US20090208537A1

US20090208537A1 - Anti-Neovasculature Preparations for Cancer

Info

Publication number: US20090208537A1
Application number: US11/772,811
Authority: US
Inventors: John J.L. SIMARD; David C. Diamond
Original assignee: Mannkind Corp
Current assignee: Mannkind Corp
Priority date: 2001-03-07
Filing date: 2007-07-02
Publication date: 2009-08-20
Also published as: US7252824B2; EP2295074A1; AU2002247304A1; WO2002069907A3; JP2005505242A; EP1372736A4; WO2002069907A8; CN1703247A; WO2002069907A2; HK1083771A1; US20050260234A1; JP2011098980A; CN100589845C; US20030046714A1; EP1372736A2

Abstract

Disclosed herein are immunogenic compositions, methods of designing immunogenic compositions, methods of treatment using immunogenic compositions, methods of evaluating cell-mediated immunity resulting from immunogenic compositions, research models, and methods of making research models, all of which relate to targeting tumor vasculature.

Description

CROSS REFERENCE

The present application is a divisional of and claims priority under 35 U.S.C. § 120 to U.S. Non-Provisional Patent Application Ser. No. 10/094,699, filed Mar. 7, 2002, which claims priority under 35 U.S.C. § 119(e) to U.S. Provisional Patent Application Ser. No. 60/274,063, filed on Mar. 7, 2001, entitled “ANTI-NEOVASCULATURE PREPARATIONS FOR CANCER,” both of which are hereby incorporated by reference in their entirety.

BACKGROUND OF THE INVENTION

Description of the Related Art

The treatment of cancer has remained challenging despite the advances in biomedicine. In recent years two approaches have been described showing much promise: therapeutic vaccines and anti-angiogenesis.
Therapeutic vaccines rely on the observation that cancerous tissues generally express certain antigens preferentially, collectively tumor-associated antigens (TuAA). TuAA include proteins normally expressed selectively by the tissue from which the cancer derives (differentiation antigens), proteins that are associated with a different stage of development (oncofetal and cancer-testis antigens), proteins that are created by aberrant chromosomal rearrangement, or proteins that are derived from oncogenic viruses. These TuAA, or fragments of them, are then used as immunogens in vaccines intended to stimulate cellular immunity, particularly cytotoxic T lymphocytes (CTL), capable of killing the tumor cells.
The anti-angiogenesis approach takes advantage of the need of tumors to recruit a blood supply to support their continued growth. To accomplish this, tumors secrete angiogenic factors that promote the growth of new blood vessels. The anti-angiogenesis approach aims to disrupt a tumor's supply of nutrients to cause it to die, or at least limit its growth. Attempts at this approach have sought chemotherapeutic drugs used directly against a variety of anti-angiogenic factors and angiogenesis.

SUMMARY OF THE INVENTION

The invention disclosed herein is directed to compositions designed to stimulate cellular immune responses targeting tumor-associated neovasculature (TuNV). In one embodiment of the invention the compositions stimulate a CTL response. Such compositions may include one or more epitopes of the target antigen. One aspect of this embodiment specifically includes a housekeeping epitope, another specifically includes an immune epitope or epitope cluster, and another aspect specifically combines housekeeping and immune epitopes.
Embodiments of the invention relate to the use of prostate specific membrane antigen (PSMA) as the target antigen of the composition. Aspects of this embodiment include various epitopes derived from PSMA provided directly as polypeptide, or as a nucleic acid capable of conferring expression of the epitope. Other embodiments relate to the use of other TuNV-associated antigens.
In other embodiments of the invention, compositions are directed against both the TuNV and against TuAA expressed by the cancerous cells, by combining immunogens derived from both sources into a single formulation or method or treatment.
Preclinical evaluation of the compositions of this invention can be accomplished using adoptive transfer of immunized T cells into SCID mice bearing microvasculature formed from implanted human dermal microvascular endothelial cells (HDMEC). Preclinical evaluation can also be accomplished through the use of HLA-transgenic mice immunized with compositions comprised of epitopes conserved between mice and humans.
Embodiments of the invention relate to methods of evaluating cell-mediated immunity. The methods can include the steps of implanting vascular cells into an immunodeficient mammal; establishing an immune response in the mammal; and assaying a characteristic to determine cell-mediated immunity in the mammal. The cell-mediated immunity can be directed against a neovasculature antigen, for example. The neovasculature antigen can be preferentially expressed by tumor-associated neovasculature, for example, and in preferred embodiments can be prostate specific membrane antigen (PSMA), vascular endothelial growth factor receptor 2 (VEGFR2), and the like. The establishing step can be achieved, for example, by adoptive transfer of T-cells to the mammal, by contacting the mammal with an antigen, and the like. The cell-mediated immunity can be mediated by cytotoxic T lymphocytes. The vascular cells can be vascular endothelial cells, such as, for example, human dermal microvascular endothelial cells (HDMEC), telomerase-transformed endothelial cells, and the like. The immunodeficient mammal can be a mouse, such as for example a SCID mouse. The characterizing step can include assessing a parameter, such as for example, vessel formation, vessel destruction, vessel density, proportion of vessels carrying blood of the host mammal, and the like.
The methods can further include the step of implanting tumor cells or tumor tissue in the mouse. The characterizing step can include assessing a parameter, such as, for example, tumor presence, tumor growth, tumor size, rapidity of tumor appearance, dose of vaccine required to inhibit or prevent tumor establishment, tumor vascularization, a proportion of necrotic tissue within the tumor, and the like.
The methods can further include the steps of providing a first population of mammals and a second populations of mammals; establishing cell-mediated immunity in the first population; differentially establishing cell-mediated immunity in the second population; and comparing a result obtained from the first population of mammals to a result obtained from the second population of mammals. The cell-mediated immunity of the first population can include, for example, naive immunity, immunity to an irrelevant epitope, and the like.
Other embodiments relate to methods of evaluating cell-mediated immunity, including immunity directed against a neovasculature antigen. The methods can include the steps of implanting or injecting MHC-transgenic tumor cells into an MHC-transgenic mammal; establishing an immune response in the mammal; and assaying a characteristic to determine cell-mediated immunity in the mammal. The MHC-transgenic mammal can be an HLA-transgenic mammal, such as, for example an HLA-A2 transgenic mammal. In preferred embodiments the mammal can be a mouse. The cell-mediated immunity can be established by vaccination, which in preferred embodiments can take place prior to, concurrent with, or subsequent to transfer of the tumor cells, for example. In preferred embodiments the cell-mediated immunity can be mediated by cytotoxic T lymphocytes. The neovasculature antigen can be preferentially expressed by tumor-associated neovasculature and can also be a tumor-associated antigen. Preferably, the antigen can be the ED-B domain of fibronectin. The characterizing step can include, for example, assessing a parameter, including tumor presence, tumor growth, tumor size, rapidity of tumor appearance, dose of vaccine required to inhibit or prevent tumor establishment, tumor vascularization, a proportion of necrotic tissue within the tumor, and the like. The methods can further include the steps of providing a first population of mammals and a second populations of mammals; establishing cell-mediated immunity in the first population; differentially establishing cell-mediated immunity in the second population; and comparing a result obtained from the first population of mammals to a result obtained from the second population of mammals. The cell-mediated immunity of the first population can include naive immunity, immunity to an irrelevant epitope, and the like.
Still further embodiments relate to methods of treating neoplastic disease, including the step of immunizing a mammal to induce a cellular immune response directed against an antigen differentially expressed by tumor-associated neovasculature. The differentially expressed antigen can be a protein, such as, for example prostate specific membrane antigen, vascular endothelial growth factor receptor 2 (VEGFR2), and the like. In other preferred embodiments, the antigen can be the ED-B domain of fibronectin. The immunization can be carried out, for example, with at least one peptide derived from the sequence of the protein, with a nucleic acid capable of conferring expression of the protein or peptides, and the like. The at least one peptide can include a housekeeping epitope, for example, and in preferred embodiments can be co-C-terminal with the housekeeping epitope. The methods can further include at least one additional peptide, wherein the at least one additional peptide includes an immune epitope. The methods can include an additional step wherein the mammal is treated with an anti-tumor therapy active directly against cancerous cells. The anti-tumor therapy can be immunization against a tumor-associated antigen. Preferably, the cellular immune response can include a CTL response.
Other embodiments relate to immunogenic compositions. The immunogenic compositions can include at least one immunogen corresponding to an antigen expressed by tumor-associated neovasculature, wherein the composition can induce a cellular immune response. The immunogen can be one that is not associated with a cell conspecific with the recipient. The antigen can be a protein, such as, for example prostate specific membrane antigen, vascular endothelial growth factor receptor 2 (VEGFR2), and the like. In other preferred embodiments the antigen can be the ED-B domain of fibronectin. The immunogen can include at least one peptide. The compositions can include a nucleic acid capable of conferring expression of the antigen, and wherein the antigen is a protein or a peptide. The compositions can include at least one peptide that includes a housekeeping epitope, and in preferred embodiments the at least one peptide can be co-C-terminal with the housekeeping epitope. Also, the compositions can additionally include at least one peptide that includes an immune epitope. The compositions can include at least one immunogen corresponding to a tumor-associated antigen. In preferred embodiments the cellular immune response can include a CTL response.
Embodiments relate to methods of anti-tumor vaccine design. The methods can include the steps of identifying an antigen differentially expressed by tumor-associated neovasculature; and incorporating a component of the antigen into a vaccine. The component can include, for example, a polypeptide fragment of the antigen, a nucleic acid encoding the antigen or a fragment of the antigen, and the like.
Further embodiments relate to methods of making a research model. The methods can include implanting a vascular cell and a tumor cell into an immunodeficient mammal. The tumor cell and the vascular cell can be implanted adjacent to one another. The vascular cell can be a vascular endothelial cell, such as for example HDMEC. In preferred embodiments the vascular endothelial cell can be telomerase-transformed. The immunodeficient mammal can be a mouse, such as, for example, a SCID mouse.
Other embodiments relate to research models. The research models can include an immunodeficient mammal. The mammal can include an implanted vascular cell and an implanted tumor cell. The vascular cell and the tumor cell can be implanted adjacent to one another.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A, B, and C show results of N-terminal pool sequencing of a T=60 min. time point aliquot of the PSMA_163-192proteasomal digest.

FIG. 2 shows binding curves for HLA-A2:PSMA_168-177and HLA-A2:PSMA_288-297with controls.

FIG. 3 shows results of N-terminal pool sequencing of a T=60 min. time point aliquot of the PSMA_281-310proteasomal digest.

FIG. 4 shows binding curves for HLA-A2:PSMA_461-469, HLA-A2:PSMA_460-469,and HLA-A2:PSMA_663-671, with controls.

FIG. 5 shows the results of a γ (gamma)-IFN-based ELISPOT assay detecting PSMA_463-471-reactive HLA-A1⁺ CD8⁺ T cells.

FIG. 6 shows blocking of reactivity of the T cells used in FIG. 10 by anti-HLA-A1 mAb, demonstrating HLA-A1-restricted recognition.

FIG. 7 shows a binding curve for HLA-A2:PSMA_663-671, with controls.

FIG. 8 shows a binding curve for HLA-A2:PSMA_662-671, with controls.

FIG. 9 shows epitope specific lysis by CTL from HHD-A2 mice immunized with ED-B 29-38 peptide.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT

Embodiments of the invention disclosed herein provide compositions, methods of composition or vaccine design, and methods of treatment related to the generation of a cellular immune response, preferably, a T cell response and, more preferably, a CTL response, directed against the neovasculature of tumors. Such methods and compositions are particularly useful in the treatment and prevention of cancer. Other embodiments relate to composition evaluation models.

