CA2560972A1 - Proteomic analysis of biological fluids - Google Patents

Abstract

The invention concerns the identification of proteomes of biological fluids and their use in determining the state of maternal/fetal conditions, including maternal conditions of fetal origin, chromosomal aneuploidies, and fetal diseases associated with fetal growth and maturation. In particular, the invention concerns the identification of the proteome of amniotic fluid (multiple proteins representing the composition of amniotic fluid) and the correlation of characteristic changes in the normal, proteome with various pathologic maternal/fetal conditions, such as intra-amniotic infection, or chromosomal defects.

Description

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PROTEOMIC ANALYSIS OF BIOLOGICAL FLUIDS
Background of the Invention Field of the Invention The invention concerns the identification of proteomes of biological fluids and their use in determining the state of maternallfetal conditions, including maternal conditions of fetal origin, chromosomal aneuploidies, and fetal diseases associated with fetal growth and maturation. In particular, the invention concerns the identification of the proteome of amniotic fluid (multiple proteins representing the composition of amniotic fluid) and the correlation of characteristic changes in the normal proteome with various pathologic maternallfetal conditions, such as infra-amniotic infection, or chromosomal defects.
Description of the Related Art PYOteomics The large-scale analysis of protein expression patterns is emerging as an important and necessary complement to current DNA cloning and gene profiling approaches (Pandey and Mann, Natur°e 405:537-46 (2000)). DNA sequence information is helpful in deducing some structural and potential protein modifications based on homology methods, but it does not provide information on regulation of protein function through post-translational modifications, proteolysis or compartmentalization.
Traditional gel-based methods, such as one- and two-dimensional gel electrophoresis are useful for small-scale protein detection (<1,000 proteins), but these require large sample quantity (Lilley KS, Razzaq A, Dupree P: Two-dimensional gel electrophoresis:
recent advances in sample preparation, detection and quantitation. Curr Opin Chem Biol. 6(1):46-50, 2002). Approaches to overcome this limitation include matrix-assisted or surface-enhanced laser desorption/ionization (MALDI or SELDI) time-of-flight mass spectrometers that accurately generate profiles showing the masses of proteins in a sample. These patterns or profiles can be used to identify and monitor various diseases. The second level of identification comes from coupling peptide mapping to tandem mass spectrometry to generate amino acid sequence information from peptide fragments. This can, for example, be achieved by coupling the MALDI/SELDI or ESI to quadrupole time- of flight MS (Qq-TOF
MS). The latter method can also be used for quantification of specific peptides (ICAT
technology).
Diayzosis ofPatholo.~ic Mate~nallFetal CohditioNs There are numerous pathologic maternal and fetal conditions, such as infra-amniotic infection (IAI), preeclampsia, preterm delivery and labor, and chromosomal aneuploidies, that may develop during pregnancy and compromise the well-being or, in some instances, threaten the life of the mother and/or the fetus or newborn. Early diagnosis of such conditions is critical to allow timely treatment and intervention. Unfortunately, early diagnosis for most of these conditions is difficult because the clinical signs and symptoms occur late, and are often non-specific and inconsistent. For example, the clinical symptoms of IAI
typically include maternal fever and leukocytosis, but these symptoms often occur later and are neither sensitive nor specific. Thus, Gravett et al., Am. J. Obstet. Gynecol. 171:1660-7 (1994), utilizing a non-human primate model, demonstrated that following experimental intra-amniotic infection with Group B streptococcus, fever and leukocytosis are present only 50%
of the time at the onset of infection-induced preterm labor, which occurs 28 to 40 hours after experimental infection. Therefore, to avoid a delay in diagnosis, a high index of suspicion and the appropriate use of adjunctive laboratory tests, are warranted. The clinical criteria commonly used t~ diagnose IAI include maternal fever (> 37.8°C), along with two or more of the following: maternal leukocytosis (>15,000 /mm3), maternal or fetal tachycardia, uterine tenderness, or foul-smelling amniotic fluid.
Because of the inconsistency of clinical features, other adjunctive laboratory tests have been utilized to aid in the diagnosis of IAI. These include: measurement of maternal C
reactive protein, direct examination of amniotic fluid for leukocytes or bacteria on Gram stain, amniotic fluid culture, measurement of amniotic fluid glucose concentrations, detection of amniotic fluid leukocyte esterase, detection of bacterial organic acids by gas-liquid chromatography, measurements of various amniotic fluid or vaginal cytokines (e.g., interleukins 2, 4, 6, granulocyte colony-stimulating factor, and tumor necrosis factor-a), matrix metalloproteinase-9, lactoferrin, and assessment of fetal activity (biophysical profile) by ultrasonography. Measurement of cytokines or other biochemical factors is expensive, generally not clinically available, and is primarily a research tool. Further, the testing efficiency of these tests has not been consistently better than more readily available traditional tests such as armliotic fluid Gram stain and culture, amniotic fluid glucose concentrations, and detection of amniotic fluid leukocyte esterase. The efficiency of these tests has been previously extensively reviewed. (Ohlsson,A. and Wang,E.: An analysis of antenatal tests to detect infection at preterm rupture of the membranes.
American .Iournal of Obstetrics and Gynecology 162:809, 1990). Although all have reasonable sensitivity, specificity, and predictive value none are sufficiently sensitive or specific to be utilized independently of clinical features in the diagnosis of IAI.
Accordingly, there is a great need for new approaches that allow early and accurate diagnosis of IAI and other pathologic maternal/fetal conditions.
It is particularly desirable to develop new, efficient and reliable non-invasive methods for the diagnosis of chromosomal aneuploidies. At present the definitive diagnosis of chromosomal aneuploidies following maternal serum screening and ultrasound requires a mid-trimester genetic amniocentesis. This is an invasive procedure associated with a 0.5%
risk of loss of the pregnancy. Further, chromosomal analysis of amniotic fluid cells is a labor-intensive and time-consuming procedure, taking up to 2 weeks. Reliable tests are therefore necessary to improve the detection of chromosomal aneuploidies from maternal serum, or other biological fluids, reduce the unacceptably high false positive rate of maternal screening, and increase the speed and efficiency of diagnosis from airmiotic fluid following amniocentesis. ~ther patahologic aneuploidic conditions, such as Klinefelter syndrome and Turner syndrome, may be entirely missed by screening with ultrasonography or conventional maternal serum screening.
Summary of the Invention The present invention provides non-invasive and sensitive methods for the early diagnosis, prognosis, and monitoring of pathologic fetal/maternal conditions, by proteomic analysis of biological fluids.
The present invention further provides proteomic profiles of biological fluids, such as amniotic fluid and maternal serum, which enable the diagnosis, prognosis, and monitoring of various pathologic fetal/maternal conditions, including, without limitation, intra-amniotic infection (IAI), chromosomal aneuploidies, and fetal diseases associated with fetal growth and maturation. In particular, the present invention provides normal and pathologic proteomic profiles for IAI and chromosomal aneuploidies. The determination of the normal proteomic profile is of great importance, since it enables the elimination of the fetal/maternal condition in question (negative diagnosis), which eliminates the need to subject the patient to unnecessary and potentially dangerous treatment or intervention.
The present invention further provides specific biomarkers for the presence and state of various fetal or maternal conditions, such as IAI and chromosomal aneuploidies, which are differentially expressed in biological fluids, such as amniotic fluid or maternal serum, when such pathologic conditions are present. Such biomaxkers and antibodies binding to such biomarkers, which may, for example, be presented on protein or antibody arrays, find utility in simple, non-invasive diagnostic assays.
In one aspect, the invention concerns a method for determining the state of a maternal or fetal condition, comprising comparing the proteomic profile of a test sample of a biological fluid obtained from a mammalian subject with the proteomic profile of a normal sample, or a reference proteomic profile comprising at least one unique expression signature characteristic of such condition.
In an embodiment of this method, the mammalian subject is a pregnant female, preferably primate or human.
In another embodiment, the maternal condition is selected from the group consisting of intrauterine infection, preeclampsia, and preteen labor.
In a further embodiment, the fetal condition is selected from the group consisting of chromosomal aneuploidies, congenital malformation, gestational age and fetal maturity, where the chromosomal aneuploidy can, for example, be I?own syndrome, trisomy-13, trisomy-18, Turner syndrome, or I~linefelter syndrome.
Any biological fluid can be used in performing the method of the invention, including, without limitation, amniotic fluid, serum, plasma, urine, cerebrospinal fluid, breast milk mucus, and saliva, preferably, amniotic fluid or maternal serum.
In a further embodiment, the proteomic profile of the test sample comprises information of at least 2 proteins or at least 5 proteins, or at least 10 proteins, .or at least 20 proteins, or at least 50 proteins.
In a specific embodiment, the proteomic profile is a mass spectrum.
In another embodiment, the mass spectrum comprises at least one unique expression signature in the 3 to 5 kl~a range of the mass spectrum.
In yet another embodiment, the mass spectrum comprises at least one unique expression signature in the 10 to 12 kDa range of the mass spectrum.
In a further embodiment, the maternal condition is infra-amniotic infection, and the unique expression signature is an extra peak in the 10 to 11 kDa molecular weight range in the test sample, which is indicative of infra-amniotic infection.
In a different embodiment, the proteomic profile is produced by Western blot analysis.
In another embodiment, the biological fluid is that of a human, and the proteomic profile includes information of the expression of one or more of the proteins selected from the group consisting of macrophage capping protein, neutrophil gelatinise-associated lipocalin, myeloperoxidase; L-plastin; azurocidin; antibacterial protein FALL-39; Gp340 variant protein; Ebner salivary gland protein homologous (GenBank Accession No.
355392);
leukocyte elastase inhibitor; calgranulin A; calgranulin B; cofilin; moesin;
profilin I, cronin-like protein p57; annexin II, fibronectin; glia-derived nexin; antithrombin-III; squamous cell carcinoma antigen 1, squamous cell carcinoma antigen 2; serpin 12; cystatin A;
cystatin B;
cystatin C; IGFBP-1; Vitamin D-binding protein; apolipoprotein A-I; 14-3-3 protein sigma;
