CA2462653C - Nucleic acid and corresponding protein entitled 161p2f10b useful in treatment and detection of cancer - Google Patents

Abstract

A novel gene 0161P2F10B (also designated 161P2F10B) and its encoded protein, and variants thereof, are described wherein 161P2F10B exhibits tissue specific expression in normal adult tissue, and is aberrantly expressed in the cancers listed in Table I. Consequently, 161P2F10B provides a diagnostic, prognostic, prophylactic and/or therapeutic target for cancer. The 161P2F10B gene of fragment thereof, or its encoded protein, or variants thereof, or a fragment thereof, can be used to elicit a humoral or cellular immune response;
antibodies or T cells reactive with 161P2F10B can be used in active or passive immunization.

Description

DEMANDES OU BREVETS VOLUMINEUX
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USEFUL IN TREATMENT AND DETECTION OF CANCER
FIELD
This disclosure relates to a gene and its encoded protein, termed 161P2F10B, expressed in certain cancers, and to diagnostic and therapeutic methods and compositions useful in the management of cancers that express 161P2F10B.
BACKGROUND
Cancer is the second leading cause of human death next to coronary disease.
Worldwide, millions of people die from cancer every year. In the United States alone, as reported by the American Cancer Society, cancer causes the death of well over a half-million people annually, with over 1.2 million new cases diagnosed per year. While deaths from heart disease have been declining significantly, those resulting from cancer generally are on the rise. In the early part of the next century, cancer is predicted to become the leading cause of death.
Worldwide, several cancers stand out as the leading killers. In particular, carcinomas of the lung, prostate, breast, colon, pancreas, and ovary represent the primary causes of cancer death. These and virtually all other carcinomas share a common lethal feature. With very few exceptions, metastatic disease from a carcinoma is fatal. Moreover, even for those cancer patients who initially survive their primary cancers, common experience has shown that their lives are dramatically altered. Many cancer patients experience strong anxieties driven by the awareness of the potential for recurrence or treatment failure. Many cancer patients experience physical debilitations following treatment.
Furthermore, many cancer patients experience a recurrence.
Worldwide, prostate cancer is the fourth most prevalent cancer in men. In North America and Northern Europe, it is by far the most common cancer in males and is the second leading cause of cancer death in men. In the United States alone, well over 30,000 men die annually of this disease - second only to lung cancer.
Despite the magnitude of these figures, there is still no effective treatment for metastatic prostate cancer. Surgical prostatectomy, radiation therapy, hormone ablation therapy, surgical castration and chemotherapy continue to be the main treatment modalities. Unfortunately, these treatments are ineffective for many and are often associated with undesirable consequences.
On the diagnostic front, the lack of a prostate tumor marker that can accurately detect early-stage, localized tumors remains a significant limitation in the diagnosis and management of this disease. Although the serum prostate specific antigen (PSA) assay has been a very useful tool, however its specificity and general utility is widely regarded as lacking in several important respects.
Progress in identifying additional specific markers for prostate cancer has been improved by the generation of prostate cancer xenografts that can recapitulate different stages of the disease in mice. The LAPC (Los Angeles Prostate Cancer) xenografts are prostate cancer xenografts that have survived passage in severe combined immune deficient (SCID) mice and have exhibited the capacity to mimic the transition from androgen dependence to androgen independence (Klein etal., 1997, Nat. Med. 3:402). More recently identified prostate cancer markers include PCTA-1 (Su et al., 1996, Proc. Natl. Acad. Sci. USA
93: 7252), prostate-specific membrane (PSM) antigen (Pinto etal., Clin Cancer Res 1996 Sep 2(9): 1445-51), STEAP (Hubert, etal., Proc Natl Acad Sci U S A. 1999 Dec 7; 96(25): 14523-8) and prostate stem cell antigen (PSCA) (Reiter etal., 1998, Proc.
Natl. Acad. Sci. USA 95: 1735).
While previously identified markers such as PSA, PSM, PCTA and PSCA have facilitated efforts to diagnose and treat prostate cancer, there is need for the identification of additional markers and therapeutic targets for prostate and related cancers in order to further improve diagnosis and therapy.

2 Renal cell carcinoma (RCC) accounts for approximately 3 percent of adult malignancies. Once adenomas reach a diameter of 2 to 3 cm, malignant potential exists. In the adult, the two principal malignant renal tumors are renal cell adenocarcinoma and transitional cell carcinoma of the renal pelvis or ureter. The incidence of renal cell adenocarcinoma is estimated at more than 29,000 cases in the United States, and more than 11,600 patients died of this disease in 1998. Transitional cell carcinoma is less frequent, with an incidence of approximately 500 cases per year in the United States.
Surgery has been the primary therapy for renal cell adenocarcinoma for many decades. Until recently, metastatic disease has been refractory to any systemic therapy. With recent developments in systemic therapies, particularly immunotherapies, metastatic renal cell carcinoma may be approached aggressively in appropriate patients with a possibility of durable responses. Nevertheless, there is a remaining need for effective therapies for these patients.
Of all new cases of cancer in the United States, bladder cancer represents approximately 5 percent in men (fifth most common neoplasm) and 3 percent in women (eighth most common neoplasm). The incidence is increasing slowly, concurrent with an increasing older population. In 1998, there was an estimated 54,500 cases, including 39,500 in men and 15,000 in women. The age-adjusted incidence in the United States is 32 per 100,000 for men and eight per 100,000 in women. The historic male/female ratio of 3:1 may be decreasing related to smoking patterns in women. There were an estimated 11,000 deaths from bladder cancer in 1998 (7,800 in men and 3,900 in women). Bladder cancer incidence and mortality strongly increase with age and will be an increasing problem as the population becomes more elderly.
Most bladder cancers recur in the bladder. Bladder cancer is managed with a combination of transurethral resection of the bladder (TUR) and intravesical chemotherapy or immunotherapy. The multifocal and recurrent nature of bladder cancer points out the limitations of TUR. Most muscle-invasive cancers are not cured by TUR alone. Radical cystectomy and urinary diversion is the most effective means to eliminate the cancer but carry an undeniable impact on urinary and sexual function.
There continues to be a significant need for treatment modalities that are beneficial for bladder cancer patients.
An estimated 130,200 cases of colorectal cancer occurred in 2000 in the United States, including 93,800 cases of colon cancer and 36,400 of rectal cancer. Colorectal cancers are the third most common cancers in men and women. Incidence rates declined significantly during 1992-1996 (-2.1% per year). Research suggests that these declines have been due to increased screening and polyp removal, preventing progression of polyps to invasive cancers. There were an estimated 56,300 deaths (47,700 from colon cancer, 8,600 from rectal cancer) in 2000, accounting for about 11% of all U.S. cancer deaths.
At present, surgery is the most common form of therapy for colorectal cancer, and for cancers that have not spread, it is frequently curative. Chemotherapy, or chemotherapy plus radiation, is given before or after surgery to most patients whose cancer has deeply perforated the bowel wall or has spread to the lymph nodes.
A permanent colostomy (creation of an abdominal opening for elimination of body wastes) is occasionally needed for colon cancer and is infrequently required for rectal cancer. There continues to be a need for effective diagnostic and treatment modalities for colorectal cancer.
There were an estimated 164,100 new cases of lung and bronchial cancer in 2000, accounting for 14% of all U.S.
cancer diagnoses. The incidence rate of lung and bronchial cancer is declining significantly in men, from a high of 86.5 per 100,000 in 1984 to 70.0 in 1996. In the 1990s, the rate of increase among women began to slow. In 1996, the incidence rate in women was 42.3 per 100,000.
Lung and bronchial cancer caused an estimated 156,900 deaths in 2000, accounting for 28% of all cancer deaths.
During 1992-1996, mortality from lung cancer declined significantly among men (-1.7% per year) while rates for women were still significantly increasing (0.9% per year). Since 1987, more women have died each year of lung cancer than breast cancer, which, for over 40 years, was the major cause of cancer death in women.
Decreasing lung cancer incidence and mortality rates most likely resulted from decreased smoking rates over the previous 30 years;
however, decreasing smoking patterns among

3 women lag behind those of men. Of concern, although the declines in adult tobacco use have slowed, tobacco use in youth is increasing again.
Treatment options for lung and bronchial cancer are determined by the type and stage of the cancer and include surgery, radiation therapy, and chemotherapy. For many localized cancers, surgery is usually the treatment of choice.
Because the disease has usually spread by the time it is discovered, radiation therapy and chemotherapy are often needed in combination with surgery. Chemotherapy alone or combined with radiation is the treatment of choice for small cell lung cancer; on this regimen, a large percentage of patients experience remission, which in some cases is long lasting.
There is however, an ongoing need for effective treatment and diagnostic approaches for lung and bronchial cancers.
An estimated 182,800 new invasive cases of breast cancer were expected to occur among women in the United States during 2000. Additionally, about 1,400 new cases of breast cancer were expected to be diagnosed in men in 2000.
After increasing about 4% per year in the 1980s, breast cancer incidence rates in women have leveled off in the 1990s to about 110.6 cases per 100,000.
In the U.S. alone, there were an estimated 41,200 deaths (40,800 women, 400 men) in 2000 due to breast cancer. Breast cancer ranks second among cancer deaths in women. According to the most recent data, mortality rates declined significantly during 1992-1996 with the largest decreases in younger women, both white and black. These decreases were probably the result of earlier detection and improved treatment.
Taking into account the medical circumstances and the patient's preferences, treatment of breast cancer may involve lumpectomy (local removal of the tumor) and removal of the lymph nodes under the arm; mastectomy (surgical removal of the breast) and removal of the lymph nodes under the arm; radiation therapy; chemotherapy; or hormone therapy. Often, two or more methods are used in combination. Numerous studies have shown that, for early stage disease, long-term survival rates after lumpectomy plus radiotherapy are similar to survival rates after modified radical mastectomy. Significant advances in reconstruction techniques provide several options for breast reconstruction after mastectomy. Recently, such reconstruction has been done at the same time as the mastectomy.
Local excision of ductal carcinoma in situ (DCIS) with adequate amounts of surrounding normal breast tissue may prevent the local recurrence of the DCIS. Radiation to the breast and/or tamoxifen may reduce the chance of DCIS
occurring in the remaining breast tissue. This is important because DCIS, if left untreated, may develop into invasive breast cancer. Nevertheless, there are serious side effects or sequelae to these treatments. There is, therefore, a need for efficacious breast cancer treatments.
There were an estimated 23,100 new cases of ovarian cancer in the United States in 2000. It accounts for 4% of all cancers among women and ranks second among gynecologic cancers. During 1992-1996, ovarian cancer incidence rates were significantly declining. Consequent to ovarian cancer, there were an estimated 14,000 deaths in 2000. Ovarian cancer causes more deaths than any other cancer of the female reproductive system.
Surgery, radiation therapy, and chemotherapy are treatment options for ovarian cancer. Surgery usually includes the removal of one or both ovaries, the fallopian tubes (salpingo-oophorectomy), and the uterus (hysterectomy). In some very early tumors, only the involved ovary will be removed, especially in young women who wish to have children. In advanced disease, an attempt is made to remove all intra-abdominal disease to enhance the effect of chemotherapy.
There continues to be an important need for effective treatment options for ovarian cancer, There were an estimated 28,300 new cases of pancreatic cancer in the United States in 2000. Over the past 20 years, rates of pancreatic cancer have declined in men. Rates among women have remained approximately constant but =
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4 may be beginning to decline. Pancreatic cancer caused an estimated 28,200 deaths in 2000 in the United States. Over the past 20 years, there has been a slight but significant decrease in mortality rates among men (about -0.9% per year) while rates have increased slightly among women.
Surgery, radiation therapy, and chemotherapy are treatment options for pancreatic cancer. These treatment options can extend survival and/or relieve symptoms in many patients but are not likely to produce a cure for most. There is a significant need for additional therapeutic and diagnostic options for pancreatic cancer.
SUMMARY
The present disclosure relates to a gene, designated 161P2F1013, that has now been found to be over-expressed in the cancer(s) listed in Table I. Northern blot expression analysis of 161P2F106 gene expression in normal tissues shows a restricted expression pattern in adult tissues. The nucleotide (Figure 2) and amino acid (Figure 2, and Figure 3) sequences of 161P2F1OB are provided. The tissue-related profile of 161P2F1OB
in normal adult tissues, combined with the over-expression observed in the tissues listed in Table I, shows that 161P2F1OB is aberrantly over-expressed in at least some cancers, and thus serves as a useful diagnostic, prophylactic, prognostic, and/or therapeutic target for cancers of the tissue(s) such as those listed in Table I.
This disclosure provides polynucleotides corresponding or complementary to all or part of the 161P2F1OB genes, mRNAs, and/or coding sequences, preferably in isolated form, including polynucleotides encoding 161P2F10B-related proteins and fragments of 4, 5, 6,7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or more than 25 contiguous amino acids; at least 30, 35, 40, 45, 50, 55, 60, 65, 70, 80, 85, 90, 95, 100 or more than 100 contiguous amino acids of a 161P2F10B-related protein, as well as the peptides/proteins themselves; DNA, RNA, DNA/RNA hybrids, and related molecules, polynucleotides or oligonucleotides complementary or having at least a 90% homology to the 161P2F1013 genes or mRNA sequences or parts thereof, and polynucleotides or oligonucleotides that hybridize to the 161P2F1OB genes, mRNAs, or to 161P2F108-encoding polynucleotides. Also provided are means for isolating cDNAs and the genes encoding 161P2F108, Recombinant DNA molecules containing 161P2F1OB
polynucleotides, cells transformed or transduced with such molecules, and host-vector systems for the expression of 161P2F1OB gene products are also provided.
This disclosure further provides antibodies that bind to 161P2F108 proteins and polypeptide fragments thereof, including polyclonal and monoclonal antibodies, murine and other mammalian antibodies, chimeric antibodies, humanized and fully human antibodies, and antibodies labeled with a detectable marker or therapeutic agent. In certain embodiments, there is a proviso that the entire nucleic acid sequence of Figure 2 is not encoded and/or the entire amino acid sequence of Figure 2 is not prepared. In certain embodiments, the entire nucleic acid sequence of Figure 2 is encoded and/or the entire amino acid sequence of Figure 2 is prepared, either of which are in respective human unit dose forms.
This disclosure further provides methods for detecting the presence and status of 161P2F108 polynucleotides and proteins in various biological samples, as well as methods for identifying cells that express 161P2F10B. A typical embodiment of this invention provides methods for monitoring 161P2F1OB gene products in a tissue or hematology sample having or suspected of having some form of growth dysregulation such as cancer.
This disclosure further provides various immunogenic or therapeutic compositions and strategies for treating cancers that express 161P2F1OB such as cancers of tissues listed in Table I, including therapies aimed at inhibiting the transcription, translation, processing or function of 161P2F1OB as well as cancer vaccines. In one aspect, this disclosure provides compositions, and methods comprising them, for treating a cancer that expresses 161P2F1OB in a human subject = CA2462653 wherein the composition comprises a carrier suitable for human use and a human unit dose of one or more than one agent that inhibits the production or function of 161P2F10B. Preferably, the carrier is a uniquely human carrier. In another aspect, the agent is a moiety that is immunoreactive with 161P2F1OB protein.
Non-limiting examples of such moieties include, but are not limited to, antibodies (such as single chain, monoclonal, polyclonal, humanized, chimeric, or human antibodies), functional equivalents thereof (whether naturally occurring or synthetic), and combinations thereof. The antibodies can be conjugated to a diagnostic or therapeutic moiety. In another aspect, the agent is a small molecule as defined herein.
In another aspect, the agent comprises one or more than one peptide which comprises a cytotoxic T lymphocyte (CTL) epitope that binds an HLA class 1 molecule in a human to elicit a CTL
response to 161P2F1OB and/or one or more than one peptide which comprises a helper T lymphocyte (HTL) epitope which binds an HLA class II molecule in a human to elicit an HTL response. The peptides may be on the same or on one or more separate polypeptide molecules. In a further aspect, the agent comprises one or more than one nucleic acid molecule that expresses one or more than one of the CTL or HTL response stimulating peptides as described above. In yet another aspect, the one or more than one nucleic acid molecule may express a moiety that is immunologically reactive with 161P2F1OB as described above. The one or more than one nucleic acid molecule may also be, or encodes, a molecule that inhibits production of 161P2F10B.
Non-limiting examples of such molecules include, but are not limited to, those complementary to a nucleotide sequence essential for production of 161P2F105 (e.g. antisense sequences or molecules that form a triple helix with a nucleotide double helix essential for 161P2F108 production) or a ribozyme effective to lyse 161P2F1OB mRNA.
Note that to determine the starting position of any peptide set forth in Tables VIII-XXI and XXII to XLIX
(collectively HLA Peptide Tables) respective to its parental protein, e.g., variant 1, variant 2, etc., reference is made to three factors: the particular variant, the length of the peptide in an HLA
Peptide Table, and the Search Peptides in Table VII. Generally, a unique Search Peptide is used to obtain HLA peptides of a particular for a particular variant. The position of each Search Peptide relative to its respective parent molecule is listed in Table VII. Accordingly, if a Search Peptide begins at position "X", one must add the value "X - 1" to each position in Tables VIII-XXI and XXII to XLIX to obtain the actual position of the HLA peptides in their parental molecule. For example, if a particular Search Peptide begins at position 150 of its parental molecule, one must add 150- 1, i.e., 149 to each HLA peptide amino acid position to calculate the position of that amino acid in the parent molecule.
One embodiment disclosed herein comprises an HLA peptide, that occurs at least twice in Tables VIII-XXI and XXII to XLIX collectively, or an oligonucleotide that encodes the HLA peptide.
Another embodiment comprises an HLA
peptide that occurs at least once in Tables VIII-XXI and at least once in tables XXII to XLIX, or an oligonucleotide that encodes the HLA peptide.
Another embodiment disclosed herein is antibody epitopes, which comprise a peptide regions, or an oligonucleotide encoding the peptide region, that has one two, three, four, or five of the following characteristics:
i) a peptide region of at least 5 amino acids of a particular peptide of Figure 3, in any whole number increment up to the full length of that protein in Figure 3, that includes an amino acid position having a value equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in the Hydrophilicity profile of Figure 5;
ii) a peptide region of at least 5 amino acids of a particular peptide of Figure 3, in any whole number increment up to the full length of that protein in Figure 3, that includes an amino acid position having a value equal to or less than 0.5, 0.4, 0.3, 0.2, 0.1, or having a value equal to 0.0, in the Hydropathicity profile of Figure 6;

iii) a peptide region of at least 5 amino acids of a particular peptide of Figure 3, in any whole number increment up to the full length of that protein in Figure 3, that includes an amino acid position having a value equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in the Percent Accessible Residues profile of Figure 7;
iv) a peptide region of at least 5 amino acids of a particular peptide of Figure 3, in any whole number increment up to the full length of that protein in Figure 3, that includes an amino acid position having a value equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in the Average Flexibility profile of Figure 8; or v) a peptide region of at least 5 amino acids of a particular peptide of Figure 3, in any whole number increment up to the full length of that protein in Figure 3, that includes an amino acid position having a value equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in the Beta-turn profile of Figure 9.
Various embodiments of the claimed invention relate to a polynucleotide that encodes the polypeptide sequence shown in SEQ ID NO:9. The polynucleotide may comprise the nucleic acid sequence of SEQ ID NO:8 from residue 44 through 2671. Also claimed are recombinant expression vectors comprising such a polynucleotide, a host cell containing such an expression vector and a process for producing the protein comprising culturing such a host cell under conditions sufficient for production of the protein.
Various embodiments of the claimed invention relate to an isolated protein that comprises SEQ ID NO:9. The protein may be produced by a claimed process. Also claimed are compositions comprising such a protein and a pharmaceutically acceptable carrier.
Various embodiments of the claimed invention relate to an antibody or antigen binding fragment thereof that immunospecifically binds to a protein comprising the amino acid sequence of SEQ ID NO:9, Also claimed are compositions comprising such an antibody or fragment thereof and a pharmaceutically acceptable carrier as well as hybridomas that produce such an antibody as a monoclonal antibody. Such an antibody or fragment thereof may be for use in inhibiting growth of a cell expressing the protein of SEQ ID NO:9. Such a use may be in preparation of a medicament for such inhibiting. Such an antibody or fragment thereof may be for use to deliver an agent to a cell expressing the protein of SEQ ID NO:9. Such a use may be in preparation of a medicament for such delivering. The agent may be a cytotoxic agent.
Various embodiments of the claimed invention relate to an in vitro method for detecting the presence of a protein (SEQ ID NO:9) or polynucleotide (SEQ ID NO:8) in a test sample comprising:
contacting the sample with an antibody or polynucleotide, respectively, that specifically binds to the protein or polynucleotide, respectively; and detecting binding of protein or polynucleotide, respectively, in the sample thereto.
Various embodiments of the claimed invention relate to use of a protein of SEQ
ID NO:9 or an epitope thereof to elicit an immune response, wherein the protein or epitope thereof is for contacting an immune system cell, whereby the immune system cell is induced. Such a use may be in preparation of a medicament for such eliciting of an immune response. The immune response may be in a subject.

= , , - CA2462653 , 6a BRIEF DESCRIPTION OF THE FIGURES
Figure 1. The 161P2F1OB SSH sequence of 182 nucleotides.
Figure 2. A) The cDNA and amino acid sequence of 161P2F1OB variant 1 (also called "161P2F1OB v.1"
or "161P2F1OB variant 1") is shown in Figure 2A. The start methionine is underlined. The open reading frame extends from nucleic acid 44-2671 including the stop codon.
B) The cDNA and amino acid sequence of 161P2F1OB variant 2 (also called "161P2F1OB v.2") is shown in Figure 2B. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 44-2671 including the stop codon.
C) The cDNA and amino acid sequence of 161P2F1OB variant 3 (also called "161P2F1OB v.3") is shown in Figure 2C. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 44-2671 including the stop codon. The cDNA and amino acid sequence of 161P2F10B variant 4 (also called "161P2F1OB v.4") is shown in D) Figure 20. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 44-2671 including the stop codon.
E) The cDNA and amino acid sequence of 161P2F1OB variant 5 (also called "161P2F1OB v.5") is shown in Figure 2E. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 44-2671 including the stop codon.
F) The cDNA and amino acid sequence of 161P2F1OB variant 6 (also called "161P2F1OB v.6") is shown in Figure 2F. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 84-2711 including the stop codon.
G) The cDNA and amino acid sequence of 161P2F1OB variant 7 (also called "161P2F1OB v.7") is shown in Figure 2G. The codon for the start methionine is underlined. The open reading frame extends from nucleic acid 276-2801 including the stop codon.
Figure 3.
A) Amino acid sequence of 161P2F1OB v.1 is shown in Figure 3A; it has 875 amino acids.
B) The amino acid sequence of 161P2F1OB v.2 is shown in Figure 3B; it has 875 amino acids.
C) The amino acid sequence of 161P2F1OB v.3 is shown in Figure 3C; it has 875 amino acids.
D) The amino acid sequence of 161P2F1OB v.4 is shown in Figure 3D; it has 875 amino acids.

E) The amino acid sequence of 161P2F1013 v.7 is shown in Figure 3E; it has 841 amino adds. As used herein, a reference to 161P2F1OB includes all variants thereof, including those shown in Figures 2 3, 10, and 11, unless the context dearly indicates otherwise.
Figure 4. Figure 4A: Alignment of 161P2F10 with variant 1 carrying a K to R
mutation. Figure 4B: Alignment of 161P2F1013 and SNP variant carrying a T to P mutation.
Figure 5. Hydrophilicity amino acid profile of 161P2F1013 determined by computer algorithm sequence analysis using the method of Hopp and Woods (Hopp T.P., Woods KR., 1981. Proc. Natl.
Acad. Sci. U.SA 78:3824-3828) accessed on the Protscale website located on the World Wide Web through the ExPasy molecular biology server.
Figure 6. Hydropathicity amino acid profile of 161P2F108 determined by computer algorithm sequence analysis using the method of Kyle and Doolittle (Kyle J., Doolittle R,F., 1982. J. Mot Blot. 157:105-132) accessed on the ProtScale website located on the World Wide Web through the ExPasy molecular biology server.
Figure 7. Percent accessible residues amino acid profile of 161P2F108 'determined by computer algorithm sequence analysis using the method of Janin (Janin J., 1979 Nature 277:491492) accessed on the ProtScale website located on the World Wide Web through the ExPasy molecular biology server.
Figure 8. Average flexibility amino add profile of 161P2F108 determined by computer algorithm sequence analysis using the method of Bhaskaran and Ponnuswamy (Bhaskaran R. and Ponnuswamy P.K., 1988.Int. J. Pept. Protein Res. 32:242-255) accessed on the ProtScale website located on the World Wide Web through the ExPasy molecular biology server.
Figure 9. Beta-turn amino add profile of 161P2F1OB -determined by computer algorithm sequence analysis using the method of Deteage and Roux (Deleage, G., Roux B. 1987 Protein Engineering 1:289-294) accessed on the ProtScale website located on the World Wide Web through the ExPasy molecular biology server.
Figure 10. Variants 161P2F1OB v.2 through v.5 are variants with single nucleotide differences. Though these SNP
variants are shown separately, they could also occur in any combinations and in any transcript variants that contains the base pairs.. Variants 161P2F1011 v.6 and v.7 are transcript variants. Variant 161 P2F1OB v.6 has extra 40 bases at the 5' end and a different 3' end portion, while variant 161P2F1OB v.7 has an insertion of 130 bases in between positions 121 and 122 of 161P2F108 v.1. Numbers in 1 ). correspond to those of 161P2F108 v.1.
Black box shows the same sequence as 161P2P108 v.1 SNPs are indicated above the box Figure 11. Protein variants correspond to nucleotide variants. Nucleotide variants 161P2F1013 v.5 and v.6 in Figure 10 code for the same protein as 161P2F1OB v.1. Nucleotide variants 161P2F1OB v.6 and v.7 are splice variants of v.1, as shown in Figure 12. Single amino acid differences were indicated above the boxes. Black boxes represent the same sequence as 161P2F1013 v.1. Numbers underneath the box correspond to 161P2F108 v.1.
Figure 12. Intentionally Omitted Figure 13. The secondary structure of 161P2F108 (SEQ ID NO: 103), namely the predicted presence and location of alpha betides, extended strands, and random coils, is predicted from the primary amino acid sequence using the HNN - Hierarchical Neural Network method (Guermeur, 1997, on the World Wide Web hinInpsa_autornalpl?page=npsum.h(ml), accessed from the ExPasy molecular biology server (on the WOrki Wide Web at expasy.chitools/). The analysis indicates that 161P2F108 is composed 31,31%
alpha helix, 11.31% extended strand, and 57.37% random coil (Figure 13A). Shown graphically in Figure 13 panels Band C
are the results of analysis using the TMpred (Figure 1313) and TMHMM (Figure 13C) prediction programs depicting the location of the transmembrane domain.
Figure 14. First strand cONA was generated from normal stomach, normal brain, normal heart, normal liver, normal skeletal muscle, normal testis, normal prostate, normal bladder, normal kidney, normal colon, normal lung, normal pancreas, and a pool of cancer specimens from prostate cancer patients, bladder cancer patients, kidney cancer patients, colon cancer patients, lung cancer patients, pancreas cancer patients, a pool of prostate cancer xenografts (LAPC-4AD, LAPC-4A1, LAPC-9AD and LAPC-9AI), and a pool of 2 patient prostate metastasis to lymph node. Normalization was performed by PCR using primers to actin. Semi-quantitative PCR, using primers to 161P2F10B, was performed at 26 and 30 cycles of amplification. Samples were run on an agarose gel, and PCR products were quantitated using the AlphaImager software. Results show strong expression in prostate cancer, bladder cancer, kidney cancer, colon cancer, lung cancer, pancreas cancer, bone cancer, lymphoma cancer, uterus cancer, compared to all normal tissues tested. Strong expression was also detected in the xenograft pool as well as the prostate cancer metastasis to lymph node specimens.
Figure 15. First strand cDNA was prepared from a panel of kidney cancer clear cell carcinoma (A), kidney cancer papillary carcinoma (B), and in uterus patient cancer specimens (C).
Normalization was performed by PCR using primers to actin. Semi-quantitative PCR, using primers to 161P2F10B, was performed at 26 and 30 cycles of amplification. Samples were run on an agarose gel, and PCR products were quantitated using the AlphaImager software. Expression was recorded as absent, low, medium or strong. Results show expression of 161P2F1OB in 94.7% of clear cell renal carcinoma, 62.5% of papillary renal cell carcinoma, and in 61.5% of uterus cancer.
Figure 16. Shows Phosphodiesterase Activity of 3T3-161P2F1OB Stable Cells.
Cell surface phosphodiesterase activity is assayed on 3T3 and 3T3-161P2F1OB using the substrate p-nitrophenyl thymidine -5'-L-monosphosphate.
Figure 17. Shows Protection from Apoptosis by 161P2F10B.
Figure 18. Shows that 161P2F1OB Protects from Apoptotic Signals.
Figure 19. Shows that 161P2F1OB Protects from Staurosporine and UV-Induced Apoptosis.
Figure 20. Shows that 161P2F1013 Expression Protects Cells from Drug and UV-Induced Apoptosis. NIH 313 cells-were treated with the staurosporine or UV, stained with Annexin V-FITC
and propidium iodide, and analyzed by FACS.
Figure 21. Shows that 161P2F1OB Protects from Apoptosis by Chemotherapeutic Agents.
Figure 22 Shows the effect of 161P2F1OB on In Vitro Invasion. Invasion was determined by measuring the fluorescence of cells in the lower chamber relative to the fluorescence of the entire cell population.
Figure 23. Shows that 161P2F1OB MAb Attenuates the Growth of Human Kidney Cancer Xenograft in SCID Mice.
Figure 24. Detection of 161P2F1013 protein by immunohistochemistry in kidney cancer patient specimens. Two renal clear cell carcinoma tissue specimens and one renal papillary cell carcinoma were obtained from three different kidney cancer patients. Frozen tissues were cut into 4 micron sections and fixed in acetone for 10 minutes. The sections were then incubated with mouse monoclonal anti-ENPP3 antibody (Coulter-Immunotech, Marseilles, France) for 3 hours. The slides were washed three times in buffer, and further incubated with DAKO
EnVision+TMI peroxidase-conjugated goat anti-mouse secondary antibody (DAKO Corporation, Carpenteria, CA) for 1 hour. The sections were then washed in buffer, developed using the DAB kit (SIGMA Chemicals), counterstained using hematoxylin, and analyzed by bright field microscopy. The - results showed strong expression of 161P2F1OB in all three renal carcinoma patient tissues (Figure 24 panels A-C). The expression was detected mostly around the cell membrane in the renal clear cell carcinoma specimens, indicating that 161P2F1OB is membrane associated in this kidney cancer, and throughout the cells in the papillary cell carcinoma with an apparent predisposition towards the cell periphery.
Figure 25. Detection of 161P2F1OB protein by immunohistochemistry in a prostate cancer patient specimen.
Tissue specimens of prostate adenocarcinoma were obtained from eight different prostate cancer patients. Frozen tissues were cut into 4 micron sections and fixed in acetone for 10 minutes. The sections were then incubated with mouse monoclonal anti-ENPP3 antibody (Coulter-lmmunotech, Marseilles, France) for 3 hours. The slides were washed three times in buffer, and further incubated with DAKO EnVision+n" peroxidase-conjugated goat anti-mouse secondary antibody (DAKO
Corporation, Carpenteria, CA) for 1 hour. The sections were then washed in buffer, developed using the DAB kit (SIGMA

Chemicals), counterstained using hematoxylin, and analyzed by bright field microscopy. The results showed expression of 161P2F1OB in six of the eight prostate cancer patient tissues, one of which is illustrated in this Figure 25. 161P2F1OB was expressed on the tumor cells with an apparent proclivity towards the luminal cell surface.
Figure 26. Detection of 161P2F108 protein by immunohistochemistry in a colon cancer patient specimen. Tissue specimens of colon adenocarcinoma were obtained from nine different colon cancer patients. Frozen tissues were cut into 4 micron sections and fixed in acetone for 10 minutes. The sections were then incubated with mouse monoclonal anti-ENPP3 antibody (Coulter-Immunotech, Marseilles, France) for 3 hours. The slides were washed three times in buffer, and further incubated with DAKO EnVision+TN peroxidase-conjugated goat anti-mouse secondary antibody (DAKO Corporation, Carpenteria, CA) for 1 hour. The sections were then washed in buffer, developed using the DAB kit (SIGMA Chemicals), counterstained using hematoxylin, and analyzed by bright field microscopy. The results showed strong expression of 161P2F1OB in two of the nine colon cancer patient tissues, one of which is illustrated in this Figure 26. 161P2F1OB was most strongly expressed on the tumor cells with a luminal cell surface but was also expressed throughout all the tumor tissue.
Figure 27. Detection by immunohistochemistry of 161P2F1OB protein expression in kidney clear cell cancer patient specimens by specific binding of mouse monoclonal antibodies. Renal clear cell carcinoma tissue and its matched normal adjacent were obtained from a kidney cancer patient. Frozen tissues were cut into 4 micron sections and fixed in acetone for 10 minutes. The sections were then incubated either mouse monoclonal anti-ENPP3 antibody (Coulter-Immunotech, Marseilles, France) for 3 hours (Figure 27 panels A, D), or mouse monoclonal antibody X41(3)50 (Figure 27 panels B, E), or mouse monoclonal antibody X41(3)37 (Figure 27 panels C, F).
The slides were washed three times in buffer and further incubated with DAKO EnVision+im peroxidase-conjugated goat anti-mouse secondary antibody (DAKO
Corporation, Carpenteria, CA) for 1 hour. The sections were then washed in buffer, developed using the DAB kit (SIGMA
Chemicals), counterstained using hematoxylin, and analyzed by bright field microscopy (Figure 27 panels A-F). The results showed strong expression of 161P2F1OB in the renal clear cell carcinoma patient tissue (Figure 27 panels A-C), but weakly in normal kidney (Figure 27 panels D-F). The expression was predominantly around the cell periphery indicating that 161P2F1OB is membrane associated in kidney cancer tissues. The weak expression detected in normal kidney was localized to the kidney proximal tubules.
Figure 28. Expression of 161P2F10b in recombinant cell lines.
A.) Rat1, NIH3T3, NSO, and 300.19 cells stably expressing either 16P2F10b or a control vector (neo) were stained with PE-conjugated anti-CD203c MAb and examined by flow cytometry.
(Light dotted line: control neo cells. Dark line: 161P2F10 cells) B.) Rat1, NIH3T3, NSO, 300.19, and UT7 cells were stained with either PE-conjugated anti-CD203c MAb or control I9G1-PE Ab and examined by flow cytometry. (Light dotted line: control MAb. Dark line: 97A6 (CO203c) MAb.) Shown is the mean fluorescence of the staining of the control and 161P2F10b cells and the ratio of the values. This was used to rank the cells for relative expression levels of 161P2F10b.
C.) The relative cell surface phosphodiesterase enzymatic activity of the recombinant cells was measured by the addition of p-nitrophenyl thymidine-5'-L-monophosphate (p-nTMP) phosphodiesterase substrate. There is a correlation between expression levels determined by flow cytometry and surface enzyme activity.
Figure 29. Surface expression and phosphodiesterase activity of 161P2F10b.
A. 161P2F10b transfected 293T cells were stained with the commercially available (Coulter Immunotech) PE-conjugated anti-CD-203c MAb, a commercially available anti-ENPP3 (161P2F10b) MAb and examined by fluorescent microscopy.

B. 161P2F10b and vector transfected 293T cells were incubated in assay buffer containing the phosphodiesterase-1 colorimetic substrate p-nitrophenyl thymidine-5'-L-monophosphate (p-nTMP) and optical densities (0.D.) were obtained at 405nm.
Figure 30. Relative expression and enzymatic activity of 161P2F10b mutants in recombinant Caki kidney cancer cells. Caki kidney cancer cells were infected with retrovirus containing either wildtype 161P2F120b cDNA, or point mutant cDNAs encoding either a threonine to serine mutation (T/S) at amino acid 205, a threonine to alanine mutation (T/A) at amino acid 205, or a aspartic acid to glutamic acid mutation (DIE) at amino acid 80.
Stably expressing cell lines were analyzed for 161P2F10b expression by flow cytometry with 97A6 (CD203c) MAb (A) and for enzymatic activity with p-nTMP substrate (B).
Mutation of threonine 205 to aspartic acid or alanine abolishes the ability to cleave the substrate, demonstrating that threonine 205 is critical to the enzymatic activity of 161P2F10b.
Figure 31. Purification of a recombinant protein encoding the extracellular domain (ECD) of 161P2F10b. 293T
cells were transfected with a Tag5 secretion expression vector encoding the ECD of 161P2F10b (amino acids 46-875). The recombinant protein was purified from the conditioned media using either metal chelate affinity chromatography (not shown) or with an immunoaffinity column comprised of anti-161P2F10b MAb X41.6 (shown). 2 ul of 2 separate purified lots were analyzed by SDS-PAGE and Coomasie staining. BSA protein was also analyzed as a quantitative standard.
Figure 32. 161P2F10b enzymatic assays utilizing P-nitrophenyl-thymidine monophosphate (p-nTMP).
A. Schematic of the calorimetric enzyme assay showing enzymatic cleavage of the p-nTMP substrate generating a soluble yellow product.
B. Kinetics and dose response of the enzymatic action of purified Tag5-ECD
161P2F10b protein on p-nTMP (2.5 mM). Optical densities (OD) of reactions were determined at 405nm.
C. Cell surface enzymatic assay of 161P2F10b-expressing Rat1 cells. The indicated number of Rat1-161P2F10b cells were incubated with p-nTMP substrate and the OD's of the wells were determined.
D. ATP and NAD (not shown) serve as competitive inhibitors 161P2F10b cleavage of p-nTMP. Purified Tag5-ECD
protein (20 ng) was incubated with p-nTMP substrate in the absence or presence of the indicated amounts of ATP. The OD's of reactions were obtained at 405 nm.
Figure 33. Analysis of the internalization of anti-161P2F10b MAb X41.6.
Panel A. Schematic of the protocol. Rat1-161P2F10b cells are incubated with anti-161P2F10b MAb at 4C, washed, and then either kept at 4C and stained with anti-mouse IgG secondary-PE conjugated Ab at 4C (B, total surface staining) or moved to 37C for various times and then stained with secondary Ab at 4C (C, residual surface staining). Panels B and C demonstrate that MAb X41.6 engagement of surface 161P2F10b causes internalization at 37C of the complex indicated by the progressive decrease in mean fluorescence intensity (MFI).
Figure 34. Internalization of selected anti-161P2F10b murine MAbs.
Internalization of selected anti-161P2F10b MAbs are by flow cytometry are shown. Internalization is indicated by a decrease in the mean fluorescence intensity (MFI) of cells moved to 37C versus cells stained at 4C.
Figure 35. Antibody engagement of 161P2F10b results in its internalization.
Internalization of the commercially available MAb 97A6, anti-CD203c, is shown by fluorescence microscopy following staining of Rat1-161P2F10b cells. The cells were incubated with CD203c-PE conjugated MAb at 4C, washed, and then moved to 37C for the indicated times and then examined by fluorescence microscopy. At 4C, the staining of the cells is cell surface (bright halo of fluorescence around individual cells). Upon moving to 37C, there is a gradual loss of the surface fluorescence, concomitant with capping of the MAb to punctate regions on the surface, followed by the appearance of punctate and diffuse intracellular fluorescence and a total loss of surface fluorescence.

Figure 36. Effects of X41.50 MAb-saporin toxin conjugate on Caki-161P2F10b cells. Shown is the morphology of Caki-161P2F10b cells that were treated with and without the indicated concentrations of the internalizing anti-161P2F10b MAb and an anti-mouse IgG-saporin toxin secondary Ab (2 ug/ml). Saporin is unable to enter cells efficiently on its own and must be internalized for its toxic mechanism (protein synthesis inhibition) to work. Cells were first incubated at 4C with X41.50 MAb to allow surface binding, than either media or the saporin-conjugated secondary Ab was added and the cells were incubated for 72 hours at 37C. Cells incubated with either media alone, X41.50 alone, or the secondary-saporin Ab alone had no effect on Caki-161P2F10b growth and morphology, exemplified by a viable confluent monolayer. However, cells incubated with X41.50 MAb (2 and 0.5 ug/ml) and the secondary saporin-conjugate exhibited signs of growth inhibition =(did not reach confluency) and apoptosis (small round floating apoptotic cells above the attached cell layer). This demonstrates the utility of anti-161P2F10b MAbs drug/toxin conjugates as a therapeutic approach for 161P2F10b-expressing cancers and diseased tissues.
Figure 37. Internalization-mediated downregulation of 161P2F10 protein by MAb X41.50. Rat1-161P2F10b cells were incubated with and without 10 ug/ml of MAb X41.50 for 72 hours. Cells were washed, fixed, permeabilized, and stained with PE-conjugated CD203c MAb to monitor total 161P2FlOb protein expression.
The data shows a marked decrease in staining following treatment of the cells with X41.50, demonstrating downregulation of 161P2F10b protein.
Figure 38. Anti-161P2F10b MAbs downregulate surface 161P2F10b enzymatic activity. Rat1-161P2F10b cells were treated with and without various concentrations of the indicated MAbs for 48 hours and then assayed for surface enzymatic activity using p-n-TMB substrate. The data demonstrates that engagement and intemalization of surface 161P2F10b by MAbs results in the concamitant loss of surface 161P2F10b enzymatic activity.
Figure 39. Characteristics of mouse 161P2F10b MAbs. Shown is a summary of various characteristics of MAbs that recognize 161P2F10b.
The relative affinity of the MAbs was determined by saturation binding ELISA
using the recombinant Tag5-ECD
protein. The Kd of the binding reaction was determined using a one-site binding non-linear regression analysis of the data using GraphPad Prism software version 3.02 (Graphpad Software, San Diego, CA).
Relative surface staining was determined using 10 ug/ml of each MAb on RAT1-161P2F10b cells.
Relative ability to internalize was also carried out on Rat1-161P2F10b cells comparing staining with 10 ug/ml of MAb at 4C versus residual staining following incubation at 37C for 30 minutes.
The ability of the MAbs to downregulate surface enzyme activity was determined by incubation of Rat1-161P2F10b cells with 10 ug/ml of each MAb for 72 hours then assaying surface enzyme activity with p-nTMP substrate.
Relative specific immunohistochemical staining (INC) was determined using 10 ug/ml of each MAb on 161P2F10b-expressing frozen section kidney clear cell carcinoma samples.
The epitope family was determined by competition binding ELISA using the Tag5-ECD protein as target. Tag5-ECD ELISA coated wells were first incubated with or without 10 ug/ml of competitor MAb, washed, and then incubated with 1 ug/ml of HRP-labeled test MAb. MAb that compete for binding (reduction of the signal of the test MAb with prior incubation with competitor) must share the same or an overlapping epitope and are thus assigned to an epitope family. Of the MAbs listed, at least 2 epitope families are defined.
Figure 40. Surface staining of selected anti-161P2F10b MAbs. Specific binding of cell surface 161P2F10b was determined by incubation of Rat1-161P2F10 (dark line) and Rat1-neo control cells (light dotted line) with 10 ug/ml of each MAb for 1.5 hours at 4C. Cells were washed, incubated with goat-anti-mouse-PE
conjugated secondary Ab, washed again, and analyzed by flow cytometry. Shown are examples of MAb derived from DNA-based immunization of mice with an FC-fusion of the ECD (X41.6, X41.15, X41.17, X41.29, X41.37, X41.50), also DNA-based immunization with Tag5-ECD , and with Rat1-161P2F10b cells (the last data was generated using the respective hybridoma supernatant at a 1:50 dilution) was performed.
Figure 41. Anti-161P2F10b MAbs X41.6 and 97A6 (CD203c) do not cross-react with ENPP1. Conditioned media from 293T cells transfected with either Tag5-161P2F10b or ENPP1 His-tagged vectors was subjected to immunoprecipitation analysis using 5 ug of MAb X41.6, MAb 97A6 (CD203c), or anti-His pAb.
Following washing of the immune complexes, phosphodiesterase activity was determined by the addition of p-nTMP substrate.
Enzymatic activity is seen in anti-His immune complexes from both Tag5 161P2F10b and Tag5 ENPP1 media due to the presence of the His epitope in both proteins. However, enzymatic activity is seen only in the immune complexes of X41.6 and 97A6 from Tag5 161P2F10 conditioned media and not with Tag5 ENPP1 media. These data demonstrate that MAbs X41.6 and 97A6 (CD203c) do not crossreact with the homologous ectonucleotide pyrophosphatase/phosphodiesterase family member ENPP1.
Figure 42. Detection of 161P2F10b in the conditioned media of 161P2F10b-expressing cells. Supernatants of the indicated 161P2F20b-expressing and non-expressing cell lines were analyzed for for shedding/secretion of 161P2F10b protein by a capture ELISA. The capture ELISA was made.using a 161P2F10b-specific MAb as the bottom capture MAb (1 ug/well), and X41.29 as the top detection MAb (2 ug/ml), and an anti-mouse IgG2a-HRP secondary and tetramethylbenzamidine as substrate for development. Recombinant 161P2F10b Tag5 ECD protein was used as a standard. 161P2F10b protein was detected in the media from 769 and Caki kidney cancer cells engineered to express 161P2F10b but not in the parental lines, indicating that 161P2F10b protein is shed or secreted. Shed/secreted 161P2F10b may exert its activity on cells in an autocrine/paracrine manner. In addition, shed/secreted 161P2F10b is useful as a diagnostic marker for 161P2F10b-expressing cancer and/or other 161P2F10b-expressing diseased tissues.
Figure 43. Detection of secreted 161P2F108 in the serum of mice bearing UGK3 human kidney cancer xenografts. SCID mice inoculated subcutaneously with UGK3 kidney cancer cells were monitored for tumor growth (1 dimensional tumor measurements) and 161P2F10b serum levels (by capture ELISA) over the indicated times. The data - demonstrates that 161P2F10b serum levels increase as the tumor size increases. This demonstrates that 161P2F10b is shed/secreted from 161P2F10b-expressing tissues in vivo and further demonstrates the utility of an ELISA to monitor 161P2F10b as a diagnostic marker.
Figure 44: Detection of 161P2F1OB protein by immunohistochemistry in kidney cancer patient specimens. Renal clear cell carcinoma tissue and its matched normal adjacent tissue as well as its metastatic cancer to lymph node were obtained from a kidney cancer patient. Frozen tissues were cut into 4 micron sections and fixed in acetone for 10 minutes.
The sections were then incubated with PE-labeled mouse monoclonal anti-ENPP3 antibody (Coulter-lmmunotech, Marseilles, France) for 3 hours (Figure 44 panels A-F), or isotype control antibody (Figure 44 panels G-I). The slides were washed three times in buffer, and either analyzed by fluorescence microscopy (Figure 44 panels A, B and C), or further incubated with DAKO EnVision+N peroxidase-conjugated goat anti-mouse secondary antibody (DAKO Corporation, Carpenterta, CA) for 1 hour (Figure 44 panels D, E, and F). The sections were then washed in buffer, developed using the DAB kit (SIGMA Chemicals), counterstained using hematoxylin, and analyzed by bright field microscopy (Figure 44 panels D, E and F). The results showed strong expression of 161P2F1OB in the renal carcinoma patient tissue (Figure 44 panels A
and D) and the kidney cancer metastasis to lymph node tissue (Figure 44 panels C and F), but weakly in normal kidney (Figure 44 B and E). The expression was detected mostly around the cell membrane indicating that 161P2F1OB is membrane associated in kidney cancer tissues. The weak expression detected in normal kidney was localized to the kidney tubules. The sections stained with the isotype control antibody were negative showing the specificity of the anti-ENPP3 antibody (Figure 44 panels G-I).
Figure 45: Expression of 161P2F1OB in Human Patient Cancers by Western Blot.
Cell lysates from kidney cancer tissues (KiCa), kidney cancer metastasis to lymph node (KiCa Met), as well as normal kidney (NK) were subjected to Western analysis using an anti-161P2F10B mouse monoclonal antibody. Briefly, tissues (-25 pg total protein) were solubilized in SOS-PAGE sample buffer and separated on a 10-20% SDS-PAGE gel and transferred to nitrocellulose. Blots were blocked in Tris-buffered saline (TBS) + 3% non-fat milk and then probed with purified anti-161P2F108 antibody in TBS
+ 0.15% Tween-201m + 1% milk. Blots were then washed and incubated with a 14,000 dilution of anti-mouse IgG-HRP
conjugated secondary antibody. Following washing, anti-161P2F108 immunoreactive bands were developed and visualized by enhanced chemiluminescence and exposure to autoradiographic film. The specific anti-161P2P1OB immunoreactive bands represent a monomeric form of the 161P2F1013 protein, which runs at approximately 130kDa. These results demonstrate that 161P2F1013 is useful as a diagnostic and therapeutic target for kidney cancers, metastatic cancers and other such as tose aas listed in Table I and other human cancers that express 161P2F106.
Figure 46: Expression of 161P2F1OB in Human Xenograft Tissues by Western Blot.
Cell lysates from kidney cancer xenograft (KiCa Xeno), kidney cancer metastasis to lymph node xenograft (Met Xeno), as well as normal kidney (NK) were subjected to Western analysis using an anti-161P2F1OB mouse monoclonal anfibody. Briefly, tissues (-25 pg total protein) were solubilized in SOS-PAGE sample buffer and separated on a 10-20%
SOS-PAGE gel and transferred to nitrocellulose. Blots were blocked in Tris-buffered saline (TBS) + 3% non-fat milk and then probed with purified anti-161P2F1OB antibody in TBS + 0,15% Tween-20 + 1% milk. Blots were then washed and incubated with a 1:4,000 dilution of anti-mouse IgG-HRP conjugated secondary antibody. Following washing, anti-161P2F1013 immunoreactive bands were=
developed and visualized by enhanced chemiluminescence and exposure to autoradiographic film. The specific anti-161P2F1OB immunoreactive bands represent a monomeric form of the 161P2F1OB
protein, which runs at approximately 130kDa, and a multimer of approximately 260kDa. These results demonstrate that the human cancer xanograft mouse models can be used to study the diagnostic and therapeutic effects of 161P2F1013.
DETAILED DESCRIPTION OF THE INVENTION
Outline of Sections 1.) Definitions IL) 161P2F108 Polynucleotides ILA.) Uses of 161P2F108 Polynucleotides II.A.1.) Monitoring of Genetic Abnormalities 11.A.2.) Antisense Embodiments II.A.3.) Primers and Primer Pairs II.A.4.) Isolation of 161P2F106-Encoding Nucleic Acid Molecules ILA.5.) Recombinant Nucleic Acid Molecules and Host-Vector Systems III.) 161P2F108-related Proteins III.A.) Motif-bearing Protein Embodiments 111.8.) Expression of 161P2F108-related Proteins III.C.) Modifications of 161P2F10B-related Proteins 111.D.) Uses of 161P2F10B-related Proteins IV.) 161P2F108 Antibodies V.) 161P2F108 Cellular Immune Responses VI.) 161P2F108 Transgenic Animals VII.) Methods for the Detection of 161P2F108 VIII.) Methods for Monitoring the Status of 161P2F108-related Genes and Their Products IX.) Identification of Molecules That Interact With 161P2F108 X.) Therapeutic Methods and Compositions X.A.) Anti-Cancer Vaccines X.B.) 161P2F1OB as a Target for Antibody-Based Therapy X.C.) 161P2F1OB as a Target for Cellular Immune Responses X.C.1. Minigene Vaccines X.C.2. Combinations of CTL Peptides with Helper Peptides X.C.3. Combinations of CTL Peptides with T Cell Priming Agents X.C.4. Vaccine Compositions Comprising DC Pulsed with CTL and/or HTL Peptides X.D.) Adoptive Immunotherapy X.E.) Administration of Vaccines for Therapeutic or Prophylactic Purposes XI.) Diagnostic and Prognostic Embodiments of 161P2F10B.
XII.) Inhibition of 161P2F1OB Protein Function XII.A.) Inhibition of 161P2F1OB With Intracellular Antibodies XII.B.) Inhibition of 161P2F1OB with Recombinant Proteins XII.C.) Inhibition of 161P2F1OB Transcription or Translation XII.D.) General Considerations for Therapeutic Strategies XIII.) Identification, Characterization and Use of Modulators of 161P2F10b XIV.) KITS/Articles of Manufacture I.) Definitions:
Unless otherwise defined, all terms of art, notations and other scientific terms or terminology used herein are intended to have the meanings commonly understood by those of skill in the art to which this invention pertains. In some cases, terms with commonly understood meanings are defined herein for clarity and/or for ready reference, and the inclusion of such definitions herein should not necessarily be construed to represent a substantial difference over what is generally understood in the art. Many of the techniques and procedures described or referenced herein are well understood and commonly employed using conventional methodology by those skilled in the art, such as, for example, the widely utilized molecular cloning methodologies described in Sambrook et al., Molecular Cloning: A Laboratory Manual 2nd. edition (1989) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. As appropriate, procedures involving the use of commercially available kits and reagents are generally carried out in accordance with manufacturer defined protocols and/or parameters unless otherwise noted.
The terms "advanced prostate cancer", "locally advanced prostate cancer", "advanced disease" and "locally advanced disease" mean prostate cancers that have extended through the prostate capsule, and are meant to include stage C disease under the American Urological Association (AUA) system, stage Cl -C2 disease under the Whitmore-Jewett system, and stage 13 - T4 and N+ disease under the TNM (tumor, node, metastasis) system. In general, surgery is not recommended for patients with locally advanced disease, and these patients have substantially less favorable outcomes compared to patients having clinically localized (organ-confined) prostate cancer. Locally advanced disease is clinically identified by palpable evidence of induration beyond the lateral border of the prostate, or asymmetry or induration above the prostate base. Locally advanced prostate cancer is presently diagnosed pathologically following radical prostatectomy if the tumor invades or penetrates the prostatic capsule, extends into the surgical margin, or invades the seminal vesicles.
"Altering the native glycosylation pattern" is intended for purposes herein to mean deleting one or more carbohydrate moieties found in native sequence 161P2F1OB (either by removing the underlying glycosylation site or by deleting the glycosylation by chemical and/or enzymatic means), and/or adding one or more glycosylation sites that are not present in the native sequence 161P2F10B. In addition, the phrase includes qualitative changes in the glycosylation of the native proteins, involving a change in the nature and proportions of the various carbohydrate moieties present.
The term "analog" refers to a molecule which is structurally similar or shares similar or corresponding attributes with another molecule (e.g. a 161P2F10B-related protein). For example, an analog of a 161P2F1OB protein can be specifically bound by an antibody or T cell that specifically binds to 161P2F10B.
The term "antibody is used in the broadest sense. Therefore, an "antibody can be naturally occurring or man-made such as monoclonal antibodies produced by conventional hybridoma technology.
Anti-161P2F1OB antibodies comprise monoclonal and polyclonal antibodies as well as fragments containing the antigen-binding domain and/or one or more complementarity determining regions of these antibodies.
An "antibody fragment" is defined as at least a portion of the variable region of the immunoglobulin molecule that binds to its target, i.e., the antigen-binding region. In one embodiment it specifically covers single anti-161P2F1OB antibodies and clones thereof (including agonist, antagonist and neutralizing antibodies) and anti-161P2F1OB antibody compositions with polyepitopic specificity.
The term "codon optimized sequences" refers to nucleotide sequences that have been optimized for a particular host species by replacing any codons having a usage frequency of less than about 20%. Nucleotide sequences that have been optimized for expression in a given host species by elimination of spurious polyadenylation sequences, elimination of exon/intron splicing signals, elimination of transposon-like repeats and/or optimization of GC content in addition to codon optimization are referred to herein as an "expression enhanced sequences."
A "combinatorial library" is a collection of diverse chemical compounds generated by either chemical synthesis or biological synthesis by combining a number of chemical "building blocks" such as reagents. For example, a linear combinatorial chemical library, such as a polypeptide (e.g., rnutein) library, is formed by combining a set of chemical building blocks called amino acids in every possible way for a given compound length (i.e., the number of amino acids in a polypeptide compound). Numerous chemical compounds are synthesized through such combinatorial mixing of chemical building blocks (Gallop et al., J. Med. Chem. 37(9): 1233-1251 (1994)).
Preparation and screening of combinatorial libraries is well known to those of skill in the art. Such combinatorial chemical libraries include, but are not limited to, peptide libraries (see, e.g., U.S. Patent No. 5,010,175, Furka, Pept. Prot.
Res. 37:487-493 (1991), Houghton et al., Nature, 354:84-88 (1991)), peptoids (PCT Publication No WO 91/19735), encoded peptides (PCT Publication WO 93/20242), random bio- oligomers (PCT Publication WO 92/00091), benzodiazepines (U.S.
Pat. No. 5,288,514), diversomers such as hydantoins, benzodiazepines and dipeptides (Hobbs et al., Proc. Nat. Acad. Sci.
USA 90:6909-6913 (1993)), vinylogous polypeptides (Hagihara et al., J. Amer.
Chem. Soc. 114:6568 (1992)), nonpeptidal peptidomimetics with a Beta-D-Glucose scaffolding (Hirschmann et al., J. Amer.
Chem. Soc. 114:9217-9218 (1992)), analogous organic syntheses of small compound libraries (Chen et al., J. Amer.
Chem. Soc. 116:2661 (1994)), oligocarbarnates (Cho, et al., Science 261:1303 (1993)), and/or peptidyl phosphonates (Campbell et al., J. Org. Chem.
59:658 (1994)). See, generally, Gordon et al., J. Med. Chem. 37:1385 (1994), nucleic acid libraries (see, e.g., Stratagene, Corp.), peptide nucleic acid libraries (see, e.g., U.S. Patent 5,539,083), antibody libraries (see, e.g., Vaughn et al., Nature Biotechnology 14(3): 309-314 (1996), and PCT/US96/10287), carbohydrate libraries (see, e.g., Liang et at, Science 274:1520-1522 (1996), and U.S. Patent No. 5,593,853), and small organic molecule libraries (see, e.g., benzodiazepines, Baum, C&EN, Jan 18, page 33 (1993); isoprenoids, U.S. Patent No. 5,569,588;
thiazolidinones and metathiazanones, U.S.
Patent No. 5,549,974; pyrrolidines, U.S. Patent Nos. 5,525,735 and 5,519,134;
morpholino compounds, U.S. Patent No.

5,506, 337; benzodiazepines, U.S. Patent No. 5,288,514; and the like).
Devices for the preparation of combinatorial libraries are commercially available (see, e.g., 357 NIPS, 390 NIPS, Advanced Chem Tech, Louisville KY; Symphony, Rainin, Woburn, MA; 433A, Applied Biosystems, Foster City, CA; 9050, Plus, Millipore, Bedford, NIA). A number of well-known robotic systems have also been developed for solution phase - chemistries. These systems include automated workstations such as the automated synthesis apparatus developed by Takeda Chemical Industries, LTD. (Osaka, Japan) and many robotic systems utilizing robotic arms (Zymate H, Zymark Corporation, Hopkinton, Mass.; Orca, Hewlett-Packard, Palo Alto, Calif.), which mimic the manual synthetic operations performed by a chemist. Any of the above devices are suitable for use with the present invention. The nature and implementation of modifications to these devices (if any) so that they can operate as discussed herein will be apparent to persons skilled in the relevant art. In addition, numerous combinatorial libraries are themselves commercially available (see, e.g., ComGenex, Princeton, NJ; Asinex, Moscow, RU; Tripos, Inc., St. Louis, MO; ChemStar, Ltd, Moscow, RU; 3D
Pharmaceuticals, Exton, PA; Martek Biosciences, Columbia, MD; etc.).
The term "cytotoxic agent" refers to a substance that inhibits or prevents the expression activity of cells, function of cells and/or causes destruction of cells. The term is intended to include radioactive isotopes chemotherapeutic agents, and toxins such as small molecule toxins or enzymatically active toxins of bacterial, fungal, plant or animal origin, including fragments and/or variants thereof. Examples of cytotoxic agents include, but are not limited to auristatins, auromycins, maytansinoids, yttrium, bismuth, ricin, ricin A-chain, combrestatin, duocarmycins, dolostatins, doxorubicin, daunorubicin, taxol, cisplatin, cc1065, ethidium bromide, mitomycin, etoposide, tenoposide, vincristine, vinblastine, colchicine, dihydroxy anthracin dione, actinomycin, diphtheria toxin, Pseudomonas exotoxin (PE) A, PE40, abrin, abrin A chain, modeccin A chain, alpha-sarcin, gelonin, mitogellin, retstrictocin, phenomycin, enomycin, curicin, crotin, calicheamicin, Sapaonaria officinalis inhibitor, and glucocorticoid and other chemotherapeutic agents, as well as radioisotopes such as At211, 1131, 1125, ro, Res, Re188, Sm153, B1212 or 213, p32 and radioactive isotopes of Lu including Luln.
Antibodies may also be conjugated to an anti-cancer pro-drug activating enzyme capable of converting the pro-drug to its active form.
The "gene product' is sometimes referred to herein as a protein or mRNA. For example, a "gene product of the invention" is sometimes referred to herein as a "cancer amino acid sequence", "cancer protein", "protein of a cancer listed in Table I", a "cancer mRNA", "mRNA of a cancer listed in Table I", etc. In one embodiment, the cancer protein is encoded by a nucleic acid of Figure 2. The cancer protein can be a fragment, or altematively, be the full-length protein to the fragment encoded by the nucleic acids of Figure 2. In one embodiment, a cancer amino acid sequence is used to determine sequence identity or similarity. In another embodiment, the sequences are naturally occurring allelic variants of a protein encoded by a nucleic acid of Figure 2. In another embodiment, the sequences are sequence variants as further described herein.
"High throughput screening" assays for the presence, absence, quantification, or other properties of particular nucleic acids or protein products are well known to those of skill in the art.
Similarly, binding assays and reporter gene assays are similarly well known. Thus, e.g., U.S. Patent No. 5,559,410 discloses high throughput screening methods for proteins; U.S. Patent No. 5,585,639 discloses high throughput screening methods for nucleic acid binding (i.e., in arrays);
while U.S. Patent Nos. 5,576,220 and 5,541,061 disclose high throughput methods of screening for ligand/antibody binding.
In addition, high throughput screening systems are commercially available (see, e.g., Amersham Biosciences, Piscataway, NJ; Zymark Corp., Hopkinton, MA; Air Technical Industries, Mentor, OH; Beckman Instruments, Inc. Fullerton, CA; Precision Systems, Inc., Natick, MA; etc.). These systems typically automate entire procedures, including all sample and reagent pipetting, liquid dispensing, timed incubations, and final readings of the microplate in detector(s) appropriate for the assay. These configurable systems provide high throughput and rapid start up as well as a high degree of flexibility and customization. The manufacturers of such systems provide detailed protocols for various high throughput systems. Thus, e.g., Zymark Corp. provides technical bulletins describing screening systems for detecting the modulation of gene transcription, ligand binding, and the like.

The term "homolog" refers to a molecule which exhibits homology to another molecule, by for example, having sequences of chemical residues that are the same or similar at corresponding-positions.
"Human Leukocyte Antigen" or "HLA" is a human class I or class II Major Histocompatibility Complex (MHC) protein (see, e.g., Stites, etal., IMMUNOLOGY, 8TH ED., Lange Publishing, Los Altos, CA (1994).
The terms "hybridize", "hybridizing", "hybridizes" and the like, used in the context of polynucleotides, are meant to refer to conventional hybridization conditions, preferably such as hybridization in 50% formamide/6XSSC/0.1% SDS/100 1.1.g/mIssDNA, in which temperatures for hybridization are above 37 degrees C
and temperatures for washing in 0.1XSSC/0.1 /0 SDS are above 55 degrees C.
The phrases "isolated" or "biologically pure" refer to material which is substantially or essentially free from components which normally accompany the material as it is found in its native state. Thus, isolated peptides in accordance with the invention preferably do not contain materials normally associated with the peptides in their in situ environment. For example, a polynucleotide is said to be "isolated" when it is substantially separated from contaminant polynucleotides that correspond or are complementary to genes other than the 161P2F1OB genes or that encode polypeptides other than 161P2F1OB
gene product or fragments thereof. A skilled artisan can readily employ nucleic acid isolation procedures to obtain an isolated 161P2F1OB polynucleotide. A protein is said to be "isolated," for example, when physical, mechanical or chemical methods are employed to remove the 161P2F1OB proteins from cellular constituents that are normally associated with the protein. A skilled artisan can readily employ standard purification methods to obtain an isolated 161P2F1OB protein. Alternatively, an isolated protein can be prepared by chemical means.
The term "mammal" refers to any organism classified as a mammal, including mice, rats, rabbits, dogs, cats, cows, horses and humans. In one embodiment of the invention, the mammal is a mouse.
In another embodiment of the invention, the mammal is a human.
The terms "metastatic prostate cancer" and "metastatic disease" mean prostate cancers that have spread to regional lymph nodes or to distant sites, and are meant to include stage D
disease under the AUA system and stage TxNxM+ under the TNM system. As is the case with locally advanced prostate cancer, surgery is generally not indicated for patients with metastatic disease, and hormonal (androgen ablation) therapy is a preferred treatment modality. Patients with metastatic prostate cancer eventually develop an androgen-refractory state within 12 to 18 months of treatment initiation.
Approximately half of these androgen-refractory patients die within 6 months after developing that status. The most common site for prostate cancer metastasis is bone. Prostate cancer bone metastases are often osteoblastic rather than osteolytic (i.e., resulting in net bone formation). Bone metastases are found most frequently in the spine, followed by the femur, pelvis, rib cage, skull and humerus. Other common sites for metastasis include lymph nodes, lung, liver and brain. Metastatic prostate cancer is typically diagnosed by open or laparoscopic pelvic lymphadenectomy, whole body radionuclide scans, skeletal radiography, and/or bone lesion biopsy.
The term "modulator" or "test compound" or "drug candidate" or grammatical equivalents as used herein describe any molecule, e.g., protein, oligopeptide, small organic molecule, polysaccharide, polynucleotide, etc., to be tested for the capacity to directly or indirectly alter the cancer phenotype or the expression of a cancer sequence, e.g., a nucleic acid or protein sequences, or effects of cancer sequences (e.g., signaling, gene expression, protein interaction, etc.) In one aspect, a modulator will neutralize the effect of a cancer protein of the invention.
By "neutralize" is meant that an activity of a protein is inhibited or blocked, along with the consequent effect on the cell. In another aspect, a modulator will neutralize the effect of a gene, and its corresponding protein, of the invention by normalizing levels of said protein. In preferred embodiments, modulators alter expression profiles, or expression profile nucleic acids or proteins provided herein, or downstream effector pathways. In one embodiment, the modulator suppresses a cancer phenotype, e.g.
to a normal tissue fingerprint. In another embodiment, a modulator induced a cancer phenotype. Generally, a plurality of assay mixtures is run in parallel with different agent concentrations to obtain a differential response to the various concentrations. Typically, one of these concentrations serves as a negative control, i.e., at zero concentration or below the level of detection.
Modulators, drug candidates or test compounds encompass numerous chemical classes, though typically they are organic molecules, preferably small organic compounds having a molecular weight of more than 100 and less than about 2,500 Daltons. Preferred small molecules are less than 2000, or less than 1500 or less than 1000 or less than 500 D.
Candidate agents comprise functional groups necessary for structural interaction with proteins, particularly hydrogen bonding, and typically include at least an amine, carbonyl, hydroxyl or carboxyl group, preferably at least two of the functional chemical groups. The candidate agents often comprise cyclical carbon or heterocyclic structures and/or aromatic or polyaromatic structures substituted with one or more of the above functional groups. Modulators also comprise biomolecules such as peptides, saccharides, fatty acids, steroids, purines, pyrimidines, derivatives, structural analogs or combinations thereof. Particularly preferred are peptides. One class of modulators are peptides, for example of from about five to about 35 amino acids, with from about five to about 20 amino acids being preferred, and from about 7 to about 15 being particularly preferred. Preferably, the cancer modulatory protein is soluble, includes a non-transmembrane region, and/or, has an N-terminal Cys to aid in solubility. In one embodiment, the C-terminus of the fragment is kept as a free acid and the N-terminus is a free amine to aid in coupling, i.e., to cysteine. In one embodiment, a cancer protein of the invention is conjugated to an immunogenic agent as discussed herein. In one embodiment, the cancer protein is conjugated to BSA. The peptides of the invention, e.g., of preferred lengths, can be linked to each other or to other amino acids to create a longer peptide/protein.
The modulatory peptides can be digests of naturally occurring proteins as is outlined above, random peptides, or "biased"
random peptides. In a preferred embodiment, peptide/protein-based modulators are antibodies, and fragments thereof, as defined herein.
Modulators of cancer can also be nucleic acids. Nucleic acid modulating agents can be naturally occurring nucleic acids, random nucleic acids, or "biased" random nucleic acids. For example, digests of prokaryotic or eukaryotic genomes can be used in an approach analogous to that outlined above for proteins.
The term "monoclonal antibody" refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the antibodies comprising the population are identical except for possible naturally occurring mutations that are present in minor amounts.
A "motif", as in biological motif of a 161P2F10B-related protein, refers to any pattern of amino acids forming part of the primary sequence of a protein, that is associated with a particular function (e.g. protein-protein interaction, protein-DNA
interaction, etc) or modification (e.g. that is phosphorylated, glycosylated or amidated), or localization (e.g. secretory sequence, nuclear localization sequence, etc.) or a sequence that is correlated with being immunogenic, either humorally or cellularly. A motif can be either contiguous or capable of being aligned to certain positions that are generally correlated with a certain function or property. In the context of HLA motifs, "motif" refers to the pattern of residues in a peptide of defined length, usually a peptide of from about 8 to about 13 amino acids for a class I HLA motif and from about 6 to about 25 amino acids for a class ll HLA motif, which is recognized by a particular HLA
molecule. Peptide motifs for HLA binding are typically different for each protein encoded by each human HLA allele and differ in the pattern of the primary and secondary anchor residues.
A "pharmaceutical excipient" comprises a material such as an adjuvant, a carrier, pH-adjusting and buffering agents, tonicity adjusting agents, wetting agents, preservative, and the like.
"Pharmaceutically acceptable" refers to a non-toxic, inert, and/or composition that is physiologically compatible with humans or other mammals.
The term "polynucleotide" means a polymeric form of nucleotides of at least 10 bases or base pairs in length, either ribonucleotides or deoxynucleotides or a modified form of either type of nucleotide, and is meant to include single and double stranded forms of DNA and/or RNA. In the art, this term if often used interchangeably with "oligonucleotide". A
polynucleotide can comprise a nucleotide sequence disclosed herein wherein thymidine (T), as shown for example in Figure 2, can also be uracil (U); this definition pertains to the differences between the chemical structures of DNA and RNA, in particular the observation that one of the four major bases in RNA is uracil (U) instead of thymidine (T).
The term "polypeptide" means a polymer of at least about 4, 5, 6, 7, or 8 amino acids. Throughout the specification, standard three letter or single letter designations for amino acids are used. In the art, this term is often used interchangeably with "peptide" or "protein".
An HLA "primary anchor residue" is an amino acid at a specific position along a peptide sequence which is understood to provide a contact point between the immunogenic peptide and the HLA molecule. One to three, usually two, primary anchor residues within a peptide of defined length generally defines a "motif" for an immunogenic peptide. These residues are understood to fit in close contact with peptide binding groove of an HLA molecule, with their side chains buried in specific pockets of the binding groove. In one embodiment, for example, the primary anchor residues for an HLA class I
molecule are located at position 2 (from the amino terminal position) and at the carboxyl terminal position of a 8, 9, 10, 11, or 12 residue peptide epitope in accordance with the invention. Alternatively, in another embodiment, the primary anchor residues of a peptide binds an HLA class II molecule are spaced relative to each other, rather than to the termini of a peptide, where the peptide is generally of at least 9 amino acids in length.
The primary anchor positions for each motif and supermotif are set forth in Table IV. For example, analog peptides can be created by altering the presence or absence of particular residues in the primary and/or secondary anchor positions shown in Table IV. Such analogs are used to modulate the binding affinity and/or population coverage of a peptide comprising a particular HLA motif or supermotif.
"Radioisotopes" include, but are not limited to the following (non-limiting exemplary uses are also set forth):
Examples of Medical Isotopes:
Isotope Description of use Actinium-225 (AC-225) See Thorium-229 (Th-229) Actinium-227 (AC-227) Parent of Radium-223 (Ra-223) which is an alpha emitter used to treat metastases in the skeleton resulting from cancer (i.e., breast and prostate cancers), and cancer radioimmunotherapy Bismuth-212 (Bi-212) See Thorium-228 (Th-228) Bismuth-213 (Bi-213) See Thorium-229 (Th-229) Cadmium-109 (Cd-109) Cancer detection Cobalt-60 (Co-60) Radiation source for radiotherapy of cancer, for food irradiators, and for sterilization of medical supplies Copper-64 (Cu-64) A positron emitter used for cancer therapy and SPECT imaging Copper-67 (Cu-67) Beta/gamma emitter used in cancer radioimmunotherapy and diagnostic studies (i.e., breast and colon cancers, and lymphoma) Dysprosium-166 (Dy-166) Cancer radioimmunotherapy Erbium-169 (Er-169) Rheumatoid arthritis treatment, particularly for the small joints associated with fingers and toes Europium-152 (Eu-152) Radiation source for food irradiation and for sterilization of medical supplies Europium-154 (Eu-154) Radiation source for food irradiation and for sterilization of medical supplies Gadolinium-153 (Gd-153) Osteoporosis detection and nuclear medical quality assurance devices Gold-198 (Au-198) Implant and intracavity therapy of ovarian, prostate, and brain cancers Holmium-166 (Ho-166) Multiple myeloma treatment in targeted skeletal therapy, cancer radioimmunotherapy, bone marrow ablation, and rheumatoid arthritis treatment Iodine-125 (1-125) Osteoporosis detection, diagnostic imaging, tracer drugs, brain cancer treatment, radiolabeling, tumor imaging, mapping of receptors in the brain, interstitial radiation therapy, brachytherapy for treatment of prostate cancer, determination of glomerular filtration rate (GFR), determination of plasma volume, detection of deep vein thrombosis of the legs Iodine-131 (1-131) Thyroid function evaluation, thyroid disease detection, treatment of thyroid cancer as well as other non-malignant thyroid diseases (i.e., Graves disease, goiters, and hyperthyroidism), treatment of leukemia, lymphoma, and other forms of cancer (e.g., breast cancer) using radioimmunotherapy Iridium-192 (Ir-192) Brachytherapy, brain and spinal cord tumor treatment, treatment of blocked arteries (i.e., arteriosclerosis and restenosis), and implants for breast and prostate tumors Lutetium-177 (Lu-177) Cancer radioimmunotherapy and treatment of blocked arteries (i.e., arteriosclerosis and restenosis) Molybdenum-99 (Mo-99) Parent of Technetium-99m (Tc-99m) which is used for imaging the brain, liver, lungs, heart, and other organs.
Currently, Tc-99m is the most widely used radioisotope used for diagnostic imaging of various cancers and diseases involving the brain, heart, liver, lungs; also used in detection of deep vein thrombosis of the legs Osmium-194 (0s-194) Cancer radioimmunotherapy Palladium-103 (Pd-103) Prostate cancer treatment Platinum-195m (Pt-195m) Studies on biodistribution and metabolism of cisplatin, a chemotherapeutic drug Phosphorus-32 (P-32) Polycythemia rubra vera (blood cell disease) and leukemia treatment, bone cancer diagnosis/treatment; colon, pancreatic, and liver cancer treatment; radiolabeling nucleic acids for in vitro research, diagnosis of superficial tumors, treatment of blocked arteries (i.e., arteriosclerosis and restenosis), and intracavity therapy Phosphorus-33 (P-33) Leukemia treatment, bone disease diagnosis/treatment, radiolabeling, and treatment of blocked arteries (i.e., arteriosclerosis and restenosis) Radium-223 (Ra-223) See Actinium-227 (Ac-227) Rhenium-186 (Re-186) Bone cancer pain relief, rheumatoid arthritis treatment, and diagnosis and treatment of lymphoma and bone, breast, colon, and liver cancers using radioimmunotherapy Rhenium-188 (Re-188) Cancer diagnosis and treatment using radioimmunotherapy, bone cancer pain relief, treatment of rheumatoid arthritis, and treatment of prostate cancer Rhodium-105 (Rh-105) Cancer radioimmunotherapy Samarium-145 (Sm-145) Ocular cancer treatment Samarium-153 (Sm-153) Cancer radioimmunotherapy and bone cancer pain relief Scandium-47 (Sc-47) Cancer radioimmunotherapy and bone cancer pain relief Selenium-75 (Se-75) Radiotracer used in brain studies, imaging of adrenal cortex by gamma-scintigraphy, lateral locations of steroid secreting tumors, pancreatic scanning, detection of hyperactive parathyroid glands, measure rate of bile acid loss from the endogenous pool Strontium-85 (Sr-85) Bone cancer detection and brain scans Strontium-89 (Sr-89) Bone cancer pain relief, multiple myeloma treatment, and osteoblastic therapy Technetium-99m (Tc-99m) See Molybdenum-99 (Mo-99) Thorium-228 (Th-228) Parent of Bismuth-212 (Bi-212) which is an alpha emitter used in cancer radioimmunotherapy Thorium-229 (Th-229) Parent of Actinium-225 (Ac-225) and grandparent of Bismuth-213 (Bi-213) which are alpha emitters used in cancer radioimmunotherapy Thulium-170 ( Tm-170) Gamma source for blood irradiators, energy source for implanted medical devices Tin-117m (Sn-117m) Cancer immunotherapy and bone cancer pain relief Tungsten-188 (W-188) Parent for Rhenium-188 (Re-188) which is used for cancer diagnostics/treatment, bone cancer pain relief, rheumatoid arthritis treatment, and treatment of blocked arteries (i.e., arteriosclerosis and restenosis) Xenon-127 (Xe-127) Neuroimaging of brain disorders, high resolution SPECT studies, pulmonary function tests, and cerebral blood flow studies Ytterbium-175 (Yb-175) Cancer radioimmunotherapy Yttrium-90 (Y-90) Microseeds obtained from irradiating Yttrium-89 (Y-89) for liver cancer treatment Yttrium-91 (Y-91) A gamma-emitting label for Yttrium-90 (Y-90) which is used for cancer radioimmunotherapy (i.e., lymphoma, breast, colon, kidney, lung, ovarian, prostate, pancreatic, and inoperable liver cancers) By "randomized" or grammatical equivalents as herein applied to nucleic acids and proteins is meant that each nucleic acid and peptide consists of essentially random nucleotides and amino acids, respectively. These random peptides (or nucleic acids, discussed herein) can incorporate any nucleotide or amino acid at any position. The synthetic process can be designed to generate randomized proteins or nucleic acids, to allow the formation of all or most of the possible combinations over the length of the sequence, thus forming a library of randomized candidate bioactive proteinaceous agents.

In one embodiment, a library is "fully randomized," with no sequence preferences or constants at any position. In another embodiment, the library is a "biased random" library. That is, some positions within the sequence either are held constant, or are selected from a limited number of possibilities. For example, the nucleotides or amino acid residues are randomized within a defined class, e.g., of hydrophobic amino acids, hydrophilic residues, sterically biased (either small or large) residues, towards the creation of nucleic acid binding domains, the creation of cysteines, for cross-finking, pralines for SH-3 domains, serines, threonines, tyrosines or histidines for phosphorylation sites, etc., or to purines, etc.
A "recombinanr DNA or RNA molecule is a DNA or RNA molecule that has been subjected to molecular manipulation in vim).
Non-limiting examples of small molecules include compounds that bind or interact with 161P2F10B, ligands including hormones, neuropeptides, chemokines, odorants, phospholipids, and functional equivalents thereof that bind and preferably inhibit 161P2F108 protein function. Such non-limiting small molecules preferably have a molecular weight of less than abou110 kDa, more preferably below about 9, about 8, about 7, about 6, about 5 or about 4 kDa. In certain embodiments, small molecules physically associate with, or bind, 161P2F1013 protein; are not found in naturally occurring metabolic pathways; and/or are more soluble in aqueous than non-aqueous solutions "Stringency" of hybridization reactions is readily determinable by one of ordinary skill in the art, and generally is an empirical calculation dependent upon probe length, washing temperature, and salt concentration. In general, longer probes require higher temperatures for proper annealing, while shorter probes need lower temperatures. Hybridization generally depends on the ability of denatured nucleic acid sequences to reanneal when complementary strands are present in an environment below their melting temperature. The higher the degree of desired homology between the probe and hybridizable sequence, the higher the relative temperature that can be used.
As a result, it follows that higher relative temperatures would tend to make the reaction conditions more stringent, while lower temperatures less so. For additional details and explanation of stringency of hybridization reactions, see Ausubel etal., Current Protocols in Molecular Biology, Wiley Interscience Publishers, (1995).
"Stringent conditions" or "high stringency conditions", as defined herein, are identified by, but not limited to, those that: (1) employ low ionic strength and high temperature for washing, for example 0.015 M sodium chloride/0.0015 M sodium citrate/0.1% sodium dodecyl sulfate at 50 C; (2) employ during hybridization a denaturing agent, such as formamide, for example, 50% (v/v) formamide with 0.1% bovine serum albumin/0.1% Ficollim10.1%
polyvinylpyrrolidine/50 mM sodium phosphate buffer at pH 6.5 with 750 mM sodium chloride, 75 mM sodium citrate at 42 C; or (3) employ 50% formamide, 5 x SSC (0.75 M NaCI, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5 x Denhardrs solution, sonicated salmon sperm DNA (50 110/m1), 0.1% SDS, and 10%
dextran sulfate at 42 C, with washes at 42 C in 0.2 x SSC (sodium chloride/sodium, citrate) and 50% formamide at 55 0C, followed by a high-stringency wash consisting of 0.1 x SSC containing EDTA at 55 C. "Moderately stringent conditions" are described by, but not limited to, those in Sambrook et al., Molecular Cloning: A Laboratory Manual, New York:
Cold Spring Harbor Press, 1989, and include the use of washing solution and hybridization conditions (e.g., temperature, ionic strength and %SDS) less stringent than those described above. An example of moderately stringent conditions is overnight incubation at 37 C in a solution comprising: 20% formamide, 5 x SSC (150 mM NaCI, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5 x Denhards solution, 10% dextran sulfate, and 20 mg/mL denatured sheared salmon sperm DNA, followed by washing the filters in 1 x SSC at about 37-50 C. The skilled artisan will recognize how to adjust the temperature, ionic strength, etc. as necessary to accommodate factors such as probe length and the like.
An HLA "supermotir is a peptide binding specificity shared by HLA molecules encoded by two or more HLA alleles.
Overall phenotypic frequencies of HtA-supertypes in different ethnic populations are set forth in Table IV (F). The non-limiting constituents of various supetypes are as follows:

A2: A*0201, A*0202, A*0203, A*0204, A* 0205, A*0206, A*6802, A*6901, A*0207 A3: A3, All, A31, A*3301, A*6801, A*0301, A*1101, A*3101 B7: B7, B*3501-03, B*51, B*5301, B*5401, B*5501, B*5502, 8*5601, 8*6701, B*7801, B*0702, B*5101, B*5602 B44: B*3701, B*4402, B*4403, B*60 (B*4001), B61 (B*4006) At A*0102, A*2604, A*3601, A*4301, A*8001 A24: A*24, A*30, A*2403, A*2404, A*3002, A*3003 B27: B*1401-02, 8*1503, B*1509, B*1510, B*1518, B*3801-02, B*3901, B*3902, B*3903-04, B*4801-02, B*7301, B*2701-08 658: 6*1516, B*1517, 6*5701, B*5702, B58 1362: B*4601, B52, B*1501 (862), B*1502 (875), B*1513 (B77) Calculated population coverage afforded by different HLA-supertype combinations are set forth in Table IV (G).
As used herein "to treat" or "therapeutic" and grammatically related terms, refer to any improvement of any consequence of disease, such as prolonged survival, less morbidity, and/or a lessening of side effects which are the byproducts of an alternative therapeutic modality; full eradication of disease is not required.
A "transgenic animal" (e.g., a mouse or rat) is an animal having cells that contain a transgene, which transgene was introduced into the animal or an ancestor of the animal at a prenatal, e.g., an embryonic stage. A "transgene" is a DNA
that is integrated into the genome of a cell from which a transgenic animal develops.
As used herein, an HLA or cellular immune response 'vaccine" is a composition that contains or encodes one or more peptides of the invention. There are numerous embodiments of such vaccines, such as a cocktail of one or more individual peptides; one or more peptides of the invention comprised by a polyepitopic peptide; or nucleic acids that encode such individual peptides or polypeptides, e.g., a minigene that encodes a polyepitopic peptide. The "one or more peptides"
can include any whole unit integer from 1-150 or more, e.g., at least 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, or 150 or more peptides of the invention.
The peptides or polypeptides can optionally be modified, such as by lipidation, addition of targeting or other sequences. HLA
class I peptides of the invention can be admixed with, or linked to, HLA class II peptides, to facilitate activation of both cytotoxic T lymphocytes and helper T lymphocytes. HLA vaccines can also comprise peptide-pulsed antigen presenting cells, e.g., dendritic cells.
The term "variant" refers to a molecule that exhibits a variation from a described type or norm, such as a protein that has one or more different amino acid residues in the corresponding position(s) of a specifically described protein (e.g. the 161P2F1OB
protein shown in Figure 2 or Figure 3. An analog is an example of a variant protein. Splice isoforms and single nucleotides polymorphisms (SNPs) are further examples of variants.
The "161P2F106-related proteins" of the invention include those specifically identified herein, as well as allelic variants, conservative substitution variants, analogs and homologs that can be isolated/generated and characterized without undue experimentation following the methods outlined herein or readily available in the art. Fusion proteins that combine parts of different 161P2F1OB proteins or fragments thereof, as well as fusion proteins of a 161P2F106 protein and a heterologous polypeptide are also included. Such 161P2F1OB proteins are collectively referred to as the 161P2F10B-related proteins, the proteins of the invention, or 161P2F106. The term "161P2F10B-related protein"
refers to a polypeptide fragment or a 161P2F1OB
protein sequence of 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,21, 22, 23, 24, 25, or more than 25 amino acids; or, at least 30, 35, 40, 45, 50, 55, 60, 65, 70, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 650, or 664 or more amino acids.