Compositions, Composition Design, and Treatment Using the Compositions

Embodiments of the invention relate to immunogenic compositions, including vaccines, for the generation of a cellular immune response, particularly a T cell response and specifically a CTL response, directed against tumor neovasculature (TuNV). “Tumor neovasculature” is broadly meant to include any vasculature found in or around tumor masses, vasculature which supports or is necessary for tumor growth, and the like. It should be noted, and one of skill in the art will appreciate, that although the discussion herein refers generally to the tumors and tumor neovasculature, the embodiments of the present invention also can be applied to other conditions or disease states associated with inappropriate angiogenesis.
Until now the design of anti-tumor vaccines has concentrated on antigens expressed by the malignant cells themselves. However, larger tumors are complex structures and not simply a homogeneous mass of cells. All cells, particularly rapidly growing cells, need a supply of nutrients (oxygen, glucose, amino acids, etc.), as well as a means of removal of metabolic wastes, in order to remain metabolically active and intact. This is normally accomplished by the flow of blood and lymph through the various organs of the body. At a cellular level, the tissues of the body are permeated by a fine network of capillaries—tiny vessels through which nutrients and waste products can be exchanged with the surrounding cells by diffusion. Diffusion is effective over relatively short distances. The capillary beds are so extensive that generally cells are at most located only a few cells away from a capillary. If a tumor merely grew by propagation of its malignant cells, soon those cells in the interior of the mass would be unable to sustain themselves. In fact, the interiors of unvascularized tumors often contain necrotic tissue. Thus, in order to grow unchecked, tumors secrete factors that promote the in-growth of new blood vessels, namely TuNV. Since the TuNV expresses antigens differentiating it from other tissues, cancer can be treated with therapeutic compositions directed against the TuNV, instead of directly targeting the cancerous cells themselves. Suitable TuNV antigens can include those that are expressed generally in neovasculature or preferentially by TuNV, for example.
In some embodiments of the invention the compositions can include, for example, an epitopic peptide or peptides. Immune epitopes may be provided embedded in epitope clusters and protein fragments. Housekeeping epitopes can be provided with the proper C-terminus. In other embodiments of the invention the compositions can include nucleic acids capable of conferring expression of these epitopes on pAPC, for example.
In preferred embodiments, the compositions can be administered directly to the lymphatic system of a mammal being treated. This can be applied to both polypeptide and nucleic acid based compositions. Administration methods of this type, and related technologies, are disclosed in U.S. patent application Ser. No. 09/380,534, filed on Sep. 1, 1999, and a Continuation-in-Part thereof, filed on Feb. 2, 2001; U.S. patent application Ser. No. 09/776,232, both entitled “A METHOD OF INDUCING A CTL RESPONSE,” which are incorporated by reference in their entirety.
In a preferred embodiment, destruction of the blood vessels in a tumor by action of a composition of the invention can eliminate all of the cells in a tumor. However, small tumors, including micrometastases, are typically unvasculaturized. Additionally, unvascularized tumors that instead apparently rely on blood flow through channels penetrating the tumor mass have been reported (Maniotis, A. J., et al. Am. J. Pathol. 155: 739-752, 1999). Thus in other embodiments, the compositions are generally effective as tumor control agents that may not eradicate all cancer cells. Accordingly, the invention provides tools for eliminating tumors, controlling tumor growth, reducing tumor burden, improving overall clinical status, and the like. In some embodiments, it can be desirable to combine these compositions with other treatments that target the cancerous cells directly. Additionally there is evidence that the vasculature in tumors can be mosaic in nature consisting of both endothelial and cancer cells (Chang, Y. S., et al. Proc. Natl. Acad. Sci. USA 97:14608-14613, 2000). Thus, in some embodiments of the invention a course of composition treatment can be followed by administration of a bio- or chemotherapeutic agent. In a particularly preferred embodiment, treatment can include administration of a TuAA directed composition concurrent or subsequent to administration of the anti-TuNV composition.
As mentioned above, suitable TuNV antigens for the compositions can include those that are expressed generally in neovasculature or preferentially by TuNV, for example. A variety of techniques for discovery of TuAA are known in the art. Examples of these techniques include, without limitation, differential hybridization and subtractive hybridization, including use of microarrays; expression cloning; SAGE (serial analysis of gene expression); SEREX (serological identification of antigens by recombinant expression cloning); in situ RT-PCT; immunohistochemistry (as was the case for PSMA); EST analysis; variously using bulk, sectioned, and/or microdissected tissue; and the like. Utilization of these and other methods provides one of skill in the art the techniques necessary to identify genes and gene products contained within a target cell that may be used as antigens of immunogenic compositions. The techniques are applicable to TuAA discovery regardless of whether the target cell is a cancer cell or an endothelial cell. Any identified antigen can be scrutinized for epitopes, which can be used in embodiments of the invention.
The endothelial cells making up the lining of the vasculature can express housekeeping proteasomes. Thus, compositions targeting endothelial cells can be comprised of peptides, or nucleic acids conferring expression of the peptides, corresponding to the digestion products of the housekeeping proteasome (i.e. housekeeping epitopes). IFN-γ (gamma), secreted by activated cells of the immune system, can induce expression of the immunoproteasome in the target cells. Generally, the immunoproteasome is constitutive in professional antigen presenting cells (pAPC). Thus, it can be helpful to include immune epitopes or epitope clusters in CTL-inducing compositions to ensure that there are CTL able to recognize the target cell regardless of the state that the target cell is in. This can be particularly true with endothelial cells, which readily assume antigen presentation functions. These concepts are more fully explained in U.S. patent application Ser. No. 09/560,465, filed on Apr. 28, 2000; U.S. patent application Ser. No. 10/005,905, filed on Nov. 7, 2001; and a continuation thereof, U.S. application Ser. No. 10/026,066 filed on Dec. 7, 2001, attorney docket number CTLIMM.21CP1C, each of which is entitled “EPITOPE SYNCHRONIZATION IN ANTIGEN PRESENTING CELLS,” and each of which is hereby incorporated by reference in its entirety.
As discussed above, the immunogenic compositions, including in preferred embodiments, vaccines, can include TuNV antigens and epitopes, for example. The epitopes can include one or more housekeeping epitopes and/or one or more immune epitopes. Specific epitopes useful in compositions can be identified using the methods disclosed in U.S. patent application Ser. No. 09/561,074 entitled “METHOD OF EPITOPE DISCOVERY,” filed on Apr. 28, 2000. For example, peptide sequences that are known or predicted to bind to some MHC restriction element can be compared to fragments produced by proteasomal digestion in order to identify those that are co-C-terminal.
Examples of useful epitopes for the embodiments of the invention, including epitopes of ED-B and PSMA, are disclosed in a U.S. Provisional Patent Application No. 60/363,210, entitled “EPITOPE SEQUENCES,” attorney docket number CTLIMM.027PR; filed on Mar. 7, 2002, and two U.S. Provisional Patent Applications, each entitled “EPITOPE SEQUENCES;” Application Ser. No. 60/282,211, filed on Apr. 6, 2001 and 60/337,017, filed on Nov. 7, 2001. Each of these applications is incorporated herein by reference in its entirety.
PSMA is one example of a TuAA that can be targeted in some embodiments. PSMA is expressed in the neovasculature of most tumor types, but not by the vascular endothelium of normal tissues (Chang, S. M. et al., Cancer Res. 59(13):3192-8,1999; Clin Cancer Res. 10:2674-81, 1999). PSMA is a membrane antigen, and as such, it may be possible to attack PSMA-expressing TuNV with monoclonal antibody (mAb). However, the effectiveness of mAb in the treatment of cancer has proved to be more difficult than initially anticipated. Moreover, as other antigens are discovered to be associated with the TuNV, it is likely that many of them will prove not to be expressed at the vasculature surface, making them inaccessible to mAb attack.
T cells, particularly CTL, on the other hand, survey the expression of internal components of the cell through the process of major histocompatability complex (MHC)-restricted antigen presentation. The parameters for determining the effectiveness of T cell-activating vaccines and compositions against self-antigens are subtle. Some of the critical features and parameters relating to appropriate epitope selection are disclosed in U.S. patent application Ser. No. 09/560,465 entitled “EPITOPE SYNCHRONIZATION IN ANTIGEN PRESENTING CELLS,” filed on Apr. 28, 2001; U.S. patent application Ser. No. 09/561,074 entitled “METHOD OF EPITOPE DISCOVERY,” filed on Apr. 28, 2001; and U.S. patent application Ser. No. 09/561,571 entitled “EPITOPE CLUSTERS,” filed on Apr. 28, 2001. Features of DNA vaccine design promoting epitope synchronization are disclosed in U.S. patent application Ser. No. 09/561,572 entitled “EXPRESSION VECTORS ENCODING EPITOPES OF TARGET-ASSOCIATED ANTIGENS,” filed on Apr. 28, 2001 and U.S. Provisional Application No. 60/336,968 entitled “EXPRESSION VECTORS ENCODING EPITOPES OF TARGET-ASSOCIATED ANTIGENS AND METHODS FOR THEIR DESIGN,” filed on Nov. 7, 2001. Particularly effective means of vaccine delivery are described in U.S. patent application Ser. No. 09/380,534, filed on Sep. 1, 1999, and a Continuation-in-Part thereof, U.S. patent application Ser. No. 09/776,232, filed on Feb. 2, 2001, both entitled “A METHOD OF INDUCING A CTL RESPONSE.” Each of the above-mentioned references is incorporated herein by reference in its entirety.
Another example of a TuNV antigen that can be used in embodiments is fibronectin, preferably the ED-B domain. Fibronectin is subject to developmentally regulated alternative splicing, with the ED-B domain being encoded by a single exon that is used primarily in oncofetal tissues. Matsuura, H. and S. Hakomori Proc. Natl. Acad. Sci. USA 82:6517-6521, 1985; Carnemolla, B. et al. J. Cell Biol. 108:1139-1148, 1989; Loridon-Rosa, B. et al. Cancer Res.50:1608-1612, 1990; Nicolo, G. et al. Cell Differ. Dev. 32:401-408, 1990; Borsi, L. et al. Exp. Cell Res. 199:98-105, 1992; Oyama, F. et al. Cancer Res. 53:2005-2011, 1993; Mandel, U. et al. APMIS 102:695-702, 1994; Farnoud, M. R. et al. Int. J. Cancer 61:27-34, 1995; Pujuguet, P. et al. Am. J. Pathol. 148:579-592, 1996; Gabler, U. et al. Heart 75:358-362, 1996; Chevalier, X. Br. J. Rheumatol. 35:407-415, 1996; Midulla, M. Cancer Res. 60:164-169, 2000.
The ED-B domain is also expressed in fibronectin of the neovasculature Kaczmarek, J. et al. Int. J. Cancer 59:11-16, 1994; Castellani, P. et al. Int. J. Cancer 59:612-618, 1994; Neri, D. et al. Nat. Biotech. 15:1271-1275, 1997; Karelina, T. V. and A. Z. Eisen Cancer Detect. Prev. 22:438-444, 1998; Tarli, L. et al. Blood 94:192-198, 1999; Castellani, P. et al. Acta Neurochir. (Wien) 142:277-282, 2000. As an oncofetal domain, the ED-B domain is commonly found in the fibronectin expressed by neoplastic cells, in addition to being expressed by the TuNV. Therefore, CTL-inducing compositions targeting the ED-B domain can exhibit two mechanisms of action: direct lysis of tumor cells, and disruption of tumor blood supply through destruction of the TuNV.
It should be noted that expression of the fibronectin ED-B domain has been reported in both tumor-associated and normal neovasculature (Castellani, P. et al. Int. J. Cancer 59:612-618, 1994). Thus, compositions based on it, or similarly expressed antigens, can be effective against other conditions associated with inappropriate angiogenesis. Further, as CTL activity can decay rapidly after withdrawal of the composition, interference with normal angiogenesis can be minimal.
Other targets for the immunogenic compositions include growth factor receptors, including those associated with vascular cells. One such example is the vascular endothelial growth factor receptor 2 (VEGFR2). U.S. Pat. No. 6,342,221 includes discussion of VEGF and VEGFR2, and is hereby incorporated by reference in its entirety. One of skill in the art will appreciate that any other antigen or protein associated with vascular cells can be a target for the immunogenic compositions, including those that are presently known and those yet to be identified.