14-3-3 protein zetaldelta; gelsolin; lactotransferrin; phosphoglycerate kinase 1;
phosphoglycerate mutase 1; and transketolase; or a fragment, precursor, or naturally occurring variant thereof.
In a further embodiment, the proteomic profile includes information of the expression of one or more of the proteins selected from the group consisting of macrophage capping protein; neutrophil gelatinise-associated lipocalin; myeloperoxidase; L-plastin; azurocidin;
antibacterial protein FALL-39; leukocyte elastase inhibitor; calgranulin A;
calgranulin B;
profilin I, glia-derived nexin; serpin 12; cystatin A; and IGFBP-1; or a fragment, precursor, or naturally occurring variant thereof.
The foregoing method is suitable for the diagnosis of various fetal and maternal conditions, including, without limitation, intra-amniotic infection, developmental defects, including defects of an organ system, musculoskeletal deformities, and conditions resulting from chromosomal aneuploidies, such as Down syndrome, trisomy-13, trisomy-18, Turner syndrome, or I~linefelter syndrome.
If the proteomic profile of the test sample is essentially the aims as the proteomic profile of the nornal sample, the subject is determined to be free of the maternal or fetal condition.
If the proteomic profile contains essentially the same unique expression signature as a diseased sample, the patient is diagnosed with the corresponding materal or fetal condition.
In another aspect, the invention concerns a method for the diagnosis of intra-amniotic infection, comprising (a) comparing the proteomic profile of a test sample of a biological fluid obtained from a pregnant female mammal with the proteomic profile of a normal sample, or a reference proteomic profile, wherein the proteomic profiles provide information of the mass of the proteins present in the samples, or the proteolytic fragments thereof;
and (b) diagnosing the mammal with infra-amniotic infection if the proteomic profile of the test sample shows a unique expression signature in the 3-5 and/or 10-12 KDa molecular weight range.
In a further aspect, the invention concerns a method for the diagnosis of infra-amniotic infection, comprising:
(a) comparing the proteomic profile of a test sample of a biological fluid obtained from a pregnant female mammal with the proteomic profile of a normal sample;
and (b) diagnosing the mammal with infra-amniotic infection if at least one protein selected from the group consisting of IGFB-1, profilin, ceruloplasmin, L-plastin, and calgraulin, or a fragment, precursor or naturally occurring variant thereof, is differentially expressed in the test sample relative to the normal sample.
In a particular embodiment, at least one of IGFBP-1, profilin, ceruloplasmin, and calgranulin, or a fragment, precursor, or naturally-occurring variant thereof, is overexpressed in the test sample relative to the normal sample.
In another embodiment, L-plastin is underexpressed in the test sample relative to the normal sample.
In yet another embodiment, the presence of IGFBP-1 is detected by identifying the proteolytic fragment shown in Figure 12, or a fragment thereof.
In another aspect, the invention concerns a method for the diagnosis of a chromosomal aneuploidy, comprising:
(a) comparing the proteomic profile of a test sample of a biological fluid obtained from a pregnant female mammal with the proteomic profile of a normal sample, or a reference proteomic profile, wherein the proteomic profiles provide information of the mass of the proteins present in the samples, or the proteolytic fragments thereof;
and (b) diagnosing the mammal with the chromosomal aneuploidy if the proteomic profile of the test sample shows a unique expression signature in the 4 to 15 Ira molecular weight range.
In a different aspect, the invention concerns a method for the diagnosis of a developmental defect of a fetus, comprising:
(a) comparing the proteomic profile of a test sample of a biological fluid obtained from a pregnant female mammal with the proteomic profile of a normal sample, or a reference proteomic profile; and (b) confirming the presence of the developmental defect if at least one actin-modulating protein, or a fragment, precursor, or naturally occurnng variant thereof, is differentially expressed in the test sample relative to the normal sample.
In a particular embodiment of this method, the actin-modulating protein is selected from the group consisting of moesin, p57, gelsolin, and a 14-3-3 protein.
In a further aspect, the invention concerns a method for the diagnosis of a maternal or fetal infection or immune-response related disorder, comprising (a) comparing the proteomic profile of a test sample of a biological fluid obtained from a pregnant female marmnal with the proteomic profile of a normal sample, or a reference proteomic profile; and (b) confirming the presence of the maternal or fetal infection or immune-response related disorder, if at least one protein selected from the group consisting of macrophage capping protein (MCP), leukocyte elastase, neutrophil gelatinase-associated lipcalcin (NGAL), myeloperoxidase, L-plastin, calgranulin, FALL-39, azyrocidin (CAP37), proteases and protease inhibitors, is differentially expressed in the test sample relative to the normal sample.
In a still further aspect, the invention concerns a method for the diagnosis of neonatal sepsis, comprising detecting in the proteomic profile of a biological fluid obtained from a pregnant females mammal the presence of Gp-340.
In yet another aspect, the invention concerns a proteomic profile of a biological fluid comprising information of one or more proteins selected from the group consisting of macrophage capping protein, neutrophil gelatinase-associated lipocalin, myeloperoxidase; L-plastin; azurocidin; antibacterial protein FALL-39; Gp340 variant protein;
Ebner salivary gland protein homologous (GenBank Accession IVo. 355392); leukocyte elastase inhibitor;
calgranulin A; calgranulin B; cofilin; moesin; profilin I, cronin-like protein p57; annexin II, fibronectin; glia-derived nexin; antithrombin-III; squamous cell carcinoma antigen 1, squamous cell carcinoma antigen 2; serpin 12; cystatin A; cystatin B; cystatin C; IGFBP-1;
Vitamin D-binding protein; apolipoprotein A-I; 14-3-3 protein sigma; 14-3-3 protein zeta/delta; gelsolin; lactotransferrin; phosphoglycerate kinase 1;
phosphoglycerate mutase 1;
and transketolase; or a fragment, precursor, or naturally occurring variant thereof.
In a further aspect, the invention concerns a proteomic profile of a biological fluid comprising information of one or more proteins selected from the group consisting of macrophage capping protein; neutrophil gelatinase-associated lipocalin;
myeloperoxidase; L-plastin; azurocidin; antibacterial protein FALL-39; leukocyte elastase inhibitor; calgranulin A; calgranulin B; profilin I, glia-derived nexin; serpin 12; cystatin A; and IGFBP-1; or a fragment, precursor, or naturally occurring variant thereof.
The invention further concerns a proteomic profile of a biological fluid characteristic of intra-amniotic infection, comprising information confirming the presence of a protein selected from the group consisting of IGFB-1, profilin, ceruloplasmin, L-plastin, and r calgraulin.
In another aspect, the invention concerns a proteomic profile of a biological fluid characteristic of intra-amniotic infection represented in a form providing information of the molecular weight of proteins present in the biological fluid, or the proteolytic fragments thereof, comprising a unique expression signature in the 3-5 KDa and/or 10-12 KDa molecular weight range.
In a further aspect, the invention concerns the proteomic profile essentially as shown in any one of Figures lA-1C, or essentially as shown in any one of Figures 2A-C, or essentially as shown in any one of Figures 3A-C, or essentially as shown in Figure 4A or 4B, or essentially as shown in any one of Figures 6-10.
In a particular embodiment, the proteomic profile is analyzed in a microarray format.
Brief Description of the Drawings Figures IA-C. Infection-induced differefatial pYOtein expnessi~n in tlae pnimate am fai~ti~ fluid. SELDI-TOF analysis of amniotic fluid extracts bound to chemically defined I~Tormal Phase chip arrays. A). Whole spectrum collected at 235 laser intensity showing the differences in the peak intensities. B) Detailed spectrum showing the differences approximately in the 10 to 12 KDa region between control and infected. C) Detailed spectrum showing the differences approximately in the 3-5 I~Da region between control and infected.
Solid lines were used to show the significant differences in expression (unique expression signatures) which could be used to develop diagnostic tests.
Figuy~es 2A-C. Time course analyses of the pYimate amniotic fluid in ~espofase to infection (GBS). Amniotic fluid was collected before the inoculation of bacteria and serially after infection and subjected to SELDI-TOF analysis as described below. Figure 2 A: before infection; 2B: 12 hours after infection; 2C: 36 hours after infection.
Figures 3A-C. Infection-induced differential pYOteifa expression in tlae hunaan amniotic fluid. SELDI-TOF analysis of amniotic fluid extracts bound to chemically defined Normal Phase chip arrays. A). Whole spectrum collected at 235 laser intensity showing the differences in the peak intensities. B) Detailed spectrum showing the differences in the 10 to 12 KDa region between control and infected. C) Detailed spectrum showing the differences in the 3-5 I~Da region between control and infected.
Figures 4A and 4B. Mass spectra acquired on a generic MALDI TOF mass spectrometer, using amniotic fluid from human A) control, without intrauterine infection and B) sample, with intrauterine infection.
Figure S. SDS-PAGE Coontassie Blue stained gel. A) 4 human control AF samples pooled; B) individual control AF sample; C) 4 human infected AF samples pooled; D) individual infected AF sample.
Figure 6. Detection of differential proteirt expression in the humayt amniotic fluid. A) Control AF sample (pooled); B) Infected AF sample (pooled).
Figure 7. Detection of differential protein expression in the human amniotic fluid. A) Control AF sample (pooled); B) Infected AF sample (pooled) Figure ~ shows the detection of differential protein expression in t7te hunaatt amniotic fluid attd maternal serum. A) control sample (pooled); B) infected sample (pooled).
Figure 9 shows the detection of differentially ~xp3"~ss~d pr~t~Zn,S Z3Z
n2atr?rflal serum a~sirtg pr~otcin arrays. 1) pseudocolor image of the protein array showing the binding of corresponding proteins with their antibodies; 2) enlarged area of the array;
3) Western blot of calgranulin IP.
Figure 10 shows differential protein expression patterns in th.c naaterttal serum with a~nique profiles to distinguish trisonties.
Figure 1l. Schematic representation of de nova protein sequence identification of amniotic fluid proteins. PRO1 HUMAN (P07737) Profilin I (SEQ ID NOs: 5-11).
Figure 12. IGFBP-1 de nova protein. identification and proteolytic fragment sequence (SEQ ID NO: 1). The peptide sequences found in samples 0426se H1_12 and 0425se H1_13 with the Ms/1VIS are shown in lower case (SEQ ~ NOs: 2 and 3).
These came from infected amniotic fluid when run on 1-D gel bands that were trypsin digested and subjected to MS/MS analysis. The proteolytic fragment of IGF-BP-1 detected in 1-D gels (low molecular weight range, Figure 5), Western blots (Figure 6) and MS/MS
analysis (Figure 13) of trypsin-digested 10.5 to 12 KDa band from infected amniotic fluid is represented in the region of the underlined sequence (SEQ ID NO: 4).