IL) 161P2F1OB Polynucleotides One aspect of the invention provides polynucleotides corresponding or complementary to all or part of a 161P2F1OB gene, mRNA, and/or coding sequence, preferably in isolated form, including polynucleotides encoding a 161P2F10B-related protein and fragments thereof, DNA, RNA, DNA/RNA hybrid, and related molecules, polynucleotides ar oligonucleotides complementary to a 161P2F1OB gene or mRNA sequence or a part thereof, and polynucleotides or oligonucleotides that hybridize to a 161P2F1OB gene, mRNA, or to a 161P2F1OB
encoding polynucleotide (collectively, "161P2F1OB polynucleotides"). In all instances when referred to in this section, T can also be U in Figure 2.
Embodiments of a 161P2F1OB polynucleotide include: a 161P2F10B polynucleotide having the sequence shown in Figure 2, the nucleotide sequence of 161P2F1OB as shown in Figure 2 wherein T
is U; at least 10 contiguous nucleotides of a polynucleotide having the sequence as shown in Figure 2; or, at least 10 contiguous nucleotides of a polynucleotide having the sequence as shown in Figure 2 where T is U. For example, embodiments of 161P2F1OB nucleotides comprise, without limitation:
(I) a polynucleotide comprising, consisting essentially of, or consisting of a sequence as shown in Figure 2, wherein T can also be U;
(II) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in Figure 2A, from nucleotide residue number 44 through nucleotide residue number 2671, including the stop codon, wherein T can also be U;
(III) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in Figure 2B, from nucleotide residue number 44 through nucleotide residue number 2671, including the stop codon, wherein T can also be U;
(IV) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in Figure 2C, from nucleotide residue number 44 through nucleotide residue number 2671, including the a stop codon, wherein T can also be U;
(V) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in Figure 2D, from nucleotide residue number 44 through nucleotide residue number 2671, including the stop codon, wherein T can also be U;
(VI) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in Figure 2E, from nucleotide residue number 44 through nucleotide residue number 2671, including the stop codon, wherein T can also be U;
(VII) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in Figure 2F, from nucleotide residue number 84 through nucleotide residue number 2711, including the stop codon, wherein T can also be U;
(VIII) a polynucleotide comprising, consisting essentially of, or consisting of the sequence as shown in Figure 2G, from nucleotide residue number 276 through nucleotide residue number 2801, including the stop codon, wherein T can also be U;

(IX) a polynucleotide that encodes a 161P2F10B-related protein that is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% homologous to an entire amino acid sequence shown in Figure 2A-G;
(X) a polynucleotide that encodes a 161P2F10B-related protein that is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% identical to an entire amino acid sequence shown in Figure 2A-G;
(XI) a polynucleotide that encodes at least one peptide set forth in Tables VIII-XXI and XXII-XLIX;
(XII) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of Figure 3A-D in any whole number increment up to 875 that includes at least 1, 2, 3,4, 5, 6,7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,35 amino acid position(s) having a value greater than 0.5 in the Hydrophilicity profile of Figure 5;
(XIII) a polynucleotide that encodes a peptide region of at least 5,6, 7, 8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,35 amino acids of a peptide of Figure 3A-D in any whole number increment up to 875 that includes 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value less than 0.5 in the Hydropathicity profile of Figure 6;
(XIV) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,35 amino acids of a peptide of Figure 3A-D in any whole number increment up to 875 that includes 1, 2, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Percent Accessible Residues profile of Figure 7;
(XV) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of Figure 3A-DF in any whole number increment up to 875 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Average Flexibility profile of Figure 8;
(XVI) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,35 amino acids of a peptide of Figure 3A-D in any whole number increment up to 875 that includes 1, 2, 3, 4, 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Beta-turn profile of Figure 9;
(XVII) a polynucleotide that encodes a peptide-region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of Figure 3E in any whole number increment up to 841 that includes 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Hydrophilicity profile of Figure 5;

(XVIII) a polynucleotide that encodes a peptide region of at least 5,6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of Figure 3E in any whole number increment up to 841 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value less than 0.5 in the Hydropathicity profile of Figure 6;
(XIX) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34,35 amino acids of a peptide of Figure 3E in any whole number increment up to 841 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Percent Accessible Residues profile of Figure 7;
(XX) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of Figure 3E in any whole number increment up to 841 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Average Flexibility profile of Figure 8;
()Oa) a polynucleotide that encodes a peptide region of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a peptide of Figure 3E in any whole number increment up to 841 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Beta-turn profile of Figure 9 (XXII) a polynucleotide that encodes monoclonal antibody or binding region thereof secreted by a hybridoma entitled X41(3)15 deposited with the American Type Culture Collection (ATCC; 10801 University Blvd., Manassas, VA
20110-2209 USA) on 07 November 2002 and assigned as Accession No. PTA-4791;
(XXIII) a polynucleotide that encodes monoclonal antibody or binding region thereof secreted by a hybridoma entitled X41(3)29 deposited with the American Type Cufture Collection (ATCC;
10801 University Blvd., Manassas, VA 20110-2209 USA) on 07 November 2002 and assigned as Accession No. PTA-4791;
(XXIV) a polynucleotide that encodes monoclonal antibody or binding region thereof secreted by a hybridoma entitled X41(3)37 deposited with the American Type Culture Collection (ATCC;
10801 University Blvd., Manassas, VA 20110-2209 USA) on 07 November 2002 and assigned as Accession No. PTA-4791;
(X0/) a polynucleotide that encodes monoclonal antibody or binding region thereof secreted by a hybridoma entitled X41(4)6 deposited with the American Type Culture Collection (ATCC;
10801 University Blvd., Manassas, VA
20110-2209 USA) on 07 November 2002 and assigned as Accession No. PTA-4794;
(XXVI) a polynucleotide that encodes monoclonal antibody or binding region thereof secreted by a hybridoma entitled X41(3)17 deposited with the American Type Culture Collection (ATCC;
10801 University Blvd., Manassas, VA 20110-2209 USA) on 07 November 2002 and assigned as Accession No. PTA-4792;

(XXVII) a polynucleotide that encodes monoclonal antibody or binding region thereof secreted by a hybridoma entitled X41(3)50 deposited with the American Type Culture Collection (ATCC;
10801 University Blvd., Manassas, VA 20110-2209 USA) on 07 November 2002 and assigned as Accession No. PTA-4793;
(XXVIII) a polynucleotide that is fully complementary to a polynucleotide of any one of (1)-(X)(V11).
(XXIX) a peptide that is encoded by any of (I) to (X)(VII); and (XXX) a composition comprising a polynucleotide of any of (1)-(XXVII) or peptide of (XXIX) together with a pharmaceutical excipient and/or in a human unit dose form.
(XXXI) a method of using a polynucleotide of any (1)-(XXVII) or peptide of (XXIX) or a composition of (XXX) in a method to modulate a cell expressing 161P2F10b, (XXXII) a method of using a polynucleotide of any (1)-(XXVII) or peptide of (XXIX) or a composition of (XXX) in a method to diagnose, prophylax, prognose, or treat an individual who bears a cell expressing 161P2F10b (XXXIII) a method of using a polynucleotide of any (I)-(XXVII) or peptide of (XXIX) or a composition of (XXX) in a method to diagnose, prophylax, prognose, or treat an individual who bears a cell expressing 161P2F10b, said cell from a cancer of a tissue listed in Table I;
(XXXIV) a method of using a polynucleotide of any (1)-(XLII) or peptide of (XXIX) or a composition of (XXX) in a method to diagnose, prophylax, prognose, or treat a cancer;
(OON) a method of using a polynucleotide of any (1)-(XLII) or peptide of (XXIX) or a composition of (XXX) in a method to diagnose, prophylax, prognose, or treat a cancer of a tissue listed in Table I; and, (XXXVI) a method of using a polynucleotide of any (1)-(XLII) or peptide of (XXIX) or a composition of (XXX) in a method to identify or characterize a modulator of a cell expressing 161P2F10b.
As used herein, a range is understood to disclose specifically all whole unit positions thereof.
Typical embodiments of the invention disclosed herein include 161P2F1OB
polynudeotides that encode specific portions of 161P2F1OB mRNA sequences (and those which are complementary to such sequences) such as those that encode the proteins and/or fragments thereof, for example:
(a) 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 650, 675, 700, 725, 750, 775, 800, 825, 850, 860, 870, 875 or more contiguous amino acids of 161P2F1OB variant 1; the maximal lengths relevant for other variants are:
variant 2, 875 amino acids; variant 3, 875 amino acids, variant 4, 875 amino acids, and variant 7, 841 amino acids.
For example, representative embodiments of the invention disclosed herein include: polynucleotides and their encoded peptides themselves encoding about amino acid Ito about amino acid 10 of the 161P2F1OB protein shown in Figure 2 or 3, polynucleotides encoding about amino acid 10 to about amino acid 20 of the 161P2F1OB protein shown in Figure 2 or Figure 3, polynucleotides encoding about amino acid 20 to about amino acid 30 of the 161P2F1OB protein shown in Figure 2 or Figure 3, polynucleotides encoding about amino acid 30 to about amino acid 40 of the 161P2F1OB
protein shown in Figure 2 or Figure 3, polynucleotides encoding about amino acid 40 to about amino acid 50 of the 161P2F1OB protein shown in Figure 2 or Figure 3, polynucleotides encoding about amino acid 50 to about amino acid 60 of the 161P2F1OB protein shown in Figure 2 or Figure 3, polynucleotides encoding about amino acid 60 to about amino acid 70 of the 161P2F1OB protein shown in Figure 2 or Figure 3, polynucleotides encoding about amino acid 70 to about amino acid 80 of the 161P2F1OB protein shown in Figure 2 or Figure 3, polynucleotides encoding about amino acid 80(0 about amino acid 90 of the 161P2F1OB protein shown in Figure 2 or Figure 3, polynucleotides encoding about amino acid 90 to about amino acid 100 of the 161P2F1OB protein shown in Figure 2 or Figure 3, in increments of about 10 amino acids, ending at the carboxyl terminal amino acid set forth in Figure 2 or Figure 3.
Accordingly, polynucleotides encoding portions of the amino acid sequence (of about 10 amino acids), of amino acids, 100 through the carboxyl terminal amino acid of the 161P2F1OB protein are embodiments of the invention. Wherein it is understood that each particular amino acid position discloses that position plus or minus five amino acid residues.
Polynucleotides encoding relatively long portions of a 161P2F1OB protein are also within the scope of the invention. For example, polynucleotides encoding from about amino acid 1 (or 20 or 30 or 40 etc.) to about amino acid 20, (or 30, or 40 or 50 etc.) of the 161P2F1OB protein "or variant" shown in Figure 2 or Figure 3 can be generated by a variety of techniques well known in the art. These polynucleotide fragments can include any portion of the 161P2F1OB sequence as shown in Figure 2.
Additional illustrative embodiments of the invention disclosed herein include 161P2F1OB polynucleotide fragments encoding one or more of the biological motifs contained within a 161P2F1OB
protein "or variant" sequence, including one or more of the motif-bearing subsequences of a 161P2F1OB protein "or variant" set forth in Tables VIII-XXI and XXII-XLIX. In another embodiment, typical polynucleotide fragments of the invention encode one or more of the regions of 161P2F1OB
protein or variant that exhibit homology to a known molecule. In another embodiment of the invention, typical polynucleotide fragments can encode one or more of the 161P2F1OB protein or variant N-glycosylation sites, cAMP and cGMP-dependent protein kinase phosphorylation sites, casein kinase II phosphorylation sites or N-myristoylation site and amidation sites.
Note that to determine the starting position of any peptide set forth in Tables VIII-XXI and Tables XXII to XLIX
(collectively HLA Peptide Tables) respective to its parental protein, e.g., variant 1, variant 2, etc., reference is made to three factors: the particular variant, the length of the peptide in an HLA Peptide Table, and the Search Peptides listed in Table LVII. Generally, a unique Search Peptide is used to obtain HLA peptides for a particular variant. The position of each Search Peptide relative to its respective parent molecule is listed in Table VII. Accordingly, if a Search Peptide begins at position "X", one must add the value "X minus 1" to each position in Tables VIII-XXI and Tables XXII-IL to obtain the actual position of the HLA peptides in their parental molecule. For example if a particular Search Peptide begins at position 150 of its parental molecule, one must add 150- 1, i.e., 149 to each HLA peptide amino acid position to calculate the position of that amino acid in the parent molecule.
ILA.) Uses of 161P2F1OB Polvnucleotides II.A.1.) Monitoring of Genetic Abnormalities The polynucleotides of the preceding paragraphs have a number of different specific uses. The human 161P2F1OB gene maps to the chromosomal location set forth in the Example entitled 'Chromosomal Mapping of 161P2F1OB." For example, because the 161P2F1OB gene maps to this chromosome, polynucleotides that encode different regions of the 161P2F1OB proteins are used to characterize cytogenetic abnormalities of this chromosomal locale, such as abnormalities that are identified as being associated with various cancers. In certain genes, a variety of chromosomal abnormalities including rearrangements have been identified as frequent cytogenetic abnormalities in a number of different cancers (see e.g. Krajinovic etal., Mutat. Res. 382(3-4): 81-83(1998);
Johansson et al., Blood 86(10): 3905-3914 (1995) and Finger etal., P.N.A.S. 85(23): 9158-9162 (1988)). Thus, polynucleotides encoding specific regions of the 161P2F1OB
proteins provide new tools that can be used to delineate, with greater precision than previously possible, cytogenetic abnormalities in the chromosomal region that encodes 161P2F1OB that may contribute to the malignant phenotype. In this context, these polynucleotides satisfy a need in the art for expanding the sensitivity of chromosomal screening in order to identify more subtle and less common chromosomal abnormalities (see e.g. Evans etal., Am. J. Obstet. Gynecol 171(4):
1055-1057 (1994)).
Furthermore, as 161P2F1OB was shown to be highly expressed in bladder and other cancers, 161P2F108 polynucleotides are used in methods assessing the status of 161P2F1OB gene products in normal versus cancerous tissues.
Typically, polynucleotides that encode specific regions of the 161P2F1OB
proteins are used to assess the presence of perturbations (such as deletions, insertions, point mutations, or alterations resulting in a loss of an antigen etc.) in specific regions of the 161P2F1OB gene, such as regions containing one or more motifs.
Exemplary assays include both RT-PCR
assays as well as single-strand conformation polymorphism (SSCP) analysis (see, e.g., Marrogi etal., J. Cutan. Pathol.
26(8): 369-378 (1999), both of which utilize polynucleotides encoding specific regions of a protein to examine these regions within the protein.
II.A.2.) Antisense Embodiments Other specifically contemplated nucleic acid related embodiments of the invention disclosed herein are genomic DNA, cDNAs, ribozymes, and antisense molecules, as well as nucleic acid molecules based on an alternative backbone, or including alternative bases, whether derived from natural sources or synthesized, and include molecules capable of inhibiting the RNA or protein expression of 161P2F1013. For example, antisense molecules can be RNAs or other molecules, including peptide nucleic acids (PNAs) or non-nucleic acid molecules such as phosphorothioate derivatives that specifically bind DNA or RNA
in a base pair-dependent manner. A skilled artisan can readily obtain these classes of nucleic acid molecules using the 161P2F1OB polynucleotides and polynudeotide sequences disclosed herein.
Antisense technology entails the administration of exogenous oligonucleotides that bind to a target polynucleotide located within the cells. The term "antisense" refers to the fact that such oligonucleotides are complementary to their intracellular targets, e.g., 161P2F10B. See for example, Jack Cohen, Oligodeoxynucleotides, Antisense Inhibitors of Gene Expression, CRC Press, 1989; and Synthesis 1:1-5 (1988). The 161P2F1OB
antisense oligonucleotides of the present invention include derivatives such as S-oligonucleotides (phosphorothioate derivatives or S-oligos, see, Jack Cohen, supra), which exhibit enhanced cancer cell growth inhibitory action. S-oligos (nucleoside phosphorothioates) are isoelectronic analogs of an oligonucleotide (0-oligo) in which a nonbridging oxygen atom of the phosphate group is replaced by a sulfur atom. The S-oligos of the present invention can be prepared by treatment of the corresponding 0-oligos with 3H-1,2-benzodithioI-3-one-1,1-dioxide, which is a sulfur transfer reagent. See, e.g., lyer, R. P. etal., J. Org. Chem. 55:4693-4698 (1990); and lyer, R. P. etal., J. Am. Chem. Soc. 112:1253-1254 (1990).
Additional 161P2F1OB antisense oligonucleotides of the present invention include morpholino antisense oligonucleotides known in the art (see, e.g., Partridge etal., 1996, Antisense & Nucleic Acid Drug Development 6: 169-175).
The 161P2F1OB antisense oligonucleotides of the present invention typically can be RNA or DNA that is complementary to and stably hybridizes with the first 100 5' codons or last 100 3' codons of a 161P2F108 genomic sequence or the corresponding mRNA. Absolute complementarity is not required, although high degrees of complementarity are preferred. Use of an oligonucleotide complementary to this region allows for the selective hybridization to 161P2F1OB
mRNA and not to mRNA specifying other regulatory subunits of protein kinase.
In one embodiment, 161P2F1OB antisense oligonucleotides of the present invention are 15 to 30-mer fragments of the antisense DNA molecule that have a sequence that hybridizes to 161P2F1OB mRNA. Optionally, 161P2F1OB antisense oligonucleotide is a 30-mer oligonucleotide that is complementary to a region in the first 105' codons or last 10 3' codons of 161P2F1OB. Alternatively, the antisense molecules are modified to employ ribozymes in the inhibition of 161P2F1OB
expression, see, e.g., L. A. Couture & D. T.
Stinchcomb; Trends Genet 12: 510-515(1996).
II.A.3.) Primers and Primer Pairs Further specific embodiments of these nucleotides of the invention include primers and primer pairs, which allow the specific amplification of polynucleotides of the invention or of any specific parts thereof, and probes that selectively or specifically hybridize to nucleic acid molecules of the invention or to any part thereof. Probes can be labeled with a detectable marker, such as, for example, a radioisotope, fluorescent compound, bioluminescent compound, a chemiluminescent compound, metal chelator or enzyme. Such probes and primers are used to detect the presence of a 161P2F1OB polynucleotide in a sample and as a means for detecting a cell expressing a 161P2F1OB protein.
Examples of such probes include polypeptides comprising all or part of the human 161P2F1OB cDNA sequence shown in Figure 2. Examples of primer pairs capable of specifically amplifying 161P2F1OB mRNAs are also described in the Examples.
As will be understood by the skilled artisan, a great many different primers and probes can be prepared based on the sequences provided herein and used effectively to amplify and/or detect a 161P2F1OB
mRNA.
The 161P2F1OB polynucleotides of the invention are useful for a variety of purposes, including but not limited to their use as probes and primers for the amplification and/or detection of the 161P2F1OB gene(s), mRNA(s), or fragments thereof; as reagents for the diagnosis and/or prognosis of prostate cancer and other cancers; as coding sequences capable of directing the expression of 161P2F1013 polypeptides; as tools for modulating or inhibiting the expression of the 161P2F1OB gene(s) and/or translation of the 161P2F1OB transcript(s); and as therapeutic agents.
The present invention includes the use of any probe as described herein to identify and isolate a 161P2F1OB or 161P2F1OB related nucleic acid sequence from a naturally occurring source, such as humans or other mammals, as well as the isolated nucleic acid sequence per se, which would comprise all or most of the sequences found in the probe used.
II.A.4.) Isolation of 161P2F10B-Encoding Nucleic Acid Molecules The 161P2F1OB cDNA sequences described herein enable the isolation of other polynucleotides encoding 161P2F1OB
gene product(s), as well as the isolation of polynucleotides encoding 161P2F1OB gene product homologs, altematively spliced isoforms, allelic variants, and mutant forms of a 161P2F108 gene product as well as polynudeotides that encode analogs of 161P2F10B-related proteins. Various molecular cloning methods that can be employed to isolate full length cDNAs encoding a 161P2F1OB gene are well known (see, for example, Sambrook, J. etal., Molecular Cloning: A Laboratory Manual, 2d edition, Cold Spring Harbor Press, New York, 1989; Current Protocols in Molecular Biology. Ausubel et al., Eds., Wiley and Sons, 1995).
For example, lambda phage cloning methodologies can be conveniently employed, using commercially available cloning systems (e.g., Lambda ZAP Express, Stratagene). Phage clones containing 161P2F1OB gene cDNAs can be identified by probing with a labeled 161P2F1OB cDNA or a fragment thereof. For example, in one embodiment, a 161P2F1OB cDNA (e.g., Figure 2) or a portion thereof can be synthesized and used as a probe to retrieve overlapping and full-length cDNAs corresponding to a 161P2F1OB gene. A 161P2F1OB gene itself can be isolated by screening genomic DNA libraries, bacterial artificial chromosome libraries (BACs), yeast artificial chromosome libraries (YACs), and the like, with 161P2F1OB DNA probes or primers.
II.A.5.) Recombinant Nucleic Acid Molecules and Host-Vector Systems The invention also provides recombinant DNA or RNA molecules containing a 161P2F1OB polynucleotide, a fragment, analog or homologue thereof, including but not limited to phages, plasmids, phagemids, cosmids, YACs, BACs, as well as various viral and non-viral vectors well known in the art, and cells transformed or transfected with such recombinant DNA or RNA
molecules. Methods for generating such molecules are well known (see, for example, Sambrook etal., 1989, supra).
The invention further provides a host-vector system comprising a recombinant DNA molecule containing a 161P2F1OB polynucleotide, fragment, analog or homologue thereof within a suitable prokaryotic or eukaryotic host cell.

Examples of suitable eukaryotic host cells include a yeast cell, a plant cell, or an animal cell, such as a mammalian cell or an insect cell (e.g., a baculovirus-infectible cell such as an Sf9 or HighFive cell). Examples of suitable mammalian cells include various prostate cancer cell lines such as DU145 and TsuPr1, other transfectable or transducible prostate cancer cell lines, primary cells (PrEC), as well as a number of mammalian cells routinely used for the expression of recombinant proteins (e.g., COS, CHO, 293, 293T cells). More particularly, a polynucleotide comprising the coding sequence of 161P2F1OB or a fragment, analog or homolog thereof can be used to generate 161P2F1OB proteins or fragments thereof using any number of host-vector systems routinely used and widely known in the art.
A wide range of host-vector systems suitable for the expression of 161P2F1OB
proteins or fragments thereof are available, see for example, Sambrook et al., 1989, supra; Current Protocols in Molecular Biology, 1995, supra). Preferred vectors for mammalian expression include but are not limited to pcDNA 3.1 myc-His-tag (Invitrogen) and the retroviral vector pSRatkneo (Muller etal., 1991, MCB 11:1785). Using these expression vectors, 161P2F1OB can be expressed in several prostate cancer and non-prostate cell lines, including for example 293, 293T, rat-1, NIH 313 and TsuPr1. The host-vector systems of the invention are useful for the production of a 161P2F1OB protein or fragment thereof. Such host-vector systems can be employed to study the functional properties of 161P2F1OB and 161P2F1OB mutations or analogs.
Recombinant human 161P2F1OB protein or an analog or homolog or fragment thereof can be produced by mammalian cells transfected with a construct encoding a 161P2F10B-related nucleotide. For example, 2931 cells can be transfected with an expression plasmid encoding 161P2F1OB or fragment, analog or homolog thereof, a 161P2F1OB-related protein is expressed in the 2931 cells, and the recombinant 161P2F1OB protein is isolated using standard purification methods (e.g., affinity purification using anti-161P2F1OB antibodies). In another embodiment, a 161P2F1OB coding sequence is subcloned into the retroviral vector pSRaMSVtkneo and used to infect various mammalian cell lines, such as NIH 313, TsuPr1, 293 and rat-1 in order to establish 161P2F1OB expressing cell lines. Various other expression systems well known in the art can also be employed. Expression constructs encoding a leader peptide joined in frame to a 161P2F1OB coding sequence can be used for the generation of a secreted form of recombinant 161P2F1OB protein.
As discussed herein, redundancy in the genetic code permits variation in 161P2F1OB gene sequences. In particular, it is known in the art that specific host species often have specific codon preferences, and thus one can adapt the disclosed sequence as preferred for a desired host. For example, preferred analog codon sequences typically have rare codons (i.e., codons having a usage frequency of less than about 20% in known sequences of the desired host) replaced with higher frequency codons. Codon preferences for a specific species are calculated, for example, by utilizing codon usage tables available on the INTERNET such as at URL
dna.affrc.go.jp/¨nakamura/codon.html.
Additional sequence modifications are known to enhance protein expression in a cellular host. These include elimination of sequences encoding spurious polyadenylation signals, exon/intron splice site signals, transposon-like repeats, and/or other such well-characterized sequences that are deleterious to gene expression. The GC content of the sequence is adjusted to levels average for a given cellular host, as calculated by reference to known genes expressed in the host cell.
Where possible, the sequence is modified to avoid predicted hairpin secondary mRNA structures. Other useful modifications include the addition of a translational initiation consensus sequence at the start of the open reading frame, as described in Kozak, MoL BioL, 9:5073-5080(1989). Skilled artisans understand that the general rule that eukaryotic ribosomes initiate translation exclusively at the 5' proximal AUG codon is abrogated only under rare conditions (see, e.g., Kozak PNAS
92(7): 2662-2666, (1995) and Kozak NAR 15(20): 8125-8148 (1987)).
III.) 161P2F10B-related Proteins Another aspect of the present invention provides 161P2F10B-related proteins.
Specific embodiments of 161P2F1OB proteins comprise a polypeptide having all or part of the amino acid sequence of human 161P2F1OB as shown in Figure 2 or Figure 3. Alternatively, embodiments of 161P2F1OB proteins comprise variant, homolog or analog polypeptides that have alterations in the amino acid sequence of 161P2F1OB
shown in Figure 2 or Figure 3.
Embodiments of a 161P2F1OB polypeptide include: a 161P2F106 polypeptide having a sequence shown in Figure 2, a peptide sequence of a 161P2F1OB as shown in Figure 2 wherein T is U; at least 10 contiguous nucleotides of a polypeptide having the sequence as shown in Figure 2; or, at least 10 contiguous peptides of a polypeptide having the sequence as shown in Figure 2 where T is U. For example, embodiments of 161P2F1OB peptides comprise, without limitation:
(I)- a protein comprising, consisting essentially of, or consisting of an amino acid sequence as shown in Figure 2A-G or Figure 3A-E;
(II) a 161P2F10B-related protein that is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% homologous to an entire amino acid sequence shown in Figure 2A-G;
(III) a 161P2F10B-related protein that is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% identical to an entire amino acid sequence shown in Figure 2A-G or 3A-E;
(IV) a protein that comprises at least one peptide set forth in Tables VIII
to XLIX, optionally with a proviso that it is not an entire protein of Figure 2;
(V) a protein that comprises at least one peptide set forth in Tables VIII-XXI, collectively, which peptide is also set forth in Tables XXII to XLIX, collectively, optionally with a proviso that it is not an entire protein of Figure 2;
(VI) a protein that comprises at least two peptides selected from the peptides set forth in Tables VIII-XLIX, optionally with a proviso that it is not an entire protein of Figure 2;
(VII) a protein that comprises at least two peptides selected from the peptides set forth in Tables VIII to XLIX
collectively, with a proviso that the protein is not a contiguous sequence from an amino acid sequence of Figure 2;
(VIII) a protein that comprises at least one peptide selected from the peptides set forth in Tables VIII-XXI; and at least one peptide selected from the peptides set forth in Tables XXII to XLIX, with a proviso that the protein is not a contiguous sequence from an amino acid sequence of Figure 2;
(IX) a polypeptide comprising at least 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a protein of Figure 3A, 3B, 3C, 3D, or 3E in any whole number increment up to 875, 875, 875, 875, or 841 respectively that includes at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Hydrophilicity profile of Figure 5;
(X) = a polypeptide comprising at least 5, 6, 7, 8, 9, 10,11, 12, 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a protein of Figure 3A, 3B, 3C, 3D, or 3E in any whole number increment up to 875, 875, 875, 875, or 841 respectively, that includes at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value less than 0.5 in the Hydropathicity profile of Figure 6;

(XI) a polypeptide comprising at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a protein of Figure 3A, 3B, 3C, 3D, or 3E in any whole number increment up to 875, 875, 875, 875, or 841 respectively, that includes at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Percent Accessible Residues profile of Figure 7;
(XII) a polypeptide comprising at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a protein of Figure 3A, 3B, 3C, 3D, or 3E in any whole number increment up to 875, 875, 875, 875, or 841 respectively, that includes at least 1, 2, 3,4, 5, 6, 7,8, 9,10, 11, 12, 13, 14, 15, 16,17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Average Flexibility profile of Figure 8;
(XIII) a polypeptide comprising at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acids of a protein of Figure 3A, 3B, 3C, 3D, or 3E in any whole number increment up to 875, 875, 875, 875, or 841 respectively, that includes at least 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value greater than 0.5 in the Beta-turn profile of Figure 9;
(XIV) a peptide that occurs at least twice in Tables VIII-XXI and XXII to XLIX, collectively;
(XV) a peptide that occurs at least three times in Tables VIII-XXI and XXII
to XLIX, collectively;
(XVI) a peptide that occurs at least four times in Tables VIII-XXI and XXII
to XLIX, collectively;
(XVII) a peptide that occurs at least five times in Tables VIII-XXI and XXII to XLIX, collectively;
(XVIII) a peptide that occurs at least once in Tables VIII-XXI, and at least once in tables XXII to XLIX;
(XIX) a peptide that occurs at least once in Tables VIII-XXI, and at least twice in tables XXII to XLIX;
(XX) a peptide that occurs at least twice in Tables VIII-XXI, and at least once in tables XXII to XLIX;
(XXI) a peptide that occurs at least twice in Tables VIII-XXI, and at least twice in tables XXII to XLIX;
(XXII) a peptide which comprises one two, three, four, or five of the following characteristics, or an oligonucleotide encoding such peptide:
i) a region of at least 5 amino acids of a particular peptide of Figure 3, in any whole number increment up to the full length of that protein in Figure 3, that includes an amino acid position having a value equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in the Hydrophilicity profile of Figure 5;
ii) a region of at least 5 amino acids of a particular peptide of Figure 3, in any whole number increment up to the full length of that protein in Figure 3, that includes an amino acid position having a value equal to or less than 0.5, 0.4, 0.3, 0.2, 0.1, or having a value equal to 0.0, in the Hydropathicity profile of Figure 6;
iii) a region of at least 5 amino acids of a particular peptide of Figure 3, in any whole number increment up to the full length of that protein in Figure 3, that includes an amino acid position having a value equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in the Percent Accessible Residues profile of Figure 7;
iv) a region of at least 5 amino acids of a particular peptide of Figure 3, in any whole number increment up to the full length of that protein in Figure 3, that includes an amino acid position having a value equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in the Average Flexibility profile of Figure 8; or, v) a region of at least 5 amino acids of a particular peptide of Figure 3, in any whole number increment up to the full length of that protein in Figure 3, that includes an amino acid position having a value equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having a value equal to 1.0, in the Beta-turn profile of Figure 9;
(XXIII) a monoclonal antibody or binding region thereof secreted by a hybridoma entitled X41(3)15 deposited with the American Type Culture Collection (ATCC; 10801 University Blvd., Manassas, VA 20110-2209 USA) on 07 November 2002 and assigned as Accession No. PTA-4791;
(XXIV) a monoclonal antibody or binding region thereof secreted by a hybridoma entitled X41(3)29 deposited with the American Type Culture Collection (ATCC; 10801 University Blvd., Manassas, VA 20110-2209 USA) on 07 November 2002 and assigned as Accession No. PTA-4791;
(XXV) a monoclonal antibody or binding region thereof secreted by a hybridoma entitled X41(3)37 deposited with the American Type Culture Collection (ATCC; 10801 University Blvd., Manassas, VA 20110-2209 USA) on 07 November 2002 and assigned as Accession No. PTA-4791;
(XXVI) a monoclonal antibody or binding region thereof secreted by a hybridoma entitled X41(4)6 deposited with the American Type Culture Collection (ATCC; 10801 University Blvd., Manassas, VA
20110-2209 USA) on 07 November 2002 and assigned as Accession No. PTA-4794;
(XXVII) a monoclonal antibody or binding region thereof secreted by a hybridoma entitled X41(3)17 deposited with the American Type Culture Collection (ATCC; 10801 University Blvd., Manassas, VA 20110-2209 USA) on 07 November 2002 and assigned as Accession No. PTA-4792;
(XXVIII) a monoclonal antibody or binding region thereof secreted by a hybridoma entitled X41(3)50 deposited with the American Type Culture Collection (ATCC; 10801 University Blvd., Manassas, VA 20110-2209 USA) on 07 November 2002 and assigned as Accession No. PTA-4793;
(XXIX) a composition comprising a peptide of (1)-(XXII) or an antibody or binding region thereof of (XXIII to XXVIII) together with a pharmaceutical excipient and/or in a human unit dose form.
(XXX) a method of using a peptide of (1)-(XXII), or an antibody or binding region thereof of (XXIII to XXVIII) or a composition of (XXIX) in a method to modulate a cell expressing 161P2F10b, (XXXI) a method of using a peptide of (I)-(XXII) or an antibody or binding region thereof of (XXIII to XX\/III)or a composition of (XXIX) in a method to diagnose, prophylax, prognose, or treat an individual who bears a cell expressing 161P2F10b (XXXII) a method of using a peptide of (I)-(XXII) or an antibody or binding region thereof of (XXIII to XXVIII) or a composition (XXIX) in a method to diagnose, prophylax, prognose, or treat an individual who bears a cell expressing 161P2F10b, said cell from a cancer of a tissue listed in Table I;

(XXXIII) a method of using a peptide of (I)-(XXII) or an antibody or binding region thereof of (XXIII to XXVIII) or a composition of (XXIX) in a method to diagnose, prophylax, prognose, or treat a a cancer;
(XXXIV) a method of using a peptide of (I)-(XXII) or an antibody or binding region thereof of (XXIII to XXVIII) or a composition of (XXIX) in a method to diagnose, prophylax, prognose, or treat a a cancer of a tissue listed in Table I; and, (XXXV) a method of using a a peptide of (I)-(XXII) or an antibody or binding region thereof of (XXIII to XXVIII) or a composition (XXIX) in a method to identify or characterize a modulator of a cell expressing 161P2F10b.
As used herein, a range is understood to specifically disclose all whole unit positions thereof.
Typical embodiments of the invention disclosed herein include 161P2F1OB
polynucleotides that encode specific portions of 161P2F1OB mRNA sequences (and those which are complementary to such sequences) such as those that encode the proteins and/or fragments thereof, for example:
(a) 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40,45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 650, 675, 700, 725, 750, 775, 800, 825, 850, 860, 870, 875 or more contiguous amino acids of 161P2F1OB variant 1;
the maximal lengths relevant for other variants are: variant 2, 875 amino acids; variant 3, 875 amino acids, variant 4, 875, and variant 7, 841 amino acids..
In general, naturally occurring allelic variants of human 161P2F1OB share a high degree of structural identity and homology (e.g., 90% or more homology). Typically, allelic variants of a 161P2F1OB protein contain conservative amino acid substitutions within the 161P2F1OB sequences described herein or contain a substitution of an amino acid from a corresponding position in a homologue of 161P2F1OB. One class of 161P2F1OB allelic variants are proteins that share a high degree of homology with at least a small region of a particular 161P2F1OB amino acid sequence, but further contain a radical departure from the sequence, such as a non-conservative substitution, truncation, insertion or frame shift. In comparisons of protein sequences, the terms, similarity, identity, and homology each have a distinct meaning as appreciated in the field of genetics. Moreover, orthology and paralogy can be important concepts describing the relationship of members of a given protein family in one organism to the members of the same family in other organisms.
Amino acid abbreviations are provided in Table II. Conservative amino acid substitutions can frequently be made in a protein without altering either the conformation or the function of the protein. Proteins of the invention can comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 conservative substitutions. Such changes include substituting any of isoleucine (I), valine (V), and leucine (L) for any other of these hydrophobic amino acids;
aspartic acid (D) for glutamic acid (E) and vice versa; glutamine (Q) for asparagine (N) and vice versa; and serine (S) for threonine (T) and vice versa. Other substitutions can also be considered conservative, depending on the environment of the particular amino acid and its role in the three-dimensional structure of the protein. For example, glycine (G) and alanine (A) can frequently be interchangeable, as can alanine (A) and valine (V). Methionine (M), which is relatively hydrophobic, can frequently be interchanged with leucine and isoleucine, and sometimes with valine. Lysine (K) and arginine (R) are frequently interchangeable in locations in which the significant feature of the amino acid residue is its charge and the differing pK's of these two amino acid residues are not significant. Still other changes can be considered "conservative" in particular environments (see, e.g. Table III herein; pages 13-15 "Biochemistry" 2nd ED. Lubert Stryer ed (Stanford University); Henikoff et al., PNAS 1992 Vol 89 10915-10919; Lei et al., J Biol Chem 1995 May 19; 270(20):11882-6).
Embodiments of the invention disclosed herein include a wide variety of art-accepted variants or analogs of 161P2F1OB proteins such as polypeptides having amino acid insertions, deletions and substitutions. 161P2F1OB variants can be made using methods known in the art such as site-directed mutagenesis, alanine scanning, and PCR mutagenesis.

Site-directed mutagenesis (Carter et al., NucL Acids Res., 13:4331 (1986);
Zoller etal., NucL Acids Res., /0:6487 (1987)), cassette mutagenesis (Wells etal., Gene, 34:315 (1985)), restriction selection mutagenesis (Wells etal., Philos. Trans. R.
Soc. London SerA, 317:415 (1986)) or other known techniques can be performed on the cloned DNA to produce the 161P2F1OB variant DNA.
Scanning amino acid analysis can also be employed to identify one or more amino acids along a contiguous sequence that is involved in a specific biological activity such as a protein-protein interaction. Among the preferred scanning amino acids are relatively small, neutral amino acids. Such amino acids include alanine, glycine, serine, and cysteine.
Alanine is typically a preferred scanning amino acid among this group because it eliminates the side-chain beyond the beta-carbon and is less likely to alter the main-chain conformation of the variant.
Alanine is also typically preferred because it is the most common amino acid. Further, it is frequently found in both buried and exposed positions (Creighton, The Proteins, (W.H. Freeman & Co., N.Y.); Chothia, J. Mol. Biol., 150:1 (1976)). If alanine substitution does not yield adequate amounts of variant, an isosteric amino acid can be used.
As defined herein, 161P2F1OB variants, analogs or homologs, have the distinguishing attribute of having at least one epitope that is "cross reactive" with a 161P2F1OB protein having an amino acid sequence of Figure 3. As used in this sentence, 'cross reactive" means that an antibody or T cell that specifically binds to a 161P2F1OB variant also specifically binds to a 161P2F1OB protein having an amino acid sequence set forth in Figure 3. A polypeptide ceases to be a variant of a protein shown in Figure 3, when it no longer contains any epitope capable of being recognized by an antibody or T cell that specifically binds to the starting 161P2F1OB protein. Those skilled in the an understand that antibodies that recognize proteins bind to epitopes of varying size, and a grouping of the order of about four or five amino acids, contiguous or not, is regarded as a typical number of amino acids in a minimal epitope. See, e.g., Nair etal., J. Immunol 2000 165(12): 6949-6955; Hebbes etal., Mol Immunol (1989) 26(9):865-73; Schwartz etal., J Immunol (1985) 135(4):2598-608.
Other classes of 161P2F108-related protein variants share 70%, 75%, 80%, 85%
or 90% or more similarity with an amino acid sequence of Figure 3, or a fragment thereof. Another specific class of 161P2F1OB protein variants or analogs comprises one or more of the 161P2F1OB biological motifs described herein or presently known in the art. Thus, encompassed by the present invention are analogs of 161P2F1OB fragments (nucleic or amino acid) that have altered functional (e.g. immunogenic) properties relative to the starting fragment. It is to be appreciated that motifs now or which become part of the art are to be applied to the nucleic or amino acid sequences of Figure 2 or Figure 3.
As discussed herein, embodiments of the claimed invention include polypeptides containing less than the full amino acid sequence of a 161P2F1OB protein shown in Figure 2 or Figure 3. For example, representative embodiments of the invention comprise peptides/proteins having any 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more contiguous amino acids of a 161P2F1OB protein shown in Figure 2 or Figure 3.
Moreover, representative embodiments of the invention disclosed herein include polypeptides consisting of about amino acid 1 to about amino acid 10 of a 161P2F1OB protein shown in Figure 2 or Figure 3, polypeptides consisting of about amino acid 10 to about amino acid 20 of a 161P2F1OB protein shown in Figure 2 or Figure 3, polypeptides consisting of about amino acid 20 to about amino acid 30 of a 161P2F1OB protein shown in Figure 2 or Figure 3, polypeptides consisting of about amino acid 30 to about amino acid 40 of a 161P2F1OB protein shown in Figure 2 or Figure 3, polypeptides consisting of about amino acid 40 to about amino acid 50 of a 161P2F1OB
protein shown in Figure 2 or Figure 3, polypeptides consisting of about amino acid 50 to about amino acid 60 of a 161P2F1OB protein shown in Figure 2 or Figure 3, polypeptides consisting of about amino acid 60 to about amino acid 70 of a 161P2F1OB protein shown in Figure 2 or Figure 3, polypeptides consisting of about amino acid 70 to about amino acid 80 of a 161P2F1OB protein shown in Figure 2 or Figure 3, polypeptides consisting of about amino acid 80 to about amino acid 90 of a 161P2F1OB protein shown in Figure 2 or Figure 3, polypeptides consisting of about amino acid 90 to about amino acid 100 of a 161P2F1OB protein shown in Figure 2 or Figure 3, etc. throughout the entirety of a 161P2F1OB amino acid sequence. Moreover, polypeptides consisting of about amino acid 1 (or 20 or 30 or 40 etc.) to about amino acid 20, (or 130, or 140 or 150 etc.) of a 161P2F1OB protein shown in Figure 2 or Figure 3 are embodiments of the invention. It is to be appreciated that the starting and stopping positions in this paragraph refer to the specified position as well as that position plus or minus 5 residues.
161P2F10B-related proteins are generated using standard peptide synthesis technology or using chemical cleavage methods well known in the art. Alternatively, recombinant methods can be used to generate nucleic acid molecules that encode a 161P2F108-related protein. In one embodiment, nucleic acid molecules provide a means to generate defined fragments of a 161P2F1OB protein (or variants, homologs or analogs thereof).
Motif-bearine Protein Embodiments Additional illustrative embodiments of the invention disclosed herein include 161P2F1OB polypeptides comprising the amino acid residues of one or more of the biological motifs contained within a 161P2F108 polypeptide sequence set forth in Figure 2 or Figure 3. Various motifs are known in the art, and a protein can be evaluated for the presence of such motifs by a number of publicly available Internet sites (see, e.g., EpimatrixTM and EpimerTM, Brown University, and BIMAS) Motif bearing subsequences of all 161P2F108 variant proteins are set forth and identified in Tables VIII-XXI and Table V sets forth several frequently occurring motifs based on pfam searches..
The columns of Table V list (1) motif name abbreviation, (2) percent identity found amongst the different member of the motif family, (3) motif name or description and (4) most common function; location information is included if the motif is relevant for location.
Polypeptides comprising one or more of the 161P2F1OB motifs discussed above are useful in elucidating the specific characteristics of a malignant phenotype in view of the observation that the 161P2F1013 motifs discussed above are associated with growth dysregulation and because 161P2F108 is overexpressed in certain cancers (See, e.g., Table l).
= Casein kinase II, cAMP and camp-dependent protein kinase, and Protein Kinase C, for example, are enzymes known to be associated with the development of the malignant phenotype (see e.g. Chen et at, Lab Invest., 78(2): 165-174 (1998);
Gaiddon etal., Endocrinology 136(10): 4331-4338(1995); Hall et at, Nucleic Acids Research 24(6): 1119-1126(1996);
Peterziel etal., Oncogene 18(46): 6322-6329(1999) and O'Brian, Oncol. Rep.
5(2): 305-309 (1998)). Moreover, both glycosylation and myristoylation are protein modifications also associated with cancer and cancer progression (see e.g, Dennis etal., Blochem. Biophys. Ada 1473(1):21-34 (1999); Raju etal., Exp.
Cell Res. 235(1): 145-154 (1997)). Amidation is another protein modification also associated with cancer and cancer progression (see e.g. Treston etal., J. Natl. Cancer Inst. Monogr. (13): 169-175(1992)).
In another embodiment, proteins of the invention comprise one or more of the immunoreacfive epitopes identified in accordance with art-accepted methods, such as the peptides set forth in Tables VIII-XXI and XXII-XLIX. CIL epitopes can =
be determined using specific algorithms to identify peptides within a 161P2F1013 protein that are capable of optimally binding to specified HtA alleles (e.g., Table IV; EpIrnatlixTM and EpimerTM, Brown University, and BIMAS ) Moreover, processes for identifying peptides that have sufficient binding affinity for FILA molecules and which are correlated with being immunogenic epitopes, are well known in the art, and are carried out without undue experimentation. In addition, processes for identifying peptides that are immunogenic epitopes, are well known in the art, and are carried out without undue experimentation either in vitro or in viva.

Also known in the art are principles for creating analogs of such epitopes in order to modulate immunogenicity. For example, one begins with an epitope that bears a CTL or HTL motif (see, e.g., the HLA Class I and HLA Class II
motifs/supermotifs of Table IV). The epitope is analoged by substituting out an amino acid at one of the specified positions, and replacing it with another amino acid specified for that position. For example, on the basis of residues defined in Table IV, one can substitute out a deleterious residue in favor of any other residue, such as a preferred residue; substitute a less-preferred residue with a preferred residue; or substitute an originally-occurring preferred residue with another preferred residue. Substitutions can occur at primary anchor positions or at other positions in a peptide; see, e.g., Table IV.
_ A variety of references reflect the art regarding the identification and generation of epitopes in a protein of interest as well as analogs thereof. See, for example, WO 97/33602 to Chesnut etal.;
Sette, Immunogenetics 1999 50(3-4): 201-212; Sette etal., J. Immunol. 2001 166(2): 1389-1397; Sidney etal., Hum.
Immunol. 1997 58(1): 12-20; Kondo etal., Immunogenetics 1997 45(4): 249-258; Sidney etal., J. Immunol. 1996 157(8):
3480-90; and Falk et al., Nature 351: 290-6 (1991); Hunt etal., Science 255:1261-3 (1992); Parker etal., J. Immunol.
149:3580-7 (1992); Parker etal., J. Immunol.
152:163-75 (1994)); Kast etal., 1994 152(8): 3904-12; Borras-Cuesta etal., Hum. Immunol. 2000 61(3): 266-278; Alexander etal., J. Immunol. 2000 164(3); 164(3): 1625-1633; Alexander etal., PMID:
7895164, Ul: 95202582; O'Sullivan etal., J.
Immunol. 1991147(8): 2663-2669; Alexander etal., Immunity 1994 1(9): 751-761 and Alexander etal., Immunol. Res. 1998 18(2): 79-92.
Related embodiments of the invention include polypeptides comprising combinations of the different motifs set forth in Table VI, and/or, one or more of the predicted CTL epitopes of Tables VIII-XXI and XXII-XLIX, and/or, one or more of the predicted HTL epitopes of Tables XLVI-XLIX, and/or, one or more of the T cell binding motifs known in the art. Preferred embodiments contain no insertions, deletions or substitutions either within the motifs or within the intervening sequences of the polypeptides. In addition, embodiments which include a number of either N-terminal and/or C-terminal amino acid residues on either side of these motifs may be desirable (to, for example, include a greater portion of the polypeptide architecture in which the motif is located). Typically, the number of N-terminal and/or C-terminal amino acid residues on either side of a motif is between about 1 to about 100 amino acid residues, preferably 5 to about 50 amino acid residues.
161P2F10B-related proteins are embodied in many forms, preferably in isolated form. A purified 161P2F1OB protein molecule will be substantially free of other proteins or molecules that impair the binding of 161P2F1OB to antibody, T cell or other ligand. The nature and degree of isolation and purification will depend on the intended use. Embodiments of a 161P2F1OB-related proteins include purified 161P2F1OB-related proteins and functional, soluble 161P2F1OB-related proteins. In one embodiment, a functional, soluble 161P2F1OB protein or fragment thereof retains the ability to be bound by antibody, T cell or other ligand.
The invention also provides 161P2F1OB proteins comprising biologically active fragments of a 161P2F1OB amino acid sequence shown in Figure 2 or Figure 3. Such proteins exhibit properties of the starting 161P2F1OB protein, such as the ability to elicit the generation of antibodies that specifically bind an epitope associated with the starting 161P2F1OB
protein; to be bound by such antibodies; to elicit the activation of HTL or CTL; and/or, to be recognized by HTL or CTL that also specifically bind to the starting protein.
161P2F10B-related polypeptides that contain particularly interesting structures can be predicted and/or identified using various analytical techniques well known in the art, including, for example, the methods of Chou-Fasman, Gamier-Robson, Kyte-Doolittle, Eisenberg, Karplus-Schultz or Jameson-Wolf analysis, or based on immunogenicity. Fragments that contain such structures are particularly useful in generating subunit-specific anti-161P2F1OB antibodies or T cells or in identifying cellular factors that bind to 161P2F10B. For example, hydrophilicity profiles can be generated, and immunogenic peptide fragments identified, using the method of Hopp, T.P. and Woods, K.R., 1981, Proc. Natl.
Acad. Sci. U.S.A. 78:3824-3828.
Hydropathicity profiles can be generated, and immunogenic peptide fragments identified, using the method of Kyte, J. and Doolittle, RE, 1982, J. Mot Biol. 157:105-132. Percent (%) Accessible Residues profiles can be generated, and immunogenic peptide fragments identified, using the method of Janin 1979, Nature 277:491.492. Average Flexibility profiles can be generated, and Immunogenic peptide fragments identified, using the method of 13haskaran R., Ponnuswamy P.K., 1988, Int, J. Pept. Protein Res. 32:242-255. Beta-turn profiles can be generated, and immunogenic peptide fragments identified, using the method of Deleage, G., Roux B., 1987, Protein Engineering 1:289-294.
CTL epitopes can be determined using specific algorithms to identify peptides within a 161P2F1OB protein that are capable of optimally binding to specified HLA alleles (e.g., by using the SYFPEITHI site at World Wide Web the listings in Table IV(A)-(E); EpirnatrixTm and EpimarTM, Brown University, and BIMAS), = Illustrating this, peptide epitopes from 161P2F1OB
that are presented in the context of human MHC Class I molecules, e.g., HLA-Al, A2, A3, All, A24, 87 and 835 were predicted (see, e.g., Tables VIII-XXI, XXII-XLIX). Specifically, the complete amino acid sequence of the 161P2F1013 protein and relevant portions of other variants, i.e., for HLA Class I predictions 9 flanking residues on either side of a point mutation or exon Odom and for HLA Class II predictions 14 flanking residues on either side of a point mutation or exon junction corresponding to that variant, were entered into the HLA Peptide Motif Search algorithm foUndl in the Bioinfonnatics and Molecular Analysis Section (BIMAS) web site listed above; in addition to the site SYFPEITH1.
The RA peptide motif search algorithm was developed by Dr. Ken Parker based on binding of specific peptide sequences in the groove of HLA Class I molecules, in particular HLA-A2 (see, e.gõ Falk etal., Nature 351: 290-8(1991):
Hunt etal., Science 255:1261-3(1992); Parker et al., J. Immunot 149:3580-7(1992): Parker et at, J. Imrnunot 152:163-75 (1994)). This algorithm allows location and ranking of 8-met, 9-met, and 10-met peptides from a complete protOn sequence for predicted binding to HLA-A2 as well as numerous other HLA Class I
molecules. Many RA class I binding peptides are 8-. 9-.10 or 11-mars. Fa' example, for Class I HLA-AZ the epitopes preferably contain a leudne (L) or methionine (M) at position 2 and a valine (V) or ieucine (L) at the C-terminus (see, e.g., Parker at at, J. In'enunol. 149:3580-7 (1992)). Selected results of 161P2F1OB predicted binding peptides are shown in Tables VIII-XXI
and XXII-Yd.IX herein. In Tables VIII-YvXI and XXII-XLVII, selected candidates, 9-mers and 10-mars, for each family member are shown along with their location, the amino acid sequence of each specific peptide, and an estimated binding score. In Tables XLVI-XLIX, selected candidates, 15-niers, for each family member are shown along with their location, the amino acid sequence of each specific peptide, and an estimated binding score. The binding score corresponds to the estimated half time of dissociation of complexes containing the peptide at 31 C at pH 6,5, Peptides with the highest binding score are predicted to be the most tightly bound to HLA
Class I on the cell surface for the greatest period of time and thus represent the best immunogenic targets for 1-cell recognition.
Actual binding of peptides lo an HLA allele can be evaluated by stabilization of HLA expression on the antigen-processing defective cell line T2 (see, e.g., Xue at at., Prostate 30:73-8 (1997) and Pestiwa etal., Prostate 36:129-38 (1998)). Immunogenidty of specific peptides can be evaluated in wiry by stimulation of CD8+ cytotmdc T lymphocytes (CIL) in the presence of antigen presenting cells such as dendritic cells.
It is to be appreciated that every epitope predicted-by the BIMAS site, EpimerTm and EplmatrixTM sites, or specified by the HLA class I or class 11 motifs available in the art or which become part of the art such as set forth in Table IV (or determined using World Wide Web site Fe. syfpeithi or BIMAS) are to be "applied' to a 161P2F1OB protein in accordance with the invention. As used in this context *applied" means that a 161P2F1013 protein is evaluated, e.g., visually or by computer-based patterns finding methods, as appreciated by those of skill in the relevant art.
Every subsequence of a 161P2F1OB protein of 8, 9, 10, or 11 amino acid residues that bears an HLA Class I motif, or a subsequence of 9 or more amino acid residues that bear an HLA Class II motif are within the scope of the invention.
=

III.B.) Expression of 161P2F10B-related Proteins In an embodiment described in the examples that follow, 161P2F1OB can be conveniently expressed in cells (such as 293T cells) transfected with a commercially available expression vector such as a CMV-driven expression vector encoding 161P2F1OB with a C-terminal 6XHis and MYC tag (pcDNA3.1/mycHIS, Invitrogen or Tag5, GenHunter Corporation, Nashville TN). The Tag5 vector provides an IgGK secretion signal that can be used to facilitate the production of a secreted 161P2F1OB protein in transfected cells. The secreted HIS-tagged 161P2F1OB in the culture media can be purified, e.g., using a nickel column using standard techniques.
III.C.) Modifications of 161P2F10B-related Proteins Modifications of 161P2F10B-related proteins such as covalent modifications are included within the scope of this invention. One type of covalent modification includes reacting targeted amino acid residues of a 161P2F1OB polypeptide with an organic derivatizing agent that is capable of reacting with selected side chains or the N- or C- terminal residues of a 161P2F1OB protein. Another type of covalent modification of a 161P2F1OB
polypeptide included within the scope of this invention comprises altering the native glycosylation pattern of a protein of the invention. Another type of covalent modification of 161P2F1OB comprises linking a 161P2F1OB polypeptide to one of a variety of nonproteinaceous polymers, e.g., polyethylene glycol (PEG), polypropylene glycol, or polyoxyalkylenes, in the manner set forth in U.S. Patent Nos.
4,640,835; 4,496,689; 4,301,144; 4,670,417; 4,791,192 or 4,179,337.
The 161P2F10B-related proteins of the present invention can also be modified to form a chimeric molecule comprising 161P2F1OB fused to another, heterologous polypeptide or amino acid sequence. Such a chimeric molecule can be synthesized chemically or recombinantly. A chimeric molecule can have a protein of the invention fused to another tumor-associated antigen or fragment thereof. Alternatively, a protein in accordance with the invention can comprise a fusion of fragments of a 161P2F1OB sequence (amino or nucleic acid) such that a molecule is created that is not, through its length, directly homologous to the amino or nucleic acid sequences shown in Figure 2 or Figure 3. Such a chimeric molecule can comprise multiples of the same subsequence of 161P2F1OB. A chimeric molecule can comprise a fusion of a 161P2F10B-related protein with a polyhistidine epitope tag, which provides an epitope to which immobilized nickel can selectively bind, with cytokines or with growth factors. The epitope tag is generally placed at the amino- or carboxyl- terminus of a 161P2F1OB protein. In an alternative embodiment, the chimeric molecule can comprise a fusion of a 161P2F10B-related protein with an immunoglobulin or a particular region of an immunoglobulin.
For a bivalent form of the chimeric molecule (also referred to as an "immunoadhesin"), such a fusion could be to the Fc region of an IgG molecule. The Ig fusions preferably include the substitution of a soluble (transmembrane domain deleted or inactivated) form of a 161P2F1OB
polypeptide in place of at least one variable region within an Ig molecule. In a preferred embodiment, the immunoglobulin fusion includes the hinge, CH2 and CH3, or the hinge, CHI, CH2 and CH3 regions of an IgGI molecule. For the production of immunoglobulin fusions see, e.g., U.S. Patent No. 5,428,130 issued June 27, 1995.
111.03 Uses of 161P2F10B-related Proteins The proteins of the invention have a number of different specific uses. As 161P2F1OB is highly expressed in prostate and other cancers, 161P2F108-related proteins are used in methods that assess the status of 161P2F1OB gene products in normal versus cancerous tissues, thereby elucidating the malignant phenotype. Typically, polypeptides from specific regions of a 161P2F1OB protein are used to assess the presence of perturbations (such as deletions, insertions, point mutations etc.) in those regions (such as regions containing one or more motifs). Exemplary assays utilize antibodies or T cells targeting 161P2F10B-related proteins comprising the amino acid residues of one Or more of the biological motifs contained within a 161P2F1OB polypeptide sequence in order to evaluate the characteristics of this region in normal versus cancerous tissues or to elicit an immune response to the epitope.
Alternatively, 161P2F10B-related proteins that contain the amino acid residues of one or more of the biological motifs in a 161P2F1OB
protein are used to screen for factors that interact with that region of 161P2F10B.
161P2F1OB protein fragments/subsequences are particularly useful in generating and characterizing domain-specific antibodies (e.g., antibodies recognizing an extracellular or intracellular epitope of a 161P2F1OB protein), for identifying agents or cellular factors that bind to 161P2F1OB or a particular structural domain thereof, and in various therapeutic and diagnostic contexts, including but not limited to diagnostic assays, cancer vaccines and methods of preparing such vaccines.
Proteins encoded by the 161P2F1OB genes, or by analogs, homologs or fragments thereof, have a variety of uses, including but not limited to generating antibodies and in methods for identifying ligands and other agents and cellular constituents that bind to a 161P2F1OB gene product Antibodies raised against a 161P2F1OB protein or fragment thereof are useful in diagnostic and prognostic assays, and imaging methodologies in the management of human cancers characterized by expression of 161P2F1OB protein, such as those listed in Table I. Such antibodies can be expressed intracellularly and used in methods of treating patients with such cancers. 161P2F10B-related nucleic acids or proteins are also used in generating HTL or CTL responses.
Various immunological assays useful for the detection of 161P2F1OB proteins are used, including but not limited to various types of radioimmunoassays, enzyme-linked immunosorbent assays (ELISA), enzyme-linked immunofluorescent assays (ELIFA), immunocytochemical methods, and the like. Antibodies can be labeled and used as immunological imaging reagents capable of detecting 161P2F10B-expressing cells (e.g., in radioscintigraphic imaging methods). 161P2F1OB proteins are also particularly useful in generating cancer vaccines, as further described herein.
IV.) 161P2F1OB Antibodies Another aspect of the invention provides antibodies that bind to 161P2F108-related proteins. Preferred antibodies specifically bind to a 161P2F10B-related protein and do not bind (or bind weakly) to peptides or proteins that are not 161P2F10B-related proteins. For example, antibodies that bind 161P2F1OB can bind 161P2F10B-related proteins such as the homologs or analogs thereof.
161P2F1OB antibodies of the invention are particularly useful in cancer (see, e.g., Table I) diagnostic and prognostic assays, and imaging methodologies. Similarly, such antibodies are useful in the treatment, diagnosis, and/or prognosis of other cancers, to the extent 161P2F1OB is also expressed or overexpressed in these other cancers. Moreover, intracellularly expressed antibodies (e.g., single chain antibodies) are therapeutically useful in treating cancers in which the expression of 161P2F1OB is involved, such as advanced or metastatic prostate cancers.
The invention also provides various immunological assays useful for the detection and quantification of 161P2F1OB and mutant 161P2F108-related proteins. Such assays can comprise one or more 161P2F108 antibodies capable of recognizing and binding a 161P2F10B-related protein, as appropriate. These assays are performed within various immunological assay formats well known in the art, including but not limited to various types of radioimmunoassays, enzyme-linked immunosorbent assays (ELISA), enzyme-linked immunofluorescent assays (ELIFA), and the like.
Immunological non-antibody assays of the invention also comprise T cell immunogenicity assays (inhibitory or stimulatory) as well as major histocompatibility complex (MHC) binding assays.
In addition, immunological imaging methods capable of detecting prostate cancer and other cancers expressing 161P2F1OB are also provided by the invention, including but not limited to radioscintigraphic imaging methods using labeled 161P2F1OB antibodies. Such assays are clinically useful in the detection, monitoring, and prognosis of 161P2F1OB expressing cancers such as prostate cancer.

161P2F1OB antibodies are also used in methods for purifying a 161P2F1OB-related protein and for isolating 161P2F1OB homologues and related molecules. For example, a method of purifying a 161P2F1OB-related protein comprises incubating a 161P2F1OB antibody, which has been coupled to a solid matrix, with a lysate or other solution containing a 161P2F10B-related protein under conditions that permit the 161P2F1OB antibody to bind to the 161P2F10B-related protein;
washing the solid matrix to eliminate impurities; and eluting the 161P2F10B-related protein from the coupled antibody. Other uses of 161P2F1OB antibodies in accordance with the invention include generating anti-idiotypic antibodies that mimic a 161P2F1OB protein.
Various methods for the preparation of antibodies are well known in the art.
For example, antibodies can be prepared by immunizing a suitable mammalian host using a 161P2F10B-related protein, peptide, or fragment, in isolated or immunoconjugated form (Antibodies: A Laboratory Manual, CSH Press, Eds., Harlow, and Lane (1988); Harlow, Antibodies, Cold Spring Harbor Press, NY (1989)). In addition, fusion proteins of 161P2F1OB can also be used, such as a 161P2F1OB GST-fusion protein. In a particular embodiment, a GST fusion protein comprising all or most of the amino acid sequence of Figure 2 or Figure 3 is produced, then used as an immunogen to generate appropriate antibodies.
In another embodiment, a 161P2F1OB-related protein is synthesized and used as an immunogen.
In addition, naked DNA immunization techniques known in the art are used (with or without purified 161P2F10B-related protein or 161P2F1OB expressing cells) to generate an immune response to the encoded immunogen (for review, see Donnelly et aL, 1997, Ann. Rev. Immunol. 15: 617-648).
The amino acid sequence of a 161P2F1OB protein as shown in Figure 2 or Figure 3 can be analyzed to select specific regions of the 161P2F1OB protein for generating antibodies. For example, hydrophobicity and hydrophilicity analyses of a 161P2F1OB amino acid sequence are used to identify hydrophilic regions in the 161P2F1OB structure. Regions of a 161P2F1OB
protein that show immunogenic structure, as well as other regions and domains, can readily be identified using various other methods known in the art, such as Chou-Fasman, Gamier-Robson, Kyte-Doolittle, Eisenberg, Karplus-Schultz or Jameson-Wolf analysis. Hydrophilicity profiles can be generated using the method of Hopp, T.P. and Woods, KR., 1981, Proc. Natl. Acad.
Sci. U.S.A. 78:3824-3828. Hydropathicity profiles can be generated using the method of Kyte, J. and Doolittle, R.F., 1982, J.
Mol. Biol. 157:105-132. Percent (%) Accessible Residues profiles can be generated using the method of Janin J., 1979, Nature 277:491-492. Average Flexibility profiles can be generated using the method of Bhaskaran R., Ponnuswamy P.K., 1988, Int. J. Pept. Protein Res. 32:242-255. Beta-turn profiles can be generated using the method of Deleage, G., Roux B., 1987, Protein Engineering 1:289-294. Thus, each region identified by any of these programs or methods is within the scope of the present invention. Methods for the generation of 161P2F1OB antibodies are further illustrated by way of the examples provided herein. Methods for preparing a protein or polypeptide for use as an immunogen are well known in the art. Also well known in the art are methods for preparing immunogenic conjugates of a protein with a carrier, such as BSA, KLH or other carrier protein. In some circumstances, direct conjugation using, for example, carbodiimide reagents are used; in other instances linking reagents such as those supplied by Pierce Chemical Co., Rockford, IL, are effective. Administration of a 161P2F1OB immunogen is often conducted by injection over a suitable time period and with use of a suitable adjuvant, as is understood in the art. During the immunization schedule, titers of antibodies can be taken to determine adequacy of antibody formation.
161P2F1OB monoclonal antibodies can be produced by various means well known in the art. For example, immortalized cell lines that secrete a desired monoclonal antibody are prepared using the standard hybridoma technology of Kohler and Milstein or modifications that immortalize antibody-producing B
cells, as is generally known. Immortalized cell lines that secrete the desired antibodies are screened by immunoassay in which the antigen is a 161P2F10B-related protein. When the appropriate immortalized cell culture is identified, the cells can be expanded and antibodies produced either from in vitro cultures or from ascites fluid.

The antibodies or fragments of the invention can also be produced, by recombinant means. Regions that bind specifically to the desired regions of a 161P2F1OB protein can also be produced in the context of chimeric or complementarity-determining region (CDR) grafted antibodies of multiple species origin.
Humanized or human 161P2F1OB antibodies can also be produced, and are preferred for use in therapeutic contexts. Methods for humanizing murine and other non-human antibodies, by substituting one or more of the non-human antibody CDRs for corresponding human antibody sequences, are well known (see for example, Jones etal., 1986, Nature 321: 522-525; Riechmann etal., 1988, Nature 332: 323-327; Verhoeyen etal., 1988, Science 239: 1534-1536). See also, Carter etal., 1993, Proc. Natl, Acad. Sci. USA 89:
4285 and Sims et al., 1993, J. Immunol, 151: 2296.
Methods for producing fully human monoclonal antibodies include phage display and transgenic methods (for review, see Vaughan et al., 1998, Nature Biotechnology 16: 535-539). Fully human 161P2F1OB monoclonal antibodies can be generated using cloning technologies employing large human Ig gene combinatorial libraries (i.e., phage display) (Griffiths and Hoogenboom, Building an in vitro immune system: human antibodies from phage display libraries. In: Protein Engineering of Antibody Molecules for Prophylactic and Therapeutic Applications in Man, Clark, M. (Ed.), Nottingham Academic, pp 45-64 (1993); Burton and Barbas, Human Antibodies from combinatorial libraries. Id., pp 65-82). Fully human 161P2F1OB monoclonal antibodies can also be produced using transgenic mice engineered to contain human immunoglobulin gene loci as described in PCT Patent Application W098/24893, Kucherlapati and Jakobovits et aL, published December 3, 1997 (see also, Jakobovits, 1998, Exp. Opin. Invest Drugs 7(4): 607-614; U.S. patents 6,162,963 issued 19 December 2000; 6,150,584 issued 12 November 2000; and, 6,114598 issued 5 September 2000). This method avoids the in vitro manipulation required with phage display technology and efficiently produces high affinity authentic human antibodies.
Reactivity of 161P2F1OB antibodies with a 161P2F10B-related protein can be established by a number of well known means, including Western blot, immunoprecipitation, ELISA, and FACS
analyses using, as appropriate, 161P2F10B-related proteins, 161P2F10B-expressing cells or extracts thereof. A 161P2F1OB
antibody or fragment thereof can be labeled with a detectable marker or conjugated to a second molecule. Suitable detectable markers include, but are not limited to, a radioisotope, a fluorescent compound, a bioluminescent compound, chemiluminescent compound, a metal chelator or an enzyme. Further, bi-specific antibodies specific for two or more 161P2F1OB
epitopes are generated using methods generally known in the art. Homodimeric antibodies can also be generated by cross-linking techniques known in the art (e.g., Wolff et al., Cancer Res. 53: 2560-2565).
V.) 161P2F1OB Cellular Immune Responses The mechanism by which T cells recognize antigens has been delineated.
Efficacious peptide epitope vaccine compositions of the invention induce a therapeutic or prophylactic immune responses in very broad segments of the world-wide population. For an understanding of the value and efficacy of compositions of the invention that induce cellular immune responses, a brief review of immunology-related technology is provided.
A complex of an HLA molecule and a peptidic antigen acts as the ligand recognized by HLA-restricted T cells (Buus, S. etal., Cell 47:1071, 1986; Babbitt, B. P. etal., Nature 317:359, 1985; Townsend, A. and Bodmer, H., Annu. Rev.
ImmunoL 7:601, 1989; Germain, R. N., Annu. Rev. Immunot 11:403, 1993). Through the study of single amino acid substituted antigen analogs and the sequencing of endogenously bound, naturally processed peptides, critical residues that correspond to motifs required for specific binding to HLA antigen molecules have been identified and are set forth in Table IV
(see also, e.g., Southwood, etal., J. ImmunoL 160:3363, 1998; Rammensee, etal., lmmunogenetics 41:178, 1995;
Rammensee etal., SYFPEITHI, access via World Wide Web at URL
(134.2.96.221/scripts.hlaserverdllihome.htm); Sette, A.
and Sidney, J. Curr. Opin. ImmunoL 10:478, 1998; Engelhard, V. H., Curr. Opin.
ImmunoL 6:13, 1994; Sette, A. and Grey, H.
M., Cum Opin. Immunot 4:79, 1992; Sinigaglia, F. and Hammer, J. Curr. BioL

6:52, 1994; Ruppert et al., Cell 74:929-937, 1993; Kondo et al., J. ImmunoL 155:4307-4312, 1995; Sidney et al., J. Immunot 157:3480-3490, 1996; Sidney et al., Human Immunot 45:79-93, 1996; Sette, A. and Sidney, J. Immunogenetics 1999 Nov; 50(3-4)201-12, Review).
Furthermore, x-ray crystallographic analyses of HLA-peptide complexes have revealed pockets within the peptide binding cleft/groove of HLA molecules which accommodate, in an allele-specific mode, residues borne by peptide ligands;
these residues in turn determine the HLA binding capacity of the peptides in which they are present. (See, e.g., Madden, D.R. Annu. Rev. ImmunoL 13:587, 1995; Smith, etal., Immunity 4:203, 1996;
Fremont etal., Immunity 8:305, 1998; Stern et al., Structure 2:245, 1994; Jones, E.Y. Cum Opin. Immunot 9:75, 1997; Brown, J. H. etal., Nature 364:33, 1993; Guo, H. C.
etal., Proc. Natl. Acad. ScL USA 90:8053, 1993; Guo, H. C. etal., Nature 360:364, 1992; Silver, M. L. etal., Nature 360:367, 1992; Matsumura, M. et aL, Science 257:927, 1992; Madden et aL, Cell 70:1035, 1992; Fremont, D. H. etal., Science 257:919, 1992; Saper, M. A. , Bjorkman, P. J. and Wiley, D. C., J. Mol. Biol.
219:277, 1991.) Accordingly, the definition of class I and class II allele-specific HLA
binding motifs, or class I or class II supermotifs allows identification of regions within a protein that are correlated with binding to particular HLA antigen(s).
Thus, by a process of HLA motif identification, candidates for epitope-based vaccines have been identified; such candidates can be further evaluated by HLA-peptide binding assays to determine binding affinity and/or the time period of association of the epitope and its corresponding HLA molecule. Additional confirmatory work can be performed to select, amongst these vaccine candidates, epitopes with preferred characteristics in terms of population coverage, and/or immunogenicity.
Various strategies can be utilized to evaluate cellular immunogenicity, including:
1) Evaluation of primary T cell cultures from normal individuals (see, e.g., Wentworth, P. A. etal., MoL Immunot 32:603, 1995; Celis, E. etal., Proc. Natt Acad. Sci. USA 91:2105, 1994; Tsai, V. et al., J. Immunot 158:1796, 1997;
Kawashima, I. etal., Human Immunot 59:1, 1998). This procedure involves the stimulation of peripheral blood lymphocytes (PBL) from normal subjects with a test peptide in the presence of antigen presenting cells in vitro over a period of several weeks. T cells specific for the peptide become activated during this time and are detected using, e.g., a lymphokine- or 51Cr-release assay involving peptide sensitized target cells.
2) Immunization of HLA transgenic mice (see, e.g., Wentworth, P. A. etal., J.
Immunot 26:97, 1996; Wentworth, P.
A. etal., mt. Immunot 8:651, 1996; Alexander, J. etal., J. Immunot 159:4753, 1997). For example, in such methods peptides in incomplete Freund's adjuvant are administered subcutaneously to HLA transgenic mice. Several weeks following immunization, splenocytes are removed and cultured in vitro in the presence of test peptide for approximately one week.
Peptide-specific T cells are detected using, e.g., a 51Cr-release assay involving peptide sensitized target cells and target cells expressing endogenously generated antigen.
3) Demonstration of recall T cell responses from immune individuals who have been either effectively vaccinated and/or from chronically ill patients (see, e.g., Rehermann, B. etal., J. Exp.
Med. 181:1047, 1995; Doolan, D. L. etal., Immunity 7:97, 1997; Bertoni, R. etal., J. Clin. Invest. 100:503, 1997;
Threlkeld, S. C. et aL, J. Immunot 159:1648, 1997;
Diepolder, H. M. etal., J. ViroL 71:6011, 1997). Accordingly, recall responses are detected by culturing PBL from subjects that have been exposed to the antigen due to disease and thus have generated an immune response "naturally", or from patients who were vaccinated against the antigen. PBL from subjects are cultured in vitro for 1-2 weeks in the presence of test peptide plus antigen presenting cells (APC) to allow activation of "memory" T cells, as compared to "naive" T cells. At the end of the culture period, T cell activity is detected using assays including 51Cr release involving peptide-sensitized targets, T cell proliferation, or lymphokine release.
VI.) 161P2F1OB Transonic Animals Nucleic acids that encode a 161P2F10B-related protein can also be used to generate either transgenic animals or "knock our animals that, in turn, are useful in the development and screening of therapeutically useful reagents. In accordance with established techniques, cDNA encoding 161P2F1OB can be used to clone genomic DNA that encodes 161P2F1OB. The cloned genomic sequences can then be used to generate transgenic animals containing cells that express DNA that encode 161P2F1OB. Methods for generating transgenic animals, particularly animals such as mice or rats, have become conventional in the art and are described, for example, in U.S. Patent Nos. 4,736,866 issued 12 April 1988, and 4,870,009 issued 26 September 1989. Typically, particular cells would be targeted for 161P2F1OB transgene incorporation with tissue-specific enhancers.
Transgenic animals that include a copy of a transgene encoding 161P2F1OB can be used to examine the effect of increased expression of DNA that encodes 161P2F10B. Such animals can be used as tester animals for reagents thought to confer protection from, for example, pathological conditions associated with its overexpression. In accordance with this aspect of the invention, an animal is treated with a reagent and a reduced incidence of a pathological condition, compared to untreated animals that bear the transgene, would indicate a potential therapeutic intervention for the pathological condition.
Alternatively, non-human homologues of 161P2F1OB can be used to construct a 161P2F1OB "knock out" animal that has a defective or altered gene encoding 161P2F1OB as a result of homologous recombination between the endogenous gene encoding 161P2F1OB and altered genomic DNA encoding 161P2F1OB
introduced into an embryonic cell of the animal. For example, cDNA that encodes 161P2F1OB can be used to clone genomic DNA encoding 161P2F1OB in accordance with established techniques. A portion of the genomic DNA encoding 161P2F1OB can be deleted or replaced with another gene, such as a gene encoding a selectable marker that can be used to monitor integration. Typically, several kilobases of unaltered flanking DNA (both at the 5' and 3' ends) are included in the vector (see, e.g., Thomas and Capecchi, Cell, 51:503 (1987) for a description of homologous recombination vectors).
The vector is introduced into an embryonic stem cell line (e.g., by electroporation) and cells in which the introduced DNA has homologously recombined with the endogenous DNA are selected (see, e.g., Li etal., Cell, 69:915 (1992)). The selected cells are then injected into a blastocyst of an animal (e.g., a mouse or rat) to form aggregation chimeras (see, e.g., Bradley, in Teratocarcinomas and Embryonic Stem Cells: A
Practical Approach, E. J. Robertson, ed. (IRL, Oxford, 1987), pp. 113-152). A
chimeric embryo can then be implanted into a suitable pseudopregnant female foster animal, and the embryo brought to term to create a "knock out" animal. Progeny harboring the homologously recombined DNA in their germ cells can be identified by standard techniques and used to breed animals in which all cells of the animal contain the homologously recombined DNA. Knock out animals can be characterized, for example, for their ability to defend against certain pathological conditions or for their development of pathological conditions due to absence of a 161P2F1OB polypeptide.
VII.) Methods for the Detection of 161P2F1OB
Another aspect of the present invention relates to methods for detecting 161P2F1OB polynucleotides and 161P2F10B-related proteins, as well as methods for identifying a cell that expresses 161P2F10B. The expression profile of 161P2F1OB
makes it a diagnostic marker for metastasized disease. Accordingly, the status of 161P2F1OB gene products provides information useful for predicting a variety of factors including susceptibility to advanced stage disease, rate of progression, and/or tumor aggressiveness. As discussed in detail herein, the status of 161P2F1OB
gene products in patient samples can be analyzed by a variety protocols that are well known in the art including immunohistochemical analysis, the variety of Northern blotting techniques including in situ hybridization, RT-PCR analysis (for example on laser capture micro-dissected samples), Western blot analysis and tissue array analysis.
More particularly, the invention provides assays for the detection of 161P2F1OB polynudeotides in a biological sample, such as serum, bone, prostate, and other tissues, urine, semen, cell preparations, and the like. Detectable 161P2F1OB

polynucleotides include, for example, a 161P2F108 gene or fragment thereof, 161P2F1OB mRNA, alternative splice variant 161P2F1OB mRNAs, and recombinant DNA or RNA molecules that contain a 161P2F1OB
polynucleotide. A number of methods for amplifying and/or detecting the presence of 161P2F1OB polynucleotides are well known in the art and can be employed in the practice of this aspect of the invention.
In one embodiment, a method for detecting a 161P2F1OB mRNA in a biological sample comprises producing cDNA
from the sample by reverse transcription using at least one primer; amplifying the cDNA so produced using a 161P2F1OB
polynucleotides as sense and antisense primers to amplify 161P2F1OB cDNAs therein; and detecting the presence of the amplified 161P2F108 cDNA. Optionally, the sequence of the amplified 161P2F1OB
cDNA can be determined.
In another embodiment, a method of detecting a 161P2F1OB gene in a biological sample comprises first isolating genomic DNA from the sample; amplifying the isolated genomic DNA using 161P2F1OB polynucleotides as sense and antisense primers; and detecting the presence of the amplified 161P2F1OB gene.
Any number of appropriate sense and antisense probe combinations can be designed from a 161P2F1OB nucleotide sequence (see, e.g., Figure 2) and used for this purpose.
The invention also provides assays for detecting the presence of a 161P2F1OB
protein in a tissue or other biological sample such as serum, semen, bone, prostate, urine, cell preparations, and the like. Methods for detecting a 161P2F10B-related protein are also well known and include, for example, immunoprecipitation, immunohistochemical analysis, Western blot analysis, molecular binding assays, ELISA, ELIFA and the like. For example, a method of detecting the presence of a 161P2F10B-related protein in a biological sample comprises first contacting the sample with a 161P2F1OB antibody, a 161P2F10B-reactive fragment thereof, or a recombinant protein containing an antigen-binding region of a 161P2F1OB antibody; and then detecting the binding of 161P2F10B-related protein in the sample.
Methods for identifying a cell that expresses 161P2F1OB are also within the scope of the invention. In one embodiment, an assay for identifying a cell that expresses a 161P2F1OB gene comprises detecting the presence of 161P2F1OB mRNA in the cell. Methods for the detection of particular mRNAs in cells are well known and include, for example, hybridization assays using complementary DNA probes (such as in situ hybridization using labeled 161P2F1OB riboprobes, Northern blot and related techniques) and various nucleic acid amplification assays (such as RT-PCR
using complementary primers specific for 161P2F10B, and other amplification type detection methods, such as, for example, branched DNA, SISBA, TMA and the like).
Alternatively, an assay for identifying a cell that expresses a 161P2F1OB gene comprises detecting the presence of 161P2F1OB-related protein in the cell or secreted by the cell. Various methods for the detection of proteins are well known in the art and are employed for the detection of 161P2F1OB-related proteins and cells that express 161P2F1OB-related proteins.
161P2F1OB expression analysis is also useful as a tool for identifying and evaluating agents that modulate 161P2F1OB
gene expression. For example, 161P2F1OB expression is significantly upregulated in prostate cancer, and is expressed in cancers of the tissues listed in Table I. Identification of a molecule or biological agent that inhibits 161P2F1OB expression or over-expression in cancer cells is of therapeutic value. For example, such an agent can be identified by using a screen that quantifies 161P2F1OB expression by RT-PCR, nucleic acid hybridization or antibody binding.
VIII.) Methods for Monitoring the Status of 161P2F10B-related Genes and Their Products Oncogenesis is known to be a multistep process where cellular growth becomes progressively dysregulated and cells progress from a normal physiological state to precancerous and then cancerous states (see, e.g., Alers etal., Lab Invest. 77(5): 437-438 (1997) and Isaacs etal., Cancer Surv. 23: 19-32 (1995)). In this context, examining a biological sample for evidence of dysregulated cell growth (such as aberrant 161P2F1OB
expression in cancers) allows for early detection of such aberrant physiology, before a pathologic state such as cancer has progressed to a stage that therapeutic options are more limited and or the prognosis is worse. In such examinations, the status of 161P2F1OB in a biological sample of interest can be compared, for example, to the status of 161P2F1OB in a corresponding normal sample (e.g. a sample from that individual or alternatively another individual that is not affected by a pathology). An alteration in the status of 161P2F1OB in the biological sample (as compared to the normal sample) provides evidence of dysregulated cellular growth. In addition to using a biological sample that is not affected by a pathology as a normal sample, one can also use a predetermined normative value such as a predetermined normal level of mRNA
expression (see, e.g., Greyer et aL, J. Comp.
Neurol. 1996 Dec 9; 376(2): 306-14 and U.S. Patent No. 5,837,501) to compare 161P2F1OB status in a sample.
The term "status" in this context is used according to its art accepted meaning and refers to the condition or state of a gene and its products. Typically, skilled artisans use a number of parameters to evaluate the condition or state of a gene and its products. These include, but are not limited to the location of expressed gene products (including the location of 161P2F1OB
expressing cells) as well as the level, and biological activity of expressed gene products (such as 161P2F1OB mRNA, polynucleotides and polypeptides). Typically, an alteration in the status of 161P2F1OB comprises a change in the location of 161P2F1OB and/or 161P2F1OB expressing cells and/or an increase in 161P2F1OB
mRNA and/or protein expression.
161P2F1OB status in a sample can be analyzed by a number of means well known in the art, including without limitation, immunohistochemical analysis, in situ hybridization, RT-PCR
analysis on laser capture micro-dissected samples, Western blot analysis, and tissue array analysis. Typical protocols for evaluating the status of a 161P2F1OB gene and gene products are found, for example in Ausubel et aL eds., 1995, Current Protocols In Molecular Biology, Units 2 (Northern Blotting), 4 (Southern Blotting), 15 (Immunoblotting) and 18 (PCR Analysis).
Thus, the status of 161P2F1OB in a biological sample is evaluated by various methods utilized by skilled artisans including, but not limited to genomic Southern analysis (to examine, for example perturbations in a 161P2F1OB gene), Northern analysis and/or PCR analysis of 161P2F1OB mRNA (to examine, for example alterations in the polynucleotide sequences or expression levels of 161P2F1OB mRNAs), and, Western and/or immunohistochemical analysis (to examine, for example alterations in polypeptide sequences, alterations in polypeptide localization within a sample, alterations in expression levels of 161P2F1OB proteins and/or associations of 161P2F1OB proteins with polypeptide binding partners). Detectable 161P2F1OB
polynucleotides include, for example, a 161P2F1OB gene or fragment thereof, 161P2F1OB mRNA, alternative splice variants, 161P2F1OB mRNAs, and recombinant DNA or RNA molecules containing a 161P2F1OB polynudeotide.
The expression profile of 161P2F1OB makes it a diagnostic marker for local and/or metastasized disease, and =
provides information on the growth or oncogenic potential of a biological sample. In particular, the status of 161P2F1OB provides information useful for predicting susceptibility to particular disease stages, progression, and/or tumor aggressiveness. The invention provides methods and assays for determining 161P2F1OB status and diagnosing cancers that express 161P2F10B, such as cancers of the tissues listed in Table I. For example, because 161P2F1OB mRNA is so highly expressed in prostate and other cancers relative to normal prostate tissue, assays that evaluate the levels of 161P2F1OB mRNA transcripts or proteins in a biological sample can be used to diagnose a disease associated with 161P2F1OB
dysregulation, and can provide prognostic information useful in defining appropriate therapeutic options.
The expression status of 161P2F1OB provides information including the presence, stage and location of dysplastic, precancerous and cancerous cells, predicting susceptibility to various stages of disease, and/or for gauging tumor aggressiveness. Moreover, the expression profile makes it useful as an imaging reagent for metastasized disease.
Consequently, an aspect of the invention is directed to the various molecular prognostic and diagnostic methods for examining the status of 161P2F1OB in biological samples such as those from individuals suffering from, or suspected of suffering from a pathology characterized by dysregulated cellular growth, such as cancer.
As described above, the status of 161P2F1OB in a biological sample can be examined by a number of well-known procedures in the art. For example, the status of 161P2F1OB in a biological sample taken from a specific location in the body can be examined by evaluating the sample for the presence or absence of 161P2F1OB expressing cells (e.g. those that express 161P2F1OB mRNAs or proteins). This examination can provide evidence of dysregulated cellular growth, for example, when 161P2F10B-expressing cells are found in a biological sample that does not normally contain such cells (such as a lymph node), because such alterations in the status of 161P2F1OB in a biological sample are often associated with dysregulated cellular growth. Specifically, one indicator of dysregulated cellular growth is the metastases of cancer cells from an organ of origin (such as the prostate) to a different area of the body (such as a lymph node). In this context, evidence of dysregulated cellular growth is important for example because occult lymph node metastases can be detected in a substantial proportion of patients with prostate cancer, and such metastases are associated with known predictors of disease progression (see, e.g., Murphy etal., Prostate 42(4): 315-317 (2000);Su etal., Semin. Surg. Oncol. 18(1): 17-28 (2000) and Freeman etal., J Urol 1995 Aug 154(2 Pt 1):474-8).
In one aspect, the invention provides methods for monitoring 161P2F1OB gene products by determining the status of 161P2F1OB gene products expressed by cells from an individual suspected of having a disease associated with dysregulated cell growth (such as hyperplasia or cancer) and then comparing the status so determined to the status of 161P2F1OB gene products in a corresponding normal sample. The presence of aberrant 161P2F1OB gene products in the test sample relative to the normal sample provides an indication of the presence of dysregulated cell growth within the cells of the individual.
In another aspect, the invention provides assays useful in determining the presence of cancer in an individual, comprising detecting a significant increase in 161P2F1OB mRNA or protein expression in a test cell or tissue sample relative to expression levels in the corresponding normal cell or tissue. The presence of 161P2F1OB mRNA can, for example, be evaluated in tissues including but not limited to those listed in Table I. The presence of significant 161P2F1OB expression in any of these tissues is useful to indicate the emergence, presence and/or severity of a cancer, since the corresponding normal tissues do not express 161P2F1OB mRNA or express it at lower levels.
In a related embodiment, 161P2F1OB status is determined at the protein level rather than at the nucleic acid level. For example, such a method comprises determining the level of 161P2F1OB protein expressed by cells in a test tissue sample and comparing the level so determined to the level of 161P2F1OB expressed in a corresponding normal sample. In one embodiment, the presence of 161P2F1OB protein is evaluated, for example, using immunohistochemical methods. 161P2F1OB antibodies or binding partners capable of detecting 161P2F1OB protein expression are used in a variety of assay formats well known in the art for this purpose.
In a further embodiment, one can evaluate the status of 161P2F1OB nucleotide and amino acid sequences in a biological sample in order to identify perturbations in the structure of these molecules. These perturbations can include insertions, deletions, substitutions and the like. Such evaluations are useful because perturbations in the nucleotide and amino acid sequences are observed in a large number of proteins associated with a growth dysregulated phenotype (see, e.g., Marrogi et al., 1999, J. Cutan. Pathol. 26(8):369-378). For example, a mutation in the sequence of 161P2F1OB may be indicative of the presence or promotion of a tumor. Such assays therefore have diagnostic and predictive value where a mutation in 161P2F1OB
indicates a potential loss of function or increase in tumor growth.
A wide variety of assays for observing perturbations in nucleotide and amino acid sequences are well known in the art.
For example, the size and structure of nucleic acid or amino acid sequences of 161P2F1OB gene products are observed by the Northern, Southern, Western, PCR and DNA sequencing protocols discussed herein. In addition, other methods for observing perturbations in nucleotide and amino acid sequences such as single strand conformation polymorphism analysis are well known =
in the art (see, e.g., U.S. Patent Nos. 5,382,510 issued 7 September 1999, and 5,952,170 issued 17 January 1995).
Additionally, one can examine the methylation status of a 161P2F1OB gene in a biological sample. Aberrant demethylation and/or hyperrnethylation of CpG islands in gene 5' regulatory regions frequently occurs in immortalized and transformed cells, and can result in altered expression of various genes. For example, promoter hypermethylation of the pi-class glutathione S-transferase (a protein expressed in normal prostate but not expressed in >90% of prostate carcinomas) appears to permanently silence transcription of this gene and is the most frequently detected genomic alteration in prostate carcinomas (De Marzo etal., Am. J. Pathol. 155(6): 1985-1992 (1999)). In addition, this alteration is present in at least 70%
of cases of high-grade prostatic intraepithelial neoplasia (PIN) (Brooks et al., Cancer Epidemiol. Biomarkers Prey., 1998,