Animal Models, Methods of Making the Models, and Composition Evaluation

Compositions designed based upon the preceding considerations are effective against the various targets. However, additional evaluation can be easily performed at any time, but preferably in a pre-clinical setting. For example, such evaluation can be used in order to further aid in composition design. Other embodiments of the invention relate to methods of evaluating the immunogenic compositions. The compositions of the present invention can be easily evaluated by one of skill in the art using animal models for composition evaluation. For example, following the routine procedures below, one of skill in the art can evaluate TuNV compositions quickly and efficiently. Thus, using the models or guidance described herein, one of skill in the art can evaluate any TuNV composition for any TuNV antigen with little or no experimentation. Further embodiments relate to methods of making the animal research models. Other embodiments relate to the research model animals. These embodiments are set forth more fully below.

Xenotransplanted Human Vasculature-Based Model

Some embodiments relate to a model system for studying the mechanisms of human microvessel formation. For example, in some embodiments, the model system can be used for preclinical evaluation of compositions. The model involves the subcutaneous implantation of telomerase-transformed human dermal microvascular endothelial cells (HDMEC) mixed with MATRIGEL (Becton Dickinson) into SCID mice. Subcutaneous implantation of telomerase-transformed HCMEC is described in Yang, J. et al. Nature Biotech 19:219-224, 2001, which is hereby incorporated by reference in its entirety. T cells activated by the compositions of this invention can be adoptively transferred, for example, into such implanted mice, and the ability of the T cells to destroy, or prevent the formation of, such human microvessels can be assessed. In other embodiments, the mouse can be directly vaccinated and evaluated. Also, in still further embodiments, the model system can be further adapted for testing compositions effective in non-human species by substituting DMEC from other species and species-matched telomerase, and by using analogous reagents to those described below for the human system.
The MHC-restriction elements presenting the epitopes of the composition being tested, preferably, are shared by the HDMEC line implanted into the mice. The T cells can be derived from in vitro immunization of human T cells, or by immunization of HLA-transgenic mice (procedures for which are well known in the art and examples of which are provided in the above incorporated patent applications). Use of T cells generated in HLA-transgeneic mice allows matching of genetic backgrounds between the adoptively transferred T cells and the host, thereby reducing the possibility of allogeneic or xenogeneic reactions that might complicate interpretation of the results. However, depending on the mouse strains available, this might require cross-breeding to get the HLA-transgene and SCID phenotype on the same genetic background. In the alternative, the donor T cells (human or murine) can be subjected to one or more rounds of in vitro stimulation to enrich for the desired population or establish a clone, and thereby similarly avoid undesired reactivities.
Techniques for in vitro immunization are know in the art, for example, Stauss et al., Proc. Natl. Acad. Sci. USA 89:7871-7875, 1992; Salgaller et al. Cancer Res. 55:4972-4979, 1995; Tsai et al., J. Immunol. 158:1796-1802, 1997; and Chung et al., J. Immunother. 22:279-287, 1999. Once generated, whether in vivo or in vitro, sufficient numbers of such T cells can be obtained by expansion in vitro through stimulation with the compositions of this invention and/or cytokines (see for example Kurokawa, T. et al., Int. J. Cancer 91:749-746, 2001) or other mitogens. These T cells can constitute a clone or a polyclonal population recognizing one or more epitopes. In preferred embodiments, on the order of 10⁵to 10⁸cells are transferred for adoptive transfer experiments in mice. (See for example Drobyski, W. R. et al. Blood 97:2506-2513, 2001; Seeley B. M. et al. Otolaryngol. Head Neck Surg. 124:436-441, 2001; Kanwar, J. R. et al. Cancer Res. 61:1948-1956, 2001). Clones and otherwise more enriched populations generally require the transfer of fewer cells.
Transfer of the T cells can take place shortly before, concurrent with, or subsequent to implantation or establishment of the HDMEC. Parameters that can be assessed to evaluate effectiveness of the compositions include vessel formation, changes in vessel density, and ability to carry mouse blood (as described in Yang et al.), and the like. Assessment can be carried out as early as one week, and at least as long as 6 weeks, after implantation of telomerase-transformed HDMEC, preferably after 2 weeks; and from a day to more than 6 weeks after T cell transfer, preferably after 1 to 3 weeks. Generally, assessment can include comparison of mice receiving T cells reactive with the target antigen with mice receiving naive (including sham-immunized), or irrelevant epitope-reactive T cells.
Relevant antigens can be expressed generally in neovasculature or preferentially by TuNV. Expression can be confirmed by a variety of techniques known in the art, including immunohistochemistry and RT-PCR. For example, tumor cells can be implanted along with the HDMEC. This can result in inducing expression of antigens preferentially expressed by TuNV. In one example, this can be accomplished by implanting a block of tumor tissue adjacent to the HDMEC-containing MATRIGEL implant, injecting tumor cells at the site of the implant, implanting tumor cell-containing MATRIGEL adjacent to the HDMEC-containing MATRIGEL implant, incorporating both tumor cells and HDMEC into the same MATRIGEL implant or by any other suitable method. As discussed above, in some embodiments, tumor cells can be implanted along with vascular cells. The animals so made, can be used as research models. Additional variations will be apparent to one of skill in the art.

HLA-Transgenic Animal Model

For antigens that are conserved, in sequence and/or expression profile, between human and the model species, HLA-transgenic strains allow another approach, namely vaccination of the model animal to combat a syngeneic tumor. The ED-B domain of fibronectin provides such an opportunity, as it is a marker of angiogenesis and has identical amino acid sequence in both humans and mice (Nilsson, F. et al. Cancer Res. 61:711-716, 2001). Moreover, spontaneous tumor tissue from a strain of HLA-A2 transgenic mice has been isolated and propagated. Epitope discovery and selection, and composition design and delivery for CTL inducing compositions are discussed above.
The tumor cell line, M1, is derived from a spontaneous salivary glandular cystadenocarcinoma. The M1 tumor cell line and methods of using the same is disclosed in U.S. Provisional Application No. 60/363,131, filed on Mar. 7, 2001, entitled “AN HLA-TRANSGENIC MURINE TUMOR CELL LINE,” which is hereby incorporated by reference in its entirety. The tumor cell line, can arise in individuals of the HHD-A2 transgenic mouse strain of S. Pascolo et al. (J. Exp. Med. 185:2043-2051, 1997). These mice express a single monochain class I molecule comprising human β (beta)2-microglobulin, and α1 (alpha-1), and α2 (alpha-2) domains of HLA-A2.1 with the balance of the molecule derived from the murine class I molecule H2D^b. Blocks of tumor can be transplanted into new individuals where the tumor will re-grow, commonly within 1-3 weeks, with 3 mm blocks growing to 3 cm. Alternatively, tumor tissue can be disaggregated and the tumor cells grown in vitro. Upon harvest, the tumor cells can be injected subcutaneously into the neck or abdomen (2.5×10⁶cells for 1-3 successive days), to result in a visible tumor in approximately 5-12 weeks for early passage cells. After the cells have become better adapted to growth in vitro, single injections of 1×10⁶to 1×10⁷cells lead to visible tumor in ten days. Generally, the initial tumor consistently occurs in the vicinity of the salivary glands, but secondary tumors can also occur in a variety of locations, including kidney, lung, liver, and abdominal muscle.
To evaluate the efficacy of a composition, it can be administered before, concurrent with, or subsequent to establishment of the tumor, depending on the expected mechanism of the composition. For therapeutic compositions intended to be used with some sort of debulking technique (e.g. surgery), concurrent administration can be appropriate. The better established the tumor is before treatment begins, the more stringent the test.
Both animal evaluation models have been described for the testing of human compositions. However, application to veterinary compositions is analogous, requiring only the substitution of species-matched endothelial cells, MHC, TuAA, etc.
All patents, patent applications, and publications referred to herein are hereby incorporated by reference in their entirety.
The following examples are intended for illustration purposes only, and should not be construed as limiting the scope of the invention in any way.

EXAMPLES

Example 1

A preclinical study was carried out using the already identified antigens PSMA and ED-B disclosed herein. The results of the study revealed excellent candidate epitopes. See table 9 below.

Example 1.1

Cluster Analysis (PSMA_163-192)

A peptide, AFSPQGMPEGDLVYVNYARTEDFFKLERDM, PSMA_163-192,(SEQ ID NO. 3), containing an A1 epitope cluster from prostate specific membrane antigen, PSMA_168-190(SEQ ID NO. 4) was synthesized using standard solid-phase F-moc chemistry on a 433A ABI Peptide synthesizer. After side chain deprotection and cleavage from the resin, peptide first dissolved in formic acid and then diluted into 30% Acetic acid, was run on a reverse-phase preparative HPLC C4 column at following conditions: linear AB gradient ( 5% B/min) at a flow rate of 4 ml/min, where eluent A is 0.1% aqueous TFA and eluent B is 0.1% TFA in acetonitrile. A fraction at time 16.642 min containing the expected peptide, as judged by mass spectrometry, was pooled and lyophilized. The peptide was then subjected to proteasome digestion and mass spectrum analysis essentially as described above. Prominent peaks from the mass spectra are summarized in Table 1.

TABLE 1

PSMA_163-192Mass Peak Identification.

			CALCU-
SEQ			LATED
ID			MASS
NO.	PEPTIDE	SEQUENCE	(MH⁺)

110	163-177	AFSPQGMPEGDLVYV	1610.0

111	178-189	NYARTEDFFKLE	1533.68

112	170-189	PEGDLVYVNYARTEDFFKLE	2406.66

113	178-191	NYARTEDFFKLERD	1804.95

114	170-191	PEGDLVYVNYARTEDFFKLERD	2677.93

115	178-192	NYARTEDFFKLERDM	1936.17

116	163-176	AFSPQGMPEGDLVY	1511.70

117	177-192	VNYARTEDFFKLERDM	2035.30

118	163-179	AFSPQGMPEGDLYYVNY	1888.12

119	180-192	ARTEDFFKLERDM	1658.89

120	163-183	AFSPQGMPEGDLVYVNYARTE	2345.61

121	184-192	DFFKLERDM	1201.40

122	176-192	YVNYARTEDFFKLERDM	2198.48

123	167-185	QGMPEGDLVYVNYARTEDF	2205.41

124	178-186	NYARTEDFF	1163.22

Boldface sequences correspond to peptides predicted to bind to MHC, see Table 2.