Figure 13. LCQ-MS profile of trypsira digestion of 10.5-Il kD ID gel band f born infected amniotic fluid. LCQ-MS showing parent ions representing potential proteins present in the sample.
Figure 14. Mass spectrum for the 17.55-18.21 minute retention tune peak drown in Figure 13.
Figure I5. MSlMS spectrum for the parent ion of the 434.9 peak shown in Figure 14.
Figure 16. Irnrnunodetection of biomarkers for IAI. 16a) Primate control (-) and infected (+) AF. 16b) Human control (-) and infected (+) AF. 16c) Human control (-) and infected (+) AF. Vitamin D binding protein (VDBP) unregulated control marker.

bands represent the intact protein (~30kDa) and proteolytic fragment (~11 kDa). 16d) Detection of IGFBP1 in pooled maternal serum from immunoprecitates. Control (-) and infected (+) serum. 16e) Detection of calgranulin B in pooled maternal serum from immunoprecitates. Control (-) and infected (+) serum.
Detailed Description of the Preferred Embodiment A. Definitions IJnlcss defined otherevise, technical and scientific ternls used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Singleton et al., Dictionary of Microbiology and Molecular Biology 2nd ed., J.
Wiley ~. Sons (~Tew fork, 19940 provides one skilled in the ark with a general guide to many of the terms used in the present application.
The term "proteome" is used herein to describe a significant portion of proteins in a biological sample at a given time. The concept of proteome is fundamentally different from the genome. While the genome is virtually static, the proteome continually changes in response to internal and external events.
The term "proteomic profile" is used to refer to a representation of the expression pattern of a plurality of proteins in a biological sample, e.g. a biological fluid at a given time.
The proteomic profile can, for example, be represented as a mass spectrum, but other representations based on any physicochemical or biochemical properties of the proteins are also included. Thus the proteomic profile may, for example, be based on differences in the electrophoretic properties of proteins, as determined by two-dimensional gel electrophoresis, e.g. by 2-D PAGE, and can be represented, e.g. as a plurality of spots in a two-dimensional electrophoresis gel. Differential expression profiles may have important diagnostic value, even in the absence of specifically identified proteins. Single protein spots can then be detected, for example, by immunoblotting, multiple spots or proteins using protein microarrays. The proteomic profile typically represents or contains information that could range from a few peaks to a complex profile representing 50 or more peaks.
Thus, for example, the proteomic profile may contain or represent at least 2, or at least 5 or at least 10 or at least 15, or at least 20, or at least 25, or at least 30, or at least 35, or at least 40, or at least 45, or at least 50 proteins.
The term "pathologic condition" is used in the broadest sense and covers all changes and phenomena that compromise the well-being of a subject. Pathologic maternal conditions include, without limitation, infra-amniotic infection, conditions of fetal or maternal origin, such as, for example preeclampsia, and preterm labor and delivery. Pathologic fetal conditions include, without limitation, chromosomal defects (aneuploidies), such as Down syndrome, and all abnormalities in gestational age and fetal maturity.
The term "state of a pathologic [maternal or fetal] condition" is used herein in the broadest sense and refers to the absence, presence, extent, stage, nature, progression or regression of the pathologic condition.
The term "unique expression signature" is used to describe a unique feature or motif within the proteomic profile of a biological sample (e.g. a reference sample) that differs from the proteomic profile of a corresponding normal biological sample (obtained from the same type of source, e.g. biological fluid) in a statistically significant mamler.
The terms "mfrs-amniotic infection (It~l','9 6Ga~iotic fluid infection,"
"amnionitis,"
and "clinical chorioamnionitis" are used interchangeably, and refer to an acute infection, including, but not restricted to bacterial, of the amniotic fluid and intrauterine contents during pregnancy.
"Patient response" can be assessed using any endpoint indicating a benefit to the patient, including, without limitation, (1) inhibition, at least to some extent, of the progression of a pathologic condition, (2) prevention of the pathologic condition, (3) relief, at least to some extent, of one or more symptoms associated with the pathologic condition;
(4) increase in the length of survival following treatment; and/or (5) decreased mortality at a given point of time following treatment.
The term "treatment" refers to both therapeutic treatment and prophylactic or preventative measures, wherein the object is to prevent or slow down (lessen) the targeted pathologic condition or disorder. Those in need of treatment include those already with the disorder as well as those prone to have the disorder or those in whom the disorder is to be prevented.
"Congenital malformation" is an abnormality which is non-hereditary but which exists at birth.
B. Detailed Description The present invention concerns methods and means for an early, reliable and non invasive testing of maternal and fetal conditions based upon the proteomic profile of a biological fluid of the mother or fetus. The invention utilizes proteomics techniques well known in the art, as described, for example, in the following textbooks, the contents of which are hereby expressly incorporated by reference: Proteome Research: New Frontiers in Functional Genomics (Principles and Practice), M.R. Wilkins et al., eds., Springer Verlag, 1007; 2-D Proteome Analysis Protocols, Andrew L Link, editor, Humana Press, 1999;
Proteome Research: Two-Dimensional Gel Electrophoresis and Identification Methods (Principles and Practice), T. Rabilloud editor, Springer Verlag, 2000;
Proteome Research:
Mass Spectrometry (Principles and Practice), P. James editor, Springer Verlag, 2001;
Introduction to Proteomics, D. C. Liebler editor, Humana Press, 2002;
Proteomics in Practice:
A Laboratory Manual of Proteome Analysis, R. Westermeier et al., eds., John Wiley ~ Sons, 2002.
~ne skilled in the art will recognize many methods and materials similar or equivalent to those described herein, which could be used in the practice of the present invention.
Indeed, the present invention is in no way limited to the methods and materials described.
1. IdefZti acatiof2 ~f Proteins ayad Polypeptides Expressed ira Piologieal Fluids According to the present invention, proteomics analysis of biological fluids can be performed using a variety of methods known in the art.
Typically, protein patterns (proteome maps) of samples from different sources, such as normal biological fluid (normal sample) and a test biological fluid (test sample), are compared to detect proteins that are up- or down-regulated in a disease. These proteins can then be excised for identification and full characterization, e.g. using peptide-mass fingerprinting and/or mass spectrometry and sequencing methods, or the normal and/or disease-specific proteome map can be used directly far the diagnosis of the disease of interest, or to confirm the presence or absence of the disease.

In comparative analysis, it is important to treat the normal and test samples exactly the same way, in order to correctly represent the relative abundance of proteins, and obtain accurate results. The required amount of total proteins will depend on the analytical technique used, and can be readily determined by one skilled in the art. The proteins present in the biological samples are typically separated by two-dimensional gel electrophoresis (2-DE) according to their pI and molecular weight. The proteins are first separated by their charge using isoelectric focusing (one-dimensional gel electrophoresis). This step can, for example, be carried out using immobilized pH-gradient (IPG) strips, which are commercially available. The second dimension is a normal SDS-PAGE analysis, where the focused IPG