7:531-536). In another example, expression of the LAGE-I tumor specific gene (which is not expressed in normal prostate but is expressed in 25-50% of prostate cancers) is induced by deoxy-azacytidine in lymphoblastoid cells, suggesting that tumoral expression is due to demethylation (Lethe etal., Int. J. Cancer 76(6):
903-908 (1998)). A variety of assays for examining methylation status of a gene are well known in the art. For example, one can utilize, in Southern hybridization approaches, methylation-sensitive restriction enzymes that cannot cleave sequences that contain methylated CpG sites to assess the methylation status of CpG islands. In addition, MSP (methylation specific PCR) can rapidly profile the methylation status of all the CpG sites present in a CpG island of a given gene. This procedure involves initial modification of DNA by sodium bisulfite (which will convert all unmethylated cytosines to uracil) followed by amplification using primers specific for methylated versus unmethylated DNA. Protocols involving methylation interference can also be found for example in Current Protocols In Molecular Biology, Unit 12, Frederick M. Ausubel etal. eds., 1995.
Gene amplification is an additional method for assessing the status of 161P2F10B. Gene amplification is measured in a sample directly, for example, by conventional Southern blotting or Northern blotting to quantitate the transcription of mRNA (Thomas, 1980, Proc. Natl. Acad. Sci. USA, 77:5201-5205), dot blotting (DNA analysis), or in situ hybridization, using an appropriately labeled probe, based on the sequences provided herein. Alternatively, antibodies are employed that recognize specific duplexes, including DNA duplexes, RNA
duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes. The antibodies in turn are labeled and the assay carried out where the duplex is bound to a surface, so that upon the formation of duplex on the surface, the presence of antibody bound to the duplex can be detected.
Biopsied tissue or peripheral blood can be conveniently assayed for the presence of cancer cells using for example, Northern, dot blot or RT-PCR analysis to detect 161P2F1OB expression. The presence of RT-PCR amplifiable 161P2F1OB
mRNA provides an indication of the presence of cancer. RT-PCR assays are well known in the art. RT-PCR detection assays for tumor cells in peripheral blood are currently being evaluated for use in the diagnosis and management of a number of human solid tumors. In the prostate cancer field, these include RT-PCR assays for the detection of cells expressing PSA and PSM (Verkaik et al., 1997, Urol. Res. 25:373-384; Ghossein et al., 1995, J. Clin. Oncol.
13:1195-2000; Heston etal., 1995, Clin. Chem. 41:1687-1688).
A further aspect of the invention is an assessment of the susceptibility that an individual has for developing cancer. In one embodiment, a method for predicting susceptibility to cancer comprises detecting 161P2F1OB mRNA or 161P2F1OB protein in a tissue sample, its presence indicating susceptibility to cancer, wherein the degree of 161P2F1OB mRNA expression correlates to the degree of susceptibility. In a specific embodiment, the presence of 161P2F1OB in prostate or other tissue is examined, with the presence of 161P2F1OB in the sample providing an indication of prostate cancer susceptibility (or the emergence or existence of a prostate tumor). Similarly, one can evaluate the integrity 161P2F1OB
nucleotide and amino acid sequences in a biological sample, in order to identify perturbations in the structure of these molecules such as insertions, deletions, substitutions and the like. The presence of one or more perturbations in 161P2F1OB gene products in the sample is an indication of cancer susceptibility (or the emergence or existence of a tumor).
The invention also comprises methods for gauging tumor aggressiveness. In one embodiment, a method for gauging aggressiveness of a tumor comprises determining the level of 161P2F1OB mRNA or 161P2F1OB protein expressed by tumor cells, comparing the level so determined to the level of 161P2F1OB mRNA or 161P2F1OB protein expressed in a corresponding normal tissue taken from the same individual or a normal tissue reference sample, wherein the degree of 161P2F1OB mRNA or 161P2F1OB protein expression in the tumor sample relative to the normal sample indicates the degree of aggressiveness. In a specific embodiment, aggressiveness of a tumor is evaluated by determining the extent to which 161P2F1OB is expressed in the tumor cells, with higher expression levels indicating more aggressive tumors.
Another embodiment is the evaluation of the integrity of 161P2F1OB nucleotide and amino acid sequences in a biological sample, in order to identify perturbations in the structure of these molecules such as insertions, deletions, substitutions and the like. The presence of one or more perturbations indicates more aggressive tumors.
Another embodiment of the invention is directed to methods for observing the progression of a malignancy in an individual over time. In one embodiment, methods for observing the progression of a malignancy in an individual over time comprise determining the level of 161P2F1OB mRNA or 161P2F1OB protein expressed by cells in a sample of the tumor, comparing the level so determined to the level of 161P2F1OB mRNA or 161P2F1OB
protein expressed in an equivalent tissue sample taken from the same individual at a different time, wherein the degree of 161P2F1OB mRNA or 161P2F1OB protein expression in the tumor sample over time provides information on the progression of the cancer. In a specific embodiment, the progression of a cancer is evaluated by determining 161P2F1OB expression in the tumor cells over time, where increased expression over time indicates a progression of the cancer. Also, one can evaluate the integrity 161P2F1OB nucleotide and amino acid sequences in a biological sample in order to identify perturbations in the structure of these molecules such as insertions, deletions, substitutions and the like, where the presence of one or more perturbations indicates a progression of the cancer.
The above diagnostic approaches can be combined with any one of a wide variety of prognostic and diagnostic protocols known in the art. For example, another embodiment of the invention is directed to methods for observing a coincidence between the expression of 161P2F1OB gene and 161P2F1013 gene products (or perturbations in 161P2F108 gene and 161P2F1OB gene products) and a factor that is associated with malignancy, as a means for diagnosing and prognosticating the status of a tissue sample. A wide variety of factors associated with malignancy can be utilized, such as the expression of genes associated with malignancy (e.g. PSA, PSCA and PSM expression for prostate cancer etc.) as well as gross cytological observations (see, e.g., Bocking et al., 1984, Anal. Quant. Cytol. 6(2):74-88;
Epstein, 1995, Hum. Pathol. 26(2):223-9; Thorson et al., 1998, Mod. Pathol. 11(6):543-51; Baisden et al., 1999, Am. J. Surg.
Pathol. 23(8):918-24). Methods for observing a coincidence between the expression of 161P2F108 gene and 161P2F1OB gene products (or perturbations in 161P2F1OB gene and 161P2F1OB gene products) and another factor that is associated with malignancy are useful, for example, because the presence of a set of specific factors that coincide with disease provides information crucial for diagnosing and prognosticating the status of a tissue sample.
In one embodiment, methods for observing a coincidence between the expression of 161P2F1OB gene and 161P2F1OB gene products (or perturbations in 161P2F1OB gene and 161P2F1OB gene products) and another factor associated with malignancy entails detecting the overexpression of 161P2F1OB mRNA or protein in a tissue sample, detecting the overexpression of PSA mRNA or protein in a tissue sample (or PSCA or PSM
expression), and observing a coincidence of 161P2F1OB mRNA or protein and PSA mRNA or protein overexpression (or PSCA or PSM expression). In a specific embodiment, the expression of 161P2F1OB and PSA mRNA in prostate tissue is examined, where the coincidence of 161P2F1OB
and PSA mRNA overexpression in the sample indicates the existence of prostate cancer, prostate cancer susceptibility or the emergence or status of a prostate tumor.
Methods for detecting and quantifying the expression of 161P2F1OB mRNA or protein are described herein, and standard nucleic acid and protein detection and quantification technologies are well known in the art. Standard methods for the detection and quantification of 161P2F108 mRNA include in situ hybridization using labeled 161P2F1OB riboprobes, Northern blot and related techniques using 161P2F1OB polynudeotide probes, RT-PCR analysis using primers specific for 161P2F1OB, and other amplification type detection methods, such as, for example, branched DNA, SISBA, TMA and the like. In a specific embodiment, semi-quantitative RT-PCR is used to detect and quantify 161P2F1OB
mRNA expression. Any number of primers capable of amplifying 161P2F1OB can be used for this purpose, including but not limited to the various primer sets specifically described herein. In a specific embodiment, polyclonal or monoclonal antibodies specifically reactive with the wild-type 161P2F1OB protein can be used in an immunohistochemical assay of biopsied tissue.
IX.) Identification of Molecules That Interact With 161P2F108 The 161P2F1OB protein and nucleic acid sequences disclosed herein allow a skilled artisan to identify proteins, small molecules and other agents that interact with 161P2F1OB, as well as pathways activated by 161P2F1OB via any one of a variety of art accepted protocols. For example, one can utilize one of the so-called interaction trap systems (also referred to as the "two-hybrid assay"). In such systems, molecules interact and reconstitute a transcription factor which directs expression of a reporter gene, whereupon the expression of the reporter gene is assayed. Other systems identify protein-protein interactions in vivo through reconstitution of a eukaryotic transcriptional activator, see, e.g., U.S. Patent Nos.
' 5,955,280 issued 21 September 1999, 5,925,523 issued 20 July 1999, 5,846,722 issued 8 December 1998 and 6,004,746 issued 21 December 1999. Algorithms are also available in the art for genome-based predictions of protein function (see, e.g., Marcotte, etal., Nature 402: 4 November 1999, 83-86).
Alternatively one can screen peptide libraries to identify molecules that interact with 161P2F1OB protein sequences.
In such methods, peptides that bind to 161P2F1OB are identified by screening libraries that encode a random or controlled collection of amino acids. Peptides encoded by the libraries are expressed as fusion proteins of bacteriophage coat proteins, the bacteriophage particles are then screened against the 161P2F1OB
protein(s).
Accordingly, peptides having a wide variety of uses, such as therapeutic, prognostic or diagnostic reagents, are thus identified without any prior information on the structure of the expected ligand or receptor molecule. Typical peptide libraries and screening methods that can be used to identify molecules that interact with 161P2F1OB protein sequences are disclosed for example in U.S. Patent Nos. 5,723,286 issued 3 March 1998 and 5,733,731 issued 31 March 1998.
Altematively, cell lines that express 161P2F1OB are used to identify protein-protein interactions mediated by 161P2F1OB. Such interactions can be examined using immunoprecipitation techniques (see, e.g., Hamilton B.J., etal.
Biochem. Biophys. Res. Commun. 1999, 261:646-51). 161P2F1OB protein can be immunoprecipitated from 161P2F1OB-expressing cell lines using anti-161P2F1OB antibodies. Altematively, antibodies against His-tag can be used in a cell line engineered to express fusions of 161P2F1OB and a His-tag (vectors mentioned above). The immunoprecipitated complex can be examined for protein association by procedures such as Western blotting, 35S-methionine labeling of proteins, protein microsequencing, silver staining and two-dimensional gel electrophoresis.
Small molecules and ligands that interact with 161P2F1OB can be identified through related embodiments of such screening assays. For example, small molecules can be identified that interfere with protein function, including molecules that interfere with 161P2F1OB's ability to mediate phosphorylation and de-phosphorylation, interaction with DNA or RNA
molecules as an indication of regulation of cell cycles, second messenger signaling or tumorigenesis. Similarly, small molecules that modulate 161P2F10B-related ion channel, protein pump, or cell communication functions are identified and used to treat patients that have a cancer that expresses 161P2F108 (see, e.g., Hille, B., Ionic Channels of Excitable Membranes 2nd Ed., Sinauer Assoc., Sunderland, MA, 1992). Moreover, ligands that regulate 161P2F1OB function can be identified based on their ability to bind 161P2F1OB and activate a reporter construct. Typical methods are discussed for example in U.S. Patent No. 5,928,868 issued 27 July 1999, and include methods for forming hybrid ligands in which at least one ligand is a small molecule. In an illustrative embodiment, cells engineered to express a fusion protein of 161P2F1OB
and a DNA-binding protein are used to co-express a fusion protein of a hybrid ligand/small molecule and a cDNA library transcriptional activator protein. The cells further contain a reporter gene, the expression of which is conditioned on the proximity of the first and second fusion proteins to each other, an event that occurs only if the hybrid ligand binds to target sites on both hybrid proteins. Those cells that express the reporter gene are selected and the unknown small molecule or the unknown ligand is identified. This method provides a means of identifying modulators, which activate or inhibit 161P2F1OB.
An embodiment of this invention comprises a method of screening for a molecule that interacts with a 161P2F1OB
amino acid sequence shown in Figure 2 or Figure 3, comprising the steps of contacting a population of molecules with a 161P2F1OB amino acid sequence, allowing the population of molecules and the 161P2F1OB amino acid sequence to interact under conditions that facilitate an interaction, determining the presence of a molecule that interacts with the 161P2F1OB
amino acid sequence, and then separating molecules that do not interact with the 161P2F1OB amino acid sequence from molecules that do. In a specific embodiment, the method further comprises purifying, characterizing and identifying a molecule that interacts with the 161P2F1OB amino acid sequence. The identified molecule can be used to modulate a function performed by 161P2F10B. In a preferred embodiment, the 161P2F1OB
amino acid sequence is contacted with a library of peptides.
X.) Therapeutic Methods and Compositions The identification of 161P2F106 as a protein that is normally expressed in a restricted set of tissues, but which is also expressed in prostate and other cancers, opens a number of therapeutic approaches to the treatment of such cancers.
As contemplated herein, 161P2F1OB functions as a transcription factor involved in activating tumor-promoting genes or repressing genes that block tumorigenesis.
Accordingly, therapeutic approaches that inhibit the activity of a 161P2F1013 protein are useful for patients suffering from a cancer that expresses 161P2F10B. These therapeutic approaches generally fall into two classes. One class comprises various methods for inhibiting the binding or association of a 161P2F1OB protein with its binding partner or with other proteins. Another class comprises a variety of methods for inhibiting the transcription of a 161P2F1OB gene or translation of 161P2F1OB mRNA.
X.A.) Anti-Cancer Vaccines The invention provides cancer vaccines comprising a 161P2F10B-related protein or 161P2F1013-related nucleic acid. In view of the expression of 161P2F106, cancer vaccines prevent and/or treat 161P2F1013-expressing cancers with minimal or no effects on non-target tissues. The use of a tumor antigen in a vaccine that generates humoral and/or cell-mediated immune responses as anti-cancer therapy is well known in the art and has been employed in prostate cancer using human PSMA and rodent PAP immunogens (Hodge et al., 1995, Int. J. Cancer 63:231-237; Fong et al., 1997, J. lmmunol. 159:3113-3117).
Such methods can be readily practiced by employing a 161P2F10B-related protein, or a 161P2F10B-encoding nucleic acid molecule and recombinant vectors capable of expressing and presenting the 161P2F1OB immunogen (which typically comprises a number of antibody or T cell epitopes). Skilled artisans understand that a wide variety of vaccine systems for delivery of immunoreactive epitopes are known in the art (see, e.g., Heryln etal., Ann Med 1999 Feb 31(1):66-78; Maruyama etal., Cancer Immunol lmmunother 2000 Jun 49(3):123-32) Briefly, such methods of generating an immune response (e.g. humoral and/or cell-mediated) in a mammal, comprise the steps of: exposing the mammal's immune system to an immunoreactive epitope (e.g. an epitope present in a 161P2F1OB protein shown in Figure 3 or analog or homolog thereof) so that the mammal generates an immune response-that is specific for that epitope (e.g. generates antibodies that specifically recognize that epitope). In a preferred method, a 161P2F1OB
immunogen contains a biological motif, see e.g., _ Tables VIII-XXI and XXII-XLIX, or a peptide of a size range from 161P2F1OB
indicated in Figure 5, Figure 6, Figure 7, Figure

8, and Figure 9.
The entire 161P2F1OB protein, immunogenic regions or epitopes thereof can be combined and delivered by various means. Such vaccine compositions can include, for example, lipopeptides (e.g.,Vitiello, A. etal., J. Clin. Invest.

95:341, 1995), peptide compositions encapsulated in poly(DL-lectIde-co-glycolide) ("PLG") microspheres (see, e.g., Eldridge, et al., *dec. trninunot 28:287-294, 1991: Alonso etal., Vaccine 12:299-306, 1994; Jones eta!,, Vaccine 13:675-681, 1995), peptide compositions contained in immune stimulating complexes (ISCOMS) (see, e.g., Takahashi et al., Nature 344:873-875, 1990; Hu et at, Cim Exp Immunot 113:235-243, 1998), multiple antigen peptide systems (MAPs) (see e.g, Tam, J. P., =
Proc. Natt Acad. Sc!. ttS.A 85:5409-5413, 1988; Tam, J.P., J !moot Methods 196:17-32, 1996), peptides formulated as multivalent peptides; peptides for use in ballistic delivery systems, typically crystallized peptides, viral delivery vectors (Perkus, M. E. etal., In: Concepts in vaccine development, Kaufmann, S. H. E., ed,, p.379, 1996; Chakrabarti, S. etal., Nature 320:535, 1986; Hu, S. L. etal., Nature 320537, 1986; Kieny, M.-P.
etal., AIDS abfrechnology 4:790, 1 '6; Top, F.
H. at at, J. Infect. Dis. 124:148, 1971; Chanda, P. K. etal., Virology 175:535, 1990), particles of viral or synthetic origin (e.g., Koller, N. et al., J. Immunot Methods. 192:25, 1996; Eldridge, J. H. et al., Sam. Hemalo). 30:16, 1993; Falo, L. D., Jr. etal., Nature Med. 7:649, 1995), adjuvants (Warren, H. S., Vogel, F. R., and Chedid, L. A. Annu. Rev. Inning 4:369, 1986;
Gupta, R. K. etal., Vaccine 11:293, 1993), liposomes (Reddy, ft etal., J.
Immunot 148:1585, 1992; Rock, K. L., Immunot Today 17:131, 1996), or, naked or particle absorbed cDNA (Ulmer, J. B. et at, Science 259:1745, 1993; Robinson, H. L., Hunt, L. A., and Webster, R. a, Vaccine 11:957, 1993; Shiver, J. W. etal., in:
Concepts in vaccine development, Kaufmann, S. H. E., ed., p. 423, 1996; Cease, K. B., and Berzofsky, J. A., Annu. Rev, Immunot 12:923, 1994 and Eldridge, J. H. etal., Sam. Hernatot 30:16, 1993). Toxin-targeted delivery technologies, also known as receptor mediated targeting, such as those of Avant Immunotherapeutics, Inc. (Needham, Massachusetts) may also be used.
In patients with 161P2F108-associated cancer, the vaccine compositions of the invention can also be used in conjunction with other treatments used for cancer, e,g., surgery, chemotherapy, drug therapies, radiation therapies, etc.
including use in combination with immune adjuvants such as 1L-2, IL-12, GM-CSF, and the like.
Cllular Vaccines:
CTL epitopes can be determined using specific algorithms to identify peptides within 161P2F108 protein that bind corresponding HLA alleles (see e.g., Table IV; Epimerm and Epimalrham, Brown University.
MIMS tgAl SYFPEITHI) .
In a preferred embodiment, a 161P2F1OB immunogen contains one or more amino acid sequences identified using techniques well known in the art, such as the sequences shown in Tables VIII-XXI and XXII-XLIX or a peptide o(8, 9, 10 or 11 amino acids specified by an HLA Classi motifisupermotif (e.g., Table IV (A), Table 1V (D), or Table IV (E)) and/or a peptide of at least 9 amino adds that comprises an HIA Class limotifisupermolif (ea, Table IV (13) or Table 81(C)). As is appreciated in the art, the HLA class I binding groove is essentially closed ended so that peptides of only a particular sire range can fit into the groove and be bound, generally HIA Class I epitopes are 8,9, 10, or 11 amino acids long. In contrast, the HLA Class II binding groove is essentially open ended; therefore a peptide of about 9 or more amino acids can be bound by an HLA Class II molecule. Due to the binding groove differences between HLA
Class 1 and IL HLA Class I motifs are length specific, Le., position two of El Class I motif is the second amino acid in an amino b carboxyl direction of the peptide.
The amino acid positions in a Class 11 motif are relative only to each other, not the overall peptide, i.e., additional amino acids can be attached to the amino and/or carboxyl termini of a motif-bearing sequence. HLA Class II epitopes are often 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20, 21, 22, D, 24, or 25 amino acids tong, or longer than 25 amino acids.
Antibody-based Vaccines A wide variety of methods for generating an immune response in a mammal are known in the art (for example as the first step in the generation of hybridomas). Methods of generating an immune response in a mammal comprise exposing the mammal's immune system to an immunogenic epitope on a protein (e.g. a 161P2F1OB protein) so that an immune response is generated. A typical embodiment consists of a method for generating an Immune response to 161P2F1OB in a host, by contacting the host with a sufficient amount of at least one 161P2F1OB B cell Or cytotoxic T-cell epitope or analog thereof; and at least one periodic interval thereafter re-contacting the host with the 161P2F1013 B cell or cytotoxic T-cell epitope or analog thereof. A specific embodiment consists of a method of generating an immune response against a 161P2F10B-related protein or a man-made multiepitopic peptide comprising:
administering 161P2F1OB immunogen (e.g. a 161P2F108 protein or a peptide fragment thereof, a 161P2F1OB fusion protein or analog etc.) in a vaccine preparation to a human or another mammal. Typically, such vaccine preparations further contain a suitable adjuvant (see, e.g., U.S. Patent No. 6,146,635) or a universal helper epitope such as a PADRErm peptide (Epimmune Inc., San Diego, CA; see, e.g., Alexander etal., J. lmmunol. 2000 164(3); 164(3): 1625-1633; Alexander etal., Immunity 1994 1(9): 751-761 and Alexander etal., Immunol. Res. 1998 18(2): 79-92). An alternative method comprises generating an immune response in an individual against a 161P2F1OB immunogen by: administering in vivo to muscle or skin of the individual's body a DNA molecule that comprises a DNA sequence that encodes a 161P2F1OB immunogen, the DNA sequence operatively linked to regulatory sequences which control the expression of the DNA sequence; wherein the DNA
molecule is taken up by cells, the DNA
sequence is expressed in the cells and an immune response is generated against the immunogen (see, e.g., U.S. Patent No.
5,962,428). Optionally a genetic vaccine facilitator such as anionic lipids;
saponins; lectins; estrogenic compounds;
hydroxylated lower alkyls; dimethyl sulfoxide; and urea is also administered.
In addition, an antiidiotypic antibody can be administered that mimics 161P2F1OB, in order to generate a response to the target antigen.
Nucleic Acid Vaccines:
Vaccine compositions of the invention include nucleic acid-mediated modalities. DNA or RNA that encode protein(s) of the invention can be administered to a patient. Genetic immunization methods can be employed to generate prophylactic or therapeutic humoral and cellular immune responses directed against cancer cells expressing 161P2F10B.
Constructs comprising DNA encoding a 161P2F10B-related protein/immunogen and appropriate regulatory sequences can be injected directly into muscle or skin of an individual, such that the cells of the muscle or skin take-up the construct and express the encoded 161P2F1OB proteinfimmunogen. Alternatively, a vaccine comprises a 161P2F10B-related protein.
Expression of the 161P2F10B-related protein immunogen results in the generation of prophylactic or therapeutic humoral and cellular immunity against cells that bear a 161P2F1OB protein. Various prophylactic and therapeutic genetic immunization techniques known in the art can be used (for review, see information and references published at Internet address genweb.com). Nucleic acid-based delivery is described, for instance, in Wolff et. al., Science 247:1465(1990) as well as U.S. Patent Nos. 5,580,859; 5,589,466; 5,804,566; 5,739,118;
5,736,524; 5,679,647; WO 98/04720. Examples of DNA-based delivery technologies include "naked DNA", facilitated (bupivicaine, polymers, peptide-mediated) delivery, cationic lipid complexes, and particle-mediated ("gene gun") or pressure-mediated delivery (see, e.g., U.S. Patent No.
5,922,687).
For therapeutic or prophylactic immunization purposes, proteins of the invention can be expressed via viral or bacterial vectors. Various viral gene delivery systems that can be used in the practice of the invention include, but are not limited to, vaccinia, fowlpox, canarypox, adenovirus, influenza, poliovirus, adeno-associated virus, lentivirus, and sindbis virus (see, e.g., Restifo, 1996, Curr. Opin. Immunol. 8:658-663; Tsang et al. J. Natl. Cancer Inst. 87:982-990(1995)). Non-viral delivery systems can also be employed by introducing naked DNA encoding a 161P2F1OB-related protein into the patient (e.g., intramuscularly or intradermally) to induce an anti-tumor response.
Vaccinia virus is used, for example, as a vector to express nucleotide sequences that encode the peptides of the invention. Upon introduction into a host, the recombinant vaccinia virus expresses the protein immunogenic peptide, and thereby elicits a host immune response. Vaccinia vectors and methods useful in immunization protocols are described in, e.g., U.S. Patent No. 4,722,848. Another vector is BCG (Bacille Calmette Guerin). BCG vectors are described in Stover et al., Nature 351:456-460 (1991). A wide variety of other vectors useful for therapeutic administration or immunization of the peptides of the invention, e.g. adeno and adeno-associated virus vectors, retroviral vectors, Salmonella typhi vectors, detoxified anthrax toxin vectors, and the like, will be apparent to those skilled in the art from the description herein.
Thus, gene delivery systems are used to deliver a 161P2F10B-related nucleic acid molecule. In one embodiment, the full-length human 161P2F1OB cDNA is employed. In another embodiment, 161P2F1OB
nucleic acid molecules encoding specific cytotoxic T lymphocyte (CTL) and/or antibody epitopes are employed.
Ex Vivo Vaccines Various ex vivo strategies can also be employed to generate an immune response. One approach involves the use of antigen presenting cells (APCs) such as dendritic cells (DC) to present 161P2F1OB antigen to a patient's immune system.
Dendritic cells express MHC class I and II molecules, B7 co-stimulator, and IL-12, and are thus highly specialized antigen presenting cells. In prostate cancer, autologous dendritic cells pulsed with peptides of the prostate-specific membrane antigen (PSMA) are being used in a Phase I clinical trial to stimulate prostate cancer patients' immune systems (Tjoa et al., 1996, Prostate 28:65-69; Murphy etal., 1996, Prostate 29:371-380). Thus, dendritic cells can be used to present 161P2F1OB peptides to T cells in the context of MHC class I or II molecules.
In one embodiment, autologous dendritic cells are pulsed with 161P2F1OB peptides capable of binding to MHC class land/or class II molecules. In another embodiment, dendritic cells are pulsed with the complete 161P2F1OB protein. Yet another embodiment involves engineering the overexpression of a 161P2F1OB gene in dendritic cells using various implementing vectors known in the art, such as adenovirus (Arthur etal., 1997, Cancer Gene Ther. 4:17-25), retrovirus (Henderson etal., 1996, Cancer Res. 56:3763-3770), lentivirus, adeno-associated virus, DNA transfection (Ribas etal., 1997, Cancer Res. 57:2865-2869), or tumor-derived RNA
transfection (Ashley etal., 1997, J. Exp. Med. 186:1177-1182). Cells that express 161P2F1OB can also be engineered to express immune modulators, such as GM-CSF, and used as immunizing agents.
X.B.) 161P2F1OB as a Target for Antibody-based Therapy 161P2F1OB is an attractive target for antibody-based therapeutic strategies. A
number of antibody strategies are known in the art for targeting both extracellular and intracellular molecules (see, e.g., complement and ADCC mediated killing as well as the use of intrabodies). Because 161P2F1OB is expressed by cancer cells of various lineages relative to corresponding normal cells, systemic administration of 161P2F10B-immunoreactive compositions are prepared that exhibit excellent sensitivity without toxic, non-specific and/or non-target effects caused by binding of the immunoreactive composition to non-target organs and tissues. Antibodies specifically reactive with domains of 161P2F1OB are useful to treat 161P2F10B-expressing cancers systemically, either as conjugates with a toxin or therapeutic agent, or as naked antibodies capable of inhibiting cell proliferation or function.
161P2F1013 antibodies can be introduced into a patient such that the antibody binds to 161P2F1OB and modulates a function, such as an interaction with a binding partner, and consequently mediates destruction of the tumor cells and/or inhibits the growth of the tumor cells. Mechanisms by which such antibodies exert a therapeutic effect can include complement-mediated cytolysis, antibody-dependent cellular cytotoxicity, modulation of the physiological function of 161P2F1OB, inhibition of ligand binding or signal transduction pathways, modulation of tumor cell differentiation, alteration of tumor angiogenesis factor profiles, and/or apoptosis.
Those skilled in the art understand that antibodies can be used to specifically target and bind immunogenic molecules such as an immunogenic region of a 161P2F1OB sequence shown in Figure 2 or Figure 3. In addition, skilled artisans understand that it is routine to conjugate antibodies to cytotoxic agents (see, e.g., Sievers etal. Blood 93:11 3678-3684 (June 1, 1999)). When cytotoxic and/or therapeutic agents are delivered directly to cells, such as by conjugating them to antibodies specific for a molecule expressed by that cell (e.g. 161P2F10B), the cytotoxic agent will exert its known biological effect (i.e. cytotoxicity) on those cells.

A wide variety of compositions and methods for using antibody-cytotoxic agent conjugates to kill cells are known in the art. In the context of cancers, typical methods entail administering to an animal having a tumor a biologically effective amount of a conjugate comprising a selected cytotoxic and/or therapeutic agent linked to a targeting agent (e.g. an anti-161P2F1OB antibody) that binds to a marker (e.g. 161P2F10B) expressed, accessible to binding or localized on the cell surfaces. A typical embodiment is a method of delivering a cytotoxic and/or therapeutic agent to a cell expressing 161P2F10B, comprising conjugating the cytotoxic agent to an antibody that immunospecifically binds to a 161P2F1OB
epitope, and, exposing the cell to the antibody-agent conjugate. Another illustrative embodiment is a method of treating an individual suspected of suffering from metastasized cancer, comprising a step of administering parenterally to said individual a pharmaceutical composition comprising a therapeutically effective amount of an antibody conjugated to a cytotoxic and/or therapeutic agent.
Cancer immunotherapy using anti-161P2F10B antibodies can be done in accordance with various approaches that have been successfully employed in the treatment of other types of cancer, including but not limited to colon cancer (Arlen et al., 1998, Crit. Rev. Immunol. 18:133-138), multiple myeloma (Ozaki etal., 1997, Blood 90:3179-3186, Tsunenari etal., 1997, Blood 90:2437-2444), gastric cancer (Kasprzyk etal., 1992, Cancer Res.
52:2771-2776), B-cell lymphoma (Funakoshi etal., 1996, J. lmmunother. Emphasis Tumor Immunol. 19:93-101), leukemia (Zhong etal., 1996, Leuk. Res. 20:581-589), colorectal cancer (Moun etal., 1994, Cancer Res. 54:6160-6166; Velders etal., 1995, Cancer Res. 55:4398-4403), and breast cancer (Shepard et al., 1991, J. Clin. Immunol. 11:117-127). Some therapeutic approaches involve conjugation of naked antibody to a toxin or radioisotope, such as the conjugation of Y91 or 1131 to anti-CD20 antibodies (e.g., ZevalinTM, IDEC
Pharmaceuticals Corp. or BexxarTM, Coulter Pharmaceuticals), while others involve co-administration of antibodies and other therapeutic agents, such as HerceptinTm (trastuzumab) with paclitaxel (Genentech, Inc.). The antibodies can be conjugated to a therapeutic agent. To treat prostate cancer, for example, 161P2F1OB
antibodies can be administered in conjunction with radiation, chemotherapy or hormone ablation. Also, antibodies can be conjugated to a toxin such as calicheamicin (e.g., MylotargN, Wyeth-Ayerst, Madison, NJ, a recombinant humanized IgG4 kappa antibody conjugated to antitumor antibiotic calicheamicin) or a maytansinoid (e.g., taxane-based Tumor-Activated Prodrug, TAP, platform, ImmunoGen, Cambridge, MA, also see e.g., US Patent 5,416,064).
Although 161P2F1OB antibody therapy is useful for all stages of cancer, antibody therapy can be particularly appropriate in advanced or metastatic cancers. Treatment with the antibody therapy of the invention is indicated for patients who have received one or more rounds of chemotherapy. Alternatively, antibody therapy of the invention is combined with a chemotherapeutic or radiation regimen for patients who have not received chemotherapeutic treatment. Additionally, antibody therapy can enable the use of reduced dosages of concomitant chemotherapy, particularly for patients who do not tolerate the toxicity of the chemotherapeutic agent very well. Fan et al.
(Cancer Res. 53:4637-4642, 1993), Prewett et al.
(International J. of Onco. 9:217-224, 1996), and Hancock et al. (Cancer Res.
51:4575-4580, 1991) describe the use of various antibodies together with chemotherapeutic agents.
Although 161P2F108 antibody therapy is useful for all stages of cancer, antibody therapy can be particularly appropriate in advanced or metastatic cancers. Treatment with the antibody therapy of the invention is indicated for patients who have received one or more rounds of chemotherapy. Alternatively, antibody therapy of the invention is combined with a chemotherapeutic or radiation regimen for patients who have not received chemotherapeutic treatment. Additionally, antibody therapy can enable the use of reduced dosages of concomitant chemotherapy, particularly for patients who do not tolerate the toxicity of the chemotherapeutic agent very well.
Cancer patients can be evaluated for the presence and level of 161P2F1OB
expression, preferably using immunohistochemical assessments of tumor tissue, quantitative 161P2F1OB
imaging, or other techniques that reliably indicate the presence and degree of 161P2F1OB expression. lmmunohistochemical analysis of tumor biopsies or surgical specimens is preferred for this purpose. Methods for immunohistochemical analysis of tumor tissues are well known in the art.
Anti-161P2F1OB monoclonal antibodies that treat prostate and other cancers include those that initiate a potent immune response against the tumor or those that are directly cytotoxic. In this regard, anti-161P2F1OB monoclonal antibodies (mAbs) can elicit tumor cell lysis by either complement-mediated or antibody-dependent cell cytotoxicity (ADCC) mechanisms, both of which require an intact Fc portion of the immunoglobulin molecule for interaction with effector cell Fc receptor sites on complement proteins. In addition, anti-161P2F1OB mAbs that exert a direct biological effect on tumor growth are useful to treat cancers that express 161P2F10B. Mechanisms by which directly cytotoxic mAbs act include:
inhibition of cell growth, modulation of cellular differentiation, modulation of tumor angiogenesis factor profiles, and the induction of apoptosis. The mechanism(s) by which a particular anti-161P2F1OB
mAb exerts an anti-tumor effect is evaluated using any number of in vitro assays that evaluate cell death such as ADCC, ADMMC, complement-mediated cell lysis, and so forth, as is generally known in the art.
In some patients, the use of murine or other non-human monoclonal antibodies, or human/mouse chimeric mAbs can induce moderate to strong immune responses against the non-human antibody.
This can result in clearance of the antibody from circulation and reduced efficacy. In the most severe cases, such an immune response can lead to the extensive formation of immune complexes which, potentially, can cause renal failure. Accordingly, preferred monoclonal antibodies used in the therapeutic methods of the invention are those that are either fully human or humanized and that bind specifically to the target 161P2F1OB antigen with high affinity but exhibit low or no antigenicity in the patient.
Therapeutic methods of the invention contemplate the administration of single anti-161P2F1OB mAbs as well as combinations, or cocktails, of different mAbs. Such mAb cocktails can have certain advantages inasmuch as they contain mAbs that target different epitopes, exploit different effector mechanisms or combine directly cytotoxic mAbs with mAbs that rely on immune effector functionality. Such mAbs in combination can exhibit synergistic therapeutic effects. In addition, anti-161P2F1OB mAbs can be administered concomitantly with other therapeutic modalities, including but not limited to various chemotherapeutic agents, androgen-blockers, immune modulators (e.g., IL-2, GM-CSF), surgery or radiation. The anti-161P2F1OB mAbs are administered in their "naked" or unconjugated form, or can have a therapeutic agent(s) conjugated to them.
Anti-161P2F1OB antibody formulations are administered via any route capable of delivering the antibodies to a tumor cell. Routes of administration include, but are not limited to, intravenous, intraperitoneal, intramuscular, intratumor, intradermal, and the like. Treatment generally involves repeated administration of the anti-161P2F1OB antibody preparation, via an acceptable route of administration such as intravenous injection (IV), typically at a dose in the range of about 0.1, .2, .3, .4, .5, .6, .7, .8, .9., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 mg/kg body weight. In general, doses in the range of 10-1000 mg mAb per week are effective and well tolerated.
Based on clinical experience with the HerceptinTM mAb in the treatment of metastatic breast cancer, an initial loading dose of approximately 4 mg/kg patient body weight IV, followed by weekly doses of about 2 mg/kg IV of the anti-161P2F1OB mAb preparation represents an acceptable dosing regimen. Preferably, the initial loading dose is administered as a 90-minute or longer infusion. The periodic maintenance dose is administered as a 30 minute or longer infusion, provided the initial dose was well tolerated. As appreciated by those of skill in the art, various factors can influence the ideal dose regimen in a particular case. Such factors include, for example, the binding affinity and half life of the Ab or mAbs used, the degree of 161P2F1OB expression in the patient, the extent of circulating shed 161P2F1OB antigen, the desired steady-state antibody concentration level, frequency of treatment, and the influence of chemotherapeutic or other agents used in combination with the treatment method of the invention, as well as the health status of a particular patient.

Optionally, patients should be evaluated for the levels of 161P2F1OB in a given sample (e.g. the levels of circulating 161P2F1OB antigen and/or 161P2F1OB expressing cells) in order to assist in the determination of the most effective dosing regimen, etc. Such evaluations are also used for monitoring purposes throughout therapy, and are useful to gauge therapeutic success in combination with the evaluation of other parameters (for example, urine cytology and/or ImmunoCyt levels in bladder cancer therapy, or by analogy, serum PSA levels in prostate cancer therapy).
Anti-idiotypic anti-161P2F1OB antibodies can also be used in anti-cancer therapy as a vaccine for inducing an immune response to cells expressing a 161P2F10B-related protein. In particular, the generation of anti-idiotypic antibodies is well known in the art; this methodology can readily be adapted to generate anti-idiotypic anti-161P2F108 antibodies that mimic an epitope on a 161P2F10B-related protein (see, for example, Wagner et al., 1997, Hybridoma 16: 33-40; Foon et al., 1995, J. Clin. Invest. 96:334-342; Herlyn etal., 1996, Cancer lmmunol.
Immunother. 43:65-76). Such an anti-idiotypic antibody can be used in cancer vaccine strategies.
X.C.) 161P2F1OB as a Target for Cellular Immune Responses Vaccines and methods of preparing vaccines that contain an immunogenically effective amount of one or more HLA-binding peptides as described herein are further embodiments of the invention. Furthermore, vaccines in accordance with the invention encompass compositions of one or more of the claimed peptides. A peptide can be present in a vaccine individually. Alternatively, the peptide can exist as a homopolymer comprising multiple copies of the same peptide, or as a heteropolymer of various peptides. Polymers have the advantage of increased immunological reaction and, where different peptide epitopes are used to make up the polymer, the additional ability to induce antibodies and/or CTLs that react with different antigenic determinants of the pathogenic organism or tumor-related peptide targeted for an immune response. The composition can be a naturally occurring region of an antigen or can be prepared, e.g., recombinantly or by chemical synthesis.
Carriers that can be used with vaccines of the invention are well known in the art, and include, e.g., thyroglobulin, albumins such as human serum albumin, tetanus toxoid, polyamino acids such as poly L-lysine, poly L-glutamic acid, influenza, hepatitis B virus core protein, and the like. The vaccines can contain a physiologically tolerable (i.e., acceptable) diluent such as water, or saline, preferably phosphate buffered saline. The vaccines also typically include an adjuvant.
Adjuvants such as incomplete Freund's adjuvant, aluminum phosphate, aluminum hydroxide, or alum are examples of materials well known in the art. Additionally, as disclosed herein, CTL
responses can be primed by conjugating peptides of the invention to lipids, such as tripalmitoyl-S-glycerylcysteinlyseryl- serine (P3CSS). Moreover, an adjuvant such as a synthetic cytosine-phosphorothiolated-guanine-containing (CpG) oligonucleotides has been found to increase CTL
responses 10- to 100-fold. (see, e.g. Davila and Celis, J. lmmunol. 165:539-547 (2000)) Upon immunization with a peptide composition in accordance with the invention, via injection, aerosol, oral, transdermal, transmucosal, intrapleural, intrathecal, or other suitable routes, the immune system of the host responds to the vaccine by producing large amounts of CTLs and/or HTLs specific for the desired antigen. Consequently, the host becomes at least partially immune to later development of cells that express or overexpress 161P2F1OB antigen, or derives at least some therapeutic benefit when the antigen was tumor-associated.
In some embodiments, it may be desirable to combine the class I peptide components with components that induce or facilitate neutralizing antibody and or helper T cell responses directed to the target antigen. A preferred embodiment of such a composition comprises class I and class ll epitopes in accordance with the invention. An alternative embodiment of such a composition comprises a class I and/or class II epitope in accordance with the invention, along with a cross reactive HTL epitope such as PADRETM (Epimmune, San Diego, CA) molecule (described e.g., in U.S. Patent Number 5,736,142).

A vaccine of the invention can also include antigen-presenting cells (APC), such as dendritic cells (DC), as a vehicle to present peptides of the invention. Vaccine compositions can be created in vitro, following dendritic cell mobilization and harvesting, whereby loading of dendritic cells occurs in vitro. For example, dendritic cells are transfected, e.g., with a minigene in accordance with the invention, or are pulsed with peptides. The dendritic cell can then be administered to a patient to elicit immune responses in vivo. Vaccine compositions, either DNA- or peptide-based, can also be administered in vivo in combination with dendritic cell mobilization whereby loading of dendritic cells occurs in vivo.
Preferably, the following principles are utilized when selecting an array of epitopes for inclusion in a polyepitopic composition for use in a vaccine, or for selecting discrete epitopes to be included in a vaccine and/or to be encoded by nucleic acids such as a minigene. It is preferred that each of the following principles be balanced in order to make the selection. The multiple epitopes to be incorporated in a given vaccine composition may be, but need not be, contiguous in sequence in the native antigen from which the epitopes are derived.
1.) Epitopes are selected which, upon administration, mimic immune responses that have been observed to be correlated with tumor clearance. For HLA Class I this includes 3-4 epitopes that come from at least one tumor associated antigen (TM). For HLA Class II a similar rationale is employed; again 3-4 epitopes are selected from at least one TM (see, e.g., Rosenberg etal., Science 278:1447-1450). Epitopes from one TM may be used in combination with epitopes from one or more additional TMs to produce a vaccine that targets tumors with varying expression patterns of frequently-expressed TMs.
2.) Epitopes are selected that have the requisite binding affinity established to be correlated with immunogenicity: for HLA Class I an IC50 of 500 nM or less, often 200 nM or less; and for Class II an IC50 of 1000 nM or less.
3.) Sufficient supermotif bearing-peptides, or a sufficient array of allele-specific motif-bearing peptides, are selected to give broad population coverage. For example, it is preferable to have at least 80% population coverage. A
Monte Carlo analysis, a statistical evaluation known in the art, can be employed to assess the breadth, or redundancy of, population coverage.
4.) When selecting epitopes from cancer-related antigens it is often useful to select analogs because the patient may have developed tolerance to the native epitope.
5.) Of particular relevance are epitopes referred to as "nested epitopes."
Nested epitopes occur where at least two epitopes overlap in a given peptide sequence. A nested peptide sequence can comprise B cell, HLA class I and/or HLA class ll epitopes. When providing nested epitopes, a general objective is to provide the greatest number of epitopes per sequence. Thus, an aspect is to avoid providing a peptide that is any longer than the amino terminus of the amino terminal epitope and the carboxyl terminus of the carboxyl terminal epitope in the peptide. When providing a multi-epitopic sequence, such as a sequence comprising nested epitopes, it is generally important to screen the sequence in order to insure that it does not have pathological or other deleterious biological properties.
6.) If a polyepitopic protein is created, or when creating a minigene, an objective is to generate the smallest peptide that encompasses the epitopes of interest This principle is similar, if not the same as that employed when selecting a peptide comprising nested epitopes. However, with an artificial polyepitopic peptide, the size minimization objective is balanced against the need to integrate any spacer sequences between epitopes in the polyepitopic protein. Spacer amino acid residues can, for example, be introduced to avoid junctional epitopes (an epitope recognized by the immune system, not present in the target antigen, and only created by the man-made juxtaposition of epitopes), or to facilitate cleavage between epitopes and thereby enhance epitope presentation. Junctional epitopes are generally to be avoided because the recipient may generate an immune response to that non-native epitope. Of particular concern is a junctional epitope that is a "dominant epitope." A dominant epitope may lead to such a zealous response that immune responses to other epitopes are diminished or suppressed.

7.) Where the sequences of multiple variants of the same target protein are present, potential peptide epitopes can also be selected on the basis of their conservancy. For example, a criterion for conservancy may define that the entire sequence of an HLA class I binding peptide or the entire 9-mer core of a class II binding peptide be conserved in a designated percentage of the sequences evaluated for a specific protein antigen.
X.C.1. Minigene Vaccines A number of different approaches are available which allow simultaneous delivery of multiple epitopes. Nucleic acids encoding the peptides of the invention are a particularly useful embodiment of the invention. Epitopes for inclusion in a minigene are preferably selected according to the guidelines set forth in the previous section. A preferred means of administering nucleic acids encoding the peptides of the invention uses minigene constructs encoding a peptide comprising one or multiple epitopes of the invention.
The use of multi-epitope minigenes is described below and in, lshioka et aL, J. Immunot 162:3915-3925, 1999; An, L. and Whitton, J. L., J. Vim!. 71:2292, 1997; Thomson, S. A. etal., J.
ImmunoL 157:822, 1996; Whitton, J. L. etal., J. ViroL
67:348, 1993; Hanke, R. etal., Vaccine 16:426, 1998. For example, a multi-epitope DNA plasmid encoding supermotif-and/or motif-bearing epitopes derived 161P2F108, the PADRE universal helper T
cell epitope or multiple HTL epitopes from 161P2F1OB (see e.g., Tables VIII-XXI and XXII to XLIX), and an endoplasmic reticulum-translocating signal sequence can be engineered. A vaccine may also comprise epitopes that are derived from other TMs.
The immunogenicity of a multi-epitopic minigene can be confirmed in transgenic mice to evaluate the magnitude of CTL induction responses against the epitopes tested. Further, the immunogenicity of DNA-encoded epitopes in vivo can be correlated with the in vitro responses of specific CTL lines against target cells transfected with the DNA plasmid. Thus, these experiments can show that the minigene serves to both: 1.) generate a CTL
response and 2.) that the induced CTLs recognized cells expressing the encoded epitopes.
For example, to create a DNA sequence encoding the selected epitopes (minigene) for expression in human cells, the amino acid sequences of the epitopes may be reverse translated. A human codon usage table can be used to guide the codon choice for each amino acid. These epitope-encoding DNA sequences may be directly adjoined, so that when translated, a continuous polypeptide sequence is created. To optimize expression and/or immunogenicity, additional elements can be incorporated into the minigene design. Examples of amino acid sequences that can be reverse translated and included in the minigene sequence include: HLA class I epitopes, HLA class II epitopes, antibody epitopes, a ubiquitination signal sequence, and/or an endoplasmic reticulum targeting signal. In addition, HLA presentation of CTL and HTL epitopes may be improved by including synthetic (e.g. poly-alanine) or naturally-occurring flanking sequences adjacent to the CTL or HTL epitopes; these larger peptides comprising the epitope(s) are within the scope of the invention.
The minigene sequence may be converted to DNA by assembling oligonucleotides that encode the plus and minus strands of the minigene. Overlapping oligonucleotides (30-100 bases long) may be synthesized, phosphorylated, purified and annealed under appropriate conditions using well known techniques. The ends of the oligonucleotides can be joined, for example, using 14 DNA ligase. This synthetic minigene, encoding the epitope polypeptide, can then be cloned into a desired expression vector.
Standard regulatory sequences well known to those of skill in the art are preferably included in the vector to ensure expression in the target cells. Several vector elements are desirable: a promoter with a down-stream cloning site for minigene insertion; a polyadenylation signal for efficient transcription termination; an E. col/ origin of replication; and an E.
coli selectable marker (e.g. ampicillin or kanamycin resistance). Numerous promoters can be used for this purpose, e.g., the human cytomegalovirus (hCMV) promoter. See, e.g., U.S. Patent Nos. 5,580,859 and 5,589,466 for other suitable promoter sequences.

Additional vector modifications may be desired to optimize minigene expression and immunogenicity. In some cases, introns are required for efficient gene expression, and one or more synthetic or naturally-occurring introns could be incorporated into the transcribed region of the minigene. The inclusion of mRNA stabilization sequences and sequences for replication in mammalian cells may also be considered for increasing minigene expression.
Once an expression vector is selected, the minigene is cloned into the polylinker region downstream of the promoter. This plasmid is transformed into an appropriate E. coil strain, and DNA is prepared using standard techniques.
The orientation and DNA sequence of the minigene, as well as all other elements included in the vector, are confirmed using restriction mapping and DNA sequence analysis. Bacterial cells harboring the correct plasmid can be stored as a master cell bank and a working cell bank.
In addition, immunostimulatory sequences (ISSs or CpGs) appear to play a role in the immunogenicity of DNA
vaccines. These sequences may be included in the vector, outside the minigene coding sequence, if desired to enhance immunogenicity.
In some embodiments, a bi-cistronic expression vector which allows production of both the minigene-encoded epitopes and a second protein (included to enhance or decrease immunogenicity) can be used. Examples of proteins or polypeptides that could beneficially enhance the immune response if co-expressed include cytokines (e.g., IL-2, 1L-12, GM-CSF), cytokine-inducing molecules (e.g., LelF), costimulatory molecules, or for NIL responses, pan-DR binding proteins (PADRETM, Epimmune, San Diego, CA). Helper (HTL) epitopes can be joined to intracellular targeting signals and expressed separately from expressed CTL epitopes; this allows direction of the HTL epitopes to a cell compartment different than that of the CTL epitopes. If required, this could facilitate more efficient entry of HTL epitopes into the HLA class II
pathway, thereby improving HTL induction. In contrast to HTL or CTL induction, specifically decreasing the immune response by co-expression of immunosuppressive molecules (e.g. TGF-(3) may be beneficial in certain diseases.
Therapeutic quantities of plasmid DNA can be produced for example, by fermentation in E. coil, followed by purification. Aliquots from the working cell bank are used to inoculate growth medium, and grown to saturation in shaker flasks or a bioreactor according to well-known techniques. Plasmid DNA can be purified using standard bioseparation technologies such as solid phase anion-exchange resins supplied by QIAGEN, Inc. (Valencia, California). If required:
supercoiled DNA can be isolated from the open circular and linear forms using gel electrophoresis or other methods.
Purified plasmid DNA can be prepared for injection using a variety of formulations. The simplest of these is reconstitution of lyophilized DNA in sterile phosphate-buffer saline (PBS).
This approach, known as "naked DNA," is currently being used for intramuscular (IM) administration in clinical trials.
To maximize the immunotherapeutic effects of minigene DNA vaccines, an alternative method for formulating purified plasmid DNA may be desirable. A variety of methods have been described, and new techniques may become available. Cationic lipids, glycolipids, and fusogenic liposomes can also be used in the formulation (see, e.g., as described by WO 93/24640;
Mannino & Gould-Fogerite, Bio Techniques 6(7):
682(1988); U.S. Pat No. 5,279,833; WO 91/06309; and Feigner, et al., Proc.
Nat'l Acad. Sci. USA 84:7413 (1987). In addition, peptides and compounds referred to collectively as protective, interactive, non-condensing compounds (PINC) could also be complexed to purified plasmid DNA to influence variables such as stability, intramuscular dispersion, or trafficking to specific organs or cell types.
Target cell sensitization can be used as a functional assay for expression and HLA class I presentation of minigene-encoded CTL epitopes. For example, the plasmid DNA is introduced into a mammalian cell line that is suitable as a target for standard CTL chromium release assays. The transfection method used will be dependent on the final formulation. Electroporation can be used for "naked" DNA, whereas cationic lipids allow direct in vitro transfection. A
plasmid expressing green fluorescent protein (GFP) can be co-transfected to allow enrichment of transfected cells using fluorescence activated cell sorting (FACS). These cells are then chromium-51 (51Cr) labeled and used as target cells for epitope-specific CTL lines; cytolysis, detected by 51Cr release, indicates both production of, and HLA presentation of, minigene-encoded CTL epitopes. Expression of HTL epitopes may be evaluated in an analogous manner using assays to assess HTL activity.
In vivo immunogenicity is a second approach for functional testing of minigene DNA formulations. Transgenic mice expressing appropriate human HLA proteins are immunized with the DNA product.
The dose and route of administration are formulation dependent (e.g., IM for DNA in PBS, intraperitoneal (i.p.) for lipid-complexed DNA). Twenty-one days after immunization, splenocytes are harvested and restimulated for one week in the presence of peptides encoding each epitope being tested. Thereafter, for CTL effector cells, assays are conducted for cytolysis of peptide-loaded, 51Cr-labeled target cells using standard techniques. Lysis of target cells that were sensitized by HLA loaded with peptide epitopes, corresponding to minigene-encoded epitopes, demonstrates DNA vaccine function for in vivo induction of CTLs.
Immunogenicity of HTL epitopes is confirmed in transgenic mice in an analogous manner.
Alternatively, the nucleic acids can be administered using ballistic delivery as described, for instance, in U.S.
Patent No. 5,204,253. Using this technique, particles comprised solely of DNA
are administered. In a further alternative embodiment, DNA can be adhered to particles, such as gold particles.
Minigenes can also be delivered using other bacterial or viral delivery systems well known in the art, e.g., an expression construct encoding epitopes of the invention can be incorporated into a viral vector such as vaccinia.
X.C.2. Combinations of CTL Peptides with Helper Peptides Vaccine compositions comprising CTL peptides of the invention can be modified, e.g., analoged, to provide desired attributes, such as improved serum half life, broadened population coverage or enhanced immunogenicity.
For instance, the ability of a peptide to induce CTL activity can be enhanced by linking the peptide to a sequence which contains at least one epitope that is capable of inducing a T helper cell response. Although a CTL peptide can be directly linked to a T helper peptide, often CTL epitope/HTL epitope conjugates are linked by a spacer molecule. The spacer is typically comprised of relatively small, neutral molecules, such as amino acids or amino acid mimetics, which are substantially uncharged under physiological conditions. The spacers are typically selected from, e.g., Ala, Gly, or other neutral spacers of nonpolar amino acids or neutral polar amino acids. It will be understood that the optionally present spacer need not be comprised of the same residues and thus may be a hetero- or homo-oligomer. When present, the spacer will usually be at least one or two residues, more usually three to six residues and sometimes 10 or more residues. The CTL
peptide epitope can be linked to the T helper peptide epitope either directly or via a spacer either at the amino or carboxy terminus of the CTL peptide. The amino terminus of either the immunogenic peptide or the T helper peptide may be acylated.
In certain embodiments, the T helper peptide is one that is recognized by T
helper cells present in a majority of a genetically diverse population. This can be accomplished by selecting peptides that bind to many, most, or all of the HLA
class II molecules. Examples of such amino acid bind many HLA Class II
molecules include sequences from antigens such as tetanus toxoid at positions 830-843 (QYIKANSKFIGITE; SEQ ID NO: 25), Plasmodium falciparum circumsporozoite (CS) protein at positions 378-398 (DIEKKIAKMEKASSVFNVVNS; SEQ ID NO: 26), and Streptococcus 18kD protein at positions 116-131 (GAVDSILGGVATYGAA; SEQ ID NO: 27). Other examples include peptides bearing a DR 1-4-7 supermotif, or either of the DR3 motifs.
Alternatively, it is possible to prepare synthetic peptides capable of stimulating T helper lymphocytes, in a loosely HLA-restricted fashion, using amino acid sequences not found in nature (see, e.g., PCT publication WO 95/07707). These synthetic compounds called Pan-DR-binding epitopes (e.g., PADRETM, Epimmune, Inc., San Diego, CA) are designed, most preferably, to bind most HLA-DR (human HLA class II) molecules. For instance, a pan-DR-binding epitope peptide having the formula: aKXVAAWILKAAa (SEQ ID NO: 28), where "X" is either cyclohexylalanine, phenylalanine, or tyrosine, and a is either 0-alanine or L-alanine, has been found to bind to most HLA-DR alleles, and to stimulate the response of T helper lymphocytes from most individuals, regardless of their HLA type. An alternative of a pan-DR binding epitope comprises all "L" natural amino acids and can be provided in the form of nucleic acids that encode the epitope.
HTL peptide epitopes can also be modified to alter their biological properties. For example, they can be modified to include 0-amino acids to increase their resistance to proteases and thus extend their serum half life, or they can be conjugated to other molecules such as lipids, proteins, carbohydrates, and the like to increase their biological activity. For example, a T helper peptide can be conjugated to one or more palmitic acid chains at either the amino or carboxyl termini.
X.C.3. Combinations of CTL Peptides with T Cell Priming Agents In some embodiments it may be desirable to include in the pharmaceutical compositions of the invention at least one component which primes B lymphocytes or T lymphocytes. Lipids have been identified as agents capable of priming CTL in vivo. For example, palmitic acid residues can be attached to the s-and a- amino groups of a lysine residue and then linked, e.g., via one or more linking residues such as Gly, Gly-Gly-, Ser, Ser-Ser, or the like, to an immunogenic peptide.
The lipidated peptide can then be administered either directly in a micelle or particle, incorporated into a liposome, or emulsified in an adjuvant, e.g., incomplete Freund's adjuvant. In a preferred embodiment, a particularly effective immunogenic composition comprises palmitic acid attached to s- and a- amino groups of Lys, which is attached via linkage, e.g., Ser-Ser, to the amino terminus of the immunogenic peptide.
As another example of lipid priming of CTL responses, E. coil lipoproteins, such as tripalmitoyl-S-glycerylcysteinlyseryl- serine (P3CSS) can be used to prime virus specific CTL
when covalently attached to an appropriate peptide (see, e.g., Deres, etal., Nature 342:561, 1989). Peptides of the invention can be coupled to P3CSS, for example, and the lipopeptide administered to an individual to prime specifically an immune response to the target antigen. Moreover, because the induction of neutralizing antibodies can also be primed with P3CSS-conjugated epitopes, two 'such compositions can be combined to more effectively elicit both humoral and cell-mediated responses.
X.C.4. Vaccine Compositions Comprising DC Pulsed with CTL and/or HTL Peptides An embodiment of a vaccine composition in accordance with the invention comprises ex vivo administration of a cocktail of epitope-bearing peptides to PBMC, or isolated DC therefrom, from the patient's blood. A pharmaceutical to facilitate harvesting of DC can be used, such as ProgenipoietinTM (Pharmacia-Monsanto, St. Louis, MO) or GM-CSF/IL-4.
After pulsing the DC with peptides and prior to reinfusion into patients, the DC are washed to remove unbound peptides. In this embodiment, a vaccine comprises peptide-pulsed DCs which present the pulsed peptide epitopes complexed with HLA
molecules on their surfaces.
The DC can be pulsed ex vivo with a cocktail of peptides, some of which stimulate CTL responses to 161P2F10B.
Optionally, a helper T cell (HTL) peptide, such as a natural or artificial loosely restricted HLA Class II peptide, can be included to facilitate the CTL response. Thus, a vaccine in accordance with the invention is used to treat a cancer which expresses or overexpresses 161P2F10B.
X.D. Adoptive Immunotherapv Antigenic 161P2F10B-related peptides are used to elicit a CTL and/or HTL
response ex vivo, as well. The resulting CTL or HTL cells, can be used to treat tumors in patients that do not respond to other conventional forms of therapy, or will not respond to a therapeutic vaccine peptide or nucleic acid in accordance with the invention. Ex vivo CTL or HTL responses to a particular antigen are induced by incubating in tissue culture the patient's, or genetically compatible, CTL
or HTL precursor cells together with a source of antigen-presenting cells (APC), such as dendritic cells, and the appropriate immunogenic peptide. After an appropriate incubation time (typically about 7-28 days), in which the precursor cells are activated and expanded into effector cells, the cells are infused back into the patient, where they will destroy (CTL) or facilitate destruction (HTL) of their specific target cell (e.g., a tumor cell). Transfected dendritic cells may also be used as antigen presenting cells.
X.E. Administration of Vaccines for Therapeutic or Prophylactic Purposes Pharmaceutical and vaccine compositions of the invention are typically used to treat and/or prevent a cancer that expresses or overexpresses 161P2F10B. In therapeutic applications, peptide and/or nucleic acid compositions are administered to a patient in an amount sufficient to elicit an effective B
cell, CTL and/or HTL response to the antigen and to cure or at least partially arrest or slow symptoms and/or complications. An amount adequate to accomplish this is defined as "therapeutically effective dose." Amounts effective for this use will depend on, e.g., the particular composition administered, the manner of administration, the stage and severity of the disease being treated, the weight and general state of health of the patient, and the judgment of the prescribing physician.
For pharmaceutical compositions, the immunogenic peptides of the invention, or DNA encoding them, are generally administered to an individual already bearing a tumor that expresses 161P2F10B. The peptides or DNA encoding them can be administered individually or as fusions of one or more peptide sequences. Patients can be treated with the immunogenic peptides separately or in conjunction with other treatments, such as surgery, as appropriate.
For therapeutic use, administration should generally begin at the first diagnosis of 161P2F10B-associated cancer.
This is followed by boosting doses until at least symptoms are substantially abated and for a period thereafter. The embodiment of the vaccine composition (i.e., including, but not limited to embodiments such as peptide cocktails, polyepitopic polypeptides, minigenes, or TM-specific CTLs or pulsed dendritic cells) delivered to the patient may vary according to the stage of the disease or the patient's health status. For example, in a patient with a tumor that expresses 161P2F10B, a vaccine comprising 161P2F10B-specific CTL may be more efficacious in killing tumor cells in patient with advanced disease than alternative embodiments.
It is generally important to provide an amount of the peptide epitope delivered by a mode of administration sufficient to stimulate effectively a cytotoxic T cell response; compositions which stimulate helper T cell responses can also be given in accordance with this embodiment of the invention.
The dosage for an initial therapeutic immunization generally occurs in a unit dosage range where the lower value is about 1, 5, 50, 500, or 1,000 pg and the higher value is about 10,000; 20,000;
30,000; or 50,000 pg. Dosage values for a human typically range from about 500 pg to about 50,000 pg per 70 kilogram patient. Boosting dosages of between about 1.0 j.tg to about 50,000 j.ig of peptide pursuant to a boosting regimen over weeks to months may be administered depending upon the patient's response and condition as determined by measuring the specific activity of CTL and HTL obtained from the patient's blood. Administration should continue until at least clinical symptoms or laboratory tests indicate that the neoplasia, has been eliminated or reduced and for a period thereafter. The dosages, routes of administration, and dose schedules are adjusted in accordance with methodologies known in the art.
In certain embodiments, the peptides and compositions of the present invention are employed in serious disease states, that is, life-threatening or potentially life threatening situations.
In such cases, as a result of the minimal amounts of extraneous substances and the relative nontoxic nature of the peptides in preferred compositions of the invention, it is possible and may be felt desirable by the treating physician to administer substantial excesses of these peptide compositions relative to these stated dosage amounts.
The vaccine compositions of the invention can also be used purely as prophylactic agents. Generally the dosage for an initial prophylactic immunization generally occurs in a unit dosage range where the lower value is about 1, 5, 50, 500, or 1000 pg and the higher value is about 10,000; 20,000; 30,000; or 50,000 pg.
Dosage values for a human typically range from about 500 pg to about 50,000 pg per 70 kilogram patient. This is followed by boosting dosages of between about 1.0 pig to about 50,000 pig of peptide administered at defined intervals from about four weeks to six months after the initial administration of vaccine. The immunogenicity of the vaccine can be assessed by measuring the specific activity of CTL and HTL obtained from a sample of the patient's blood.
The pharmaceutical compositions for therapeutic treatment are intended for parenteral, topical, oral, nasal, intrathecal, or local (e.g. as a cream or topical ointment) administration.
Preferably, the pharmaceutical compositions are administered parentally, e.g., intravenously, subcutaneously, intradermally, or intramuscularly. Thus, the invention provides compositions for parenteral administration which comprise a solution of the immunogenic peptides dissolved or suspended in an acceptable carrier, preferably an aqueous carrier.
A variety of aqueous carriers may be used, e.g., water, buffered water, 0.8%
saline, 0.3% glycine, hyaluronic acid and the like. These compositions may be sterilized by conventional, well-known sterilization techniques, or may be sterile filtered. The resulting aqueous solutions may be packaged for use as is, or lyophilized, the lyophilized preparation being combined with a sterile solution prior to administration.
The compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as pH-adjusting and buffering agents, tonicity adjusting agents, wetting agents, preservatives, and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, triethanolamine oleate, etc.
The concentration of peptides of the invention in the pharmaceutical formulations can vary widely, i.e., from less than about 0.1%, usually at or at least about 2% to as much as 20% to 50% or more by weight, and will be selected primarily by fluid volumes, viscosities, etc., in accordance with the particular mode of administration selected.
A human unit dose form of a composition is typically included in a pharmaceutical composition that comprises a human unit dose of an acceptable carrier, in one embodiment an aqueous carrier, and is administered in a volume/quantity that is known by those of skill in the art to be used for administration of such compositions to humans (see, e.g., Remington's Pharmaceutical Sciences, 17th Edition, A. Gennaro, Editor, Mack Publishing Co., Easton, Pennsylvania, 1985). For example a peptide dose for initial immunization can be from about 1 to about 50,000 pig, generally 100-5,000 pig, for a 70 kg patient.
For example, for nucleic acids an initial immunization may be performed using an expression vector in the form of naked nucleic acid administered IM (or SC or ID) in the amounts of 0.5-5 mg at multiple sites. The nucleic acid (0.1 to 1000 pig) can also be administered using a gene gun. Following an incubation period of 3-4 weeks, a booster dose is then administered. The booster can be recombinant fowlpox virus administered at a dose of 5-107 to 5x109 pfu.
For antibodies, a treatment generally involves repeated administration of the anti-161P2F1OB antibody preparation, via an acceptable route of administration such as intravenous injection (IV), typically at a dose in the range of about 0.1 to about 10 mg/kg body weight. In general, doses in the range of 10-500 mg mAb per week are effective and well tolerated.
Moreover, an initial loading dose of approximately 4 mg/kg patient body weight IV, followed by weekly doses of about 2 mg/kg IV of the anti- 161P2F1OB mAb preparation represents an acceptable dosing regimen. As appreciated by those of skill in the art, various factors can influence the ideal dose in a particular case. Such factors include, for example, half life of a composition, the binding affinity of an Ab, the immunogenicity of a substance, the degree of 161P2F1OB expression in the patient, the extent of circulating shed 161P2F1OB antigen, the desired steady-state concentration level, frequency of treatment, and the influence of chemotherapeutic or other agents used in combination with the treatment method of the invention, as well as the health status of a particular patient. Non-limiting preferred human unit doses are, for example, 500pg - 1mg, 1mg - 50mg, 50mg - 100mg, 100mg - 200mg, 200mg - 300mg, 400mg -500mg, 500mg - 600mg, 600mg -700mg, 700mg - 800mg, 800mg - 900mg, 900mg - 1g, or 1mg - 700mg. In certain embodiments, the dose is in a range of 2-mg/kg body weight, e.g., with follow on weekly doses of 1-3 mg/kg; 0.5mg, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10mg/kg body weight followed, e.g., in two, three or four weeks by weekly doses; 0.5- 10mg/kg body weight, e.g., followed in two, three or four weeks by weekly doses; 225, 250, 275, 300, 325, 350, 375, 400mg m2 of body area weekly; 1-600mg m2 of body area weekly; 225-400mg m2 of body area weekly; these does can be followed by weekly doses for 2, 3, 4, 5, 6, 7, 8, 9, 19, 1112 or more weeks.
In one embodiment, human unit dose forms of polynucleotides comprise a suitable dosage range or effective amount that provides any therapeutic effect. As appreciated by one of ordinary skill in the art a therapeutic effect depends on a number of factors, including the sequence of the polynucleotide, molecular weight of the polynucleotide and route of administration. Dosages are generally selected by the physician or other health care professional in accordance with a variety of parameters known in the art, such as severity of symptoms, history of the patient and the like. Generally, for a polynucleotide of about 20 bases, a dosage range may be selected from, for example, an independently selected lower limit such as about 0.1, 0.25, 0.5, 1,2, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400 or 500 mg/kg up to an independently selected upper limit, greater than the lower limit, of about 60, 80, 100, 200, 300, 400, 500, 750, 1000, 1500, 2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000 or 10,000 mg/kg. For example, a dose may be about any of the following:
0.1 to 100 mg/kg, 0.1 to 50 mg/kg, 0.1 to 25 mg/kg, 0.1 to 10 mg/kg, 1 to 500 mg/kg, 100 to 400 mg/kg, 200 to 300 mg/kg, 1 to 100 mg/kg, 100 to 200 mg/kg, 300 to 400 mg/kg, 400 to 500 mg/kg, 500 to 1000 mg/kg, 500 to 5000 mg/kg, or 500 to 10,000 mg/kg. Generally, parenteral routes of administration may require higher doses of polynucleotide compared to more direct application to the nucleotide to diseased tissue, as do polynucleotides of increasing length.
In one embodiment, human unit dose forms of T-cells comprise a suitable dosage range or effective amount that provides any therapeutic effect. As appreciated by one of ordinary skill in the art, a therapeutic effect depends on a number of factors. Dosages are generally selected by the physician or other health care professional in accordance with a variety of parameters known in the art, such as severity of symptoms, history of the patient and the like. A dose may be about 104 cells to about 106 cells, about 106 cells to about 108 cells, about 108 to about 1011 cells, or about 108 to about 5 x 1010 cells.
A dose may also about 106 cells/m2 to about 1010 cells/m2, or about 106 cells/m2 to about 108 cells/m2 Proteins(s) of the invention, and/or nucleic acids encoding the protein(s), can also be administered via liposomes, which may also serve to: 1) target the proteins(s) to a particular tissue, such as lymphoid tissue; 2) to target selectively to diseases cells; or, 3) to increase the half-life of the peptide composition.
Liposomes include emulsions, foams, micelles, insoluble monolayers, liquid crystals, phospholipid dispersions, lamellar layers and the like. In these preparations, the peptide to be delivered is incorporated as part of a liposome, alone or in conjunction with a molecule which binds to a receptor prevalent among lymphoid cells, such as monoclonal antibodies which bind to the CD45 antigen, or with other therapeutic or immunogenic compositions. Thus, liposomes either filled or decorated with a desired peptide of the invention can be directed to the site of lymphoid cells, where the liposomes then deliver the peptide compositions. Liposomes for use in accordance with the invention are formed from standard vesicle-forming lipids, which generally include neutral and negatively charged phospholipids and a sterol, such as cholesterol. The selection of lipids is generally guided by consideration of, e.g., liposome size, acid lability and stability of the liposomes in the blood stream. A variety of methods are available for preparing liposomes, as described in, e.g., Szoka, etal., Ann.
Rev. Biophys, Bioeng. 9:467 (1980), and U.S.
Patent Nos. 4,235,871, 4,501,728, 4,837,028, and 5,019,369.
For targeting cells of the immune system, a ligand to be incorporated into the liposome can include, e.g., antibodies or fragments thereof specific for cell surface determinants of the desired immune system cells. A liposome suspension containing a peptide may be administered intravenously, locally, topically, etc. in a dose which varies according to, inter alia, the manner of administration, the peptide being delivered, and the stage of the disease being treated.
For solid compositions, conventional nontoxic solid carriers may be used which include, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium carbonate, and the like. For oral administration, a pharmaceutically acceptable nontoxic composition is formed by incorporating any of the normally employed excipients, such as those carriers previously listed, and generally 10-95% of active ingredient, that is, one or more peptides of the invention, and more preferably at a concentration of 25%-75%.
For aerosol administration, immunogenic peptides are preferably supplied in finely divided form along with a surfactant and propellant. Typical percentages of peptides are about 0.01%-20%
by weight, preferably about 1%-10%. The surfactant must, of course, be nontoxic, and preferably soluble in the propellant. Representative of such agents are the esters or partial esters of fatty acids containing from about 6 to 22 carbon atoms, such as caproic, octanoic, lauric, palmitic, stearic, linoleic, linolenic, olesteric and oleic acids with an aliphatic polyhydric alcohol or its cyclic anhydride. Mixed esters, such as mixed or natural glycerides may be employed. The surfactant may constitute about 0.1%-20% by weight of the composition, preferably about 0.25-5%. The balance of the composition is ordinarily propellant. A carrier can also be included, as desired, as with, e.g., lecithin for intranasal delivery.
XI.) Diagnostic and Prognostic Embodiments of 161P2F1OB.
As disclosed herein, 161P2F1OB polynucleotides, polypeptides, reactive cytotoxic T cells (CTL), reactive helper T
cells (HTL) and anti-polypeptide antibodies are used in well known diagnostic, prognostic and therapeutic assays that examine conditions associated with dysregulated cell growth such as cancer, in particular the cancers listed in Table I (see, e.g., both its specific pattern of tissue expression as well as its overexpression in certain cancers as described for example in the Example entitled "Expression analysis of 161P2F1OB in normal tissues, and patient specimens").
161P2F1OB can be analogized to a prostate associated antigen PSA, the archetypal marker that has been used by medical practitioners for years to identify and monitor the presence of prostate cancer (see, e.g., Merrill etal., J. Urol. 163(2):
503-5120(2000); Polascik etal., J. Urol. Aug; 162(2):293-306 (1999) and Fortier etal., J. Nat. Cancer Inst. 91(19): 1635-1640(1999)). A variety of other diagnostic markers are also used in similar contexts including p53 and K-ras (see, e.g., Tulchinsky et al., Int J Mol Med 1999 Jul 4(1):99-102 and Minimoto etal., Cancer Detect Prey 2000;24(1):1-12). Therefore, this disclosure of 161P2F1OB polynucleotides and polypeptides (as well as 161P2F1OB polynucleotide probes and anti-161P2F1OB antibodies used to identify the presence of these molecules) and their properties allows skilled artisans to utilize these molecules in methods that are analogous to those used, for example, in a variety of diagnostic assays directed to examining conditions associated with cancer.
Typical embodiments of diagnostic methods which utilize the 161P2F1OB
polynucleotides, polypeptides, reactive T
cells and antibodies are analogous to those methods from well-established diagnostic assays, which employ, e.g., PSA
polynucleotides, polypeptides, reactive T cells and antibodies. For example, just as PSA polynucleotides are used as probes (for example in Northern analysis, see, e.g., Sharief et al., Biochem. Mol.
Biol. Int. 33(3):567-74(1994)) and primers (for example in PCR analysis, see, e.g., Okegawa etal., J. Urol. 163(4): 1189-1190 (2000)) to observe the presence and/or the level of PSA mRNAs in methods of monitoring PSA overexpression or the metastasis of prostate cancers, the 161P2F1OB
polynucleotides described herein can be utilized in the same way to detect 161P2F1OB overexpression or the metastasis of prostate and other cancers expressing this gene. Alternatively, just as PSA
polypeptides are used to generate antibodies specific for PSA which can then be used to observe the presence and/or the level of PSA proteins in methods to monitor PSA protein overexpression (see, e.g., Stephan etal., Urology 55(4):560-3 (2000)) or the metastasis of prostate cells (see, e.g., Alanen etal., Pathol. Res. Pract. 192(3):233-7 (1996)), the 161P2F1OB
polypeptides described herein can be utilized to generate antibodies for use in detecting 161P2F1OB overexpression or the metastasis of prostate cells and cells of other cancers expressing this gene.
Specifically, because metastases involves the movement of cancer cells from an organ of origin (such as the lung or prostate gland etc.) to a different area of the body (such as a lymph node), assays which examine a biological sample for the presence of cells expressing 161P2F1OB polynucleotides and/or polypeptides can be used to provide evidence of metastasis. For example, when a biological sample from tissue that does not normally contain 161P2F10B-expressing cells (lymph node) is found to contain 161P2F10B-expressing cells such as the 161P2F1OB expression seen in LAPC4 and LAPC9, xenografts isolated from lymph node and bone metastasis, respectively, this finding is indicative of metastasis.
Alternatively 161P2F108 polynucleotides and/or polypeptides can be used to provide evidence of cancer, for example, when cells in a biological sample that do not normally express 161P2F1OB or express 161P2F1OB at a different level are found to express 161P2F1OB or have an increased expression of 161P2F1OB (see, e.g., the 161P2F1OB
expression in the cancers listed in Table I and in patient samples etc. shown in the accompanying Figures). In such assays, artisans may further wish to generate supplementary evidence of metastasis by testing the biological sample for the presence of a second tissue restricted marker (in addition to 161P2F10B) such as PSA, PSCA etc. (see, e.g., Alanen etal., Pathol. Res. Pract. 192(3): 233-237 (1996)).
Just as PSA polynucleotide fragments and polynucleotide variants are employed by skilled artisans for use in methods of monitoring PSA, 161P2F1OB polynucleotide fragments and polynucleotide variants are used in an analogous = manner. In particular, typical PSA polynucleotides used in methods of monitoring PSA are probes or primers which consist of fragments of the PSA cDNA sequence. Illustrating this, primers used to PCR
amplify a PSA polynucleotide must include less than the whole PSA sequence to function in the polymerase chain reaction.
In the context of such PCR reactions, skilled artisans generally create a variety of different polynucleotide fragments that can be used as primers in order to amplify different portions of a polynucleotide of interest or to optimize amplification reactions (see, e.g., Caetano-Anolles, G.
Biotechniques 25(3): 472-476, 478-480 (1998); Robertson etal., Methods Mol.
Biol. 98:121-154 (1998)). An additional illustration of the use of such fragments is provided in the Example entitled "Expression analysis of 161P2F1OB in normal tissues, and patient specimens," where a 161P2F1OB polynucleotide fragment is used as a probe to show the expression of 161P2F1OB RNAs in cancer cells. In addition, variant polynucleotide sequences are typically used as primers and probes for the corresponding mRNAs in PCR and Northern analyses (see, e.g., Sawai etal., Fetal Diagn. Ther. 1996 Nov-Dec 11(6):407-13 and Current Protocols In Molecular Biology, Volume 2, Unit 2, Frederick M. Ausubel etal. eds., 1995)).
Polynucleotide fragments and variants are useful in this context where they are capable of binding to a target polynucleotide sequence (e.g., a 161P2F1OB polynucleotide shown in Figure 2 or variant thereof) under conditions of high stringency.
Furthermore, PSA polypeptides which contain an epitope that can be recognized by an antibody or T cell that specifically binds to that epitope are used in methods of monitoring PSA.
161P2F1OB polypeptide fragments and polypeptide analogs or variants can also be used in an analogous manner. This practice of using polypeptide fragments or polypeptide variants to generate antibodies (such as anti-PSA antibodies or T
cells) is typical in the art with a wide variety of systems such as fusion proteins being used by practitioners (see, e.g., Current Protocols In Molecular Biology, Volume 2, Unit 16, Frederick M. Ausubel etal. eds., 1995). In this context, each epitope(s) functions to provide the architecture with which an antibody or T cell is reactive. Typically, skilled artisans create a variety of different polypeptide fragments that can be used in order to generate immune responses specific for different portions of a polypeptide of interest (see, e.g., U.S.
Patent No. 5,840,501 and U.S. Patent No. 5,939,533). For example it may be preferable to utilize a polypeptide comprising one of the 161P2F1OB biological motifs discussed herein or a motif-bearing subsequence which is readily identified by one of skill in the art based on motifs available in the art. Polypeptide fragments, variants or analogs are typically useful in this context as long as they comprise an epitope capable of generating an antibody or T cell specific for a target polypeptide sequence (e.g. a 161P2F1OB polypeptide shown in Figure 3).
As shown herein, the 161P2F1OB polynucleotides and polypeptides (as well as the 161P2F1OB polynucleotide probes and anti-161P2F1OB antibodies or T cells used to identify the presence of these molecules) exhibit specific properties that make them useful in diagnosing cancers such as those listed in Table I.
Diagnostic assays that measure the presence of 161P2F1OB gene products, in order to evaluate the presence or onset of a disease condition described herein, such as prostate cancer, are used to identify patients for preventive measures or further monitoring, as has been done so successfully with PSA. Moreover, these materials satisfy a need in the art for molecules having similar or complementary characteristics to PSA in situations where, for example, a definite diagnosis of metastasis of prostatic origin cannot be made on the basis of a test for PSA alone (see, e.g., Alanen etal., Pathol. Res.
Pract. 192(3): 233-237 (1996)), and consequently, materials such as 161P2F1OB polynucleotides and polypeptides (as well as the 161P2F1OB polynucleotide probes and anti-161P2F1OB antibodies used to identify the presence of these molecules) need to be employed to confirm a metastases of prostatic origin.
Finally, in addition to their use in diagnostic assays, the 161P2F1OB
polynucleotides disclosed herein have a number of other utilities such as their use in the identification of oncogenetic associated chromosomal abnormalities in the chromosomal region to which the 161P2F1OB gene maps (see the Example entitled "Chromosomal Mapping of 161P2F1OB"
below). Moreover, in addition to their use in diagnostic assays, the 161P2F10B-related proteins and polynucleotides disclosed herein have other utilities such as their use in the forensic analysis of tissues of unknown origin (see, e.g., Takahama K Forensic Sci Int 1996 Jun 28;80(1-2): 63-9).
Additionally, 161P2F1OB-related proteins or polynucleotides of the invention can be used to treat a pathologic condition characterized by the over-expression of 161P2F10B. For example, the amino acid or nucleic acid sequence of Figure 2 or Figure 3, or fragments of either, can be used to generate an immune response to a 161P2F1OB antigen.
Antibodies or other molecules that react with 161P2F1OB can be used to modulate the function of this molecule, and thereby provide a therapeutic benefit.
XII.) Inhibition of 161P2F1OB Protein Function The invention includes various methods and compositions for inhibiting the binding of 161P2F1OB to its binding partner or its association with other protein(s) as well as methods for inhibiting 161P2F1OB function.
XII.A.) Inhibition of 161P2F1OB With Intracellular Antibodies In one approach, a recombinant vector that encodes single chain antibodies that specifically bind to 161P2F1OB
are introduced into 161P2F1OB expressing cells via gene transfer technologies.
Accordingly, the encoded single chain anti-161P2F1OB antibody is expressed intracellularly, binds to 161P2F1OB protein, and thereby inhibits its function. Methods for engineering such intracellular single chain antibodies are well known. Such intracellular antibodies, also known as "intrabodies", are specifically targeted to a particular compartment within the cell, providing control over where the inhibitory activity of the treatment is focused. This technology has been successfully applied in the art (for review, see Richardson and Marasco, 1995, TIBTECH vol. 13). Intrabodies have been shown to virtually eliminate the expression of otherwise abundant cell surface receptors (see, e.g., Richardson etal., 1995, Proc. Natl. Acad.
Sci. USA 92: 3137-3141; Beerli etal., 1994, J.
Biol. Chem. 289: 23931-23936; Deshane eta!;, 1994, Gene Ther. 1: 332-337).
Single chain antibodies comprise the variable domains of the heavy and light chain joined by a flexible linker polypeptide, and are expressed as a single polypeptide. Optionally, single chain antibodies are expressed as a single chain variable region fragment joined to the light chain constant region. Well-known intracellular trafficking signals are engineered into recombinant polynucleotide vectors encoding such single chain antibodies in order to target precisely the intrabody to the desired intracellular compartment. For example, intrabodies targeted to the endoplasmic reticulum (ER) are engineered to incorporate a leader peptide and, optionally, a C-terminal ER retention signal, such as the KDEL amino acid motif.
Intrabodies intended to exert activity in the nucleus are engineered to include a nuclear localization signal. Lipid moieties are joined to intrabodies in order to tether the intrabody to the cytosolic side of the plasma membrane. Intrabodies can also be targeted to exert function in the cytosol. For example, cytosolic intrabodies are used to sequester factors within the cytosol, thereby preventing them from being transported to their natural cellular destination.
In one embodiment, intrabodies are used to capture 161P2F1OB in the nucleus, thereby preventing its activity within the nucleus. Nuclear targeting signals are engineered into such 161P2F1OB intrabodies in order to achieve the desired targeting. Such 161P2F1OB intrabodies are designed to bind specifically to a particular 161P2F1OB domain. In another embodiment, cytosolic intrabodies that specifically bind to a 161P2F1OB protein are used to prevent 161P2F1OB
from gaining access to the nucleus, thereby preventing it from exerting any biological activity within the nucleus (e.g., preventing 161P2F1OB from forming transcription complexes with other factors).
In order to specifically direct the expression of such intrabodies to particular cells, the transcription of the intrabody is placed under the regulatory control of an appropriate tumor-specific promoter and/or enhancer. In order to target intrabody expression specifically to prostate, for example, the PSA promoter and/or promoter/enhancer can be utilized (See, for example, U.S. Patent No. 5,919,652 issued 6 July 1999).
XII.B.) Inhibition of 161P2F1OB with Recombinant Proteins In another approach, recombinant molecules bind to 161P2F1OB and thereby inhibit 161P2F106 function. For example, these recombinant molecules prevent or inhibit 161P2F1OB from accessing/binding to its binding partner(s) or associating with other protein(s). Such recombinant molecules can, for example, contain the reactive part(s) of a 161P2F1OB
specific antibody molecule. In a particular embodiment, the 161P2F108 binding domain of a 161P2F1OB binding partner is engineered into a dimeric fusion protein, whereby the fusion protein comprises two 161P2F1OB ligand binding domains linked to the Fc portion of a human IgG, such as human IgG1. Such IgG portion can contain, for example, the CH2 and CH3 domains and the hinge region, but not the CH1 domain. Such dimeric fusion proteins are administered in soluble form to patients suffering from a cancer associated with the expression of 161P2F1013, whereby the dimeric fusion protein specifically binds to 161P2F1013 and blocks 161P2F1OB interaction with a binding partner. Such dimeric fusion proteins are further combined into multimeric proteins using known antibody linking technologies.
XII.C.) Inhibition of 161P2F1OB Transcription or Translation The present invention also comprises various methods and compositions for inhibiting the transcription of the 161P2F1OB gene. Similarly, the invention also provides methods and compositions for inhibiting the translation of 161P2F108 mRNA into protein.
In one approach, a method of inhibiting the transcription of the 161P2F1OB
gene comprises contacting the 161P2F1OB gene with a 161P2F1OB antisense polynucleotide. In another approach, a method of inhibiting 161P2F1OB
mRNA translation comprises contacting a 161P2F1OB mRNA with an antisense polynucleotide. In another approach, a 161P2F1OB specific ribozyme is used to cleave a 161P2F1OB message, thereby inhibiting translation. Such antisense and ribozyme based methods can also be directed to the regulatory regions of the 161P2F1OB gene, such as 161P2F1OB
promoter and/or enhancer elements. Similarly, proteins capable of inhibiting a 161P2F1OB gene transcription factor are used to inhibit 161P2F1OB mRNA transcription. The various polynucleotides and compositions useful in the aforementioned methods have been described above. The use of antisense and ribozyme molecules to inhibit transcription and translation is well known in the art.
Other factors that inhibit the transcription of 161P2F1OB by interfering with 161P2F1OB transcriptional activation are also useful to treat cancers expressing 161P2F10B. Similarly, factors that interfere with 161P2F106 processing are useful to treat cancers that express 161P2F10B. Cancer treatment methods utilizing such factors are also within the scope of the invention.