N-Terminal Pool Sequence Analysis

One aliquot at one hour of the proteasomal digestion was subjected to N-terminal amino acid sequence analysis by an ABI 473A Protein Sequencer (Applied Biosystems, Foster City, Calif.). Determination of the sites and efficiencies of cleavage was based on consideration of the sequence cycle, the repetitive yield of the protein sequencer, and the relative yields of amino acids unique in the analyzed sequence. That is if the unique (in the analyzed sequence) residue X appears only in the nth cycle a cleavage site exists n-i residues before it in the N-terminal direction. In addition to helping resolve any ambiguity in the assignment of mass to sequences, these data also provide a more reliable indication of the relative yield of the various fragments than does mass spectrometry.
For PSMA_163-192(SEQ ID NO. 3) this pool sequencing supports a single major cleavage site after V₁₇₇and several minor cleavage sites, particularly one after Y₁₇₉. Reviewing the results presented in FIGS. 1A-C reveals the following:

- S at the 3^rdcycle indicating presence of the N-terminus of the substrate.
- Q at the 5^thcycle indicating presence of the N-terminus of the substrate.
- N at the 1^stcycle indicating cleavage after V₁₇₇.
- N at the 3^rdcycle indicating cleavage after V₁₇₅. Note the fragment 176-192 in Table 1.
- T at the 5^thcycle indicating cleavage after V₁₇₇.
- T at the 1^st-3^rdcycles, indicating increasingly common cleavages after R₁₈₁, A₁₈₀and Y₁₇₉. Only the last of these correspond to peaks detected by mass spectrometry; 163-179 and 180-192, see Table 1. The absence of the others can indicate that they are on fragments smaller than were examined in the mass spectrum.
- K at the 4^th, 8^th, and 10^thcycles indicating cleavages after E₁₈₃, Y₁₇₉, and V₁₇₇, respectively, all of which correspond to fragments observed by mass spectroscopy. See Table 1.
- A at the 1^stand 3^rdcycles indicating presence of the N-terminus of the substrate and cleavage after V₁₇₇, respectively.
- P at the 4^thand 8^thcycles indicating presence of the N-terminus of the substrate.
- G at the 6^thand 10^thcycles indicating presence of the N-terminus of the substrate.
- M at the 7^thcycle indicating presence of the N-terminus of the substrate and/or cleavage after F₁₈₅.
- M at the 15^thcycle indicating cleavage after V₁₇₇.
- The 1^stcycle can indicate cleavage after D₁₉₁, see Table 1.
- R at the 4^thand 13^thcycle indicating cleavage after V₁₇₇.
- R at the 2^ndand 11^thcycle indicating cleavage after Y₁₇₉.
- V at the 2^nd, 6^th, and 13^thcycle indicating cleavage after V₁₇₅, M₁₆₉and presence of the N-terminus of the substrate, respectively. Note fragments beginning at 176 and 170 in Table 1.
- Y at the 1^st, 2^nd, and 14^thcycles indicating cleavage after V₁₇₅, V₁₇₇, and presence of the N-terminus of the substrate, respectively.
- L at the 11^thand 12^thcycles indicating cleavage after V₁₇₇, and presence of the N-terminus of the substrate, respectively, is the interpretation most consistent with the other data. Comparing to the mass spectrometry results we see that L at the 2^nd, 5^th, and 9^thcycles is consistent with cleavage after F₁₈₆, E₁₈₃or M₁₆₉, and Y₁₇₉, respectively. See Table 1.

Epitope Identification

Fragments co-C-terminal with 8-10 amino acid long sequences predicted to bind HLA by the SYFPEITHI or NIH algorithms were chosen for further analysis. The digestion and prediction steps of the procedure can be usefully practiced in any order. Although the substrate peptide used in proteasomal digest described here was specifically designed to include a predicted HLA-A1 binding sequence, the actual products of digestion can be checked after the fact for actual or predicted binding to other MHC molecules. Selected results are shown in Table 2.

TABLE 2

Predicted HLA binding by proteasomally
generated fragments

I. SEQ ID NO	II. PEPTIDE	HLA	SYFPEITHI	NIH

5 & (6)	(G)MPEGDLVYV	A*0201	17(27)	(2605)
		B*0702	20	<5
		B*5101	22	314

7 & (8)	(Q)GMPEGDLVY	A1	24(26)	<5
		A3	16(18)	36
		B*2705	17	25

9	MPEGDLVY	B*5101	15	NP†

10 & (11)	(P)EGDLVYVNY	A1	27(15)	12
		A26	23(17)	NP

12	LVYVNYARTE	A3	21	<5

13 & (14)	(Y)VNYARTEDF	A26	(20)	NP
		B*08	15	<5
		B*2705	12	50

15	NYARTEDFF	A24	NP†	100
		Cw*0401	NP	120

16	YARTEDFF	B*08	16	<5

17	RTEDFFKLE	A1	21	<5
		A26	15	NP

†No prediction

HLA-A*0201 Binding Assay

Binding of the candidate epitope PSMA_168-177, GMPEGDLVYV, (SEQ ID NO. 6) to HLA-A2.1 was assayed using a modification of the method of Stauss et al., (Proc Natl Acad Sci USA 89(17):7871-5 (1992)). Specifically, T2 cells, which express empty or unstable MHC molecules on their surface, were washed twice with Iscove's modified Dulbecco's medium (IMDM) and cultured overnight in serum-free AIM-V medium (Life Technologies, Inc., Rockville, Md.) supplemented with human β2-microglobulin at 3μg/ml (Sigma, St. Louis, Mo.) and added peptide, at 800, 400, 200, 100, 50, 25, 12.5, and 6.25 μg/ml. in a 96-well flat-bottom plate at 3×10⁵cells/200 μl/well. Peptide was mixed with the cells by repipeting before distributing to the plate (alternatively peptide can be added to individual wells), and the plate was rocked gently for 2 minutes. Incubation was in a 5% CO₂incubator at 37° C. The next day the unbound peptide was removed by washing twice with serum free RPMI medium and a saturating amount of anti-class I HLA monoclonal antibody, fluorescein isothiocyanate (FITC)-conjugated anti-HLA A2, A28 (One Lambda, Canoga Park, Calif.) was added. After incubation for 30 minutes at 4° C., cells were washed 3 times with PBS supplemented with 0.5% BSA, 0.05%(w/v) sodium azide, pH 7.4-7.6 (staining buffer). (Alternatively W6/32 (Sigma) can be used as the anti-class I HLA monoclonal antibody the cells washed with staining buffer and then incubated with fluorescein isothiocyanate (FITC)-conjugated goat F(ab′) antimouse-IgG (Sigma) for 30 min at 4° C. and washed 3 times as before.) The cells were resuspended in 0.5 ml staining buffer. The analysis of surface HLA-A2.1 molecules stabilized by peptide binding was performed by flow cytometry using a FACScan (Becton Dickinson, San Jose, Calif.). If flow cytometry is not to be performed immediately the cells can be fixed by adding a quarter volume of 2% paraformaldehyde and storing in the dark at 4° C.
As seen in FIG. 2, this epitope exhibits significant binding at even lower concentrations than the positive control peptides. The Melan-A peptide used as a control in this assay (and throughout this disclosure), ELAGIGILTV (SEQ ID NO: 106), is actually a variant of the natural sequence (EAAGIGILTV; SEQ ID NO: 107)) and exhibits a high affinity in this assay. The known A2.1 binder FLPSDYFPSV (HBV_18-27; SEQ ID NO: 107) was also used as a positive control. An HLA-B44 binding peptide, AEMGKYSFY (SEQ ID NO: 109), was used as a negative control. The fluorescence obtained from the negative control was similar to the signal obtained when no peptide was used in the assay. Positive and negative control peptides were chosen from Table 18.3.1 in Current Protocols in Immunology p. 18.3.2, John Wiley and Sons, New York, 1998.

Example 1.2

Cluster Analysis (PSMA_281-310)

Another peptide, RGIAEAVGLPSIPVHPIGYYDAQKLLEKMG, PSMA_281-310, (SEQ ID NO. 18), containing an A1 epitope cluster from prostate specific membrane antigen, PSMA_283-307(SEQ ID NO. 19), was synthesized using standard solid-phase F-moc chemistry on a 433A ABI Peptide synthesizer. After side chain deprotection and cleavage from the resin, peptide in ddH2O was run on a reverse-phase preparative HPLC C18 column at following conditions: linear AB gradient (5% B/min) at a flow rate of 4 ml/min, where eluent A is 0.1% aqueous TFA and eluent B is 0.1% TFA in acetonitrile. A fraction at time 17.061 min containing the expected peptide as judged by mass spectrometry, was pooled and lyophilized. The peptide was then subjected to proteasome digestion and mass spectrum analysis essentially as described above. Prominent peaks from the mass spectra are summarized in Table 3.

TABLE 3

PSMA_281-310Mass Peak Identification.

			CAL-
SEQ			CULATED
ID			MASS
NO.	PEPTIDE	SEQUENCE	(MH⁺)

125	281-297	RGIAEAVGLPSIPVHPI*	1727.07

126	286-297	AVGLPSIPVHPI**	1200.46

127	287-297	VGLPSIPVHPI	1129.38

128	288-297	GLPSIPVHPI ^†	1030.25

129	298-310	GYYDAQKLLEKMG‡	1516.5

130	298-305	GYYDAQKL§	958.05

131	281-305	RGIAEAVGLPSIPVHPIGYYDAQKL	2666.12

132	281-307	RGIAEAVGLPSIPVHPIGYYDAQKLLE	2908.39

133	286-307	AVGLPSIPVHPIGYYDAQKLLE¶	2381.78

134	287-307	VGLPSIPVHPIGYYDAQKLLE	2310.70

135	288-307	GLPSIPVHPIGYYDAQKLLE#	2211.57

136	281-299	RGIAEAVGLPSIPVHPIGY	1947

137	286-299	AVGLPSIPVHPIGY	1420.69

138	287-299	VGLPSIPVHPIGY	1349.61

139	288-299	GLPSIPVHPIGY	1250.48

140	287-310	VGLPSIPVHPIGYYDAQKLLEKMG	2627.14

141	288-310	GLPSIPVHPIGYYDAQKLLEKMG	2528.01

Boldface sequences correspond to peptides predicted to bind to MHC, see Table 4.
*By mass alone this peak could also have been 296-310 or 288-303.
**By mass alone this peak could also have been 298-307. Combination of HPLC and mass spectrometry show that at some later time points this peak is a mixture of both species.
†By mass alone this peak could also have been 289-298.
≠By mass alone this peak could also have been 281-295 or 294-306.
§By mass alone this peak could also have been 297-303.
¶By mass alone this peak could also have been 285-306.
#By mass alone this peak could also have been 288-303.
None of these alternate assignments are supported N-terminal pool sequence analysis.

N-Terminal Pool Sequence Analysis

One aliquot at one hour of the proteasomal digestion (see Example 3 part 3 above) was subjected to N-terminal amino acid sequence analysis by an ABI 473A Protein Sequencer (Applied Biosystems, Foster City, Calif.). Determination of the sites and efficiencies of cleavage was based on consideration of the sequence cycle, the repetitive yield of the protein sequencer, and the relative yields of amino acids unique in the analyzed sequence. That is if the unique (in the analyzed sequence) residue X appears only in the nth cycle a cleavage site exists n-1 residues before it in the N-terminal direction. In addition to helping resolve any ambiguity in the assignment of mass to sequences, these data also provide a more reliable indication of the relative yield of the various fragments than does mass spectrometry.
For PSMA_281-310(SEQ ID NO. 18) this pool sequencing supports two major cleavage sites after V₂₈₇and I₂₉₇among other minor cleavage sites. Reviewing the results presented in FIG. 3 reveals the following:

- S at the 4^thand 11^thcycles indicating cleavage after V₂₈₇and presence of the N-terminus of the substrate, respectively.
- H at the 8^thcycle indicating cleavage after V₂₈₇. The lack of decay in peak height at positions 9 and 10 versus the drop in height present going from 10 to 11 can suggest cleavage after A₂₈₆and E₂₈₅as well, rather than the peaks representing latency in the sequencing reaction.
- D at the 2^nd, 4^th, and 7^thcycles indicating cleavages after Y₂₉₉, I₂₉₇, and V₂₉₄, respectively. This last cleavage is not observed in any of the fragments in Table 4 or in the alternate assignments in the notes below.
- Q at the 6^thcycle indicating cleavage after I₂₉₇.
- M at the 10^thand 12^thcycle indicating cleavages after Y₂₉₉and I₂₉₇, respectively.

Epitope Identification

Fragments co-C-terminal with 8-10 amino acid long sequences predicted to bind HLA by the SYFPEITHI or NIH algorithms were chosen for further study. The digestion and prediction steps of the procedure can be usefully practiced in any order. Although the substrate peptide used in proteasomal digest described here was specifically designed to include a predicted HLA-A1 binding sequence, the actual products of digestion can be checked after the fact for actual or predicted binding to other MHC molecules. Selected results are shown in Table 4.