strip is used as the sample. After 2-DE separation, proteins can be visualized with conventional dyes, like Coomassie Blue or silver staining, and imaged using known techniques and equipment, such as, e.g. Bio-Rad GS800 densitometer and PDQUEST
software, both of which are commercially available. Individual spots are then cut from the gel, destained, and subjected to tryptic digestion. The peptide mixtures can be analyzed by mass spectrometry (MS). Alternatively, the peptides can be separated, for example by capillary high pressure liquid chromatography (IiPLC) and can be analyzed by MS either individually, or in pools.
Mass spectrometers consist of an ion source, mass analyzer, ion detector, and data, acquisition unit. First, the peptides are ionized in the ion source. Then the ionized peptides are separated according to their mass-to-charge ratio in the mass analyzer and the separate ions are detected. Mass spectrometry has been widely used in protein analysis, especially since the invention of matrix-assisted laser-desorption ionisation/time-of flight (MALDI-T~F) and electrospray ionisation (EST) methods. There are several versions of mass analyzer, including, for example, MALDI-T~F and triple or quadrupole-T~F, or ion trap mass analyzer coupled to ESI. Thus, for example, a Q-Tof 2 mass spectrometer utilizes an orthogonal time-of flight analyzer that allows the simultaneous detection of ions across the full mass spectrum range.
For further details see, e.g. Chemusevich et al., J. Mass Spectrom. 36:849-865 (2001).
If desired, the amino acid sequences of the peptide fragments and eventually the proteins from which they derived can be determined by techniques known in the art, such as certain variations of mass spectrometry, or Edman degradation.
2. Fetal-Maternal ConditiofZS Bene atih~ fYOjn Early and Noh Ih.vasive Dia~hosis a. Intra-amniotic infection Infra-amniotic infection (IAI) is an acute bacterial infection of the amniotic fluid and intrauterine contents during pregnancy. Prospective studies indicate that IAI
occurs in 4% to 10% of all deliveries (Newton, E.R., Prihoda, T.J., and Gibbs, R.S.: Logistic regression analysis of risk factors for infra-amniotic infection. Obstet. Gynecol.
73:571, 1989; Soper, D.E., Mayhall, C.G., and Dalton, H.P.: Risk factors for intraamniotic infection: a prospective epidemicologic study. American Journal of Obstetrics and Gynecology 161:562, 1989; and Lopez-Zeno, J.A., Peaceman, A.M., Adashek, J.A., and Socol, M.L.: A controlled trial of a program for the active management of labor. N .Engl .J Med. 326:450, 1992).
Other terms used to describe IAI include amniotic fluid infection, amnionitis, and clinical chorioamnioutis. W tra-armiotic infection is clinically diagnosed by maternal fever, uterine tenderness, leukocytosis, and fetal tachycardia and should be distinguished from histologic chorioamnionitis. Infra-amniotic infection is an important cause of maternal and neonatal morbidity. Infra-amniotic infection accounts for 10-40% of cases of febrile morbidity in the peripartum period and is associated with 20-40% of cases of early neonatal sepsis and pneumonia (Newton, E.R.: Chorioamnionitis and intraamniotic infection.
Clin.Obstet.Gynecol. 36:795, 1993). Maternal bacteremia occurs in 2-6% of patients with IAI and postpartum infectious morbidity is increased. There is also an increased risk of dysfunctional labor and cesarean delivery among patients vaith IAI. Duff et al. reported a 75% incidence of dysfunctional labor and a 34% incidence of cesarean delivery among patients who developed infra-amniotic infection while in labor (Duff, P., Sanders, R., and Gibbs, R.S.: The course of labor in term pregnancies with chorioamnionitis.
Anaef~ieafa Journal of Obsteta~ics and Gynecology 147:391, 1983). Infra-amniotic infection is also associated with increased neonatal morbidity and mortality, particularly among preterm neonates. W general, there is a three to four-fold increase in perinatal mortality among low birth weight neonates born to mothers with IAI (Gibbs, R.S., Castillo, M.A., and Rodgers, P.J.: Management of acute chorioamnionitis. Arney°ican Jouf°nal of Obstetrics and Gynaecology 136:709, 1980; Gilstrap, L.C., III, Leveno, K.J., Cox, S.M., Burns, J.S., Mashburn, M., and Rosenfeld, C.R.: Intrapartum treatment of acute chorioamnionitis: impact i on neonatal sepsis. Ann. J .Obstet. Gynecol. 159:579, 1988). There are also increases in respiratory distress syndrome, intraventricular hemorrhage, and neonatal sepsis Morales, W.J.: The effect of chorioamnionitis on the developmental outcome of preterm infants at one year. Obstetrics and Gynaecology 70:183, 1987). Recently, IAI has been implicated in neonatal periventricular leukomalacia and cerebral palsy; the risks of cerebral white matter damage and cerebral palsy are nine-fold greater in the setting of infra-amniotic infection Bejar, R., Wozniak, P., Allard, M., Benirschke, K., Vaucher, Y., Coen, R., Berry, C., Schragg, P., Villegas, L, and Resnik, R.: Antenatal origin of neurologic damage in newborn infants. I. Preterm infants. Am. J.Obstet .Gynecol. 159:357, 1988; Grether ,J
.K. and Nelson, K. B.: Maternal infection and cerebral palsy in infants of normal birth weight. JAMA
278:207, 1997). Finally, subclinical IAI has been found in at least 10% of women in preterm labor with intact fetal membranes, suggesting that IAI is an important, and potentially preventable, cause of prematurity (Romero, R., Avila, C., Brekus, C.A., and Morotti, R.: The role of systemic and intrauterine infection in preterm parturition. Annuals of the New Yoy~k Academy of Sciences 622:355, 1991). A literature review by Newton demonstrated incidences of clinical IAI of 41% at gestational ages less than 27 weeks, 15%
at gestational ages of 27-37 weeks, and 2% at gestations of 38 weeks or greater (Newton et al., supra).
Bacteria indigenous to the lower genital tract have also been recovered from the armiiotic fluid of 10-20% of all women in preterm labor with intact fetal membranes without clinical signs of intraarmliotic infection (Romero et czl., supf~a), and in up to 67%
of women in preterm labor with pregnancies ending at 23-24 weeks (Watts, D. H., Krohn, M. A., Hillier, S. L., and Eschenbach, D. A.: The association of occult amniotic fluid infection with gestational age and neonatal outcome among women in pretenn labor. ~bstet Gyn.ec~l 79:351, 1992).
Lost of these patients deliver rapidly, and clinically apparent IAI develops in many.
These observations support the hypothesis that ascending, initially subclinical intrauterine infections precede preterm labor and may be an important cause of extreme preterm deliveries.
b. Preeclam s~'ia Preeclampsia, defined as maternal hypertension accompanied by proteinuria, edema, or both, occurs in 7% of pregnancies not terminating in the first trimester.
Although the cause is unknown, it is more common in extremes of age in childbearing, maternal diabetes, pregnancies with multiple gestations, and pre-existing maternal renal disease and or hypertension. Preeclampsia is associated with increases in perinatal mortality, and may also lead to eclampsia, characterized by maternal seizures and increased maternal mortality.
Currently the mainstay of therapy for preeclampsia is delivery and anticonvulsant prophylaxis with magnesium sulfate. Prior to the advent of magnesium sulfate therapy, the observed maternal mortality was 20-30%. However, with prompt diagnosis, allowing anticonvulsant therapy with magnesium sulfate, anti-hypertensives, and delivery the maternal mortality has been reduced to near zero.