XII.D.) General Considerations for Therapeutic Strategies Gene transfer and gene therapy technologies can be used to deliver therapeutic polynucleotide molecules to tumor cells synthesizing 161P2F108 (i.e., antisense, ribozyme, polynucleotides encoding intrabodies and other 161P2F108 inhibitory molecules). A number of gene therapy approaches are known in the art.
Recombinant vectors encoding 161P2F1OB antisense polynucleotides, ribozymes, factors capable of interfering with 161P2F1OB
transcription, and so forth, can be delivered to target tumor cells using such gene therapy approaches.
The above therapeutic approaches can be combined with any one of a wide variety of surgical, chemotherapy or radiation therapy regimens. The therapeutic approaches of the invention can enable the use of reduced dosages of chemotherapy (or other therapies) and/or less frequent administration, an advantage for all patients and particularly for those that do not tolerate the toxicity of the chemotherapeutic agent well.
The anti-tumor activity of a particular composition (e.g., antisense, ribozyme, intrabody), or a combination of such compositions, can be evaluated using various in vitro and in vivo assay systems. In vitro assays that evaluate therapeutic activity include cell growth assays, soft agar assays and other assays indicative of tumor promoting activity, binding assays capable of determining the extent to which a therapeutic composition will inhibit the binding of 161P2F1OB to a binding partner, etc.
In vivo, the effect of a 161P2F1OB therapeutic composition can be evaluated in a suitable animal model. For example, xenogenic prostate cancer models can be used, wherein human prostate cancer explants or passaged xenograft tissues are introduced into immune compromised animals, such as nude or SCID mice (Klein etal., 1997, Nature Medicine 3: 402-408). For example, PCT Patent Application W098/16628 and U.S. Patent 6,107,540 describe various xenograft models of human prostate cancer capable of recapitulating the development of primary tumors, micrometastasis, and the formation of osteoblastic metastases characteristic of late stage disease. Efficacy can be predicted using assays that measure inhibition of tumor formation, tumor regression or metastasis, and the like.
In vivo assays that evaluate the promotion of apoptosis are useful in evaluating therapeutic compositions. In one embodiment, xenografts from tumor bearing mice treated with the therapeutic composition can be examined for the presence of apoptotic foci and compared to untreated control xenograft-bearing mice.
The extent to which apoptotic foci are found in the tumors of the treated mice provides an indication of the therapeutic efficacy of the composition.
The therapeutic compositions used in the practice of the foregoing methods can be formulated into pharmaceutical compositions comprising a carrier suitable for the desired delivery method.
Suitable carriers include any material that when combined with the therapeutic composition retains the anti-tumor function of the therapeutic composition and is generally non-reactive with the patient's immune system. Examples include, but are not limited to, any of a number of standard pharmaceutical carriers such as sterile phosphate buffered saline solutions, bacteriostatic water, and the like (see, generally, Remington's Pharmaceutical Sciences 16th Edition, A. Osal., Ed., 1980).
Therapeutic formulations can be solubilized and administered via any route capable of delivering the therapeutic composition to the tumor site. Potentially effective routes of administration include, but are not limited to, intravenous, parenteral, intraperitoneal, intramuscular, intratumor, intradermal, intraorgan, orthotopic, and the like. A preferred formulation for intravenous injection comprises the therapeutic composition in a solution of preserved bacteriostatic water, sterile unpreserved water, and/or diluted in polyvinylchloride or polyethylene bags containing 0.9% sterile Sodium Chloride for Injection, USP. Therapeutic protein preparations can be lyophilized and stored as sterile powders, preferably under vacuum, and then reconstituted in bacteriostatic water (containing for example, benzyl alcohol preservative) or in sterile water prior to injection.
Dosages and administration protocols for the treatment of cancers using the foregoing methods will vary with the method and the target cancer, and will generally depend on a number of other factors appreciated in the art.

XIII.) Identification, Characterization and Use of Modulators of 161P2FlOb Methods to Identify and Use Modulators In one embodiment, screening is performed to identify modulators that induce or suppress a particular expression profile, suppress or induce specific pathways, preferably generating the associated phenotype thereby. In another embodiment, having identified differentially expressed genes important in a particular state; screens are performed to identify modulators that alter expression of individual genes, either increase or decrease. In another embodiment, screening is performed to identify modulators that alter a biological function of the expression product of a differentially expressed gene.
Again, having identified the importance of a gene in a particular state, screens are performed to identify agents that bind and/or modulate the biological activity of the gene product.
In addition, screens are done for genes that are induced in response to a candidate agent. After identifying a modulator (one that suppresses a cancer expression pattern leading to a normal expression pattern, or a modulator of a cancer gene that leads to expression of the gene as in normal tissue) a screen is performed to identify genes that are specifically modulated in response to the agent. Comparing expression profiles between normal tissue and agent-treated cancer tissue reveals genes that are not expressed In normal tissue or cancer tissue, but are expressed in agent treated tissue, and vice versa. These agent-specific sequences are identified and used by methods described herein for cancer genes or proteins. In particular these sequences and the proteins they encode are used in marking or identifying agent-treated cells. In addition, antibodies are raised against the agent-induced proteins and used to target novel therapeutics to the treated cancer tissue sample.
Modulator-related Identification and Screening Assays:
Gene Expression-related Assays Proteins, nucleic acids, and antibodies of the invention are used in screening assays. The cancer-associated proteins, antibodies, nucleic acids, modified proteins and cells containing these sequences are used in screening assays, such as evaluating the effect of drug candidates on a "gene expression profile," expression profile of polypeptides or alteration of biological function. In one embodiment, the expression profiles are used, preferably in conjunction with high throughput screening techniques to allow monitoring for expression profile genes after treatment with a candidate agent (e.g., Davis, GE, et at, J Biol Screen 7:69(2002); Zlokamik, et al., Science 279:84-8 (1998); Heid, Genome Res 6:986-94,1996).
= The cancer proteins, antibodies, nucleic acids, modified proteins and cells containing the native or modified cancer proteins or genes are used in screening assays. That is, the present invention comprises methods for screening for compositions which modulate the cancer phenotype or a physiological function of a cancer protein of the invention. This is done on a gene itself or by evaluating the effect of drug candidates on a "gene expression profile" or biological function. In one embodiment, expression profiles are used, preferably in conjunction with high throughput screening techniques to allow monitoring after treatment with a candidate agent, see Zlokamik, supra.
A variety of assays are executed directed to the genes and proteins of the invention. Assays are run on an individual nucleic acid or protein level. That is, having identified a particular gene as up regulated in cancer, test compounds are screened for the ability to modulate gene expression or for binding to the cancer protein of the invention. "Modulation" in this context includes an increase or a decrease in gene expression. The preferred amount of modulation will depend on the original change of the gene expression in normal versus tissue undergoing cancer, with changes of at least 10%, preferably 50%, more preferably 100-300%, and in some embodiments 300-1000% or greater.
Thus, if a gene exhibits a 4-fold increase in cancer tissue compared to normal tissue, a decrease of about four-fold is often desired; similarly, a 10-fold decrease in cancer tissue compared to normal tissue a target value of a 10-fold increase in expression by the test compound is often desired. Modulators that exacerbate the type of gene expression seen in cancer are also useful, e.g., as an upregulated target in further analyses.
The amount of gene expression is monitored using nucleic acid probes and the quantification of gene expression levels, or, alternatively, a gene product itself is monitored, e.g., through the use of antibodies to the cancer protein and standard immunoassays. Proteomics and separation techniques also allow for quantification of expression.
Expression Monitoring to Identify Compounds that Modify Gene Expression In one embodiment, gene expression monitoring, i.e., an expression profile, is monitored simultaneously for a number of entities. Such profiles will typically involve one or more of the genes of Figure 2. In this embodiment, e.g., cancer nucleic acid probes are attached to biochips to detect and quantify cancer sequences in a particular cell. Altematively, PCR
can be used. Thus, a series, e.g., wells of a microtiter plate, can be used with dispensed primers in desired wells. A PCR
reaction can then be performed and analyzed for each well.
Expression monitoring is performed to identify compounds that modify the expression of one or more cancer-associated sequences, e.g., a polynucleotide sequence set out in Figure 2.
Generally, a test modulator is added to the cells prior to analysis. Moreover, screens are also provided to identify agents that modulate cancer, modulate cancer proteins of the invention, bind to a cancer protein of the invention, or interfere with the binding of a cancer protein of the invention and an antibody or other binding partner.
In one embodiment, high throughput screening methods involve providing a library containing a large number of potential therapeutic compounds (candidate compounds). Such "combinatorial chemical libraries" are then screened in one or more assays to identify those library members (particular chemical species or subclasses) that display a desired characteristic activity. The compounds thus identified can serve as conventional "lead compounds," as compounds for screening, or as therapeutics.
In certain embodiments, combinatorial libraries of potential modulators are screened for an ability to bind to a cancer polypeptide or to modulate activity. Conventionally, new chemical entities with useful properties are generated by identifying a chemical compound (called a "lead compound") with some desirable property or activity, e.g., inhibiting activity, creating variants of the lead compound, and evaluating the property and activity of those variant compounds. Often, high throughput screening (HTS) methods are employed for such an analysis.
As noted above, gene expression monitoring is conveniently used to test candidate modulators (e.g., protein, nucleic acid or small molecule). After the candidate agent has been added and the cells allowed to incubate for a period, the sample containing a target sequence to be analyzed is, e.g., added to a biochip.
If required, the target sequence is prepared using known techniques. For example, a sample is treated to lyse the cells, using known lysis buffers, electroporation, etc., with purification and/or amplification such as PCR performed as appropriate. For example, an in vitro transcription with labels covalently attached to the nucleotides is performed. Generally, the nucleic acids are labeled with biotin-FITC or PE, or with cy3 or cy5.
The target sequence can be labeled with, e.g., a fluorescent, a chemiluminescent, a chemical, or a radioactive signal, to provide a means of detecting the target sequence's specific binding to a probe. The label also can be an enzyme, such as alkaline phosphatase or horseradish peroxidase, which when provided with an appropriate substrate produces a product that is detected. Alternatively, the label is a labeled compound or small molecule, such as an enzyme inhibitor, that binds but is not catalyzed or altered by the enzyme. The label also can be a moiety or compound, such as, an epitope tag or biotin which specifically binds to streptavidin. For the example of biotin, the streptavidin is labeled as described above, thereby, providing a detectable signal for the bound target sequence. Unbound labeled streptavidin is typically removed prior to analysis.

As will be appreciated by those in the art, these assays can be direct hybridization assays or can comprise "sandwich assays", which include the use of multiple probes, as is generally outlined in U.S. Patent Nos. 5, 681,702;
5,597,909; 5,545,730; 5,594,117; 5,591,584; 5,571,670; 5,580,731; 5,571,670;
5,591,584; 5,624,802; 5,635,352; 5,594,118;
5,359,100; 5,124, 246; and 5,681,697. In this embodiment, in general, the target nucleic acid is prepared as outlined above, and then added to the biochip comprising a plurality of nucleic acid probes, under conditions that allow the formation of a hybridization complex.
A variety of hybridization conditions are used in the present invention, including high, moderate and low stringency conditions as outlined above. The assays are generally run under stringency conditions which allow formation of the label probe hybridization complex only in the presence of target. Stringency can be controlled by altering a step parameter that is a thermodynamic variable, including, but not limited to, temperature, formamide concentration, salt concentration, chaotropic salt concentration pH, organic solvent concentration, etc. These parameters may also be used to control non-specific binding, as is generally outlined in U.S. Patent No. 5,681,697. Thus, it can be desirable to perform certain steps at higher stringency conditions to reduce non-specific binding.
The reactions outlined herein can be accomplished in a variety of ways.
Components of the reaction can be added simultaneously, or sequentially, in different orders, with preferred embodiments outlined below. In addition, the reaction may include a variety of other reagents. These include salts, buffers, neutral proteins, e.g. albumin, detergents, etc. which can be used to facilitate optimal hybridization and detection, and/or reduce nonspecific or background interactions. Reagents that otherwise improve the efficiency of the assay, such as protease inhibitors, nuclease inhibitors, anti-microbial agents, etc., may also be used as appropriate, depending on the sample preparation methods and purity of the target. The assay data are analyzed to determine the expression levels of individual genes, and changes in expression levels as between states, forming a gene expression profile.
Biological Activity-related Assays The invention provides methods identify or screen for a compound that modulates the activity of a cancer-related gene or protein of the invention. The methods comprise adding a test compound, as defined above, to a cell comprising a cancer protein of the invention. The cells contain a recombinant nucleic acid that encodes a cancer protein of the invention.
In another embodiment, a library of candidate agents is tested on a plurality of cells.
In one aspect, the assays are evaluated in the presence or absence or previous or subsequent exposure of physiological signals, e.g. hormones, antibodies, peptides, antigens, cytokines, growth factors, action potentials, pharmacological agents including chemotherapeutics, radiation, carcinogenics, or other cells (i.e., cell-cell contacts). In another example, the determinations are made at different stages of the cell cycle process. In this way, compounds that modulate genes or proteins of the invention are identified. Compounds with pharmacological activity are able to enhance or interfere with the activity of the cancer protein of the invention. Once identified, similar structures are evaluated to identify critical structural features of the compound.
In one embodiment, a method of modulating ( e.g., inhibiting) cancer cell division is provided; the method comprises administration of a cancer modulator. In another embodiment, a method of modulating ( e.g., inhibiting) cancer is provided; the method comprises administration of a cancer modulator. In a further embodiment, methods of treating cells or individuals with cancer are provided; the method comprises administration of a cancer modulator.
In one embodiment, a method for modulating the status of a cell that expresses a gene of the invention is provided.
As used herein status comprises such art-accepted parameters such as growth, proliferation, survival, function, apoptosis, senescence, location, enzymatic activity, signal transduction, etc. of a cell.
In one embodiment, a cancer inhibitor is an antibody as discussed above. In another embodiment, the cancer inhibitor is an antisense molecule. A variety of cell growth, proliferation, and metastasis assays are known to those of skill in the art, as described herein.
High Throughput Screening to Identify Modulators The assays to identify suitable modulators are amenable to high throughput screening. Preferred assays thus detect enhancement or inhibition of cancer gene transcription, inhibition or enhancement of polypeptide expression, and inhibition or enhancement of polypeptide activity.
In one embodiment, modulators evaluated in high throughput screening methods are proteins, often naturally occurring proteins or fragments of naturally occurring proteins. Thus, e.g., cellular extracts containing proteins, or random or directed digests of proteinaceous cellular extracts, are used. In this way, libraries of proteins are made for screening in the methods of the invention. Particularly preferred in this embodiment are libraries of bacterial, fungal, viral, and mammalian proteins, with the latter being preferred, and human proteins being especially preferred. Particularly useful test compound will be directed to the class of proteins to which the target belongs, e.g., substrates for enzymes, or ligands and receptors.
Use of Soft Agar Growth and Colony Formation to Identify and Characterize Modulators Normal cells require a solid substrate to attach and grow. When cells are transformed, they lose this phenotype and grow detached from the substrate. For example, transformed cells can grow in stirred suspension culture or suspended in semi-solid media, such as semi-solid or soft agar. The transformed cells, when transfected with tumor suppressor genes, can regenerate normal phenotype and once again require a solid substrate to attach to and grow. Soft agar growth or colony formation in assays are used to identify modulators of cancer sequences, which when expressed in host cells, inhibit abnormal cellular proliferation and transformation. A modulator reduces or eliminates the host cells' ability to grow suspended in solid or semisolid media, such as agar.
Techniques for soft agar growth or colony formation in suspension assays are described in Freshney, Culture of Animal Cells a Manual of Basic Technique (3rd ed., 1994). See also, the methods section of Garkavtsev et al. (1996), supra.
Evaluation of Contact Inhibition and Growth Density Limitation to Identify and Characterize Modulators Normal cells typically grow in a flat and organized pattern in cell culture until they touch other cells. When the cells touch one another, they are contact inhibited and stop growing. Transformed cells, however, are not contact inhibited and continue to grow to high densities in disorganized foci. Thus, transformed cells grow to a higher saturation density than corresponding normal cells. This is detected morphologically by the formation of a disoriented monolayer of cells or cells in foci. Alternatively, labeling index with (3H)-thymidine at saturation density is used to measure density limitation of growth, similarly an MU or Alamar blue assay will reveal proliferation capacity of cells and the the ability of modulators to affect same. See Freshney (1994), supra. Transformed cells, when transfected with tumor suppressor genes, can regenerate a normal phenotype and become contact inhibited and would grow to a lower density.
In this assay, labeling index with 3H)-thymidine at saturation density is a preferred method of measuring density limitation of growth. Transformed host cells are transfected with a cancer-associated sequence and are grown for 24 hours at saturation density in non-limiting medium conditions. The percentage of cells labeling with (3H)-thymidine is determined by incorporated cpm.
Contact independent growth is used to identify modulators of cancer sequences, which had led to abnormal cellular proliferation and transformation. A modulator reduces or eliminates contact independent growth, and returns the cells to a normal phenotype.
Evaluation of Growth Factor or Serum Dependence to Identify and Characterize Modulators Transformed cells have lower serum dependence than their normal counterparts (see, e.g., Temin, J. Natl. Cancer Inst. 37:167-175(1966); Eagle et al., J. Exp. Med 131:836-879 (1970));
Freshney, supra. This is in part due to release of various growth factors by the transformed cells The degree of growth factor or serum dependence of transformed host cells can be compared with that of control. For example, growth factor or serum dependence of a cell is monitored in methods to identify and characterize compounds that modulate cancer-associated sequences of the invention.
Use of Tumor-specific Marker Levels to Identify and Characterize Modulators Tumor cells release an increased amount of certain factors (hereinafter "tumor specific markers") than their normal counterparts. For example, plasminogen activator (PA) is released from human glloma at a higher level than from normal brain cells (see, e.g., Guilin , Angiogenesis, Tumor Vascularization, and Potential Interference with Tumor Growth, in Biological Responses in Cancer, pp. 178-184 (Mihich (ed.) 1985)). Similarly, Tumor Angiogenesis Factor (TAF) is released at a higher level in tumor cells than their normal counterparts. See, e.g., Folkman, Angiogenesis and Cancer, Sem Cancer Biol.
(1992)), while bFGF is released from endothelial tumors (Ensoli, Bet al).
Various techniques which measure the release of these factors are described in Freshney (1994), supra. Also, see, Unkless et at,, J. Biol. Chem. 249:4295-4305 (1974); Strickland & Beers, J. Biol. Chem. 251:5694-5702(1976): Whur at al, Br. J. Cancer 42:305 312 (1980); Guilin , Angiogenesis, Tumor Vascularization, and Potential Interference with Tumor Growth, in Biological Responses in Cancer, pp. 178-184 (Mihich (ed.) 1985);
Freshney, Anticancer Res. 5:111-130(1985).
For example, tumor specific marker levels are monitored in methods to identify and characterize compounds that modulate cancer-associated sequences of the invention.
Invasiveness into Matrioel to Identify and Characterize Modulators The degree of invasiveness into Matrigellm or an extracellular matrix constituent can be used as an assay to identify and characterize compounds that modulate cancer associated sequences. Tumor cells exhibit a positive correlation between malignancy and invasiveness Of cells into Matrigel or some other extracellular matrix constituent. In this assay, tumorigenic cells are typically used as host cells. Expression of a tumor suppressor gene in these host cells would decrease invasiveness of the host cells. Techniques described in Cancer Res. 1999;
59:6010; Freshney (1994), supra, can be used.
Briefly, the level of invasion of host cells is measured by using filters coated with Matrigel or some other extracellular matrix constituent. Penetration into the gel, or through to the distal side of the filter, is rated as invasiveness, and rated histologically by number of cells and distance moved, or by prelabeling the cells with I251 and counting the radioactivity on the distal side of the filter or bottom of the dish. See, e.g., Freshney (1984), supra.
Evaluation of Tumor Growth in Vivo to identify and Characterize Modulators Effects of cancer-associated sequences on cell growth are tested in transgenic or immune-suppressed organisms.
Transgenic organisms are prepared in a variety of art-accepted ways. For example, knock-out transgenic organisms, e.g., mammals such as mice, are made, in which a cancer gene is disrupted or in which a cancer gene is inserted. Knock-out transgenic mice are made by insertion of a marker gene or other heterologous gene into the endogenous cancer gene site in the mouse genome via homologous recombination. Such mice can also be made by substituting the endogenous cancer gene with a mutated version of the cancer gene, or by mutaling the endogenous cancer gene, e.g., by exposure to carcinogens.
To prepare transgenic chimeric animals, e.g., mice, a DNA construct is introduced into the nuclei of embryonic stem cells. Cells containing the newly engineered genetic lesion are injected into a host mouse embryo, which is re-implanted into a recipient female. Some of these embryos develop into chimeric mice that possess germ cells some of which are derived from the mutant cell line. Therefore, by breeding the chimeric mice it is possible to obtain a new line of mice containing the introduced genetic lesion (see, e.g., Capecchi et al., Science 244:1288(1989)). Chimeric mice can be derived according to US Patent 6,365,797, issued 2 April 2002; US Patent 6,107,540 issued 22 August 2000; Hogan et at., Manipulating the Mouse Embryo: A laboratory Manual, Cold Spring Harbor Laboratory (1988) and Teratocarcinomas and Embryonic Stem Cells: A Practical Approach, Robertson, ed., IRL Press, Washington, D.C., (1987).
Alternatively, various immune-suppressed or immune-deficient host animals can be used. For example, a genetically athymic "nude" mouse (see, e.g., Giovanella et al., J. Natl.
Cancer Inst. 52:921 (1974)), a SCID mouse, a thymectornized mouse, or an irradiated mouse (see, e.g., Bradley et al., Br.
J. Cancer 38:263 (1978); Selby et al., Br. J.
Cancer 41:52 (1980)) can be used as a host. Transplantable tumor cells (typically about 106 cells) injected into isogenic hosts produce invasive tumors in a high proportion of cases, while normal cells of similar origin will not. In hosts which developed invasive tumors, cells expressing cancer-associated sequences are injected subcutaneously or orthotopically.
Mice are then separated into groups, including control groups and treated experimental groups) e.g. treated with a modulator). After a suitable length of time, preferably 4-8 weeks, tumor growth is measured (e.g., by volume or by its two largest dimensions, or weight) and compared to the control. Tumors that have statistically significant reduction (using, e.g., Student's T test) are said to have inhibited growth.
In Vitro Assays to Identify and Characterize Modulators Assays to identify compounds with modulating activity can be performed in vitro. For example, a cancer polypeptide is first contacted with a potential modulator and incubated for a suitable amount of time, e.g., from 0.5 to 48 hours. In one embodiment, the cancer polypeptide levels are determined in vitro by measuring the level of protein or mRNA.
The level of protein is measured using immunoassays such as Western blotting, ELISA and the like with an antibody that selectively binds to the cancer polypeptide or a fragment thereof. For measurement of mRNA, amplification, e.g., using PCR, LCR, or hybridization assays, e. g., Northern hybridization, RNAse protection, dot blotting, are preferred. The level of protein or mRNA is detected using directly or indirectly labeled detection agents, e.g., fluorescently or radioactively labeled nucleic acids, radioactively or enzymatically labeled antibodies, and the like, as described herein.
Alternatively, a reporter gene system can be devised using a cancer protein promoter operably linked to a reporter gene such as luciferase, green fluorescent protein, CAT, or P-gal. The reporter construct is typically transfected into a cell.
After treatment with a potential modulator, the amount of reporter gene transcription, translation, or activity is measured according to standard techniques known to those of skill in the art (Davis GF, supra; Gonzalez, J. & Negulescu, P. Curr.
Opin. Biotechnol. 1998: 9:624).
As outlined above, in vitro screens are done on individual genes and gene products. That is, having identified a particular differentially expressed gene as important in a particular state, screening of modulators of the expression of the gene or the gene product itself is performed.
In one embodiment, screening for modulators of expression of specific gene(s) is performed. Typically, the expression of only one or a few genes is evaluated. In another embodiment, screens are designed to first find compounds that bind to differentially expressed proteins. These compounds are then evaluated for the ability to modulate differentially expressed activity. Moreover, once initial candidate compounds are identified, variants can be further screened to better evaluate structure activity relationships.
Binding Assays to Identify and Characterize Modulators In binding assays in accordance with the invention, a purified or isolated gene product of the invention is generally used. For example, antibodies are generated to a protein of the invention, and immunoassays are run to determine the amount and/or location of protein. Alternatively, cells comprising the cancer proteins are used in the assays.
Thus, the methods comprise combining a cancer protein of the invention and a candidate compound such as a ligand, and determining the binding of the compound to the cancer protein of the invention. Preferred embodiments utilize the human cancer protein; animal models of human disease of can also be developed and used. Also, other analogous mammalian proteins also can be used as appreciated by those of skill in the art. Moreover, in some embodiments variant or derivative cancer proteins are used.
Generally, the cancer protein of the invention, or the ligand, is non-diffusibly bound to an insoluble support. The support can, e.g., be one having isolated sample receiving areas (a microtiter plate, an array, etc.). The insoluble supports can be made of any composition to which the compositions can be bound, is readily separated from soluble material, and is otherwise compatible with the overall method of screening. The surface of such supports can be solid or porous and of any convenient shape.
Examples of suitable insoluble supports include microtiter plates, arrays, membranes and beads. These are typically made of glass, plastic (e.g., polystyrene), polysaccharide, nylon, nitrocellulose, or Teflon etc. Microtiter plates and arrays are especially convenient because a large number of assays can be carried out simultaneously, using small amounts of reagents and samples. The particular manner of binding of the composition to the support is not crucial so long as it is compatible with the reagents and overall methods of the invention, maintains the activity of the composition and is nondiffusable. Preferred methods of binding include the use of antibodies which do not sterically block either the ligand binding site or activation sequence when attaching the protein to the support, direct binding to "sticky" or ionic supports, chemical crosslinking, the synthesis of the protein or agent on the surface, etc. Following binding of the protein or ligand/binding agent to the support, excess unbound material is removed by washing. The sample receiving areas may then be blocked through incubation with bovine serum albumin (BSA), casein or other innocuous protein or other moiety.
Once a cancer protein of the invention is bound to the support, and a test compound is added to the assay.
Altematively, the candidate binding agent is bound to the support and the cancer protein of the invention is then added.
Binding agents include specific antibodies, non-natural binding agents identified in screens of chemical libraries, peptide analogs, etc.
Of particular interest are assays to identify agents that have a low toxicity for human cells. A wide variety of assays can be used for this purpose, including proliferation assays, cAMP assays, labeled in vitro protein-protein binding assays, electrophoretic mobility shift assays, immunoassays for protein binding, functional assays (phosphorylation assays, etc.) and the like.
A determination of binding of the test compound (ligand, binding agent, modulator, etc.) to a cancer protein of the invention can be done in a number of ways. The test compound can be labeled, and binding determined directly, e.g., by attaching all or a portion of the cancer protein of the invention to a solid support, adding a labeled candidate compound (e.g., a fluorescent label), washing off excess reagent, and determining whether the label is present on the solid support. Various blocking and washing steps can be utilized as appropriate.
In certain embodiments, only one of the components is labeled, e.g., a protein of the invention or ligands labeled.
Alternatively, more than one component is labeled with different labels, e.g., 1125, for the proteins and a fluorophor for the compound. Proximity reagents, e.g., quenching or energy transfer reagents are also useful.
Competitive Binding to !den* and Characterize Modulators In one embodiment, the binding of the "test compound" is determined by competitive binding assay with a "competitor." The competitor is a binding moiety that binds to the target molecule (e.g., a cancer protein of the invention).
Competitors include compounds such as antibodies, peptides, binding partners, ligands, etc. Under certain circumstances, the competitive binding between the test compound and the competitor displaces the test compound. In one embodiment, the test compound is labeled. Either the test compound, the competitor, or both, is added to the protein for a time sufficient to allow binding. Incubations are performed at a temperature that facilitates optimal activity, typically between four and 40 C.

Incubation periods are typically optimized, e.g., to facilitate rapid high throughput screening; typically between zero and one hour will be sufficient. Excess reagent is generally removed or washed away.
The second component is then added, and the presence or absence of the labeled component is followed, to indicate binding.
In one embodiment, the competitor is added first, followed by the test compound. Displacement of the competitor is an indication that the test compound is binding to the cancer protein and thus is capable of binding to, and potentially modulating, the activity of the cancer protein. In this embodiment, either component can be labeled. Thus, e.g., if the competitor is labeled, the presence of label in the post-test compound wash solution indicates displacement by the test compound. Alternatively, if the test compound is labeled, the presence of the label on the support indicates displacement.
In an alternative embodiment, the test compound is added first, with incubation and washing, followed by the competitor. The absence of binding by the competitor indicates that the test compound binds to the cancer protein with higher affinity than the competitor. Thus, if the test compound is labeled, the presence of the label on the support, coupled with a lack of competitor binding, indicates that the test compound binds to and thus potentially modulates the cancer protein of the invention.
Accordingly, the competitive binding methods comprise differential screening to identity agents that are capable of modulating the activity of the cancer proteins of the invention. In this embodiment, the methods comprise combining a cancer protein and a competitor in a first sample. A second sample comprises a test compound, the cancer protein, and a competitor. The binding of the competitor is determined for both samples, and a change, or difference in binding between the two samples indicates the presence of an agent capable of binding to the cancer protein and potentially modulating its activity. That is, if the binding of the competitor is different in the second sample relative to the first sample, the agent is capable of binding to the cancer protein.
Alternatively, differential screening is used to identify drug candidates that bind to the native cancer protein, but cannot bind to modified cancer proteins. For example the structure of the cancer protein is modeled and used in rational drug design to synthesize agents that interact with that site, agents which generally do not bind to site-modified proteins.
Moreover, such drug candidates that affect the activity of a native cancer protein are also identified by screening drugs for the ability to either enhance or reduce the activity of such proteins.
Positive controls and negative controls can be used in the assays. Preferably control and test samples are performed in at least triplicate to obtain statistically significant results.
Incubation of all samples occurs for a time sufficient to allow for the binding of the agent to the protein. Following incubation, samples are washed free of non-specifically bound material and the amount of bound, generally labeled agent determined. For example, where a radiolabel is employed, the samples can be counted in a scintillation counter to determine the amount of bound compound.
A variety of other reagents can be included in the screening assays. These include reagents like salts, neutral proteins, e.g. albumin, detergents, etc. which are used to facilitate optimal protein-protein binding and/or reduce non-specific or background interactions. Also reagents that otherwise improve the efficiency of the assay, such as protease inhibitors, nuclease inhibitors, anti-microbial agents, etc., can be used. The mixture of components is added in an order that provides for the requisite binding.
Use of Polynucleotides to Down-regulate or Inhibit a Protein of the Invention.

Polynucleotide modulators of cancer can be introduced into a cell containing the target nucleotide sequence by formation of a conjugate with a ligand-binding molecule, as described in WO
91/04753. Suitable ligand-binding molecules include, but are not limited to, cell surface receptors, growth factors, other cytokines, or other ligands that bind to cell surface receptors. Preferably, conjugation of the ligand binding molecule does not substantially interfere with the ability of the ligand binding molecule to bind to its corresponding molecule or receptor, or block entry of the sense or antisense oligonucleotide or its conjugated version into the cell. Alternatively, a polynucleotide modulator of cancer can be introduced into a cell containing the target nucleic acid sequence, e.g., by formation of a polynucleotide-lipid complex, as described in WO
90/10448. It is understood that the use of antisense molecules or knock out and knock in models may also be used in screening assays as discussed above, in addition to methods of treatment.
Inhibitory and Antisense Nucleotides In certain embodiments, the activity of a cancer-associated protein is down-regulated, or entirely inhibited, by the use of antisense polynucleotide or inhibitory small nuclear RNA (snRNA), i.e., a nucleic acid complementary to, and which can preferably hybridize specifically to, a coding mRNA nucleic acid sequence, e.g., a cancer protein of the invention, mRNA, or a subsequence thereof. Binding of the antisense polynucleotide to the mRNA
reduces the translation and/or stability of the mRNA.
In the context of this invention, antisense polynucleotides can comprise naturally occurring nucleotides, or synthetic species formed from naturally occurring subunits or their close homologs. Antisense polynucleotides may also have altered sugar moieties or inter-sugar linkages. Exemplary among these are the phosphorothioate and other sulfur containing species which are known for use in the art. Analogs are comprised by this invention so long as they function effectively to hybridize with nucleotides of the invention. See, e.g., Isis Pharmaceuticals, Carlsbad, CA; Sequitor, Inc., Natick, MA.
Such antisense polynucleotides can readily be synthesized using recombinant means, or can be synthesized in vitro. Equipment for such synthesis is sold by several vendors, including Applied Biosystems. The preparation of other oligonucleotides such as phosphorothioates and alkylated derivatives is also well known to those of skill in the art.
Antisense molecules as used herein include antisense or sense oligonucleotides. Sense oligonucleotides can, e.g., be employed to block transcription by binding to the anti-sense strand.
The antisense and sense oligonucleotide comprise a single stranded nucleic acid sequence (either RNA or DNA) capable of binding to target mRNA (sense) or DNA
(antisense) sequences for cancer molecules. Antisense or sense oligonucleotides, according to the present invention, comprise a fragment generally at least about 12 nucleotides, preferably from about 12 to 30 nucleotides. The ability to derive an antisense or a sense oligonucleotide, based upon a cDNA sequence encoding a given protein is described in, e.g., Stein &Cohen (Cancer Res. 48:2659 (1988 and van der Krol et al. (BioTechniques 6:958 (1988)).
Ribozymes In addition to antisense polynucleotides, ribozymes can be used to target and inhibit transcription of cancer-associated nucleotide sequences. A ribozyme is an RNA molecule that catalytically cleaves other RNA molecules. Different kinds of ribozymes have been described, including group I ribozymes, hammerhead ribozymes, hairpin ribozymes, RNase P, and axhead ribozymes (see, e.g., Castanotto et al., Adv. in Pharmacology 25:
289-317 (1994) for a general review of the properties of different ribozymes).
The general features of hairpin ribozymes are described, e.g., in Hampel et al., Nucl. Acids Res. 18:299-304 (1990); European Patent Publication No. 0360257; U.S. Patent No. 5,254,678.
Methods of preparing are well known to those of skill in the art (see, e.g., WO 94/26877; Ojwang et al., Proc. Natl.
Acad. Sci. USA 90:6340-6344 (1993); Yamada et al., Human Gene Therapy 1:39-45 (1994); Leavitt et al., Proc. Natl. Acad Sci.
USA 92:699- 703 (1995); Leavitt et al., Human Gene Therapy 5: 1151-120(1994); and Yamada et al., Virology 205: 121-126 (1994)).
Use of Modulators in Phenotypic Screening In one embodiment, a test compound is administered to a population of cancer cells, which have an associated cancer expression profile. By "administration" or "contacting" herein is meant that the modulator is added to the cells in such a manner as to allow the modulator to act upon the cell, whether by uptake and intracellular action, or by action at the cell surface. In some embodiments, a nucleic acid encoding a proteinaceous agent (i.e., a peptide) is put into a viral construct such as an adenoviral or retroviral construct, and added to the cell, such that expression of the peptide agent is accomplished, e.g., PCT US97/01019. Regulatable gene therapy systems can also be used. Once the modulator has been administered to the cells, the cells are washed if desired and are allowed to incubate under preferably physiological conditions for some period. The cells are then harvested and a new gene expression profile is generated. Thus, e.g., cancer tissue is screened for agents that modulate, e.g., induce or suppress, the cancer phenotype. A change in at least one gene, preferably many, of the expression profile indicates that the agent has an effect on cancer activity. Similarly, altering a biological function or a signaling pathway is indicative of modulator activity. By defining such a signature for the cancer phenotype, screens for new drugs that alter the phenotype are devised.
With this approach, the drug target need not be known and need not be represented in the original gene/protein expression screening platform, nor does the level of transcript for the target protein need to change. The modulator inhibiting function will serve as a surrogate marker As outlined above, screens are done to assess genes or gene products. That is, having identified a particular differentially expressed gene as important in a particular state, screening of modulators of either the expression of the gene or the gene product itself is performed.
Use of Modulators to Affect Peptides of the Invention Measurements of cancer polypeptide activity, or of the cancer phenotype are performed using a variety of assays.
For example, the effects of modulators upon the function of a cancer polypeptide(s) are measured by examining parameters described above. A physiological change that affects activity is used to assess the influence of a test compound on the polypeptides of this invention. When the functional outcomes are determined using intact cells or animals, a variety of effects can be assesses such as, in the case of a cancer associated with solid tumors, tumor growth, tumor metastasis, neovascularization, hormone release, transcriptional changes to both known and uncharacterized genetic markers (e.g., by Northern blots), changes in cell metabolism such as cell growth or pH changes, and changes in intracellular second messengers such as cGNIP.
Methods of Identifying Characterizing Cancer-associated Sequences Expression of various gene sequences is correlated with cancer. Accordingly, disorders based on mutant or variant cancer genes are determined. In one embodiment, the invention provides methods for identifying cells containing variant cancer genes, e.g., determining the presence of, all or part, the sequence of at least one endogenous cancer gene in a cell. This is accomplished using any number of sequencing techniques. The invention comprises methods of identifying the cancer genotype of an individual, e.g., determining all or part of the sequence of at least one gene of the invention in the individual. This is generally done in at least one tissue of the individual, e.g., a tissue set forth in Table I, and may include the evaluation of a number of tissues or different samples of the same tissue.
The method may include comparing the sequence of the sequenced gene to a known cancer gene, i.e., a wild-type gene to determine the presence of family members, homologies, mutations or variants. The sequence of all or part of the gene can then be compared to the sequence of a known cancer gene to determine if any differences exist. This is done using any number of known homology programs, such as BLAST, Bestfit, etc. The presence of a difference in the sequence between the cancer gene of the patient and the known cancer gene correlates with a disease state or a propensity for a disease state, as outlined herein.
In a preferred embodiment, the cancer genes are used as probes to determine the number of copies of the cancer gene in the genome. The cancer genes are used as probes to determine the chromosomal localization of the cancer genes.
Information such as chromosomal localization finds use in providing a diagnosis or prognosis in particular when chromosomal abnormalities such as translocations, and the like are identified in the cancer gene locus.

XIV.) KitslArticles of Manufacture For use in the diagnostic and therapeutic applications described herein, kits are also within the scope of the invention. Such kits can comprise a carrier, package or container that is compartmentalized to receive one or more containers such as vials, tubes, and the like, each of the container(s) comprising one of the separate elements to be used in the method. For example, the container(s) can comprise a probe that is or can be detectably labeled. Such probe can be an antibody or polynucleotide specific for a Figure 2-related protein or a Figure 2 gene or message, respectively. Where the method utilizes nucleic acid hybridization to detect the target nucleic acid, the kit can also have containers containing nucleotide(s) for amplification of the target nucleic acid sequence and/or a container comprising a reporter-means, such as a biotin-binding protein, such as avidin or streptavidin, bound to a reporter molecule, such as an enzymatic, florescent, or radioisotope label. The kit can include all or part of the amino acid sequences in Figure 2 or Figure 3 or analogs thereof, or a nucleic acid molecules that encodes such amino acid sequences.
The kit of the invention will typically comprise the container described above and one or more other containers comprising materials desirable from a commercial and user standpoint, including buffers, diluents, filters, needles, syringes;
carrier, package, container, vial and/or tube labels listing contents and/or instructions for use, and package inserts with instructions for use.
A label can be present on the container to indicate that the composition is used for a specific therapy or non-therapeutic application, such as a diagnostic or laboratory application, and can also indicate directions for either in vivo or in vitro use, such as those described herein. Directions and or other information can also be included on an insert(s) or label(s) which is included with or on the kit The terms "kit" and "article of manufacture" can be used as synonyms.
In another embodiment of the invention, an article(s) of manufacture containing compositions, such as amino acid sequence(s), small molecule(s), nucleic acid sequence(s), and/or antibody(s), e.g., materials useful for the diagnosis, prognosis, prophylaxis and/or treatment of neoplasias of tissues such as those set forth in Table I is provided. The article of manufacture typically comprises at least one container and at least one label.
Suitable containers include, for example, bottles, vials, syringes, and test tubes. The containers can be formed from a variety of materials such as glass or plastic.
The container can hold amino acid sequence(s), small molecule(s), nucleic acid sequence(s), and/or antibody(s), in one embodiment the container holds a polynucleotide for use in examining the mRNA
expression profile of a cell,. together with reagents used for this purpose.
The container can alternatively hold a composition which is effective for treating, diagnosis, prognosing or prophylaxing a condition and can have a sterile access port (for example the container can be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle). The active agents in the composition can be an antibody capable of specifically binding 161P2F1OB and modulating the function of 161P2F10B.
The label can be on or associated with the container. A label a can be on a container when letters, numbers or other characters forming the label are molded or etched into the container itself; a label can be associated with a container when it is present within a receptacle or carrier that also holds the container, e.g., as a package insert. The label can indicate that the composition is used for diagnosing, treating, prophylaxing or prognosing a condition, such as a neoplasia of a tissue set forth in Table I. The article of manufacture can further comprise a second container comprising a pharmaceutically-acceptable buffer, such as phosphate-buffered saline, Ringers solution and/ordextrose solution. It can further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, stirrers, needles, syringes, and/or package inserts with indications and/or instructions for use.

EXAMPLES:
Various aspects of the invention are further described and illustrated by way of the several examples that follow, none of which are intended to limit the scope of the invention.
Example 1: SSH-Generated Isolation of cDNA Fragment of the STEAP Gene To isolate genes that are over-expressed in kidney cancer we used the Suppression Subtractive Hybridization (SSH) procedure using cDNA derived from kidney cancer patient tissues.
The 161P2F1OB SSH cDNA sequence was derived from a subtraction consisting of a kidney cancer minus normal kidney and a mixture of 9 normal tissues: stomach, skeletal muscle, lung, brain, liver, kidney, pancreas, small intestine and heart. By RT-PCR, the 161P2F10B cDNA was identified as highly expressed in kidney cancer pool, with lower expression detected in prostate cancer xenograft pool, prostate cancer pool, colon cancer pool, lung cancer pool, ovary cancer pool, breast cancer pool, metastasis cancer pool, pancreas cancer pool, 2 different prostate cancer metastasis to lymph node, VP1 and VP2. (Figure 14).
The 161P2F1OB SSH cDNA sequence of 182 bp matches the cDNA for phosphodiesterase 1/nucleotide pyrophosphatase 3 (PDNP3). The full-length 161P2F1OB cDNA and ORF are described in Figure 2 with the protein sequence listed in Figure 3.
Materials and Methods RNA Isolation:
Tumor tissues were homogenized in Trizol reagent (Life Technologies, Gibco BRL) using 10 ml/ g tissue or 10 ml/
108 cells to isolate total RNA. Poly A RNA was purified from total RNA using Qiagen's Oligotex mRNA Mini and Midi kits.
Total and mRNA were quantified by spectrophotometric analysis (0.D. 260/280 nm) and analyzed by gel electrophoresis.
Oligonucleotides:
The following HPLC purified oligonudeotides were used.
DPNCDN (cDNA synthesis primer):
5'TTTTGATCAAGCTT3o3' (SEQ ID NO: 29) Adaptor 1:
5'CTAATACGACTCACTATAGGGCTCGAGCGGCCGCCCGGGCAG3' (SEQ ID NO: 30) 3'GGCCCGTCCTAG5' (SEQ ID NO-. 31) Adaptor 2:
5'GTAATACGACTCACTATAGGGCAGCGTGGTCGCGGCCGAG3' (SEQ ID NO: 32) 3'CGGCTCCTAG5' (SEQ ID NO: 33) PCR primer 1:
5'CTAATACGACTCACTATAGGGC3' (SEQ ID NO: 34) Nested primer (NP)1:
5'TCGAGCGGCCGCCCGGGCAGGA3' (SEQ ID NO: 35) Nested primer (NP)2:

5'AGCGTGGTCGCGGCCGAGGA3' (SEQ ID NO: 36) Suppression Subtractive Hybridization:
Suppression Subtractive Hybridization (SSH) was used to identify cDNAs corresponding to genes that may be differentially expressed in prostate cancer. The SSH reaction utilized cDNA
from kidney cancer patient specimens. The gene 161P2F1OB was derived from kidney cancer patient tissues minus normal kidney and a mixture of 9 normal tissues:
stomach, skeletal muscle, lung, brain, liver, kidney, pancreas, small intestine and heart. The SSH DNA sequence (Figure 1) was identified.
The cDNA derived from kidney cancer patient tissues was used as the source of the "driver" cDNA, while the cDNA
from normal tissues was used as the source of the "tester" cDNA. Double stranded cDNAs corresponding to tester and driver cDNAs were synthesized from 2 pg of poly(A) - RNA isolated from the relevant tissue, as described above, using CLONTECH's PCR-Select cDNA Subtraction Kit and 1 ng of oligonucleotide DPNCDN
as primer. First- and second-strand synthesis were carried out as described in the Kit's user manual protocol (CLONTECH Protocol No. PT1117-1, Catalog No.
K1804-1). The resulting cDNA was digested with Dpn II for 3 his at 37 C.
Digested cDNA was extracted with phenol/chloroform (1:1) and ethanol precipitated.
Tester cDNA was generated by diluting 1 I of Dpn II digested cDNA from the relevant tissue source (see above) (400 ng) in 5 I of water. The diluted cDNA (2 I, 160 ng) was then ligated to 2 I of Adaptor 1 and Adaptor 2(10 M), in separate ligation reactions, in a total volume of 10 I at 16 C overnight, using 400 u of T4 DNA ligase (CLONTECH).
Ligation was terminated with 1 I of 0.2 M EDTA and heating at 72 C for 5 min.
The first hybridization was performed by adding 1.5 I (600 ng) of driver cDNA
to each of two tubes containing 1.5 (20 ng) Adaptor 1- and Adaptor 2- ligated tester cDNA. In a final volume of 4 I, the samples were overlaid with mineral oil, denatured in an MJ Research thermal cycler at 98 C for 1.5 minutes, and then were allowed to hybridize for 8 hrs at 68 C. The two hybridizations were then mixed together with an additional 1 jAl of fresh denatured driver cDNA and were allowed to hybridize overnight at 68 C. The second hybridization was then diluted in 200 I of 20 mM Hepes, pH 8.3, 50 mM
NaCI, 0.2 mM EDTA, heated at 70 C for 7 min. and stored at -20 C.
PCR Amplification, Cloning and Sequencing of Gene Fragments Generated from SSH:
To amplify gene fragments resulting from SSH reactions, two PCR amplifications were performed. In the primary PCR reaction 1 1.11 of the diluted final hybridization mix was added to 1 I
of PCR primer 1(10 M), 0.5 I dNTP mix (10 M), 2.5 I 10 x reaction buffer (CLONTECH) and 0.5 1.11 50 x Advantage cDNA
polymerase Mix (CLONTECH) in a final volume of 25 pl. PCR 1 was conducted using the following conditions: 75 C for 5 min., 94 C for 25 sec., then 27 cycles of 94 C for 10 sec, 66 C for 30 sec, 72 C for 1.5 min. Five separate primary PCR
reactions were performed for each experiment. The products were pooled and diluted 1:10 with water. For the secondary PCR reaction, 1 1.11 from the pooled and diluted primary PCR reaction was added to the same reaction mix as used for PCR 1, except that primers NP1 and NP2 (10 M) were used instead of PCR primer 1. PCR 2 was performed using 10-12 cycles of 94 C for 10 sec, 68 C for 30 sec, and 72 C for 1.5 minutes. The PCR products were analyzed using 2% agarose gel electrophoresis.
The PCR products were inserted into pCR2.1 using the T/A vector cloning kit (Invitrogen). Transformed E. coli were subjected to blue/white and ampicillin selection. White colonies were picked and arrayed into 96 well plates and were grown in liquid culture overnight To identify inserts, PCR amplification was performed on 1 ml of bacterial culture using the conditions of PCR1 and NP1 and NP2 as primers. PCR products were analyzed using 2% agarose gel electrophoresis.
Bacterial clones were stored in 20% glycerol in a 96 well format. Plasmid DNA
was prepared, sequenced, and subjected to nucleic acid homology searches of the GenBank, dBest, and NCI-CGAP databases.

R1-PCR Expression Analysis:
First strand cDNAs can be generated from 1 pg of mRNA with oligo (dT)12-18 priming using the Gibco-BRL
SuperscriptTM Preamplification system. The manufacturers protocol was used which included an incubation for 50 mm at 42 C
with reverse transcriptase followed by RNAse H treatment at 37 C for 20 min.
After completing the reaction, the volume can be increased to 200 ul with water prior to normalization. First strand cDNAs from 16 different normal human tissues can be obtained from Clontech.
Normalization of the first strand cDNAs from multiple tissues was performed by using the primers 5`atatcgccgcgctcgtcgtcgacaa3' (SE0 ID NO: 37) and 5'agccacacgcagctcattgtagaagg 3' (SEQ ID NO: 38) to amplify 0-actin.
First strand cDNA (5 pl) were amplified in a total volume of 50 ul containing 0.4 uM primers, 0.2 0M each dNTPs, 1XPCR
buffer (Clontech, 10 mM Tris4ICI, 1.5 mM M9C12, 50 mM KCI, 0.18.3) and 1X
Klentaq DNA polymerase (Clontech). Five ul of the PCR reaction can be removed at 18, 20, and 22 cycles and used for agarose gel electrophoresis. PCR was performed using an MJ Research thermal cycler under the following conditions: initial denaturation can be at 94 C for 15 sec, followed by a 18, 20, and 22 cycles of 94 C for 15,65 C for 2 min, 72 C for 5 sec. A
final extension at 72 C was carried out for 2 min.
After agarose gel electrophoresis, the band intensities of the 283 bp 0-actin bands from multiple tissues were compared by visual inspection. Dilution factors for the first strand cDNAs were calculated to result in equal 0-actin band intensities in all tissues after 22 cycles of PCR. Three rounds of normalization can be required to achieve equal band intensities in all tissues after 22 cycles of PCR.
To determine expression levels of the 161P2F108 gene, 5 el of normalized first strand cDNA were analyzed by PCR using 26, and 30 cycles of amplification. Semi-quantitative expression analysis can be achieved by comparing the PCR
products at cycle numbers that give light band intensities.
A typical RT-PCR expression analysis is shown in Figure 14. RT-PCR expression analysis was performed on first strand cDNAs generated using pools of tissues from multiple samples. The cDNAs were shown to be normalized using beta-actin PCR. Strong expression of 161P2F1OB was observed in kidney cancer pool Expression was also detected in VP1, prostate cancer xenograft pool, prostate cancer pool and colon cancer pool.
Low expression was observed in VP2, lung cancer pool, ovary cancer pool, breast cancer pool, metastasis pool, pancreas cancer pool, and in the 2 different prostate cancer metastasis to lymph node.
Example 2: Isolation of Full Lenoth 161P2F1OB Encoding cONA
To isolate genes that are involved in kidney cancer, an experiment was conducted using kidney cancer patient specimens. The gene 161P2F1OB was derived from a subtraction consisting of kidney cancer specimens, minus normal kidney mixed with a cocktail of 9 normal tissues: stomach, skeletal muscle, lung, brain, liver, kidney, pancreas, small intestine and heart The SSH DNA sequence (Figure 1) was designated 161P2F1013.
cDNA clone 161P2F108 was cloned from kidney cancer specimens (Figure 2 and Figure 3). 161P2F1OB showed homology to the gene ENPP3. The amino acid alignment of 161P2F1OB with ENPP3 is shown in Figure 4 (also, see, e.g., Buhring, et al., Blood 97:3303-3305(2001)).
Example 3: Chromosomal Mapping of 161P2F1OB
Chromosomal localization can implicate genes in disease pathogenesis. Several chromosome mapping approaches are available including fluorescent in situ hybridization (FISH), human/hamster radiation hybrid (RH) panels (Walter at al., 1994; Nature Genetics 7:22; Research Genetics, Huntsville Al), human-rodent somatic cell hybrid panels such as is available from the Corlett Institute (Camden, New Jersey), and genomic viewers utilizing BLAST homologies to sequenced and mapped genomic clones (NCBI, Bethesda, Maryland).

161P2F1OB maps to chromosome 6q22, using 161P2F108 sequence and the NCBI BLAST
tool located at the World Wide Web.
Example 4: Expression Analysis of 161P2F1OB
To compare expression of 161P2F108 in normal versus patient cancer tissues, RT-PCR experiment was performed using normal and patient cancer tissues (Figure 14). First strand cDNA was generated from normal stomach, normal brain, normal heart, normal liver, normal skeletal muscle, normal testis, normal prostate, normal bladder, normal kidney, normal colon, normal lung, normal pancreas, and a pool of cancer specimens from prostate cancer patients, bladder cancer patients, kidney cancer patients, colon cancer patients, lung cancer patients, pancreas cancer patients, a pool of prostate cancer xenografts (LAPC-4AD, LAPC-4A1, LAPC-9AD and LAPC-9AI), and a pool of 2 patient prostate metastasis to lymph node. Normalization was performed by PCR using primers to actin. Semi-quantitative PCR, using primers to 161P2F10B, was performed at 26 and 30 cycles of amplification. Samples were run on an agarose gel, and PCR products were quantitated using the Alphalmager software. Results show strong expression in prostate cancer, bladder cancer, kidney cancer, colon cancer, lung cancer, pancreas cancer, bone cancer, lymphoma cancer, uterus cancer, compared to all normal tissues tested, Strong expression was also detected in the xenograft pool as well as the prostate cancer metastasis to lymph node specimens.
Figure 15 & Table LIX shows expression of 161P2F1OB in a panel of kidney cancer clear cell carcinoma (A), kidney cancer papillary carcinoma (B), and in uterus patient cancer specimens (C). First strand cDNA was prepared from the patient specimens. Normalization was performed by PCR using primers to actin.
Semi-quantitative PCR, using primers to 161P2F108, was performed at 26 and 30 cycles of amplification. Samples were run on an agarose gel, and PCR products were quantitated using the Alphalmager software. Expression was recorded as absent, low, medium or strong. Results show expression of 161P2F1OB in 94.7% of clear cell renal carcinoma, 6Z5% of papillary renal cell carcinoma, and in 61.5%
of uterus cancer.
The restricted expression of 161P2F1OB in normal tissues and the upregulation detected in kidney cancer, in kidney cancer metastasis, as well as in prostate, bladder, colon, lung, pancreas, bone, lymphoma, uterus, breast, and ovary cancers, suggest that 161P2F108 is a potential therapeutic target and a diagnostic marker for human cancers.
Example 5: Transcript Variants of 161P2F1OB
Transcript variants are variants of mature mRNA from the same gene, which arise by alternative transcription or alternative splicing. Alternative transcripts are transcripts from the same gene but start transcription at different points. Splice variants are mRNA variants spliced differently from the same transcript In eukaryotes, when a multi-exon gene is transcribed from genomic DNA, the initial RNA is spliced to produce functional mRNA, which has only exons and is used for translation into an amino acid sequence. Accordingly, a given gene can have zero to many alternative transcripts and each transcript can have zero to many splice variants. Each transcript variant has a unique exon makeup, and can have different coding and/or non-coding (5' or 3' end) portions, from the original transcript Transcript variants can code for similar or different proteins with the same or a similar function or can encode proteins with different functions, and can be expressed in the same tissue at the same time, or in different tissues at the same time, or in the same tissue at different times, or in different tissues at different times. Proteins encoded by transcript variants can have similar or different cellular or extracellular localizations, e.g., secreted versus intracellular.
Transcript variants are identified by a variety of art-accepted methods. For example, alternative transcripts And splice variants are identified by full-length cloning experiment or by use of full-length transcript and EST sequences. First, all human ESTs were grouped into clusters which show direct or indirect identity with each other. Second, ESTs in the same cluster were further grouped into sub-clusters and assembled into a consensus sequence. The original gene sequence is compared to the consensus sequence(s) or other full-length sequences. Each consensus sequence is a potential splice variant for that gene. Even when a variant is identified that is not a full-length clone, that portion of the variant is very useful Ear antigen generation and for further cloning of the full-length splice variant, using techniques known in the art Moreover, computer programs are available in the art that identify transcript variants based on genomic sequences. Genomic-based transcript variant identification programs include FgenesH (A. Salamov and V. Solovyev, "Ab inilio gene finding in Drosophila genomic DNA: Genorne Research. 2000 April;
10(4):516-22); Grail and GenScan For a general discussion of splice variant identification protocols see., e.g., Southan, C., A genomic perspective on human proteases, FEBS Lett.
2001 Jun 8; 498(2-3):214-8; de Souza, S.J., et at, Identification of human chromosome 22 transcribed sequences with ORF
expressed sequence tags, Proc. Nail Acad Sci U S A. 2000 Nov 7; 97(23):12690-3.
To further confirm the parameters of a transcript variant, a variety of techniques are available in the art, such as full-length cloning, proteomic validation, PCR-based validation, and 5' RACE
validation, etc. (see e.g, Proteornic Validation:
Brennan, S.O., etal., Albumin banks peninsula: a new termination variant characterized by electrospray mass spectrometry, Biochem Biophys Acta. 1999 Aug 17;1433(1-2):321-6; Ferranti P. etal., Differential splicing of pre-messenger RNA produces multiple forms of mature caprine alpha(s1)-casein, Eur J Biochem. 1997 Oct 1;249(1):1-7. For PCR-based Validation:
Wellmann S, etal., Specific reverse transcription-PCR quantification of vascular endothelial growth factor (VEGF) splice variants by LightCycler technology, Clin Chem. 2001 Apr;47(4):654-60; Jia, H,P., et al., Discovery of new human beta-defensins using a genomics-based approach, Gene. 2001 Jan 24; 263(1-2):211-8.
For PCR-based and 5' RACE Validation:
Brigle, K.E., etal., Organization of the mudne reduced rotate carrier gene and identification of variant splice forms, Biochem Biophys Ada. 1997 Aug 7; 1353(2): 191-8).
It is known in the art that genomic regions are modulated in cancers. When the genornic region to which a gene maps is modulated in a particular cancer, the alternative transcripts or splice variants of the gene are modulated as well.
Disclosed herein is that 161P2F1OB has a particular expression profile related to cancer. Alternative transcripts and splice variants of 161P2F1013 may also be involved in cancers in the same or different tissues, thus serving as tumor-associated markers/antigens.
Using the full-length gene and EST sequences, two transcript variants were identified, designated as 161P2F1OB
v.6 and v.7. Compared with 161 P2F1OB v.1, transcript variant 161P2F1013 v.6 has extra 40 bases to the 5' starting site of variant 161P2F10E3 v.1 transcript and has a different 3' end portion, which is on the same chromosome as other exons in the current version of human genome. Variant 161P2F108 v.7 inserted 130 bases in between positions 121 and 122 of variant 161P2F10B v.1. Theoretically, each different combination of exons in spatial order, e.g. exons 2 and 3, is a potential splice variant. Due to the incorrect assembly of the chromosome region in the current version of human genome, the transcript structure cannot be derived computationally.
Tables LI through LAI! are set forth on a variant by variant bases. Tables LI
and LV show the nucleotide sequence of the transcript variant. Tables LII and LVI show the alignment of the transcript variant with nucleic acid sequence of 161P2F108 v.l. Tables LIII and LVII lay out amino acid translation of the transcript variant for the identified reading frame orientation. Tables LIV and LVIII display alignments of the amino acid sequence encoded by the splice variant with that of 161P2F1OB v.1.
Example 6: Single Nucleotide Polymorphisms of 161P2F1013 A Single Nucleotide Polymorphism (SNP) is a single base pair variation in a nucleotide sequence at a specific location. At any given point of the genome, there are four possible nucleotide base pairs: AfT, C/G, G/C and T/A. Genotype refers to the specific base pair sequence of one or more locations in the genome of an individual. Haplotype refers to the base pair sequence of more than one location on the same DNA molecule (or the same chromosome in higher organisms), often in the context of one gene or in the context of several tightly linked genes. SNPs that occur on a cDNA are called cSNPs. These cSNPs may change amino acids of the protein encoded by the gene and thus change the functions of the protein. Some SNPs cause inherited diseases; others contribute to quantitative variations in phenotype and reactions to environmental factors including diet and drugs among individuals. Therefore, SNPs and/or combinations of alleles (called haplotypes) have many applications, including diagnosis of inherited diseases, determination of drug reactions and dosage, identification of genes responsible for diseases, and analysis of the genetic relationship between individuals (P. Nowotny, J.
M. Kwon and A. M. Goate, "SNP analysis to dissect human traits," Curr. Opin.
Neurobiol. 2001 Oct; 11(5):637-641; M.
Pirmohamed and B. K. Park, "Genetic susceptibility to adverse drug reactions,"
Trends Pharmacol. Sci. 2001 Jun; 22(6):298-305; J. H. Riley, C. J. Allan, E. Lai and A. Roses, "The use of single nucleotide polymorphisms in the isolation of common disease genes," Pharmacogenomics. 2000 Feb; 1(1):39-47; R. Judson, J. C.
Stephens and A. Windemuth, "The predictive power of haplotypes in clinical response," Pharmacogenomics. 2000 feb; 1(1):15-26).
SNPs are identified by a variety of art-accepted methods (P. Bean, "The promising voyage of SNP target discovery," Am. Clin. Lab. 2001 Oct-Nov; 20(9):18-20; K. M. Weiss, "In search of human variation," Genome Res. 1998 Jul;
8(7):691-697; M. M. She, "Enabling large-scale pharmacogenetic studies by high-throughput mutation detection and genotyping technologies," Clin. Chem. 2001 Feb; 47(2):164-172). For example, SNPs are identified by sequencing DNA
fragments that show polymorphism by gel-based methods such as restriction fragment length polymorphism (RFLP) and denaturing gradient gel electrophoresis (DGGE). They can also be discovered by direct sequencing of DNA samples pooled from different individuals or by comparing sequences from different DNA
samples. With the rapid accumulation of sequence data in public and private databases, one can discover SNPs by comparing sequences using computer programs (Z. Cu, L.
Hillier and P. Y. Kwok, "Single nucleotide polymorphism hunting in cyberspace," Hum. Mutat. 1998; 12(4):221-225). SNPs can be verified and genotype or haplotype of an individual can be determined by a variety of methods including direct sequencing and high throughput microarrays (P. Y. Kwok, "Methods for genotyping single nucleotide polymorphisms," Annu.
Rev. Genomics Hum. Genet. 2001; 2:235-258; M. Kokoris, K. Dix, K. Moynihan, J.
Mathis, B. Erwin, P. Grass, B. Hines and A. Duesterhoeft, "High-throughput SNP genotyping with the Masscode system,"
Mol. Diagn. 2000 Dec; 5(4):329-340).
Using the methods described above, four SNPs were identified in the original transcript, 161P2F1OB v.1, at positions 408 (NC), 2502 (NG), 2663 (NC) and 3233 (NC). The transcripts or proteins with alternative alleles were designated as variants 161P2F1OB v.2, v.3, v.4, and v.5, respectively. Figure 10 shows the schematic alignment of the SNP variants.
Figure 11 shows the schematic alignment of protein variants, corresponding to nucleotide variants. Nucleotide variants that code for the same amino acid sequence as variant 1 are not shown in Figure 11.
These alleles of the SNPs, though shown separately here, can occur in different combination (haplotypes) and in any one of the transcript variants (such as 161P2F1OB v.7) that contains the sequence context of the SNPs.
Example 7: Production of Recombinant 161P2F1OB in Prokaryotic Systems To express recombinant 161P2F1OB in prokaryotic cells, the full or partial length 161P2F1OB cDNA sequences can be cloned into any one of a variety of expression vectors known in the art.
One or more of the following regions of 161P2F1OB are expressed in these contructs, amino acids 1 to 875; or any 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more contiguous amino acids from 161P2F10B, variants, or analogs thereof.
A. In vitro transcription and translation constructs:
pCRII: To generate 161P2F1OB sense and anti-sense RNA probes for RNA in situ investigations, pCRII constructs (lnvitrogen, Carlsbad CA) are generated encoding either all or fragments of the 161P2F1OB cDNA. The pCRII vector has Sp6 and 17 promoters flanking the insert to drive the transcription of 161P2F1OB RNA for use as probes in RNA in situ hybridization experiments. These probes are used to analyze the cell and tissue expression of 161P2F1OB at the RNA level.
Transcribed 161P2F1OB RNA representing the cDNA amino acid coding region of the 161P2F1OB gene is used in in vitro translation systems such as the TnTT^^ Coupled Reticulolysate System (Promega, Corp., Madison, WI) to synthesize 161P2F1OB protein.
B. Bacterial Constructs:
pGEX Constructs: To generate recombinant 161P2F1OB proteins in bacteria that are fused to the Glutathione S-transferase (GST) protein, all or parts of the 161P2F1OB cDNA protein coding sequence are fused to the GST gene by cloning into pGEX-6P-1 or any other GST- fusion vector of the pGEX family (Amersham Pharmacia Biotech, Piscataway, NJ). These constructs allow controlled expression of recombinant 161P2F1OB
protein sequences with GST fused at the amino-terminus and a six histidine epitope (6X His) at the carboxyl-terminus.
The GST and 6X His tags permit purification of the recombinant fusion protein from induced bacteria with the appropriate affinity matrix and allow recognition of the fusion protein with anti-GST and anti-His antibodies. The 6X His tag is generated by adding 6 histidine codons to the cloning primer at the 3' end, e.g., of the open reading frame (ORF). A proteolytic cleavage site, such as the PreScissionTM recognition site in pGEX-6P-1, may be employed such that it permits cleavage of the GST tag from 161P2F10B-related protein. The ampicillin resistance gene and pBR322 origin permits selection and maintenance of the pGEX plasmids in E. co/i.
pMAL Constructs: To generate, in bacteria, recombinant 161P2F1OB proteins that are fused to maltose-binding protein (MBP), all or parts of the 161P2F1OB cDNA protein coding sequence are fused to the MBP gene by cloning into the pMAL-c2X and pMAL-p2X vectors (New England Biolabs, Beverly, MA). These constructs allow controlled expression of recombinant 161P2F1OB protein sequences with MBP fused at the amino-terminus and a 6X His epitope tag at the carboxyl-terminus. The MBP and 6X His tags permit purification of the recombinant protein from induced bacteria with the appropriate affinity matrix and allow recognition of the fusion protein with anti-MBP and anti-His antibodies. The 6X His epitope tag is generated by adding 6 histidine codons to the 3' cloning primer. A Factor Xa recognition site permits cleavage of the pMAL
tag from 161P2F1OB. The pMAL-c2X and pMAL-p2X vectors are optimized to express the recombinant protein in the cytoplasm or periplasm respectively. Periplasm expression enhances folding of proteins with disulfide bonds.
pET Constructs: To express 161P2F1OB in bacterial cells, all or parts of the 161P2F1OB cDNA protein coding sequence are cloned into the pET family of vectors (Novagen, Madison, WI).
These vectors allow tightly controlled expression of recombinant 161P2F1OB protein in bacteria with and without fusion to proteins that enhance solubility, such as NusA and thioredoxin (Trx), and epitope tags, such as 6X His and S-Tag that aid purification and detection of the recombinant protein. For example, constructs are made utilizing pET NusA
fusion system 43.1 such that regions of the 161P2F1OB protein are expressed as amino-terminal fusions to NusA.
C. Yeast Constructs:
pESC Constructs: To express 161P2F1OB in the yeast species Saccharomyces cerevisiae for generation of recombinant protein and functional studies, all or parts of the 161P2F1OB cDNA
protein coding sequence are cloned into the pESC family of vectors each of which contain 1 of 4 selectable markers, HIS3, TRP1, LEU2, and URA3 (Stratagene, La Jolla, CA). These vectors allow controlled expression from the same plasmid of up to 2 different genes or cloned sequences containing either FlagTM or Myc epitope tags in the same yeast cell. This system is useful to confirm protein-protein interactions of 161P2F1OB. In addition, expression in yeast yields similar post-translational modifications, such as glycosylations and phosphorylations, that are found when expressed in eukaryotic cells.
pESP Constructs: To express 161P2F1OB in the yeast species Saccharomyces pombe, all or parts of the 161P2F1OB cDNA protein coding sequence are cloned into the pESP family of vectors. These vectors allow controlled high level of expression of a 161P2F1OB protein sequence that is fused at either the amino terminus or at the carboxyl terminus to GST which aids purification of the recombinant protein. A FlagTM epitope tag allows detection of the recombinant protein with anti- FlagTM antibody.
Example 8: Production of Recombinant 161P2F1OB in Higher Eukaryotic Systems A. Mammalian Constructs:
To express recombinant 161P2F1OB in eukaryotic cells, the full or partial length 161P2F1OB cDNA sequences can be cloned into any one of a variety of expression vectors known in the art.
One or more of the following regions of 161P2F1OB are expressed in these constructs, amino acids 1 to 875; or any 8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,29, 30 or more contiguous amino acids from 161P2F10B, variants, or analogs thereof.
The constructs were transfected into any one of a wide variety of mammalian cells such as 2931 cells or kidney cancer cell lines. Transfected 2931 cell lysates were probed with the anti-161P2F1OB polyclonal serum and monoclonal antibodies, described herein.
pcDNA3.11MycHis Constructs: To express 161P2F1OB in mammalian cells, the 161P2F1OB ORF, or portions thereof, of 161P2F1OB with a consensus Kozak translation initiation site were cloned into pcDNA3.1/MycHis Version A
(Invitrogen, Carlsbad, CA). Protein expression is driven from the cytomegalovirus (CMV) promoter. The recombinant proteins have the myc epitope and 6X His epitope fused to the carboxyl-terminus. The pcDNA3.1/MycHis vector also contains the bovine growth hormone (BGH) polyadenylation signal and transcription termination sequence to enhance mRNA
stability, along with the SV40 origin for episomal replication and simple vector rescue in cell lines expressing the large T
antigen. The Neomycin resistance gene can be used, as it allows for selection of mammalian cells expressing the protein and the ampicillin resistance gene and C0lE1 origin permits selection and maintenance of the plasmid in E. coli.
The pcDNA3.1/mycHis encoding 161P2F1OB was transfected in 2931 cells. Cells were harvested 24 hours later and analyzed showing cell surface expression of 161P2F1OB driven from the pcDNA3.1/mycHis vector (Figure 29).
pTact5: The 161P2F1OB ORF, or portions thereof, of 161P2F1OB were cloned into pTag-5. This vector is similar to pAPtag but without the alkaline phosphatase fusion. This construct generates 161P2F1OB protein with an amino-terminal IgGic signal sequence and myc and 6X His epitope tags at the carboxyl-terminus that facilitate detection and affinity purification. The resulting recombinant 161P2F1OB protein was optimized for secretion into the media of transfected mammalian cells, and was used as immunogen or ligand to identify proteins such as ligands or receptors that interact with the 161P2F1OB proteins. Protein expression is driven from the CMV promoter.
The Zeocin resistance gene present in the vector allows for selection of mammalian cells expressing the protein, and the ampicillin resistance gene permits selection of the plasmid in E. co/i. Figures 31 and 32 show expression and enzymatic activity of the soluble pTag5 expressing 161P2F1OB.
PsecFc: The 161P2F1OB ORF, or portions thereof, of 161P2F1OB were cloned into psecFc. The psecFc vector was assembled by cloning the human immunoglobulin G1 (IgG) Fc (hinge, CH2, CH3 regions) into pSecTag2 (Invitrogen, California). This construct generates an IgG1 Fc fusion at the amino-terminus of the 161P2F1OB proteins. 161P2F1OB
fusions utilizing the murine IgG1 Fc region was also generated and expressed.
The resulting recombinant 161P2F1OB
proteins are optimized for secretion into the media of transfected mammalian cells, and can be used as immunogens or to identify proteins such as ligands or receptors that interact with the 161P2F1OB protein. Protein expression is driven from the CMV promoter. The hygromycin resistance gene present in the vector allows for selection of mammalian cells that express the recombinant protein, and the ampicillin resistance gene permits selection of the plasmid in E. coll.
pSRa Constructs: To generate mammalian cell lines that express 161P2F1OB
constitutively, 161P2F1OB ORF, or portions thereof, of 161P2F1OB are cloned into pSRa constructs. Amphotropic and ecotropic retroviruses were generated by transfection of pSRa constructs into the 293T-10A1 packaging line or co-transfection of pSRa and a helper plasmid (containing deleted packaging sequences) into the 293 cells. The retrovirus is used to infect a variety of mammalian cell lines, resulting in the integration of the cloned gene, 161P2F10B, into the host cell-lines. Protein expression is driven from a long terminal repeat (LTR). The Neomycin resistance gene present in the vector allows for selection of mammalian cells that express the protein, and the ampicillin resistance gene and ColE1 origin permit selection and maintenance of the plasmid in E. coll. The retroviral vectors were thereafter used for infection and generation of various cell lines using, for example, NIH
3T3, 293 Rat-1 cells or kidney cancer cell lines such as Caki and 769 cells.
Figures 16 and 30 show cell surface expression of 161P2F1OB driven from the pSRa construct in Caki and NIH3T3 cells respectively.
Additional pSRa constructs were generated encoding 3 different mutants of 161P2F1OB. The first mutant is D80E, converted the D amino acid residue of the RGD domain at position 80 into E.
The other mutants are mutants of the active site of 161P2F10B, converting the T205 amino acid residue at position 205 into either A (T205A), or S (T205S). The 3 mutant pSRa constructs were transfected into a variety of mammalian cell lines such as 293T cells and CaKi kidney cancer cells. Expression was confirmed using anti-161P2F108 monoclonal antibody and phosphodiesterase enzyme activity was tested (Figure 30).
pcDNA411-lisMax Constructs: To express 161P2F1OB in mammalian cells, the 161P2F1OB ORE, or portions thereof, of 161P2F108 are cloned into pcDNA4/HisMax Version A (lnvitrogen, Carlsbad, CA). Protein expression is driven from the cytomegalovirus (CMV) promoter and the SP16 translational enhancer.
The recombinant protein has XpressTM and six histidine (6X His) epitopes fused to the amino-terminus. The pcDNA4/HisMax vector also contains the bovine growth hormone (BGH) polyadenylation signal and transcription termination sequence to enhance mRNA stability along with the SV40 origin for episomal replication and simple vector rescue in cell lines expressing the large T antigen. The Zeocin resistance gene allows for selection of mammalian cells expressing the protein and the ampicillin resistance gene and ColE1 origin permits selection and maintenance of the plasmid in E. coll.
pcDNA3.11CT-GFP-TOPO Construct: To express 161P2F1OB in mammalian cells and to allow detection of the recombinant proteins using fluorescence, the 161P2F1OB ORF, or portions thereof, of 161P2F1OB with a consensus Kozak translation initiation site are cloned into pcDNA3.1/CT-GFP-TOPO (Invitrogen, CA). Protein expression is driven from the cytomegalovirus (CMV) promoter. The recombinant proteins have the Green Fluorescent Protein (GFP) fused to the carboxyl-terminus facilitating non-invasive, in vivo detection and cell biology studies. The pcDNA3.1/CT-GFP-TOPO vector also contains the bovine growth hormone (BGH) polyadenylation signal and transcription termination sequence to enhance mRNA stability along with the SV40 origin for episomal replication and simple vector rescue in cell lines expressing the large T antigen. The Neomycin resistance gene allows for selection of mammalian cells that express the protein, and the ampicillin resistance gene and ColE1 origin permits selection and maintenance of the plasmid in E. coll. Additional constructs with an amino-terminal GFP fusion are made in pcDNA3.1/NT-GFP-TOPO
spanning the entire length of the 161P2F1OB proteins.
PAPtau: The 161P2F1OB ORE, or portions thereof, of 161P2F1OB are cloned into pAPtag-5 (GenHunter Corp.
Nashville, TN). This construct generates an alkaline phosphatase fusion at the carboxyl-terminus of the 161P2F1OB proteins while fusing the IgGic signal sequence to the amino-terminus. Constructs are also generated in which alkaline phosphatase with an amino-terminal IgGic signal sequence is fused to the amino-terminus of 161P2F1OB proteins. The resulting recombinant 161P2F1OB proteins are optimized for secretion into the media of transfected mammalian cells and can be used to identify proteins such as ligands or receptors that interact with the 161P2F1OB proteins. Protein expression is driven from the CMV promoter and the recombinant proteins also contain myc and 6X His epitopes fused at the carboxyl-terminus that facilitates detection and purification. The Zeocin resistance gene present in the vector allows for selection of mammalian cells expressing the recombinant protein and the ampicillin resistance gene permits selection of the plasmid in E. coll.

Additional Viral Vectors: Additional constructs are made for viral-mediated delivery and expression of 161P2F10B. High virus titer leading to high-level expression of 161P2F1OB is achieved in viral delivery systems such as adenoviral vectors and herpes amplicon vectors. The 161P2F1OB coding sequences or fragments thereof are amplified by PCR and subcloned into the AdEasy shuttle vector (Stratagene). Recombination and virus packaging are performed according to the manufacturer's instructions to generate adenoviral vectors.
Alternatively, 161P2F1OB coding sequences or fragments thereof are cloned into the HSV-1 vector (Imgenex) to generate herpes viral vectors. The viral vectors are thereafter used for infection of various cell lines such as PC3, NIH 313, 293 or rat-1 cells.
Regulated Expression Systems: To control expression of 161P2F1OB in mammalian cells, coding sequences of 161P2F10B, or portions thereof, are cloned into regulated mammalian expression systems such as the 1-Rex System (lnvitrogen), the GeneSwitch System (Invitrogen) and the tightly-regulated Ecdysone System (Sratagene). These systems allow the study of the temporal and concentration dependent effects of recombinant 161P2F10B. These vectors are thereafter used to control expression of 161P2F1OB in various cell lines such as PC3, NIH 373, 293 or rat-1 cells.
B. Baculovirus Expression Systems To generate recombinant 161P2F1OB proteins in a Baculovirus expression system, 161P2F1OB ORF, or portions thereof, are cloned into the Baculovirus transfer vector pBlueBac 4.5 (lnvitrogen), which provides a His-tag at the N-terminus.
Specifically, pBlueBac-161P2F1OB is co-transfected with helper plasmid pBac-N-Blue (lnvitrogen) into SF9 (Spodoptera frugiperda) insect cells to generate recombinant Baculovirus (see Invitrogen instruction manual for details). Baculovirus is then collected from cell supernatant and purified by plaque assay.
Recombinant 161P2F1OB protein is then generated by infection of HighFive insect cells (Invitrogen) with purified Baculovirus. Recombinant 161P2F1OB protein can be detected using anti-161P2F1OB or anti-His-tag antibody. 161P2F1OB
protein can be purified and used in various cell-based assays or as immunogen to generate polyclonal and monoclonal antibodies specific for 161P2F10B.
Example 9: AnticieniciV Profiles and Secondary Structure Figure 5, Figure 6, Figure 7, Figure 8, and Figure 9 depict graphically five amino acid profiles of the 161P2F1OB
amino acid sequence, each assessment available by accessing the ProtScale website located on the World Wide Web at (.expasy.ch/cgi-bin/protscale.p1) on the ExPasy molecular biology server.
These profiles: Figure 5, Hydrophilicity, (Hopp T.P., Woods K.R., 1981. Proc.
Natl. Acad. Sci. U.S.A. 78:3824-3828); Figure 6, Hydropathicity, (Kyte J., Doolittle R.F., 1982. J. Mol. Biol.
157:105-132); Figure 7, Percentage Accessible Residues (Janin J., 1979 Nature 277:491-492); Figure 8, Average Flexibility, (Bhaskaran R., and Ponnuswamy P.K., 1988.
Int. J. Pept. Protein Res. 32:242-255); Figure 9, Beta-turn (Deleage, G., Roux B. 1987 Protein Engineering 1:289-294); and optionally others available in the art, such as on the ProtScale website, were used to identify antigenic regions of the 161P2F1OB protein. Each of the above amino acid profiles of 161P2F1OB were generated using the following ProtScale parameters for analysis: 1) A window size of 9; 2) 100% weight of the window edges compared to the window center; and, 3) amino acid profile values normalized to lie between 0 and 1.
Hydrophilicity (Figure 5), Hydropathicity (Figure 6) and Percentage Accessible Residues (Figure 7) profiles were used to determine stretches of hydrophilic amino acids (i.e., values greater than 0.5 on the Hydrophilicity and Percentage Accessible Residues profile, and values less than 0.5 on the Hydropathicity profile). Such regions are likely to be exposed to the aqueous environment, be present on the surface of the protein, and thus available for immune recognition, such as by antibodies.
Average Flexibility (Figure 8) and Beta-turn (Figure 9) profiles determine stretches of amino acids (i.e., values greater than 0.5 on the Beta-turn profile and the Average Flexibility profile) that are not constrained in secondary structures such as beta sheets and alpha helices. Such regions are also more likely to be exposed on the protein and thus accessible to immune recognition, such as by antibodies.
Antigenic sequences of the 161P2F1OB protein indicated, e.g., by the profiles set forth in Figure 5, Figure 6, Figure 7, Figure 8, and/or Figure 9 are used to prepare immunogens, either peptides or nucleic acids that encode them, to generate therapeutic and diagnostic anti-161P2F1OB antibodies. The immunogen can be any 5, 6, 7, 8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50 or more than 50 contiguous amino acids, or the corresponding nucleic acids that encode them, from the 161P2F1013 protein. In particular, peptide immunogens of the invention can comprise, a peptide region of at least 5 amino acids of Figure 2 in any whole number increment up to 875 that includes an amino acid position having a value greater than 0.5 in the Hydrophilicity profile of Figure 5; a peptide region of at least 5 amino acids of Figure 2 in any whole number increment up to 875 that includes an amino acid position having a value less than 0.5 in the Hydropathicity profile of Figure 6; a peptide region of at least 5 amino acids of Figure 2 in any whole number increment up to 875 that includes an amino acid position having a value greater than 0.5 in the Percent Accessible Residues profile of Figure 7; a peptide region of at least 5 amino acids of Figure 2 in any whole number increment up to 875 that includes an amino acid position having a value greater than 0.5 in the Average Flexibility profile on Figure 8; and, a peptide region of at least 5 amino acids of Figure 2 in any whole number increment up to 875 that includes an amino acid position having a value greater than 0.5 in the Beta-turn profile of Figure 9. Peptide immunogens of the invention can also comprise nucleic acids that encode any of the forgoing.
All immunogens of the invention, peptide or nucleic acid, can be embodied in human unit dose form, or comprised by a composition that includes a pharmaceutical excipient compatible with human physiology.
The secondary structure of 161P2F10B, namely the predicted presence and location of alpha helices, extended strands, and random coils, is predicted from the primary amino acid sequence using the HNN -Hierarchical Neural Network method (Guermeur, 1997) accessed from the ExPasy molecular biology server The analysis indicates that 161P2F1013 is composed 31.31% alpha helix, 11.31% extended strand, and 57.37% random coil (Figure 19A).
Analysis for the potential presence of transmembrane domains in 161P2F1OB was carried out using a variety of transmembrane prediction algorithms accessed from the ExPasy molecular biology server The programs predict the presence oil transmembrane domain in 161P2F108, consistent with that of a Type II cell surface protein. Shown graphically in Figure 19 are the results of analysis using the TMpred (Figure 19B) and TMHMM (Figure 19C) prediction programs depicting the location of the transmembrane domain.
Example 10: Generation of 161P2F1OB Polyclonal Antibodies Polyclonal antibodies can be raised in a mammal, for example, by one or more injections of an immunizing agent and, if desired, an adjuvant. Typically, the immunizing agent and/or adjuvant will be injected in the mammal by multiple subcutaneous or intrapentoneal injections. In addition to immunizing with the full length 161P2F1OB protein, computer algorithms are employed in design of immunogens that, based on amino acid sequence analysis contain characteristics of being antigenic and available for recognition by the immune system of the immunized host (see the Example entitled "Antigenicity Profiles"). Such regions would be predicted to be hydrophilic, flexible, in beta-turn conformations, and be exposed on the surface of the protein (see, e.g., Figure 5, Figure 6, Figure 7, Figure 8, or Figure 9 for amino acid profiles that indicate such regions of 161P2F10B).
For example, 161P2F1OB recombinant bacterial fusion proteins or peptides containing hydrophilic, flexible, beta-turn regions of the 161P2F10B, in which numerous regions are found in the predicted extraceflular domain coded by amino acids 45-870, are used as antigens to generate polyclonal antibodies in New Zealand White rabbits. For example, such regions include, but are not limited to, amino acids 43-93, 100-134, 211-246,467-492, 500-517, and amino acids 810-870. In addition, recombinant proteins are made that encode the whole extracellular domain, amino acids 45-870, or halves of the domain, such as amino acids 45-450 and amino acids 451-870. Antigens are also created encoding the Somatomedin-B-like domain (amino acids 53-133), the catalytic domain (amino acids 158-538), and the nuclease like domain (amino acids 609-875) of 161P2F1OB (Bogen et. al., 2000. Grit. Rev. Biochem. Mot. Biol., 35: 393-432), in order to generate antibodies specific to these regions. Ideally antibodies are raised to non-conserved regions of these domains such that they do not crossreact with other homologous nucleotide pyrophosphatases/phosphodiesterases. It is useful to conjugate the immunizing agent to a protein known to be immunogenic in the mammal being immunized. Examples of such immunogenic proteins include, but are not limited to, keyhole limpet hemocyanin (KLH), serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor. In one embodiment, a peptide encoding amino acids 500-517 of 161P2F108 is conjugated to KLH and used to immunize the rabbit. Alternatively the immunizing agent may include altar portions of the 161P2F1OB protein, analogs or fusion proteins thereof. For example, the 161P2F1013 amino acid sequence can be fused using recombinant DNA
techniques to any one of a variety of fusion protein partners that are well known in the art, such as glutalhione-S-transferase (GST) and HIS tagged fusion proteins. Such fusion proteins are purified from induced bacteria using the appropriate affinity matrix.
In one embodiment, a GST-fusion protein encoding amino acids 45-875 is produced and purified and used as immunogen. Other recombinant bacterial fusion proteins that may be employed include maltose binding protein, LacZ, thioredoxin, NusA, or an immunoglobulin constant region (see the section entitled "Production of 161P2F1OB in Prokaryotic Systems" and Current Protocols In Molecular Biology, Volume 2, Unit 16, Frederick M. Ausubul et at. eds., 1995; Linsley, P.S., Brady, W., limes, M., Grosmaire, L., Damle, N., and Ledbetter, L.(1991) J.Exp. Med. 174, 561-566).
In addition to bacterial derived fusion proteins, mammalian expressed protein antigens are also used. These antigens are expressed from mammalian expression vectors such as the Tag5 and Fc-fusion vectors (see the section entitled "Production of Recombinant 161P2F1OB in Eukaryotic Systems"), and retain post-translational modifications such as glycosylations found in native protein. in one embodiment, amino acids 45-875 is cloned into the Tag5 mammalian secretion vector. The recombinant protein is purified by metal chelate chromatography from tissue culture supernatants of 2931 cells stably expressing the recombinant vector. The purified Tag5 161P2F1OB protein is then used as immunogen.
During the immunization protocol, it is useful to mix or emulsify the antigen in adjuvants that enhance the immune response of the host animal. Examples of adjuvants include, but are not limited to, complete Freund's adjuvant (CFA) and MPL-TDM adjuvant (monophosphoryl Lipid A, synthetic trehalose dicorynomycolate).
In a typical protocol, rabbits are initially immunized subcutaneously with up to 200 pg, typically 100-200 pg, of fusion protein or peptide conjugated to KLH mixed in complete Freund's adjuvant (CFA). Rabbits are then injected subcutaneously every two weeks with up to 200 pg, typically 100-200 p.g, of the immunogen in incomplete Freund's adjuvant (IFA). Test bleeds are taken approximately 7-10 days following each immunization and used to monitor the titer of the antiserum by ELISA.
To test reactivity and specificity of immune serum, such as the rabbit serum derived from immunization with Tag5 161P2F1OB encoding amino acids 58-538, the full-length 161P2F1OB cDNA is cloned into pCDNA 3.1 myc-his expression vector (lnvitrogen, see the Example entitled "Production of Recombinant 161P2F1OB in Eukaryotic Systems"). After transfection of the constructs into 293T cells, cell lysates are probed with the anti-161P2F108 serum and with anti-His antibody (Santa Cruz Biotechnologies, Santa Cruz, CA) to determine specific reactivity to denatured 161P2F108 protein using the Western blot technique. Immunoprecipitation and flow cytometric analyses of 2931 and other recombinant 161P2F106-expressing cells determine recognition of native protein by the antiserum. In addition, Western blot, immunoprecipitation, fluorescent microscopy, and flow cytometric techniques using cells that endogenously express 161P2F106 are carried out to test specificity.
The anti-serum from the Tag5 161P2F1OB immunized rabbit is affinity purified by passage over a column composed of the Tag5 antigen covalentiy coupled to Affigel matrix (BioRad, Hercules, Calif.). The serum is then further purified by protein G affinity chromatography to isolate the IgG fraction. Serum from rabbits immunized with fusion proteins, such as GST
and MBP fusion proteins, are purified by depletion of antibodies reactive to the fusion partner sequence by passage over an affinity column containing the fusion partner either alone or in the context of an irrelevant fusion protein. Sera from other His-tagged antigens and peptide immunized rabbits as well as fusion partner depleted sera are affinity purified by passage over a column matrix composed of the original protein immunogen or free peptide.
Example 11: Generation of 161P2F1OB Monoclonal Antibodies (mAbs) The use of agents to identify the presence of 161P2F1OB in biopsy specimens or to neutralize the effect of 161P2F10B has a beneficial effect in diagnosis, prognosis, prophylaxis and/or therapy. One particularly useful class of anti 161P2F1OB agents is antibodies, in particular monoclonal antibodies (Mabs) to 161P2F10B. Anti 161P2F1OB Abs, such as Mabs, are generated that react with the epitopes of the 161P2F1OB protein such that they either indicate it's presence, disrupt or modulate it's biological function (for example those that would disrupt the interaction with ligands or proteins that mediate or are involved in it's biological activity) or are able to carry a toxin to the cell which is expressing 161P2F10B.
The term anti 161P2F106 antibody as used herein is to be understood to cover antibodies to any epitope of the 161P2F1OB gene product. Diagnostic Mabs, e.g. those used for imaging or immunocytochemistry, comprise those that specifically bind epitopes of 161P2F106 protein and thus demonstrate its presence. Therapeutic Mabs include those that are useful for diagnosis but also comprise those that specifically bind epitopes of 161P2F1OB exposed on the cell surface and thus are useful to modulate growth and survival of cells expressing 161P2F1OB by disrupting the function of a cell expressing 161P2F1OB and/or disrupting the interaction of cells expressing 161P2F1OB and the ligand for 161P2F10B.
Preferred antibodies which form one aspect of the invention include but are not limited to antibodies entitled X41(4)6, X41(3)17, X41(3)50, X41(3)15, X41(3)29 and X41(3)37 secreted by a hybridoma deposited with the American Type Culture Collection (ATCC; 10801 University Blvd., Manassas, VA 20110-2209 USA) on 07 November 2002 and assigned as Accession No's. PTA-4794, PTA-4792, PTA-4793, PTA-4791, PTA-4791, and PTA-4791, respectively; and derivatives thereof, the production of which is described herein.
Pathological conditions which are characterized by the presence of 161P2F106 expression include, but are not restricted to, neoplasms of tissues such as those listed in Table I. One aspect of the invention provides a method of detecting the presence of 161P2F108. A further aspect of the invention provides a method of treatment of conditions characterized by the presence of 161P2F10B, comprising administering an effective amount of an anti 161P2F1OB antibody. The administration of anti-161P2F1OB antibody is particularly advantageous in the treatment of conditions characterized by the presence of 161P2F10B.
The antibodies against 161P2F1OB for use according to the invention can be from any species, and can belong to any immunoglobulin class. Thus, for example, the anti 161P2F1OB antibody for use according to the invention can be an immunoglobulin G (IgG), Immunoglobulin M (IgM), immunoglobulin A (IgA), Immunoglobulin E (IgE) or immunoglobulin D
(IgD).
The anti 161P2F1OB antibody can be from an animal, for example mammaliam or avian origin, and can be for example of murine, rat or human origin. The antibody can be a whole immunoglobulin, or a fragment thereof, for example a fragment derived by proteolytic cleavage of a whole antibody, such as F(a13')2, Fab' or Fab fragments or fragments obtained by recombinant DNA techniques, for example Fv fragments.