TABLE 4

Predicted HLA binding by proteasomally
generated fragments: PSMA_281-310

III. SEQ ID
NO.	IV. PEPTIDE	HLA	SYFPEITHI	NIH

20 & (21)	(G)LPSIPVHPI	A*0201	16(24)	(24)
		B*0702/B7	23	12
		B*5101	24	572
		Cw*0401	NP†	20

22 & (23)	(P)IGYYDAQKL	A*0201	(16)	<5
		A26	(20)	NP
		B*2705	16	25
		B*2709	15	NP
		B*5101	21	57
		Cw*0301	NP	24

24 & (25)	(P)SIPVHPIGY	A1	21(27)	<5
		A26	22	NP
		A3	16	<5

26	IPVHPIGY	B*5101	16	NP

27	YYDAQKLLE	A1		22	<5

†No prediction

As seen in Table 4, N-terminal addition of authentic sequence to epitopes can often generate still useful, even better epitopes, for the same or different MHC restriction elements. Note for example the pairing of (G)LPSIPVHPI with HLA-A*0201, where the 10-mer can be used as a vaccine useful with several MHC types by relying on N-terminal trimming to create the epitopes for HLA-B7,-B*5101, and Cw*0401.

HLA-A*0201 Binding Assay

HLA-A*0201 binding studies were preformed with PSMA_288-297, GLPSIPVHPI, (SEQ ID NO. 21) essentially as described in Example 1.1 above. As seen in FIG. 2, this epitope exhibits significant binding at even lower concentrations than the positive control peptides.

Example 1.3

Cluster Analysis (PSMA_454-481)

Another peptide, SSIEGNYTLRVDCTPLMYSLVHLTKEL, PSMA_454-481, 5 (SEQ ID NO. 28) containing an epitope cluster from prostate specific membrane antigen, was synthesized by MPS (purity>95%) and subjected to proteasome digestion and mass spectrum analysis as described above. Prominent peaks from the mass spectra are summarized in Table 5.

TABLE 5

PSMA_454-481Mass Peak Identification.

SEQ ID	MS PEAK			CALCULATED
NO.	(measured)	PEPTIDE	SEQUENCE	MASS (MH⁺)

142	1238.5	454-464	SSIEGNYTLRV	1239.78

143	1768.38 ± 0.60	454-469	SSIEGNYTLRVDCTPL	1768.99

144	1899.8	454-470	SSIEGNYTLRVDCTPLM	1900.19

145	1097.63 ± 0.91	463-471	RVDCTPLMY	1098.32

146	2062.87 ± 0.68	454-471*	SSIEGNYTLRVDCTPLMY	2063.36

147	1153	472-481**	SLVHNLTKEL	1154.36

148	1449.93 ± 1.79	470-481	MYSLVHNLTKEL	1448.73

Boldface sequence correspond to peptides predicted to bind to MHC, see Table 6.
*On the basis of mass alone this peak could equally well be assigned to the peptide 455-472 however proteasomal removal of just the N-terminal amino acid is considered unlikely. If the issue were important it could be resolved by N-terminal sequencing.
**On the basis of mass this fragment might also represent 455-464.

Epitope Identification

Fragments co-C-terminal with 8-10 amino acid long sequences predicted to bind HLA by the SYFPEITHI or NIH algorithms were chosen for further study. The digestion and prediction steps of the procedure can be usefully practiced in any order. Although the substrate peptide used in proteasomal digest described here was specifically designed to include predicted HLA-A2.1 binding sequences, the actual products of digestion can be checked after the fact for actual or predicted binding to other MHC molecules. Selected results are shown in Table 6.

TABLE 6

Predicted HLA binding by proteasomally
generated fragments

V.
SEQ ID NO	VI. PEPTIDE	HLA	SYFPEITHI	NIH

29 & (30)	(S)IEGNYTLRV	A1	(19)	<5

31	EGNYTLRV	A*0201	16(22)	<5
		B*5101	15	NP†

32 & (33)	(Y)TLRVDCTPL	A*0201	20(18)	(5)
		A26	16(18)	NP
		B7
	14	40
		B8	23	<5
		B*2705	12	30
		Cw*0301	NP	(30)

34	LRVDCTPLM	B*2705	20	600
		B*2709	20	NP

35 & (36)	(L)RVDCTPLMY	A2	32(22)	125
				(13.5)
		A3	25	<5
		A26	22	NP
		B*2702	NP	(200)
		B*2705	13(NP)	(1000)

†No prediction

As seen in Table 6, N-terminal addition of authentic sequence to epitopes can often generate still useful, even better epitopes, for the same or different MHC restriction elements. Note for example the pairing of (L)RVDCTPLMY (SEQ ID NOS 35 and (36)) with HLA-B*2702/5, where the 10-mer has substantial predicted halftimes of dissociation and the co-C-terminal 9-mer does not. Also note the case of SIEGNYTLRV (SEQ ID NO 30) a predicted HLA-A*0201 epitope which can be used as a vaccine useful with HLA-B*5101 by relying on N-terminal trimming to create the epitope.

HLA-A*0201 Binding Assay

HLA-A*0201 binding studies were preformed, essentially as described in Example 1.1 above, with PSMA_460-469, YTLRVDCTPL, (SEQ ID NO.33). As seen in FIG. 4, this epitope was found to bind HLA-A2.1 to a similar extent as the known A2.1 binder FLPSDYFPSV (HBV_18-27; SEQ ID NO: 108) used as a positive control. Additionally, PSMA_461-469, (SEQ ID NO. 32) binds nearly as well.

ELISPOT Analysis: PSMA_463-471(SEQ ID NO. 35)

The wells of a nitrocellulose-backed microtiter plate were coated with capture antibody by incubating overnight at 4° C. using 50 μl/well of 4 μg/ml murine anti-human □-IFN monoclonal antibody in coating buffer (35 mM sodium bicarbonate, 15 mM sodium carbonate, pH 9.5). Unbound antibody was removed by washing 4 times 5 min. with PBS. Unbound sites on the membrane then were blocked by adding 200 μl/well of RPMI medium with 10% serum and incubating 1 hr. at room temperature. Antigen stimulated CD8⁺ T cells, in 1:3 serial dilutions, were seeded into the wells of the microtiter plate using 100 μl/well, starting at 2×10⁵cells/well. (Prior antigen stimulation was essentially as described in Scheibenbogen, C. et al. Int. J. Cancer 71:932-936, 1997; which is incorporated herein by reference in its entirety.) PSMA_462-471(SEQ ID NO. 36) was added to a final concentration of 10 μg/ml and IL-2 to 100 U/ml and the cells cultured at 37° C. in a 5% CO₂, water-saturated atmosphere for 40 hrs. Following this incubation the plates were washed with 6 times 200 μl/well of PBS containing 0.05% Tween-20 (PBS-Tween). Detection antibody, 50 μl/well of 2 g/ml biotinylated murine anti-human □-IFN monoclonal antibody in PBS+10% fetal calf serum, was added and the plate incubated at room temperature for 2 hrs. Unbound detection antibody was removed by washing with 4 times 200 μl of PBS-Tween. 100 μl of avidin-conjugated horseradish peroxidase (Pharmingen, San Diego, Calif.) was added to each well and incubated at room temperature for 1 hr. Unbound enzyme was removed by washing with 6 times 200 μl of PBS-Tween. Substrate was prepared by dissolving a 20 mg tablet of 3-amino 9-ethylcoarbasole in 2.5 ml of N, N-dimethylformamide and adding that solution to 47, 5 ml of 0.05 M phosphate-citrate buffer (pH 5.0). 25 μl of 30% H₂O₂was added to the substrate solution immediately before distributing substrate at 100 μl/well and incubating the plate at room temperature. After color development (generally 15-30 min.), the reaction was stopped by washing the plate with water. The plate was air dried and the spots counted using a stereomicroscope.
FIG. 5 shows the detection of PSMA_463-471(SEQ ID NO. 35)-reactive HLA-A1⁺ CD8⁺ T cells previously generated in cultures of HLA-A1⁺ CD8⁺ T cells with autologous dendritic cells plus the peptide. No reactivity is detected from cultures without peptide (data not shown). In this case it can be seen that the peptide reactive T cells are present in the culture at a frequency between 1 in 2.2×10⁴and 1 in 6.7×10⁴. That this is truly an HLA-A1-restricted response is demonstrated by the ability of anti-HLA-A1 monoclonal antibody to block □-IFN production; see FIG. 6.

Example 1.4

Cluster Analysis (PSMA_653-687)

Another peptide, FDKSNPIVLRMMNDQLMFLERAFIDPLGLPDRPFY PSMA_653-687, (SEQ ID NO. 37) containing an A2 epitope cluster from prostate specific membrane antigen, PSMA_660-681(SEQ ID NO. 38), was synthesized by MPS (purity>95%) and subjected to proteasome digestion and mass spectrum analysis as described above. Prominent peaks from the mass spectra are summarized in Table 7.

TABLE 7

PSMA_653-687Mass Peak Identification.

SEQ
ID	MS PEAK			CALCULATED
NO.	(measured)	PEPTIDE	SEQUENCE	MASS (MH⁺)

149	906.17 ± 0.65	681-687**	LPDRPFY	908.05

150	1287.73 ± 0.76	677-687**	DPLGLPDRPFY	1290.47

151	1400.3 ± 1.79	676-687	IDPLGLPDRPFY	1403.63

152	1548.0 ± 1.37	675-687	FIDPLGLPDRPFY	1550.80

153	1619.5 ± 1.51	674-687**	AFIDPLGLPDRPFY	1621.88

154	1775.48 ± 1.32	673-687*	RAFIDPLGLPDRPFY	1778.07

155	2440.2 ± 1.3	653-672	FDKSNPIVLRMMNDQLMFLE	2442.932313.82

156	1904.63 ± 1.56	672-687*	ERAFIDPLGLPDRPFY	1907.19

157	2310.6 ± 2.5	653-671	FDKSNPIVLRMMNDQLMFL	2313.82

158	2017.4 ± 1.94	671-687	LERAFIDPLGLPDRPFY	2020.35

159	2197.43 ± 1.78	653-670	FDKSNPIVLRMMNDQLMF	2200.66

Boldface sequence correspond to peptides predicted to bind to MHC, see Table 7.
*On the basis of mass alone this peak could equally well be assigned to a peptide beginning at 654, however proteasomal removal of just the N-terminal amino acid is considered unlikely. If the issue were important it could be resolved by N-terminal sequencing.
**On the basis of mass alone these peaks could have been assigned to internal fragments, but given the overall pattern of digestion it was considered unlikely.

Epitope Identification

Fragments co-C-terminal with 8-10 amino acid long sequences predicted to bind HLA by the SYFPEITHI or NIH algorithms were chosen for further study. The digestion and prediction steps of the procedure can be usefully practiced in any order. Although the substrate peptide used in proteasomal digest described here was specifically designed to include predicted HLA-A2.1 binding sequences, the actual products of digestion can be checked after the fact for actual or predicted binding to other MHC molecules. Selected results are shown in Table 8.

TABLE 8

Predicted HLA binding by proteasomally
generated fragments

VII.
SEQ ID NO	VIII. PEPTIDE	HLA	SYFPEITHI	NIH

39 & (40)	(R)MMNDQLMFL	A*0201	24 (23)	1360 (722)
		A*0205	NP†	71 (42)
		A26	15	NP
		B*2705	12	50

41	RMMNDQLMF	B*2705	17	75

†No prediction

As seen in Table 8, N-terminal addition of authentic sequence to epitopes can generate still useful, even better epitopes, for the same or different MHC restriction elements. Note for example the pairing of (R)MMNDQLMFL (SEQ ID NOS. 39 and (40)) with HLA-A*02, where the 10-mer retains substantial predicted binding potential.