Unfortunately, the diagnosis of preeclampsia based upon commonly recognized symptoms and signs is frequently difficult, and occurs late in the course of the disease.
Frequently fetal compromise in growth or well-being is the first recognized manifestation of preeclampsia. Laboratory markers for preeclampsia include quantitation of proteinuria, and elevated serum concentrations of uric acid or creatinine. There are no currently available serum markers for early preeclampsia or markers which identify women which will develop preeclampsia. Recently prospective serum markers including leptin and uric acid have been associated with subsequent preeclampsia in one study (Gursoy T, et al.
Preeclampsia disrupts the normal physiology of leptin.: Am J Perinatol.l9(6):303-10, 2002) but much work is needed to confirm these findings. Development of early and reliable markers for preeclampsia is imperative to allow for therapy and intervention to optimize the outcome for the neonate and mother.
c. Preterm Labor and Delivery Preterm delivery is defined as birth prior to the 37th completed week of gestation. The incidence of preterm birth in the United States is 10-11% of all live births, and is increasing despite aggressive treatment of preterm labor. ~verall, prematurity and its consequences are responsible for 80°/~ of perinatal deaths not attributable to congenital malformations and add approximately ~5 billion annually to the national health care budget. Risk factors for preterm birth include non-white race, young age, low socioeconomic status, maternal weight below 55 kg, nulliparity, 1St trimester bleeding, multiple gestations (Meis PJ, Michielutte R, Peters TJ, et al. Factors associated with pretemn birth in Cardiff, Vales: II. Indicated and spontaneous preterm birth. ~lrn J ~bstet (Jyraec~l 173:597-602, 1995) Unfortunately the prediction of patients at risk for spontaneous preterm birth has been generally disappointing (Greasy RIB, Iams JD. Preterm labor and delivery. In Maternal-Fetal Medicine, Greasy RK, Resnik R (eds.). W.B. Saunders Company, Philadelphia, PA
4tt' edition, 1999. Pages 498-531). Previous attempts at defining the population at greatest risk for preterm birth, and thereby potentially benefiting from early intervention have included risk-scoring indices, biochemical detection of cervical fetal fibronectin, ultrasound measurement of cervical length, and home uterine activity monitoring. These programs have been both costly, and, have been hampered by the inability to predict with accuracy which patients might benefit from early intervention or prophylaxis. All suffer from poor positive predictive value of approximately 30%, with the majority of patients identified as "at risk"
delivering at term. Interventions, including pharmacologic treatment to inhibit uterine contractions, are efficacious, but depend upon the early and reliable diagnosis of preterm labor. Early and reliable markers to identify patients at greatest risk for preterm birth are therefore necessary to reduce the tremendous costs and neonatal mortality and morbidity associated with preterm birth.
d. Chromosomal Aneuploidies Chromosomal abnormalities are a frequent cause of perinatal morbidity and mortality.
Chromosomal abnormalities occur with an incidence of 1 in 200 live births. The major cause of these abnormalities is chromosomal aneuploidy, an abnormal number of chromosomes inherited from the parents. One of the most frequent chromosomal aneuploidies is trisomy-21 (Down syndrome), which has an occurrence of 1 in 800 livebirths (Hook EB, Hamerton JL:
The frequency of chromosome abnormalities detected in consecutive newborn studies:
Differences between studies: Results by sex and by severity of phenotypic involvement. In Hook EB, Porter IH (eds): Population Cytogenetics, pp 63-79. New York, Academic Press, 1978). The primary risk factor for trisomy-21 is maternal age greater than 35, but 80% of children with trisomy-21 are born to women younger than 35 years of age. Other common aneuploidic conditions include trisomies 13 and 18, Turner Syndrome and I~linefelter syndrome.
Because 80°/~ of children with trisomy-21 are born to women younger than 35 years of age, prenatal diagnostic screening programs designed on the basis of maternal age alone axe inefficient. Prenatal screening programs have therefore been supplemented with maternal serum screening for analytes associated with fetal chromosomal aneuploidy, ultrasound, or a combination of both. Candidate serum markers that have been widely utilized include alpha-fetoprotein (AFP), unconjugated estriol, human choriogonadotrophic hormone (hHCG), and inhibin-A. However, with a screen positive rate of 2-5%, the detection rate for trisomy-21 and other aneuploidies has been disappointing, with detection rates of only 70-86% (Cuckle H. Biochemical screening for Down syndrome. Eur J Obstet Gynecol Reprod Biol.
92(1):97-101, 2000). Further, the rate of true positive tests, i.e., trisomy-21 among those with a screen positive test is only 1-2%, resulting in an overall false positive rate in excess of 98%.
The definitive diagnosis of chromosomal aneuploidies following maternal serum screening and ultrasound requires a mid-trimester genetic amniocentesis. This is an invasive procedure associated with a 0.5% risk of loss of the pregnancy. Further, chromosomal analysis of amniotic fluid cells is a labor-intensive and time consuming procedure, taking up to 2 weeks. Reliable tests are therefore necessary to improve the detection of chromosomal aneuploidies from maternal serum, reduce the unacceptably high false positive rate of maternal screening, and increase the speed and efficiency of diagnosis from amniotic fluid following amniocentesis.
3. Diagnosis of Mater~nallFetal Conditions Ilsin~ the Pf~oteornic Pro ale of Biological Fluids The present invention provides an early and reliable, non-invasive method for the diagnosis of the foregoing and other similar maternal/fetal conditions by proteomic analysis of biological fluids, such as, for example, amniotic fluid, serum, plasma, urine, cerebrospinal fluid, breast milk, mucus, or saliva.
As noted before, in the context of the present invention the term "proteomic profile" is used to refer to a representation of the expression pattern of a plurality of proteins in a biological sample, e.g. a biological fluid at a given time. The proteomic profile can, for example, be represented as a mass spectrum, but other representations based on any physicochemical or biochemical properties of the proteins are also included.
Although it is possible to identify and sequence all or some of the proteins present in the proteome of a biological fluid, this is not necessary for the diagnostic use of the proteomic profiles generated in accordance with the present invention. Diagnosis of a particular disease can be based on characteristic differences (unique expression signatures) betv~een a normal proteomic profile, and proteomic profile of the same biological fluid obtained under the same circumstances, when the disease or pathologic condition to be diagnosed is present. The unique expression signature can be any unique feature or motif within the proteomic profile of a test or reference biological sample that differs from the proteomic profile of a corresponding normal biological sample obtained from the same type of source, in a statistically significant manner. For example, if the proteomic profile is presented in the form of a mass spectrum, the unique expression signature is typically a peak or a combination of peaks that differ, qualitatively or quantitatively, from the mass spectrum of a corresponding normal sample. Thus, the appearance of a new peak or a combination of new peaks in the mass spectrum, or any statistically significant change in the amplitude or shape of an existing peak or combination of existing peaks in the mass spectrum can be considered a unique expression signature. When the proteomic profile of the test sample obtained from a mammalian subject is compared with the proteomic profile of a reference sample comprising a unique expression signature characteristic of a pathologic maternal or fetal condition, the mammalian subject is diagnosed with such pathologic condition if it shares the unique expression signature with the reference sample.