Particularly useful antibodies for use according to the invention include humanized or fully human anti 161P2F1OB
antibodies and fragments thereof. These antibodies are produced by any suitable procedure including, but not restricted to, mammalian cell and bacterial cell fermentation systems.
The anti 161P2F1OB Mabs are prepared by immunological techniques employing 161P2F1OB antigens. Thus, for example, any suitable host can be injected (immunized) with a suitable reagent which makes 161P2F1OB available as an immunogen. Examples of reagents which make 161P2F1OB available as an immunogen are purified protein (e.g. the whole extra-cellular domain (ecd) or fragments there of), peptides designed using the full length protein as a template (e.g peptides encompass ing the catalytic domain), DNA vectors encoding all or truncated fragments of the ecd, recombinant cells expressing 161P2F1OB (e.g. Rat-1, Mouse 3T3, Mouse 300.19, and mouse NSO), Cell lines with endogenous 161P2F1OB
expression (e.g. human UT-7) or xenografts (i.e. patient derived clear cell and papillary xenografts).
Immune cells , for example splenocytes or lymphocytes, are recovered from the immunized host and immortalized, using for example the method of Kohler et al, Eur. J. Immunol 6, 511 (1976), or their immunoglobulin genes can be isolated and transferred to an appropriate DNA vector for expression in an appropriate cell type. The resulting cells, generated by either technique, will be selected to obtain a single genetic line producing a single unique type of antibody more commonly known as a monoclonal antibody. Antibody fragments can be produced using techniques such as enzymatic digestion of whole antibodies e.g. with pepsin (Parham, J. Immunol 131:2895 (1983)) or papain (Lamoyi and Nisonoff, J. Immunol Meth. 56:235(1983)), or by recombinant DNA techniques.
Suitable hosts for the production of Mab's to 161P2F1OB include mice, rats, hamsters and rabbits. For example, mice are immunized with a number of different reagents which make 161P2F1OB
available as a source of antigenic material (immunogen). The route and timing if the immunizations will depend on the source and/or embodiment of the immunogen.
Sources of immunogen for 161P2F1OB include, but are not restricted to, peptide, protein, fusion protein, DNA, RNA, cells or cell membranes as detailed above.. These can be used separately as immunogens or in combination to produce a specific immune reaction to 161P2F1OB. The use and application of these various immunogens is described fully in the accompanying examples.
Example 12: HLA Class I and Class II Binding Assays HLA class I and class ll binding assays using purified HLA molecules are performed in accordance with disclosed protocols (e.g., PCT publications WO 94/20127 and WO 94/03205; Sidney et al., Current Protocols in Immunology 18.3.1 (1998); Sidney, et al., J. Immunol. 154:247 (1995); Sette, et al., Mol.
Immunol. 31:813 (1994)). Briefly, purified MHC
molecules (5 to 500 nM) are incubated with various unlabeled peptide inhibitors and 1-10 nM 125I-radiolabeled probe peptides as described. Following incubation, MHC-peptide complexes are separated from free peptide by gel filtration and the fraction of peptide bound is determined. Typically, in preliminary experiments, each MHC preparation is titered in the presence of fixed amounts of radiolabeled peptides to determine the concentration of HLA
molecules necessary to bind 10-20% of the total radioactivity. All subsequent inhibition and direct binding assays are performed using these HLA concentrations.
Since under these conditions [labeINHLA] and 1C5o[HL.A1 the measured ICso values are reasonable approximations of the true Ke values. Peptide inhibitors are typically tested at concentrations ranging from 120 pg/m1 to 1.2 ng/ml, and are tested in two to four completely independent experiments. To allow comparison of the data obtained in different experiments, a relative binding figure is calculated for each peptide by dividing the ICso of a positive control for inhibition by the ICso for each tested peptide (typically unlabeled versions of the radiolabeled probe peptide). For database purposes, and inter-experiment comparisons, relative binding values are compiled. These values can subsequently be converted back into ICso nM values by dividing the ICso nM of the positive controls for inhibition by the relative binding of the peptide of interest. This method of data compilation is accurate and consistent for comparing peptides that have been tested on different days, or with different lots of purified MHC.
Binding assays as outlined above may be used to analyze HLA supermotif and/or HLA motif-bearing peptides (see Table IV).
Example 13: Identification of HLA Supermotif- and Motif-Bearinq CTL Candidate Epitopes HLA vaccine compositions of the invention can include multiple epitopes. The multiple epitopes can comprise multiple HLA supermotifs or motifs to achieve broad population coverage. This example illustrates the identification and confirmation of supermotif- and motif-bearing epitopes for the inclusion in such a vaccine composition. Calculation of population coverage is performed using the strategy described below.
Computer searches and algorithms for identification of supermotif and/or motif-bearing epitopes The searches performed to identify the motif-bearing peptide sequences in the Example entitled "Antigenicity Profiles' and Tables VIII-XXI and XXII-XLIX employ the protein sequence data from the gene product of 161P2F1OB set forth in Figures 2 and 3, the specific search peptides used to generate the tables are listed in Table VII.
Computer searches for epitopes bearing HLA Class I or Class II supermotifs or motifs are performed as follows. All translated 161P2F1OB protein sequences are analyzed using a text string search software program to identify potential peptide sequences containing appropriate HLA binding motifs; such programs are readily produced in accordance with information in the art in view of known motif/supermotif disclosures.
Furthermore, such calculations can be made mentally.
Identified A2-, A3-, and DR-supermotif sequences are scored using polynomial algorithms to predict their capacity to bind to specific HLA-Class I or Class II molecules. These polynomial algorithms account for the impact of different amino acids at different positions, and are essentially based on the premise that the overall affinity (or AG) of peptide-HLA molecule interactions can be approximated as a linear polynomial function of the type:
"AG" = aii x azi x a3; ........ x an;
where ar is a coefficient which represents the effect of the presence of a given amino acid (j) at a given position (i) along the sequence of a peptide of n amino acids. The crucial assumption of this method is that the effects at each position are essentially independent of each other (i.e., independent binding of individual side-chains). When residue j occurs at position i in the peptide, it is assumed to contribute a constant amount ji to the free energy of binding of the peptide irrespective of the sequence of the rest of the peptide.
The method of derivation of specific algorithm coefficients has been described in Gulukota et al., J. Mol. BioL
267:1258-126, 1997; (see also Sidney etal., Human Immunol. 45:79-93, 1996; and Southwood etal., J. Immunol. 160:3363-3373, 1998). Briefly, for all i positions, anchor and non-anchor alike, the geometric mean of the average relative binding (ARB) of all peptides carrying j is calculated relative to the remainder of the group, and used as the estimate of ji. For Class II peptides, if multiple alignments are possible, only the highest scoring alignment is utilized, following an iterative procedure.
To calculate an algorithm score of a given peptide in a test set, the ARB
values corresponding to the sequence of the peptide are multiplied. If this product exceeds a chosen threshold, the peptide is predicted to bind. Appropriate thresholds are chosen as a function of the degree of stringency of prediction desired.
Selection of HLA-A2 supertype cross-reactive peptides Protein sequences from 161P2F1OB are scanned utilizing motif identification software, to identify 8-, 9- 10- and 11-mer sequences containing the HLA-A2-supermotif main anchor specificity.
Typically, these sequences are then scored using the protocol described above and the peptides corresponding to the positive-scoring sequences are synthesized and tested for their capacity to bind purified HLA-A*0201 molecules in vitro (HLA-A*0201 is considered a prototype A2 supertype molecule).
These peptides are then tested for the capacity to bind to additional A2-supertype molecules (A*0202, A*0203, A*0206, and A*6802). Peptides that bind to at least three of the five A2-supertype alleles tested are typically deemed A2-supertype cross-reactive binders. Preferred peptides bind at an affinity equal to or less than 500 nM to three or more HLA-A2 supertype molecules.
Selection of HLA-A3 supermotif-bearing epitopes The 161P2F1OB protein sequence(s) scanned above is also examined for the presence of peptides with the HLA-A3-supermotif primary anchors. Peptides corresponding to the HLA A3 supermotif-bearing sequences are then synthesized and tested for binding to HLA-A*0301 and HLA-A*1101 molecules, the molecules encoded by the two most prevalent A3-supertype alleles. The peptides that bind at least one of the two alleles with binding affinities of ..500 nM, often 200 nM, are then tested for binding cross-reactivity to the other common A3-supertype alleles (e.g., A*3101, A*3301, and A*6801) to identify those that can bind at least three of the five HLA-A3-supertype molecules tested.
Selection of HLA-B7 supermotif bearing epitopes The 161P2F1OB protein(s) scanned above is also analyzed for the presence of 8-, 9- 10-, or 11-mer peptides with the HLA-B7-supermotif. Corresponding peptides are synthesized and tested for binding to HLA-B*0702, the molecule encoded by the most common B7-supertype allele (i.e., the prototype 87 supertype allele). Peptides binding B*0702 with IC50 of .500 nM are identified using standard methods. These peptides are then tested for binding to other common B7-supertype molecules (e.g., 8*3501, B*5101, B*5301, and 8*5401). Peptides capable of binding to three or more of the five B7-supertype alleles tested are thereby identified.
Selection of Al and A24 motif-bearing epitopes To further increase population coverage, HLA-A1 and -A24 epitopes can also be incorporated into vaccine compositions. An analysis of the 161P2F1OB protein can also be performed to identify HLA-Al- and A24-motif-containing sequences.
High affinity and/or cross-reactive binding epitopes that bear other motif and/or supermotifs are identified using analogous methodology.
Example 14: Confirmation of Immunogenicity Cross-reactive candidate CTL A2-supermotif-bearing peptides that are identified as described herein are selected to confirm in vitro immunogenicity. Confirmation is performed using the following methodology:
Target Cell Lines for Cellular Screening:
The .221A2.1 cell line, produced by transferring the HLA-A2.1 gene into the HLA-A, -B, -C null mutant human B-Iymphoblastoid cell line 721.221, is used as the peptide-loaded target to measure activity of HLA-A2.1-restricted CTL. This cell line is grown in RPMI-1640 medium supplemented with antibiotics, sodium pyruvate, nonessential amino acids and 10%
(v/v) heat inactivated FCS. Cells that express an antigen of interest, or transfectants comprising the gene encoding the antigen of interest, can be used as target cells to confirm the ability of peptide-specific CTLs to recognize endogenous antigen.
Primary CTL Induction Cultures:

Generation of Dendlitic Cells (DC): PBMCs are thawed in RPM' with 30 g/m1 DNAse, washed twice and resuspended in complete medium (RPMI-1640 plus 5% AB human serum, non-essential amino acids, sodium pyruvate, L-glutamine and penicillin/streptomycin). The monocytes are purified by plating 10 x 106 PBMC/well in a 6-well plate. After 2 hours at 37 C, the non-adherent cells are removed by gently shaking the plates and aspirating the supernatants. The wells are washed a total of three times with 3 ml RPMI to remove most of the non-adherent and loosely adherent cells. Three ml of complete medium containing 50 ng/ml of GM-CSF and 1,000 Wm! of IL-4 are then added to each well. TNFa is added to the DCs on day 6 at 75 ng/ml and the cells are used for CTL induction cultures on day 7.
Induction of CTL with DC and Peptide: CD8+ T-cells are isolated by positive selection with Dynal immunomagnetic beads (Dynabeads@ M-450) and the detacha-bead reagent. Typically about 200-250x106 PBMC are processed to obtain 24x106 CD8 T-cells (enough for a 48-well plate culture). Briefly, the PBMCs are thawed in RPMI with 30pg/m1 DNAse, washed once with PBS containing 1% human AB serum and resuspended in PBS/1% AB
serum at a concentration of 20x106cells/ml. The magnetic beads are washed 3 times with PBS/AB serum, added to the cells (140p1 beads/20x106 cells) and incubated for 1 hour at 4 C with continuous mixing. The beads and cells are washed 4x with PBS/AB serum to remove the nonadherent cells and resuspended at 100x106 cells/ml (based on the original cell number) in PBS/AB serum containing 100p1/m1 detacha-bead reagent and 30 pg/ml DNAse. The mixture is incubated for 1 hour at room temperature with continuous mixing. The beads are washed again with PBS/AB/DNAse to collect the CD8+ T-cells. The DC are collected and centrifuged at 1300 rpm for 5-7 minutes, washed once with PBS with 1% BSA, counted and pulsed with 40pg/m1 of peptide at a cell concentration of 1-2x106/m1 in the presence of 3pg/m1112-microglobulin for 4 hours at 20 C. The DC are then irradiated (4,200 rads), washed 1 time with medium and counted again.
Setting up induction cultures: 0.25 ml cytokine-generated DC (at 1x105 cells/ml) are co-cultured with 0.25m1 of CD8+ T-cells (at 2x106 cell/mil) in each well of a 48-well plate in the presence of 10 ng/ml of IL-7. Recombinant human IL-10 is added the next day at a final concentration of 10 ng/ml and rhuman IL-2 is added 48 hours later at 10 Restimulation of the induction cultures with peptide-pulsed adherent cells:
Seven and fourteen days after the primary induction, the cells are restimulated with peptide-pulsed adherent cells. The PBMCs are thawed and washed twice with RPMI and DNAse. The cells are resuspended at 5x106 cells/ml and irradiated at ¨4200 rads. The PBMCs are plated at 2x106 in 0.5 ml complete medium per well and incubated for 2 hours at 37 C.
The plates are washed twice with RPM! by tapping the plate gently to remove the nonadherent cells and the adherent cells pulsed with 10pg/m1 of peptide in the presence of 3 pg/ml l2 microglobulin in 0.25m1 RPMI/5%AB per well for 2 hours at 37 C. Peptide solution from each well is aspirated and the wells are washed once with RPMI. Most of the media is aspirated from the induction cultures (CD8+ cells) and brought to 0.5 ml with fresh media. The cells are then transferred to the wells containing the peptide-pulsed adherent cells. Twenty four hours later recombinant human IL-10 is added at a final concentration of 10 ng/ml and recombinant human IL2 is added the next day and again 2-3 days later at 501U/m1 (Tsai et al., Critical Reviews in Immunology 18(1-2):65-75, 1998). Seven days later, the cultures are assayed for CTL
activity in a 51Cr release assay. In some experiments the cultures are assayed for peptide-specific recognition in the in situ IFNy ELISA at the time of the second restimulation followed by assay of endogenous recognition 7 days later. After expansion, activity is measured in both assays for a side-by-side comparison.
Measurement of CTL lvtic activity by 51Cr release.
Seven days after the second restimulation, cytotoxicity is determined in a standard (5 hr) 51Cr release assay by assaying individual wells at a single E:T. Peptide-pulsed targets are prepared by incubating the cells with 10pg/nnl peptide overnight at 37 C.
Adherent target cells are removed from culture flasks with trypsin-EDTA.
Target cells are labeled with 200pCi of 5ICr sodium chromate (Dupont, Wilmington, DE) for 1 hour at 37 C. Labeled target cells are resuspended at 106 per ml and diluted 1:10 with K562 cells at a concentration of 3.3x106/m1 (an NK-sensitive erythroblasloma cell line used to reduce non-specific lysis). Target cells (100 pl) and effectors (100p1) are plated in 96 well round-bottom plates and incubated for 5 hours at 37 C. At that time, 100 pl of supernatant are collected from each well and percent lysis is determined according to the formula:
((cpm of the test sample- cpm of the spontaneous 5ICr release sample)/(cpm of the maximal 5ICr release sample-cpm of the spontaneous 5ICr release sample)) x 100.
Maximum and spontaneous release are determined by incubating the labeled targets with 1% Triton X-1001m and media alone, respectively. A positive culture is defined as one in which the specific lysis (sample- background) is 10% or higher in the case of individual wells and is 15% or more at the two highest E:T ratios when expanded cultures are assayed.
in situ Measurement of Human IENy Production as an Indicator of Peptide-specific and Endogenous Recognition Immulon 2 plates are coated with mouse anti-human IFNy monoclonal antibody (4 pg/m1 0,1M NaHCO3, pH8.2) overnight at 4 C. The plates are washed with Cal*, Mg2+-free P88/0.05% Tween 20 and blocked with PBS/10% FCS for two hours, after which the CTLs (100 pl/well) and targets (100 pl/well) are added to each well, leaving empty wells for the standards and blanks (which received media only). The target cells, either peptide-pulsed or endogenous targets, are used at a concentration of lx106oells/ml, The plates are incubated for 48 hours at 37 C with 5% CO2.
Recombinant human IFN-gamma is added to the standard wells starting at 400 pg or 1200pg/100 microliter/well and the plate incubated for two hours at 37 C. The plates are washed and 100 pl of biotinylated mouse anti-human IFN-gamma monoclonal antibody (2 microgram/ml in PBS/3%FCS/0.05% Tween 20) are added and incubated for 2 hours at room temperature. After washing again, 100 microliter HRP-streptavidin (1:4000) are added and the plates incubated for one hour at room temperature. The plates are then washed 6x with wash buffer, 100 microliter/well developing solution (TMB
1:1) are added, and the plates allowed to develop for 5-15 minutes. The reaction is stopped with 50 microliter/well 1M H3PO4 and read at 0D450. A culture is considered positive if it measured at least 50 pg of IFN-gamma/well above background and is twice the background level of expression, CTL Expansion.
Those cultures that demonstrate specific lytic activity against peptide-pulsed targets and/or tumor targets are expanded over a two week period with anti-CD3. Briefly, 5x104 C08+ cells are added to a 125 flask containing the following:
1x106 irradiated (4,200 rad) PBMC (autologous or allogeneic) per ml, 2x105 irradiated (8,000 rad) EBV- transformed cells per ml, and 01(13 (anti-CD3) at 3Ong per ml in RPMI-1640 containing 10% (v/v) human AB serum, non-essential amino adds, sodium pyruvate, 25pM 2-mercaptoethanol, L-glutamine and penicillin/streptomycin. Recombinant human 112 is added 24 hours later at a final concentration of 2001U/m1 and every three days thereafter with fresh media at 501U/mi. The cells are split lithe cell concentration exceeds 1x106/m1 and the cultures are assayed between days 13 and 15 at E:T ratios of 30, 10, 3 and 1:1 in the 5ICr release assay or at 1x1 05/m1 in the in situ IFNy assay using the same targets as before the expansion.
Cultures are expanded in the absence of anti-CD3+ as follows. Those cultures that demonstrate specific lytic activity against peptide and endogenous targets are selected and 5x104 CDS+
cells are added to a 125 flask containing the following: 1x105 autologous PBMC per ml which have been peptide-pulsed with 10 pgirril peptide for two hours at 37 C and irradiated (4,200 rad); 2x105 irradiated (8,000 rad) EBV-transformed cells per ml RPMI-1640 containing 10%(v/v) human AB
serum, non-essential AA, sodium pyruvate, 25mM 2-ME, 1-glutamine and gentamicin.
Immunogenicitv of A2 supermotif-bearing peptides A2-supermotif cross-reactive binding peptides are tested In the cellular assay for the ability to induce, peptide-specific CTL in normal individuals. In this analysis, a peptide is typically considered to be an epitope lilt induces peptide-specific CTLs in at least individuals, and preferably, also recognizes the endogenously expressed peptide.

Immunogenicity can also be confirmed using PBMCs isolated from patients bearing a tumor that expresses 161P2F10B. Briefly, PBMCs are isolated from patients, re-stimulated with peptide-pulsed monocytes and assayed for the ability to recognize peptide-pulsed target cells as well as transfected cells endogenously expressing the antigen.
Evaluation of A*03/A11 immunogenicity HLA-A3 supermotif-bearing cross-reactive binding peptides are also evaluated for immunogenicity using methodology analogous for that used to evaluate the immunogenicity of the HLA-A2 supermotif peptides.
Evaluation of B7 immunogenicity lmmunogenicity screening of the B7-supertype cross-reactive binding peptides identified as set forth herein are confirmed in a manner analogous to the confirmation of A2-and A3-supermotif-bearing peptides.
Peptides bearing other supermotifs/motifs, e.g., HLA-A1, HLA-A24 etc. are also confirmed using similar methodology Example 15: Implementation of the Extended Supermotif to Improve the Binding Capacity of Native Epitopes by Creating Analogs HLA motifs and supermotifs (comprising primary and/or secondary residues) are useful in the identification and preparation of highly cross-reactive native peptides, as demonstrated herein.
Moreover, the definition of HLA motifs and supermotifs also allows one to engineer highly cross-reactive epitopes by identifying residues within a native peptide sequence which can be analoged to confer upon the peptide certain characteristics, e.g. greater cross-reactivity within the group of HLA molecules that comprise a supertype, and/or greater binding affinity for some or all of those HLA molecules.
Examples of analoging peptides to exhibit modulated binding affinity are set forth in this example.
Analoginq at Primary Anchor Residues Peptide engineering strategies are implemented to further increase the cross-reactivity of the epitopes. For example, the main anchors of A2-supermotif-bearing peptides are altered, for example, to introduce a preferred L, I, V, or M
at position 2, and I or V at the C-terminus.
To analyze the cross-reactivity of the analog peptides, each engineered analog is initially tested for binding to the prototype A2 supertype allele A*0201, then, if A*0201 binding capacity is maintained, for A2-supertype cross-reactivity.
Alternatively, a peptide is confirmed as binding one or all supertype members and then analoged to modulate binding affinity to any one (or more) of the supertype members to add population coverage.
The selection of analogs for immunogenicity in a cellular screening analysis is typically further restricted by the capacity of the parent wild type (WT) peptide to bind at least weakly, i.e., bind at an IC90 of 5000nM or less, to three of more A2 supertype alleles. The rationale for this requirement is that the WT
peptides must be present endogenously in sufficient quantity to be biologically relevant. Analoged peptides have been shown to have increased immunogenicity and cross-reactivity by T cells specific for the parent epitope (see, e.g., Parkhurst etal., J. Immunol. 157:2539, 1996; and Pogue et al., Proc. Natl. Acad. Sci. USA 92:8166, 1995).
In the cellular screening of these peptide analogs, it is important to confirm that analog-specific CTLs are also able to recognize the wild-type peptide and, when possible, target cells that endogenously express the epitope.
Analoginq of HLA-A3 and B7-supermotif-bearinq peptides Analogs of HLA-A3 supermotif-bearing epitopes are generated using strategies similar to those employed in analoging HLA-A2 supermotif-bearing peptides. For example, peptides binding to 3/5 of the A3-supertype molecules are engineered at primary anchor residues to possess a preferred residue (V, S, M, or A) at position 2.

The analog peptides are then tested for the ability to bind A*03 and A*11 (prototype A3 supertype alleles). Those peptides that demonstrate 5. 500 nM binding capacity are then confirmed as having A3-supertype cross-reactivity.
Similarly to the A2- and A3- motif bearing peptides, peptides binding 3 or more B7-supertype alleles can be improved, where possible, to achieve increased cross-reactive binding or greater binding affinity or binding half life. B7 supermotif-bearing peptides are, for example, engineered to possess a preferred residue (V, I, L, or F) at the C-terminal primary anchor position, as demonstrated by Sidney etal. (J. ImmunoL 157:3480-3490, 1996).
Analoging at primary anchor residues of other motif and/or supermotif-bearing epitopes is performed in a like manner.
The analog peptides are then be confirmed for immunogenicity, typically in a cellular screening assay. Again, it is generally important to demonstrate that analog-specific CTLs are also able to recognize the wild-type peptide and, when possible, targets that endogenously express the epitope.
Analoqing at Secondary Anchor Residues Moreover, HLA supermotifs are of value in engineering highly cross-reactive peptides and/or peptides that bind HLA molecules with increased affinity by identifying particular residues at secondary anchor positions that are associated with such properties. For example, the binding capacity of a B7 supermotif-bearing peptide with an F residue at position 1 is analyzed. The peptide is then analoged to, for example, substitute L for F at position 1. The analoged peptide is evaluated for increased binding affinity, binding half life and/or increased cross-reactivity. Such a procedure identifies analoged peptides with enhanced properties.
Engineered analogs with sufficiently improved binding capacity or cross-reactivity can also be tested for immunogenicity in HLA-B7-transgenic mice, following for example, IFA
immunization or lipopeptide immunization. Analoged peptides are additionally tested for the ability to stimulate a recall response using PBMC from patients with 161P2F10B-expressing tumors.
Other analoging strategies Another form of peptide analoging, unrelated to anchor positions, involves the substitution of a cysteine with a-amino butyric acid. Due to its chemical nature, cysteine has the propensity to form disulfide bridges and sufficiently alter the peptide structurally so as to reduce binding capacity. Substitution of a-amino butyric acid for cysteine not only alleviates this problem, but has been shown to improve binding and crossbinding capabilities in some instances (see, e.g., the review by Sette etal., In: Persistent Viral Infections, Eds. R. Ahmed and I. Chen, John Wiley & Sons, England, 1999).
Thus, by the use of single amino acid substitutions, the binding properties and/or cross-reactivity of peptide ligands for HLA supertype molecules can be modulated.
Example 16: Identification and confirmation of 161P2F10B-derived sequences with HLA-DR binding motifs Peptide epitopes bearing an HLA class II supermotif or motif are identified and confirmed as outlined below using methodology similar to that described for HLA Class I peptides.
Selection of HLA-DR-supermotif-bearinq epitopes.
To identify 161P2F10B-derived, HLA class ll HTL epitopes, a 161P2F1OB antigen is analyzed for the presence of sequences bearing an HLA-DR-motif or supermotif. Specifically, 15-mer sequences are selected comprising a DR-supermotif, comprising a 9-mer core, and three-residue N- and C-terminal flanking regions (15 amino acids total).
Protocols for predicting peptide binding to DR molecules have been developed (Southwood et aL, J. Immunot 160:3363-3373, 1998). These protocols, specific for individual DR molecules, allow the scoring, and ranking, of 9-mer core regions. Each protocol not only scores peptide sequences for the presence of DR-supermotif primary anchors (i.e., at position 1 and position 6) within a 9-mer core, but additionally evaluates sequences for the presence of secondary anchors.
Using allele-specific selection tables (see, e.g., Southwood etal., ibid.), it has been found that these protocols efficiently select peptide sequences with a high probability of binding a particular DR
molecule. Additionally, it has been found that performing these protocols in tandem, specifically those for DR1, DR4w4, and DR7, can efficiently select DR cross-reactive peptides.
The 161P2F10E3-derived peptides identified above are tested for their binding capacity for various common HLA-DR molecules. All peptides are initially tested for binding to the DR
molecules in the primary panel: DR1, DR4w4, and DR7.
Peptides binding at least two of these three DR molecules are then tested for binding to DR2w2 131, DR2w2132, DR6w19, and DR9 molecules in secondary assays. Finally, peptides binding at least two of the four secondary panel DR molecules, and thus cumulatively at least four of seven different DR molecules, are screened for binding to DR4w15, DR5w11, and DR8w2 molecules in tertiary assays. Peptides binding at least seven of the ten DR molecules comprising the primary, secondary, and tertiary screening assays are considered cross-reactive DR
binders. 161P2F10B-derived peptides found to bind common HLA-DR alleles are of particular interest Selection of DR3 motif peptides Because HLA-DR3 is an allele that is prevalent in Caucasian, Black, and Hispanic populations, DR3 binding capacity is a relevant criterion in the selection of HTL epitopes. Thus, peptides shown to be candidates may also be assayed for their DR3 binding capacity. However, in view of the binding specificity of the DR3 motif, peptides binding only to DR3 can also be considered as candidates for inclusion in a vaccine formulation.
To efficiently identify peptides that bind DR3, target 161P2F1OB antigens are analyzed for sequences carrying one of the two DR3-specific binding motifs reported by Geluk et aL (J. ImmunoL
152:5742-5748, 1994). The corresponding peptides are then synthesized and confirmed as having the ability to bind DR3 with an affinity of lp.M or better, i.e., less than 1 M. Peptides are found that meet this binding criterion and qualify as HLA
class II high affinity binders.
DR3 binding epitopes identified in this manner are included in vaccine compositions with DR supermotif-bearing peptide epitopes.
Similarly to the case of HLA class I motif-bearing peptides, the class ll motif-bearing peptides are analoged to improve affinity or cross-reactivity. For example, aspartic acid at position 4 of the 9-mer core sequence is an optimal residue for DR3 binding, and substitution for that residue often improves DR 3 binding.
Example 17: lmmunogenicity of 161P2F10B-derived HTL epitopes This example determines immunogenic DR supermotif- and DR3 motif-bearing epitopes among those identified using the methodology set forth herein.
Immunogenicity of HTL epitopes are confirmed in a manner analogous to the determination of immunogenicity of CTL epitopes, by assessing the ability to stimulate HTL responses and/or by using appropriate transgenic mouse models.
Immunogenicity is determined by screening for: 1.) in vitro primary induction using normal PBMC or 2.) recall responses from patients who have 161P2F10B-expressing tumors.
Example 18: Calculation of phenotypic frequencies of HLA-supertypes in various ethnic backgrounds to determine breadth of population coverage This example illustrates the assessment of the breadth of population coverage of a vaccine composition comprised of multiple epitopes comprising multiple supermotifs and/or motifs.
In order to analyze population coverage, gene frequencies of HLA alleles are determined. Gene frequencies for each HLA allele are calculated from antigen or allele frequencies utilizing the binomial distribution formulae gf=1-(SQRT(1-af)) (see, e.g., Sidney etal., Human Immunol. 45:79-93, 1996). To obtain overall phenotypic frequencies, cumulative gene frequencies are calculated, and the cumulative antigen frequencies derived by the use of the inverse formula [af=1-(1-Cgf)2].
Where frequency data is not available at the level of DNA typing, correspondence to the serologically defined antigen frequencies is assumed. To obtain total potential supertype population coverage no linkage disequilibrium is assumed, and only alleles confirmed to belong to each of the supertypes are included (minimal estimates). Estimates of total potential coverage achieved by inter-loci combinations are made by adding to the A coverage the proportion of the non-A
covered population that could be expected to be covered by the B alleles considered (e.g., tota1=A+B*(1-A)). Confirmed members of the A3-like supertype are A3, All, A31, A*3301, and A*6801.
Although the A3-like supertype may also include A34, A66, and A*7401, these alleles were not included in overall frequency calculations. Likewise, confirmed members of the A2-like supertype family are A*0201, A*0202, A*0203, A*0204, A*0205, A*0206, A*0207, A*6802, and A*6901. Finally, the B7-like supertype-confirmed alleles are: B7, B*3501-03, B51, B*5301, B*5401, B*5501-2, B*5601, B*6701, and B*7801 (potentially also B*1401, B*3504-06, B*4201, and B*5602).
Population coverage achieved by combining the A2-, A3- and B7-supertypes is approximately 86% in five major ethnic groups. Coverage may be extended by including peptides bearing the Al and A24 motifs. On average, Al is present in 12% and A24 in 29% of the population across five different major ethnic groups (Caucasian, North American Black, Chinese, Japanese, and Hispanic). Together, these alleles are represented with an average frequency of 39% in these same ethnic populations. The total coverage across the major ethnicities when Al and A24 are combined with the coverage of the A2-, A3- and B7-supertype alleles is >95%, see, e.g., Table IV (G). An analogous approach can be used to estimate population coverage achieved with combinations of class II motif-bearing epitopes.
lmmunogenicity studies in humans (e.g., Bertoni etal., J. Clin. Invest.
100:503, 1997; Doolan etal., Immunity 7:97, 1997; and Threlkeld etal., J. Immunol. 159:1648, 1997) have shown that highly cross-reactive binding peptides are almost always recognized as epitopes. The use of highly cross-reactive binding peptides is an important selection criterion in identifying candidate epitopes for inclusion in a vaccine that is immunogenic in a diverse population.
With a sufficient number of epitopes (as disclosed herein and from the art), an average population coverage is predicted to be greater than 95% in each of five major ethnic populations. The game theory Monte Carlo simulation analysis, which is known in the art (see e.g., Osborne, M.J. and Rubinstein, A. "A
course in game theory" MIT Press, 1994), can be used to estimate what percentage of the individuals in a population comprised of the Caucasian, North American Black, Japanese, Chinese, and Hispanic ethnic groups would recognize the vaccine epitopes described herein. A preferred percentage is 90%. A more preferred percentage is 95%.
Example 19: CTL Recognition Of Endogenously Processed Antigens After Priming This example confirms that CTL induced by native or analoged peptide epitopes identified and selected as described herein recognize endogenously synthesized, i.e., native antigens.
Effector cells isolated from transgenic mice that are immunized with peptide epitopes, for example HLA-A2 supermotif-bearing epitopes, are re-stimulated in vitro using peptide-coated stimulator cells. Six days later, effector cells are assayed for cytotoxicity and the cell lines that contain peptide-specific cytotoxic activity are further re-stimulated. An additional six days later, these cell lines are tested for cytotoxic activity on 51Cr labeled Jurkat-A2.1/Kb target cells in the absence or presence of peptide, and also tested on 51Cr labeled target cells bearing the endogenously synthesized antigen, i.e. cells that are stably transfected with 161P2F1OB expression vectors.
The results demonstrate that CTL lines obtained from animals primed with peptide epitope recognize endogenously synthesized 161P2F1OB antigen. The choice of transgenic mouse model to be used for such an analysis depends upon the epitope(s) that are being evaluated. In addition to HLA-A*0201/Kb transgenic mice, several other transgenic mouse models including mice with human All, which may also be used to evaluate A3 epitopes, and 87 alleles have been characterized and others (e.g., transgenic mice for HLA-A1 and A24) are being developed. HLA-DR1 and HLA-DR3 mouse models have also been developed, which may be used to evaluate HTL
epitopes.
Example 20: Activity Of CTL-HTL Conjugated Epitopes In Transcienic Mice This example illustrates the induction of CTLs and HTLs in transgenic mice, by use of a 161P2F10B-derived CTL
and HTL peptide vaccine compositions. The vaccine composition used herein comprise peptides to be administered to a patient with a 161P2F10B-expressing tumor. The peptide composition can comprise multiple CTL and/or HTL epitopes. The epitopes are identified using methodology as described herein. This example also illustrates that enhanced immunogenicity can be achieved by inclusion of one or more HTL epitopes in a CTL vaccine composition; such a peptide composition can comprise an HTL epitope conjugated to a CTL epitope. The CTL epitope can be one that binds to multiple HLA family members at an affinity of 500 nM or less, or analogs of that epitope. The peptides may be lipidated, if desired.
Immunization procedures: Immunization of transgenic mice is performed as described (Alexander etal., J.
Immunol. 159:4753-4761, 1997). For example, A2/Kb mice, which are transgenic for the human HLA A2.1 allele and are used to confirm the immunogenicity of HLA-A*0201 motif- or HLA-A2 supermotif-bearing epitopes, and are primed subcutaneously (base of the tail) with a 0.1 ml of peptide in Incomplete Freund's Adjuvant, or if the peptide composition is a lipidated CTLJHTL conjugate, in DMSO/saline, or if the peptide composition is a polypeptide, in PBS or Incomplete Freund's Adjuvant. Seven days after priming, splenocytes obtained from these animals are restimulated with syngenic irradiated LPS-activated lymphoblasts coated with peptide.
Cell lines: Target cells for peptide-specific cytotoxicity assays are Jurkat cells transfected with the HLA-A2.1/Kb chimeric gene (e.g., Vitiello etal., J. Exp. Med. 173:1007, 1991) In vitro CTL activation: One week after priming, spleen cells (30x106 cells/flask) are co-cultured at 37 C with syngeneic, irradiated (3000 rads), peptide coated lymphoblasts (10x106 cells/flask) in 10 ml of culture medium/T25 flask.
After six days, effector cells are harvested and assayed for cytotoxic activity.
Assay for cytotoxic activity: Target cells (1.0 to 1.5x106) are incubated at 37 C in the presence of 200 pl of 610r.
After 60 minutes, cells are washed three times and resuspended in R10 medium.
Peptide is added where required at a concentration of 1 pg/ml. For the assay, 10461Cr-labeled target cells are added to different concentrations of effector cells (final volume of 200 pl) in U-bottom 96-well plates. After a six hour incubation period at 37 C, a 0.1 ml aliquot of supematant is removed from each well and radioactivity is determined in a Micromedic automatic gamma counter. The percent specific lysis is determined by the formula: percent specific release = 100 x (experimental release - spontaneous release)/(maximum release - spontaneous release). To facilitate comparison between separate CTL
assays run under the same conditions, %
61Cr release data is expressed as lytic units/106 cells. One lytic unit is arbitrarily defined as the number of effector cells required to achieve 30% lysis of 10,000 target cells in a six hour 61Cr release assay. To obtain specific lytic units/106, the lytic units/106 obtained in the absence of peptide is subtracted from the lytic units/106 obtained in the presence of peptide.
For example, if 30% 61Cr release is obtained at the effector (E): target (T) ratio of 50:1 (i.e., 5x106 effector cells for 10,000 targets) in the absence of peptide and 5:1 (i.e., 5x104 effector cells for 10,000 targets) in the presence of peptide, the specific lytic units would be: R1/50,000)41/500,000)] x 106 = 18 LU.
The results are analyzed to assess the magnitude of the CTL responses of animals injected with the immunogenic CTUHTL conjugate vaccine preparation and are compared to the magnitude of the CTL response achieved using, for example, CTL epitopes as outlined above in the Example entitled "Confirmation of Immunogenicity." Analyses similar to this may be performed to confirm the immunogenicity of peptide conjugates containing multiple CTL epitopes and/or multiple HTL
epitopes. In accordance with these procedures, it is found that a CTL response is induced, and concomitantly that an HTL
response is induced upon administration of such compositions.

Example 21: Selection of CTL an HTL epitopes for inclusion in a 161P2F108-specific vaccine.
This example illustrates a procedure for selecting peptide epitopes for vaccine compositions of the invention. The peptides in the Composition can be in the form of a nucleic acid sequence, either single or one or more sequences (i.e., minlgene) that Encodes peptide(s), or can be single and/or polyepitopic peptides.
The following principles are utilized when selecting a plurality of epitopes for inclusion in a vaccine composition.
Each of the resowing principles is balanced in order to make the selection.
' Epitopes are selected which, upon administration, mimic immune responses that are correlated with 161P2F1013 cleatana7 Thehumber of epitopes used depends on observations of patients who spontaneously clear 161P2F1013. For example, if it has been observed that patients who spontaneously clear 161P2F10B-expressing cells generate an immune response to at least three (3) epitopes from 161P2F108 antigen, then at least three epitopes should be included for RA
class I. A similar rationale is used to determine HLA class II epitopes.
Epitopes are often selected that have a binding affinity of an ICso of 500 nM
or less for an HLA class I molecule, or for class IL¨an-less of 1000 nM or less; or HLA Class I peptides with high binding scores from the BIMAS web site.
In order to achieve broad coverage of the vaccine through out a diverse population, sufficient supermotif bearing peptides, or a sufficient array of allele-specific mobl bearing peptides, are selected to give broad poptdation coverage. In one embodiment, epitopes are selected to provide at least 80% population coverage. A Monte Carlo analysis, a statistical evaluation knOwit In the art, can be employed to assess breadth, or redundancy, of population coverage.
When creating poiyepitopic compositions, or a minigene that encodes same, it is fp:46'211y desirable to generate the smallest peptide possible that encompasses the epitopes of interest. The principles employed are similar, if not the same, as those employed when selecting a peptide somprising nested epitopes. For example, a protein sequence for the vaccine composition is selected because it has maximal number of epitopes contained within the sequence, i.e., It has a high concentration of epitopes. Epitopes may be nested or overlapping (La, frame shifted relative to one another). For example, with overlapping epitopes, two 9-mer epitopes and one 10-mar epftope can be present in a 10 amino acid peptide. Each epitope can be exposed and bound by an HLA molecule upon administration of such a peptide. A multi-epitopic, peptide can he generated synthetically, recombinantly, or via-cleavage from the native source. Alternatively, an analog can be made of this native sequence, whereby one or more of the epitopes comprise substitutions that alter the cross-reactivity and/or binding affinity properties of the polyepitopic peptide. Such a vaccine composition is administered for therapeutic or prophylactic purposes. This embodiment provides for the possibility that an as yet undiscovered aspect of immune system processing will apply to the native nested sequence and thereby facilitate the production of therapeutic or prophylactic immune response-inducing vaccine compositions. Additionally such an embodiment provides for the possibility of motif-bearing epitopes for an HLA makeup that Is presently unknown. Furthermore, this embodiment (absent the creating of any analogs) directs the immune response to multiple peptide sequences that are actually present in 161P2F10B, thus avoiding the need to evaluate any junctional epitopes. Lastly, the embodiment provides an economy of scale when producing nucleic acid vaccine compositions. Related to this embodiment, computer programs can be derived in accordance with principles in the art, which identify in a target sequence, the greatest number of epitopes per sequence length.
A vaccine composition comprised of selected peptides, when administered, is safe, efficacious, and elicits an immune response similar in magnitude to an immune response that controls or clears cells that bear or overexpress 161P2F10B.

Example 22: Construction of "Minigene" Multi-Epitope DNA Plasmids This example discusses the construction of a minigene expression plasmid.
Minigene plasmids may, of course, contain various configurations of B cell, CTL and/or HTL epitopes or epitope analogs as described herein.
A minigene expression plasmid typically includes multiple CTL and HTL peptide epitopes. In the present example, HLA-A2, -A3, -B7 supermotif-bearing peptide epitopes and HLA-A1 and -A24 motif-bearing peptide epitopes are used in conjunction with DR supermotif-bearing epitopes and/or DR3 epitopes. HLA class I supermotif or motif-bearing peptide epitopes derived 161P2F10B, are selected such that multiple supermotifs/motifs are represented to ensure broad population coverage. Similarly, RA class II epitopes are selected from 161P2F1OB to provide broad population coverage, i.e. both HLA DR-1-4-7 supermotif-bearing epitopes and HLA DR-3 motif-bearing epitopes are selected for inclusion in the minigene construct. The selected CTL and HTL epitopes are then incorporated into a minigene for expression in an expression vector.
Such a construct may additionally include sequences that direct the HTL
epitopes to the endoplasmic reticulum.
For example, the Ii protein may be fused to one or more HTL epitopes as described in the art, wherein the CLIP sequence of the Ii protein is removed and replaced with an HLA class II epitope sequence so that HLA class II epitope is directed to the endoplasmic reticulum, where the epitope binds to an HLA class II molecules.
This example illustrates the methods to be used for construction of a minigene-bearing expression plasmid. Other expression vectors that may be used for minigene compositions are available and known to those of skill in the art.
The minigene DNA plasmid of this example contains a consensus Kozak sequence and a consensus murine kappa lg-light chain signal sequence followed by CTL and/or HTL epitopes selected in accordance with principles disclosed herein.
The sequence encodes an open reading frame fused to the Myc and His antibody epitope tag coded for by the pcDNA 3.1 Myc-His vector.
Overlapping oligonucleotides that can, for example, average about 70 nucleotides in length with 15 nucleotide overlaps, are synthesized and HPLC-purified. The oligonucleotides encode the selected peptide epitopes as well as appropriate linker nucleotides, Kozak sequence, and signal sequence. The final multiepitope minigene is assembled by extending the overlapping oligonucleotides in three sets of reactions using PCR. A Perkin/Elmer 9600 PCR machine is used and a total of 30 cycles are performed using the following conditions: 95 C
for 15 sec, annealing temperature (5 below the lowest calculated Tm of each primer pair) for 30 sec, and 72 C for 1 min.
For example, a minigene is prepared as follows. For a first PCR reaction, 51.1.g of each of two oligonucleotides are annealed and extended: In an example using eight oligonucleotides, i.e., four pairs of primers, oligonucleotides 1+2, 3+4, 5+6, and 7+8 are combined in 100111 reactions containing Pfu polymerase buffer (1r: 10 mM KCL, 10 mM (NH4)2SO4, 20 mM Tris-chloride, pH 8.75, 2 mM MgSO4, 0.1% Triton X-100, 100 p.g/mIBSA), 0.25 mM each dNTP, and 2.5 U of Pfu polymerase. The full-length=dinner products are gel-purified, and two reactions containing the product of 1+2 and 3+4, and the product of 5+6 and 7+8 are mixed, annealed, and extended for 10 cycles.
Half of the two reactions are then mixed, and cycles of annealing and extension carried out before flanking primers are added to amplify the full length product. The full-length product is gel-purified and cloned into pCR-blunt (Invitrogen) and individual clones are screened by sequencing.
Example 23: The Plasmid Construct and the Degree to Which It Induces Immunogenicity.
The degree to which a plasmid construct, for example a plasmid constructed in accordance with the previous Example, is able to induce immunogenicity is confirmed in vitro by determining epitope presentation by APC following transduction or transfection of the APC with an epitope-expressing nucleic acid construct. Such a study determines "antigenicity" and allows the use of human APC. The assay determines the ability of the epitope to be presented by the APC
in a context that is recognized by a T cell by quantifying the density of epitope-HLA class I complexes on the cell surface.
Quantitation can be performed by directly measuring the amount of peptide eluted from the APC (see, e.g., Sijts etal., J.

Immunot 156:683-692, 1996; Demotz et al., Nature 342:682-684, 1989); or the number of peptide-HLA class I complexes can be estimated by measuring the amount of lysis or lymphokine release induced by diseased or transfected target cells, and then determining the concentration of peptide necessary to obtain equivalent levels of lysis or lymphokine release (see, e.g., Kageyama etal., J. lmmunol. 154:567-576, 1995).
Alternatively, immunogenicity is confirmed through in vivo injections into mice and subsequent in vitro assessment of CTL and HTL activity, which are analyzed using cytotoxicity and proliferation assays, respectively, as detailed e.g., in Alexander etal., Immunity 1:751-761, 1994.
For example, to confirm the capacity of a DNA minigene construct containing at least one HLA-A2 supermotif peptide to induce CTLs in vivo, HLA-A2.1/Kb transgenic mice, for example, are immunized intramuscularly with 100 pg of naked cDNA. As a means of comparing the level of CTLs induced by cDNA
immunization, a control group of animals is also immunized with an actual peptide composition that comprises multiple epitopes synthesized as a single polypeptide as they would be encoded by the minigene.
Splenocytes from immunized animals are stimulated twice with each of the respective compositions (peptide epitopes encoded in the minigene or the polyepitopic peptide), then assayed for peptide-specific cytotoxic activity in a 51Cr release assay. The results indicate the magnitude of the CTL response directed against the A2-restricted epitope, thus indicating the in vivo immunogenicity of the minigene vaccine and polyepitopic vaccine.
It is, therefore, found that the minigene elicits immune responses directed toward the HLA-A2 supermotif peptide epitopes as does the polyepitopic peptide vaccine. A similar analysis is also performed using other HLA-A3 and HLA-B7 .
transgenic mouse models to assess CTL induction by HLA-A3 and HLA-B7 motif or supermotif epitopes, whereby it is also found that the minigene elicits appropriate immune responses directed toward the provided epitopes.
To confirm the capacity of a class II epitope-encoding minigene to induce HTLs in vivo, DR transgenic mice, or for those epitopes that cross react with the appropriate mouse MHC molecule, I-Ab-restricted mice, for example, are immunized intramuscularly with 100 pg of plasmid DNA. As a means of comparing the level of HTLs induced by DNA immunization, a group of control animals is also immunized with an actual peptide composition emulsified in complete Freund's adjuvant.
CD4+ T cells, i.e. HTLs, are purified from splenocytes of immunized animals and stimulated with each of the respective compositions (peptides encoded in the minigene). The HTL response is measured using a 3H-thymidine incorporation proliferation assay, (see, e.g., Alexander et al. Immunity 1:751-761, 1994).
The results indicate the magnitude of the HTL
response, thus demonstrating the in vivo immunogenicity of the minigene.
DNA minigenes, constructed as described in the previous Example, can also be confirmed as a vaccine in combination with a boosting agent using a prime boost protocol. The boosting agent can consist of recombinant protein (e.g., Barnett etal., Aids Res. and Human Retroviruses 14, Supplement 3:S299-S309, 1998) or recombinant vaccinia, for example, expressing a minigene or DNA encoding the complete protein of interest (see, e.g., Hanke etal., Vaccine 16:439-445, 1998; Sedegah etal., Proc. Natl. Acad. Sci USA 95:7648-53, 1998; Hanke and McMichael, Immunot Letters 66:177-181, 1999; and Robinson etal., Nature Med. 5:526-34, 1999).
For example, the efficacy of the DNA minigene used in a prime boost protocol is initially evaluated in transgenic mice. In this example, A2.1/Kb transgenic mice are immunized IM with 10014 of a DNA minigene encoding the immunogenic peptides including at least one HLA-A2 supermotif-bearing peptide.
After an incubation period (ranging from 3-

9 weeks), the mice are boosted IP with 107 pfu/mouse of a recombinant vaccinia virus expressing the same sequence encoded by the DNA minigene. Control mice are immunized with 100 pg of DNA or recombinant vaccinia without the minigene sequence, or with DNA encoding the minigene, but without the vaccinia boost. After an additional incubation period of two weeks, splenocytes from the mice are immediately assayed for peptide-specific activity in an ELISPOT assay.

Additionally, splenocytes are stimulated in vitro with the A2-restricted peptide epitopes encoded in the minigene and recombinant vaccinia, then assayed for peptide-specific activity in an alpha, beta and/or gamma IFN ELISA.
It is found that the minigene utilized in a prime-boost protocol elicits greater immune responses toward the HLA-A2 supermotif peptides than with DNA alone. Such an analysis can also be performed using HLA-A11 or HLA-B7 transgenic mouse models to assess CTL induction by HLA-A3 or HLA-B7 motif or supermotif epitopes. The use of prime boost protocols in humans is described below in the Example entitled "Induction of CTL Responses Using a Prime Boost Protocol."
Example 24: Peptide Compositions for Prophylactic Uses Vaccine compositions of the present invention can be used to prevent 161P2F1OB
expression in persons who are at risk for tumors that bear this antigen. For example, a polyepitopic peptide epitope composition (or a nucleic acid comprising the same) containing multiple CTL and HTL epitopes such as those selected in the above Examples, which are also selected to target greater than 80% of the population, is administered to individuals at risk for a 161P2F10B-associated tumor.
For example, a peptide-based composition is provided as a single polypeptide that encompasses multiple epitopes.
The vaccine is typically administered in a physiological solution that comprises an adjuvant, such as Incomplete Freunds Adjuvant. The dose of peptide for the initial immunization is from about 1 to about 50,000 1.1g, generally 100-5,000 pg, for a 70 kg patient The initial administration of vaccine is followed by booster dosages at 4 weeks followed by evaluation of the magnitude of the immune response in the patient, by techniques that determine the presence of epitope-specific CTL
populations in a PBMC sample. Additional booster doses are administered as required. The composition is found to be both safe and efficacious as a prophylaxis against 161P2F10B-associated disease.
Alternatively, a composition typically comprising transfecting agents is used for the administration of a nucleic acid-based vaccine in accordance with methodologies known in the art and disclosed herein.
Example 25: Polyepitopic Vaccine Compositions Derived from Native 161P2F1OB
Sequences A native 161P2F1OB polyprotein sequence is analyzed, preferably using computer algorithms defined for each class I and/or class II supermotif or motif, to identify "relatively short"
regions of the polyprotein that comprise multiple epitopes. The "relatively short' regions are preferably less in length than an entire native antigen. This relatively short sequence that contains multiple distinct or overlapping, "nested" epitopes can be used to generate a minigene construct.
The construct is engineered to express the peptide, which corresponds to the native protein sequence. The "relatively short"
peptide is generally less than 250 amino acids in length, often less than 100 amino acids in length, preferably less than 75 amino acids in length, and more preferably less than 50 amino acids in length.
The protein sequence of the vaccine composition is selected because it has maximal number of epitopes contained within the sequence, i.e., it has a high concentration of epitopes. As noted herein, epitope motifs may be nested or overlapping (i.e., frame shifted relative to one another). For example, with overlapping epitopes, two 9-mer epitopes and one

10-mer epitope can be present in a 10 amino acid peptide. Such a vaccine composition is administered for therapeutic or prophylactic purposes.
The vaccine composition will include, for example, multiple CTL epitopes from 161P2F1OB antigen and at least one HTL epitope. This polyepitopic native sequence is administered either as a peptide or as a nucleic acid sequence which encodes the peptide. Alternatively, an analog can be made of this native sequence, whereby one or more of the epitopes comprise substitutions that alter the cross-reactivity and/or binding affinity properties of the polyepitopic peptide.
The embodiment of this example provides for the possibility that an as yet undiscovered aspect of immune system processing will apply to the native nested sequence and thereby facilitate the production of therapeutic or prophylactic immune response-inducing vaccine compositions. Additionally, such an embodiment provides for the possibility of motif-bearing epitopes for an HLA makeup(s) that is presently unknown. Furthermore, this embodiment (excluding an analoged embodiment) directs the immune response to multiple peptide sequences that are actually present in native 161P2F10B, thus avoiding the need to evaluate any junctional epitopes. Lastly, the embodiment provides an economy of scale when producing peptide or nucleic acid vaccine compositions.
Related to this embodiment, computer programs are available in the art which can be used to identify in a target sequence, the greatest number of epitopes per sequence length.
Example 26: Polyepitopic Vaccine Compositions from Multiple Antigens The 161P2F1OB peptide epitopes of the present invention are used in conjunction with epitopes from other target tumor-associated antigens, to create a vaccine composition that is useful for the prevention or treatment of cancer that expresses 161P2F1OB and such other antigens. For example, a vaccine composition can be provided as a single polypeptide that incorporates multiple epitopes from 161P2F1OB as well as tumor-associated antigens that are often expressed with a target cancer associated with 161P2F1OB expression, or can be administered as a composition comprising a cocktail of one or more discrete epitopes. Alternatively, the vaccine can be administered as a minigene construct or as dendritic cells which have been loaded with the peptide epitopes in vitro.
Example 27: Use of peptides to evaluate an immune response Peptides of the invention may be used to analyze an immune response for the presence of specific antibodies, CTL or HTL directed to161P2F10B. Such an analysis can be performed in a manner described by Ogg etal., Science 279:2103-2106, 1998. In this Example, peptides in accordance with the invention are used as a reagent for diagnostic or prognostic purposes, not as an immunogen.
In this example highly sensitive human leukocyte antigen tetrameric complexes ('tetramers) are used for a cross-sectional analysis of, for example, 161P2F1OB HLA-A*0201-specific CTL
frequencies from HLA A*0201-positive individuals at different stages of disease or following immunization comprising a 161P2F106 peptide containing an A*0201 motif.
Tetrameric complexes are synthesized as described (Musey etal., N. Engl. J.
Med. 337:1267, 1997). Briefly, purified HLA
heavy chain (A*0201 in this example) and 32-microglobulin are synthesized by means of a prokaryotic expression system.
The heavy chain is modified by deletion of the transmembrane-cytosolic tail and COOH-terminal addition of a sequence containing a BirA enzymatic biotinylation site. The heavy chain, 32-microglobulin, and peptide are refolded by dilution. The 45-kD refolded product is isolated by fast protein liquid chromatography and then biotinylated by BirA in the presence of biotin (Sigma, St. Louis, Missouri), adenosine 5' triphosphate and magnesium.
Streptavidin-phycoerythrin conjugate is added in a 1:4 molar ratio, and the tetrameric product is concentrated to 1 mg/ml. The resulting product is referred to as tetramer-phycoerythrin.
For the analysis of patient blood samples, approximately one million PBMCs are centrifuged at 300g for 5 minutes and resuspended in 50 1.11 of cold phosphate-buffered saline. Tr-color analysis is performed with the tetramer-phycoerythrin, along with anti-CD8-Tricolor, and anti-CD38. The PBMCs are incubated with tetramer and antibodies on ice for 30 to 60 min and then washed twice before formaldehyde fixation. Gates are applied to contain >99.98% of control samples. Controls for the tetramers include both A*0201-negative individuals and A*0201-positive non-diseased donors. The percentage of cells stained with the tetramer is then determined by flow cytometry. The results indicate the number of cells in the PBMC sample that contain epitope-restricted CTLs, thereby readily indicating the extent of immune response to the 161P2F1OB epitope, and thus the status of exposure to 161P2F10B, or exposure to a vaccine that elicits a protective or therapeutic response.
Example 28: Use of Peptide Epitopes to Evaluate' Recall Responses The peptide epitopes of the invention are used as reagents to evaluate T cell responses, such as acute or recall responses, in patients. Such an analysis may be performed on patients who have recovered from 161P2F10B-associated disease or who have been vaccinated with a 161P2F1OB vaccine.
For example, the class I restricted CTL response of persons who have been vaccinated may be analyzed. The vaccine may be any 161P2F1OB vaccine. PBMC are collected from vaccinated individuals and HLA typed. Appropriate peptide epitopes of the invention that, optimally, bear supermotifs to provide cross-reactivity with multiple HLA supertype family members, are then used for analysis of samples derived from individuals who bear that HLA type.
PBMC from vaccinated individuals are separated on Ficoll-Histopaque density gradients (Sigma Chemical Co., St.
Louis, MO), washed three times in HBSS (GIBCO Laboratories), resuspended in RPMI-1640 (GIBCO Laboratories) supplemented with L-glutamine (2mM), penicillin (50U/m1), streptomycin (50 g/m1), and Hepes (10mM) containing 10%
heat-inactivated human AB serum (complete RPM') and plated using microculture formats. A synthetic peptide comprising an epitope of the invention is added at 10 g/mIto each well and HBV core 128-140 epitope is added at 1 g/mIto each well as a source of T cell help during the first week of stimulation.
In the microculture format, 4 x 105 PBMC are stimulated with peptide in 8 replicate cultures in 96-well round bottom plate in 100 l/well of complete RPMI. On days 3 and 10, 100 pl of complete RPM' and 20 Uhl final concentration of rIL-2 = are added to each well. On day 7 the cultures are transferred into a 96-well flat-bottom plate and restimulated with peptide, rIL-2 and 105 irradiated (3,000 rad) autologous feeder cells. The cultures are tested for cytotoxic activity on day 14. A
positive CTL response requires two or more of the eight replicate cultures to display greater than 10% specific 51Cr release, based on comparison with non-diseased control subjects as previously described (Rehernnann, etal., Nature Med.
= 2:1104,1108, 1996; Rehermann etal., J. Clin. Invest. 97:1655-1665, 1996;
and Rehermann etal. J. Clin. Invest. 98:1432-1440, 1996).
Target cell lines are autologous and allogeneic EBV-transformed B-LCL that are either purchased from the American Society for Histocompatibility and lmmunogenetics (ASHI, Boston, MA) or established from the pool of patients as - described (Guilhot, etal. J. ViroL 66:2670-2678, 1992).
Cytotoxicity assays are performed in the following manner. Target cells consist of either allogeneic HLA-matched or autologous EBV-transformed B lymphoblastoid cell line that are incubated overnight with the synthetic peptide epitope of the invention at 10 M, and labeled with 100 Ci of 51Cr (Amersham Corp., Arlington Heights, IL) for 1 hour after which they are washed four times with HBSS.
Cytolytic activity is determined in a standard 4-h, split well 51Cr release assay using U-bottomed 96 well plates containing 3,000 targets/well.- Stimulated PBMC are tested at effector/target (UT) ratios of 20-50:1 on day 14. Percent cytotoxicity is determined from the formula: 100 x [(experimental release-spontaneous release)/maximum release-spontaneous release)]. Maximum release is determined by lysis of targets by detergent (2% Triton X-100; Sigma Chemical Co., St. Louis, MO). Spontaneous release is <25% of maximum release for all experiments.
The results of such an analysis indicate the extent to which HLA-restricted CTL populations have been stimulated by previous exposure to 161P2F1OB or a 161P2F1OB vaccine.
Similarly, Class II restricted HTLresponses may also be analyzed. Purified PBMC are cultured in'a 96-well flat bottom plate at a density of 1.5x105 cells/well and are stimulated with 10 g/mIsynthetic peptide of the invention, whole 161P2F1OB antigen, or PHA. Cells are routinely plated in replicates of 4-6 wells for each condition. After seven days of culture, the medium is removed and replaced with fresh medium containing 10U/m1 IL-2. Two days later, 1 Ci 3H-thymidine is added to each well and incubation is continued for an additional 18 hours.
Cellular DNA is then harvested on glass fiber mats and analyzed for 3H-thymidine incorporation. Antigen-specific T cell proliferation is calculated as the ratio of 3H-thymidine incorporation in the presence of antigen divided by the 3H-thymidine incorporation in the absence of antigen.

Example 29: Induction Of Specific CTL Response In Humans A human clinical trial for an immunogenic composition comprising CTL and HTL
epitopes of the invention is set up as an IND Phase I, dose escalation study and carried out as a randomized, double-blind, placebo-controlled trial. Such a trial is designed, for example, as follows:
A total of about 27 individuals are enrolled and divided into 3 groups:
Group I: 3 subjects are injected with placebo and 6 subjects are injected with 5 lig of peptide composition;
Group II: 3 subjects are injected with placebo and 6 subjects are injected with 50 pg peptide composition;
Group III: 3 subjects are injected with placebo and 6 subjects are injected with 500 ug of peptide composition.
After 4 weeks following the first injection, all subjects receive a booster inoculation at the same dosage.
The endpoints measured in this study relate to the safety and tolerability of the peptide composition as well as its immunogenicity. Cellular immune responses to the peptide composition are an index of the intrinsic activity of this the peptide composition, and can therefore be viewed as a measure of biological efficacy. The following summarize the clinical and laboratory data that relate to safety and efficacy endpoints.
Safety: The incidence of adverse events is monitored in the placebo and drug treatment group and assessed in terms of degree and reversibility.
Evaluation of Vaccine Efficacy: For evaluation of vaccine efficacy, subjects are bled before and after injection.
Peripheral blood mononuclear cells are isolated from fresh heparinized blood by Ficoll-Hypaque density gradient centrifugation, aliquoted in freezing media and stored frozen. Samples are assayed for CTL and HTL activity.
The vaccine is found to be both safe and efficacious.
Example 30: Phase II Trials In Patients Expressing 161P2F1OB
Phase ll trials are performed to study the effect of administering the CTL-HTL
peptide compositions to patients having cancer that expresses 161P2F10B. The main objectives of the trial are to determine an effective dose and regimen for inducing CTLs in cancer patients that express 161P2F10B, to establish the safety of inducing a CTL and HTL response in these patients, and to see to what extent activation of CTLs improves the clinical picture of these patients, as manifested, e.g., by the reduction and/or shrinking of lesions. Such a study is designed, for example, as follows:
The studies are performed in multiple centers. The trial design is an open-label, uncontrolled, dose escalation protocol wherein the peptide composition is administered as a single dose followed six weeks later by a single booster shot of the same dose. The dosages are 50, 500 and 5,000 micrograms per injection.
Drug-associated adverse effects (severity and reversibility) are recorded.
There are three patient groupings. The first group is injected with 50 micrograms of the peptide composition and the second and third groups with 500 and 5,000 micrograms of peptide composition, respectively. The patients within each group range in age from 21-65 and represent diverse ethnic backgrounds. All of them have a tumor that expresses 161P2F10B.
Clinical manifestations or antigen-specific T-cell responses are monitored to assess the effects of administering the peptide compositions. The vaccine composition is found to be both safe and efficacious in the treatment of 161P2F10B-associated disease.
Example 31: Induction of CTL Responses Using a Prime Boost Protocol A prime boost protocol similar in its underlying principle to that used to confirm the efficacy of a DNA vaccine in transgenic mice, such as described above in the Example entitled The Plasmid Construct and the Degree to Which It Induces Immunogenicity," can also be used for the administration of the vaccine to humans. Such a vaccine regimen can include an initial administration of, for example, naked DNA followed by a boost using recombinant virus encoding the vaccine, or recombinant protein/polypeptide or a peptide mixture administered in an adjuvant.
For example, the initial immunization may be performed using an expression vector, such as that constructed in the Example entitled "Construction of "Minigene" Multi-Epitope DNA Plasmids" in the form of naked nucleic acid administered IM
(or SC or ID) in the amounts of 0.5,5 mg at multiple sites. The nucleic acid (0.1 to 1000 1.1g) can also be administered using a gene gun. Following an incubation period of 3-4 weeks, a booster dose is then administered. The booster can be recombinant fowlpox virus administered at a dose of 5-107 to 5x108 pfu. An alternative recombinant virus, such as an MVA, canarypox, adenovirus, or adeno-associated virus, can also be used for the booster, or the polyepitopic protein or a mixture of the peptides can be administered. For evaluation of vaccine efficacy, patient blood samples are obtained before immunization as well as at intervals following administration of the initial vaccine and booster doses of the vaccine.
Peripheral blood mononuclear cells are isolated from fresh heparinized blood by Ficoll-Hypaque density gradient - centrifugation, aliquoted in freezing media and stored frozen. Samples are assayed for CTL and HTL activity.
Analysis of the results indicates that a magnitude of response sufficient to achieve a therapeutic or protective immunity against 161P2F1OB is generated.
Example 32: Administration of Vaccine Compositions Using Dendritic Cells (DC) Vaccines comprising peptide epitopes of the invention can be administered using APCs, or "professional" APCs .such as DC. In this example, peptide-pulsed DC are administered to a patient to stimulate a CTL response in vivo. In this method, dendritic cells are isolated, expanded, and pulsed with a vaccine comprising peptide CTL and HTL epitopes of the invention. The dendritic cells are infused back into the patient to elicit CTL
and HTL responses in vivo. The induced CTL
and HTL then destroy or facilitate destruction, respectively, of the target cells that bear the 161P2F1OB protein from which the epitopes in the vaccine are derived.
For example, a cocktail of epitope-comprising peptides is administered ex vivo to PBMC, or isolated DC therefrom.
A pharmaceutical to facilitate harvesting of DC can be used, such as ProgenipoietinTM (Monsanto, St. Louis, MO) or GM-CSF/IL-4. After pulsing the DC with peptides, and prior to reinfusion into patients, the DC are washed to remove unbound peptides.
As appreciated clinically, and readily determined by one of skill based on clinical outcomes, the number of DC
reinfused into the patient can vary (see, e.g., Nature Med. 4:328, 1998;
Nature Med. 2:52, 1996 and Prostate 32:272, 1997).
Although 2-50 x 106 DC per patient are typically administered, larger number of DC, such as 107 or 108 can also be provided.
Such cell populations typically contain between 50-90% DC.
In some embodiments, peptide-loaded PBMC are injected into patients without purification of the DC. For example, PBMC generated after treatment with an agent such as ProgenipoiellnTM
are injected into patients without purification of the DC. The total number of PBMC that are administered often ranges from 108 to 1010. Generally, the cell doses injected into patients is based on the percentage of DC in the blood of each patient, as determined, for example, by immunofluorescence analysis with specific anti-DC antibodies. Thus, for example, if ProgenipoietinTM mobilizes 2% DC in the peripheral blood of a given patient, and that patient is to receive 5 x 106 DC, then the patient will be injected with a total of 2.5 x 108 peptide-loaded PBMC. The percent DC mobilized by an agent such as ProgenipoietinTM is typically estimated to be between 2-10%, but can vary as appreciated by one of skill in the art.
Ex vivo activation of CTUHTL responses Alternatively, ex vivo CTL or HTL responses to 161P2F1OB antigens can be induced by incubating, in tissue culture, the patient's, or genetically compatible, CTL or HTL precursor cells together with a source of APC, such as DC, and immunogenic peptides. After an appropriate incubation time (typically about 7-28 days), in which the precursor cells are activated and expanded into effector cells, the cells are infused into the patient, where they will destroy (CTL) or facilitate destruction (NIL) of their specific target cells, i e., tumor cells.
Example 33: An Alternative Method of Identifying and Confirming Motif-Bearing Peptides Another method of identifying and confirming motif-bearing peptides is to elute them from cells bearing defined MI-IC molecules. For example, Ef3V transformed B cell lines used for tissue typing have been extensively characterized to determine which HLA molecules they express. In certain cases these cells express only a single type of HLA molecule.
These cells can be transfected with nucleic acids that express the antigen of interest, e.g. 161P2F10B. Peptides produced by endogenous antigen processing of peptides produced as a result of transfection will then bind to HLA molecules within the cell and be transported and displayed on the cell's surface. Peptides are then eluted from the MLA molecules by exposure to mild acid conditions and their amino acid sequence determined, e.g., by mass spectral analysis (e.g., Kubo of al., J.
Immune!. 152:3913,1994). Because the majority of peptides that bind a particular HLA molecule are mofiebearing, this is an alternative modality for obtaining the motif-bearing peptides correlated with the particular HLA molecule expressed on the cell Alternatively, cell lines that do not express endogenous RA molecules can be trandected with an expression construct encoding a single HLA allele. These cells can then be used as described, I.e., they can then be transfected with nucleic acids that encode 161P2F100 to isolate peptides corresponding to 161P2F1OB that have been presented on the cell surface. Peptides obtained from such an analysis will bear motif(s) that correspond to binding to the single HLA allele that is expressed in the cell.
= As appreciated by one in the ad, one am perform a similar analysis on a cell bearing more than one FAA allele and subsequently determine peptides specific for each HLA allele expressed.
Moreover, one of skill would also recognize that means other than transfection, such-as loading with a protein antigen, can be used to provide a source of antigen to the cell Example 34: Complementary Polvnucleotides Sequences complementary to the 161P2F10B-encoding sequences, or any parts thereof, are used to detect, decrease, or inhibit expression of naturally occurring 161P2F108. Although use of oligonudeotides comprising from about 15 to 30 base pairs is described, essentially the same procedure is used with smaller or with larger sequence fragments.
= Appropriate oligonucleolides are designed using, e.g., OLIGO 4.06 software (National Biosciences) and the coding sequence of 161P2F100, To inhibit transcription, a complementary oligonucleotide is designed from the most unique 5' sequence and used to prevent promoter binding to the coding sequence. To inhibit translation, a complementary ofigonucleolide is designed to prevent ribosomal binding to a 161 P2F108-encoding transcript.
Example 35: Purification of Naturally-occurring or Recombinant 161P2P104Usina 161P2F10B-Specific Antibodies Naturally occurring or recombinant 161P2F100 is substantially purified by immunoaffinity chromatography using antibodies specific for 16IP2F100. An immunoaffinity column is constructed by covalently coupling anti-161P2F100 antibody to an activated chromatographic min, such as CNBr-activated SEPHAROSETM (Amersham Pharmacia Biotech).
After the coupling, the resin Is blocked and washed according to the manufacturer's instructions.
Media containing 161P2F1013 are passed over the immurioaffinity column, and the column is washed under.
conditions that allow the preferential absorbance of 161P2F1OB (e.g., high ionic strength buffers in the presence of detergent). The column is eluted under conditions that disrupt antibody/161P2F1OB binding (e.g., a buffer of pH 2 to pH 3, or a high concentration of a chaotrope, such as urea or thiocyanate ion), and GCR.P is collected.
Example 36: Identification of Molecules Which Interact with 161P2F1OB
161P2F10B, or biologically active fragments thereof, are labeled with 121 1 Bolton-Hunter reagent. (See, e.g., Bolton etal. (1973) Biochem. J. 133:529.) Candidate molecules previously arrayed in the wells of a multi-well plate are incubated with the labeled 161P2F10B, washed, and any wells with labeled 161P2F1OB complex are assayed. Data obtained using different concentrations of 161P2F1OB are used to calculate values for the number, affinity, and association of 161P2F1OB with the candidate molecules.
Example 37: In Vivo Assay for 161P2F1OB Tumor Growth Promotion The effect of the 161P2F1OB protein on tumor cell growth is evaluated in vivo by gene overexpression in tumor-bearing mice. For example, SCID mice are injected subcutaneously on each flank with 1 x 106 of either PC3, TSUPR1, or DU145 cells containing tkNeo empty vector or 161P2F10B. At least two strategies may be used: (1) Constitutive 161P2F108 expression under regulation of a promoter such as a constitutive promoter obtained from the genomes of viruses such as polyoma virus, fowlpox virus (UK 2,211,504 published 5 July 1989), adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus and Simian Virus 40 (SV40), or from heterologous mammalian promoters, e.g., the actin promoter or an immunoglobulin promoter, provided such promoters are compatible with the host cell systems, and (2) regulated expression under control of an inducible vector system, such as ecdysone, tet, etc., provided such promoters are compatible with the host cell systems. Tumor volume is then monitored at the appearance of palpable tumors and followed over time and determines that 161P2F10B-expressing cells grow at a faster rate and/or tumors produced by 161P2F10B-expressing cells demonstrate characteristics of altered aggressiveness (e.g.
enhanced metastasis, vascularization, reduced responsiveness to chemotherapeutic drugs).
Additionally, mice can be implanted with 1 x 106 of the same cells orthotopically to determine that 161P2F1OB has an effect on local growth in the prostate and/or on the ability of the cells to metastasize, e.g., to lungs, lymph nodes, and bone marrow.
The assay is also useful to determine the 161P2F10B-inhibitory effect of candidate therapeutic compositions, such as for example, small molecule drugs, 161P2F1OB intrabodies, 161P2F1OB
antisense molecules and ribozymes.
Example 38: 161P2F1OB Monoclonal Antibody-mediated Inhibition of Prostate Tumors In Vivo.
The significant expression of 161P2F10B, in cancer tissues, together with its restricted expression in normal tissues along with its cell surface expression makes 161P2F1OB an excellent target for antibody therapy. Similarly, 161P2F1OB is a target for T cell-based innmunotherapy. Thus, the therapeutic efficacy of anti-161P2F1OB mAbs is evaluated, e.g., in human prostate cancer xenograft mouse models using androgen-independent LAPC-4 and LAPC-9 xenografts (Craft, N., etal.,. Cancer Res, 1999. 59(19): p. 5030-6), kidney cancer xenografts (AGS-K3, AGS-K6), kidney cancer metastases to lymph node (AGS-K6 met) xenografts, and kidney cancer cell lines transfected with 161P2F10B, such as 769P-161P2F10B, A498-161P2F10B.
Antibody efficacy on tumor growth and metastasis formation is studied, e.g., in mouse orthotopic prostate cancer xenograft models and mouse kidney xenograft models. The antibodies can be unconjugated, as discussed in this Example, or can be conjugated to a therapeutic modality, as appreciated in the art.
Anti-161P2F1OB mAbs inhibit formation of both the androgen-dependent LAPC-9 and androgen-independent PC3-161P2F1OB tumor xenografts. Anti-161P2F1OB mAbs also retard the growth of established orthotopic tumors and prolonged survival of tumor-bearing mice. These results indicate the utility of anti-161P2F10B mAbs in the treatment of local and advanced stages of prostate cancer. (See, e.g., Saffran, D., et al., PNAS 10:1073-1078 or www.pnas.org/cgi/doi/10.1073/pnas.051624698).
Similarly, anti-161P2F1OB mAbs can inhibit formation of AGS-K3 and AGS-K6 tumors in SCID mice, and prevent or retard the growth A498-161P2F1OB tumor xenografts. These results indicate the use of anti-161P2F1OB mAbs in the treatment of prostate and/or kidney cancer.
Administration of the anti-161P2F1OB mAbs leads to retardation of established orthotopic tumor growth and inhibition of metastasis to distant sites, resulting in a significant prolongation in the survival of tumor-bearing mice. These studies indicate that 161P2F1OB is an attractive target for immunotherapy and demonstrate the therapeutic use of anti-161P2F1OB mAbs for the treatment of local and metastatic prostate cancer. This example demonstrates that unconjugated 161P2F1OB monoclonal antibodies are effective to inhibit the growth of human prostate tumor xenografts and human kidney xenografts grown in SCID mice.
Tumor inhibition using multiple unconjugated 161P2F1OB mAbs Materials and Methods 161P2F1OB Monoclonal Antibodies:
Monoclonal antibodies are raised against 161P2F1OB as described in the Example entitled "Generation of 161P2F1OB Monoclonal Antibodies (mAbs)" or are obtained commercially, e.g., 97A6 (Coulter lmmunotech). The antibodies are characterized by ELISA, Western blot, FACS, and immunoprecipitation for their capacity to bind 161P2F10B. Epitope mapping data for the anti-161P2F1OB mAbs, as determined by ELISA and Western analysis, recognize epitopes on the 161P2F1OB protein. The 97A6 antibody binds to amino acids 393-405 of the 161P2F1OB protein shown in Figure 2.
Immunohistochemical analysis of cancer tissues and cells is performed with these antibodies.
The monoclonal antibodies are purified from ascites or hybridoma tissue culture supematants by Protein-G
Sepharose chromatography, dialyzed against PBS, filter sterilized, and stored at -20 C. Protein determinations are performed by a Bradford assay (Bio-Rad, Hercules, CA). A therapeutic monoclonal antibody or a cocktail comprising a mixture of individual monoclonal antibodies is prepared and used for the treatment of mice receiving subcutaneous or orthotopic injections of LAPC-9 prostate tumor xenografts.
Cancer Xenografts and Cell Lines The LAPC-9 xenograft, which expresses a wild-type androgen receptor and produces prostate-specific antigen (PSA), is passaged in 6- to 8-week-old male ICR-severe combined immunodeficient (SCID) mice (Taconic Farms) by s.c.
trocar implant (Craft, N., etal., supra). The AGS-K3 and AGS-K6 kidney xenografts are also passaged by subcutaneous implants in 6- to 8- week old SCID mice. Single-cell suspensions of tumor cells are prepared as described in Craft, etal.
The prostate carcinoma cell line PC3 (American Type Culture Collection) is maintained in RPM; supplemented with L-glutamine and 10% FBS, and the kidney carcinoma line A498 (American Type Culture Collection) is maintained in DMEM
supplemented with L-glutamine and 10% FBS.
PC3-161P2F1OB and A498-161P2F1OB cell populations are generated by retroviral gene transfer as described in Hubert, R.S., et at., STEAP: A Prostate-specific Cell-surface Antigen Highly Expressed in Human Prostate Tumors, Proc Natl Acad Sci U S A, 1999. 96(25): p. 14523-8. Anti-161P2F1OB staining is detected by using an FITC-conjugated goat anti-mouse antibody (Southern Biotechnology Associates) followed by analysis on a Coulter Epics-XL flow cytometer.
Xenociraft Mouse Models.
Subcutaneous (s.c.) tumors are generated by injection of 1 x 106 LAPC-9, AGS-K3, AGS-K6, PC3, PC3-161P2F10B, A498 or A498-i61P2F1OB cells mixed at a 1:1 dilution with Matrigel (Collaborative Research) in the right flank of male SCID mice. To test antibody efficacy on tumor formation, i.p. antibody injections are started on the same day as tumor-cell injections. As a control, mice are injected with either purified mouse IgG (ICN) or PBS; or a purified monoclonal antibody that recognizes an irrelevant antigen not expressed in human cells.
In preliminary studies, no difference is found between mouse IgG or PBS on tumor growth. Tumor sizes are determined by vernier caliper measurements, and the tumor volume is calculated as length x width x height Mice with s.c. tumors greater than 1$ an in diameter are sacrificed. PSA
levels are determined by using a PSA ELISA kit (Anogen, Mississauga, Ontario), Circulating levels of anti-161P2F1OB mAbs are determined by a capture ELISA kit (Bethyl Laboratories. Montgomery, TX), (See, e.g., (Saffran. D., et al., PNAS
10:1073-1078), Orthotopic prostate injections are performed under anesthesia by using ketaminekylazine. For prostate orthotopic studies, an incision is made through the abdominal muscles to expose the bladder and seminal vesicles, which then are delivered through the incision to expose the dorsal prostate 1APC-9 cells (5x 105) mixed with Matrigel are injected into each dorsal lobe in a 10-pt volume. To monitor tumor growth, mice are bled on a weekly basis for determination of PSA
levels. For kidney orthopotic models, an incision Is made through the abdominal muscles to expose the kidney. AGS-K3 or AGS-K6 cells mixed with Matrigel are injected under the kidney capsule. The mice are segregated into groups for the appropriate treatments, with anti-161P2F1OB or control mAbs being injected i.p.
Anti461P2F1OB mAbs Inhibit Growth of 1 1P2F1013-Expressine Xenoeraft-Cancer Tumors The effect of anti-161P2F1013 mAbs on tumor formation is tested by using LAPC-9 anclior AGS-K3 orthotopic models. As compared with the s.c. tumor model, the orthotopic model, which requires Injection of tumor cells directly in the mouse prostate or kidney, respectively, results in a local tumor growth, development of metastasis in distal sites, deterioration of mouse health, and subsequent death (Saffran, D., at at., PNAS
supra; Fu, X., at at, Int J Cancer, 1992.
52(6): p. 987-90; Kubota, T., J Cell Biochem, 1994. 56(1): p. 4-8). The features make the orthotopic model more representative of human disease progression and allowed for tracking of the therapeutic effect of mAbs on clinically relevant end points.
Accordingly, tumor cells are injected into the mouse prostate or kidney, and 2 days later, the mice are segregated into two groups and treated with either: a) 200-500pg, of anti-161P2F1013 Ab, orb) PBS three times per week for two to five weeks.
A major advantage of the orthotopic prostate-cancer model is the abifity to study the development of metastases.
Formation of metastasis in mice bearing established orthotopic tumors is studies by INC analysis on lung sections using an antibody against a prostate-specific cell-surface protein STEAP expressed at high levels in LAPC-9 xenografts (Hubert, R.S., of A, Proc Nail Aced Sci U S A, 1999.98(25): p. 14523-8) or anti-G250 antibody for kidney cancer models.
Mice bearing established orthotopic LAPC-9 tumors are administered 1000pg injections of either ant1-161P2F1OB
mAb or PBS over a 4-week period. Mice in both groups are allowed to establish a high tumor burden (PSA levels greater than 300 ng/m1), to ensure a high frequency of metastasis formation in mouse lungs. Mice then are killed and their prostate/kidney and lungs are analyzed for the presence of tumor cells by 11-1Canalysis.
These studies demonstrate a broad anti-tumor efficacy of anti-161P2F1013 antibodies on initiation and progression of prostate and kidney cancer in xenograft mouse models. Anti-161P2F1013 antibodies Inhibit tumor formation of both androgen-dependent and androgen-independent prostate tumors as well as retarding the growth of already established tumors and prolong the survival of treated mice. Moreover, anti-161P2F108 mAbs demonstrate a dramatic inhibitory effect on the spread of local prostate tumor to distal sites, even in the presence of a large tumor burden. Similar therapeutic effects are seen in the kidney cancer model. Thus, anti-161P2F1OB mAbs are efficacious on major clinically relevant end points (tumor growth), prolongation of survival, and health, Example 39: Therapeutic and Diagnostic use of Anti-161P2F1OB Antibodies in Humans.
Anti-161P2F1OB monoclonal antibodies are safely and effectively used for diagnostic, prophylactic, prognostic and/or therapeutic purposes in humans. Western blot and immunohistochemical analysis of cancer tissues and cancer xenografts with anti-161P2F1OB mAb show strong extensive staining in carcinoma but significantly lower or undetectable levels in normal tissues. Detection of 161P2F1OB in carcinoma and in metastatic disease demonstrates the usefulness of the mAb as a diagnostic and/or prognostic indicator. Anti-161P2F1OB antibodies are therefore used in diagnostic applications such as immunohistochemistry of kidney biopsy specimens to detect cancer from suspect patients.
As determined by flow cytometry, anti-161P2F1OB mAb specifically binds to carcinoma cells. Thus, anti-161P2F108 antibodies are used in diagnostic whole body imaging applications, such as radioimmunoscintigraphy and radioimmunotherapy, (see, e.g., Potamianos S., et. al. Anticancer Res 20(2A):925-948 (2000)) for the detection of localized and metastatic cancers that exhibit expression of 161P2F1OB. Shedding or release of an extracellular domain of 161P2F1OB into the extracellular milieu, such as that seen for alkaline phosphodiesterase B10 (Meerson, N. R., Hepatology 27:563-568 (1998)), allows diagnostic detection of 161P2F1OB by anti-161P2F1OB
antibodies in serum and/or urine samples from suspect patients.
Anti-161P2F1OB antibodies that specifically bind 161P2F1OB are used in therapeutic applications for the treatment of cancers that express 161P2F1OB. Anti-161P2F1OB antibodies are used as an unconjugated modality and as conjugated form in which the antibodies are attached to one of various therapeutic or imaging modalities well known in the art, such as a prodrugs, enzymes or radioisotopes. In preclinical studies, unconjugated and conjugated anti-161P2F1OB antibodies are tested for efficacy of tumor prevention and growth inhibition in the SCID
mouse cancer xenograft models, e.g., kidney cancer models AGS-K3 and AGS-K6, (see, e.g., the Example entitled "161P2F1OB
Monoclonal Antibody-mediated Inhibition of Bladder and Lung Tumors In Vivo"). Either conjugated and unconjugated anti-161P2F1OB antibodies are used as a therapeutic modality in human clinical trials either alone-or in combination with other treatments as described in following Examples.
Example 40: Human Clinical Trials for the Treatment and Diagnosis of Human Carcinomas through use of Human Anti-161P2F1OB Antibodies In vivo Antibodies are used in accordance with the present invention which recognize an epitope on 161P2F10B, and are used in the treatment of certain tumors such as those listed in Table I. Based upon a number of factors, including 161P2F1OB expression levels, tumors such as those listed in Table I are presently preferred indications. In connection with each of these indications, three clinical approaches are successfully pursued.
I.) Adjunctive therapy: In adjunctive therapy, patients are treated with anti-161P2F1OB antibodies in combination with a chemotherapeutic or antineoplastic agent and/or radiation therapy. Primary cancer targets, such as those listed in Table I, are treated under standard protocols by the addition anti-161P2F1OB antibodies to standard first and second line therapy. Protocol designs address effectiveness as assessed by reduction in tumor mass as well as the ability to reduce usual doses of standard chemotherapy. These dosage reductions allow additional and/or prolonged therapy by reducing dose-related toxicity of the chemotherapeutic agent. Anti-161P2F1OB antibodies are utilized in several adjunctive clinical trials in combination with the chemotherapeutic or antineoplastic agents adriamycin (advanced prostrate carcinoma), cisplatin (advanced head and neck and lung carcinomas), taxol (breast cancer), and doxorubicin (preclinical).
IL) Monotherapy: In connection with the use of the anti-161P2F1OB
antibodies in monotherapy of tumors, the antibodies are administered to patients without a chemotherapeutic or antineoplastic agent. In one embodiment, monotherapy is conducted clinically in end stage cancer patients with extensive metastatic disease. Patients show some disease stabilization. Trials demonstrate an effect in refractory patients with cancerous tumors.
III.) Imaging Agent: Through binding a radionuclide (e.g., iodine or yttrium (1131, (90) to anti-161P2F1OB
antibodies, the radiolabeled antibodies are utilized as a diagnostic and/or imaging agent. In such a role, the labeled antibodies localize to both solid tumors, as well as, metastatic lesions of cells expressing 161P2F10B. In connection with the use of the anti-161P2F1OB antibodies as imaging agents, the antibodies are used as an adjunct to surgical treatment of solid tumors, as both a pre-surgical screen as well as a post-operative follow-up to determine what tumor remains and/or returns.
In one embodiment, a (111In)-161P2F1OB antibody is used as an imaging agent in a Phase I human clinical trial in patients having a carcinoma that expresses 161P2F1OB (by analogy see, e.g., Divgi etal.
J. Natl. Cancer Inst. 83:97-104 (1991)).
Patients are followed with standard anterior and posterior gamma camera. The results indicate that primary lesions and metastatic lesions are identified Dose and Route of Administration As appreciated by those of ordinary skill in the art, dosing considerations can be determined through comparison with the analogous products that are in the clinic. Thus, anti-161P2F1OB
antibodies can be administered with doses in the range of 5 to 400 mg/m 2, with the lower doses used, e.g., in connection with safety studies. The affinity of anti-161P2F1OB
antibodies relative to the affinity of a known antibody for its target is one parameter used by those of skill in the art for determining analogous dose regimens. Further, anti-161P2F1OB antibodies that are fully human antibodies, as compared to the chimeric antibody, have slower clearance; accordingly, dosing in patients with such fully human anti-161P2F1OB
antibodies can be lower, perhaps in the range of 50 to 300 mg/m2, and still remain efficacious. Dosing in mg/m2, as opposed to the conventional measurement of dose in mg/kg, is a measurement based on surface area and is a convenient dosing measurement that is designed to include patients of all sizes from infants to adults.
Three distinct delivery approaches are useful for delivery of anti-161P2F1OB
antibodies. Conventional intravenous delivery is one standard delivery technique for many tumors. However, in connection with tumors in the peritoneal cavity, such as tumors of the ovaries, biliary duct, other ducts, and the like, intraperitoneal administration may prove favorable for obtaining high dose of antibody at the tumor and to also minimize antibody clearance. In a similar manner, certain solid tumors possess vasculature that is appropriate for regional perfusion.
Regional perfusion allows for a high dose of antibody _ at the site of a tumor and minimizes short term clearance of the antibody.
Clinical Development Plan (CDP) Overview: The CDP follows and develops treatments of anti-161P2F1OB antibodies in connection with adjunctive therapy, monotherapy, and as an imaging agent. Trials initially demonstrate safety and thereafter confirm efficacy in repeat doses. Trails are open label comparing standard chemotherapy with standard therapy plus anti-161P2F1OB antibodies. As will be appreciated, one criteria that can be utilized in connection with enrollment of patients is 161P2F1OB expression levels in their tumors as determined by biopsy.
As with any protein or antibody infusion-based therapeutic, safety concerns are related primarily to (i) cytokine release syndrome, i.e., hypotension, fever, shaking, chills; (ii) the development of an immunogenic response to the material (i.e., development of human antibodies by the patient to the antibody therapeutic, or HAHA response); and, (iii) toxicity to normal cells that express 161P2F10B. Standard tests and follow-up are utilized to monitor each of these safety concerns.
Anti-161P2F1OB antibodies are found to be safe upon human administration.