HLA-A*0201 Binding Assay

HLA-A*0201 binding studies were preformed, essentially as described in Example 1.1 above, with PSMA_663-671, (SEQ ID NO. 39) and PSMA_662-671, RMMNDQLMFL (SEQ NO. 67). As seen in FIGS. 4, 7 and 8, this epitope exhibits significant binding at even lower concentrations than the positive control peptide (FLPSDYFPSV (HBV_18-27); SEQ ID NO. 108). Though not run in parallel, comparison to the controls suggests that PSMA_662-671(which approaches the Melan A peptide in affinity) has the superior binding activity of these two PSMA peptides.

Example 2

A multi-center clinical study is carried out using compositions as disclosed herein. The results of the study show the compositions to be useful and effective for debulking solid tumors and for generally inducing anti-angiogenic activity.

Example 3 Evaluation of a PSMA Composition in the Xenotransplanted Human Vasculature Model

Generation of Target Antigen-Reactive CTL

A. In Vivo Immunization of Mice

HHD1 transgenic A*0201 mice (Pascolo, S., et al. J. Exp. Med. 185:2043-2051, 1997) were anesthetized and injected subcutaneously at the base of the tail, avoiding lateral tail veins, using 100 μl containing 100 nmol of PSMA_288-297(SEQ ID NO. 21) and 20 μg of a HTL epitope peptide in PBS emulsified with 50 μl of IFA (incomplete Freund's adjuvant).

B. Preparation of Stimulating Cells (LPS Blasts)

Using spleens from 2 naïve mice for each group of immunized mice, un-immunized mice were sacrificed and their carcasses placed in alcohol. Using sterile instruments, the top dermal layer of skin on the mouse's left side (lower mid-section) was cut through, exposing the peritoneum. The peritoneum was saturated with alcohol, and the spleen aseptically extracted. The spleens were placed in a petri dish with serum-free media. Splenocytes were isolated by using sterile plungers from 3 ml syringes to mash the spleens. Cells were collected in a 50 ml conical tubes in serum-free media, rinsing dish well. Cells were centrifuged (12000 rpm, 7 min) and washed one time with RPMI. Fresh spleen cells were resuspended to a concentration of 1×10⁶cells per ml in RPMI-10%FCS (fetal calf serum). 25 g/ml lipopolysaccharide and 7 μg/ml Dextran Sulfate were added. Cell were incubated for 3 days in T-75 flasks at 37° C., with 5% CO₂. Splenic blasts were collected in 50 ml tubes pelleted (12,000 rpm, 7 min) and resuspended to 3×10⁷/ml in RPMI. The blasts were pulsed with the priming peptide at 50 μg/ml, RT 4 hr. mitomycin C-treated at 25 μg/ml, 37° C., 20 min and washed three times with DMEM.

C. In Vitro Stimulation

Three days after LPS stimulation of the blast cells and the same day as peptide loading, the primed mice were sacrificed (at 14 days post immunization) to remove spleens as above. 3×10⁶splenocytes were co-cultured with 1×10⁶LPS blasts/well in 24-well plates at 37° C., with 5% CO₂in DMEM media supplemented with 10% FCS, 5×10⁻⁵M β(beta)-mercaptoethanol, 100 μg/ml streptomycin and 100 IU/ml penicillin. Cultures were fed 5% (vol/vol) ConA supernatant on day 3 and can be transferred on day 7. An aliquot of the CTL are also tested in a standard chromium release assay to ensure activity.

Implantation and Adoptive Transfer

1×10⁶telomerase-transformed HDMEC in 10 μl of EGM-2-VM medium (Clonetics, San Diego, Calif.) are mixed with 0.5 ml of MATRIGEL (Becton Dickinson) on ice. The mixture is injected subcutaneously, through a 25 gauge needle, along the ventral midline of the thorax of SCID mice. One week later 1×10⁷T cells (target epitope-reactive or sham-immunized) in 0.2 ml are injected intravenously (alternatively they can be injected intraperitoneally).

Assessment (Micromorphometry)

At one and two weeks after transfer remove implants, fix in 10% buffered overnight, embed in paraffin, and section. For immunofluorescence detection of human microvessels using anti-human type IV collagen IgG and fluorescently-labeled secondary antibody, deparifinize and retrieve antigen by microwaving thin sections 2×7 minutes in 10 mM citric acid, pH 6.0. Vessel density is assessed as a function of the average number of positively stained annular structures observed in five separate, randomly selected 20× fields-of-view, from at least three sections per implant.

Example 4 A Fibronectin ED-B Vaccine in the HLA-Transgenic Mouse Model

A. Establishment of Tumor

M1 tumor cells grown in complete RPMI plus 10% serum were harvested and washed with PBS by centrifugation. The cells were suspended in PBS at 5×10⁶cells/ml and 0.5 ml of the suspension (early passage) was injected subcutaneously into the abdomen.

B. Vaccination

A nucleotide sequence encoding an HLA-A2-restricted fibronectin ED-B domain-derived housekeeping epitope, for example ED-B_29-38(SEQ ID NO. 103), is inserted into an appropriate vaccine vector (e.g. pVAX1 (Invitrogen Inc, Carlsbad, Calif.) or one of the vectors described in U.S. patent application Ser. No. 09/561,572 entitled “EXPRESSION VECTORS ENCODING EPITOPES OF TARGET-ASSOCIATED ANTIGENS,” filed on Apr. 28, 2001, and incorporated by reference above. HHD-A2 mice are injected intranodally in the inguinal lymph node with 0, 2, 10, 50, 100, and 200 μg of vector in PBS every other day over 8 days (4 injections) alternating sides for each injection (single dosage per mouse or group of mice). Injection series are started the day of tumor cell injection, at 2 weeks before, and at 4 and 10 weeks after.

C. Evaluation

At approximately 12 weeks after injection of tumor cells visible tumors are observed in the mice receiving the vehicle instead of the vaccine. Effectiveness of the vaccine is expressed as the proportion of vaccinated animals that fail to develop a tumor in the same time frame, the relative size of tumors at the same time point, the delay in time before tumors appear in the vaccinated animals, and the dose and number of composition cycles needed to inhibit or prevent the establishment of tumor.

D. Alternative Schedule

The availability of more aggressive later passage M1 cells enables a more compressed experimental schedule. Instead mice are vaccinated on the day of tumor cell inoculation, 1 and 2 weeks before, and 3 or 4 days after injections of 1×10⁶cells. Effectiveness of vaccination is assessed at approximately 10 days after tumor cell inoculation.

E. Immunization With Peptide

HHD-A2 mice were immunized with ED-B29-38 (SEQ ID NO. 103) in complete Freund's adjuvants and spleen cells were harvested and re-stimulated in vitro using standard methodology. The resulting CTL were able to specifically lyse peptide pulsed T2 cells, which are HLA-A2+ (FIG. 9).

Example 5 Epitopes and Epitope Clusters

Table 9 discloses epitopes and epitope clusters from PSMA and ED-B that can be useful in construction of compositions according to the present invention.

TABLE 9

SEQ ID NOS.*

SEQ ID NO	IDENTITY	SEQUENCE

1	PSMA protein	Accession number**: NP_004467

2	PSMA cDNA	Accession number: NM_004476

3	PSMA 163-192	AFSPQGMPEGDLVYVNYARTEDFFKLERDM

4	PSMA 168-190	GMPEGDLVYVNYARTEDFFKLER

5	PSMA 169-177	MPEGDLVYV

6	PSMA 168-177	GMPEGDLVYV

7	PSMA 168-176	GMPEGDLVY

8	PSMA 167-176	QGMPEGDLVY

9	PSMA 169-176	MPEGDLVY

10	PSMA 171-179	EGDLVYVNY

11	PSMA 170-179	PEGDLVYVNY

12	PSMA 174-183	LVYVNYARTE

13	PSMA 177-185	VNYARTEDF

14	PSMA 176-185	YVNYARTEDF

15	PSMA 178-186	NYARTEDFF

16	PSMA 179-186	YARTEDFF

17	PSMA 181-189	RTEDFFKLE

18	PSMA 281-310	RGIAEAVGLPSIPVHPIGYYDAQKLLEKMG

19	PSMA 283-307	IAEAVGLPSIPVHPIGYYDAQKLLE

20	PSMA 289-297	LPSIPVHPI

21	PSMA 288-297	GLPSIPVHPI

22	PSMA 297-305	IGYYDAQKL

23	PSMA 296-305	PIGYYDAQKL

24	PSMA 291-299	SIPVHPIGY

25	PSMA 290-299	PSIPVHPIGY

26	PSMA 292-299	IPVHPIGY

27	PSMA 299-307	YYDAQKLLE

28	PSMA 454-481	SSIEGNYTLRVDCTPLMYSLVHLTKEL

29	PSMA 456-464	IEGNYTLRV

30	PSMA 455-464	SIEGNYTLRV

31	PSMA 457-464	EGNYTLRV

32	PSMA 461-469	TLRVDCTPL

33	PSMA 460-469	YTLRVDCTPL

34	PSMA 462-470	LRVDCTPLM

35	PSMA 463-471	RVDCTPLMY

36	PSMA 462-471	LRVDCTPLMY

37	PSMA 653-687	FDKSNPIVLRMMNDQLMFLERAFIDPLGLPDRPFY

38	PSMA 660-681	VLRMMNDQLMFLERAFIDPLGL

39	PSMA 663-671	MMNDQLMFL

40	PSMA 662-671	RMMNDQLMFL

41	PSMA 662-670	RMMNDQLMF

42	PSMA 4-12	LLHETDSAV

43	PSMA 13-21	ATARRPRWL

44	PSMA 53-61	TPKHNMKAF

45	PSMA 64-73	ELKAENIKKF

46	PSMA 69-77	NIKKFLH¹NF

47	PSMA 68-77	ENIKKFLH¹NF

48	PSMA 220-228	AGAKGVILY

49	PSMA 468-477	PLMYSLVHNL

50	PSMA 469-477	LMYSLVHNL

51	PSMA 463-471	RVDCTPLMY

52	PSMA 465-473	DCTPLMYSL

53	PSMA 507-515	SGMPRISKL

54	PSMA 506-515	FSGMPRISKL

55	PSMA 211-218	GNKVKNAQ

56	PSMA 202-209	IARYGKVF

57	PSMA 217-225	AQLAGAKGV

58	PSMA 207-215	KVFRGNKVK

59	PSMA 211-219	GNKVKNAQL

60	PSMA 269-277	TPGYPANEY

61	PSMA 268-277	LTPGYPANEY

62	PSMA 271-279	GYPANEYAY

63	PSMA 270-279	PGYPANEYAY

64	PSMA 266-274	DPLTPGYPA

65	PSMA 492-500	SLYESWTKK

66	PSMA 491-500	KSLYESWTKK

67	PSMA 486-494	EGFEGKSLY

68	PSMA 485-494	DEGFEGKSLY

69	PSMA 498-506	TKKSPSPEF

70	PSMA 497-506	WTKKSPSPEF

71	PSMA 492-501	SLYESWTKKS

72	PSMA 725-732	WGEVKRQI

73	PSMA 724-732	AWGEVKRQI

74	PSMA 723-732	KAWGEVKRQI

75	PSMA 723-730	KAWGEVKR

76	PSMA 722-730	SKAWGEVKR

77	PSMA 731-739	QIYVAAFTV

78	PSMA 733-741	YVAAFTVQA

79	PSMA 725-733	WGEVKRQIY

80	PSMA 727-735	EVKRQIYVA

81	PSMA 738-746	TVQAAAETL

82	PSMA 737-746	FTVQAAAETL

83	PSMA 729-737	KRQIYVAAF

84	PSMA 721-729	PSKAWGEVK

85	PSMA 723-731	KAWGEVKRQ

86	PSMA 100-108	WKEFGLDSV

87	PSMA 99-108	QWKEFGLDSV

88	PSMA 102-111	EFGLDSVELA

89	ED-B domain of	EVPQLTDLSFVDITDSSIGLRWTPLNSSTIIGYRI
	Fibronectin	TVVAAGEGIPIFEDFVDSSVGYYTVTGLEPGID
		YDISVITLINGGESAPTTLTQQT