A particular pathologic maternal/fetal condition can be diagnosed by comparing the proteomic profile of a biological fluid obtained from the subject to be diagnosed with the S proteomic profile of a normal biological fluid of the same kind, obtained and treated the same manner. If the proteomic profile of the test sample is essentially the same as the proteomic profile of the normal sample, the subj ect is considered to be free of the subj ect pathologic maternal/fetal condition. If the proteomic profile of the test sample shows a unique expression signature relative to the proteomic profile of the normal sample, the subject is diagnosed with the maternal/fetal condition in question.
Alternatively or in addition, the proteomic profile of the test sample may be compared with the proteomic profile of a reference sample, obtained from a biological fluid of a subject independently diagnosed with the pathologic maternal/fetal condition in question. In this case, the subject is diagnosed with the pathologic condition if the proteomic profile of the test sample shares at least one feature, or a combination of features representing a unique expression signature, with the proteomic profile of the reference sample.
In the methods of the present invention the proteomic profile of a normal biological sample plays an important diagnostic role. As discussed above, if the proteomic profile of the test sample is essentially the same as the proteomic profile of the normal biological sample, the patient is diagnosed as being free of the pathologic maternal/fetal condition to be identified. This bsnegative~' diagnosis is of great significance, since it eliminates the need of subjecting a patient to unnecessary treatment or intervention, which could have potential side-effects, or may otherwise put the patient, fetus, or neonate at risk. The data are analyzed to determine if the differences are statistically significant.
The sensitivity of the diagnostic methods of the present invention can be enhanced by removing the proteins found both in normal and diseased proteome at essentially the same expression levels (common proteins, such as albumin and immunoglobulins) prior to analysis using conventional protein separation methods. The removal of such common proteins, which are not part of the unique expression signature, results in improved sensitivity and diagnostic accuracy. Alternatively or in addition, the expression signatures of the common proteins can be eliminated (or signals can be removed) during computerized analysis of the results, typically using spectral select algorithms, that are machine oriented, to make diagnostic calls. The results detailed in the Examples below present proteomic profiles characteristics of intraamniotic infection (IAI) that differ from the normal proteomic profile of amniotic fluid in a statistically significant manner. In addition, the Examples present expression markers and unique expression signatures characteristic of IAI and Down syndrome, respectively.
Statistical methods for comparing proteomic profiles are well known in the art. For example, in the case of a mass spectrum, the proteomic profile is defined by the peak amplitude values at key mass/charge (M/Z) positions along the horizontal axis of the spectrum. Accordingly, a characteristic proteomic profile can, for example, be characterized by the pattern formed by the combination of spectral amplitudes at given M/Z
vales. The presence or absence of a characteristic expression signature, or the substantial identity of two profiles can be determined by matching the proteomic profile (pattern) of a test sample with the proteomic profile (pattern) of a reference or normal sample, with an appropriate algorithm. A statistical method for analyzing proteomic patterns is disclosed, for example, in Petricoin III, et al., The Lancet 359:572-77 (2002).; Issaq et al., Biochefrl Biophys Comrnura 292:587-92 (2002); Ball et al., Bioir for~matics 18:395-404 (2002); and Li et al., Clinical Chemist~.Iout~nczl, 48:1296-1304 (2002).
In a particular embodiment, a sample obtained from the patient is applied to a protein chip, an the proteomic pattern is generated by mass spectrometry. The pattern of the peaks within the spectrum can be analyzed by suitable bioinoformatic software, as described above.
4. S'cf~eerain~ Assays The proteomic profiles of the invention find f~.u-ther utility in screening assays to identify drug candidates for the treatment of a particular maternal/fetal condition. Such screening assays are based on the ability of a test molecule to convert a proteomic profile containing an expression signature characteristic of the maternal/fetal condition to be treated into a proteomic profile devoid of the expression signature. In one particular embodiment, the ability of the test compound to convert a pathologic expression profile into a normal expression profile is tested. In another embodiment, the screening assay tests the ability of a test compound to convert a unique expression signature characteristic of a pathologic condition into a corresponding normal expression signature.
Such screening assays ca.n be performed in vitro by treatment of a diseased biological sample and comparing the proteomics expression profiles before and after treatment.
Alternatively or in addition, drug screening can be performed by treating a laboratory animal exhibiting the target pathologic maternal/fetal condition with a test compound, taking samples of a biological fluid of the animal before and after treatment, and comparing the proteomic profiles of the two samples. In this assay, it is also possible to take samples of biological fluid at various time points following treatment, and follow the time course of treatment.
These methodologies may be applied also to characterize the toxicology of pharmaceutical agents, as well as to identify optimal candidates for specific therapies.
The test compounds can, for example, be peptides, non-peptide small organic molecules, proteins, polypeptides, antibodies (including antibody fragments), antisense molecules, oligonucleotide decoys, and any other classes of molecules that have been used previously as drugs or drug candidates.
The biological fluid can, for example, be amniotic fluid, serum (e.g. maternal serum), plasma, urine, cerebrospinal fluid, breast milk, mucus, or saliva.
Therapeutically active compounds identified can be formulated in conventional pharmaceutical formulations. A compendium of art-known formulations is found in Remin: on's Pharmaceutical Sciences, latest edition, Mack Publishing Company, Easton, PA.
Reference to this manual is routine in the art.
5. Pt~~tean. cz~cl AfZtib~cl f1f°~ays >3oth the diagnostic and the screening assays discussed above can be performed using protein arrays. In recent years, protein arrays have gained wide recognition as a powerful means to detect proteins, monitor their expression levels, and investigate protein interactions and functions. They enable high-throughput protein analysis, when large numbers of detem~inations can be performed simultaneously, using automated means. In the microarray or chip format, that was originally developed for DIVA arrays, such determinations can be carried out with minimum use of materials while generating large amounts of data.
Although proteome analysis by 2D gel electrophoresis and mass spectrometry, as described above, is very effective, it does not always provide the needed high sensitivity and this might miss many proteins that are expressed at low abundance. Protein microarrays, in addition to their high efficiency, provide improved sensitivity.
Protein arrays are formed by immobilizing proteins on a solid surface, such as glass, silicon, micro-wells, nitrocellulose, PVDF membranes, and microbeads, using a variety of covalent and non-covalent attachment chemistries well known in the art. The solid support should be chemically stable before and after the coupling procedure, allow good spot morphology, display minimal nonspecific binding, should not contribute a background in detection systems, and should be compatible with different detection systems.