Example 41: Human Clinical Trial Adiunctiye Therapy with Human Anti-161P2F1OB
Antibody and Chemotherapeutic Agent A phase I human clinical trial is initiated to assess the safety of six intravenous doses of a human anti-161P2F1OB
antibody in connection with the treatment of a solid tumor, e.g., a cancer of a tissue listed in Table I. In the study, the safety of single doses of anti-161P2F1OB antibodies when utilized as an adjunctive therapy to an antineoplastic or chemotherapeutic agent as defined herein, such as, without limitation:
cisplatin, topotecan, doxorubicin, adriamycin, taxol, or the like, is assessed. The trial design includes delivery of six single doses of an anti-161P2F1OB antibody with dosage of antibody escalating from approximately about 25 mg/m 2to about 275 mg/m 2over the course of the treatment in accordance with the following schedule:
Day 0 Day 7 Day 14 Day 21 Day 28 Day 35 mAb Dose 25 75 125 175 225 275 mg/m 2 mg/m 2 mg/m 2 mg/m 2 mg/m 2 mg/m 2 Chemotherapy +
(standard dose) Patients are closely followed for one-week following each administration of antibody and chemotherapy. In particular, patients are assessed for the safety concerns mentioned above: (i) cytokine release syndrome, i.e., hypotension, fever, shaking, chills; (ii) the development of an immunogenic response to the material (i.e., development of human antibodies by the patient to the human antibody therapeutic, or HAHA
response); and, (iii) toxicity to normal cells that express 161P2F10B. Standard tests and follow-up are utilized to monitor each of these safety concerns. Patients are also assessed for clinical outcome, and particularly reduction in tumor mass as evidenced by MRI or other imaging.
The anti-161P2F1OB antibodies are demonstrated to be safe and efficacious, Phase II trials confirm the efficacy and refine optimum dosing.
Example 42: Human Clinical Trial: Monotherapy with Human Anti-161P2F1OB
Antibody Anti-161P2F1OB antibodies are safe in connection with the above-discussed adjunctive trial, a Phase II human clinical trial confirms the efficacy and optimum dosing for monotherapy. Such trial is accomplished, and entails the same safety and outcome analyses, to the above-described adjunctive trial with the exception being that patients do not receive chemotherapy concurrently with the receipt of doses of anti-161P2F1OB
antibodies.
Example 43: Human Clinical Trial: Diagnostic Imaging with Anti-161P2F1OB
Antibody Once again, as the adjunctive therapy discussed above is safe within the safety criteria discussed above, a human clinical trial is conducted concerning the use of anti-161P2F1OB antibodies as a diagnostic imaging agent The protocol is designed in a substantially similar manner to those described in the art, such as in Divgi et al. J. Natl. Cancer Inst. 83:97-104 (1991). The antibodies are found to be both safe and efficacious when used as a diagnostic modality.
Example 44: Homology Comparison of 161P2F1OB to Known Sequences The 161P2F1OB gene is identical to a previously cloned and sequenced gene, namely ectonucleotide pyrophosphatase/phosphodiesterase 3 (gi 4826896) (Jin-Hua Petal, Genomics 1997,45:412), also known as phosphodiesterase-I beta; gp13ORB13-6; E-NPP3 (ENPP3), PDNP3 and CD203c. The 161P2F1OB protein shows 100%
identity to human ectonucleotide pyrophosphatase/phosphodiesterase 3 (gi 4826896), and 81% homology and 89% identity to rat alkaline phosphodiesterase (gi 1699034). The 161P2F1OB protein consists of 875 amino acids, with calculated molecular weight of 100.09 kDa, and pl of 6.12. 161P2F1OB is a cell surface protein as shown by immunostaining in basophils (Buhring HJ et al, Blood 2001, 97:3303) and in epithelial tumor cells as shown in the example entitled "Expression of 161P2F1OB protein in kidney cancer xenograft tissues". Some localization to the golgi-endoplasmic fraction has also been observed (Geoffroy Vet al, Arch Biochem Biophys. 2001, 387:154). Two isoforms of phosphodiesterase 3 have been identified, with one protein containing an additional 145 aa at its amino-terminus (Choi YH et al, Biochem J. 2001, 353:41).
In addition, two variants of 161P2F1OB have been identified. The first variant contains a point mutation at amino acid 122 of the 161P2F1OB protein, changing a lysine to an arginine at that position. The second variant contains a single nucleotide polymorphisms, identified at position 383, resulting in a change in amino acid from threonine to proline at that position see URL located on the World Wide Web at (mcbi.nlm.nih.gov/SNP/snp_ref.cgi?typer-rs&rs=1054222) (figure 4A and 4B). In addition, we have recently identified another variant of 161P2F10B, namely 161P2F1OB v.7. This variant differs from v.1 at its N-terminus as it lacks the first 34 aa found in v.1. The loss of the N-terminal 34 aa affects the localization of 161P2F1OB
v.7. PSort analysis reveled that, while 161P2F1OB v.1 is primarily located at the plasma memebrane, 161P2F1OB v.7 primarily localizes to the cytoplasm (52%) with some localization to the nucleus (17%).
Motif analysis revealed the presence of several known motifs, including 2-3 somatostatin B domains located at the amino terminus of the 161P2F1OB protein, a phosphodiesterase domain and an endonuclease domain at the C-terminus.
161P2F1OB belongs to a family of closely related phosphodiesterases, consisting of PDNP1, -2, and -3 (Bollen Metal, Crit.
Rev. Biochem Mol. Biol. 2000, 35: 393). M three members of this family are type II proteins, with a short N-terminus domain located intracellularly. They contain one transmembrane domain, a catalytic phosphodiesterase domain and a C-terminal nuclease domain.
Phosphodiesterase 3 expression has been detected in human neoplastic submandibular cells, glioma cells, and tansformed lymphocytes (Murata T et al, Anticancer Drugs 2001, 12:79; Andoh K
et a), Biochim Biophys Acta 1999, 1446:213; Ekholm D et al, Biochem Pharmacol 1999, 58: 935).
Phosphodiesterase 3 plays an important role in several biological processes, including release of nucleotides, cell differentiation, metabolism, cell growth, survival, angiogenesis and cell motility (Bollen M et al, Grit. Rev. Biochem Mol. Biol.
2000, 35: 393; Rawadi Get al, Endocrinol 2001, 142:4673; DeFouw Let al, Microvasc Res 2001, 62:263). In addition, Phosphodiesterase 3 regulates gene expression in epithelial cells, including the expression of key adhesion molecules such as VCAM-1 (Blease K et al, Br J Pharmacol. 1998, 124:229).
This information indicates that 161P2F1OB plays a role in the growth of mammalian cells, supports cell survival and motility, and regulate gene transcription by regulating events in the nucleus.
Accordingly, when 161P2F1OB functions as a regulator of cell transformation, tumor formation, or as a modulator of transcription involved in activating genes associated with inflammation, tumorigenesis or proliferation, 161P2F1OB is used for therapeutic, diagnostic, prognostic and/or preventative purposes. In addition, when a molecule, such as a a variant, polymorphism or SNP of 161P2F110B is expressed in cancerous tissues, such as those listed in Table I, they are used for therapeutic, diagnostic, prognostic and/or preventative purposes.
Example 45: Regulation of Transcription The cell surface localization of 161P2F1OB and ability to regulate VCAM
expression indicate that 161P2F1OB is effectively used as a modulator of the transcriptional regulation of eukaryotic genes. Regulation of gene expression is confirmed, e.g., by studying gene expression in cells expressing or lacking 161P2F1OB. For this purpose, two types of experiments are performed.

In the first set of experiments, RNA from parental and 161P2F108-expressing cells are extracted and hybridized to commercially available gene arrays (Clontech) (Smid-Koopnnan E et al. Br J
Cancer. 2000. 83:246). Resting cells as well as cells treated with FBS or androgen are compared. Differentially expressed genes are identified in accordance with procedures known in the art. The differentially expressed genes are then mapped to biological pathways (Chen K et al.
Thyroid. 2001. 11:41.).
In the second set of experiments, specific transcriptional pathway activation is evaluated using commercially available (Stratagene) luciferase reporter constructs including: NFkB-luc, SRE-Iuc, ELK1-luc, ARE-Iuc, p53-luc, and CRE-Iuc.
These transcriptional reporters contain consensus binding sites for known transcription factors that lie downstream of well-characterized signal transduction pathways, and represent a good tool to ascertain pathway activation and screen for positive and negative modulators of pathway activation.
Thus, 161P2F1OB plays a role in gene regulation, and it is used as a target for diagnostic, prognostic, preventative and/or therapeutic purposes.
Example 46: Identification and Confirmation of Potential Simla' Transduction Pathways Many mammalian proteins have been reported to interact with signaling molecules and to participate in regulating signaling pathways. (J Neurochem. 2001; 76:217-223). In particular, GPCRs have been reported to activate MAK cascades as well as G proteins, and been associated with the EGFR pathway in epithelial cells (Naor, Z., et al, Trends Endocrinol Metab. 2000, 11:91; Vacca F et al, Cancer Res. 2000, 60:5310; Della Rocca GJ
et al, J Biol Chem. 1999, 274:13978).
Using immunoprecipitation and Western blotting techniques, proteins are identified that associate with 161P2F1OB and mediate signaling events. Several pathways known to play a role in cancer biology can be regulated by 161P2F10B, including phospholipid pathways such as PI3K, AKT, etc, adhesion and migration pathways, including FAK, Rho, Rac-1, etc, as well as mitogenic/survival cascades such as ERK, p38, etc (Cell Growth Differ. 2000,11:279; J Biol Chem. 1999, 274:801; Oncogene. 2000, 19:3003, J. Cell Biol. 1997, 138:913.).
To confirm that 161P2F1OB directly or indirectly activates known signal transduction pathways in cells, luciferase (luc) based transcriptional reporter assays are carried out in cells expressing individual genes. These transcriptional reporters contain consensus-binding sites for known transcription factors that lie downstream of well-characterized signal transduction pathways. The reporters and examples of these associated transcription factors, signal transduction pathways, and activation stimuli are listed below.
1. NFkB-luc, NFkB/Rel; lk-kinase/SAPK; growth/apoptosis/stress 2. SRE-luc, SRF/TCF/ELK1; MAPK/SAPK; growth/differentiation 3. AP-1-luc, FOS/JUN; MAPK/SAPK/PKC; growth/apoptosis/stress 4. ARE-Iuc, androgen receptor; steroids/MAPK;
growth/differentiation/apoptosis 5. p53-luc, p53; SAPK; growth/differentiation/apoptosis 6. CRE-Iuc, CREB/ATF2; PKNp38; growth/apoptosis/stress Gene-mediated effects can be assayed in cells showing mRNA expression.
Luciferase reporter plasmids can be introduced by lipid-mediated transfection (TFX-50, Promega). Luciferase activity, an indicator of relative transcriptional activity, is measured by incubation of cell extracts with luciferin substrate and luminescence of the reaction is monitored in a luminometer.

Signaling pathways activated by 161P2F1OB are mapped and used for the identification and validation of therapeutic targets. When 161P2F1OB is involved in cell signaling, it is used as target for diagnostic, prognostic, preventative and/or therapeutic purposes.
Example 47: Involvement in Tumor Progression The 161P2F1OB gene can contribute to the growth of cancer cells. The role of 161P2F1OB in tumor growth is confirmed in a variety of primary and transfected cell lines including prostate, colon, bladder and kidney cell lines, as well as NIH 3T3 cells engineered to stably express 161P2F1OB. Parental cells lacking 161P2F1OB and cells expressing 161P2F1OB
are evaluated for cell growth using a well-documented proliferation assay (Fraser SP, Grimes JA, Djamgoz MB. Prostate.
2000;44:61, Johnson DE, Ochieng J, Evans SL. Anticancer Drugs. 1996, 7:288).
To confirm the role of 161P2F1OB in the transformation process, its effect in colony forming assays is investigated.
Parental NIH-3T3 cells lacking 161P2F1OB are compared to NIH-3T3 cells expressing 161P2F10B, using a soft agar assay under stringent and more permissive conditions (Song Z. et al. Cancer Res.
2000;60:6730).
To confirm the role of 161P2F1OB in invasion and metastasis of cancer cells, a well-established assay is used, e.g., a Transwell Insert System assay (Becton Dickinson) (Cancer Res. 1999;
59:6010). Control cells, including prostate, colon, bladder and kidney cell lines lacking 161P2F1OB are compared to cells expressing 161P2F1OB. Cells are loaded with the fluorescent dye, calcein, and plated in the top well of the Transwell insert coated with a basement membrane analog.
Invasion is determined by fluorescence of cells in the lower chamber relative to the fluorescence of the entire cell population.
. Using this approach we have demonstrated that 161P2F1OB induces the invasion of 3T3 cells through the basement membrane analog matrigel (Figure 22). As shown in figure 22, 3T3-neo cells that do not express 161P2F1OB exhibit - negligible levels of invasion though matrigel. Compared to 3T3-neo cells, 3T3-161P2F1OB cells, which express abundant levels of 161P2F1OB (Figure 16), invade through matrigel and migrate to the lower chamber of the transwell system in a manner similar to that observed with cells expressing the strong protooncogene 12V-Ras.
161P2F1OB can also play a role in cell cycle and apoptosis. Parental cells and cells expressing 161P2F1OB are compared for differences in cell cycle regulation using a well-established BrdU assay (Abdel-Malek ZA. J Cell Physiol.
1988, 136:247). In short, cells are grown under both optimal (full serum) and limiting (low serum) conditions are labeled with BrdU and stained with anti-BrdU Ab and propidium iodide. Cells are analyzed for entry into the G1, S, and G2M phases of the cell cycle.
In contrast to normal cells, cancer cells have been shown to withstand stress, growth factor deprivation and pro-apoptotic signals, thereby providing tumors with a growth and survival advantage. The effect of stress on apoptosis is evaluated in control parental cells and cells expressing 161P2F10B, including normal and tumor prostate, colon and lung cells using standard assays methods including annexin V binding and caspase activation (Moore A,et al, Methods Cell Biol.
1998;57:265; Porter AG, Janicke RU. Cell Death Differ. 1999; 6:99). Engineered and parental cells were treated with various chemotherapeutic agents, such as etoposide, doxorubicinõ kinase inhibitors such as staurosporine, DNA damaging agents such as UV, hypoxia and protein synthesis inhibitors, such as cycloheximide. Cells were stained with annexin V-FITC
and cell death measured by FACS analysis. Figure 20 shows that expression of 161P2F1OB prevent the apoptosis of 3T3 cells exposed to staurosporine or UV irradiation. While 64% and 62% of 3T3-neo cells underwent apoptosis in response to staurosporine and UV irradiation, respectively, only 14% and 30% of 161P2F10B-expressing 3T3 cells died under the same conditions. Similar results were obtained in another experiment comparing the effect of staurosporine and UV irradiation on 3T3-neo cells and clonal populations of 3T3-161P2F1OB cell lines (Figure 19).
As with the population of 3T3-161P2F1OB, clones 3T3-161P2F1OB-C and 3T3-161P2F1OB-10B were resistant to staurosporine-induced cell death. Since caspase activation is a hallmark of apoptosis and serves to distinguish apoptosis from other forms of cell death, we investigated the effect of to chemotherapeutic agent and, staurosporine on the apoptosis of kidney cancer cells using caspase activation as assy read out (Figure 21). The 769 kidney tumor cells that normally lack 161P2F1OB were engineered to express the 161P2F1OB protein as describe in example 8, Production of Recombinant 161P2F1OB in Higher Eukaryotic Systems, above.
The cells were treated with chemotherapeutic agents or staurosporine, lysed and analyzed for caspase activity. Figure 21 shows that expression of 161P2F1OB prevents caspase activation in 161P2F1OB-expressing kidney cancer cells treated with doxorubicin or staurosporine. These results show that 161P2F1OB imparts resistance to the chemotherapeutic drug doxorubicin and to saurosporine-induced cell death in kidney cancer cells.
A characteristic that distinguishes cancer cells from normal cells is their ability to become serum independent and survive in low serum conditions. The effect of serum deprivation on the survival of 161P2F1OB expressing cells was studied using caspase activation as a read out. The fibroblast cell line Rat-1 becomes growth arrested when serum deprived, thereby mimicking normal non-transformed cells (James L, Eisenman RN. Proc Natl Acad Sci U S A. 2002, 99:10429). Rat-1 cells expressing c-Myc (Rat-Myc) undergo apoptosis under serum deprivation conditions (James L, Eisenman RN, Proc Natl Acad Sci U S A. 2002, 99:10429). Rat-1 and Rat-Myc cells were engineered to stably express 161P2F10B. The cells were grown in 0.1% or 10% FBS and examined for apoptosis by microscopy and caspase activity (Figures 17 and 18). When 161P2F1OB is stably expressed in Rat-Myc cells, it inhibits Myc-induced apoptosis and reduces caspase ativity to background levels. The inhibition of cell death by 161P2F1OB plays a critical role in regulating tumor progression and tumor load.
When 161P2F1OB plays a role in cell growth, transformation, invasion or apoptosis, it is used as a target for diagnostic, prognostic, preventative and/or therapeutic purposes.
Example 48: Involvement in Anctiogenesis Angiogenesis or new capillary blood vessel formation is necessary for tumor growth (Hanahan D, Folkman J. Cell.
1996, 86:353; Folkman J. Endocrinology. 1998 139:441). Based on the effect of phsophodieseterase inhibitors on endothelial cells, and the homology of 161P2F1OB to other ENPP family members, 161P2F1OB plays a role in angiogenesis (DeFouw Let al, Microvasc Res 2001, 62:263). Several assays have been developed to measure angiogenesis in vitro and in vivo, such as the tissue culture assays endothelial cell tube formation and endothelial cell proliferation. Using these assays as well as in vitro neo-vascularization, the role of 161P2F1OB in angiogenesis, enhancement or inhibition, is confirmed.
For example, endothelial cells engineered to express 161P2F1OB are evaluated using tube formation and proliferation assays. The effect of 161P2F1OB is also confirmed in animal models in vivo. For example, cells either expressing or lacking 161P2F1OB are implanted subcutaneously in immunocompromised mice. Endothelial cell migration and angiogenesis are evaluated 5-15 days later using immunohistochennistry techniques. Similarly, the secreted extracellular portion of 161P2F1OB can function as an angiogenic factor and enhance the proliferation and tube formation of endothelial cells. The effect of the extracellular domain of 161P2F1013 on angiogenesis is supported by its similarity to other ENPPs, with biologically active secreted extracellular domain. When 161P2F1OB
affects angiogenesis, and it is used as a target for diagnostic, prognostic, preventative and/or therapeutic purposes.
Example 49: Involvement in Protein-Protein Interactions Several phsophodiesterases have been shown to interact with other proteins, thereby regulating gene transcription, as well as cell growth (Butt E et al, Mol Pharmacol. 1995, 47:340). Using immunoprecipitation techniques as well as two yeast hybrid systems, proteins are identified that associate with 161P2F10B.
Immunoprecipitates from cells expressing 161P2F1OB and cells lacking 161P2F1OB are compared for specific protein-protein associations.

Studies are performed to confirm the extent of association of 161P2F1OB with effector molecules, such as nuclear proteins, transcription factors, kinases, phsophates etc. Studies comparing 161P2F1OB positive and 161P2F1OB negative cells as well as studies comparing unstimulatediresting cells and cells treated with epithelial cell activators, such as cytokines, growth factors, androgen and anti-integrin Ab reveal unique interactions.
In addition, protein-protein interactions are confirmed using two yeast hybrid methodology (Curr Opin Chem Biol.
1999, 3:64). A vector carrying a library of proteins fused to the activation domain of a transcription factor is introduced into yeast expressing a 161P2F1OB-DNA-binding domain fusion protein and a reporter construct. Protein-protein interaction is detected by colorimetric reporter activity. Specific association with effector molecules and transcription factors directs one of skill to the mode of action of 161P2F1OB, and thus identifies therapeutic, prognostic, preventative and/or diagnostic targets for cancer. This and similar assays are also used to identify and screen for small molecules that interact with 161P2F10B.
Thus it is found that 161P2F1OB associates with proteins and small molecules.
Accordingly, 161P2F10Band these proteins and small molecules are used for diagnostic, prognostic, preventative and/or therapeutic purposes.
Example 50: Involvement in Cell Adhesion Cell adhesion plays a critical role in tissue colonization and metastasis.
161P2F1OB can participate in cellular organization, and as a consequence cell adhesion and motility. To confirm that 161P2F1OB regulates cell adhesion, control cells lacking 161P2F1OB are compared to cells expressing 161P2F10B, using techniques previously described (see, e.g., Haier et al, Br. J. Cancer. 1999, 80:1867; Lehr and Pienta, J. Natl. Cancer Inst. 1998, 90:118). Briefly, in one embodiment, cells labeled with a fluorescent indicator, such as calcein, are incubated on tissue culture wells coated with media alone or with matrix proteins. Adherent cells are detected by fluorimetric analysis and percent adhesion is calculated.
In another embodiment, cells lacking or expressing 161P2F1OB are analyzed for their ability to mediate cell-cell adhesion using similar experimental techniques as described above. Both of these experimental systems are used to identify proteins, antibodies and/or small molecules that modulate cell adhesion to extracellular matrix and cell-cell interaction. Cell adhesion plays a critical role in tumor growth, progression, and, colonization, and 161P2F1OB is involved in these processes. Thus, it serves as a diagnostic, prognostic, preventative and/or therapeutic modality.
Example 51: Phosphodiesterase Activity of 161P2F1OB expressing recombinant cell lines.
In order to delineate the function 161P2F1OB, several cell lines that lack 161P2F1OB were transduced with 161P2F1OB-encoding retovirus as described in example 8, Production of Recombinant 161P2F1OB in Higher Eukaryotic Systems, above. Cell lines were characterized for 161P2F1OB cell surface expression by FACS analysis (figures 28, 29, 30, and 16). cDNA was stably introduced into the fibroblast lines NIH 313 and Rat-1, myeloma NSO cells, and kidney cancer CaKi cells. The cells were immunostained with anti-CD203c mAb and analyzed by flow cytometry. Figures 28, 29, 30, and 16 show that while parental cells fail to express 161P2F1OB, engineered lines demonstrate abundant expression of 161P2F1OB on their cell surface. Expression of 161P2F1OB in engineered cells was compared to that in UT7, a cell line that expresses 161P2F1OB endogenously (Figure 28). Our results show that engineered Rat-1- and 313 cells express 161P2F1OB at levels comparable to UT7 cells.
Since 161P2F1OB is identical to the ecto-enzyme ENPP3 phosphodieterase, and members of the ENPP family possess pyrophosphatase activities, the recombinant cell lines were also characterized for phosphodiesterase activity (figures 28, 29, 30, and 16). Control and 161P2F10B-expressing cells were lysates or intact cells were incubated for at 37 degrees in 20mM Tris/HCL, pH 9.6 containing 5 mM MgCl2 and 1mM p-nitrophenyl thymidine-5'-L-monophosphate. The reaction was terminated by the addition of 0.1 N NaOH and the reaction product quantified by reading absorbance at 410nm.
Figures 28, 29, 30, and 16 show that 161P2F1OB expression parallels phosphodiesterase activity. Using CaKi cells expressing either wild type or mutant 161P2F10B, we show that mutation of T205 inhibits phosphodiesterase activity (figure 30). When 161P2F1OB shows phosphodiesterase activity, it is used as a target for diagnostic, prognostic, preventative and/or therapeutic purposes.
In addition to phosphodiesterase activity, members of the ENPP family exhibit lysophospholipase D (lysoPLD) activity (Umezu-Goto M et at, J Cell Biol. 2002, 158: 227). ENPP-2 (aka autotoxin) in particular was found to act on lysophosphatidylcholine (LPC) to generate lysophosphatidic acid (LPA) (Umezu-Goto M et at, J Cell Biol. 2002, 158: 227;
Tokumura A et al, J boil. Chem 2002, 277:39436). LPA is involved in various biological functions associated with tumor development, including cell proliferation and invasion (Gschwind A, Prenzel N, Ultich A. Cancer Res. 2002, 62:6329).
Based on the homology of 161P1F1OB to other ENPP family members, 161P2F1OB has lysoPLD activity. The lysoPLD
activity of 161P2F1OB expressing cells is compared to cells lacking 161P2F1OB
using a standard choline release assay. In short, cell lysates are incubated with LPC for 1 hr at 37 C. Liberated choline is detected by fluoremetry following the addition of choline oxidase. When 161P2F1OB shows lysoPLD activity, it is used as a target for diagnostic, prognostic, preventative and/or therapeutic purposes.
Example 52: RNA interference (RNAil Several methods of reducing or abolishing the expression of specific genes have been used for confirming the importance of said genes in tumor growth and progression. These methods include antisense oligonucleotides, morpholino, ribozyme, etc that function in a sequence specific manner to prevent gene transcription or translation. More recently, RNA
interference by duplexes of short nucleotide RNAs has been shown to inhibit gene expression in a sequence specific manner in mammalian cells (Elbashir S et at, Nature 2001, 411:494). RNA interference (RNAi) makes use of sequence specific double stranded RNA known as small interfering RNAs (siRNAs) to prevent gene expression. Small interfering RNA (siRNA) are transfected into mammalian cells and thereby mediate sequence specific mRNA degradation. (Elbashir, eta!, Nature, 2001; 411: 494). Similarly, siRNA have been used to generate stable vector systems that can be delivered in vitro and in vivo to mammalian cells, thereby providing therapeutic use for siRNAs (Lee N
et al, Nature Biotechnol 2002, 19:500).
Several siRNAs can be used to modulate the expression of 161P2F1OB in mammalian cells, including for example the following siRNA oligonucleotide sequences:
161P2F1OB (1) target: GAAUCUACGUUGACUUUAG (corresponding to nucleotides 4-23 of 161P2F1OB ORF) (SEQ ID NO: 39) The sense strand of 161P2F1OB (1) can labeled at 3' with fluorescein, 6-FAM
(ABS 494nm, EMM 525 nm, green) for easy detection. The siRNA is dissolved in RNA-free sterile buffer (100mM KOAc, 30 mM HEPES KOH, 2mM MOAc, at pH 7.4) to make 20 pM stock (200x). The siRNa is transfected into various normal and tumor cells, including UT7, 3T3-161P2F1OB, CaKi-161P2F1OB and Rat-161P2F1OB cells. Control, non-specific oligonucleotide is used as a control to rule out any non-specific effect of 161P2F1OB siRNA
oligonucleotides Protein expression is determined 24-48 hours after transfection by immunostaining followed by flow cytometry. In addition, confirmation of altered gene expression is performed by Western blotting.
Cells transfected with control or 161P2F10B-specific siRNAi are compared using functional assays described above, including invasion, proliferation, colony formation and response to apoptotic stimuli. Therefore, the RNA oligonucleotide sequences are used to assess how modulating the expression of a 161P2F1OB gene affects function of cancer cells and/or tissues.
Accordingly, the RNA oligonucleotide sequences are used in therapeutic and prophylactic applications.

Example 53: Generation of antibodies to 161P2F1OB using peptide encoding the caalytic domain of 161P2F1OB
as the immunogen.
In one embodiment peptides of 22 amino acids encompassing the161P2F1OB
catalytic domain (Threonine (T) at position 205), CGIHSKYMRAMYPTKTFPNHYT (SEQ ID NO: 40) were generated. These were, synthesized and the peptides were coupled to KLH through the N-terminal cysteine residue.
Balb/c mice were immunized intraperitoneally (i.p.) with 10gg of peptide every 2 weeks over a 4 week period. The initial immunization was given i.p. in Complete Freunds Adjuvant (CFA) and the subsequent two immunizations were given i.p. in Incomplete Freunds Adjuvant (IFA).
To determine the specificity of the response following immunization, mice were bled 10 days after the final immunization. Reactivity was determined by Enzyme Linked lmmunosorbent Assay (ELISA) using non-KLH conjugated (free) peptide as a target.Mice with the highest titers were given a final boost of 10 pg peptide in PBS and sacrificed for fusion 3 days later. Spleen cells from the immunized mice were fused with mouse Sp2/0 myeloma cells using PEG 1500 according to standard protocols (Kohler et al, Eur. J. Immunol 6: 511 (1976)).
Fused cells were plated in 10 96 well microtiter plates and hybridomas were selected using HAT media supplement. Supernatants from fusion wells were screened 10-17 days later by ELISA against 161P2F1OB peptide, and clones were then checked for the ability of the monoclonal antibody to recognize cell membrane 161P2F1OB by FACS on 161P2F10 expressing Rat-1 cells.
Example 54: Generation of antibodies to 161P2F1OB using protein encoding the whole extra cellular domain (aa 1-975) of 161P2F1OB as the immunogen.
In one embodiment the whole extra cellular domain of 161P2F1OB fused at the C' terminal with 6 Histidines (6-His for purification was purified hor use as an immunogen.
Balb/c mice were immunized intraperitoneally (i.p.) with lOgg of protein every 2 weeks over a 4 week period. The initial immunization was given i.p. in Complete Freunds Adjuvant (CFA) and thesubsequent two immunizations were given i.p. in Incomplete Freunds Adjuvant (IFA).
To determine the specificity of the response following immunization, mice were bled 10 days after the final immunization. Reactivity was determined by Enzyme Linked Immunosorbent Assay (ELISA) using purified protein as a screening agent.
Mice with the highest titers were given a final boost of 10 pg protein in PBS
and sacrificed for fusion 3 days later.
Spleen cells from the immunized mice were fused with mouse Sp2/0 myeloma cells using PEG 1500 according to standard protocols (Kohler et at, Eur. J. Immunol 6: 511 (1976)). Fused cells were plated in 10 96 well microtiter plates and hybridomas were selected using HAT media supplement. Supematants from fusion wells were screened 10-17 days later by ELISA against 161P2F1OB protein, and clones were then checked for the ability of the monoclonal antivody to recognize cell membrane 161P2F1OB by FACS on 161P2F10 expressing Rat-1 cells.
Example 55: Generation Mabs to 161P2F1OB Using DNA Immunization with a vector encoding 161P2F1OB fused at the C' terminus with human IgG Fc.
In another embodiment, a vector was constructed that encodes the 975 amino acids of the 161P2F10 extra cellular domain fused at the C-terminus to the human immunoglobulin G1 (IgG) Fc (hinge, CH2, CH3 regions). This construct was used in a DNA based immunization strategy.
Balb/c mice were immunized intra-dermally (ID) at the base of their tail.
Three immunizations were given to each mouse of 100gg of DNA in PBS over a two-week period. To increase the immune response, each mouse was given an i.p.
boost of 2 pg of 161P2F1OB-Fc protein in tissue culture media 10 days after the final DNA immunization. Bleeds were , collected 10 days after the final immunization and reactivity in the sera to the middle loop of 161P2F1OB was tested by ELISA
using 161P2F10B-Fc fusion protein as a target (test 1). In parallel the sera were also tested on an unrelated human Fc fusion protein (test 2). Specific reactivity to the 161P2F1OB portion of the fusion protein was indicated.
All mice were sacrificed and fusions and hybridoma selection was carried out as described in Example 54. Hybridoma supernatants were screened 10-17 days later by ELISA using 161P2F10B-Fc protein as target. 161P2F10B-Fc positives were subsequently cross-screened on irrelevant Fc proteins to identify 161P2F10 specific clones. Monoclonal antibodies were tested for specificity and reactivity to cell surface 161p2F1OB using recombinant Rat 1 cells. Several antibodies were identified this way including X41(4)6, X41(3)15, X41(3)17, X41(3)29, X41(3)37 and X41(3)50. These antibodies or binding region thereof secreted by a hybridoma entitled X41(3)15/29/37, X41(4)6, X41(3)17, and X41(3)50 were deposited with the American Type Culture Collection (ATCC; 10801 University Blvd., Manassas, VA
20110-2209 USA) on 07 November 2002 and assigned as Accession No. PTA-4791, PTA-4794, PTA-4792, and PTA-4793, respectively. FACS data for these monoclonal antibodies is shown on (Figure 40).
Example 56: Generation of Maim to 161P2F1OB Using DNA Immunization with a vector encoding 161P2F1OB fused at the C' terminus with the mvc His Tag.
In another embodiment, a vector was constructed that encodes the 975 amino acids of the 161P2F10 extra cellular domain fused at the C-terminus to the myc-His tag. This construct was used in a DNA based immunization strategy.
Balb/c mice were immunized intra-dermally (ID) at the base of their tail.
Three immunizations were given to each mouse of 10014 of DNA in PBS over a two-week period. To increase the immune response, each mouse was given an i.p.
boost of 2 pg of 161P2F10B-Fc protein in tissue culture media 10 days after the final DNA immunization. Bleeds were collected 10 days after the final immunization and reactivity in the sera to the middle loop of 161P2F1OB was tested by ELISA
using 161P2F10B-Fc fusion protein as a target (test 1). In parallel the sera were also tested on an unrelated human Fc fusion protein (test 2). Specific reactivity to the 161P2F1OB portion of the fusion protein was indicated.
All mice were sacrificed and fusions and hybridoma selection was carried out as described in Example 11. Hybridoma supematants were screened 10-17 days later by ELISA using 161P2F10B-Fc protein as target 161P2F10B-Fc positives were subsequently cross-screened on irrelevant Fc proteins to identify 161P2F10 specific clones. Monoclonal antibodies were tested for specificity and reactivity to cell surface 161p2F1OB using recombinant Rat 1 cells.
Example 57: Generation of Monoclonal Antibodies specific for 161P2F1OB using UT7 cells endogenously expressing 161P2F1OB.
It has been reported in the literature that antibodies to 161P2F1OB can be made by immunization with the human erythro-megakaryoblastic cell line UT-7 cultured with IL3 (Buhring et.al.
Blood 94(7): 2343. 1999). Antibodies described in this publication are available commercially and have been used as controls in the invention described here.
In another embodiment, mice were immunized intea-peritoneally with UT-7 cells, 106 cells per immunization. A total of 5 immunizations were given approximately 2 weeks apart with the final injection being given three days befor mice were sacrificed for fusions. Mice were bled 10 days after the third injection and the 161P2F1OB specific titer of the sera was determined by ELISA using 161P2F10 as a screening agent. Mice with high titers were then used for fusions as described in Example 11. Monoclonal antibodies generated in this way were selected by ELISA and their ability to recognize cells surface 161P2F1OB was confirmed by FACS on Rat 1 cells expressing 161P2F1OB.
Example 58: Generation of Monoclonal Antibodies specific for 161P2F1OB using the recombinant cell line 3T3 expressing 161P2F1OB.

In another embodiment, mice were immunized intea-peritoneally with 313 cells expressing 161P2F1OB, 106cells per immunization. A total of 5 immunizations were given approximately 2 weeks apart with the final injection being given three days before mice were sacrificed for fusions. Mice were bled 10 days after the third injection and the 161P2F108 specific titer of the sera was determined by ELISA using 161P2F10 as a screening agent. Mice with high titers were then used for fusions as described in Example

11. Monoclonal antibodies generated in this way were selected by ELISA and their ability to recognize cells surface 161P2F1OB was confirmed by FACS on Rat 1 cells expressing 161P2F10B.
Example 59: Generation of Monoclonal Antibodies specific for 161P2F1OB using the recombinant cell line Rat 1 expressing 161P2F1OB.
In another embodiment mice were immunized with Rat-1 cells expressing 161P2F10B, Mice were then used for fusions as described in Example 11. Monoclonal antibodies generated in this way were selected by ELISA and their ability to recognize cells surface 161P2F108 was confirmed by FACS on Rat 1 cells expressing 161P2F1OB.
Example 60: Detection of 161P2F1OB protein in kidney cancer patient specimens To confirm the expression of 161P2F1OB protein, kidney cancer specimens were obtained from kidney cancer patients, and stained using the commercially available antibody 97A6 specific for ENPP3 protein (also called anti-CD203c) (Immunotech, Marseilles, France). Briefly, frozen tissues were cut into 4 micron sections and fixed in acetone for 10 minutes. The sections were then incubated with PE-labeled mouse monoclonal anti-ENPP3 antibody for 3 hours (Figure 24 A-C), or isotype control antibody (Figure 44 G-I). The slides were washed three times in buffer, and either analyzed by fluorescence microscopy (Figure 44 A, B and C), or further incubated with DAKO
EnVision+n' peroxidase-conjugated goat anti-mouse secondary antibody (DAKO Corporation, Carpenteria, CA) for 1 hour (Figure 44 D, E, and F FIG 24 A-C). The sections were then washed in buffer, developed using the DAB kit (SIGMA
Chemicals), counterstained using hematoxylin, and analyzed by bright field microscopy (Figure 44 D, E and F). The results showed strong expression of 161P2F1OB in the renal carcinoma patient tissue (Figure 44A and D) and the kidney cancer metastasis to lymph node tissue (Figure 44 C and F), but weakly in normal kidney (Figure 44 B and E). The expression was detected mostly around the cell periphery in renal clear cell carcinoma (FIG 44 A and D, FIG 24 A and B) and was strongly expressed throughout the cells with an apparent predisposition towards the cell periphery in renal papillary carcinoma (FIG 24 C) indicating that 161P2F1OB is membrane associated in kidney cancer tissues. The weak expression detected in normal kidney was localized to the kidney tubules.
The sections stained with the isotype control antibody were negative showing the specificity of the anti- ENPP3 antibody (Figure 44 G-I). Kidney cancer specimens were obtained from patients with different types of renal tumor including renal clear cell carcinoma; papillary cell carcinoma; renal cell carcinoma, chromophobe type; transitional cell carcinoma and oncocytoma and were stained for 161P2F1OB using the commercially available antibody 97A6 specific for ENPP3 protein (also called anti-CD203c) (Immunotech, Marseilles, France). All tissue specimens for renal clear cell carcinoma and papillary cell carcinoma were positive for 161P2F1OB (Table LIX).
Figure 45 shows expression of 161P2F1OB in human patient cancers by Western blot analysis. Cell lysates from kidney cancer tissues (KiCa), kidney cancer metastasis to lymph node (KiCa Met), as well as normal kidney (NK) were subjected to western analysis using an anti-161P2F1OB mouse monoclonal antibody. Briefly, tissues (-25 pg total protein) were solubilized in SDS-PAGE sample buffer and separated on a 10-20% SDS-PAGE
gel and transferred to nitrocellulose.
Blots were blocked in Iris-buffered saline (TBS) + 3% non-fat milk and then probed with purified anti-161P2F1OB antibody in TBS + 0.15% Tween-20 + 1% milk. Blots were then washed and incubated with a 1:4,000 dilution of anti-mouse IgG-HRP
conjugated secondary antibody. Following washing, anti-161P2F1OB
immunoreactive bands were developed and visualized by enhanced chemiluminescence and exposure to autoradiographic film. The specific anti-161P2F1OB immunoreactive bands represent a monomeric form of the 161P2F1OB protein, which runs at approximately 130kDa. These results demonstrate that 161P2F1OB is useful as a diagnostic and therapeutic target for kidney cancers, metastatic cancers and other human cancers that express this protein.
The strong expression of 161P2F1OB in kidney cancer tissues and its restricted expression in normal kidney as well as its membrane localization show that 161P2F1OB is a target, e.g., for kidney cancer diagnosis and therapy. The expression detected in kidney cancer metastatic tissue indicates that 161P2F1OB is also a target for metastatic disease. As disclosed herein, Western blot and immunohistochemical analysis of kidney cancer tissues and kidney cancer xenografts with mAb 97A6 showed strong extensive staining of ENPP3 in clear cell kidney carcinoma but significantly lower or undetectable levels in normal kidney (Figures 44, 45, 46, and 24). Detection of 161P2F1OB (ENPP3) in high grade clear cell carcinoma and in metastatic disease.
Example 61: Detection of 161P2F1OB protein in colon cancer patient specimens Tissue specimens of colon adenocarcinoma were obtained from nine different colon cancer patients. Frozen tissues were cut into 4 micron sections and fixed in acetone for 10 minutes.
The sections were then incubated with mouse monoclonal anti-ENPP3 antibody (Coulter-Immunotech, Marseilles, France) for 3 hours. The slides were washed three times in buffer, and further incubated with DAKO EnVision+n" peroxidase-conjugated goat anti-mouse secondary antibody (DAKO
Corporation, Carpenteria, CA) for 1 hour. The sections were then washed in buffer, developed using the DAB kit (SIGMA
Chemicals), counterstained using hematoxylin, and analyzed by bright field microscopy. The results showed strong expression of 161P2F1OB in two of the nine colon cancer patient tissues, one of which is illustrated (Figure 26). 161P2F1OB
was most strongly expressed on the tumor cells with a luminal cell surface but was also expressed throughout all the tumor tissue.
Example 62: Detection of 161P2F1OB protein by immunohistochemistry in a prostate cancer patient specimens.
Tissue specimens of prostate adenocarcinoma were obtained from eight different prostate cancer patients. Frozen tissues were cut into 4 micron sections and fixed in acetone for 10 minutes.
The sections were then incubated with mouse monoclonal anti-ENPP3 antibody (Coulter-Immunotech, Marseilles, France) for 3 hours. The slides were washed three times in buffer, and further incubated with DAKO EnVision+m peroxidase-conjugated goat anti-mouse secondary antibody (DAKO
Corporation, Carpenteria, CA) for 1 hour. The sections were then washed in buffer, developed using the DAB kit (SIGMA
Chemicals), counterstained using hematoxylin, and analyzed by bright field microscopy. The results showed expression of 161P2F1OB in six of the eight prostate cancer patient tissues, one of which is illustrated (Figure 25). 161P2F1OB was expressed on the tumor cells with an apparent proclivity towards the luminal cell surface.
Example 63: Detection of 161P2F1OB protein by immunohistochemistry in normal tissue specimens.
Normal tissue specimens from a number of organs were obtained either from patients undergoing surgery or from autopsy. Frozen tissues were cut into 4 micron sections and fixed in acetone for 10 minutes. The sections were then incubated with mouse monoclonal anti-ENPP3 antibody (Coulter-Immunotech, Marseilles, France) for 3 hours. The slides were washed three times in buffer, and further incubated with DAKO EnVision+Tm peroxidase-conjugated goat anti-mouse secondary antibody (DAKO Corporation, Carpenteria, CA) for 1 hour. The sections were then washed in buffer, developed using the DAB kit (SIGMA Chemicals), counterstained using hematoxylin, and analyzed by bright field microscopy. The results showed weak expression of 161P2F1OB in some of the tubules in all of the kidney specimens and weak staining of some glandular epithelium in half of the prostate tissues. There was no expression of 161P2F1OB in any of the other normal tissues studied except for expression in a very few cells within one lung, one bladder and two colon samples which could be mast cells (TABLE LX). As disclosed herein, Western blot and immunohistochemical analysis of kidney cancer tissues and kidney cancer xenografts with mAb 97A6 showed strong extensive staining of ENPP3 in clear cell kidney carcinoma but significantly lower or undetectable levels in normal kidney (Figures 44,45, 46, and 24). Detection of 161P2F1OB (ENPP3) in high grade clear cell carcinoma and in metastatic disease.
Example 64: Detection by immunohistochemistry of 161P2F1OB protein expression in kidney clear cell cancer patient specimens by specific binding of mouse monoclonal antibodies.
Renal clear cell carcinoma tissue and its matched normal adjacent were obtained from a kidney cancer patient.
Frozen tissues were cut into 4 micron sections and fixed in acetone for 10 minutes. The sections were then incubated either mouse monoclonal anti-ENPP3 antibody (Coulter-Immunotech, Marseilles, France) for 3 hours (Figure 27 panels A, D), or mouse monoclonal antibody X41(3)50 (Figure 27 panels B, E), or mouse monoclonal antibody X41(3)37 (Figure 27 panels C, F). The slides were washed three times in buffer and further incubated with DAKO EnVision+TTM peroxidase-conjugated goat anti-mouse secondary antibody (DAKO Corporation, Carpenteria, CA) for 1 hour. The sections were then washed in buffer, developed using the DAB kit (SIGMA Chemicals), counterstained using hematoxylin, and analyzed by bright field microscopy (Figure 27 panels A-F). The results showed strong expression of 161P2F1OB in the renal clear cell carcinoma patient tissue (Figure 27 panels A-C), but weakly in normal kidney (Figure 27 panels D-F). The expression was predominantly around the cell periphery indicating that 161P2F1OB is membrane associated in kidney cancer tissues. The weak expression detected in normal kidney was localized to the kidney proximal tubules. As disclosed herein, Western blot and immunohistochemical analysis of kidney cancer tissues and kidney cancer xenografts with mAb 97A6 showed strong extensive staining of ENPP3 in clear cell kidney carcinoma but significantly lower or undetectable levels in normal kidney (Figures 44, 45, 46, and 24). Detection of 161P2F1OB (ENPP3) in high grade clear cell carcinoma and in metastatic disease.
Example 65: Characteristics and utility of anti-161P2F10b MAbs.
Using a variety of immunization strategies as described in Example 11, a panel of MAbs that specifically bind 161P2F10b protein was generated. The characteristics of this panel is summarized in Figure 39 These antibodies specifically bind with high affinity to 161P2F10b on the surface of endogenously-expressing and recombinant cell lines as determined by flow cytometry (Figures 28 and 40). Upon engagement of surface 161P2F10b, these MAbs mediate internalization of the MAb-protein complex (Figures 33, 34, and 35). These MAbs are thus useful as a specific targeting modality for toxin-conjugates, as exemplified by the growth inhibition and induction of apoptosis of Caki-161P2F10b cells by MAb X41.50 with a saporin toxin-conjugated secondary Ab (Figure 36). Treatment of 161P2F10-expressing cancerous cells with the naked MAb also has a therapeutic effect in vivo as exemplified by the inhibition of UGK3 tumor formation in SCID
mice injected with MAb X41.50 (Figure 23).
161P2F10b encodes phosphodiesterase enzymatic activity that is easily monitored both in recombinant purified protein (Figure 31) and on cells (Figure 32). The relevance of the enzymatic activity to the function of 161P2F10b may be monitored by utilization of mutants that disrupt this activity (Figure 30).
Engagement of 161P2F10b with MAbs may alter, disrupt, block, or downregulate 161P2F10 enzymatic activity, which may serve as a potential therapeutic mechanism for targeting 161P2F10b-expressing cancers and diseased tissues. Engagement of cell surface 161P2F10b cells with a subset of the MAbs listed in Figure 39 does mediate internalization and marked downregulation of cell surface enzymatic activity (Figure 37 and 38) thus demonstrating the utility of the MAbs for disrupting the function of 161P2F10b in cells and tissues.
161P2F10b protein and the MAbs that bind it are useful in the diagnosis of 161P2F10b-expressing cancer and diseased tissues. Immunohistochemical analysis of the panel of MAbs, as summarized in Figure 39, specifically stain (to varying degrees) a variety of kidney cancer samples with little to no staining of adjacent normal tissues. These MAbs are thus useful as diagnostic reagents for a variety of 161P2F10b-expressing cancers by immunohistochemistry and are potentially useful as imaging reagents in patients. In addition, the MAbs were used (specifically X48.54 and X41.29, but others that do not compete for the same epitope are also used) to demonstrate the shedding and/or secretion of the protein from 161P2F10b-expressing cancer cells and tissues (Figures 42 and 43). This supports the utility of 161P2F10b as a serum and/or urine diagnostic marker and the MAbs as reagents to quantitatively measure serum and/or urine concentrations of 161P2F10b protein.

TABLES: 134 TABLE I: Tissues that Express 161P2F10B:
a. Exemplary Normal Tissues:
Prostate Kidney b. Malignant Tissues Kidney Uterus Pancreas Prostate Colon Lung Bone Lymphoma Breast Ovary TABLE II: Amino Acid Abbreviations SINGLE LETTER THREE LETTER FULL NAME
Phe phenylalanine Leu leucine Ser serine Tyr tyrosine Cys cysteine Trp tryptophan Pro proline His histidine Gin glutamine Arg arginine Ile isoleucine Met methionine Thr threonine Asn asparagine Lys lysine V Val valine A Ala alanine Asp aspartic acid Glu glutamic acid Gly glycine TABLE III: Amino Acid Substitution Matrix Adapted from the GCG Software 9.0 BLOSUM62 amino acid substitution matrix (block substitution matrix). The higher the value, the more likely a substitution is found in related, natural proteins.
ACDEF.GHIKLMNPQRSTVWY.

6 -3 -1 0 -3 '0 0 -3 ,4 -3 -3 -2 *-2 -1 1 3 F "
.6 -2 -4 -2 -4 -3 0 -2 -2 -2 0 -2 -3 -2 -3 = 4-32 1 -3 -3 -3 -1-2 -1 3 -3 -1 I
= 5 -2 -1 0-1 I 2 0 -1 -2 -3 -2 K

=

7 -1 -2 -1 -I -2 -4 -3 P .

1y =
=
=

TABLE IV:
HLA Class I/II MotifsISupermotifs TABLE IV (A): HLA Class I Supermotifs/Motifs SUPERMOTIF POSITION POSITION POSITION
2 (Primary Anchor) 3 (Primary Anchor) C Terminus (Primary Anchor) Al TIL VMS FVVY

A24 YFW/VLMT Fl YWLM

MOTIFS
Al TSM
Al DEAS
A2.1 LMVQIAT VLIMAT

All VTMLISAGNCDF KRYH

A*3101 MVTALIS RK
A*3301 MVALFIST RK
A*6801 AVTMSLI RK
8*0702 P LMFWYAIV
B*3501 P LMFVVY/VA

B*5301 P IMFWYAL V
B*5401 P ATIVLMFWY
Bolded residues are preferred, italicized residues are less preferred: A
peptide is considered motif-bearing if it has primary anchors at each primary anchor position for a motif or supermotif as specified in the above table.
TABLE IV (B): HLA Class II Supermotif W, F, Y, V, .1, L A, V, 1, L, P, C, S, T A, V, I, L, C, S, T, M, Y

TABLE IV (C): HLA Class II Motifs MOTIFS 10 anchor 1 2 3 4 5 10 anchor 6 7 8 9 DR4 preferred FMYLIVW M T I VSTCPALIM MH MH
deleterious W R WDE
DR1 preferred MFLIVWY PAMQ VMATSPLIC M AVM
deleterious C CH FD CWD GDE D
DR7 preferred MFLIVWY M W A IVMSACTPL M IV
deleterious C G GRD N G
DR3 MOTIFS 10 anchor 1 2 3 10 anchor 4 5 10 anchor 6 Motif a preferred LIVMFY
Motif b preferred LIVMFAY DNQEST KRH
DR Supermotif MFLIVWY VMSTACPLI
Italicized residues indicate less preferred or "tolerated" residues TABLE IV (D): HLA Class I Supermotifs POSITION: 1 2 3 4 5 6 7 8 C-terminus SUPER-MOTIFS
Al 10 Anchor 10 Anchor TIL VMS FWY
A2 1 Anchor 1 Anchor LIVMATQ LIVMAT
A3 Preferred 10 Anchor YFW YEW YEW P 10 Anchor VSMATLI (4/5) (3/5) (4/5) (4/5) RK
deleterious DE (3/5); DE
P (5/5) (4/5) A24 10 Anchor 1 Anchor YFWIVLMT FIYWLM
B7 Preferred FWY (5/5) 10 Anchor FWY FWY 1 Anchor LIVM (3/5) P (4/5) (3/5) VILFMWYA
deleterious DE (3/5); DE G QN DE
P(5/5); (3/5) (4/5) (4/5) (4/5) G(4/5);
A(3/5);
QN(3/5) B27 1 Anchor 1 Anchor RHK FYLWMIVA
B44 10 Anchor 1 Anchor ED FVVYLIMVA
658 10 Anchor 10 Anchor ATS FWYLIVMA
B62 10 Anchor 1 Anchor QLIVMP FWYMIVLA
Italicized residues indicate less preferred or "tolerated" residues TABLE IV (E): HLA Class I Motifs terminus Or C-terminus Al preferred GFYW 1 Anchor DEA YFW P DEQN YFW 1 Anchor 9-mer STM
deleterious DE RHKLIVMP A G A
Al preferred GRHK ASTCLIVM 1 Anchor GSTC ASTC LIVM DE
1 Anchor 9-mer DEAS
deleterious A RHKDEPYFW DE PQN RHK PG GP
Al preferred YFW 1 Anchor DEAQN A YFWQN PASTC GDE
P 1 Anchor mer deleterious GP RHKGLIVM DE RHK QNA RHI<WW RHK A
Al preferred YFW STCLIVM 1 Anchor A YFW PG G YFW 1 Anchor 10- = DEAS
mer deleterious RHK RHKDEPYFW P G PRHK QN
A2.1 preferred YFW 1 Anchor YFW STC YFW A P 1 Anchor 9-mer LMIVQAT VLIMAT
deleterious DEP DERKH RKH DERKH
POSITION:1 2 3 4 5 6 7 8 9 C-Terminus A2.1 preferred AYFW 1 Anchor LVIM G G FYWL 1 Anchor mer deleterious DEP DE RKHA P RKH DERK RKH
A3 preferred RHK 1 Anchor YFW PRHKYF A YFW P .. 1 Anchor LMVISATFCGD W KYRHFA
deleterious DEP DE
All preferred A 1 Anchor YFW YFW A YFW YFW P 1 Anchor VTLMISAGNCD KRYH
deleterious DEP A
A24 preferred YFWRHK 1 Anchor SIC YFW YFW 1 Anchor 9-mer YFWM FLIW
deleterious DEG DE G QNP DERH G AQN
A24 Preferred 1 Anchor P YFWP P 1 Anchor mer Deleterious GDE QN RHK DE A QN DEA
A310 Preferred RHK 1 Anchor YFW P YFW YFW .. AP ..
1 Anchor Deleterious DEP DE ADE DE DE DE
A330 Preferred 1 Anchor YFW AYFW 1 Anchor Deleterious GP DE
A680 Preferred YFWSTC 1 Anchor YFWLIV YFW P 1 Anchor deleterious GP DEG RHK A
6070 Preferred RHKFWY 1 Anchor RHK RHK RHK RHK PA 1 Anchor V
deleterious DEQNP DEP DE DE GDE QN DE

terminus Or C-terminus Al preferred GFYW 1 Anchor DEA YFW P DEQN YFW 1 Anchor 9-mer STM
deleterious DE RHKLIVMP A G A
Al preferred GRHK ASTCLIVM 1 Anchor GSTC ASTC LIVM DE
1 Anchor 9-mer DEAS
deleterious A RHKDEPYFW DE PQN RHK PG GP
B350 Preferred FWYLIVM 1 Anchor FWY FWY 1 Anchor A
deleterious AGP
B51 Preferred LIVMFVVY 1 Anchor FWY SIC FWY G FWY 1 Anchor LIVFWYA
deleterious AGPDER DE G DEQN GDE
HKSTC
B530 preferred LIVMFVVY 1 Anchor FWY SIC FWY LIVMFW FWY 1 Anchor V
deleterious AGPQN G RHKQN DE
B540 preferred FWY 1 Anchor FWYLIVM LIVM ALIVM FVVYA 1 Anchor WY
deleterious GPQNDE GDESTC RHKDE DE QNDGE DE

TABLE IV (F):
Summary of HLA-supertypes Overall phenotypic frequencies of HLA-supertypes in different ethnic populations Specificity Phenoty ic frequency SupertypePosition 2 C-TerminusCaucasian N.A.
BlackJapanesethineseHispanicAverage B7 P AILMVFVVY43.2 5.1 57.1 43.0 49.3 49.5 A3 AILMVST RK 37.5 2.1 45.8 52.7 43.1 44.2 A2 AILMVT AILMVT 45.8 9.0 42.4 45.9 43.0 42.2 A24 YE (WIVLMT)FI (YWLM) 23.9 8.9 58.6 40.1 38.3 40.0 B44 E (D) FVVYLIMVA43.0 1.2 42.9 39.1 39.0 37.0 Al TI (LVMS) FVVY 47.1 16.1 21.8 14.7 26.3 25.2 B27 RHK FYL (WM1) 28.4 6.1 13.3 13.9 35.3 23.4 B62 QL (IVMP) FVVY (MIV) 12.6 .8 36.5 25.4 11.1 18.1 B58 ATS FWY (LIV) 10.0 5.1 1.6 9.0 5.9 10.3 TABLE IV (G):
Calculated population coverage afforded by different HLA-supertype combinations HLA-supertypes Phenotypic frequency Caucasian N.A Blacks Japanese Chinese Hispanic Average 83.0 86.1 87.5 88.4 86.3 86.2 A2, A3 and B7 99.5 98.1 100.0 99.5 99.4 99.3 A2, A3, B7, A24, B4499.9 99.6 100.0 99.8 99.9 99.8 and Al A2, A3, B7, A24, B44, Al, B27, B62, and B 58 Motifs indicate the residues defining supertype specificites. The motifs incorporate residues determined on the basis of published data to be recognized by multiple alleles within the supertype.
Residues within brackets are additional residues also predicted to be tolerated by multiple alleles within the supertype.
Table V: Frequently Occurring Motifs avrg. %
Name Description Potential Function identity Nucleic acid-binding protein functions as transcription factor, nuclear location zf-C2H2 34% Zinc finger, C2H2 type probable Cytochrome b(N- membrane bound oxidase, generate cytochrome_b_N 68% terminal)/b6/petB superoxide domains are one hundred amino acids long and include a conserved Ig 19% lmmunoglobulin domain intradomain disulfide bond.
tandem repeats of about 40 residues, each containing a Trp-Asp motif.
Function in signal transduction and WD40 18% WD domain, G-beta repeat protein interaction may function in targeting signaling PDZ 23% PDZ domain molecules to sub-membranous sites LRR 28% Leucine Rich Repeat short sequence motifs involved in protein-protein interactions conserved catalytic core common to both serine/threonine and tyrosine protein kinases containing an ATP
Pkinase 23% Protein kinase domain binding site and a catalytic site pleckstrin homology involved in intracellular signaling or as constituents PH 16% PH domain of the cytoskeleton 30-40 amino-acid long found in the extracellular domain of membrane-EGF 34% EGF-like domain bound proteins or in secreted proteins Reverse transcriptase (RNA-dependent DNA
Rvt 49% polymerase) Cytoplasmic protein, associates integral Ank 25% Ank repeat membrane proteins to the cytoskeleton NADH- membrane associated. Involved in Ubiquinone/plastoquinone proton translocation across the Oxidored_q1 32% (complex 1), various chains membrane calcium-binding domain, consists of al 2 residue loop flanked on both sides by a Efhand 24% EF hand 12 residue alpha-helical domain Retroviral aspartyl Aspartyl or acid proteases, centered on Rvp 79% protease a catalytic aspartyl residue extracellular structural proteins involved in formation of connective tissue. The Collagen triple helix repeat sequence consists of the G-X-Y and the Collagen 42% (20 copies) polypeptide chains forms a triple helix.
Located in the extracellular ligand-binding region of receptors and is about 200 amino acid residues long with two pairs of cysteines involved in disulfide Fn3 20% Fibronectin type III domain bonds seven hydrophobic transmembrane regions, with the N-terminus located 7 transmembrane receptor extracellularly while the C-terminus is 7tm_1 19% (rhodopsin family) cytoplasmic. Signal through G proteins Table VI: Motifs and Post-translational Modifications of 161P2F1OB
N-glycosylation site:
Number of matches: 10 1 236-239 NFSL (SEQ ID NO: 41) 2 279-282 NGSF (SEQ ID NO: 42) 3 290-293 NGSV (SEQ ID NO: 43) 4 426-429 NLSC (SEQ ID NO: 44) 533-536 NGTH (SEQ ID NO: 45) 6 582-585 NSTQ (SEQ ID NO: 46) 7 594-597 NLTQ (SEQ ID NO: 47) 8 687-690 N1TH (SEQ ID NO: 48) 9 699-702 NRTS (SEQ ID NO: 49) 789-792 NKSH (SEQ ID NO: 50) cAMP- and cGMP-dependent protein kinase phosphorylation site 14-17 KKNT (SEQ ID NO: 51) Protein kinase C phosphorylation site Number of matches: 13

12 676-678 SQK

13 698-700 SNR
Casein kinase II phosphorylation site Number of matches: 15 1 88-91 TCVE (SEQ ID NO: 52) 2 106-109 TRLE (SEQ ID NO: 53) 3 114-117 SCSD (SEQ ID NO: 54) 4 138-141 SWLE (SEQ ID NO: 55) 5 240-243 SSKE (SEQ ID NO: 56) 6 502-505 SFKE (SEQ ID NO: 57) 7 507-510 TEVE (SEQ ID NO: 58) 8 551-554 SHAE (SEQ ID NO: 59) 9 584-587 TQLE (SEQ ID NO: 60) 10 596-599 TQEE (SEQ ID NO: 61) 11 660-663 TVPD (SEQ ID NO: 62) 12 704-707 SQYD (SEQ ID NO: 63) 13 813-816 TNVE (SEQ ID NO: 64)

14 817-820 SCPE (SEQ ID NO: 65) 846-849 TGLD (SEQ ID NO: 66) Tyrosine kinase phosphorylation site 700-706 RTSDSQY (SEQ ID NO: 67) N-myristoylation site Number of matches: 11 1 38-43 GLGLGL (SEQ ID NO: 68) 2 40-45 GLGLGL (SEQ ID NO: 69) 3 38-43 GLGLGL (SEQ ID NO: 70) 4 40-45 GLGLGL (SEQ ID NO: 71) 65-70 GLENCR (SEQ ID NO: 72) 6 222-227 GIIDNN (SEQ ID NO: 73) 7 263-268 GLKAAT (SEQ ID NO: 74) 8 273-278 GSEVAI (SEQ ID NO: 75) 9 280-285 GSFPSI (SEQ ID NO: 76) 331-336 GGPVSA (SEQ ID NO: 77) 11 374-379 GMDQTY (SEQ ID NO: 78) Cell attachment sequence Somatomedin B domain signature Number of matches: 2 1 69-89 CRCDVACKDRGDCCWDFEDTC (SEQ ID NO: 79) 2 113-133 CSCSDDCLQKKDCCADYKSVC (SEQ ID NO: 80) Table VII:
Search Peptides 161P2F1OB variant 1 (SEQ ID NO: 81) Variant 2 9-mers SCSDDCLQEKDCCADYK (SEQ ID NO: 82) 10-mers CSCSDDCLQHKDCCADYKS (SEQ ID NO: 83)

15-mers LEASLCSCSDDCLQEKDCCADYKSVCQGE (SEQ ID NO: 84) =
Variant 3 9-mers PTNVESCPGGKPEALWV (SEQ ID NO: 85) 10-mers RPTNVESCPGGKPEALWVE (SEQ ID NO: 86) 15-mers FIIPHRPTNVESCPGGKPEALWVEERFTA (SEQ ID NO: 87) Variant 4 9-mers TYLPTFETPI (SEQ ID NO: 88) 10-mers KTYLPTFETPI (SEQ ID NO: 89) 15-mers EILQLKTYLPTFETPI (SEQ ID NO: 90) Table VIII-V1-HLA-A1-9mers- Table VIII-V1-HLA-A1-9mers-161P2F1OB 161P2F1OB Table VIII-V2-HLA-A1-9mers-Each peptide is a portion of SEQ ID Each peptide is a portion of SEQ ID 161P2F1OB
NO: 3; each start position is NO: 3; each start position is Each peptide is a portion of SEQ ID
specified, the length of peptide is 9 specified, the length of peptide is 9 NO: 5; each start position is amino acids, and the end position amino acids, and the end position specified, the length of peptide is 9 for each peptide is the start position for each peptide is the start position amino acids, and the end position plus eight. plus eight. for each peptide is the start position Start Subsequence Score Start Subsequence Score plus eight 105 SMDGFRAEY 25.000 167 NMYDVNLNK 0.500 Start Subsequence Score 754 NVESCPEGK 18.000 562 HCLLYHREY 0.500 2 CSDDCLQRK 15.000 55 CSDDCLQKK 15.000 197 LTAMYQGLK 0.500 9 RKDCCADYK 0.500 446 KTEVEPFEN 11.250 699 FDAPDEITK 0.500 1 SCSDDCLQR 0.500 245 WLDLPMER 10.000 787 GLDFYQDKV 0.500 5 DCLQRKDCC 0.010 798 VSEILQLKT 6.750 83 NCDTAQQSQ 0.500 8 QRKDCCADY 0.005 317 QTYCNKMEY 6.250 593 DTSPLPPTV 0.500 3 SDDCLQRKD 0.003 371 KPDQHFKPY 6.250 284 WDHAFGML 0.500 6 CLQRKDCCA 0.001 RCDVACKDR 5.000 144 KTFPNHYTI 0.500 4 DDCLQRKDC
0.001 314 GMDQTYCNK 5.000 417 NCGGGNHGY 0.500 7 LQRKDCCAD 0.000 322 KMEYMTDYF 4.500 350 NIPHDFFSF 0.500 454 NIEVYNLMC 4.500 97 DLPPVILFS 0.500 Table VIII-V3-HLA-A1-9mers-29 CVESTRIWM 4.500 742 DVLPFIIPH 0.500 161P2F1OB
650 ITSNLVPMY 2.500 250 KAERPRFYT 0.450 Each peptide is a portion of SEQ ID
118 DTLMPNINK 2.500 292 LMEGLKQRN 0.450 NO: 7;
each start position is 685 , WSGPIFDY 2.500 677 ATERNGVNV 0.450 specified, the length of peptide is 9 559 NVDHCLLYH 2.500 261 FEEPDSSGH 0.450 amino acids, and the end position 711 NTDVPIPTH 2.500 618 KCSFYLADK , 0.400 for each peptide is the start position 740 WLDVLPFII 2.500 571 VSGFGKAMR 0.300 plus eight.
402 FVDQQWLAV 2.500 536 TQEEITATV 0.270 Start Subsequence Score 431 SMEAIFLAH 2.250 193 QPMWLTAMY 0.250 3 610 RVPPSESQK 2.000 687 SGPIFDYNY 0.250 6 SCPGGKPEA 0.02 379 YLTPDLPKR 2.000 772 FTAHIARVR 0.250 5 ESCPGGKPE 0.015 613 PSESQKCSF 1.350 655 VPMYEEFRK 0.250 9 GGKPEALWV 0.013 213 GSEVAINGS 1.350 476 HGSLNHLLK 0.250 2 TNVESCPGG 0.005 359 NSEEIVRNL 1.350 712 TDVPIPTHY 0.250 7 CPGGKPEAL 0.003 128 KTCGIHSKY 1.250 550 FGRPRVLQK 0.250 1 PTNVESCPG 0.003 326 MTDYFPRIN 1.250 601 VPDCLRADV 0.250 4 426 NNEFRSMEA 1.125 578 MRMPMWSSY 0.250 8 632 FLYPPASNR 1.000 546 VNLPFGRPR 0.250 163 IIDNNMYDV 1.000 461 MCDLLRIQP 0.250 Table VIII-V4-HLA-A1-9mers-512 SLDCFCPHL 1.000 395 RIDKVHLFV 0.250 161P2F1OB
66 CADYKSVCQ 1.000 586 YTVPQLGDT 0.250 Each peptide is a portion of SEQ ID
653 NLVPMYEEF 1.000 96 FDLPPVILF 0.250 NO: 9;
each start position is 606 RADVRVPPS 1.000 509 PTESLDCFC 0.225 specified, the length of peptide is 9 54 SCSDDCLQK 1.000 758 CPEGKPEAL 0.225 amino acids, and the end position 767 WVEERFTAH 0.900 733 TPENCPGWL 0.225 for each peptide is the start position 448 EVEPFENIE 0.900 493 AEEVSKFSV 0.225 plus eight.
525 QLEQVNQML 0.900 43 CGETRLEAS 0.225 Start Subsequence Score 79 WLEENCDTA 0.900 722 VVLTSCKNK 0.200 2 YLPTFETPI 0.01 492 HAEEVSKFS 0.900 746 FIIPHRPTN 0.200 1 TYLPTFETP 0.001 537 QEEITATVK 0.900 436 FLAHGPSFK 0.200 5 GLENCRCDV 0.900 743 VLPFIIPHR 0.200 Table IX-V1-HLA-A1-10mers-47 RLEASLCSC 0.900 133 HSKYMRAMY 0.150 161P2F1OB
641 TSDSQYDAL 0.750 201 YQGLKANTY 0.150 Each peptide is a portion of SEQ ID
626 KNITHGFLY 0.625 231 GSVPFEERI 0.150 NO: 3; each start position is 558 KNVDHCLLY 0.625 686 VSGPIFDYN 0.150 specified, the length of peptide is 10 783 ELLTGLDFY 0.500 382 PDLPKRLHY 0.125 amino acids, and the end position _ 62 KKDCCADYK , 0.500 , 191 HGQPMWLTA 0.125 for each peptide is the start position 310 LADHGMDQT 0.500 701 APDEITKHL 0.125_ plus nine.

Start Subsequence Score-Table IX-V1-HLA-A1-10mers-Table IX-V2-HLA-A1-10mers-798 VSEILQLKTY 67.500 161P2F1OB 161P2F1OB
711 NTDVPIPTHY 62.500 Each peptide is a portion of SEQ ID Each peptide is a portion of SEQ ID
326 MTDYFPRINF 62.500 NO: 3; each start position is NO: 5; each start position is 781 DVELLTGLDF 45.000 specified, the length of peptide is 10 specified, the length of peptide is 10 448 EVEPFENIEV 45.000 amino acids, and the end position amino acids, and the end position 220 GSFPS1YMPY 37.500 for each peptide is the start position for each peptide is the start position 381 TPDLPKRLHY 31.250 plus nine, plus nine.
310 LADHGMDQTY 25.000 Start Subsequence Score , Start Subsequence Score 686 VSGPIFDYNY 15.000 292 LMEGLKQRNL 0.450 1 CSCSDDCLQR 0.750 213 GSEVAINGSF 13.500 487 FYEPSHAEEV 0.450 2 SCSDDCLQRK 0.200 -402 FVDQQWLAVR 10.000 92 CPEGFDLPPV 0.450 3 CSDDCLQRKD 0.075 559 NVDHCLLYHR 10.000 43 CGETRLEASL 0.450 _ 10 RKDCCADYKS 0.050 613 PSESQKCSFY 6.750 235 FEERISTLLK 0.450 4 SDDCLQRKDC 0.025 525 QLEQVNQMLN 4.500 454 NIEVYNLMCD 0.450 6 DCLQRKDCCA 0.010 567 HREYVSGFGK 4.500 261 FEEPDSSGHA 0.450 8 LQRKDCCADY 0.002 492 HAEEVSKFSV 4.500 758 CPEGKPEALW 0.450 9 QRKDCCADYK 0.001 536 TQEEITATVK 2.700 338 MYEGPAPRIR 0.450 5 DDCLQRKDCC 0.001 684 NVVSGPIFDY 2.500 316 DQTYCNKMEY 0.375 7 CLORKDCCAD 0.000 698 HFDAPDEITK 2.500 756 ESCPEGKPEA 0.300 284 VVDHAFGMLM 2.500 263 EPDSSGHAGG 0.250 Table IX-V3-HLA-A1-10mers-658 YEEFRKMWDY 2.250 740 WLDVLPFIIP 0.250 161P2F1OB
446 KTEVEPFENI 2.250 586 YTVPQLGDTS 0.250 Each peptide is a portion of SEQ ID
762 KPEALWVEER 2.250 314 GMDQTYCNKM 0.250 NO: 7;
each start position is 742 DVLPFIIPHR 2.000 479 LNHLLKVPFY 0.250 specified, the length of peptide is 10 119 TLMPNINKLK 2.000 139 AMYPTKTFPN 0.250 amino acids, and the end position 767 INVEERFTAHI 1.800 168 MYDVNLNKNF 0.250 for each peptide is the start position 53 CSCSDDCLQK 1.500 25 , FEDTCVESTR 0.250 plus nine.
641 TSDSQYDALI 1.500 377 KPYLTPDLPK 0.250 Start Subsequence Score 104 FSMDGFRAEY 1.500 105 SMDGFRAEYL 0.250 6 ESCPGGKPEA 0.3 359 NSEEIVRNLS 1.350 591 LGDTSPLPPT 0.250 4 NVESCPGGKP 0.09 349 HNIPHDFFSF 1.250 166 NNMYDVNLNK 0.250 3 TNVESCPGGK 0.05 328 DYFPRINFFY 1.250 144 KTFPNHYTIV 0.250 7 SCPGGKPEAL 0.01 601 VPDCLRADVR 1.250 371 KPDQHFKPYL 0.250 2 PTNVESCPGG 0.005 95 GFDLPPVILF 1.250 690 IFDYNYDGHF 0.250 8 CPGGKPEALW 0.005 157 YPESHGIIDN 1.125 426 NNEFRSMEAI 0.225 1 RPTNVESCPG 0.003 654 LVPMYEEFRK 1.000 74 QGETSWLEEN 0.225 10 653 NLVPMYEEFR 1.000 360 SEEIVRNLSC 0.225 9 649 LITSNLVPMY 1.000 677 ATERNGVNVV 0.225 5 47 RLEASLCSCS 0.900 570 YVSGFGKAMR 0.200 29 CVESTRIWMC 0.900 129 TCGIHSIMR 0.200 Table IX-V4-HLA-A1-10mers-GLENCRCDVA 0.900 721 FVVLTSCKNK 0.200 161P2F1OB
110 RAEYLYTWDT 0.900 682 GVNVVSGPIF 0.200 Each peptide is a portion of SEQ ID
79 WLEENCDTAQ 0.900 196 WLTAMYQGLK 0.200 NO: 9;
each start position is 431 SMEAIFLAHG 0.900 434 AIFLAHGPSF 0.200 specified, the length of peptide is 10 356 FSFNSEEIVR 0.750 54 SCSDDCLQKK 0.200 amino acids, and the end position 785 LTGLDFYQDK 0.500 478 SLNHLLKVPF 0.200 . for each peptide is the start position 623 LADKNITHGF 0.500 437 LAHGPSFKEK 0.200 plus nine.
83 NCDTAQQSQC 0.500 250 KAERPRFYTM 0.180 _ Start Subsequence Score 66 CADYKSVCQG 0.500 231 GSVPFEERIS 0.150 2 TYLPTFETPI 0.005 541 TATVKVNLPF 0.500 192 GQPMWLTAMY 0.150 1 KTYLPTFETP 0.003 RCDVACKDRG 0.500 794 KVQPVSE1LQ 0.500 Table X-V1-HLA-A0201-9mers-787 GLDFYQDKVQ 0.500 161P2F1OB
163 IIDNNMYDVN 0.500 Each peptide is a portion of SEQ ID
512 SLDCFCPHLQ 0.500 NO: 3; each start position is 461 MCDLLRIQPA 0.500 specified, the length of peptide is 9 217 AINGSFPSIY 0.500 amino acids, and the end position - 97 DLPPVILFSM 0.500 for each peptide is the start position plus eight. Table X-V1-HLA-A0201-9mers- for each peptide is the start position Start Subsequence Score 161P2F1OB plus eight.
663 KMWDYFHSV 11367.476 , Each peptide is a portion of SEQ ID Start Subsequence Score 563 CLLYHREYV 693.538 NO: 3; each start position is 6 CLQRKDCCA 4.968 325 YMTDYFPRI 270.002 specified, the length of peptide is 9 5 DCLQRKDCC 0.004 807 YLPTFETTI 182.365 amino acids, and the end position 4 DDCLQRKDC 0.001 119 TLMPNINKL 181.794 foreach peptide is the start position 1 SCSDDCLQR 0.000 196 WLTAMYQGL 147.401 plus eight. 2 CSDDCLQRK 0.000 459 NLMCDLLRI 88.783 Start Subsequence Score 7 LQRKDCCAD
0.000 113 .. YLYTWDTLM 73.129 144 KTFPNHYTI 1.876 9 RKDCCADYK 0.000 547 NLPFGRPRV 69.552 297 KQRNLHNCV 1.876 _ 3 SDDCLQRKD 0.000 765 AL1NVEERFT 68.037 240 STLLKWLDL 1.866 8 QRKDCCADY 0.000 740 WLDVLPFII 45.649 536 TQEEITATV 1.850 238 RISTLLKWL 37.157 535 LTQEEITAT 1.659 Table X-V3-HLA-A2-9mers-155 GLYPESHGI 33.385 356 FSFNSEEIV 1.552 512 SLDCFCPHL 32.471 528 QVNQMLNLT 1.500 Each peptide is a portion of SEQ ID
579 RMPMWSSYT 29.601 583 WSSYTVPQL 1.475 NO: 7; each start position is 199 AMYQGLKAA 26.408 622 YLADKNITH 1.405 _ specified, the length of peptide is 9 395 RIDKVHLFV 21.039 , 525 QLEQVNQML 1.367 amino acids, and the end position 402 FVDQQWLAV 19.036 794 IMPVSEIL 1.314 for each peptide is the start position 524 TQLEQVNQM 17.575 72 VCQGETSWL 1.304 plus eight.
747 IIPHRPTNV 16.258 467 IQPAPNNGT 1.284 Start Subsequence Score 163 IIDNNMYDV 14.957 233 VPFEERIST 1.255 9 GGKPEALVVV 0.087 400 HLFVDQQWL 14.781 192 GQPMWLTAM 1.159 7 CPGGKPEAL 0.068 787 GLDFYQDKV 13.632 456 EVYNLMCDL 1.032 6 SCPGGKPEA 0.032 90 SQCPEGFDL 12.562 131 GIHSKYMRA 1.025 2 TNVESCPGG 0.002 693 YNYDGHFDA 11.352 280 KALQVVDHA 1.007 4 VESCPGGKP 0 283 QVVDHAFGM 10.337 291 MLMEGLKQR 0.884 1 PTNVESCPG 0 300 NLHNCVNII 9.838 427 NEFRSMEAI 0.846 3 NVESCPGGK 0 555 VLQKNVDHC 9.518 784 LLTGLDFYQ 0.808 8 PGGKPEALW 0 532 MLNLTQEEI 8.691 447 TEVEPFENI 0.774 5 ESCPGGKPE 0 570 YVSGFGKAM 7.599 715 PIPTHYFVV 0.750 802 LQLKTYLPT 7.129 250 KNERPRFYT 0.740 Table X-V4-HLA-A2-9mers-500 SVCGFANPL 7.103 98 LPPVILFSM 0.735 805 KTYLPTFET 6.723 47 RLEASLCSC 0.731 Each peptide is a portion of SEQ ID
430 RSMEAIFLA 6.563 330 FPRINFFYM 0.687 NO: 9 each start position is 277 RVII<ALQVV 5.739 474 GTHGSLNHL 0.682 _ specified, the length of peptide is 9 171 VNLNKNFSL 5.087 337 YMYEGPAPR 0.650 amino acids, and the end position 59 CLQKKDCCA 4.968 274 VSARVIKAL 0.545 for each peptide is the start position 534 NLTQEEITA 4.968 521 QNSTQLEQV 0.512 plus eight.
383 DLPKRLHYA 4.713 540 ITATVKVNL 0.504 Start Subsequence Score 800 EILQLKTYL 4.483 493 AEEVSKFSV 0.502 2 YLPTFETPI 182.365 5 GLENCRCDV 4.451 270 AGGPVSARV 0.454 1 TYLPTFETP 0 452 FENIEVYNL 4.395 665 WDYFHSVLL 0.437 307 IILLADHGM 4.297 790 FYQDKVQPV 0.419 Table XI-V1-HLA-A0201-10mers-714 VPIPTHYFV 4.245 44 GETRLEASL 0.415 161P2F1OB
477 GSLNHLLKV 3.864 190 WHGQPMWLT 0.411 Each peptide is a portion of SEQ ID
111 AEYLYTWDT 3.478 656 PMYEEFRKM 0.394 NO: 3; each start position is 488 YEPSHAEEV 3.048 436 FLAHGPSFK 0.377 specified, the length of peptide is 10 79 WLEENCDTA 2.938 527 EQVNQMLNL 0.374 amino acids, and the end position 580 MPMWSSYTV 2.856 115 YTWDTLMPN 0.373 for each peptide is the start position 30 VESTRIWMC 2.833 708 HLANTDVPI 0.355 plus nine.
Start Subsequence Score 217 AINGSFPSI 2.726 663 KMWDYFHSVL 2862.980 . 649 LITSNLVPM 2.671 Table X-V2-A0201-9mers-337 YMYEGPAPRI 454.740 51 SLCSCSDDC 2.434 161P2F1OB
765 ALVVVEERFTA 239.160 670 SVLLIKHAT 2.413 Each peptide is a portion of SEQ ID
449 VEPFENIEV 2.299 NO: 5; each start position is 102 ILFSMDGFRA 181.243 -380 LTPDLPKRL 2.068 specified, the length of peptide is 9 632 FLYPPASNRT 109.693 - 379 YLTPDLPKRL 98.267 21 CCWDFEDTC 2.055 amino acids, and the end position Table XI-V1-HLA-A0201-10mers- Table XI-V1-HLA-A0201-10mers- amino acids, and the end position 161P2F1OB 161P2F1OB for each peptide is the start position Each peptide is a portion of SEQ ID Each peptide is a portion of SEQ ID plus nine.
NO: 3; each start position is NO: 3; each start position is Start Subsequence Score specified, the length of peptide is 10 specified, the length of peptide is 10 7 CLQRKDCCAD 0.015 amino acids, and the end position amino acids, and the end position 6 DCLQRKDCCA 0.009 for each peptide is the start position for each peptide is the start position 4 SDDCLQRKDC 0.003 plus nine, plus nine. 8 LQRKDCCADY 0.001 Start Subsequence Score Start Subsequence Score 2 SCSDDCLQRK 0.001 162 GIIDNNMYDV 90.183 547 NLPFGRPRVL 1.752 5 DDCLQRKDCC 0.000 309 LLADHGMDQT 58.537 455 IEVYNLMCDL 1.624 1 CSCSDDCLQR 0.000 115 YTWDTLMPNI 52.169 526 LEQVNQMLNL 1.624 10 RKDCCADYKS 0.000 579 RMPMWSSYTV 50.232 167 NMYDVNLNKN 1.624 3 CSDDCLQRKD 0.000 746 FIIPHRPTNV 43.992 484 KVPFYEPSHA 1.521 9 QRKDCCADYK 0.000 555 VLQKNVDHCL 36.316 314 GMDQTYCNKM 1.435 407 WLAVRSKSNT 34.279 123 NINKLKTCGI 1.435 Table XI-V3-HLA-A2-10mers-34 RIWMCNKFRC 32.884 317 QTYCNKMEYM 1.369 161P2F1OB
524 TQLEQVNQML 32.857 128 KTCGIHSKYM 1.328 Each peptide is a portion of SEQ ID
600 TVPDCLRADV 24.952 508 LPTESLDCFC 1.243 NO: 7; each start position is 801 ILQLKTYLPT 19.003 358 FNSEEIVRNL 1.210 specified, the length of peptide is 10 199 AMYQGLKAAT 17.222 284 VVDHAFGMLM 1.123 amino acids, and the end position 534 NLTQEEITAT 17.140 111 AEYLYTWDTL 1.107 for each peptide is the start position 105 SMDGFRAEYL 16.632 805 KTYLPTFETT 1.079 plus nine.
21 CCWDFEDTCV 15.450 466 RIQPAPNNGT 1.025 Start Subsequence Score 531 QMLNLTQEEI 13.661 139 AMYPTKTFPN 0.999 7 SCPGGKPEAL 0.068 520 LQNSTQLEQV 13.511 329 YFPRINFFYM 0.962 9 PGGKPEALWV 0.055 614 SESQKCSFYL 13.251 640 RTSDSQYDAL 0.894 6 ESCPGGKPEA 0.002 648 ALITSNLVPM 11.426 170 DVNLNKNFSL 0.813 5 VESCPGGKPE 0 51 SLCSCSDDCL 10.468 89 QSQCPEGFDL 0.809 8 CPGGKPEALW 0 387 RLHYAKNVRI 10.433 28 TCVESTRIWM 0.731 1 71 SVCQGETSWL 10.281 716 IPTHYFVVLT 0.723 3 TNVESCPGGK 0 120 LMPNINKLKT 9.149 306 NIILLADHGM 0.683 10 300 NLHNCVNIIL 8.759 242 LLKWLDLPI<A 0.680 2 PTNVESCPGG 0 795 VQPVSEILQL 8.469 662 RKMVVDYFHSV 0.679 4 NVESCPGGKP 0 233 VPFEERISTL 8.271 504 FANPLPTESL 0.669 144 KTFPNHYTIV 7.693 452 FENIEVYNLM 0.667 Table XI-V4-HLA-A2-10mers-4 RGLENCRCDV 6.887 232 SVPFEERIST 0.652 161P2F1OB
535 LTQEEITATV 6.733 425 YNNEFRSMEA 0.612 Each peptide is a portion of SEQ ID
97 DLPPVILFSM 4.970 564 LLYHREYVSG 0.608 NO: 9; each start position is 282 LQVVDHAFGM 4.966 511 ESLDCFCPHL 0.603 specified, the length of peptide is 10 , 400 HLFVDQQWLA 4.687 198 TAMYQGLKAA 0.587 amino acids, and the end position 767 VVVEERFTAHI 4.187 401 LFVDQQWLAV 0.572 for each peptide is the start position 371 KPDQHFKPYL 4.080 399 VHLFVDQQVVL 0.513 plus nine.
224 SIYMPYNGSV 3.978 63 KDCCADYKSV 0.507 Start Subsequence Score 786 TGLDFYQDKV 3.375 665 WDYFHSVLLI 0.491 2 TYLPTFETPI 0.02 622 YLADKNITHG 3.233 392 KNVRIDKVHL 0.488 1 KTYLPTFETP 0.002 207 ATYFWPGSEV 3.091 29 CVESTRIWMC 0.480 546 VNLPFGRPRV 2.856 216 VAINGSFPSI 0.468 Table X1141-HLA-A3-9mers-714 VPIPTHYFVV 2.753 440 GPSFKEKTEV 0.454 161P2F1OB
458 YNLMCDLLRI 2.666 773 TAHIARVRDV 0.444 Each peptide is a portion of SEQ ID
532 MLNLTQEEIT 2.545 339 YEGPAPRIRA 0.444 NO: 3; each start position is 713 DVPIPTHYFV 2.510 646 YDALITSNLV 0.444 specified, the length of peptide is 9 499 FSVCGFANPL 2.438 610 RVPPSESQKC 0.435 amino acids, and the end position 799 SEILQLKTYL 2.285 for each peptide is the start position 291 MLMEGLKQRN 1.922 Table XI-V2-A0201-10mers-plus eight.
S Sc 283 QVVDHAFGML 1.893 161P2F1OB = tart Subsequence ore 167 NMYDVNLNK 300.000 136 ,YMRAMYPTKT 1.882 Each peptide is a portion of SEQ ID
314 GMDQTYCNK 60.000 554 RVLQKNVDHC 1.813 NO: 5; each start position is 632 FLYPPASNR 45.000 155 GLYPESHGII 1.779 specified, the length of peptide is 10 Table XII-V1-HLA-A3-9mers- Table XII-V1-HLA-A3-9mers- Table XII-V2-HLA-A3-9mers-Each peptide is a portion of SEQ ID Each peptide is a portion of SEQ ID Each peptide is a portion of SEQ ID
NO: 3; each start position is NO: 3; each start position is NO: 5; each start position is specified, the length of peptide is 9 specified, the length of peptide is 9 specified, the length of peptide is 9 amino acids, and the end position amino acids, and the end position amino acids, and the end position for for each peptide is the start position for each peptide is the start position each peptide is the start position plus plus eight. plus eight. eight. .
Start Subsequence Score Start Subsequence Score Start Subsequence Score 242 LLKWLDLPK 40.000 568 REYVSGFGK 0.900 6 CLQRKDCCA 0.200 337 YMYEGPAPR 30.000 , 525 QLEQVNQML 0.900 2 CSDDCLQRK 0.150 663 KMWDYFHSV 27.000 199 AMYQGLKAA 0.750 1 SCSDDCLQR 0.080 436 FLAHGPSFK 20.000 797 PVSEILQLK 0.675 9 RKDCCADYK 0.020 136 YMRAMYPTK 20.000 532 MLNLTQEEI 0.600 8 QRKDCCADY 0.004 105 SMDGFRAEY 18.000 5 GLENCRCDV 0.600 5 DCLQRKDCC 0.001 _ 120 LMPNINKLK 15.000 8 NCRCDVACK 0.600 7 LQRKDCCAD
0.001 155 GLYPESHGI 13.500 564 LLYHREYVS 0.600 4 DDCLQRKDC 0.000 379 YLTPDLPKR 9.000 555 VLQKNVDHC 0.600 3 SDDCLQRKD 0.000 803 QLKTYLPTF 9.000 384 LPKRLHYAK 0.600 743 VLPFIIPHR 9.000 708 HLANTDVPI 0.600 Table XII-V3-HLA-A3-9mers-291 MLMEGLKQR 6.750 650 ITSNLVPMY 0.600 161P2F1OB
245 WLDLPKAER 6.000 196 WLTAMYQGL 0.600 Each peptide is a portion of SEQ ID
322 KMEYMTDYF 6.000 390 YAKNVRIDK 0.600 NO: 7; each start position is 102 ILFSMDGFR 6.000 542 ATVKVNLPF 0.450 specified, the length of peptide is 9 672 LLIKHATER 6.000 101 VILFSMDGF 0.450 amino acids, and the end position 325 YMTDYFPRI 5.400 794 KVQPVSEIL 0.405 for each peptide is the start position 653 NLVPMYEEF 4.500 534 NLTQEEITA 0.400 plus eight.
32 STRIWMCNK 4.500 54 SCSDDCLQK 0.400 Start Subsequence Score 685 VVSGPIFDY 4.050 622 YLADKNITH 0.400 3 NVESCPGGK 0.6 387 RLHYAKNVR 4.000 805 KTYLPTFET 0.338 7 CPGGKPEAL 0.009 610 RVPPSESQK 3.000 79 WLEENCDTA 0.300 6 SCPGGKPEA 0.003 400 HLFVDQQWL 3.000 579 RMPMWSSYT 0.300 9 GGKPEALVVV 0.002 281 ALQVVDHAF 3.000 47 RLEASLCSC 0.3001 PTNVESCPG 0 _ 113 YLYTWDTLM 3.000 563 CLLYHREYV 0.300 2 459 NLMCDLLRI 2.700 577 AMRMPMWSS ' 0.270 8 618 KCSFYLADK 2.700 362 EIVRNLSCR 0.270 4 783 ELLTGLDFY 2.700 217 AINGSFPSI 0.270 5 119 TLMPNINKL 2.025 482 LLKVPFYEP 0.270 144 KTFPNHYTI 2.025 500 SVCGFANPL 0.270 Table XII-V4-HLA-A3-9mers-. 317 QTYCNKMEY 2.000 269 HAGGPVSAR 0.270 .