90	ED-B domain of	CTFDNLSPGLEYNVSVYTVKDDKESVPISDTIIP
	Fibronectin with	EVPQLTDLSFVDITDSSIGLRWTPLNSSTIIGYRI
	flanking sequence	TVVAAGEGIPIFEDFVDSSVGYYTVTGLEPGID
	from Fribronectin	YDISVITLINGGESAPTTLTQQT
		AVPPPTDLRFTNIGPDTMRVTW

91	ED-B domain of	Accession number: X07717
	Fibronectin cds

92	ED-B 4′-5	TIIPEVPQL

93	ED-B 5′-5	DTIIPEVPQL

94	ED-B 1-10	EVPQLTDLSF

95	ED-B 23-30	TPLNSSTI

96	ED-B 18-25	IGLRWTPL

97	ED-B 17-25	SIGLRWTPL

98	ED-B 25-33	LNSSTIIGY

99	ED-B 24-33	PLNSSTIIGY

100	ED-B 23-31	TPLNSSTII

101	ED-B 31-38	IGYRITVV

102	ED-B 30-38	IIGYRITVV

103	ED-B 29-38	TIIGYRITVV

104	ED-B 31-39	IGYRITVVA

105	ED-B 30-39	IIGYRITVVA

106	Melan-A 26-35_A>L	ELAGIGILTV

107	Melan-A 26-35	EAAGIGILTV

108	HBV 18-27	FLPSDYFPSV

109	HLA-B 44 binder	AEMGKYSFY

¹This H was reported as Y in the SWISSPROT database.
*Any of SEQ ID NOS. 5-17, 20-27, 29-36, 39-88, and 92-105 can be useful as epitopes in the various embodiments of the invention. Any of SEQ ID NOS. 3, 4, 18, 19, 28, 37, 38, 89 and 90 can be useful as sequences containing epitopes or epitope clusters, as described in various embodiments of the invention.
**All accession numbers used here and throughout can be accessed through the NCBI databases, for example, through the Entrez seek and retrieval system on the world wide web.

PSMA
LOCUS	NM_004476 2653 bp mRNA PRI 01-NOV-2000

DEFINITION	Homo sapiens folate hydrolase (prostate-specific membrane
	antigen)
	1 (FOLH1), mRNA.

ACCESSION	NM_004476

VERSION	NM_004476.1 GI: 4758397

KEYWORDS	.

SOURCE	human.

ORGANISM	Homo sapiens
	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
	Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini;
	Hominidae; Homo.

REFERENCE	1 (bases 1 to 2653)

AUTHORS	Israeli, R. S., Powell, C. T., Fair, W. R. and Heston, W. D.

TITLE	Molecular cloning of a complementary DNA encoding a
	prostate-specific membrane antigen

JOURNAL	Cancer Res. 53 (2), 227-230 (1993)

MEDLINE	93113576

REFERENCE	2 (bases 1 to 2653)

AUTHORS	Rinker-Schaeffer C W, Hawkins A L, Su S L, Israeli R S,
	Griffin C A, Isaacs J T and Heston W D.

TITLE	Localization and physical mapping of the prostate-specific
	membrane antigen (PSM) gene to human chromosome 11

JOURNAL	Genomics 30 (1), 105-108 (1995)

MEDLINE	96129312

PUBMED	8595888

REFERENCE	3 (bases 1 to 2653)

AUTHORS	O'Keefe D S, Su S L, Bacich D J, Horiguchi Y, Luo Y, Powell
	C T, Zandvliet D, Russell P J, Molloy P L, Nowak N J, Shows T B,
	Mullins C, Vonder Haar R A, Fair W R and Heston W D.

TITLE	Mapping, genomic organization and promoter analysis of the
	human prostate-specific membrane antigen gene

JOURNAL	Biochim. Biophys. Acta 1443 (1-2), 113-127 (1998)

MEDLINE	99057588

PUBMED	9838072

REFERENCE	4 (bases 1 to 2653)

AUTHORS	Maraj B H, Leek J P, Karayi M, Ali M, Lench N J and Markham
	A F.

TITLE	Detailed genetic mapping around a putative prostate-
	specific membrane antigen locus on human chromosome 11p11.2

JOURNAL	Cytogenet. Cell Genet. 81 (1), 3-9 (1998)

MEDLINE	98358137

PUBMED	9691167

COMMENT	PROVISIONAL REFSEQ: This record has not yet been subject
	to final NCBI review. The reference sequence was derived from
	M99487.1.

FEATURES	Location/Qualifiers

source
	1 . . . 2653

	/organism = “Homo sapiens”

	/db_xref = “taxon: 9606”

	/chromosome = “11”

	/map = “11p11.2”

	/sex = “male”

	/cell_line = “LNCaP-ATCC”

	/cell_type = “prostate”

	/tissue_type = “prostatic carcinoma metastatic
	lymph node”

	/tissue_lib = “LNCaP cDNA of Ron Israeli”

gene	1 . . . 2653

	/gene = “FOLH1”

	/note = “FOLH; PSM; PSMA”

	/db_xref = “LocusID: 2346”

	/db_xref = “MIM: 600934”

CDS	262 . . . 2514

	/gene = “FOLH1”

	/note = “folate hydrolase 1 (prostate-specific
	membrane antigen)”

	/codon_start = 1

	/db_xref = “LocusID: 2346”

	/db_xref = “MIM: 600934”

	/evidence = experimental

	/product = “folate hydrolase (prostate-specific
	membrane antigen) 1”

	/protein_id = “NP_004467.1”

	/db_xref = “GI: 4758398”

/translation = “MWNLLHETDSAVATARRPRWLCAGALVLAGGFFLLGFLFGWFIK	(SEQ ID NO. 1)

SSNEATNITPKHNMKAFLDELKAENIKKFLYNFTQIPHLAGTEQNFQLAKQIQSQWKE

FGLDSVELAHYDVLLSYPNKTHPNYISIINEDGNEIFNTSLFEPPPPGYENVSDIVPP

FSAFSPQGMPEGDLVYVNYARTEDFFKLERDMKINCSGKIVIARYGKVFRGNKVKNAQ

LAGAKGVILYSDPADYFAPGVKSYPDGWNLPGGGVQRGNILNLNGAGDPLTPGYPANE

YAYRRGIAEAVGLPSIPVHPIGYYDAQKLLEKMGGSAPPDSSWRGSLKVPYNVGPGFT

GNFSTQKVKMHIHSTNEVTRIYNVIGTLRGAVEPDRYVILGGHRDSWVFGGIDPQSGA

AVVHEIVRSFGTLKKEGWRPRRTILFASWDAEEFGLLGSTEWAEENSRLLQERGVAYI

NADSSIEGNYTLRVDCTPLMYSLVHNLTKELKSPDEGFEGKSLYESWTKKSPSPEFSG

MPRISKLGSGNDFEVFFQRLGIASGRARYTKNWETNKFSGYPLYHSVYETYELVEKFY

DPMFKYHLTVAQVRGGMVFELANSIVLPFDCRDYAVVLRKYADKIYSISMKHPQEMKT

YSVSFDSLFSAVKNFTEIASKFSERLQDFDKSNPIVLRMMNDQLMFLERAFIDPLGLP

DRPFYRHVIYAPSSHNKYAGESFPGIYDALFDIESKVDPSKAWGEVKRQIYVAAFTVQ

AAAETLSEVA”

misc feature	778 . . . 1029

	/note = “PA; Region: PA domain”

BASE COUNT	782 a 524 c 640 g 707 t

ORIGIN

1	ctcaaaaggg gccggatttc cttctcctgg aggcagatgt tgcctctctc tctcgctcgg	(SEQ ID NO. 2)

61	attggttcag tgcactctag aaacactgct gtggtggaga aactggaccc caggtctgga

121	gcgaattcca gcctgcaggg ctgataagcg aggcattagt gagattgaga gagactttac

181	cccgccgtgg tggttggagg gcgcgcagta gagcagcagc acaggcgcgg gtcccgggag

241	gccggctctg ctcgcgccga gatgtggaat ctccttcacg aaaccgactc ggctgtggcc

301	accgcgcgcc gcccgcgctg gctgtgcgct ggggcgctgg tgctggcggg tggcttcttt

361	ctcctcggct tcctcttcgg gtggtttata aaatcctcca atgaagctac taacattact

421	ccaaagcata atatgaaagc atttttggat gaattgaaag ctgagaacat caagaagttc

481	ttatataatt ttacacagat accacattta gcaggaacag aacaaaactt tcagcttgca

541	aagcaaattc aatcccagtg gaaagaattt ggcctggatt ctgttgagct agcacattat

601	gatgtcctgt tgtcctaccc aaataagact catcccaact acatctcaat aattaatgaa

661	gatggaaatg agattttcaa cacatcatta tttgaaccac ctcctccagg atatgaaaat

721	gtttcggata ttgtaccacc tttcagtgct ttctctcctc aaggaatgcc agagggcgat

781	ctagtgtatg ttaactatgc acgaactgaa gacttcttta aattggaacg ggacatgaaa

841	atcaattgct ctgggaaaat tgtaattgcc agatatggga aagttttcag aggaaataag

901	gttaaaaatg cccagctggc aggggccaaa ggagtcattc tctactccga ccctgctgac

961	tactttgctc ctggggtgaa gtcctatcca gatggttgga atcttcctgg aggtggtgtc

1021	cagcgtggaa atatcctaaa tctgaatggt gcaggagacc ctctcacacc aggttaccca

1081	gcaaatgaat atgcttatag gcgtggaatt gcagaggctg ttggtcttcc aagtattcct

1141	gttcatccaa ttggatacta tgatgcacag aagctcctag aaaaaatggg tggctcagca

1201	ccaccagata gcagctggag aggaagtctc aaagtgccct acaatgttgg acctggcttt

1261	actggaaact tttctacaca aaaagtcaag atgcacatcc actctaccaa tgaagtgaca

1321	agaatttaca atgtgatagg tactctcaga ggagcagtgg aaccagacag atatgtcatt

1381	ctgggaggtc accgggactc atgggtgttt ggtggtattg accctcagag tggagcagct

1441	gttgttcatg aaattgtgag gagctttgga acactgaaaa aggaagggtg gagacctaga

1501	agaacaattt tgtttgcaag ctgggatgca gaagaatttg gtcttcttgg ttctactgag

1561	tgggcagagg agaattcaag actccttcaa gagcgtggcg tggcttatat taatgctgac

1621	tcatctatag aaggaaacta cactctgaga gttgattgta caccgctgat gtacagcttg

1681	gtacacaacc taacaaaaga gctgaaaagc cctgatgaag gctttgaagg caaatctctt

1741	tatgaaagtt ggactaaaaa aagtccttcc ccagagttca gtggcatgcc caggataagc

1801	aaattgggat ctggaaatga ttttgaggtg ttcttccaac gacttggaat tgcttcaggc

1861	agagcacggt atactaaaaa ttgggaaaca aacaaattca gcggctatcc actgtatcac

1921	agtgtctatg aaacatatga gttggtggaa aagttttatg atccaatgtt taaatatcac

1981	ctcactgtgg cccaggttcg aggagggatg gtgtttgagc tagccaattc catagtgctc

2041	ccttttgatt gtcgagatta tgctgtagtt ttaagaaagt atgctgacaa aatctacagt

2101	atttctatga aacatccaca ggaaatgaag acatacagtg tatcatttga ttcacttttt

2161	tctgcagtaa agaattttac agaaattgct tccaagttca gtgagagact ccaggacttt

2221	gacaaaagca acccaatagt attaagaatg atgaatgatc aactcatgtt tctggaaaga

2281	gcatttattg atccattagg gttaccagac aggccttttt ataggcatgt catctatgct

2341	ccaagcagcc acaacaagta tgcaggggag tcattcccag gaatttatga tgctctgttt

2401	gatattgaaa gcaaagtgga cccttccaag gcctggggag aagtgaagag acagatttat

2461	gttgcagcct tcacagtgca ggcagctgca gagactttga gtgaagtagc ctaagaggat

2521	tctttagaga atccgtattg aatttgtgtg gtatgtcact cagaaagaat cgtaatgggt

2581	atattgataa attttaaaat tggtatattt gaaataaagt tgaatattat atataaaaaa

2641	aaaaaaaaaa aaa

ED-B domain of Fibronectin

LOCUS	HSFIBEDB 2823 bp DNA linear PRI 09-AUG-1999

DEFINITION	Human fibronectin gene ED-B region.