In general, protein microarrays use the same detection methods commonly used for the reading of DNA arrays. Similarly, the same instrumentation as used for reading DNA
microarrays is applicable to protein arrays.
Thus, capture arrays (e.g. antibody arrays) can be probed with fluorescently labelled proteins from two different sources, such as normal and diseased biological fluids. In this case, the readout is based on the change in the fluorescent signal as a reflection of changes in the expression level of a target protein. Alternative readouts include, without limitation, fluorescence resonance energy transfer, surface plasmon resonance, rolling circle DNA
amplification, mass spectrometry, resonance light scattering, and atomic force microscopy.
For further details, see, for example, Zhou H, et al., Trends Biotechnol.
19:534-9 (2001); Zhu et al., Current Opirt. Claem. Biol. 5:40-45-(2001); Wilson and Nock, Angew Chena Int Ed Engl 42:494-500 (2003); and Schweitzer and Kingsmore, Curr Opin Bioteclanol 13:14-9 (2002). Biomolecule arrays are also disclosed in United States Patent No. 6,406,921, issued June 18, 2002, the entire disclosure of which is hereby expressly incorporated by reference.
Further details of the invention will be apparent fiom the following non-limiting examples.
Example 1 General Protocols Primate Model of Intra-amniotic Infection This protocol was approved by the Institutional Animal Care Utilization Committee of the Oregon National Primate Research Center, and guidelines for humane care were followed.
Nineteen pregnant rhesus monkeys (Macaca mulatta) with timed gestations were chronically catheterized and maintained postoperatively as previously described (Haluska GJ, et al., Temporal changes in uterine activity and prostaglandin response to RU 486 in rhesus macaques in late gestation., Ana .I Obstet Gynecol 157: 1487-95 (1987); and Gravett MG, et al., An experimental model for intra-amniotic infection and preteen labor in rhesus monkeys.
Ana JObstet Gynecol 171: 1660-7 (1994)).
Briefly, at approximately day 110 of gestation (term is 167 days) pregnant animals were conditioned to a jacket and tether system (Ducssay CA, et al., Simplified vest and tether system for maintenance of chronically catheterized pregnant rhesus monkeys.
Lab. Anim Sci 38:343-4 (1988)). After conditioning, intrauterine surgery was performed between days 119 and 126 of gestation under general anesthesia. Maternal femoral arterial and venous catheters, fetal arterial and venous catheters, two open-ended infra-amniotic pressure catheters, myometrial electromyographic electrodes, and fetal electrocardiographic electrodes were surgically implanted. All animals received terbutaline sulfate (1 mg intravenously over 3 to 5 hours twice daily) for 1 to 5 days after surgery to control uterine irritability. Animals also received cefazolin (250 mg intravenously every 12 hours), which was discontinued at least 48 hours before inoculation of bacteria.
After postoperative stabilization for 8 to 13 days (day 126 to 138 of gestation), experimental infra-amniotic infection (IAI) was established by infra-amniotic inoculation of a) 106 colony-formiong units (cfu) of Group B streptococcus, type III, suspended in saline (n=7), b) 107 cfu of U~eaplasnaa par~ur~a (formerly Uf°eaplasma u~ealyticum, serovar 1) suspended in l OB media (n=6), or c) 106 - 107 cfu of Mycoplasnaa homirZis (n=6), suspended in phosphate buffered saline with 10% sucrose and 2% endotoxin-free fetal calf serum. The Group B streptococcus isolate was originally recovered from a neonate with meningitis. The Us~eaplasma pa~vufyz was from a low passaged clinical isolate from placenta and membranes of a patient with chorioamnionitis and neonatal sepsis. The Myc~plasnaa la~minis was an endometrial isolate from a patient with postmartum endomyometritis.
Amniotic fluid samples were collected serially from all animals during the study period (daily before inoculation and every 4 to 12 hours after inoculation) for quantitative bacterial cultures, white blood cell analysis by hemocytometer, and cytokine and prostaglandin concentrations (previously reported - Gravett MG, et al., An experimental model for infra-amniotic infection and preterm labor in rhesus monkeys. Am ~
~bstet CPyraec~Z 171: 1660-7 (1994)), and for proteomic analysis.
Fetal electrocardiographic and uterine activity (electromyographic and infra-amniotic pressure) were continuously recorded from surgery until delivery. Uterine contractility was recorded as the area under the contraction curve per hour and expressed as the hourly contraction area (HCA) in millimeters of mercury times seconds/hour.
The maternal cervix was palpated vaginally before infection and serially thereafter.
Consistency, effacement, and dilatation were recorded at each examination.
After delivery, by Cesarean section in all except one animal and vaginally in one animal, fetal, decidual, placental, and inter-membrane bacterial cultures were obtained to confirm infection and histopathologic studies were performed to document chorioamnionitis.
Infection was rapidly established following infra-amniotic inoculation performed as described above. Uterine contractility which increased from basal levels of 100 to greater than 10,000 mmHg x sec/hr occurred in an average of 33 ~ 9 hours after inoculation with Group B streptococci, in 43 ~ ~14 hours after inoculation with Ureaplasma parvurn; and in 62 ~ 14 hours after inoculation with Mycoplasma hominis. Uterine contractions led to progressive cervical dilation and effacement in all instances. Increases in uterine contractility were preceded by significant elevations in the pro-inflammatory cytokines TNF-alpha, IL-1 [3, IL-6, and IL-8, and prostaglandins EZ and F2a as previously reported (Graven et al., Am J.
Obstet Gynecol 171:1660-7 (1994)). No animal demonstrated clinical signs of IAI prior to the onset of labor. Chorioamnionitis was confirmed in all cases.
Human Studx~Sub-clinical IAI in Women) The study population was drawn from 309 women admitted in premature labor at to 34 weeks of gestation with intact fetal membranes to the University of Washington Medical Center or associated hospitals in Seattle between June 25, 1991 and June 30, 1997, as previously described (Hitti J, et al., Amniotic fluid tumor necrosis factor-a and the risk of respiratory distress syndrome among preterm infants. ~hra J ~bstet Gyrtecol 177:50-6 (1997)).
All women provided written informed consent, and the study protocol was approved by the Institutional Izeview Boards for all participating hospitals. All participants had intact fetal membranes at study enrollment. Preternl labor was defined as regular uterine contractions at a frequency of <_ 10 minutes with either documented cervical change or a cervical dilatation of >1 centimeter or effacement of > 50~/~.
Subclinical IAI was defined by a positive AF microbial culture and/or an AF
interleukin-6 (IL-6) concentration > 2ng/ml, histologic evidence for chorioanmionitis (defined by the presence of >_ 10 polyrnorphonuclear leukocytes per 400X field in 10 nonadjacent fields and the absence of uterine tenderness or fever. We have previously reported tat an AF IL-6 concentration > 2 ng/ml was at or above the 75th percentile for the entire study population and was associated with the detection of bacteria by polymerase chain reaction (Hitti et al., Clin Infect Dis 24:1228-32 (1997)). Women with cervical dilatation > 4 centimeters or ruptured membranes at admission were excluded. Women with multiple gestations, cervical cerclage, placenta previa, abruptio placentae, diabetes, hypertension, and pre-eclampsia were considered eligible if they otherwise met study criteria.
Transabdominal amniocentesis was performed under ultrasound guidance for all study participants and maternal venous blood was also collected by venipuncture at the time of enrollment From this study population, a subset (Tables 1A and B) was retrospectively identified for proteomic analysis as reported here. This subset included three groups of 11 patients each: Group I - patients with evidence of sub-clinical IAI as defined above; Group I -a randomly selected subset of patients without documented intrauterine infection, but with preterm birth <_ 34 weeks gestation, and Group III - patients without infection and with preterm labor responsive to tocolyltic therapy who subsequently delivered near term (at > 35 weeks of gestation). There were no differences in maternal age, race, or parity between these three groups (Tables 1A and B). However, patients with intrauterine infection were seen at a somewhat earlier gestational age at enrollment (p=0.10) and delivered at a significantly earlier gestation age than those patients with preterm delivery without infection or those with term delivery (27.3 + 0.9 weeks versus 29.8 + 1.0 and 37.0 + 0.9 weeks respectively, p<0.0001). hi addition, those with intrauterine infection had a significantly shorter enrollment to delivery interval (2.1 + 5.6 days, compared to 8.4 + 6.3 and 46.9 + 5.6 days for the other two groups, p<0.0001). Ninety-one percent of those with intrauterine infection delivered within seven days of enrollment. Samples were stored at -20°C
until analysis and not thawed more than twice.
Among those eleven patients with infection, microorganisms were recovered from four (2 with EsclaeYichia coli, 1 with Cafadida albicafTS, and 1 with mixed anaerobes); all of these patients delivered within seven days. Seven other patients were identified based upon amniotic fluid IL-6 concentrations of greater than 2,000 pg/ml. The mean amniotic fluid concentration of interleukin-6 was 27.7 + 7.8 ng/ml among these patients, compared to 0.68 +
0.20 ng/ml among those with preterm delivery without infection and 0.25 + 0.13 ng/ml among those with preterm labor and term delivery (p < 0.01).