754 NVESCPEGK 2.000 126 KLKTCGIHS 0.240 Each peptide is a portion of SEQ ID
363 IVRNLSCRK 2.000 474 GTHGSLNHL 0.203 NO: 9; each start position is 350 NIPHDFFSF 1.800 51 SLCSCSDDC 0.200 specified, the length of peptide is 9 431 SMEAIFLAH 1.800 258 TMYFEEPDS 0.200 amino acids, and the end position - for each peptide is the start position 203 GLKAATYFW 1.800 547 NLPFGRPRV 0.200 512 SLDCFCPHL 1.800 59 CLQKKDCCA 0.200 plus eight.
Start Subsequence Score 300 ^ NLHNCVNII 1.800 550 FGRPRVLQK 0.180 _ 2 YLPTFETPI 1.8 807 YLPTFETTI 1.800 290 GMLMEGLKQ 0.180 740 WLDVLPFII 1.800 484 KVPFYEPSH 0.180 787 GLDFYQDKV 1.800 371 KPDQHFKPY 0.180 Table XIII-V1-HLA-A3-10mers-722 VVLTSCKNK 1.500 55 CSDDCLQKK 0.150 128 KTCGIHSKY 1.350 139 AMYPTKTFP 0.150 Each peptide is a portion of SEQ ID
118 DTLMPNINK 1.350 450 EPFENIEVY 0.135 NO: 3; each start position is 654 LVPMYEEFR 1.200 481 HLLKVPFYE 0.135 specified, the length of peptide is 10 34 RIWMCNKFR 1.000 241 TLLKWLDLP 0.135 - amino acids, and the end position 272 GPVSARVIK 0.900 456 EVYNLMCDL 0.135 for each peptide is the start position 655 VPMYEEFRK 0.900 plus nine.
405 QQWLAVRSK 0.900 Start Subsequence Score 197 ' LTAMYQGLK 0.900 126 KLKTCGIHSK 90.000 Table XIII-V1-HLA-A3-10mers- Table XIII-V1-HLA-A3-10mers- Table XIII-V2-HLA-A3-10mers-Each peptide is a portion of SEQ ID Each peptide is a portion of SEQ ID Each peptide is a portion of SEQ ID
NO: 3; each start position is NO: 3; each start position is NO: 5; each start position is specified, the length of peptide is 10 specified, the length of peptide is 10 specified, the length of peptide is amino acids, and the end position amino acids, and the end position amino acids, and the end position for each peptide is the start position for each peptide is the start position for each peptide is the start position plus nine, plus nine, plus nine.
Start , Subsequence Score Start Subsequence Score Start Subsequence Score 241 TLLKWLDLPK 60.000 199 AMYQGLKAAT 0.500 2 SCSDDCLQRK 0.300 119 TLMPNINKLK 33.750 139 AMYPTKTFPN 0.450 8 LQRKDCCADY , 0.120 663 KMWDYFHSVL 27.000 648 ALITSNLVPM 0.450 1 CSCSDDCLQR 0.040 653 NLVPMYEEFR 27.000 379 YLTPDLPKRL 0.450 7 CLQRKDCCAD 0.020 383 DLPKRLHYAK 18.000 437 LAHGPSFKEK 0.450 9 QRKDCCADYK 0.020 196 WLTAMYQGLK 18.000 802 LQLKTYLPTF 0.405 6 DCLQRKDCCA 0.001 290 GMLMEGLKQR 13.500 162 GIIDNNMYDV 0.405 10 RKDCCADYKS 0.000 377 KPYLTPDLPK 9.000 481 HLLKVPFYEP 0.405 4 SDDCLQRKDC 0.000 337 YMYEGPAPRI 6.750 446 KTEVEPFENI , 0.405 5 DDCLQRKDCC
0.000 654 LVPMYEEFRK 6.000 545 KVNLPFGRPR 0.360 3 CSDDCLQRKD 0.000 671 VLLIKHATER 6.000 192 GQPMWLTAMY 0.360 155 GLYPESHGII 4.050 34 RIWMCNKFRC 0.300 Table XIII-V3-HLA-A3-10mers-684 NVVSGPIFDY 4.050 326 MTDYFPRINF 0.300 161P2F1OB
577 AMRMPMWSSY 4.000 711 NTDVPIPTHY 0.300 Each peptide is a portion of SEQ ID
102 ILFSMDGFRA 3.000 54 SCSDDCLQKK 0.300 NO: 7; each start position is 785 LTGLDFYQDK 3.000 507 PLPTESLDCF 0.300 specified, the length of peptide is 10 765 ALVVVEERFTA 3.000 136 YMRAMYPTKT 0.300 amino acids, and the end position 400 HLFVDQQWLA 3.000 242 LLKWLDLPI<A 0.300 for each peptide is the start position 478 SLNHLLKVPF 2.000 686 VSGPIFDYNY 0.270 plus nine.
226 YMPYNGSVPF 2.000 784 LLTGLDFYQD 0.270 Start Subsequence Score 559 NVDHCLLYHR 1.800 767 WVEERFTAHI 0.270 3 TNVESCPGGK 0.027 314 GMDQTYCNKM 1.800 172 NLNKNFSLSS 0.240 7 SCPGGKPEAL 0.009 300 NLHNCVNIIL 1.800 656 PMYEEFRKMW 0.225 8 CPGGKPEALW 0.005 402 FVDQQWLAVR 1.800 115 YTWDTLMPNI 0.225 4 NVESCPGGKP 0.001 217 AINGSFPSIY 1.800 805 KTYLPTFETT 0.225 6 ESCPGGKPEA 0 721 FVVLTSCKNK 1.500 144 KTFPNHYTIV 0.225 10 GGKPEALVVVE 0 .
220 GSFPSIYMPY 1.350 366 NLSCRKPDQH 0.200 1 RPTNVESCPG 0 543 TVKVNLPFGR 1.200 801 ILQLKTYLPT 0.200 2 PTNVESCPGG 0 649 LITSNLVPMY 1.200 356 FSFNSEEIVR 0.200 9 PGGKPEALINV 0 330 FPRINFFYMY 1.080 53 CSCSDDCLQK 0.200 5 VESCPGGKPE 0 762 KPEALVVVEER 1.080 120 LMPNINKLKT 0.200 434 AIFLAHGPSF 1.000 258 TMYFEEPDSS 0.200 Table XIII-V4-HLA-A3-10mers-531 QMLNLTQEEI 0.900 368 SCRKPDQHFK 0.200 161P2F1OB
105 SMDGFRAEYL 0.900 113 YLYTWDTLMP , 0.200 Each peptide is a portion of SEQ ID
295 GLKQRNLHNC 0.900 166 NNMYDVNLNK 0.180 NO: 9; each start position is 555 VLQKNVDHCL 0.900 495 EVSKFSVCGF 0.180 specified, the length of peptide is 10 362 EIVRNLSCRK 0.900 740 WLDVLPFIIP 0.180 amino acids, and the end position 536 TQEEITATVK 0.900 323 MEYMTDYFPR 0.180 for each peptide is the start position 632 FLYPPASNRT 0.750 563 CLLYHREYVS 0.180 plus nine.
Start Subsequence Score 796 QPVSEILQLK 0.675 101 VILFSMDGFR 0.180 1 KTYLPTFETP 0.045 97 DLPPVILFSM 0.608 203 GLKAATYFWP 0.180 2 TYLPTFETPI 0.004 742 DVLPFIIPHR 0.608 322 KMEYMTDYFP 0.180 , 51 SLCSCSDDCL 0.600 534 NLTQEEITAT 0.150 Table XIV-V1-HLA-A11-9mers-682 GVNVVSGPIF 0.600 167 NMYDVNLNKN , 0.150 579 RMPMWSSYTV 0.600 309 ,., LLADHGMDQT 0.150 Each peptide is a portion of SEQ ID
5 GLENCRCDVA 0.600 596 PLPPTVPDCL 0.135 NO: 3; each start position is 387 RLHYAKNVRI 0.600 280 KALQWDHAF 0.135 ..
specified, the length of peptide is 9 247 DLPKAERPRF 0.600 31 ESTRIWMCNK 0.135 _ amino acids, and the end position 570 YVSGFGKAMR 0.600 474 GTHGSLNHLL 0.135 _ for each peptide is the start position 393 NVRIDKVHLF 0.600 plus eight , Start Subsequence Score Table XIV-V1-HLA-A11-9mers- Table XIV-V2-HLA-A11-9mers-610 RVPPSESQK 6.000 161P2F1OB 161P2F1OB
363 1VRNLSCRK 2.000 Each peptide is a portion of SEQ ID Each peptide is a portion of SEQ ID
754 NVESCPEGK 2.000 NO: 3; each start position is NO: 5;
each start position is 167 NMYDVNLNK 1.600 specified, the length of peptide is 9 specified, the length of peptide is 9 722 VVLTSCKNK 1.500 amino acids, and the end position amino acids, and the end position 314 GMDQTYCNK 1.200 for each peptide is the start position for each peptide is the start position 655 VPMYEEFRK 1.200 plus eight. plus eight.
568 REYVSGFGK 1.080 Start Subsequence Score Start Subsequence Score 32 STRIWMCNK 1.000 550 FGRPRVLQK 0.040 1 SCSDDCLQR 0.080 197 LTAMYQGLK 1.000 402 FVDQQWLAV 0.040 9 RKDCCADYK 0.060 272 GPVSARVIK 0.900 269 HAGGPVSAR 0.040 , 2 CSDDCLQRK 0.020 118 DTLMPNINK 0.900 236 EERISTLLK 0.036 6 CLQRKDCCA 0.004 242 LLKWLDLPK 0.800 362 EIVRNLSCR 0.036 7 LQRKDCCAD 0.001 618 KCSFYLADK 0.600 786 TGLDFYQDK 0.030 8 QRKDCCADY 0.000 390 YAKNVRIDK 0.400 240 STLLKWLDL 0.030 5 DCLQRKDCC 0.000 654 LVPMYEEFR 0.400 128 KTCGIHSKY 0.030 4 DDCLQRKDC 0.000 136 YMRAMYPTK 0.400 474 GTHGSLNHL 0.030 3 SDDCLQRKD 0.000 384 LPKRLHYAK 0.400 542 ATVKVNLPF 0.030 436 FLAHGPSFK 0.400 458 YNLMCDLLR 0.024 Table XIV-V3-HLA-A11-9mers-54 SCSDDCLQK 0.400 663 KMWDYFHSV 0.024 667 YFHSVLLIK 0.400 131 GIHSKYMRA 0.024 Each peptide is a portion of SEQ ID
720 _ YFVVLTSCK 0.300 345 RIRAHNIPH 0.024 NO: 7; each start position is 387 RLHYAKNVR 0.240 155 GLYPESHGI 0.024 _ specified, the length of peptide is 9 34 RIWMCNKFR 0.240 203 GLKAATYFW 0.024 amino acids, and the end position 797 PVSEILQLK 0.200 395 RIDKVHLFV 0.024 for each peptide is the start position 8 NCRCDVACK 0.200 393 NVRIDKVHL 0.020 plus eight.
120 LMPNINKLK 0.200 284 VVDHAFGML 0.020 Start Subsequence Score 632 , FLYPPASNR 0.160 500 SVCGFANPL 0.020 3 NVESCPGGK 2 337 YMYEGPAPR 0.160 772 FTAHIARVR 0.020 7 CPGGKPEAL 0.002 102 ILFSMDGFR 0.160 369 CRKPDQHFK 0.020 6 SCPGGKPEA 0.002 324 EYMTDYFPR 0.144 71 SVCQGETSW 0.020 9 GGKPEALWV 0.001 405 QQWLAVRSK 0.120 55 CSDDCLQKK 0.020 _ 1 378 PYLTPDLPK 0.120 127 LKTCG1HSK 0.020 2 TNVESCPGG 0 144 , KTFPNHYTI 0.120 767 VVVEERFTAH 0.020 4 VESCPGGKP 0 672 , LLIKHATER 0.120 , 174 NKNFSLSSK 0.020 ' 8 554 RVLQKNVDH 0.090 544 VKVNLPFGR 0.018 5 ESCPGGKPE 0 283 QVVDHAFGM 0.090 742 DVLPFIIPH 0.018 277 RVIKALQW 0.090 805 KTYLPTFET 0.018 Table XIV-V4-HLA-A11-9mers-743 VLPFIIPHR 0.080 192 GQPMWLTAM 0.018 161P2F1OB
291 . MLMEGLKQR 0.080 90 SQCPEGFDL 0.018 Each peptide is a portion of SEQ ID
357 SFNSEEIVR 0.080 297 KQRNLHNCV 0.018 NO: 9;
each start position is 379 YLTPDLPKR 0.080 459 NLMCDLLRI 0.016 . specified, the length of peptide is 9 245 WLDLPKAER 0.080 130 CGIHSKYMR 0.012 amino acids, and the end position 62 KKDCCADYK 0.060 5 GLENCRCDV 0.012 . for each peptide is the start position 794 KVQPVSEIL 0.060 42 RCGETRLEA 0.012 plus eight.
537 QEEITATVK 0.060 253 RPRFYTMYF 0.012 Start Subsequence Score , 682 GVNVVSGPI 0.060 740 WLDVLPFII 0.012 2 YLPTFETPI 0.004 484 KVPFYEPSH 0.060 787 GLDFYQDKV 0.012 1 TYLPTFETP 0.001 10 RCDVACKDR 0.060 616 SQKCSFYLA 0.012 685 WSGPIFDY 0.060 350 NIPHDFFSF 0.012 - Table XV-V1-HLA-A11-10mers-640 RTSDSQYDA 0.060 Each peptide is a portion of SEQ ID
2 SFRGLENCR 0.040 NO: 3;
each start position is 476 HGSLNHLLK 0.040 specified, the length of peptide is 10 289 FGMLMEGLK ' 0.040 amino acids, and the end position 559 NVDHCLLYH 0.040 for each peptide is the start position 317 QTYCNKMEY 0.040 plus nine.
, 699 - FDAPDEITK 0.040 Start Subsequence Score 29 CVESTRIWM 0.040 654 LVPMYEEFRK 6.000 Table V-V1-HLA-A11-10mers- Table XV-V1-HLA-A11-10mers- Table XV-V2-HLA-A-11-10mers-Each peptide is a portion of SEQ ID Each peptide is a portion of SEQ ID Each peptide is a portion of SEQ ID
NO: 3; each start position is NO: 3; each start position is NO: 5; each start position is specified, the length of peptide is 10 specified, the length of peptide is 10 specified, the length of peptide is 10 amino acids, and the end position amino acids, and the end position amino acids, and the end position for each peptide is the start position for each peptide is the start position for each peptide is the start position plus nine, plus nine, plus nine.
Start Subsequence Score Start Subsequence Score Start Subsequence Score 377 KPYLTPDLPK 2.400 173 LNKNFSLSSK 0.040_ 2 SCSDDCLQRK 0.200 135 KYMRAMYPTK 2.400 313 HGMDQTYCNK 0.040 9 QRKDCCADYK 0.020 721 FVVLTSCKNK 1.500 597 LPPTVPDCLR 0.040 1 CSCSDDCLQR 0.008 543 TVKVNLPFGR 1.200 284 VVDHAFGMLM 0.040 8 LQRKDCCADY 0.006 241 TLLKWLDLPK 1.200 53 CSCSDDCLQK 0.040 6 DCLQRKDCCA 0.001 126 KLKTCGIHSK 1.200 601 VPDCLRADVR 0.040 7 CLQRKDCCAD 0.000 _ 785 LTGLDFYQDK 1.000 549 PFGRPRVLQK 0.040 10 RKDCCADYKS 0.000 559 NVDHCLLYHR 0.800 162 GIIDNNMYDV 0.036 4 SDDCLQRKDC 0.000 719 HYFWLTSCK 0.800 609 VRVPPSESQK 0.030 5 DDCLQRKDCC 0.000 389 HYAKNVRIDK 0.800 283 QVVDHAFGML 0.030 3 CSDDCLQRKD 0.000 536 TQEEITATVK 0.600 640 RTSDSQYDAL 0.030 666 DYFHSVLLIK 0.480 446 KTEVEPFENI 0.030 Table XV-V3-HLA-A11-10mers-, 196 WLTAMYQGLK 0.400 474 GTHGSLNHLL 0.030 161P2F1OB
402 FVDQQWLAVR 0.400 282 LQVVDHAFGM 0.027 Each peptide is a portion of SEQ ID
= 570 YVSGFGKAMR 0.400 421 GNHGYNNEFR 0.024 NO: 7; each start position is 119 TLMPNINKLK 0.400 663 KMWDYFHSVL 0.024 specified, the length of peptide is 10 698 HFDAPDEITK 0.400 765 ALVVVEERFTA 0.024 amino acids, and the end position . 435 IFLAHGPSFK 0.300 579 RMPMWSSYTV 0.024 for each peptide is the start position 796 QPVSEILQLK 0.300 155 GLYPESHGII 0.024 plus nine.
383 DLPKRLHYAK 0.240 102 ILFSMDGFRA 0.024 Start Subsequence Score 54 SCSDDCLQKK 0.200 152 IVTGLYPESH 0.020 3 TNVESCPGGK 0.06 288 AFGMLMEGLK 0.200 71 SVCQGETSWL 0.020 8 CPGGKPEALW ' 0.002 368 SCRKPDQHFK 0.200 304 CVNIILLADH 0.020 7 SCPGGKPEAL 0.002 742 DVLPFIIPHR , 0.180 207 ATYFWPGSEV 0.020 4 NVESCPGGKP 0.002 631 GFLYPPASNR 0.180 767 WVEERFTAHI 0.020 1 RPTNVESCPG 0.001 290 GMLMEGLKQR 0.180 197 LTAMYQGLI<A 0.020 10 GGKPEALVVVE

362 EIVRNLSCRK 0.180 600 TVPDCLRADV 0.020 2 PTNVESCPGG 0 336 FYMYEGPAPR 0.160 115 YTWDTLMPNI 0.020 6 ESCPGGKPEA 0 457 VYNLMCDLLR 0.160 617 QKCSFYLADK 0.020 9 PGGKPEALWV 0 166 NNMYDVNLNK 0.160 326 MTDYFPRINF 0.020 ' 5 VESCPGGKPE 0 671 VLLIKHATER 0.120 317 QTYCNKMEYM 0.020 235 ' FEERISTLLK 0.120 61 QKKDCCADYK 0.020 Table XV-V4-HLA-A11-10mers-545 KVNLPFGRPR 0.120 393 NVRIDKVHLF 0.020 161P2F1OB
762 KPEALVVVEER 0.120 386 KRLHYAKNVR 0.018 Each peptide is a portion of SEQ ID
653 NLVPMYEEFR 0.120 244 KWLDLPKAER 0.018 NO: 9; each start position is 101 VILFSMDGFR 0.120 192 GQPMWLTAMY 0.018 specified, the length of peptide is 10 437 LAHGPSFKEK 0.100 272 GPVSARVIM 0.018 amino acids, and the end position 684 NVVSGPIFDY 0.090 170 DVNLNKNFSL 0.018 for each peptide is the start position 129 TCGIHSKYMR 0.080 404 DQQWLAVRSK 0.018 plus nine.
Start Subsequence Score 323 MEYMTDYFPR 0.072 400 HLFVDQQWLA 0.016 2 TYLPTFETPI 0.006 567 HREYVSGFGK 0.060 356 FSFNSEEIVR 0.016 1 KTYLPTFETP 0.006 753 TNVESCPEGK 0.060 128 KTCGIHSKYM _ 0.015 271 GGPVSARVIK 0.060 378 PYLTPDLPKR 0.012 Table XVI-V1-HLA-A24-9mers-682 GVNVVSGPIF 0.060 771 RFTAHIARVR 0.012 489 EPSHAEEVSK - 0.060 268 GHAGGPVSAR 0.012 484 KVPFYEPSHA 0.060 250 KAERPRFYTM 0.012 Each peptide is a portion of SEQ ID
NO: 3; each start position is 144 KTFPNHYTIV 0.060 108 GFRAEYLYTVV 0.012 specified, the length of peptide is 9 398 KVHLFVDQQW 0.060 _ 573 GFGKAMRMPM 0.012 amino acids, and the end position 475 THGSLNHLLK 0.040 387 RLHYAKNVRI 0.012 for each peptide is the start position 117 WDTLMPNINK 0.040 plus eight.

, Start Subsequence Score Table XV1-Vi-HLA-A24-9mers-Table XVI-V2-HLA-A24-9mers-112 EYLYTWDTL 300.000 161P2F1OB 161P2F1OB
457 VYNLMCDLL 300.000 Each peptide is a portion of SEQ
ID Each peptide is a portion of SEQ ID
328 DYFPRINFF 144.000 NO: 3;
each start position is NO: 5; each start position is 156 LYPESHGII 90.000 specified, the length of peptide is 9 specified, the length of peptide is 9 338 MYEGPAPRI 75.000 amino acids, and the end position amino acids, and the end position 666 DYFHSVLL1 50.000 for each peptide is the start position for each peptide is the start position 424 GYNNEFRSM 45.000 plus eight. plus eight.
40 KFRCGETRL 40.000 Start Subsequence Score Start Subsequence Score 318 TYCNKMEYM 25.000 474 GTHGSLNHL 4.800 5 DCLQRKDCC 0.150 288 AFGMLMEGL 24.000 456 EVYNLMCDL 4.800 6 CLQRKDCCA 0.150 794 KVQPVSEIL 20.160 716 IPTHYFVVL 4.800 2 CSDDCLQRK 0.014 95 GFDLPPVIL 20.000 . 196 WLTAMYQGL 4.800 8 QRKDCCADY 0.012 435 IFLAHGPSF 15.000 90 SQCPEGFDL 4.800 1 SCSDDCLQR 0.012 135 KYMRAMYPT 15.000 500 SVCGFANPL 4.800 4 DDCLQRKDC 0.010 633 LYPPASNRT 10.800 400 HLFVDQQWL 4.800 7 LQRKDCCAD 0.010 790 FYQDKVQPV 10.800 284 VVDHAFGML 4.800 9 RKDCCADYK 0.002 806 TYLPTFETT 10.800 776 IARVRDVEL 4.400 3 SDDCLQRKD 0.001 359 NSEEIVRNL 10.080 542 ATVKVNLPF 4.200 525 QLEQVNQML 10.080 764 EALVVVEERF 4.200 Table XVI-V3-HLA-A24-9mers-660 EFRKMWDYF 10.000 281 ALQVVDHAF 4.200 161P2F1OB
428 EFRSMEAIF 10.000 189 WVVHGQPMWL 4.000 Each peptide is a portion of SEQ ID
569 EYVSGFGKA 9.900 512 SLDCFCPHL 4.000 NO: 7;
each start position is 238 RISTLLKWL 9.600 393 NVRIDKVHL 4.000 specified, the length of peptide is 9 119 TLMPNINKL 9.504 583 WSSYTVPQL 4.000 amino acids, and the end position 657 MYEEFRKMW 9.000 302 HNCVNIILL 4.000 for each peptide is the start position 621 FYLADKNIT 9.000 664 MWDYFHSVL 4.000 plus eight.
225 IYMPYNGSV 9.000 548 LPFGRPRVL 4.000 Start Subsequence Score 200 MYQGLKAAT 9.000 52 LCSCSDDCL 4.000 7 CPGGKPEAL 4 380 LTPDLPKRL 8.640 253 RPRFYTMYF 4.000 6 SCPGGKPEA 0.165 597 LPPTVPDCL 8.400 641 TSDSQYDAL 4.000 9 GGKPEALWV 0.12 140 MYPTKTFPN 7.500 653 NLVPMYEEF 3.960 2 TNVESCPGG 0.018 800 EILQLKTYL 7.200 234 PFEERISTL 3.600 3 NVESCPGGK 0.015 149 HYTIVTGLY 7.000 350 NIPHDFFSF 3.600 5 ESCPGGKPE 0.012 719 HYFVVLTSC 7.000 101 VILFSMDGF 3.000 8 PGGKPEALW 0.01 701 APDEITKHL 6.720 299 RNLHNCVNI 3.000 1 PTNVESCPG 0.002 168 MYDVNLNKN 6.600 713 DVPIPTHYF 3.000 4 VESCPGGKP 0.001 736 NCPGWLDVL 6.000 683 VNVVSGP1F 3.000 259 MYFEEPDSS 6.000 202 QGLKAATYF 3.000 Table XVI-V4-HLA-A24-9mers-138 RAMYPTKTF 6.000 421 GNHGYNNEF 2.640 161P2F1OB
758 CPEGKPEAL 6.000 739 GWLDVLPFI 2.520 Each peptide is a portion of SEQ ID
733 TPENCPGWL 6.000 144 KTFPNHYTI 2.400 NO: 9; each start position is 527 EQVNQMLNL 6.000 368 SCRKPDQHF 2.400 specified, the length of peptide is 9 240 STLLKWLDL 6.000 479 LNHLLKVPF 2.400 amino acids, and the end position 615 ESQKCSFYL 6.000 508 LPTESLDCF 2.400 for each peptide is the start position 165 DNNMYDVNL 6.000 682 GVNVVSGPI 2.100 plus eight.
Subsequence Score , 72 VCQGETSWL 6.000 88 QQSQCPEGF 2.000 Start 322 KMEYMTDYF 6.000 227 MPYNGSVPF 2.000 2 YLPTFETPI 1.5, 645 QYDALITSN 6.000 496 VSKFSVCGF 2.000 1 TYLPTFETP 1.08 796 QPVSEILQL 6.000 248 LPKAERPRF 2.000 , 171 VNLNKNFSL 6.000 803 QLKTYLPTF 2.000 Table XVII-V1-HLA-A24-10mers-505 , ANPLPTESL 6.000 Each peptide is a portion of SEQ ID
556 LQKNVDHCL 5.600 NO: 3;
each start position is 347 RAHNIPHDF 5.600 specified, the length of peptide is 10 540 ITATVKVNL 5.600 amino acids, and the end position 274 VSARVIKAL 5.600 for each peptide is the start position 208 TYFWPGSEV 5.500 plus nine.
355 FFSFNSEEI 5.500 Start Subsequence Score 620 SFYLADKNI 5.000 645 QYDALITSNL 280.000 Table XVII-V1-HLA-A24-10mers- Table XVII-V1-HLA-A24-10mers- Table XVII-V2-HLA-A24-10mers-Each peptide is a portion of SEQ ID Each peptide is a portion of SEQ ID Each peptide is a portion of SEQ ID
NO: 3; each start position is NO: 3; each start position is NO: 5; each start position is specified, the length of peptide is 10 specified, the length of peptide is 10 specified, the length of peptide is 10 amino acids, and the end position amino acids, and the end position amino acids, and the end position for each peptide is the start position for each peptide is the start position for each peptide is the start position plus nine, plus nine, plus nine.
Start Subsequence Score Start Subsequence Score Start Subsequence Score 168 MYDVNLNKNF 120.000 208 TYFWPGSEVA 5.000 6 DCLQRKDCCA 0.150 _ 565 LYHREYVSGF 100.000 585 SYTVPQLGDT 5.000 8 LQRKDCCADY 0.100 806 TYLPTFETTI 90.000 735 ENCPGWLDVL 4.800 10 RKDCCADYKS 0.022 324 EYMTDYFPRI 90.000 287 HAFGMLMEGL 4.800 3 CSDDCLQRKD 0.016 569 EYVSGFGKAM 37.500 473 NGTHGSLNHL 4.800 7 CLQRKDCCAD 0.015 112 EYLYTWDTLM 37.500 474 GTHGSLNHLL 4.800 2 SCSDDCLQRK 0.014 375 HFKPYLTPDL 28.800 233 VPFEERISTL 4.800 4 SDDCLQRKDC 0.010 428 EFRSMEAIFL 20.000 94 EGFDLPPVIL 4.800 1 CSCSDDCLQR 0.010 790 FYQDKVQPVS 12.600 329 YFPRINFFYM 4.500 5 DDCLQRKDCC 0.010 524 TQLEQVNQML 12.096 775 HIARVRDVEL 4.400 9 QRKDCCADYK 0.001 392 KNVRIDKVHL 12.000 349 HNIPHDFFSF 4.320 700 DAPDEITKHL 10.080 213 GSEVAINGSF 4.200 Table XVII-V3-HLA-A24-10mers-690 IFDYNYDGHF 10.000 51 SLCSCSDDCL , 4.000 161P2F1OB
95 GFDLPPVILF 10.000 71 SVCQGETSWL 4.000 Each peptide is a portion of SEQ ID
487 FYEPSHAEEV 9.900 239 ISTLLKWLDL 4.000 NO: 7 each start position is 663 KMWDYFHSVL 9.600 517 CPHLQNSTQL 4.000 specified, the length of peptide is 10 640 RTSDSQYDAL 9.600 582 MWSSYTVPQL 4.000 amino acids, and the end position . 633 LYPPASNRTS 9.000 188 AVWVHGQPMVVL 4.000 for each peptide is the start position 283 QVVDHAFGML 8.640 776 IARVRDVELL 4.000 plus nine.
328 DYFPRINFFY 8.400 347 RAHNIPHDFF 4.000 Start Subsequence Score 280 KALQVVDHAF 8.400 105 SMDGFRAEYL 4.000 7 SCPGGKPEAL 6 555 VLQKNVDHCL 8.400 556 LQKNVDHCLL 4.000 6 ESCPGGKPEA 0.132 371 KPDQHFKPYL 8.000 456 EVYNLMCDLL 4.000 8 CPGGKPEALW 0.1 118 DTLMPNINKL 7.920 664 MWDYFHSVLL 4.000 1 RPTNVESCPG 0.02 200 MYQGLKAATY 7.500 420 GGNHGYNNEF 3.960 3 TNVESCPGGK 0.018 692 DYNYDGHFDA 7.500 478 SLNHLLKVPF 3.600 4 NVESCPGGKP 0.017 757 SCPEGKPEAL 7.200 299 RNLHNCVNII 3.600 10 GGKPEALVVVE 0.012 504 FANPLPTESL 7.200 446 KTEVEPFENI 3.600 9 PGGKPEALVVV 0.01 511 ESLDCFCPHL 7.200 652 SNLVPMYEEF 3.300 2 PTNVESCPGG 0.002 195 MWLTAMYQGL 7.200 247 DLPKAERPRF 3.000 5 VESCPGGKPE 0.001 732 HTPENCPGWL 7.200 802 LQLKTYLPTF 3.000 499 FSVCGFANPL 7.200 87 AQQSQCPEGF 3.000 Table XVII-V4-HLA-A24-10mers-43 CGETRLEASL 7.200 226 YMPYNGSVPF 3.000 161P2F1OB
358 FNSEEIVRNL 6.720 451 PFENIEVYNL 3.000 Each peptide is a portion of SEQ ID
547 NLPFGRPRVL 6.000 682 GVNVVSGPIF 3.000 NO: 9; each start position is 170 DVNLNKNFSL 6.000 781 DVELLTGLDF 3.000 specified, the length of peptide is 10 795 VQPVSEILQL 6.000 623 LADKNITHGF 2.800 amino acids, and the end position 89 QSQCPEGFDL 6.000 541 TATVKVNLPF 2.800 for each peptide is the start position 470 APNNGTHGSL 6.000 32 STRIWMCNKF 2.640 plus nine.
Start Subsequence Score 209 YFWPGSEVAI 6.000 573 GFGKAMRMPM 2.500 588 VPQLGDTSPL 6.000 367 LSCRKPDQHF 2.400 1 KTYLPTFETP 0.024 292 LMEGLKQRNL 6.000 739 GWLDVLPFII 2.160 379 YLTPDLPKRL 5.760 681 NGVNVVSGPI 2.100 Table XVIII-V1-HLA-B7-9mers-300 NLHNCVNIIL 5.600 434 AIFLAHGPSF 2.000 539 EITATVKVNL 5.600 393 NVRIDKVHLF 2.000 -Each peptide is a portion of SEQ ID
68 DYKSVCQGET 5.500 737 CPGWLDVLPF 2.000 NO: 3;
each start position is 354 DFFSFNSEEI 5.500 495 EVSKFSVCGF 2.000 -234 PFEERISTLL 5.040 326 MTDYFPRINF 2.000 specified, the length of peptide is 9amino acids, and the end position 114 LYTWDTLMPN 5.000 201 YQGLKAATYF 2.000 for each peptide is the start position 318 TYCNKMEYMT 5.000 plus eight.

Start Subsequence Score Table XVIII-V1-HLA-B7-9mers-Table XVIII-V2-HLA-B7-9mers-343 APRIRAHNI 240.000 161P2F1OB 161P2F1OB
330 FPRINFFYM 200.000 Each peptide is a portion of SEQ ID Each peptide is a portion of SEQ ID
393 NVRIDKVHL 200.000 NO: 3;
each start position is NO: 5; each start position is 776 IARVRDVEL 120.000 specified, the length of peptide is 9 specified, the length of peptide is 9 , 548 LPFGRPRVL 80.000 amino acids, and the end position amino acids, and the end position 716 IPTHYFVVL 80.000 for each peptide is the start position for each peptide is the start position 796 QPVSEILQL 80.000 plus eight.
plus eight.
597 LPPTVPDCL 80.000 Start Subsequence Score Start Subsequence Score 701 APDEITKHL 72.000 574 FGKAMRMPM 1.500 5 DCLQRKDCC 0.100 552 RPRVLQKNV 40.000 219 NGSFPSIYM 1.500 6 CLQRKDCCA 0.100 _ 758 CPEGKPEAL 24.000 288 AFGMLMEGL 1.200 7 LQRKDCCAD 0.100 733 TPENCPGWL 24.000 459 NLMCDLLRI 1.200 4 DDCLQRKDC 0.015 =
500 SVCGFANPL 20.000 525 QLEQVNQML 1.200 1 SCSDDCLQR 0.010 456 EVYNLMCDL 20.000 512 SLDCFCPHL 1.200 2 CSDDCLQRK 0.003 98 LPPVILFSM 20.000 193 QPMVVLTAMY , 1.200 8 QRKDCCADY 0.002 794 KVQPVSEIL 20.000 217 AINGSFPSI 1.200 3 SDDCLQRKD 0.000 505 ANPLPTESL 18.000 641 TSDSQYDAL 1.200 9 RKDCCADYK 0.000 580 MPMWSSYTV 12.000 777 ARVRDVELL 1.200 119 TLMPNINKL 12.000 359 NSEEIVRNL 1.200 Table XVIII-V3-HLA-B7-9mers-284 VVDHAFGML 6.000 470 APNNGTHGS 1.200 161P2F1OB
283 QVVDHAFGM 5.000 453 ENIEVYNLM 1.000 Each peptide is a portion of SEQ ID
570 YVSGFGI<AM 5.000 307 IILLADHGM 1.000 NO: 7; each start position is 778 RVRDVELLT 5.000 113 YLYTWDTLM 1.000 specified, the length of peptide is 9 274 VSARVIKAL 4.000 572 SGFGKAMRM 1.000 amino acids, and the end position 240 STLLKVVLDL 4.000 524 TQLEQVNQM 1.000 for each peptide is the start position 736 NCPGWLDVL 4.000 . 129 TCGIHSKYM 1.000 plus eight 90 SQCPEGFDL 4.000 192 GQPMWLTAM 1.000 Start Subsequence Score 714 VPIPTHYFV 4.000 649 LITSNLVPM 1.000 7 CPGGKPEAL 80 800 EILQLKTYL 4.000 45 ETRLEASLC 1.000 9 GGKPEALVVV 0.2 196 WLTAMYQGL 4.000 277 RVIKALQVV 1.000 6 SCPGGKPEA 0.1 540 ITATVKVNL 4.000 198 TAMYQGL1<A 0.900 3 NVESCPGGK 0.015 238 RISTLLKWL 4.000 577 AMRMPMWSS 0.900 5 ESCPGGKPE 0.01 253 RPRFYTMYF 4.000 248 LPKAERPRF 0.600 2 TNVESCPGG 0.01 72 VCQGETSWL 4.000 655 VPMYEEFRK 0.600 8 PGGKPEALW 0.003 474 GTHGSLNHL 4.000 647 DALITSNLV 0.600 4 VESCPGGKP 0.002 40 KFRCGETRL 4.000 270 AGGPVSARV 0.600 1 PTNVESCPG 0.001 400 HLFVDQQWL 4.000 528 QVNQMLNLT 0.500 615 ESQKCSFYL 4.000 363 IVRNLSCRK 0.500 Table XV1II-V4-HLA-B7-9mers-171 VNLNKNFSL 4.000 670 SVLLIKHAT 0.500 161P2F1OB
527 EQVNQMLNL 4.000 13 VACKDRGDC 0.450 Each peptide is a portion of SEQ ID
165 DNNMYDVNL 4.000 589 PQLGDTSPL 0.400 NO: 9; each start position is 583 WSSYTVPQL 4.000 708 HLANTDVPI 0.400 specified, the length of peptide is 9 380 LTPDLPKRL 4.000 299 RNLHNCVNI 0.400 amino acids, and the end position 556 LQKNVDHCL 4.000 807 YLPTFETTI 0.400 for each peptide is the start position 52 LCSCSDDCL 4.000 475 THGSLNHLL 0.400 plus eight.
302 HNCVNIILL 4.000 452 FENIEVYNL 0.400 Start Subsequence Score 251 AERPRFYTM 3.000 94 EGFDLPPVI 0.400 2 YLPTFETPI 0.4 233 VPFEERIST 3.000 227 MPYNGSVPF 0.400 1 TYLPTFETP 0.001 409 AVRSKSNTN 3.000 471 PNNGTHGSL 0.400 29 CVESTRIWM 2.250 211 WPGSEVAIN 0.400 Table XIX-V1-HLA-B7-10mers-146 FPNHYTIVT 2.000 Each peptide is a portion of SEQ ID
682 GVNVVSGPI 2.000 NO: 3; each start position is 485 VPFYEPSHA 2.000 specified, the length of peptide is 10 611 VPPSESQKC 2.000 amino acids, and the end position 297 KQRNLHNCV 2.000 for each peptide is the start position 121 MPNINKLKT 2.000 plus nine.
601 VPDCLRADV 1.800 Start Subsequence Score 608 DVRVPPSES 1.500 470 APNNGTHGSL 240.000 Table XIX-V1-HLA-B7-10mers- Table XIX-V1-HLA-B7-10mers- Table XIX-V2-HLA-B7-10mers-Each peptide is a portion of SEQ ID Each peptide is a portion of SEQ ID Each peptide is a portion of SEQ ID
NO: 3; each start position is NO: 3; each start position is NO: 5;
each start position is specified, the length of peptide is 10 specified, the length of peptide is 10 specified, the length of peptide is 10 amino acids, and the end position amino acids, and the end position amino acids, and the end position _ for each peptide is the start position for each peptide is the start position for each peptide is the start position plus nine, plus nine, plus nine.
Start Subsequence Score Start Subsequence Score _ Start Subsequence Score 776 IARVRDVELL 120.000 595 SPLPPTVPDC 2000. 8 LQRKDCCADY 0.200 588 VPQLGDTSPL 80.000 - 272 GPVSARVIKA 2.000 _ 6 DCLQRKDCCA 0.100 517 CPHLQNSTQL 80.000 273 PVSARVIKAL 2.000 _ 7 CLQRKDCCAD 0.010 233 VPFEERISTL 80.000 508 LPTESLDCFC 2.000 1 CSCSDDCLQR 0.010 655 VPMYEEFRKM 60.000 253 RPRFYTMYFE 2.000 5 DDCLQRKDCC 0.010 371 KPDQHFKPYL 24.000 121 MPNINKLKTC 2.000 2 SCSDDCLQRK 0.010 283 QVVDHAFGML 20.000 506 NPLPTESLDC 2.000 4 SDDCLQRKDC 0.004 186 NPAWVVHGQPM 20.000 701 APDEITKHLA 1.800 3 CSDDCLQRKD 0.003 170 DVNLNKNFSL 20.000 600 TVPDCLRADV 1.500 9 QRKDCCADYK 0.001 456 EVYNLMCDLL 20.000 218 INGSFPSIYM 1.500 10 RKDCCADYKS 0.001 71 SVCQGETSWL 20.000 28 TCVESTRIWM 1.500 504 FANPLPTESL 18.000 284 VVDHAFGMLM 1.500 Table XIX-V3-HLA-B7-10mers-409 AVRSKSNTNC 15.000 43 CGETRLEASL 1.200 161P2F1OB
287 HAFGMLMEGL 12.000 270 AGGPVSARVI
1.200 Each peptide is a portion of SEQ ID
700 DAPDEITKHL 12.000 292 LMEGLKQRNL 1.200 NO: 7; each start position is 94 EGFDLPPVIL 6.000 105 , SMDGFRAEYL
1.200 specified, the length of peptide is 10 343 APRIRAHNIP 6.000 624 ADKNITHGFL 1.200 amino acids, and the end position 275 SARVIKALQV 6.000 188 AVVWHGQPMVVL 1.200 for each peptide is the start position 300 NLHNCVNIIL 4.000 216 VAINGSFPSI 1.200 plus nine.
89 QSQCPEGFDL 4.000 92 CPEGFDLPPV 1.200 Start Subsequence Score 775 HIARVRDVEL 4.000 111 AEYLYTWDTL 1.200 7 SCPGGKPEAL 4 239 ISTLLKWLDL 4.000 571 VSGFGKAMRM 1.000 8 CPGGKPEALW 0.6 392 , KNVRIDKVHL 4.000 423 HGYNNEFRSM 1.000 1 RPTNVESCPG 0.2 440 GPSFKEKTEV 4.000 713 DVPIPTHYFV 1.000 6 ESCPGGKPEA 0.1 547 NLPFGRPRVL 4.000 191 HGQPMWLTAM 1.000 4 NVESCPGGKP 0.023 795 VQPVSEILQL 4.000 393 NVRIDKVFILF 1.000 9 PGGKPEALVVV 0.02 732 HTPENCPGWL 4.000 159 ESHGIIDNNM 1.000 10 GGKPEALVVVE 0.01 473 NGTHGSLNHL 4.000 523 STQLEQVNQM 1.000 3 TNVESCPGGK 0.01 555 VLQKNVDHCL 4.000 282 LQVVDHAFGM 1.000 2 PTNVESCPGG 0.001 511 ESLDCFCPHL 4.000 97 DLPPVILFSM 1.000 5 VESCPGGKPE 0.001 51 SLCSCSDDCL 4.000 136 YMRAMYPTKT 1.000 714 VPIPTHYFVV 4.000 306 NIILLADHGM 1.000 , Table XIX-V4-HLA-B7-10mers-757 SCPEGKPEAL 4.000 317 QTYCNKMEYM 1.000 161P2F1OB
330 FPRINFFYMY 4.000 131 GIHSIMIRAM
1.000 Each peptide is a portion of SEQ ID
663 KMWDYFHSVL 4.000 128 KTCGIHSKYM 1.000 NO: 9; each start position is 640 RTSDSQYDAL 4.000 207 , ATYFWPGSEV 0.900 specified, the length of peptide is 10 524 TQLEQVNQML 4.000 198 TAMYQGLKAA 0.900 amino acids, and the end position 428 EFRSMEAIFL 4.000 250 MERPRFYTM 0.900 for each peptide is the start position 358 FNSEEIVRNL 4.000 12 DVACKDRGDC 0.750 plus nine.
Start Subsequence Score 735 ENCPGWLDVL 4.000 232 _ SVPFEERIST 0.750 2 TYLPTFETPI 0.04 118 DTLMPNINKL 4.000 608 DVRVPPSESQ 0.750 1 KTYLPTFETP 0.01 539 EITATVKVNL 4.000 337 YMYEGPAPRI 0.600 556 LQKNVDHCLL 4.000 676 HATERNGVNV 0.600 Table XX-V1-HLA-B3501-9mers-474 GTHGSLNHLL 4.000 390 YAKNVRIDKV 0.600 ' 499 FSVCGFANPL 4.000 773 TAHIARVRDV 0.600 , Each peptide is a portion of SEQ ID
379 YLTPDLPKRL 4.000 193 _,QPMWLTAMYQ 0.600 NO: 3; each start position is 744 LPFIIPHRPT 3.000 767 VVVEERFTAHI
0.600 specified, the length of peptide is 9 648 ALITSNLVPM 3.000 = 580 _ MPMWSSYTVP 0.600 amino acids, and the end position 716 IPTHYFVVLT 2.000 269 HAGGPVSARV 0.600 for each peptide is the start position 552 RPRVLQKNVD 2.000 plus eight. =

"
Start Subsequence Score Table XX-V1-HLA-B3501-9mers- Table XX-V2-HLA-B35-9mers-253 RPRFYTMYF 120.000 161P2F1OB 161P2F1OB
330 FPRINFFYM 120.000 Each peptide is a portion of SEQ ID Each peptide is a portion of SEQ ID
248 LPI<AERPRF 90.000 NO:
3; each start position is NO: 5; each start position is 450 EPFENIEVY 80.000 specified, the length of peptide is 9 specified, the length of peptide is 9 98 , LPPVILFSM 40.000 amino acids, and the end position amino acids, and the end position 508 _ LPTESLDCF 40.000 for each peptide is the start position for each peptide is the start position 193 QPMWLTAMY 40.000 plus eight.
plus eight.
, 133 HSKYMRAMY 30.000 Start Subsequence Score _ Start Subsequence Score 796 QPVSEILQL 30.000 107 DGFRAEYLY 2.000 8 QRKDCCADY 1.200 552 RPRVLQKNV 24.000 783 ELLTGLDFY 2.000 _ 5 DCLQRKDCC 0.100 371 KPDQHFKPY 24.000 570 YVSGFGKAM 2.000 6 CLQRKDCCA 0.100 343 APRIRAHNI 24.000 121 MPNINKLKT 2.000 7 LQRKDCCAD 0.045 597 LPPTVPDCL 20.000 113 YLYTWDTLM 2.000 1 SCSDDCLQR 0.030 , 548 LPFGRPRVL 20.000 . 317 QTYCNKMEY 2.000 2 CSDDCLQRK 0.030 716 IPTHYFWL 20.000 231 GSVPFEERI 2.000 4 DDCLQRKDC 0.010 227 MPYNGSVPF 20.000 417 NCGGGNHGY 2.000 9 RKDCCADYK 0.001 496 VSKFSVCGF 15.000 219 NGSFPSIYM 2.000 3 SDDCLQRKD , 0.000 701 APDEITKHL 12.000 129 TCGIHSKYM 2.000 776 IARVRDVEL 9.000 201 YQGLKAATY 2.000 Table XX-V3-HLA-B35-9mers-558 KNVDHCLLY 8.000 307 IILLADHGM 2.000 . 161P2F1OB
733 TPENCPGVVL 6.000 687 SGPIFDYNY 2.000 Each peptide is a portion of SEQ ID
758 CPEGKPEAL 6.000 192 GQPMWLTAM 2.000 NO: 7 each start position is . 347 RAHNIPHDF 6.000 489 EPSHAEEVS 2.000 specified, the length of peptide is 9 138 RAMYPTKTF , 6.000 794 , KVQPVSEIL 2.000 amino acids, and the end position 638 SNRTSDSQY 6.000 470 APNNGTHGS 2.000 for each peptide is the start position 233 VPFEERIST 6.000 572 , SGFGKAMRM 2.000 plus eight 574 FGKAMRMPM 6.000 430 RSMEAIFLA 2.000 Start Subsequence Score 583 WSSYTVPQL 5.000 380 , LTPDLPKRL
2.000 7 CPGGKPEAL 20 _ 615 ESQKCSFYL 5.000 641 TSDSQYDAL 1.500 _ 9 GGKPEALWV 0.9 274 VSARVIKAL 5.000 203 GLKAATYFW
1.500 6 , SCPGGKPEA 0.1 393 NVRIDKVHL 4.500 350 NIPHDFFSF , 1.500 8 PGGKPEALW 0.05 453 ENIEVYNLM 4.000 400 HLFVDQQWL 1.500 _ 5 ESCPGGKPE
0.05 .
128 KTCGIHSKY 4.000 90 SQCPEGFDL 1.500 _ 2 TNVESCPGG 0.02 580 MPMWSSYTV 4.000 72 VCQGETSWL 1.500 3 NVESCPGGK 0.003 714 VPIPTHYFV 4.000 124 INKLKTCGI 1.200 1 PTNVESCPG 0.002 -351 IPHDFFSFN 4.000 ' 61 QKKDCCADY 1.200 ' 4 VESCPGGKP 0.001 626 KNITHGFLY 4.000 778 RVRDVELLT 1.200 _. .
283 QVVDHAFGM 4.000 601 VPDCLRADV 1.200 Table XX-V4-HLA-B35-9mers-524 TQLEQVNQM 4.000 297 KQRNLHNCV 1.200 161P2F1OB
803 QLKTYLPTF 3.000736 NCPGWLDVL 1.000 Each peptide is a portion of SEQ ID
_ 611 VPPSESQKC 3.000 732 HTPENCPGW
1.000 NO: 9; each start position is 368 SCRKPDQHF = 3.000 196 WLTAMYQGL 1.000 specified, the length of peptide is 9 359 NSEEIVRNL 3.000 28 TCVESTRIW 1.000 amino acids, and the end position 556 LQKNVDHCL 3.000 683 VNVVSGPIF 1.000 for each peptide is the start position 764 EALWVEERF 3.000 202 QGLKAATYF 1.000 plus eight.
485 VPFYEPSHA 3.000 500 SVCGFANPL 1.000 Start Subsequence Score 161 HGIIDNNMY 3.000 527 EQVNQMLNL 1.000 2 YLPTFETPI 0.4 180 SSKEQNNPA 3.000 88 QQSQCPEGF 1.000 1 TYLPTFETP 0.001 211 WPGSEVAIN 3.000 713 DVPIPTHYF 1.000 238 RISTLLKWL 2.000 302 HNCVNIILL 1.000 Table XXI-V1-HLA-B35-10mers-222 FPSIYMPYN 2.000 _ Each peptide is a portion of SEQ ID

2.000 NO: 3; each start position is 685 VVSGPIFDY . 2.000 specified, the length of peptide is 10 _ 649 LITSNLVPM 2.000 amino acids, and the end position 650 ITSNLVPMY 2.000 for each peptide is the start position _ 146 FPNHYTIVT 2.000 plus nine.
218 INGSFPSIY 2.000 Start Subsequence Score 634 YPPASNRTS 2.000_ , 248 LPKAERPRFY
120.000 Table XXI-V1-HLA-B35-10mers- Table XXI-V1-HLA-B35-10mers-161P2F103 161P2F1013 Table XXI-V2=HLA-B35-10mers-Each peptide is a portion of SEQ ID Each peptide is a portion of SEQ ID 161P2F10B
NO: 3; each start position is NO: 3; each start position is Each peptide is a portion of SEQ ID
specified, the length of peptide is 10 specified, the length of peptide is 10 NO: 5; each start position is amino acids, and the end position amino acids, and the end position specified, the length of peptide is 10 for each peptide is the start position for each peptide is the start position amino acids, and the end position plus nine, plus nine, for each peptide is the start position - Start Subsequence Score Start , Subsequence Score plus nine. _ 330 FPRINFFYMY 120.000 758 CPEGKPEALW 3.000 Start Subsequence Score _ 655 VPMYEEFRKM 60.000 541 _ TATVKVNLPF 3.000 8 LQRKDCCADY 6.000 233 VPFEERISTL 40.000 423 HGYNNEFRSM 3.000 6 DCLQRKDCCA 0.100 141 YPTKTFPNHY 40.000 506 _ NPLPTESLDC 3.000 1 CSCSDDCLQR 0.075 3.000 3 CSDDCLQRKD 0.030 40. -M 504 FANPLPTESL 3.000 2 SCSDDCLQRK 0.020 .
737 CPGWLDVLPF 30.000 97 DLPPVILFSM 2.000 7 CLQRKDCCAD 0.015 _ 588 VPQLGDTSPL 30.000 316 DQTYCNKMEY 2.000_ 5 DDCLQRKDCC 0.010 _ 104 FSMDGFRAEY 20.000 595 SPLPPTVPDC 2.000 9 QRKDCCADYK 0.006 470 APNNGTHGSL 20.000 272 GPVSARVIK4 2.000 10 RKDCCADYKS 0.006 _ 517 CPHLQNSTQL 20.000 648 ALITSNLVPM 2.000 4 SDDCLQRKDC 0.003 180 SSKEQNNPAW 15.000 479 LNHLLKVPFY 2.000 776 IARVRDVELL 13.500 283 QVVDHAFGML 2.000 Table XXI-V3-1335-10mers-371 KPDQHFKPYL 12.000 416 TNCGGGNHGY 2.000 161P2F1OB
_ 381 TPDLPKRLHY 12.000 131 GIHSKYMRAM 2.000 Each peptide is a portion of SEQ ID
_ 686 VSGPIFDYNY 10.000 649 LITSNLVPMY 2.000 NO: 7;-each start position is 220 GSFPSIYMPY 10.000 684 NWSGPIFDY , 2.000 specified, the length of peptide is 10 571 ,VSGFGKAMRM 10.000 306 NIILLADHGM 2.000 amino acids, and the end position _ 511 ESLDCFCPHL 10.000 121 MPNINKLKTC 2.000 for each peptide is the start position 159 ESHGIIDNNM 10.000 358 FNSEEIVRNL 2.000 plus nine.
_ 637 -ASNRTSDSQY 10.000 218 INGSFPSIYM 2.000 Start Subsequence Score 89 QSQCPEGFDL 7.500 192 GQPMWLTAMY 2.000 8 280 KALQVVDHAF 6.000 317 QTYCNKMEYM , 2.000 7 700 DAPDEITKHL , 6.000 757 SCPEGKPEAL 2.000 1 RPTNVESCPG 0.6 347 RAHNIPHDFF 6.000 611 VPPSESQKCS 2.000 6 ESCPGGKPEA 0.5 _ .
_ 577 AMRMPMWSSY 6.000 744 LPFIIPHRPT 2.000 9 PGGKPEALVVV 0.03 320 CNKMEYMTDY 6.000 217 AINGSFPSIY 2.000 10 GGKPEALVVVE 0.03 440 GPSFKEKTEV 6.000 191 F _ IGQPMWLTAM 2.000 _ 3 TNVESCPGGK 0.02 _ 384 LPKRLHYAKN 6.000 341 GPAPRIRAHN 2.000 4 NVESCPGGKP 0.003 60 LQKKDCCADY 6.000 . 732 HTPENCPGWL 2.000 _ 2 PTNVESCPGG 0.001 499 FSVCGFANPL 5.000 282 LQVVDHAFGM 2.000 _ 5 VESCPGGKPE 0.001 239 ISTLLKVVLDL 5.000 _ 716 IPTHYFWLT 2.000 367 LSCRKPDQHF 5.000 94 EGFDLPPVIL 2.000 Table XXI-V4-HLA-B35-10mers-70 KSVCQGETSW 5.000 523 STQLEQVNQM 2.000 161P2F1OB
556 LQKNVDHCLL 4.500 619 CSFYLADKNI 2.000 Each peptide is a portion of SEQ ID
612 PPSESQKCSF 4.000 524 TQLEQVNQML 2.000 NO: 9;
each start position is 640 RTSDSQYDAL 4.000 748 IPHRPTNVES 2.000 specified, the length of peptide is 10 351 IPHDFFSFNS 4.000 390 YAKNVRIDKV 1.800 amino acids, and the end position 508 LPTESLDCFC 4.000 310 LADHGMDQTY 1.800 for each peptide is the start position 663 KMWDYFHSVL 4.000 275 SARVIKALQV 1.800 plus nine.
714 VPIPTHYFW 4.000 92 CPEGFDLPPV 1.800 Start Subsequence Score 28 _TCVESTRIWM 4.000 71 SVCQGETSWL 1.500 2 TYLPTFETPI 0.04 450 EPFENIEVYN 4.000 213 GSEVAINGSF 1.500 1 KTYLPTFETP 0.02 128 KTCG1HSKYM 4.000 349 HNIPHDFFSF 1.500 250 KAERPRFYTM 3.600 795 VQPVSEILQL 1.500 287 HAFGMLMEGL 3.000 574 FGKAMRMPMW' 1.500 32 STRIWMCNKF 3.000 496 VSKFSVCGFA 1.500 393 NVRIDKVHLF 3.000 247 , DLPMERPRF 1.500 14 , ACKDRGDCCW 3.000 552 RPRVLQKNVD 1.200 392 KNVRIDKVHL 3.000 676 HATERNGVNV 1.200 . __ Tables XXII-XLIX: Table XXII-V1-HLA-A1 -9mers-Table XXIII-V1-HLA-A0201-9mers-Table XXII-V1-HLA-A1-9mers- Pos 123456789 score Pos 123456789 score _ 161P2F1OB 659 PTVPDCLRA 16 723 KMWDYFHSV 25 _ Pos 123456789 score 673 PSESQKCSF 16 27 _ 431 KPDQHFKPY 28 89 CVESTRIWM 15 _ 442 - PDLPKRLHY 26 : 121 QKKDCCADY 15 , . 188 KTCGIHSKY 24 210 YTIVTGLYP 15 277 AINGSFPSI 24 710 ITSNLVPMY 23 _309 PI<AERPRFY 15 858 VSEILQLKT 23 _ 321 FEEPDSSGH 15 33 , 23 847 , GLDFYQDIN 23 202 PTKTFPNHY 21 521 MCDLLRIQP 15_ 867 _ _ _ 477 NCGGGNHGY 19 _116 SDDCLQKKD 14 24 514 NIEVYNLMC 19 , 273 GSEVAINGS 14 _ _ 638 MRMPMWSSY 19 300 STLLKWLDL 14 _ 223 IIDNNMYDV

859 SEILQLKTY 19_ 646 YTVPQLGDT 14 _ 389 YFPRINFFY 18. 847 GLDFYQDKV 14 , 455 RIDKVHLFV _ 18 21 YKIACIVLL

686 KNITHGFLY , 18 Table XXII-V2-HLA-A1-9mers-737 ATERNGVNV , 18 161P2F108 25 CIVLLALLV

_ 745 WSGPIFDY , 18 Pos 123456789 score 65 GLENCRCDV 20 _ 843 ELLTGLDFY 18 8 QRKDCCADY 15 256 167 DGFRAEYLY 17 3 , SDDCLQRKD 14 _ 337 RVIKALQVV 20 YLTPDLPKR 20 , Table XXII-V3-HLAA1-9mers-Pos 123456789 score 836 IARVRDVEL 20 , , LLALLVIMS 19 LGLGLGLGL 19 _ _ 451 AKNVRIDKV 19 115 , CSDDCLQKK 16 455 RIDKVHLFV 19 Table XXII-V4-HLA-A1-9mers-253 QPMWLTAMY , 16 .653 DTSPLPPTV , 19 = 161P2F1013 Pos 123456789 score 800 , WLDVLPFII 19 506 KTEVEPFEN 16 , - 36 510 EPFENIEVY 16 , 285 , IYMPYNGSV 18 = 540 NHLLKVPFY 16 , 351 , MLMEGLKQR 18 Table XXIII-V1-HLA-A0201-9mers-619 NVDHCLLYH 16 Pos 123456789 score 622 HCLLYHREY 16 _ 731 VLLIKHATE 18 651 LGDTSPLPP 16 ¨
_ ._ Table XXIII-V1-HLA-A0201-9mers- Table XXIII-V1-HLA-A0201-9mers- Table XXIII-V2-HLA-A0201-9mers-Pos 123456789 score Pos 123456789 score Pos 123456789 score ..

35 MSLGLGLGL _ 17 _ 615 VLQKNVDHC 15 Table XXIII-V3-HLA-A0201-9mers-_ .
139 WLEENCDTA 17 708 ALITSNLVP 15 Pos 123456789 score 334 VSARVIKAL 17 _ 775 PIPTHYFW 15 9 GGKPEALVVV 13 _ _ 440 LTPDLPKRL 17 831 RFTAFIIARV 15 Table XXIII-V4-HLA-A0201-9mers-462 FVDQQWLAV , 17 843 ELLTGLDFY 15 161P2F1OB
_ 512 FENIEVYNL 17 856QPVSEILQL 15 - Pos 123456789 score Table )00V-V1-HLA-A0203-9mers-596 TQEEITATV , 17 150 SQCPEGFDL 14 161P2F1OB
737 ATERNGVNV 17 155 GFDLPPVIL 14 Pos 123456789 score 738 TERNGVNVV 17 _ 191 GIHSKYMRA 14 No Results Found.
799 , GWLDVLPFI 17 268 TYFWPGSEV 14 825 ALWVEERFT 17 , 270 FWPGSEVAI 14 850 FYQDKVQPV 17 284 SIYMPYNGS 14 Table XXIV-V2-HLA-A0203-9mers-854 KVQPVSEIL 17 . 294 PFEERISTL 14 161P2F1OB
863 QLKTYLPTF 17 303 LKWLDLPKA 14 Pos 123456789 score 34 IMSLGLGLG 16 336 ARVIKALQV 14 No Results Found.

208 NHYTIVTGL 16 348 AFGMLMEGL 14 Table XXIV-V3-HLA-A0203-9mers--301 TLLKWLDLP 16 362 HNCVNIILL 14 Pos 123456789 score 330 AGGPVSARV 16 368 ILLADHGMD 14 No Results Found.

520 LMCDLLRIQ 16 448 LHYAKNVR1 14 Table XXIV-V4-1-ILA-A0203-9mers-.
_ 646 YTVPQLGDT 16 524 LLRIQPAPN 14 = 161P2F1OB
706 _ YDALITSNL 16 548 YEPSHAEEV 14 - Pos 123456789 score 707 DALITSNLV 16 581 QNSTQLEQV 14 No Results Found.
732 LLIKHATER 16 _ 588 QVNQMLNLT 14 774 VPIPTHYFV 16 624 LLYHREYVS 14 ' Table XXV-V1-HLA-A3-9mers-806 FIIPHRPTN 16 643 WSSYTVPQL 14Pos 123456789 score 837 ARVRDVELL 16 . 656 PLPPTVPDC 14 _ 670 RVPPSESQK 33 861 ILQLKTYLP 16 661 VPDCLRADV 14 _ 496 FLAHGPSFK 27 18 LKKYKIACI 15 _ _ _ 692 FLYPPASNR 27 .
_ 104 GETRLEASL 15 688 ITHGFLYPP 14 _ 42 GLGLRKLEK 26 119 CLQKKDCCA 15 - 716 PMYEEFRKM 14 . 6 TLATEQPVK 25 132 VCQGETSWL 15 730 SVLLIKHAT 14 _ _ 614 . .

344 VVDHAFGML , 15 853 DOQPVSEI 14 708 ALITSNLVP 23 419 NSEEIVRNL 15 Table XXIII-V2-HLA-A0201-9mers-_ 447 RLHYAKNVR 22 542 LLKVPFYEP 15 Pos 123456789 score. 838 RVRDVELLT 22 _ 594 NLTQEE1TA 15 2 CSDDCLQRK 5_ 405 RIRAHNIPH 21 Table XXV-V1-HLA-A3-9mers- Table XXV-V1-HLA-A3-9mers- Table XXVI-V1-HLA-A26-9mers-Pos 123456789 score Pos 123456789 score Pos 123456789 score 857 PVSEILQLK 21 _ 526 RIQPAPNNG 16 32 39 LGLGLGLRK 20 630 YVSGFGKAM 16 _ 105 ETRLEASLC 19 196 YMRAMYPTK _ 19 300 STLLKWLDL 19 227 NMYDVNLNK 19 Table MV-V2-HLA-A3-9mers- 377 QTYCNKMEY 19 341 ALQVVDHAF - 19 Pos 123456789 score 560 664 CLRADVRVP _ 19 6 CLQRKDCCA 14 653 802 DVLPFIIPH 19 8 QRKDCCADY 13 _ 668 30 ALLVIMSLG 18 Table XXV-V3-HLA-A3-9mers- 856 QPVSEILQL

107 RLEASLCSC 18 Pos 123456789 score 337 RVIKALQVV 18 Table MV-V4-HLA-A3-9mers-161P2F1OB .

Pos 123456789 score 2, YLPTFETPI 11 Table XXVI-V1-HLA-A26-9mers-Pos 123456789 score 157 DLPPVILFS 17 _ 178 DTLMPNINK 17 458 KVHLFVDQQ 17 _ 660 TVPDCLRAD 17 668 DVRVPPSES 17 853 DKVQPVSEI 17 .

713 NLVPMYEEF 17 2 ESTLTLATE 16 , 854 KVQPVSEIL 17 21 YKIACIVLL 16 _ 7 LATEQPVKK 16 33 VIMSLGLGL , 16 .

188 KTCGIHSKY_ 22 _ _ .
312 ERPRFYTMY _ 21 .

131 SVCQGETSW 16 _ 219 ESHGI1DNN 16 Table XXVI-V1-HLA-A26-9mers- Table XXV1I-V1-HLA-B0702-9mers- Table XXVII-V1-HLA-B0702-9mers-Pos 123456789score Pos 123456789 - score Pos 123456789 score 225 DNNMYDVNL - 16 776. IPTHYFVVL - 25 13 ' , 695 PPASNRTSD 13 618 KNVDHCLLY 16 _ 793 TPENCPGWL 20 1 744 NVVSGPIFD 16 , 287 MPYNGSVPF 19 11 830 ERFTAHIAR ' 16 , 308 LPKAERPRF 19 20 221 _ HGIIDNNMY 15 206 FPNHYTIVT 18 198 343 QVVDHAFGM 15 655 , SPLPPTVPD 18 208 458 KVHLFVDQQ 15 , 293 , VPFEERIST 17 _ 595 , LTQEEITAT 15 545 VPFYEPSHA 16 _ 334 598 EEITATVKV 15 565 _ ANPLPTESL 16 626 YHREYVSGF 15 808 _ IPHRPTNVE 16 763 DEITKHLAN 15 _ 37 LGLGLGLGL 15 428 Table XXVI-V2-HLA-A26-9mers- 23 - IACIVLLAL 14 500 GPSFKEKTE 12 Pos 123456789 score 100 KFRCGETRL 14 . 528 QPAPNNGTH 12 _ DCLQRKDCC _ 8 441 TPDLPKRLH 14 572 Table )00/1-V3-HLA-A26-9mers- 600 ITATVKVNL 14 672 Pos 123456789 score 649 PQLGDTSPL 14 701 1 PTNVESCPG , -8 _ 58 CFDASFRGL 13 _ 201 YPTKTFPNH 13 860 El LQLKTYL 12 Table XXVI-V4-HLA-A26-9mers-271 WPGSE VAIN 13 " Table XXVII-V2-130702-9mers-Pos 123456789 score -298 RISTLLKWL 13 Pos 123456789 score [-348 AFGMLMEGL 13 . 1 SCSDDCLQR 4 Table XXVII-V1-HLA-B0702-9mers- 401 GPAPRIRAH 13 7 Pos 123456789 score , 489 FRSMEA1FL , 13 , Table XXVII-V2-130702-9mers- Table XXVIII-V1-HLA-B08-9mers- Table XXVIII-V4-HLA-B08-9mers-_ _ _ Pos 123456789 score Pos 123456789 score Pos 123456789 score ,_ , 3 SDDCLQ(RKD 1 , _ 42 GLGLRKLEK 17 2 8 QRKDCCADY 1 263 GLKAATYFW 17 Table XXIX-V1-HLA-B1510-9mers-.

Table XXVII-V3-HLA-B0702-9mers- 444 LPKRLHYAK 17 Pos 123456789 score _ 161P2F1OB 453 NVRIDKVHL 17_ 192 IHSKYMRAM 24 .
Pos 123456789 score 504 KEKTEVEPF 17 578 PHLQNSTQL 22 7 CPGGKPEAL 24 585 QLEQVNQML 17 ¨ 208 NHYTIVTGL 21 _ Table XXVII-V4-HLA-B0702-9mers- 731 VLLIKHATE 17 , 361 Pos 123456789 score 23 IACIVLIAL _ 16 626 YHREYVSGF 19 .
2 YLPTFETPI 8 29 LALLVIMSL _ 16 328 GHAGGPVSA 17 31 LLVIMSLGL, 16 408 AHNIPHDFF 17 Table XXVIII-V1-HLA-B08-9mers-_ 161P2F1OB .
100 KFRCGETRL _ 16 600 ITATVKVNL 16 Pos 123456789 score 119 CLQKKDCCA 16 608 LPFGRPRVL 16 836 IARVRDVEL 32 _ 126 CADYKSVCQ 16 776 18 LKIMIACI 28 186 _ KLKTCGIHS 16 836 IARVRDVEL 16 .

818 CPEGKPEAL 27 302 LLKWLDLPK . 16 179 TLMPNINKL 15 355 GLKQRNLHN 26 338 VIKALQVVD . 16 419 NSEEIVRNL 15 308 LPKAERPRF 22 736 HATERNGVN 16 . 448 LHYAKNVRI 14 786 SCKNKSHTP 22 TPENCPGWL 16 757 _ 294 PFEERISTL 21 VIMSLGLGL 15 _ 23 240 SSKEQNNPA 15 334 , .

626 YHREYVSGF 15 434 QHFKPYLTP . 13 74 ACKDRGDCC 18 Table XXVIII-V2-B08-9mers-_ 643 WSSYTVPQL 13 238 SLSSKEQNN 18 Pos 123456789 score 767 KHLANTDVP 13 _ 448 LHYAKNVRI 18 _ 8 QRKDCCADY 10 793 454 VRIDKVHLF 18 _ 5 DCLQRKDCC 8 796 460 HLFVDQQVVL 18 7 LQRKDCCAD 7 _ 834 AHIARVRDV 13 542 LLKVPFYEP 18 Table XXVIII-V3-HLA-B08-9mers- 20 IMIACIVL

556 VSKFSVCGF 18. 161 P2F1OB 58 CFDASFRGL 12 572 SLDCFCPHL 18 Pos 123456789 score 150 SQCPEGFDL 12 11 QPVKKNTLK 17 Table XXVIII-V4-HLA-B08-9mers- 249 15 KNTLKKYKI 17_ _ 161P2F1OB 353 MEGLKQRNL , 12 17 TLKKYKIAC , 17 Pos 123456789 score 432 PDQHFKPYL

_ Table XXIX-V1-HLA-B1510-9mers- Table XXIX-V3-HLA-B1510-9mers. Table XXX-V1-HLA-B2705-9mers-Pos 123456789 score Pos 123456789 score Pos 123456789 score _ . 585 QLEQVNQML 12 Table XXIX-V4-HLA-B1510-9mers- 35 -587 EQVNQMLNL 12 161P2F1OB 37 _ 621 DHCLLYHRE 12 Pos 123456789 score 104 , GETRLEASL 16 706 YDALITSNL 12 Table XXX-V1-HLA-B2705-9mers- 188 725 WDYFHSVLL 12 Pos 123456789 score _ _ 791 SHTPENCPG 12. 830 ERFTAHIAR 24 297 ERISTLLKW 16 ARVIKALQV _ 16 29 LALLVIMSL 11 _ 837 ARVRDVELL 23 353 35 MSLGLGLGL 11 77 _ DRGDCCWDF 21 387 TDYFPRINF 16 _ 298 RISTLLKVVL 11 _ 436 FKPYLTPDL 11 _ 525 LRIQPAPNN 19 _ 6 TLATEQPVK

460 HLFVDQQWL 11 614 RVLQKNVDH 19 _ 12 482 NHGYNNEFR 11 _ _ 512 FENIEVYNL 11 388 DYFPRINFF 18 _ 63 FRGLENCRC

560 SVCGFANPL 11 _ 481 GNHGYNNEF 18 _ 106 . 565 ANPLPTESL 11 534 GTHGSLNHL 18 162 ILFSMDGFR 15 572 SLDCFCPHL 11 578 PHLQNSTQL 18 _ 190 CGIHSKYMR 15 r 617 QKNVDHCLL . 11 632 SGFGKAMRM 18 _ 229 YDVNLNKNF 15 837 ARVRDVELL 11 860 EILQLKTYL 18 _ 313 RPRFYTMYF 15 Table XXIX-V2-B1510-9mers: 48 LEKQGSCRK 17 _ 359 RNLHNCVNI

Pos 123456789 score 178 DTLMPNINK 17 ' 406 IRAHNIPHD , 15 2 CSDDCLQRK 3 179 TLMPNINKL 17 * 407 1 SCSDDCLQR , 2 _ 227 NMYDVNLNK 17 419 NSEEIVRNL 15 3 SDDCLQRKD 2 , 262 QGLKAATYF 17 423 IVRNLSCRK 15 .
DCLQRKDCC 2 374 GMDQTYCNK 17 438 PYLTPDLPK 15 _ _ 4 DDCLQRKDC 1 447 RLHYAKNVR 17 _ 460 _ _ _ 611 GRPRVLQKN 17 _ 495 IFLAHGPSF 15 628 REYVSGFGK ' 17 1 512 FENIEVYNL _ 15 _ 856 QPVSEILQL 17 _ 613 PRVLQKNVD 15 -Table XXX-V1-HLA-B2705-9mers- Table XXX-V1-HLA-B2705-9mers- Table XXX-V1-HLA-B2705-9mers-Pos 123456789 score Pos 123456789 score Pos 123456789 score 706 YDALITSNL 15 836 , IARVRDVEL 14 _ 802 DVLPFIIPH 15 842 VELLTGLDF 14 759 FDAPDEITK 13 .
, _ 824 EALWVEERF 15 , 27 VLLALL VIM 13 _ 772 , 854 KVQPVSE1L 15 , 31 _ LLVIMSLGL 13 776 _ _ 10 EQPVKKNTL 14 _ 86 EDTCVESTR 13 798 PGWLDVLPF 13 14 KKNTLKKYK 14 _ 101 FRCGETRLE 13 818 CPEGKPEAL 13 20 KYKIACIVL 14 _ 122 KKDCCADYK 13 23 IACIVILAL 14 _ 161 VILFSMDGF 13 , 56 KKCFDASFR 14 _ 172 EYLYTWDTL 13 853 DKVQPVSEI 13 62 SFRGLENCR 14 173 YLYTWDTLM , 13 857 PVSEILQLK

, 13 132 VCQGETSWL 14 261 YQGLKAATY 13 _ 54 _ CRKKCFDAS 12 _ 169 FRAEYLYTVV 14 291 GSVPFEERI 13 _ 68 NCRCDVACK

_ _ 215 GLYPESHGI 14 _ 354 EGLKQRNLH 13 _ 252 GQPMWLTAM 14 365 VNIILLADH 13 150 SQCPEGFDL 12 , 274 SEVAINGSF 14 367 IILLADHGM 13 154 295 , FEERISTLL 14 371 ADHGMDQTY 13 , 165 SMDGFRAEY 12 180 , LMPNINKLK 12 221 _ HGIIDNNMY 12 428 SCRKPDQHF _ 14 442 , PDLPKRLHY 13 498 AHGPSFKEK 14 465 QQWLAVRSK , 13 504 KEKTEVEPF - 14 477 _ NCGGGNHGY 13 _ 533 NGTHGSLNH 14 _ 496 FLAHGPSFK 13 _ _ 431 KPDQHFKPY 12 597 QEEITATVK 14_ 626 YHREYVSGF 13 LPKRLHYAK _ 12 678 KCSFYLADK 14 675 ESQKCSFYL 13 , 453 NVRIDKVHL 12 , . _ HGSLNHLLK , 12 771 NTDVPIPTH 14 , 727 YFHSVLLIK 13 544 KVPFYEPSH 12 _ Table XXX-V1-HLA-B2705-9mers- Table XXXI-V1-HLA-132709-9mers; Table XXX1-V1-HLA-B2709-9mers-Pos 123456789 score Pos 123456789 score Pos 123456789 score _ 604 VI<VNLPFGR 12 19 KKYKIACIV 14 331 GGPVSARVI 12 __ 616 LQKNVDHCL 12 104 GETRLEASL 14 391 PRINFFYMY 12 _ . 622 HCLLYHREY 12 204 KTFPNHYT I 14 429 CRKPDQHFK 12 _ _ 665 LRADVRVPP 12 291 GSVPFEERI 14 495 IFLAHGPSF 12 _ 680 SFYLADKN I 12 537 GSLNHLLKV 14 608 LPFGRPRVL 12 684 ADKNITHGF 12 831 RFTAH1ARV 14 663 DCLRADVRV _ 12 698 SNRTSDSQY 12 35 MSLGLGLGL 13 _ 706 YDALITSNL 12 710 1TSNLVPMY 12 37 LGLGLGLGL 13 . 726 DYFHSVLLI 12 726 , DYFHSVLLI 12 , 106 TRLEASLCS 13 836 IARVRDVEL 12 747 SGPIFDYNY 12 297 ERISTLLKW 13 860 El LQLKTYL 12 Table XM-V2-HLA-B2705-9mers- 407 RAHNIPHDF 13 _ .
Pos 123456789 score 455 RIDKVHLFV 13 150 Table XXX-V3-HLA-B2705-9mers- 600 ITATVKVNL 13 Pos 123456789 score 612 RPRVLQKNV 13 287 MPYNGSVPF _ 11 6 SCPGGKPEA 7 _ 699 NRTSDSQYD 13 330 AGGPVSARV 11 725 WDYFHSVLL 13 " 348 AFGMLMEGL 11 Table XXX-V4-HLA-B2705-9mers-- Pos 123456789 score -20 , IMIACIVL 12 388 DYFPRINFF 11 21 YKIAC1VLL 12 398 , MYEGPAPRI 11 23. IACIVLLAL 12 403 APRIRAH N I 11 Table XXXI-V1-HLA-B2709-9mers- 24 ACIVLLALL 12 404 _ 26 IVLLALLVI 12 432 PDQHFKPYL , 11 Pos 123456789 score 29 LALLVIMSL 12 436 _ 33 VI MSLGLGL 12 470 VRSKSNTNC 11 _ 93 TRIWMCNKF 19 -225 , DNNMYDVNL 12 535 THGSLNHLL 11 _ 359 RNLHNCVN I 16 313 _ RPRFYTMYF 12 565 ANPLPTESL 11 Table XXXI-V1-HLA-B2709-9mers- Table XXXII-V1-HLA-134402-9mers- Table XXXII-V1-HLA-B4402-9mers-Pos 123456789 score Pos 123456789 score Pos 123456789 score . 602 ATVKVNLPF 11 819 PEGKPEALW 21 165 SMDGFRAEY

_ 774 VPIPTHYFV 11 761 APDEITKHL 18 . 419 798 PGWLDVLPF = 11 156 FDLPPVILF 17 420 204 KTFPNHYTI 16 . 713 NLVPMYEEF 14 Table )0(XI-V2-HLA-B2709-9mers- 341 ALQVVDHAF 16 738 Pos 123456789 score = 442 PDLPKRLHY 16 _ 829 837 ARVRDVELL 16 Table XXX1I-V2-HLA-B4402-9mers-Table XXXI-V3-HLA-B2709-9mers- 9 TEQPVKKNT 15 161P2F1OB
161P2F1OB 10 EQPVKKNTL 15 Pos ' 123456789 score Pos 123456789 score 13 VKKNTLKKY 15 8 _ 154 EGFDLPPVI 15 Table XXXII-V3-HLA-B4402-9m ers-Table XXXI-V4-HLA-B2709-9mers- 161P2F1OB

161P2F1OB Pos 123456789 score _ Pos 123456789 score 7 CPGGKPEAL 14 1 TYLPTFETP 3 ' 8 298 , RISTLLKWL 15 5 ESCPGGKPE 7 Table XXXII-V1-HLA-B4402-9mers- 391 PRINFFYMY 15 161P2F1OB Table )000I-V4-HLA-B4402-9mers-Pos 123456789 score 161P2F1OB

859 SE ILQLKTY 29 Pos 123456789 score YLPTFETPI . 10 772 TDVPIPTHY 15 ¨

295 FEERISTLL 23 - Table XXXIIII-V1-HLA-B5101-9mers-842 VELLTGLDF 23 Pos 123456789 score -51 QGSCRKKCF ' 14 _ Table XXXIIII-V1-HLA-B5101-9mers- Table XXXIIII-V1-HLA-B5101-9mers-Table XXXIIII-V1-1-1LA-B5101-9mers-Pos 123456789 score - -- Pos 123456789 score Pos 123456789 score = 23 IACIVLLAL 22 43 154 EGFDLPPVI 22 _ 124 DCCADYKSV 14 285 IYMPYNGSV 12 640 MPMWSSYTV 22_ 158 LPPVILFSM 14 361 LHNCVNIIL

403 , APRIRAHNI 21 181 MPNINKLKT 14 370 LADHGMDQT 12 448 LHYAKNVRI 21 215 GLYPESHGI 14 390 , FPRINFFYM 12 761 APDEITKHL 20 _ 308 LPKAERPRF 14 402 PAPRIRAHN 12 774 " VPIPTHYFV 20 347 HAFGMLMEG 14 419 NSEEIVRNL 12 612 RPRVLQKNV 19 _ 398 WEGPAPRI 14 441 TPDLPKRLH 12 694 YPPASNRTS 19 500 GPSFKEIgE 14_ 455 726 DYFHSVLLI 19 507 TEVEPFENI 14 509 VEPFENIEV 12 _ 37 LGLGLGLGL 18 566 NPLPTESLD 14 , 600 VPQLGDTSP , 12 340 KALQVVDHA 17 _ 39 LGLGLGLRK 13 666 RADVRVPPS 12 510 EPFENIEVY 17 _ 184 INKLKTCGI 13 715 867 YLPTFETTI= , 17 198 RAMYPTKTF 13 723 KMWDYFHSV 12 87 DTCVESTRI 16 204 KTFPNHYTI 13 , 742 GVNVVSGPI 12 206 FPNHYTIVT _ 16 217 YPESHGIID 13 768 HLANTDVPI 12 287 , MPYNGSVPF 16 277 AINGSFPSI 13 811 RPTNVESCP 12 _ 385 YMTDYFPRI 16 329 HAGGPVSAR 13 _ 822 KPEALVVVEE 12 437 KPYLTPDLP 16 337 RVIKALQVV 13 . 828 VEERFTAHI 12 683 LADKNITHG 16 _ 446 KRLHYAKNV 13 Table XXXIIII-V2-HLA-B5101-9mers-799 , GWLDVLPFI 16 487 NEFRSMEAI 13 Pos 123456789 score 820 EGKPEALVVV 16 529 PAPNNGTHG 13_ =
60 DASFRGLEN , 15 _ 564 FANPLPTES 13 3 SODCLQRKD 3 _ 208 NHYTIVTGL 15 596 TQEEITATV 13 1 SCSDDCLQR 2 _ 293 VPFEERIST 15 757 GHFDAPDEI 13 Table XXXIIII-V3-HLA-B5101-9mers-_ 497 LAHGPSFKE 15 796 NCPGWLDVL 13 Pos 123456789 score 601 TATVKVNLP 15 833 TAHIARVRD 13 _ 653 DTSPLPPTV 15 850 FYQDKVQPV 13 , Table XXXIIII-V4-HLA-B5101-9mers-769 LANTDVPIP 15 , 126 CADYKSVCQ 12 - Pos 123456789 score _ 804 LPFIIPHRP 15 146 TAQQSQCPE 12 2 YLPTFETPI 15 LTLATEQPV 14 176 TWDTLMPNI 12 _ -_ 169 , Table XXXIV-V1-HLA-A1-10MERS- Table XXXIV-V1-HLA-A1-10MERS- Table X:00/-V1-HLA-A0201-161P2F1OB 161P2F1OB 10mers-161P2F1OB
Pos 1234567890 score Pos 1234567890 score Pos 1234567890 score _ 858 VSEILQLKTY 30 , 621 DHCLLYHREY 15 673 PSESQKCSFY 29 744 NVVSGPIFDY 15_ 723 370 LADHGMDQTY 25 Table XXXIV-V2-HLA-A1-10mers- 293 VPFEERISTL 20 280 GSFPSIYMPY 23 _Pos 1234567890 score 564 617 QKNVDHCLLY 23_ 3 CSDDCLQRKD 16 591 QMLNLTQEEI 20 697 ASNRTSDSQY 20 Table XXXIV-V3-HLA-A1-10mers- 607 NLPFGRPRVL 19 295 FEERISTLLK 19 Pos 1234567890 score 682 _ 420 SEEIVRNLSC 19 4 NVESCPGGKP 13 692 . 506 KTEVEPFENI 19 6 ESCPGGKPEA 8 825 ALWVEERFTA

185 DKNITHGFLY¨ 18 259 AMYQGLKAAT 18 Table XXXIV-V4-HLA-A1-10mers-8 ATEQPVKKNT 17 . 276 VAINGSFPSI 18 Pos 1234567890 score 2 'TYLPTFETPI 4 Table XXXV-V1-HLA-A0201-10mers-161P2F1OB

Pos 1234567890 score 208 NHYTIVTGLY 17 . 42 GLGLRKLEKQ 17 509 VEPFENIEVY 17 . 186 709 LITSNLVPMY 17 _ 227 NMYDVNLNKN 17 _ 841 DVELLTGLDF 17 335 SARVIKALQV 17 115 CSDDCLQKKD 16 i 361 LHNCVNIILL 17 217 YPESHGlION 16 418 FNSEEIVRNL 17 . 34 IMSLGLGLGL 22 . 111 SLCSCSDDCL 22 165 ' SMDGFRAEYL 22 _ 397 YMYEGPAPRI 22 - .