ACCESSION	X07717

VERSION	X07717.1 GI: 31406

KEYWORDS	alternate splicing; fibronectin.

SOURCE	human.

ORGANISM	Homo sapiens
	Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
	Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.

REFERENCE	1 (bases 1 to 2823)

AUTHORS	Paolella, G., Henchcliffe, C., Sebastio, G. and Baralle, F. E.

TITLE	Sequence analysis and in vivo expression show that alternative
	splicing of ED-B and ED-A regions of the human fibronectin gene are
	independent events

JOURNAL	Nucleic Acids Res. 16 (8), 3545-3557 (1988)

MEDLINE	88233940

FEATURES	Location/Qualifiers

source
	1 . . . 2823

	/organism = “Homo sapiens”

	/db_xref = “taxon: 9606”

	/clone = “MA10”

exon	1 . . . 104

	/number = 1

	/product = “fibronectin”

CDS	join(<2 . . . 104, 1375 . . . 1647, 2758 . . . >2823)

	/codon_start = 1

	/product = “fibronectin”

	/protein_id = “CAB52437.1”

	/db_xref = “GI: 5725425”

	/translation = “CTFDNLSPGLEYNVSVYTVKDDKESVPISDTIIPEVPQLTDLSF	(SEQ ID NO. 90)

VDITDSSIGLRWTPLNSSTIIGYRITVVAAGEGIPIFEDFVDSSVGYYTVTGLEPGID

YDISVITLINGGESAPTTLTQQTAVPPPTDLRFTNIGPDTMRVTW”

intron	105 . . . 1374

	/number = 1

exon	1375 . . . 1647

	/note = “ED-B exon”

	/number = 2

	/product = “fibronectin”

intron	1648 . . . 2757

	/number = 2

exon	2758 . . . 2823

	/number = 3

	/product = “fibronectin”

BASE COUNT	824 a 556 c 528 g 915 t

ORIGIN

1	ctgcactttt gataacctga gtcccggcct ggagtacaat gtcagtgttt acactgtcaa	(SEQ ID NO. 91)

61	ggatgacaag gaaagtgtcc ctatctctga taccatcatc ccaggtaata gaaaataagc

121	tgctatcctg agagtgacat tccaataaga gtggggatta gcatcttaat ccccagatgc

181	ttaagggtgt caactatatt tgggatttaa ttccgatctc ccagctgcac tttccaaaac

241	caagaagtca aagcagcgat ttggacaaaa tgcttgctgt taacactgct ttactgtctg

301	tgcttcactg ggatgctgtg tgttgcagcg agtatgtaat ggagtggcag ccatggcttt

361	aactctgtat tgtctgctca catggaagta tgactaaaac actgtcacgt gtctgtactc

421	agtactgata ggctcaaagt aatatggtaa atgcatccca tcagtacatt tctgcccgat

481	tttacaatcc atatcaattt ccaacagctg cctatttcat cttgcagttt caaatccttc

541	tttttgaaaa ttggatttta aaaaaaagtt aagtaaaagt cacaccttca gggttgttct

601	ttcttgtggc cttgaaagac aacattgcaa aggcctgtcc taaggatagg cttgtttgtc

661	cattgggtta taacataatg aaagcattgg acagatcgtg tccccctttg gactcttcag

721	tagaatgctt ttactaacgc taattacatg ttttgattat gaatgaacct aaaatagtgg

781	caatggcctt aacctaggcc tgtctttcct cagcctgaat gtgcttttga atggcacatt

841	tcacaccata cattcataat gcattagcgt tatggccatg atgttgtcat gagttttgta

901	tgggagaaaa aaaatcaatt tatcacccat ttattatttt ttccggttgt tcatgcaagc

961	ttattttcta ctaaaacagt tttggaatta ttaaaagcat tgctgatact taettcagat

1021	attatgtcta ggctctaaga atggtttcga catcctaaac agccatatga tttttaggaa

1081	tctgaacagt tcaaattgta ccctttaagg atgttttcaa aatgtaaaaa atatatatat

1141	atatatatat tccctaaaag aatattcctg tttattcttc tagggaagca aactgttcat

1201	gatgcttagg aagtcttttc agagaattta aaacagattg catattacca tcattgcttt

1261	aacattccac caattttact actagtaacc tgatatacac tgctttattt tttcctcttt

1321	ttttccctct attttccttt tgcctccccc tccctttgct ttgtaactca atagaggtgc

1381	cccaactcac tgacctaagc tttgttgata taaccgattc aagcatcggc ctgaggtgga

1441	ccccgctaaa ctcttccacc attattgggt accgcatcac agtagttgcg gcaggagaag

1501	gtatccctat ttttgaagat tttgtggact cctcagtagg atactacaca gtcacagggc

1561	tggagccggg cattgactat gatatcagcg ttatcactct cattaatggc ggcgagagtg

1621	cccctactac actgacacaa caaacgggtg aattttgaaa acttctgcgt ttgagacata

1681	gatggtgttg catgctgcca ccagttactc cggttaaata tggatgtttc atgggggaag

1741	tcagcaattg gccaaagatt cagataggtg gaattggggg gataaggaat caaatgcatc

1801	tgctaaactg attggagaaa aacacatgca atatcttcag tacactctca tttaaaccac

1861	aagtagatat aaagcctaga gaaatacaga tgtctgctct gttaaatata aaatagcaaa

1921	tgttcattca atttgaagac ctagaatttt tcttcttaaa taccaaacac gaataccaaa

1981	ttgcgtaagt accaattgat aagaatatat caccaaaatg taccatcatg ctcttccttc

2041	taccctttga taaactctac catgctcctt ctttgtagct aaaaacccat caaaatttag

2101	ggtagagtgg atgggcattg ttttgaggta ggagaaaagt aaacttggga ccattctagg

2161	ttttgttgct gtcactaggt aaagaaacac ctctttaacc acagtctggg gacaagcatg

2221	caacatttta aaggttctct gctgtgcatg ggaaaagaaa catgctgaga accaatttgc

2281	atgaacatgt tcacttgtaa gtagaattca ctgaatggaa ctgtagctct agatatctca

2341	catgggggga agtttaggac cctcttgtct ttttgtctgt gtgcatgtat ttctttgtaa

2401	agtactgcta tgtttctctt tgctgtgtgg caacttaagc ctcttcggcc tgggataaaa

2461	taatctgcag tggtattaat aatgtacata aagtcaacat atttgaaagt agattaaaat

2521	cttttttaaa tatatcaatg atggcaaaaa ggttaaaggg ggcctaacag tactgtgtgt

2581	agtgttttat ttttaacagt agtacactat aacttaaaat agacttagat tagactgttt

2641	gcatgattat gattctgttt cctttatgca tgaaatattg attttacctt tccagctact

2701	tcgttagctt taattttaaa atacattaac tgagtcttcc ttcttgttcg aaaccagctg

2761	ttcctcctcc cactgacctg cgattcacca acattggtcc agacaccatg cgtgtcacct

2821	ggg

//

Claims

1. A method of treating non-prostatic neoplastic disease comprising the step of immunizing a mammal to induce a cellular immune response directed against an antigen differentially expressed by tumor-associated neovasculature, wherein the immunization comprises delivering a therapeutic vaccine comprising at least one immunogen corresponding to an antigen expressed by tumor-associated neovasculature to a mammal having a non-prostatic neoplastic disease, wherein said antigen is prostate specific membrane antigen (PSMA).

2. The method of claim 1, further comprising the step of treating the mammal with an anti-tumor therapy active directly against cancerous cells.

3. The method of claim 2, wherein the anti-tumor therapy comprises immunization against a tumor-associated antigen.

4. The method of claim 1, wherein the cellular immune response comprises a CTL response.

5. The method of claim 1, further comprising the step of detecting the cellular immune response.

6. The method of claim 5, wherein the detecting step comprises detection of tumor growth inhibition, tumor size reduction, inhibition of tumor metastasis, or increase in life expectancy of the mammal.

7. The method of claim 5, wherein the detecting step comprises an assay selected from the group consisting of a cytokine assay, a chromium release assay, an immunofluorescence assay, a cytotoxic T lymphocyte (CTL) assay, an Elispot assay, and observation of the health of the mammal.

8. The method of claim 1 wherein the vaccine is a therapeutic nucleic acid vaccine.

9. The method of claim 8, wherein the immunogen comprises a nucleic acid capable of conferring expression of at least a portion of said antigen.

10. The method of claim 1 wherein the immunogen comprises a protein, or fragment thereof.

11. The method of claim 1 wherein the immunogen comprises or encodes at least one peptide derived from the sequence of said antigen.

12. The method of claim 11, wherein the at least one peptide comprises a housekeeping epitope.

13. The method of claim 12, wherein the at least one peptide is co-C-terminal with the housekeeping epitope.

14. The method of claim 13, further comprising at least one additional peptide wherein the at least one additional peptide comprises an immune epitope.

15. The method of claim 1 further comprising immunizing the mammal to induce a cellular immune response directed against a second antigen associated with a tumor wherein the immunization comprises delivering a therapeutic vaccine comprising at least a first immunogen corresponding to PSMA and a second immunogen corresponding to the second antigen to a mammal having a non-prostatic neoplastic disease.

16. A method of treating non-prostatic neoplastic disease comprising the steps of:

selecting a patient in need of treatment for a non-prostatic neoplastic disease; and

delivering to said patient a first means for inducing a cellular immune response directed against a first antigen which is differentially expressed by tumor associated neovasculature, wherein the antigen is prostate specific membrane antigen (PSMA).

17. The method of claim 16 further comprising delivering a second means for inducing a cellular immune response directed against a second antigen which is associated with a tumor.

18. The method of claim 16 wherein the first means induces a cellular immune response directed against at least one housekeeping epitope derived from said first antigen.

19. The method of claim 18 further comprising a second means for inducing a cellular immune response directed against said first antigen, where in the second means induces a cellular immune response directed against at least one immune epitope derived from said first antigen.

20. A therapeutic vaccine comprising a first immunogen corresponding to a first antigen differentially expressed by tumor-associated neovasculature and a second immunogen corresponding to a second antigen associated with a tumor, wherein the first antigen is prostate specific membrane antigen (PSMA), and wherein the vaccine can induce a cellular immune response.

21. The therapeutic vaccine of claim 20 comprising at least one housekeeping epitope derived from the antigen.

22. The therapeutic vaccine of claim 21 further comprising at least one immune epitope derived from the antigen.

23. A therapeutic nucleic acid vaccine comprising a means for inducing a cellular immune response directed against an antigen differentially expressed by tumor associated neovasculature, wherein the antigen is prostate specific membrane antigen (PSMA), and wherein the vaccine can induce a cellular immune response, and a pharmaceutically acceptable buffer.