_ 595 LTQEEITATV 22 -_ . 152 547 FYEPSHAEEV ' 15 196 YMRAMYPTKT 16 Table XXXV-V1-HLA-A0201- Table XXV-V1-HLA-A0201- Table YJONI-V1-HLA-10mers-161P2F1OB 10mers-161P2F1OB 10mers-161P2F1OB
Pos 1234567890 score_ Pos 1234567890 score Pos 1234567890 . score _ _ 467 WLAVRSKSNT 16 _ 773 DVPIPTHYFV 14 489 FRSMEAIFLA 10 ' 526 RIQPAPNNGT 16_ 830 ERFTAHIARV 14 599 EITATVKVNL 16 844 LLTGLDFYQD 14 544 KVPFYEPSHA 10 .
606 VNLPFGRPRV 16 _ 849 DFYQDKVQPV 14 700 RTSDSQYDAL 16 859 SEILQLKTYL 14_ 593 792 HTPENCPGWL 16 866 TYLPTFETTI 14_ 628 855 VQPVSEILQL 16 Table XXXV-V2-HLA-A0201- 675 9 TEQPVKKNTL 15 10mers-161P2F1OB 688 ITHGFLYPPA 10 24 ACIVLLALLV 15 Pos 1234567890 score 699 NRTSDSQYDA 10 257 LTAMYQGLI<A 15 6 DCLQRKDCCA 5 761 APDEITKHLA 10 333 PVSARVIKAL 15 816 ESCPEGKPEA 10 .
343 QVVDHAFGML 15 Table )00:V-V3-HLA-A0201- 825 ALWVEERFTA 10 _ 355 GLKQRNLHNC 15 10mers-161P2F1OB _828 359 RNLHNCVNII 15 Pos 1234567890 score 16 NTLKKYKIAC 9 454 VRIDKVHLFV 15 7 SCPGGKPEAL 15 22 KIACIVLLAL 9 .

Table XXXV-V4-HLA-A0201-10mers-161P2F1OB

Pos 1234567890 score 538 . SLNHLLKVPF 15 191 GIHSKYMRAM 9 _ Table )000/1-V1-HLA-A0203-10mers-161P2F1OB
642 MWSSYTVPQL 15 303 LKWLDLPKAE 9 .
Pos 1234567890 score 706 YDALITSNLV 15 322 EEPDSSGHAG 9 .

259 AMYQGLKAAT , 17 827 _ VVVEERFTAHI 15 395 FFYMYEGPAP 9 33 VIMSLGLGLG 14 . 443 , 64 RGLENCRCDV 14 _ 486 65 _ GLENCRCDVA 14 490 RSMEAIFLAH 9 , 190 CGIHSKYMRA 10 173 _ YLYTWDTLMP 14 522 CDLLRIQPAP 9 191 _ GIHSKYMRAM 14 545 VPFYEPSHAE 9 232 _ NLNKNFSLSS 14 557 SKFSVCGFAN 9 338 . VIKALQVVDH 14 594 NLTQEEITAT 9 350: GMLMEGLKQR 14 659 PTVPDCLRAD 9 368 _ ILLADHGMDQ 14 676 SQKCSFYLAD 9 494 _ AIFLAHGPSF 14 689 THGFLYPPAS 9 332 GPVSARVIKA. 10 508 _ EVEPFENIEV 14 700 RTSDSQYDAL 9 533 _ NGTHGSLNHL 14 729 HSVLLIKHAT 9 _ 362 HNCVNIILLA 10 547 FYEPSHAEEV 14 753 .YNYDGHFDAP 9 Table XXXVI-V1-HLA-A0203- Table XXXVII-V1-HLA-A3-10mers- Table XXXVII-V1-HLA-A3-10mers-10mers-161P2F1OB 161P2F1OB 161P2F1OB
Pos 1234567890 score Pos 1234567890 score Pos 1234567890 score _ 762 , PDEITKHLAN 9 714 LVPMYEEFRK 20 744 NWSGPIFDY 16 829 EERFTAFIIAR 9 107 _ RLEASLCSCS 19 783 VLTSCKNKSH 16 Table XXXWV2-HLA-A0203- 523 DLLRIQPAPN 19 - 835 H1ARVRDVEL

16 10mers-161P2F1OB 538 SLNHLLKVPF 19 854 Pos 1234567890 score 588 QVNQMLNLTQ 19 861 ILQLKTYLPT 16 7 CLQRKDCCAD 9 _ 609 PFGRPRVLQK 19 8 LQRKDCCADY 8 669 _ VRVPPSESQK 19 28 LLALLVIMSL 15 Table XXXV1-V3-HLA-A0203- 5 LTLATEQPVK 18 65 GLENCRCDVA 15 10mers-161P2F1OB 30 ALLVIMSLGL 18 131 Pos 1234567890 score 36 SLGLGLGLGL 18 157 DLPPVILFSM 15 _ Table XXXV1-V4-HLA-A0203-10mers-161P2F1OB

Pos 1234567890 score No Results Found.

Table XXXVII-V1-HLA-A3-10mers- 12 PVKKNTLKKY 17 Pos 1234567890 score 46 RKLEKQGSCR 17 607 NLPFGRPRVL 15 38 GLGLGLGLRK 27 121 QKKDCCADYK 17 , 437 KPYLTPDLPK 21 , 713 NLVPMYEEFR 17 348 AFGMLMEGLK 14 781 FVVLTSCKNK 21 284 SIYMPYNGSV 16 599 EITATVKVNL 14 .

.

495 IFLAHGPSFK 20 455 RIDKVHLFVD 16 827 WVEERFTAHI 14 _ GLDFYQDKVQ ' 14 614 RVLQKNVDHC 16 . 44 , "

Table X)00/11-V1-HLA-A3-10mers- Table XXXVIII-V1-HLA-A26-10mers- Table )(XXVIII-V1-HLA-A26-10mers-Pos 1234567890 score Pos 1234567890 score Pos 1234567890 score .

_ 726 DYFHSVLLIK 13 293 VPFEERISTL 20 Table XXXVIII-V2-HLA-A26-10mers-749 PIFDYNYDGH 13 853 DKVQPVSEIL 20 Pos 1234567890 score Table XXXVII-V2-HLA-A3-10mers- 421 EEIVRNLSCR 19 2 Pos- 1234567890 score 668 DVRVPPSESQ 19 Table )000/111-V3-HLA-A26-10mers-7 CLQRKDCCAD 14 742 GVNWSGPIF 19 Pos 1234567890 score 6 ESCPGGKPEA , 11 Table XXXVII-V3-HLA-A3-10mers- 312 ERPRFYTMYF 18 3 Pos 1234567890 score 494 AIFLAHGPSF 18 Table )000/111-V4-HLA-A26-10mers-3 TNVESCPGGK 13 587 EQVNQMLNLT 18 Pos 1234567890 score Table XXXIX-V1-HLA-B0702-Table XXXVII-V4-HLA-A3-10mers- 10mers-161P2F1OB

161 P2F1OB Pos 1234567890 score Pos 1234567890 score 431 KPDQHFKPYL 23 2 TYLPTFETPI 6 648 VPQLGDTSPL 22 .

Table XXXVIII-V1-HLA-A26-10mers- 797 CPGVVLDVLPF 21 Pos 1234567890 score 293 VPFEERISTL 20 , 555 EVSKFSVCGF 32 776 IPTHYFVVLT 20 Table XXXIX-V1-HLA-B0702- Table XXXIX-V1-HLA-B0702- Table XXXIX-V2-10mers-161P2F1OB 10mers-161P2F1OB 10mers-Pos 1234567890 score Pos 1234567890 score Pos 1234567890 score 549 EPSHAEEVSK 15 534 GTHGSLNHLL 12 Table XXXIX-V3-HLA-B0702-608 LPFGRPRVLQ 15 564 FAN PLPTESL 12 10mers-11 QPVKKNTLKK 14 571 ESLDCFCPHL 12 Pos 1234567890 score 488 EFRSMEAIFL 14 855 VQPVSEILQL 12 Table XXXIX-V4-HLA-B0702-599 EITATVKVNL 14 9 TEQPVKKNTL 11 10mers-612 RPRVLQKNVD 14 28 LLALLVIMSL 11 Pos 1234567890 score 775 PI PTHYFVVL 14 101 FRCGETRLEA 11 Table XL-V1-HLA-B08-10m ers-19 KKYKIACIVL 13 131 SVCQGETSWL 11 Pos 1234567890 score 20 KYKIACIVLL 13 158 LPPVILFSMD 11 No Results Found.

165 SMDGFRAEYL 13 271 WPGSEVAING 11 Table XL-V2-H LA-B08-10mers-287 MPYNGSVPFE 13 297 ERISTLL.KWL 11 Pos 1234567890 score 299 ISTLLKWLDL 13 325 DSSGHAGGPV 11 No Results Found.

390 FPRINFFYMY 13 343 QVVDHAFGML 11 Table XL-V3-HLA-B08-10mers-435 HFKPYLTPDL 13 439 YLTPDLPKRL 11 Pos 123456789 score 452 KNVRIDKVHL 13 444 LPKRLHYAKN 11 No Results Found.

528 QPAPNNGTHG 13 515 IEVYNLMCDL 11 Table XL-V4-H LA-B08-10mers-640 MPMWSSYTVP 13 545 VPFYEPSHAE 11 Pos 123456789 score 655 SPLPPTVPDC 13 555 EVSKFSVCGF 11 No Results Found.

694 YPPASNRTSD 13 568 LPTESLDCFC 11 Table XLI-V1-HLA-B1510-10 m ers-724 MWDYFHSVLL 13 615 VLQKNVDHCL 11 Pos 1234567890 score 795 ENCPGWLDVL 13 656 PLPPTVPDCL 11 No Results Found.

818 CPEGKPEALW 13 708 ALITSNLVPM 11 Table XLI-V2-HLA-B1510-10 me rs-835 HIARVRDVEL 13 767 KHLANTDVPI 11 Pos 1234567890 score 23 IACIVLLALL 12 817 SCPEGKPEAL 11 No Results Found.

Table XLI-V3-HLA-B1510-10mers- Table XLIV-V1-HLA-B4402-10mers- Table XLIV-V1-1-1LA-B4402-10mers-Pos 123456789 score Pos 1234567890 score Pos 1234567890 score No Results Found. 509 VEPFENIEVY 25 147 AQQSQCPEGF 14 _ _ Table XLI-V4-HLA-B1510-10mers- 859 SEILQLKTYL 25 165 SMDGFRAEYL 14 _ Pos 123456789 score 842 VELLTGLDFY 23 208 No Results Found. 674 SESQKCSFYL 22 218 PESHGIIDNN 14 Table XLII-V1-HLA-B2705-10mers- 823 PEALWVEERF 21 Pos 1234567890 score 515 IEVYNLMCDL 20 353 MEGLKQRNLH 14 No Results Found. 598 EEITATVKVN 20 387 TDYFPRINFF 14 , 718 YEEFRKMVVDY 20 435 HFKPYLTPDL 14 Table XLII-V2-HLA-B2705-10mers-Pos 1234567890 score No Results Found.

Table XLII-V3-HLA-B2705-10mers- 795 ENCPGWLDVL 17 Pos 123456789 score 57 KCFDASFRGL 16 684 No Results Found. 178 DTLMPNINKL 16 700 RTSDSQYDAL 14 . Table XLII-V4-HLA-B2705-10mers- 421 EEIVRNLSCR 16 Pos 123456789 score 494 AIFLAHGPSF 16 19 No Results Found. 855 VQPVSEILQL 16 34 IMSLGLGLGL

Table XLIII-V1-HLA-B2709-10mers- 30 ALLVIMSLGL 15 Pos 1234567890 score 155 GFDLPPVILF 15 85 No Results Found. 277 AINGSFPSIY 15 92 STRIVVMCNKF 13 Table XLIII-V2-HLA-B2709-10mers- 312 ERPRFYTMYF 15 Pos 1234567890 score 361 LHNCVNIILL 15 228 MYDVNLNKNF 13 No Results Found. 388 DYFPRINFFY 15 240 SSKEQNNPAW 13 Table XLIII-V3-HLA-B2709-10mers- 430 RKPDQHFKPY 15 Pos 123456789 score 607 NLPFGRPRVL 15 321 No Results Found. 656 PLPPTVPDCL 15 347 HAFGMLMEGL 13 Table XLIII-V4-HLA-B2709-10mers-Pos 123456789 score 772 TDVPIPTHYF 15 386 No Results Found. -Table XLIV-V1-HLA-B4402-10mers- 1 MESTLTLATE 14 533 Pos 1234567890 score _ 311 , AERPRFYTMY 26 _ ¨ 141 EENCDTAQQS 14 599 a EITATVKVNL

Table XLIV-V1-HLA-B4402-10mers- Table XLIV-V1-HLA-B4402-10mers-Pos 1234567890 score Pos 1234567890 score 683 LADKNITHGF 13 _ 679 CSFYLADKNI 12 866 TYLPTFETTI 13 _ 841 DVELLTGLDF 12 25 CIVLLALLVI 12 Table XLIV-V2-HLA-B4402-10mers-76 KDRGDCCINDF 12 Pos 1234567890 score 192 IHSI<YMRAMY 12 201 YPTKTFPNHY 12 Table XLIV-V3-HLA-B4402-10mers-224 IDNNMYDVNL 12 Pos 1234567890 score 262 QGLKAATYFW 12 Table XLIV-V4-HLA-B4402-10mers-299 ISTLLKWLDL 12 Pos 1234567890 score Table XLV-V1-HLA-B5101-10mers-Pos 1234567890 score No Results Found.
406 , IRAHNIPHDF 12 431 KPDQHFKPYL 12 Table XLV-V2-HLA-B5101-10mers-492 MEAIFLAHGP 12 Pos 1234567890 score 504 KEKTEVEPFE 12 No Results Found.

512 FENIEVYNLM 12 Table XLV-V3-HLA-B5101-10mers-539 LNHLLINPFY 12 Pos 123456789 score 548 YEPSHAEEVS 12 No Results Found.

559 FSVCGFANPL 12 Table XLV-V4-HLA-B5101-10mers-616 LQKNVDHCLL 12 Pos 123456789 score 617 QKNVDHCLLY 12 No Results Found.

Table XLVI-V1-DRB1-0101-15mers-Table XLVI-V1-DRB1-0101-15mers- 161P2F1OB
161P2F1OB Pos 123456789012345 score Pos 123456789012345 score 518 486 NNEFRSMEAIFLAHG .35-589 VNQMLNLTQEEITAT 24 GIHSI<YMRAMYPTKT 23 858 VSEILQLKTYLPTFE 30 _ 210 YTIVTGLYPESHGII

30 ALLVIMSLGLGLGLG 27 _ 562 313 RPRFYTMYFEEPDSS 24 _ 98 CNKFRCGETRLEASL 20 Table XLVI-V1-DRB1-0101-15mers- Table XLVI-V1-DRB1-0101-15mers-Pos 123456789012345 score Pos _ 123456789012345 score _ _ 158 LPPVILFSMDGFRAE 19 227 302 LLKWLDLPKAERPRF 18 _ 726 DYFHSVLLIKHATER 17 382 KMEYMTDYFPRINFF 18 _ 823 _ PEALVVVEERFTAHIA 17 515 IEVYNLMCDLLRIQP 18 _ 836 IARVRDVELLTGLDF 17 640 MPMWSSYTVPQLGDT 18 Table XLV1-V2-DRB1-0101-15mers-681 FYLADKNITHGFLYP 18 _ Pos 123456789012345 score . 847 GLDFYQDKVQPVSEI 18 _ 13 16 NTLKKYKIACIVLLA 17 _ 9 SDDCLQRKDCCADYK 8 _ 8 36 SLGLGLGLGLRKLEK 17 Table XLVI-V3-HLA-DRB1-0101-15mers-103 CGETRLEASLCSCSD 17 Pos 123456789012345 score 139 VVLEENCDTAQQSQCP 17 12 SCPGGKPEX.WVEER 19 Table XLVI-V3-HLA-DRB1-0101-15mers- Table XLVII-V1-HLA-DRB1-0301-15mers-Pos 123456789012345 score Pos 123456789012345 score = Table XLVI-V4-HLA-DRB1-0101-15mers-Pos 123456789012345 score 524 2 ILQLKTYLPTFETPI 16 _ 553 _ Table XLV1I-V1-HLA-DRB1-0301-15mers- 679 CSFYLADKNITHGFL

Pos 123456789012345 score 740 662 PDCLRADVRVPPSES 28_ 812 PTNVESCPEGKPEAL = 19 305 WLDLPKAERPRFYTM 25_ 178 DTLMPNINKLKTCGI

366 NIILLADHGMDQTYC 22 =267 10 EQPVKKNTLKOKIA 20_ 586 LEQVNQMLNLTQEEI

847 GLDFYQDKVQPVSEI 20 _ 92 KFSVCGFANPLPTES 17 _ NQMLNLTQEEITATV 17 =

Table XLV1I-V1-HLA-DRB1-0301-15mers-161P2F1OB Table XLV1I-V4-HLA-DRB1-0301-15mers-Pos 123456789012345 score 161P2F1OB
714 LVPMYEEFRKMWDYF 17 Pos 123456789012345 score 60 DASFRGLENCRCDVA 16 Table XLVIII-V1-HLA-DRB1-0401-15mers-78 RGDCCWDFEDTCVES 16 Pos 123456789012345 score 226 NNMYDVNLNKNFSLS 16 631 VSGFGI<AMRMPMWSS 28 234 NKNFSLSSKEQNNPA 16 _ 691 GFLYPPASNRTSDSQ

384 EYMTDYFPRINFFYM 16 . 722 RKMVVDYFHSVLLIKH 28 -450 YAKNVRIDKVHLFVD 16 750 IFDYNYDGHFDAPDE 28 , , 532 NNGTHGSLNHLLKVP , 16 777 678 KCSFYLADKNITHGF 16 28 LtALLVIMSLGLGLG 26 478 CGGGNHGYNNEFRSM 15 60 DASFRGLENCRCDVA 22 _ Table XLVII-V2-DRB1-0301-15mers- 253 QPMWLTAMYQGLKAA 22 Pos 123456789012345 score 279 NGSFPSIYMPYNGSV 22 15 RKDCCADYKSVCQGE 16 , 387 TDYFPRINFFYMYEG 22 NHGYNNEFRSMEAIF .. 22 Table XLVII-V3-HLA-DRB1-0301-15mers- 509 VEPFEN I EVYNLMCD

161 P2F1OB 573 , LDCFCPHLQNSTQLE 22 Pos 123456789012345 score 678 KCSFYLADKNITHGF 22 Table XLV1II-V1-HLA-DRB1-0401-15mers- Table XLVIII-V1-HLA-DRB1-0401-15mers-Pos 123456789012345 score Pos 123456789012345 score 690 HGFLYPPASNRTSDS 20 170 FtAEYLYTVVDTLMPNI 16 833 TAHIARVRDVELLTG ' 20 258 TAMYQGLKAATYFWP 16 Table XLVIII-V1-HLA-D1281-0401-15mers- Table XLVIll-V1-HLA-DRB1-0401-15mers-Pos 123456789012345 score Pos 123456789012345 score _ 30 ALLVIMSLGLGLGLG 14 _ 706 YDAL1TSNLVPMYEE 14 ' 160 PVILFSMDGFRAEYL 14 801 257 LTAMYQGLKAATYFW 14 Table XLVIII-V2-DR1-0401-15mers-284 SIYMPYNGSVPFEER 14 Pos 123456789012345 score Table XLIX-V1-HLA-DRB1-1101-15mers-Table XLIX-V1-HLA-DRB1-1101-15mers- 161P2F1OB
161P2F1OB Pos 123456789012345 score Pos 123456789012345 score 556 VSKFSVCGFANPLPT 17 -339_ IKALQVVDHAFGMLM 27 . 691 GFLYPPASNRTSDSQ 17 207 _ PNHYTIVTGLYPESH 24 92 STRIWMCNKFRCGET -, 16 302 , LLKWLDLPKAERPRF 24126 CADYKSVCQGETSWL 16 _ _ 750 _ IFDYNYDGHFDAPDE 24 136 ETSVVLEENCDTAQQS 16 392 _ RINFFYMYEGPAPRI 23_ 258 TAMYQGLKAATYFWP 16 662 _ PDCLRADVRVPPSES 22 _ 349 FGMLMEGLKQRNLHN 16 160 , PVILFSMDGFRAEYL 21 387 TDYFPR1NFFYMYEG 16 178 DTLMPNINKLKTCGI 21 j 393 296 . EERISTLLKWLDLPK 21 397 YMYEGPAPRIRAHNI _ 16 -780 YFVVLTSCKNKSHTP 21 464 _ 823 PEALWVEERFTAHIA 21 _ 486 _ 227 NMYDVNLNKNFSLSS 20. 500 _ 421 EEIVRNLSCRKPDQH 20_ 509 _ 447 RLHYAKNVRIDKVH _ _ L 20 561 536 HGSLNHLLKVPFYEP 20 _ 703 DSQYDALITSNLVPM 16 728 FHSVLLIKHATERNG 20_ 718 801 LDVLPFIIPHRPTNV 20 _ 830 _ 29 LALLVIMSLGLGLGL 19 _ _ 12 _ 56 KKCFDASFRGLENCR 19 213 VTGLYPESHGIIDNN 15 _ 678 KCSFYLADKNITHGF 19 332 _ GPVSARVIKALQWD 15 , 858 VSEILQLKTYLPTFE , 19. 427 25 CIVLLALLVIMSLGL 18 458 KVHLFVDQQWLAVRS 15 _ FRKMVVDYFHSVLLIK 15 =

LATEQPVKKNTLKKY 14 .
, 544 KVPFYEPSHAEEVSK 18 20 IVLLALLVIMSLGLG - 14 _ 778 THYFVVLTSCKNKSH 18 114 SCSDDCLQKKDCCAD 14 .

283 PSIYMPYNGSVPFEE 17 290 _ NGSVPFEERISTLLK_ 14 346 DHAFGMLMEGLKQRN 17 321 , FEEPDSSGHAGGPVS 14 Table XLIX-V1-FILA-DRB1 -1101-15mers- Table XLVIII-V4-HLA-DR1-0401-15mers-Pos 123456789012345 score Pos 123456789012345 score 550 PSHAEEVSKFSVCGF 14 Table XLIX-V2-DRB1-1101-15mers-628 REYVSGFGKAMRMPM 14 Pos 123456789012345 score 814 NVESCPEGKPEALWV 14 Table XLIX-V3-HLA-DRB1-1101-15mers-842 VELLTGLDFYQDINQ 14 Pos 123456789012345 score 33 VIMSLGLGLGLGLRK 13_ 3 IPHRPTNVESCPGGK

434 QHFKPYLTPDLPKRL 13 Table XLIX-V4-11LA-DRB1-1101-15mers-514 NIEVYNLMCDLLRIQ 13 Pos 123456789012345 score 558 KFSVCGFANPLPTES 13 _ Table XLV111-V3-HLA-DR1-0401-15mers-Pos 123456789012345 score =

Table L: Properties of 161P2F-1013 Bioinformatic Outcome Program Feature Bioinformatic Outcome Program ORF (includes stop ORE finder codon) # of amino acids = Transmembrane region TM Pred One TM, aa 23-41 HMMTop One TM, aa 23-45 Sosui One TM, aa 23-45 TMHMM
= One TM, aa 23-45 Signal Peptide Signal P
None PI p1/MW tool 6.12 Molecular weight p1/MW tool 100.0g kDa Localization PSORT Plasma membrane 74%
Golgi 30%
PSORT II .
Endoplasmic 304% , Golgi 21.7%
Motifs Pfam - - - Somatomedin B, Type I
phosphodiesterase /
nucleotide pyrophosphatase --Prints Cell Attachement ROD
Blocks Somatomedin B, DNA/RNA non-specific endonuclease, Prosite Somatomedin B
Table LI. Nucleotide sequence of transcript variant 161P2P1OS v.6 (SEQ ID NO:
91) atacagtttc tctttgccag actagactaa agaaggagca ctactttatt ctgataaaac 60 aggtctatgc agctaccagg acaatggaat ctacgttgac tttagcaacg gaacaacdtg 120 ttaagaagaa cactcttaag aaatataaaa tagcttgcat tgttcttctt gctttgctgg 180 tgatcatgtc acttggatta ggcctggggc ttggactcag gaaactggaa aagcaaggca 240 gctgcaggaa gaagtgcttt gatgcatcat ttagaggact ggagaactgc cggtgtgatg 300 tggcatgtaa agaccgaggt gattgctgct gggattttga agacacctgt gtggaatcaa 360 ctcgaatatg gatgtgcaat aaatttcgtt gtggagagac cagattagag gCcagccttt 420 gctcttgttc agatgactgt ttgcagagga aagattgctg tgctgactat aagagtgttt 480 gccaaggaga aacctcatgg ctggaagaaa actgtgacac agcccagcag tctcagtgcc 540 cagaagggtt tgacctgcca ccagttatct tgttttctat ggatggattt agagctgaat 600 atttatacac atgggatact ttaatgccaa atateaataa actgaaaaca tgtggaattc 660 attcaaaata catgagagct atgtatccta ccaaaacctt cccaaatcat tacaccattg 720 tcacgggctt gtatccggag tcacatggca tcattgacaa taatatgtat gatgtaaatc 780 tcaacaagaa tttttcactt tcttcaaagg aacaaaataa tccagcctgg tggcatgggc 840 aaccaatgtg gctgacagca atgtatcaag gtttaaaagc cgctacctac ttttggcccg 900 gatcagaagt ggctataaat ggctcctttc cttccatata catgccttac aacggaagtg 960 tcccatttga agagaggatt tctacactgt taaaatggct ggacctgccc aaagctgaga 1020 gacccaggtt ttataccatg ttttttgaag aacctgattc ctctggacat gcaggtggac 1080 cagtcagtgc cagagtaatt aaagccttac aggtagtaga tcatgctttt gggatgttga 1140 tggaaggcct gaagcagcgg aatttgcaca actgtgtcaa tatcatcctt ctggctgacc 1200 oot DP6E5E.66q6q16oqqlepTevo6161e66qeqpe6pqopeolvv554615qoopoe6u TtE :9=A

09E 0g5e6P65164350qqpepqep35161p66qelve6oq3veolpu65q636q00e0P62 TOE :T'A
OtE P611;1p666qo5qo51qe6q66P5oop6ePpq.61PD66.461v5q6q663o6qapv5u65 Tgz :9.A

00E e6 66666 TtZ
:T'A
ogz q3v66p6eqqqvoqeo6qu616q6eebee66eo6436e365epD6Pepp661ouPe6 izz :9=A

otz lou66s6pqlltolpo6qp6qqqa6q6uebee66eD6o6PD66veobevvvBE.qovse6 181 :T.A
OZZ Epoqop66q1o666613366vqqP661qov3q6qeDqp6.466q35qq40634014pq461 191 :9.A

081 6E0q0P66qq36686q=66s14v6Eq;oe016qP03P5466q06q4q061q0416q izi :T.A
091 366 633565666: TOT
:9=A

ozT qpo6qqo6eqp.epelPwev6selloq3eove6pu6evq6qooup3ep66oPPo6vqlq T9 :T.A
OOT 3q66 565:3 Tt :9-A

09 op6qq5ovloquE.65queop68poov;o6s36qv;pq65poPupequEqolluqqqopq3 T.A
Snid / Snid = pue.14S (%0) 08LZ/T = sdpp '%%66, oeLz/vLcz = seTTpuaPI0'0 = qoadxa '(LSLZ) slIq TOES = aaopS
(E6 :O( aiOES) 9 Et0taniT9T
ply (E6 :ON ai Oas) T'A 80TaZd191 quemu5TI2 90UenbeS epTloeTonN 'lig eTc[EI
591E poppEt 3v2vPeqqpp .evlqe5qD.61 ppD66qoe6q qlplEqlqqq OZTE
3vve3e3q6 qq145epqev pqoloppoqp u6qose6664 osoqoq6;p q6pp6pePeo ep6e666pue PoPPvqolvq qpp6P0005q ollpqpq vv6qqqolue Evololqoq vqqqq5qqDP lqvq1DoqqD opTequSep pElqsoloqpv qoqoeveqqo lqq.684q5q4 0t6Z
13qq333q3 pepelTeqeq z6 666 poepeoqqq1 lpqvqq5ese lqqleq3eq6 qPlvv54P10 lqePolq4;1 ;D3D'44qq40 ollvq4P144 qWeqP306e P'eq00D015 vplqooqqq1 Teqolqq16E. suqvPveq64 lETE.E.E.qpq qq14q;e6q6 vt.luqpv.eeD

66qqq;epq6 uuplvq.6qos qqqe'elvqq elqopq345 quequ,P;qos PqqqP1DPDD
OOLZ
epe611vot. PoovqqQvqv oebeyylopp 35lq11.epv6 oloq6qooE, po6.45pes.gy 0t9Z
66e3qP1olq ov6qq3686q proloqloPv 6uq6qp5q6o o16663338q lpoeowEvo vqqqP5vE,P6 t,e6qq665qg qoqp6vp6vo 3uvp466pP6 lo3l6loEce6 p66q6ovvoo OZSZ
pqoppEooPo wooqeoqeq lqoDoeqopq Eqp6633661 666woo613 vepu6600v3 09tZ
poPo3Bp6 ovve-epSlq 6pDDP6qD6q 66q51.443v1 3VDPOPE000 qeopoql6qe 00tZ
SqovoQeDDE, r;q1voepPo ouqlve5qP 66e6 qqqqeoo66q P64E1qve4P
OVEZ
qqv5qqqeqv vooe66q6pq 166364evPq BE664vspE, EyBypeop6q POUPPPEqq olq3qq5q5s oppoqwpqo p6E6q6.4E.E.v ve6Poqqes6 eu61u16qP3 DDPq56144P
OZZZ
voSvwellu Pqqqa6qp61 pqpeop6eqp 6voTeopp5E. Tevo6poo6q poqoolvqoq 33qq3663u3 3ovo3vqt.P6 peoebeobeq qTeqoqiopq 6.3rPPE.E,Do E.v66qoqqo OOTZ 3q33qq66.6v 3q6qv5q3.66 63633q813e 6p333q6qop 333336;31 3353 D3 OtOZ
6v666qq6po 3333q6p3v3 Ps3qq6P66 q6qP0006qP 55PEqeQ06e eee66444P8 6q6P3q6qsq ep655poepo plq1Dowq6 qopope6645 osv6ev6po6 3el666pqo 366t.E.661q4 uoo6q1qupp 16per,5463 veobeoevlp ve6pp6pepo ovoqolpesq 0981 36qE,6e3qvp 6q6peopp85 ;36v3qopq6 eqs'eepopqo 3P3q3o363 q6.qovE.qq o;oq6u6eoP 3336qqv33l epl3611;35 6q6qqq6qoi q;16PPeoq6 6E.E,66e6so OVLT
6Teopolsoo Be6q.elqqq4 o35166ET54 oqq31P33eP E.;q15eq66q e333ee65qe e3Pe33e36 pooveoqqeD 6De3DqqoqP 64616qepqo 3velP43;6e v6qqsqvuep ql6Pp5lo25 pp8v8pspql qq8poope66 le3u366q3; qqolp;366E.

664vo6u66e ;q16u6qepo evqvq;66qv 33PE,366u86 P65q6qTeTP DP1Pse0;PP

eq6P56p116 qD56w6646 v3ev3qu66q 6q1.4313;p3 q;6Pee3p53 lpy6e3qE3v Otti e6eep36leq 3v36q3sE36 epvoo6qqqP 5woweSql qP1000Beep 363 08E1 6.433ppse53 35 6333 ppe6P;6qq ETE.66v6qpq ;veq111be Q14qq0v6q OZET
3.433.4pq2 1v3q36p633 q6DE.DooDpo 643365Erep6 3v.461v3-el3 .134q3e-eP4 eP6e333lqq ;v1qe6l3v5 Te3e1pe66q e6ePopeqbq ls,q3e5voo p6Eqee66qe Z009/ZOSII/I3c1 0170170/0 OM
1O-170-1700Z ES9Z9tZ0 VD

v.1: 361 cagattagaggccagcctttgctcttgttcagatgactgtttgcagaagaaagattgctg 420 v.6: 401 cagattagaggccagcctttgctcttgttcagatgactgtttgcagaggaaagattgctg 460 v.1: 421 tgctgactataagagtgtttgccaaggagaaacctcatggctggaagaaaactgtgacac 480 v.6: 461 tgctgactataagagtgtttgccaaggagaaacctcatggctggaagaaaactgtgacac 520 v.1: 481 agcccagcagtctcagtgcccagaagggtttgacctgccaccagttatcttgttttctat 540 v.6: 521 agcccagcagtctcagtgcccagaagggtttgacctgccaccagttatcttgttttctat 580 v.1: 541 ggatggatttagagctgaatatttatacacatgggatactttaatgccaaatatcaataa 600 v.6: 581 ggatggatttagagctgaatatttatacacatgggatactttaatgccaaatatcaataa 640 v.1: _601 actgaaaacatgtggaattcattcaaaatacatgagagctatgtatcctaccaaaacctt 660 v.6: 641 actgaaaacatgtggaattcattcaaaatacatgagagctatgtatcctaccaaaacctt 700 v.1: 661 cccaaatcattacaccattgtcacgggcttgtatccagagtcacatggcatcattgacaa 720 v.6: 701 cccaaatcattacaccattgtcacgggcttgtatccggagtcacatggcatcattgacaa 760 v.1: 721 taatatgtatgatgtaaatctcaacaagaatttttcactttcttcaaaggaacaaaataa 780 v.6: 761 taatatgtatgatgtaaatctcaacaagaatttttcactttcttcaaaggaacaaaataa 820 v.1: 781 tccagcctggtggcatgggcaaccaatgtggctgacagcaatgtatcaaggtttaaaagc 840 v.6: 821 tccagcctggtggcatgggcaaccaatgtggctgacagcaatgtatcaaggtttaaaagc 880 v.1: 841 cgctacctacttttggcccggatcagaagtggctataaatggctcctttccttccatata 900 v.6: 881 cgctacctacttttggcccggatcagaagtggctataaatggctcctttccttccatata 940 v.1: 901 catgccttacaacggaagtgtcccatttgaagagaggatttctacactgttaaaatggct 960 v.6: 941 catgccttacaacggaagtgtcccatttgaagagaggatttctacactgttaaaatggct 1000 v.1: 961 ggacctgcccaaagctgaaagacccaggttttataccatgtattttgaagaacctgattc 1020 v.6: 1001 ggacctgcccaaagctgagagacccaggttttataccatgttttttgaagaacctgattc 1060 v.1: 1021 ctctggacatgcaggtggaccagtcagtgccagagtaattaaagccttacaggtagtaga 1080 v.6: 1061 ctctggacatgcaggtggaccagtcagtgccagagtaattaaagccttacaggtagtaga 1120 v.1: 1081 tcatgcttttgggatgttgatggaaggcctgaagcagcggaatttgcacaactgtgtcaa 1140 v.6: 1121 tcatgcttttgggatgttgatggaaggcctgaagcagcggaatttgcacaactgtgtcaa 1180 v.1: 1141 tatcatccttctggctgaccatggaatggaccagacttattgtaacaagatggaatacat 1200 v.6: 1181 tatcatccttctggctgaccatggaatggaccagacttattgtaacaagatggaatacat 1240 v.1: 1201 gactgattattttcccagaataaacttcttctacatgtacgaagggcctgccccccgcat 1260 v.6: 1241 gactgattattttcccagaataaacttcttctacatgtacgaagggcctgccccccgcgt 1300 v.1: 1261 ccgagctcataatatacctcatgacttttttagttttaattctgaggaaattgttagaaa 1320 v.6: 1301 ccgagctcataatatacctcatgacttttttagttttaattctgaggaaattgttagaaa 1360 v.1: 1321 cctcagttgccgaaaacctgatcagcatttcaagccctatttgactcctgatttgccaaa 1380 v.6: 1361 cctcagttgccgaaaacctgatcagcatttcaagccctatttgactcctgatttgccaaa 1420 v.1: 1381 gcgactgcactatgccaagaacgtcagaatcgacaaagttcatctctttgtggatcaaca 1440 v.6: 1421 gcgactgcactatgccaagaacgtcagaatcgacaaagttcatctctttgtggatcaaca 1480 v.1: 1441 gtggctggctgttaggagtaaatcaaatacaaattgtggaggaggcaaccatggttataa 1500 v.6: 1481 gtggctggctgttaggagtaaatcaaatacaaattgtggaggaggcaaccatggttataa 1540 v.1: 1501 caatgagtttaggagcatggaggctatctttctggcacatggacccagttttaaagagaa 1560 v.6: 1541 caatgagtttaggagcatggaggctatctttctggcacatggacccagttttaaagagaa 1600 v.1: 1561 gactgaagttgaaccatttgaaaatattgaagtctataacctaatgtgtgatcttctacg 1620 v.6: 1601 gactgaagttgaaccatttgaaaatattgaagtctataacctaatgtgtgatcttctacg 1660 v.1: 1621 cattcaaccagcaccaaacaatggaacccatggtagtttaaaccatcttctgaaggtgcc 1680 v.6: 1661 cattcaaccagcaccaaacaatggaacccatggtagtttaaaccatcttctgaaggtgcc 1720 v.1: 1681 tttttatgagccatcccatgcagaggaggtgtcaaagttttctgtttgtggctttgctaa 1740 v.6: 1721 tttttatgagccatcccatgcagaggaggtgtcaaagttttctgtttgtggctttgctaa 1780 v.1: 1741 tccattgcccacagagtctcttgactgtttctgccctcacctacaaaatagtactcagct 1800 v.6: 1781 tccattgcccacagagtctcttgactgtttctgccctcacctacaaaatagtactcagct 1840 v.1: 1801 ggaacaagtgaatcagatgctaaatctcacccaagaagaaataacagcaacagtgaaagt 1860 v.6: 1841 ggaacaagtgaatcagatgctaaatctcacccaagaagaaataacagcaacagtgaaagt 1900 v.1: 1861 aaatttgccatttgggaggcctagggtactgcagaagaacgtggaccactgtctccttta 1920 v.6: 1901 aaatttgccatttgggaggcctagggtactgcagaagaacgtggaccactgtctccttta 1960 v.1: 1921 ccacagggaatatgtcagtggatttggaaaagctatgaggatgcccatgtggagttcata 1980 v.6: 1961 ccacagggaatatgtcagtggatttggaaaagctatgaggatgcccatgtggagttcata 2020 v.1: 1981 cacagtcccccagttgggagacacatcgcctctgcctcccactgtcccagactgtctgcg 2040 V.6: 2021 cacagtcccccagttgggagacacatcgcctctgcctcccactgtcccagactgtctgcg 2080 v.1: 2041 ggctgatgtcagggttcctccttctgagagccaaaaatgttccttctatttagcagacaa 2100 v.6: 2081 ggctgatgtcagggttcctccttctgagagccaaaaatgttccttctatttagcagacaa 2140 v.1: 2101 gaatatcacccacggcttcctctatcctcctgccagcaatagaacatcagatagccaata 2160 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
v.6: 2141 gaatatcacccacggcttcctctatcctcctgccagcaatagaacatcagatagccaata 2200 v.1: 2161 tgatgctttaattactagcaatttggtacctatgtatgaagaattcagaaaaatgtggga 2220 v.6: 2201 tgatgctttaattactagcaatttggtacctatgtatgaagaattcagaaaaatgtggga 2260 v.1: 2221 ctacttccacagtgttcttcttataaaacatgccacagaaagaaatggagtaaatgtggt 2280 v.6: 2261 ctacttccacagtgttcttcttataaaacatgccacagaaagaaatggagtaaatgtggt 2320 v.1: 2281 tagtggaccaatatttgattataattatgatggccattttgatgctccagatgaaattac 2340 v.6: 2321 tagtggaccaatatttgattataattatgatggccattttgatgctccagatgaaattac 2380 v.1: 2341 caaacatttagccaacactgatgttcccatcccaacacactactttgtggtgctgaccag 2400 v.6: 2381 caaacatttagccaacactgatgttcccatcccaacacactactttgtggtgctgaccag 2440 v.1: 2401 ttgtaaaaacaagagccacacaccggaaaactgccctgggtggctggatgtcctaccctt 2460 v.6: 2441 ttgtaaaaacaagagccacacaccggaaaactgccctgggtggctggatgtcctaccctt 2500 v.1: 2461 tatcatccctcaccgacctaccaacgtggagagctgtcctgaaggtaaaccagaagctct 2520 v.6: 2501 tatcatccctcaccgacctaccaacgtggagagctgtcctgaaggtaaaccagaagctct 2560 v.1: 2521 ttgggttgaagaaagatttacagctcacattgcccgggtccgtgatgtagaacttctcac 2580 v.6: 2561 ttgggttgaagaaagatttacagctcacattgcccgggtccgtgatgtagaacttctcac 2620 v.1: 2581 tgggcttgacttctatcaggataaagtgcagcctgtctctgaaattttgcaactaaagac 2640 v.6: 2621 tgggcttgacttctatcaggataaagtgcagcctgtctctgaaattttgcaactaaagac 2680 v.1: 2641 atatttaccaacatttgaaaccactatttaacttaataatgtctacttaatatataattt 2700 v.6: 2681 atatttaccaacatttgaaaccactatttaacttaataatgtctacttaatatataattt 2740 v.1: 2701 actgtataaagtaattttggcaaaatataagtga-ttttttctggagaattgtaaaataa 2759 v.6: 2741 actgtataaagtaattttggcaaaatataagtgatttttttctggagaattgtaaaataa 2800 v.1: 2760 agttttctatttttccttaa 2779 v.6: 2801 agttttctatttttccttaa 2820 Table LITT. Peptide sequences of protein coded by 161P2F1OB v.6 (SEQ ID NO:
94) = EEIVRNLSCR

Table LIV. Amino acid sequence alignment of 161P2F1OBv.1 v:1 (SEQIDNO: 95) and 161P2F1OB v.6 (5EQH)NO: 96) Score = 1855 bits (4804), Expect = 0.0Identities = 875/875 (100%), Positives =

875/875 (100%) 161P2F1OBv.1: 1 MESTLTLATEQPVKKNTLKKYKIACIVLLALLVIMSLGLGLGLGLRKLEKQGSCRKKCFD

MESTLTLATEQPVKKNTLKKYKIACIVLLALLVIMSLGLGLGLGLRKLEKQGSCRKKCFD
161P2F1OBv.6: 1 MESTLTLATEQPVKKNTLKKYKIACIVLLALLVIMSLGLGLGLGLRKLEKQGSCRKKCFD

161P2F1OBv.1: 61 ASFRGLENCRCDVACKDRGDCCWDFEDTCVESTRIWMCNKFRCGETRLEASLCSCSDDCL

ASFRGLENCRCDVACKDRGDCCWDFEDTCVESTRIWMCNKFRCGETRLEASLCSCSDDCL
161P2F1OBv.6: 61 ASFRGLENCRCDVACKDRGDCCWDFEDTCVESTRIWMCNKFRCGETRLEASLCSCSDDCL

161P2F1OBv.1: 121 QKKDCCADYKSVCQGETSWLEENCDTAQQSQCPEGFDLPPVILFSMDGFRAEYLYTWDTL

QKKDCCADYKSVCQGETSWLEENCDTAQQSQCPEGFDLPPVILFSMDGFRAEYLYTWDTL
161P2F1OBv.6: 121 QKKDCCADYKSVCQGETSWLEENCDTAQQSQCPEGFDLPPVILFSMDGFRAEYLYTWDTL

161P2F1OBv.1: 181 MPNINKLKTCGIHSKYMRAMYPTKTFPNHYTIVTGLYPESHGIIDNNMYDVNLNKNFSLS

MPNINKLKTCGIHSKYMRAMYPTKTFPNHYTIVTGLYPESHGIIDNNMYDVNLNKNFSLS
161P2F1OBv.6: 181 MPNINKLKTCGIHSKYMRAMYPTKTFPNHYTIVTGLYPESHGIIDNNMYDVNLNKNFSLS
240 =
161P2F1OBv.1: 241 SKEQNNPAWWHGQPMWLTAMYQGLKAATYFWPGSEVAINGSFPSIYMPYNGSVPFEERIS

SKEQNNPAWWHGQPMWLTAMYQGLKAATYFWPGSEVAINGSFPSIYMPYNGSVPFEERIS
161P2F1OBv.6: 241 SKEQNNPAWWHGQPMWLTAMYQGLKAATYFWPGSEVAINGSFPSIYMPYNGSVPFEERIS

161P2F1OBv.1: 301 TLLKWLDLPKAERPRFYTMYFEEPDSSGHAGGPVSARVIKALQVVDHAFGMLMEGLKQRN

- TLLKWLDLPKAERPRFYTMYFEEPDSSGHAGGPVSARVIKALQVVDHAFGMLMEGLKQRN
161P2F1OBv.6: 301 TLLKWLDLPKAERPRFYTMYFEEPDSSGHAGGPVSARVIKALQVVDHAFGMLMEGLKQRN

161P2F1OBv.1: 361 LHNCVNIILLADHGMDQTYCNKMEYMTDYFPRINFFYMYEGPAPRIRAHNIPHDFFSFNS

LHNCVNIILLADHGMDQTYCNKMEYMTDYFPRINFFYMYEGPAPRIRAHNIPHDFFSFNS
161P2F1OBv.6: 361 LHNCVNIILLADHGMDQTYCNKMEYMTDYFPRINFFYMYEGPAPRIRAHNIPHDFFSFNS

161P2F1OBv.1: 421 EEIVRNLSCRKPDQHFKPYLTPDLPKRLHYAKNVRIDKVHLFVDQQWLAVRSKSNTNCGG

EEIVRNLSCRKPDQHFKPYLTPDLPKRLHYAKNVRIDKVHLFVDQQWLAVRSKSNTNCGG
161P2F1OBv.6: 421 EEIVRNLSCRKPDQHFKPYLTPDLPKRLHYAKNVRIDKVHLFVDQQWLAVRSKSNTNCGG

161P2F1OBv.1: 481 GNHGYNNEFRSMEAIFLAHGPSFKEKTEVEPFENIEVYNLMCDLLRIQPAPNNGTHGSLN

GNHGYNNEFRSMEAIFLAHGPSFKEKTEVEPFENIEVYNLMCDLLRIQPAPNNGTHGSLN
161P2F1OBv.6: 481 GNHGYNNEFRSMEAIFLAHGPSFKEKTEVEPFENIEVYNLMCDLLRIQPAPNNGTHGSLN

-161P2F1OBv.1: 541 HLLKVPFYEPSHAEEVSKFSVCGFANPLPTESLDCFCPHLQNSTQLEQVNQMLNLTQEEI
161P2F1OBv.6: 541 HLLKVPFYEPSHAEEVSKFSVCGFANPLPTESLDCFCPHLQNSTQLEQVNQMLNLTQEEI

161P2F1OBv.1: 601 TATVKVNLPFGRPRVLQKNVDHCLLYHREYVSGFGKAMRMPMWSSYTVPQLGDTSPLPPT

TATVKVNLPFGRPRVLQKNVDHCLLYHREYVSGFGKAMRMPMWSSYTVPQLGDTSPLPPT
161P2F1OBv.6: 601 TATVKVNLPFGRPRVLQKNVDHCLLYHREYVSGFGKAMRMPMWSSYTVPQLGDTSPLPPT

161P2F1OBv.1: 661 VPDCLRADVRVPPSESQKCSFYLADKNITHGFLYPPASNRTSDSQYDALITSNLVPMYEE

VPDCLRADVRVPPSESQKCSFYLADKNITHGFLYPPASNRTSDSQYDALITSNLVPMYEE
161P2F1013v.6: 661 161P2F1OBv.1: 721 FRKMWDYFHSVLLIKHATERNGVNVVSGPIFDYNYDGHFDAPDEITKHLANTDVPIPTHY

FRKMWDYFHSVLLIKHATERNGVNVVSGPIFDYNYDGHFDAPDEITKHLANTDVPIPTHY
161P2F1OBv.6: 721 FRKMWDYFHSVLLIKHATERNGVNVVSGPIFDYNYDGHFDAPDEITKHLANTDVPIPTHY

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PPqPPEEDET
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5L8 III3aIdaLLYIMISSAdOANGOAaGIDITIEACI Tt8 :1'AE0TaZd191 0t8 UAUYIHVJAEHEAMWSMEdDSaANIdEHdIIadrIACIMOdONSUMMINNOSIgAAS 18L :9-AEO1dZd191 UAUVIHYSAESSAWIVSdNO3dDS3ANIdUHdIIddrIAMMDdONadIHMINNDSZIAAA
Ot8 UAHVIHVIaliaaAMqVadX0SdDSSANIdHHdIIddrIAMMOdDNSdIHMINNDSEIAAA T8L
:T'ASOTaZdT9T

Z009/Z0SII/I3c1 TO-t0-t003 ES939t30 YD

6ZL P1sso1vqsseopEqueqqqoeqe666qppeoele111Plue6136e6v411s65qp66q 0L9 665 sqpsoquqsspoo6qssq;qosqs6661p3sosqvqqqsles6qo65eqqle66s661 OtS :T.A
699 e10111161101u116upospobloosEqqq666sp6spoo536voqa16e36sopo6P3 019 :L.A

6E9 P10111164qplesopeop6loov5q1q665eP6soo3616soaq5s36sopo5so 08t :VA
609 D56 666653 oSS
:CA

6Lt, Eos6.46weesebes65w65qeoqooses6s56ssoo5111616E6se1e10e640515 OZt :VA
61S 106qqP6seeftv6e35qq15los51s6solq5q101061;q336e3366s8s11E6e33 06' :L -A

6Tt 108q4s6ses6se6E36q1Q6lopEqs8P0145410406114336poo56s6vq4e6e= 09E :T'A
68t P5s5p6616146olqqsesTeep6q6q65qvlsvEoqDPpoqss661615qops3s6s 007 1LA

6SE e6s6s55q6qq5aqqqesqupp661e66TeqesEoqossoqeu6516q6qopvps6se 00E :T.A
6Zt 51111e6564D6qp6qqs5166sEops5see;Eqso5Eq5qv5q6q663o5lopp5s68q 0LE :L-A

66Z 51111s566w6loblqs6166p5oov5sesq6qpo66q6qs6q5166Do6wep5s55q :T -A
69E DP56s6PqqlsopoEqs5q1w646ssevs56pD6qo6e366uvoSeeus66qossu6.6 0TE :L.A

6Ez 3s66s5vqqqsozeo6ls5qqqa6q6ve5vs65s36q36s366vv36ssEs66losse6E. 081 :T -A
60E PD1os66qq366661=56eqqs664wepq6qvoqs6q651oSqllo611014011611 Osz :L.A

6L1 P010P56q1p666643366sqls66qqop3q6qs3qs61661o6qq13611014041511 :T-A
snid / snid = pusa1S (%001) 6ELE/6ELE = s9T1T1u3PIO-0 = Dadxs µ(6ELE) s1Tc( 681L =
aJoDS
TZT 1 TZT :CA

TZT 1 TzT :VA
0zi qp36qqo6uqvsseqslpes6esqwweos96es5vslq6q03vE3Pe660PP05s114 19 :CA

OZT 1so5q135slesseqsqese5elqoqoPop96up5vqq6qopsepes63sso5sql1 19 :T'A
09 325qq63swqes6b1se326623osqo52351s43466sosesqu6w;qeqq13243 I L =A

09 326qq63pl3lp256qp23256233e35236qsq3q6623ssus;s6q341s1110210 T :VA
snid / $nTd = pusa1S ($00T) TZT/TZT = sa-p-puspILS-GZ = qoadxs '(1I) s1N EEZ = e-(66 :OH Ca OHS) L'A iniaZdt9T
pue (86:0X ax Oas) tA ROLEZdI9T ;o quoutu5TT2 eouenbes epT409T3nli wurey 886E oqqse653 D6Bsoqqsoo peoppoBwo 096E 34366233l3 qq66q6s5oo oDoosEqoos soqspobqw oloso66sq oftoe6poop 006E 36006q3ls 332eE,333 86e6266q33 3861's01231 0059010186 111e010051 Ot8E 86q3q6sssl esolbeopoq 0000252032 3365Eq36qe 5u66qosool POPOSPODEP
08LE 5sqq;q5s6u 56 e666 5qv3qq6q15 sE66q66155 8356226669 2o262.66613 OZLE 33523296.43 8823222693 36g3e3o52q leq32616ep 83e3eq6232 638q2s2236 099E 65;828q365 683e5eq33q 3qq35q322q 236836;q2 2068508222 1661622008 009E 222933;556 1P11essqqq 666es58668 23533236 6228362620 sEqqlsooqq Z009/ZOSI1IIDcl 0170170/0 OAN
T0-t0-t00Z ES9Z9tZ0 vp v.1: 600 aactgaaaacatgtggaattcattcaaaatacatgagagctatgtatcctaccaaaacct 659 v.7: 730 aactgaaaacatgtggaattcattcaaaatacatgagagctatgtatcctaccaaaacct 789 v.1: 660 tcccaaatcattacaccattgtcacgggcttgtatccagagtcacatggcatcattgaca 719 v.7: 790 tcccaaatcattacaccattgtcacgggcttgtatccagagtcacatggcatcattgaca 849 v.1: 720 ataatatgtatgatgtaaatctcaacaagaatttttcactttcttcaaaggaacaaaata 779 v.7: 850 ataatatgtatgatgtaaatctcaacaagaatttttcactttcttcaaaggaacaaaata 909 v.1: 780 atccagcctggtggcatgggcaaccaatgtggctgacagcaatgtatcaaggtttaaaag 839 v.7: 910 atccagcctggtggcatgggcaaccaatgtggctgacagcaatgtatcaaggtttaaaag 969 v.1: 840 ccgctacctacttttggcccggatcagaagtggctataaatggctcctttccttccatat 899 v.7: 970 ccgctacctacttttggcccggatcagaagtggctataaatggctcctttccttccatat 1029 v.1: 900 acatgccttacaacggaagtgtcccatttgaagagaggatttctacactgttaaaatggc 959 v.7: 1030 acatgccttacaacggaagtgtcccatttgaagagaggatttctacactgttaaaatggc 1089 v.1: 960 tggacctgcccaaagctgaaagacccaggttttataccatgtattttgaagaacctgatt 1019 v.7: 1090 tggacctgcccaaagctgaaagacccaggttttataccatgtattttgaagaacctgatt 1149 v.1: 1020 cctctggacatgcaggtggaccagtcagtgccagagtaattaaagccttacaggtagtag 1079 v.7: 1150 cctctggacatgcaggtggaccagtcagtgccagagtaattaaagccttacaggtagtag 1209 v.1: 1080 atcatgcttttgggatgttgatggaaggcctgaagcagcggaatttgcacaactgtgtca 1139 11111111111111)111111111111111111111111111111111111111111111 v.7: 1210 atcatgcttttgggatgttgatggaaggcctgaagcagcggaatttgcacaactgtgtca 1269 v.1: 1140 atatcatccttctggctgaccatggaatggaccagacttattgtaacaagatggaataca 1199 v.7: 1270 atatcatccttctggctgaccatggaatggaccagacttattgtaacaagatggaataca 1329 v.1: 1200 tgactgattattttcccagaataaacttcttctacatgtacgaagggcctgccccccgca 1259 v.7: 1330 tgactgattattttcccagaataaacttcttctacatgtacgaagggcctgccccccgca 1389 v.1: 1260 tccgagctcataatatacctcatgacttttttagttttaattctgaggaaattgttagaa 1319 v.7: 1390 tccgagctcataatatacctcatgacttttttagttttaattctgaggaaattgttagaa 1449 v.1: 1320 acctcagttgccgaaaacctgatcagcatttcaagccctatttgactcctgatttgccaa 1379 111[11111111111111111111111111111111111111111111111111111111 v.7: 1450 acctcagttgccgaaaacctgatcagcatttcaagccctatttgactcctgatttgccaa 1509 v.1: 1380 agcgactgcactatgccaagaacgtcagaatcgacaaagttcatctctttgtggatcaac 1439 v.7: 1510 agcgactgcactatgccaagaacgtcagaatcgacaaagttcatctctttgtggatcaac 1569 v.1: 1440 agtggctggctgttaggagtaaatcaaatacaaattgtggaggaggcaaccatggttata 1499 v.7: 1570 agtggctggctgttaggagtaaatcaaatacaaattgtggaggaggcaaccatggttata 1629 v.1: 1500 acaatgagtttaggagcatggaggctatctttctggcacatggacccagttttaaagaga 1559 111,11111111111111111111111111111111111111111111111111111111 v.7: 1630 acaatgagtttaggagcatggaggctatctttctggcacatggacccagttttaaagaga 1689 v.1: 1560 agactgaagttgaaccatttgaaaatattgaagtctataacctaatgtgtgatcttctac 1619 v.7: 1690 agactgaagttgaaccatttgaaaatattgaagtctataacctaatgtgtgatctectac 1749 v.1: 1620 gcattcaaccagcaccaaacaatggaacccatggtagtttaaaccatcttctgaaggtgc 1679 v.7: 1750 gcattcaaccagcaccaaacaatggaacccatggtagtttaaaccatcttctgaaggtgc 1809 v.1: 1680 ctttttatgagccatcccatgcagaggaggtgtcaaagttttctgtttgtggctttgcta 1739 v.7: 1810 ctttttatgagccatcccatgcagaggaggtgtcaaagttttctgtttgtggctttgcta 1869 v.1: 1740 atccattgcccacagagtctcttgactgtttctgccctcacctacaaaatagtactoagc 1799 v.7: 1870 atccattgcccacagagtctcttgactgtttctgccctcacctacaaaatagtactcagc 1929 v.1: 1800 tggaacaagtgaatcagatgctaaatctcacccaagaagaaataacagcaacagtgaaag 1859 v.7: 1930 tggaacaagtgaatcagatgctaaatctcacccaagaagaaataacagcaacagtgaaag 1989 v.1: 1860 taaatttgccatttgggaggcctagggtactgcagaagaacgtggaccactgtctccttt 1919 v.7: 1990 taaatttgccatttgggaggcctagggtactgcagaagaacgtggaccactgtctccttt 2049 v.1: 1920 accacagggaatatgtcagtggatttggaaaagctatgaggatgcccatgtggagttcat 1979 v.7: 2050 accacagggaatatgtcagtggatttggaaaagctatgaggatgcccatgtggagttcat 2109 v.1: 1980 acacagtcccccagttgggagacacatcgcctctgcctcccactgtcccagactgtctgc 2039 v.7: 2110 acacagtcccccagttgggagacacatcgcctctgcctcccactgtcccagactgtctgc 2169 v.1: 2040 gggctgatgtcagggttcctccttctgagagccaaaaatgttccttctatttagcagaca 2099 11111111111111111,111111111111111111111111111111111111111111 v.7: 2170 gggctgatgtcagggttcctccttctgagagccaaaaatgttccttctatttagcagaca 2229 v.1: 2100 agaatatcacccacggcttcctctatcctcctgccagcaatagaacatcagatagccaat 2159 v.7: 2230 agaatatcacccacggcttcctctatcctcctgccagcaatagaacatcagatagccaat 2289 v.1: 2160 atgatgctttaattactagcaatttggtacctatgtatgaagaattcagaaaaatgtggg 2219 v.7: 2290 atgatgctttaattactagcaatttggtacctatgtatgaagaattcagaaaaatgtggg 2349 v.1: 2220 actacttccacagtgttcttcttataaaacatgccacagaaagaaatggagtaaatgtgg 2279 11111111111111111111111111111111iiii111111111111111111111111 v.7: 2350 actacttccacagtgttcttcttataaaacatgccacagaaagaaatggagtaaatgtgg 2409 v.1: 2280 ttagtggaccaatatttgattataattatgatggccattttgatgctccagatgaaatta 2339 v.7: 2410 ttagtggaccaatatttgattataattatgatggccattttgatgctccagatgaaatta 2469 v.1: 2340 ccaaacatttagccaacactgatgttcccatcccaacacactactttgtggtgctgacca 2399 v.7: 2470 ccaaacatttagccaacactgatgttcccatcccaacacactactttgtggtgctgacca 2529 v.1: 2400 gttgtaaaaacaagagccacacaccggaaaactgccctgggtggctggatgtcctaccct 2459 v.7: 2530 gttgtaaaaacaagagccacacaccggaaaactgccctgggtggctggatgtcctaccct 2589 v.1: 2460 ttatcatccetcaccgacctaccaacgtggagagctgtcctgaaggtaaaccagaagctc 2519 v.7: 2590 ttatcatccctcaccgacctaccaacgtggagagctgtcctgaaggtaaaccagaagetc 2649 v.1: 2520 tttgggttgaagaaagatttacagctcacattgcccgggtccgtgatgtagaacttctca 2579 11111111111111111111111,111111111111111111111111111111111111 v.7: 2650 tttgggttgaagaaagatttacagctcacattgcccgggtccgtgatgtagaacttctca 2709 v.1: 2580 ctgggcttgacttctatcaggataaagtgcagcctgtctctgaaattttgcaactaaaga 2639 IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
v.7: 2710 ctgggcttgacttctatcaggataaagtgcagcctgtctctgaaattttgcaactaaaga 2769 v.1: 2640 catatttaccaacatttgaaaccactatttaacttaataatgtctacttaatatataatt 2699 v.7: 2770 catatttaccaacatttgaaaccactatttaacttaataatgtctacttaatatataatt 2829 v.1: 2700 tactgtataaagtaattttggcaaaatataagtgattttttctggagaattgtaaaataa 2759 v.7: 2830 tactgtataaagtaattttggcaaaatataagtgattttttctggagaattgtaaaataa 2889 v.1: 2760 agttttctatttttccttaaaaaaaaaaccggaattccgggcttgggaggctgaggcagg 2819 v.7: 2890 agttttctatttttccttaaaaaaaaaaccggaattccgggcttgggaggctgaggcagg 2949 v.1: 2820 agactcgcttgaacccgggaggcagaggttgcagtgagccaagattgcgccattgcactc 2879 v.7: 2950 agactcgcttgaacccgggaggcagaggttgcagtgagccaagattgcgccattgcactc 3009 v.1: 2880 cagagcctgggtgacagagcaagactacatctcaaaaaataaataaataaaataaaagta 2939 v.7: 3010 cagagcctgggtgacagagcaagactacatctcaaaaaataaataaataaaataaaagta 3069 v.1: 2940 acaataaaaataaaaagaacagcagagagaatgagcaaggagaaatgtcacaaactattg 2999 V.7: 3070 acaataaaaataaaaagaacagcagagagaatgagcaaggagaaatgtcacaaactattg 3129 v.1: 3000 caaaatactgttacactgggttggctctccaagaagatactggaatctcttcagccattt 3059 V.7: 3130 caaaatactgttacactgggttggctctccaagaagatactggaatctcttcagccattt 3189 v.1: 3060 gcttttcagaagtagaaaccagcaaaccacctctaagcggagaacatacgattctttatt 3119 V.7: 3190 gcttttcagaagtagaaaccagcaaaccacctctaagcggagaacatacgattctttatt 3249 v.1: 3120 aagtagctctggggaaggaaagaataaaagttgatagctccctgattgggaaaaaatgca 3179 v.7: 3250 aagtagctctggggaaggaaagaataaaagttgatagctccctgattgggaaaaaatgca 3309 v.1: 3180 caattaataaagaatgaagatgaaagaaagcatgcttatgttgtaacacaaaaaaaattc 3239 v.7: 3310 caattaataaagaatgaagatgaaagaaagcatgcttatgttgtaacacaaaaaaaattc 3369 v.1: 3240 acaaacgttggtggaaggaaaacagtatagaaaacattactttaactaaaagctggaaaa 3299 v.7: 3370 acaaacgttggtggaaggaaaacagtatagaaaacattactttaactaaaagctggaaaa 3429 v.1: 3300 attttcagttgggatgcgactgacaaaaagaacgggatttccaggcataaagttggcgtg 3359 v.7: 3430 attttcagttgggatgcgactgacaaaaagaacgggatttccaggcataaagttggcgtg 3489 v.1: 3360 agctacagagggcaccatgtggctcagtggaagacccttcaagattcaaagttccatttg 3419 v.7: 3490 agctacagagggcaccatgtggctcagtggaagacccttcaagattcaaagttccatttg 3549 v.1: 3420 acagagcaaaggcacttcgcaaggagaagggtttaaattatgggtccaaaagccaagtgg 3479 v.7: 3550 acagagcaaaggcacttcgcaaggagaagggtttaaattatgggtccaaaagccaagtgg 3609 v.1: 3480 taaagcgagcaatttgcagcataactgcttctcctagacagggctgagtgggcaaaatac 3539 v.7: 3610 taaagcgagcaatttgcagcataactgcttctcctagacagggctgagtgggcaaaatac 3669 v.1: 3540 gacagtacacacagtgactattagccactgccagaaacaggctgaacagccctgggagac 3599 v.7: 3670 gacagtacacacagtgactattagccactgccagaaacaggctgaacagccctgggagac 3729 v.1: 3600 aagggaaggcaggtggtgggagttgttcatggagagaaaggagagttttagaaccagcac 3659 v.7: 3730 aagggaaggcaggtggtgggagttgttcatggagagaaaggagagttttagaaccagcac 3789 v.1: 3660 atccactggagatgctgggccaccagacccctcccagtcaataaagtctggtgcctcatt 3719 v.7: 3790 atccactggagatgctgggccaccagacccctcccagtcaataaagtctggtgcctcatt 3849 v.1: 3720 tgatctcagcctcatcatgaccctggagagaccctgataccatctgccagtccccgacag 3779 v.7: 3850 tgatctcagcctcatcatgaccctggagagaccctgataccatctgccagtccccgacag 3909 v.1: 3780 cttaggcactccttgccatcaacctgaccccccgagtggttctccaggctccctgcccca 3839 v.7: 3910 cttaggcactccttgccatcaacctgaccccccgagtggttctccaggctccctgcccca 3969 v.1: 3840 cccattcaggccggaattc 3858 v.7: 3970 cccattcaggccggaattc 3988 Table LVII. Peptide sequences of protein coded by 161P2F1OB v.7 (SBQ ID NO:
100) Table LVIII. Amino acid sequence alignment of 161P2F1OBv.1 v.1 ORX0)N0:100 and 161P2F1OB v.7 (53EWIDNCP.1W4 Score = 1789 bits (4634), Expect = 0.0Identities = 838/841 (99%), Positives =
841/841 (99%) 161P2F1OBv.1: 35 MSLGLGLGLGLRKLEKQGSCRKKCFDASFRGLENCRCDVACKDRGDCCWDFEDTCVESTR

MSLGLGLGLGLRKLEKQGSCRKKCFDASFRGLENCRCDVACKDRGDCCWDFEDTCVESTR
161P2F1OBv.7: 1 MSLGLGLGLGLRKLEKQGSCRKKCFDASFRGLENCRCDVACKDRGDCCWDFEDTCVESTR

161P2F1OBv.1: 95 IWMCNKFRCGETRLEASLCSCSDDCLQKKDCCADYKSVCQGETSWLEENCDTAQQSQCPE

IWMCNKFRCGETRLEASLCSCSDDCLQ+KDCCADYKSVCQGETSWLEENCDTAQQSQCPE
161P2F1OBv.7: 61 IWMCNKFRCGETRLEASLCSCSDDCLQRKDCCADYKSVCQGETSWLEENCDTAQQSQCPE

161P2F1OBv.1: 155 GFDLPPVILFSMDGFRAEYLYTWDTLMPNINKLKTCGIHSKYMRAMYPTKTFPNHYTIVT

GFDLPPVILFSMDGFRAEYLYTWDTLMPNINKLKTCGIHSKYMRAMYPTKTFPNHYTIVT
161P2F1OBv.7: 121 GFDLPPVILFSMDGFRAEYLYTWDTLMPNINKLKTCGIHSKYMRAMYPTKTFPNHYTIVT

161P2F1OBv.1: 215 GLYPESHGIIDNNMYDVNLNKNFSLSSKEQNNPAWWHGOPMWLTAMYQGLKAATYFWPGS

GLYPESHGIIDNNMYDVNLNKNFSLSSKEQNNPAWWHGQPMWLTAMYQGLKAATYFWPGS
161P2F1OBv.7: 181 GLYPESHGIIDNNMYDVNLNKNFSLSSKEQNNPAWWHGQPMWLTAMYQGLKAATYFWPGS

161P2F1OBv.1: 275 EVAINGSFPSIYMPYNGSVPFEERISTLLKWLDLPKAERPRFYTMYFEEPDSSGHAGGPV

EVAINGSFPSIYMPYNGSVPFEERISTLLKWLDLPKAERPRFYTM+FEEPDSSGHAGGPV
161P2F1OBv.7: 241 EVAINGSFPSIYMPYNGSVPFEERISTLLKWLDLPKAERPRFYTMFFEEPDSSGHAGGPV

161P2F1OBv.1: 335 SARVIKALQVVDHAFGMLMEGLKQRNLHNCVNIILLADHGMDQTYCNKMEYMTDYFPRIN

SARVIKALQVVDHAFGMLMEGLKQRNLHNCVNIILLADHGMDQTYCNKMEYMTDYFPRIN
161P2F1OBv.7: 301 SARVIKALQVVDHAFGMLMEGLKQRNLHNCVNIILLADHGMDQTYCNKMEYMTDYFPRIN

161P2F1OBv.1: 395 FFYMYEGPAPRIRAHNIPHDFFSFNSEEIVRNLSCRKPDQHFKPYLTPDLPKRLHYAKNV

FFYMYEGPAPR+RAHNIPHDFFSFNSEEIVRNLSCRKPDQHFKPYLTPDLPKRLHYAKNV
161P2F1OBv.7: 361 FFYMYEGPAPRVRAHNIPHDFFSFNSEEIVRNLSCRKPDQHFKPYLTPDLPKRLHYAKNV

161P2F1OBv.1: 455 RIDKVHLFVDQQWLAVRSKSNTNCGGGNHGYNNEFRSMEAIFLAHGPSFKEKTEVEPFEN

RIDKVHLFVDQQWLAVRSKSNTNCGGGNHGYNNEFRSMEAIFLAHGPSFKEKTEVEPFEN
161P2F1OBv.7: 421 RIDKVHLFVDQQWLAVRSKSNTNCGGGNHGYNNEFRSMEAIFLAHGPSFKEKTEVEPFEN

161P2F1OBv.1: 515 IEVYNLMCDLLRIQPAPNNGTHGSLNHLLKVPFYEPSHAEEVSKFSVCGFANPLPTESLD

IEVYNLMCDLLRIQPAPNNGTHGSLNHLLKVPFYEPSHAEEVSKFSVCGFANPLPTESLD
161P2F1OBv.7: 481 IEVYNLMCDLLRIQPAPNNGTHGSLNHLLKVPFYEPSHAEEVSKFSVCGFANPLPTESLD

161P2F1OBv.1: 575 CFCPHLQNSTQLEQVNQMLNLTQEEITATVKVNLPFGRPRVLQKNVDHCLLYHREYVSGF

CFCPHLQNSTQLEQVNQMLNLTQEEITATVKVNLPFGRPRVLQKNVDHCLLYHREYVSGF
161P2F1OBv.7: 541 CFCPHLQNSTQLEQVNQMLNLTQEEITATVKVNLPFGRPRVLQKNVDHCLLYHREYVSGF

161P2F1OBv.1: 635 GKAMRMPMWSSYTVPQLGDTSPLPPTVPDCLRADVRVPPSESQKCSFYLADKNITHGFLY

GKAMRMPMWSSYTVPQLGDTSPLPPTVPDCLRADVRVPPSESQKCSFYLADKNITHGFLY
161P2F1OBv.7: 601 GKAMRMPMWSSYTVPQLGDTSPLPPTVPDCLRADVRVPPSESQKCSFYLADKNITHGFLY

161P2F1OBv.1: 695 PPASNRTSDSQYDALITSNLVPMYEEFRKMWDYFHSVLLIKHATERNGVNVVSGPIFDYN

PPASNRTSDSQYDALITSNLVPMYEEFRKMWDYFHSVLLIKHATERNGVNVVSGPIFDYN
161P2F1OBv.7: 661 PPASNRTSDSQYDALITSNLVPMYEEFRKMWDYFHSVLLIKHATERNGVNVVSGPIFDYN

161P2F1OBv.1: 755 YDGHFDAPDEITKHLANTDVPIPTHYFVVLTSCKNKSHTPENCPGWLDVLPFIIPHRPTN

YDGHFDAPDEITKHLANTDVPIPTHYFVVLTSCKNKSHTPENCPGWLDVLPFIIPHRPTN

161P2F1013v.7: 721 161P2F1OBv.1: 815 VESCPEGKPEALWVEERFTAHIARVRDVELLTGLDFYQDKVQPVSEILQLKTYLPTFETT

VESCPEGKPEALWVEERFTAHIARVRDVELLTGLDFYQDKVQPVSEILQLKTYLPTFETT
161P2F1OBv.7: 781 VESCPEGKPEALWVEERFTAHIARVRDVELLTGLDFYQDKVQPVSEILQLKTYLPTFETT

161P2F1OBv.1: 875 I 875 161P2F1OBv.7: 841 I 841 Table LIX: 161P2F1OB Expression in Kidney Cancer RNA
analysis:
Clear PapillaryChromophob Transitiona Oncocytoma cell e 1 33/34 16/19 2/3 (67%) 3/7 (42%) 0/3 (0%) (97%) (84%) Protein analysis:
Clear PapillaryChromophob Transitiona Oncocytoma cell e 1 12/12 5/5 1/3 (33%) 0/3 (0%) 0/2 (0%) (100%) (100%) Table LX: 161P2F1OB protein expression in normal tissues TISSUE FREQUENCY
Kidney 5/5 Prostate 4/8 Bladder 1/4*
Colon 2/5*
Lung 1/4*
Brain 0/1 Breast 0/2 Heart 0/1 Liver 0/3 Ovary 0/1 Pancreas 0/2 Placenta 0/1 Skin 0/1 Spleen 0/1 Testis 0/4 Thymus 0/1 Uterus 0/1 DEMANDES OU BREVETS VOLUMINEUX
LA PRESENTE PARTIE DE CETTE DEMANDE OU CE BREVETS
COMPREND PLUS D'UN TOME.

NOTE. Pour les tomes additionels, veillez contacter le Bureau Canadien des Brevets.
JUMBO APPLICATIONS / PATENTS
THIS SECTION OF THE APPLICATION / PATENT CONTAINS MORE
THAN ONE VOLUME.

NOTE For additional volumes please contact the Canadian Patent Office.

Claims (44)

CLAIMS:

1. A polynucleotide that encodes the polypeptide sequence shown in SEQ ID
NO:9.

2. The polynucleotide of claim 1, comprising the nucleic acid sequence of SEQ ID
NO:8 from nucleotide residue numbers 44 through 2671.

3. A recombinant expression vector comprising the polynucleotide of claim 1 or 2.

4. A host cell that contains the expression vector of claim 3.

5. A process for producing a protein consisting of the amino acid sequence of SEQ ID
NO:9 comprising culturing the host cell of claim 4 under conditions sufficient for the production of the protein.

6. The process of claim 5, further comprising recovering the protein so produced.

7. The process of claim 6, wherein the protein is recovered using chromatography.

8. The protein produced by the process as described in claim 5, 6 or 7.

9. A composition comprising a pharmaceutically acceptable carrier and the protein of claim 8.

10. An isolated protein, wherein the protein comprises SEQ ID NO:9.

11. An antibody or antigen binding fragment thereof that immunospecifically binds to a protein comprising the amino acid sequence of SEQ ID NO:9.

12. The antibody or fragment thereof of claim 11, which is monoclonal.

13. The antibody or fragment thereof of claim 11 or 12, which is a Fab, F(ab')2, or Fv fragment.

14. The antibody or fragment thereof of claim 11, which is a human antibody.

15. The antibody or fragment thereof of any one of claims 11 to 14, wherein the antibody or fragment thereof is conjugated to a cytotoxic agent.

16. The antibody or fragment thereof of claim 15, wherein the cytotoxic agent is selected from the group consisting of radioactive isotopes, chemotherapeutic agents and toxins.

17. The antibody or fragment thereof of claim 16, wherein the radioactive isotope is selected from the group consisting of 211At, 131I, 125I, 90Y, 186Re, 188Re, 153Sm, 212Bi, 32P, and radioactive isotopes of Lu.

18. The antibody or fragment thereof of claim 16, wherein the chemotherapeutic agent is selected from the group consisting of taxol, actinomycin, mitomycin, etoposide, tenoposide, vincristine, vinblastine, colchicine, gelonin, and calicheamicin.

19. The antibody or fragment thereof of claim 16, wherein the toxin is selected from the group consisting of diphtheria toxin, enomycin, phenomycin, Pseudomonas exotoxin (PE) A, PE40, abrin, abrin A chain, mitogellin, modeccin A chain, and alpha-sarcin.

20. A composition comprising the antibody or fragment thereof of any one of claims 11 to 19, and a pharmaceutically acceptable carrier.

21. A hybridoma that produces the antibody of claim 12.

22. An in vitro method for detecting the presence of a protein consisting of the amino acid sequence of SEQ ID NO: 9 or a polynucleotide consisting of the nucleic acid sequence of SEQ ID NO:8 in a test sample comprising:
contacting the sample with an antibody or polynucleotide, respectively, that specifically binds to the protein or polynucleotide, respectively; and detecting binding of protein or polynucleotide, respectively, in the sample thereto.

23. The method of claim 22, wherein the polynucleotide is an mRNA.

24. The method of claim 22, wherein the polynucleotide is a cDNA produced from the sample by reverse transcription.

25. The method according to claim 22, 23 or 24, wherein the detecting step comprises comparing an amount of binding of the antibody or polynucleotide that specifically binds to the protein or polynucleotide to the presence of the protein or polynucleotide in a corresponding normal sample.

26. The method of claim 25, wherein the presence of elevated polynucleotide or protein in the test sample relative to the normal tissue sample provides an indication of the presence of prostate cancer, or a cancer of kidney, bone, pancreas, colon, or lung.

27. Use of the antibody or fragment thereof of any one of claims 15 to 19, for preparation of a medicament to inhibit growth of a cell expressing the protein consisting of the amino acid sequence of SEQ ID NO:9.

28. Use of the antibody or fragment thereof of any one of claims 15 to 19, to inhibit growth of a cell expressing the protein consisting of the amino acid sequence of SEQ ID NO:9.

29. Use of the antibody or fragment thereof of any one of claims 15 to 19, to deliver said cytotoxic agent to a cell expressing the protein consisting of the amino acid sequence of SEQ ID NO:9.

30. Use of the antibody or fragment thereof of any one of claims 15 to 19, for preparation of a medicament to deliver said cytotoxic agent to a cell expressing the protein consisting of the amino acid sequence of SEQ ID NO:9.

31. Use of a protein consisting of the amino acid sequence of SEQ ID NO:9 to elicit an immune response specific to said protein, wherein the protein is for contacting an immune system cell, whereby the immune system cell is induced.

32. Use of a medicament comprising a protein consisting of the amino acid sequence of SEQ ID NO:9 to elicit an immune response specific to said protein, wherein the medicament is for contacting an immune system cell, whereby the immune system cell is induced.

33. The use of claim 31 or 32, wherein the immune system cell is a B cell, whereby the induced B cell generates antibodies that specifically bind to the protein.

34. The use of claim 31 or 32, wherein the immune system cell is a T cell that is a cytotoxic T cell (CTL), whereby the activated CTL kills an autologous cell that expresses the protein.

35. The use of claim 31 or 32, wherein the immune system cell is a T cell that is a helper T cell (HTL), whereby the activated HTL secretes cytokines that facilitate the cytotoxic activity of a CTL or the antibody producing activity of a B cell.

36. Use of a protein consisting of the amino acid sequence of SEQ ID NO:9, for preparation of a medicament to induce an immune response specific to the protein in a subject.

37. Use of a protein consisting of the amino acid sequence of SEQ ID NO:9, to induce an immune response in a subject.

38. The use of claim 36 or 37, wherein the immune response comprises activation of a B
cell, wherein the activated B cells generate antibodies that specifically bind to the protein.

39. The use of claim 36 or 37, wherein the immune response comprises activation of a T
cell, wherein the activated T cell is a cytotoxic T cell (CTL), which, when activated kills an autologous cell that expresses the protein.

40. The use of claim 36 or 37, wherein the immune response comprises activation of a T
cell, wherein the activated T cell is a helper T cell (HTL), which, when activated secretes cytokines that facilitate cytotoxic activity of a CTL or antibody producing activity of a B cell.

41. Use of an antibody for preparation of a medicament which delivers an agent to a cell expressing a protein consisting of the amino acid sequence of SEQ ID NO:9, wherein the antibody is the antibody or a fragment thereof according to any one of claims 11 to 19.

42. Use of an antibody to deliver an agent to a cell expressing a protein consisting of the amino acid sequence of SEQ ID NO:9, wherein the antibody is the antibody or a fragment thereof according to any one of claims 11 to 19.

43. Use of an effective amount of the antibody or fragment thereof according to any one of claims 15 to 19, for preparation of a medicament which inhibits growth of a cell expressing a protein consisting of the amino acid sequence of SEQ ID NO:9.

44. Use of an effective amount of the antibody or fragment thereof according to any one of claims 15 to 19, to inhibit growth of a cell expressing a protein consisting of the amino acid sequence of SEQ ID NO:9.