Table 1A. Characteristics of the Study Population Group vs PML with 1 subsequent PMD with IUI PMD without term IUI

Characteristic(n=11) (n=11) delivery (n=11) p value Maternal Age 24.55.4 26.69.0 25.66.0 NS

White Race 6(55%) 4(36%) 6(55/~) NS

Parity 1.91.6 1.91.5 3.02.5 NS

Nulliparity 3(27%) 1(9%) 1(9/~) NS

Gestational Age at 26.9l.l 28.61.1 30.31.1 0.10 Enrollment (wks) Gestational Age at 27.30.9 29.81.0 37.00.9 <0.0001 Delivery (wks) Enrollment to Delivery 2.15.6 ~.46.3 46.95.6 <0.0001 Interval (days) Delivery 7 10(91%) 6(55%) 0 <0.001 days Data expressed as mean standard deviation. Analysis by ANOVA for continuous data and Chi-square for categorical data. Abbreviations: PMD, premature delivery < 35 weeks; IUI, intrauterine infection; PML, premature labor without delivery.

Table 1B. Screening Results.
Group PML with subsequent term PMD with IUI PMD without delivery ICTI

Characteristic (n=11 ) (n=11 ) (n=11 ) p valueL

Bacterial culture 4/11 0/11 0/11 p<0.01 positive IL-6 positive 7/11 0/11 0/11 p<0.01 Diagnostic protein11/11 2/11* 0/11 p<0.01 profiles ''=The two positive samples in this pool represent subclinical infection since the Ar of the two subjects demonstrated low levels of bacteria, positive by PCR
procedures. This indicates that protein profiling can be used to identify subclinical intraamniotic infection.
In the foregoing tables, data are expressed as mean standard deviation.
Analysis by A1~TOVA for continuous data and Chi-square for categorical data.
Abbreviations: hl~Ill), premature delivery < 35 weeks; IUI, intrauterine infection; I'11~IL, premature labor without delivery.

Table 1C. Fisher's test sigiuficance values for screening test results.
Fisher's Exact: p< 0.05 (one-sided) PMD with IUI
vs PML

Bacterial Culture Class Positive Negative Total PMD with IUI 4 7 11 PML, term delivery0 11 11 Total 4 18 22 Fisher's Exact: p< 0.01 (one-sided) PMD with IUI
vs PML

IL-6 Status Class Positive Negative Total MD with ILTI 7 4 11 ML, term delivery0 11 11 Total 7 15 22 fisher's Exact: p< 0.005 (one-sided) PMD with IUI
vs PML

Diagnostic Protein Profile Class Positive Negative Total MD with IIJI 11 0 11 ML, term delivery0 11 11 Total 11 11 22 fisher's Exact: < 0.005 (one-sided) PIE with ILJI
vs PIE without ILJI

Diagnostic Protein Profile Class Positive Negative Total MD with ICTI 11 0 11 MD without ItJI 2 9 11 Total 13 9 22 fisher's Exact: p n.s.
PMD without 1ZJI
vs PML

Diagnostic Protein Profile Class Positive Negative Total MD without lUI 2 9 11 ML, term delivery0 11 11 Total 2 20 22 Four of eleven patients with occult IAI had micoorganisms recovered (2 with Esclaericlzia coli, 1 with Candida albicaras, and 1 with mixed anaerobes). The other seven patients with infection were identified on the basis of markedly elevated AF

concentrations > 2 ng/ml. The mean AF concentration of IL-6 was 27.7 ~ 7.8 ng/ml among these patients, compared to 0.68 ~ 0.20 ng/ml among those with preterm delivery without infection and 0.25 ~ 0.13 ng/ml among those in Group III with preterm contractions but term delivery (p < 0.01 ).

Proteomic Analysis ofAmniotic Fluid Protein Identification by LC-MS/MS Anal 100~,g of amniotic fluid from control and infected samples was reduced with iodoacetamide and resolved on a 15% SDS-PAGE gel. Electrophoresis was conducted at 80V to separate the proteins in the sample. After electrophoresis the gel was stained with Coomassie blue R-250 and images were collected using Bio-Rad GS800 densitometer and PDQUEST software. Distinct bandsfrom each lane were cut from the gel, destained and digested in-gel with trypsin for 24-48 hrs at 37 °C using the method of Courchesne and Patterson (Methods Mol Biol 112:487-S11 (1999)). The peptides were extracted with 0.1 %TFA and dried in a speedvac. The extract was dissolved in 0.1 %TFA and purified using Zip Tip~lB pipette tips from Millipore.(Marvin L., et al. Identification of proteins from one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis using electrospray quadrupole-time-of flight tandem mass spectrometry. Rapid Commun Mass Spectrom.
14(14):1287-92, 2000) using a Q-Tof 2 mass spectrometer (Micromass, UI~) coupled to a CapLC (Waters, W c) and/or on an ion trap (LCQ, ThermoFinnigan, San Jose, CA) coupled to a 110 Capillary LC System (Agilent Technologies, Foster City, CA).
2-Dimensional (2-D~~el electrophoresis Armiotic fluid (4.00 - 2000p,g) with or without removal of albumin was dissolved in IEF buffer and rehydrated on to a 24 cm IPG strip (pH 3-10) for 12 h at room temperature.
After rehydration, the IPG strip was subjected to 1-dimension electrophoresis at 70 ~90 kVhrs. The IPG strip was then equilibrated with DTT equilibration buffer I and IAA
equilibration buffer II for 15 minutes sequentially, before second dimension SDS-PAGE
analysis. The IPG strip was then loaded on to a 4 ~ 20% SDS-PAGE gel and electrophoresis conducted at 120 V for 12 hrs to resolve proteins in the second dimension. The gel was stained with Coomassie Blue R-250 and imaged using Bio-Rad GS800 densitometer and PDQUEST software. Individual spots were cut from the gel, destained and digested in-gel with trypsin for 24-48hrs at 37C. The peptides were extracted with 0.1%TFA and purified using Zip Tip~lB pipette tips from Millipore (2-D Proteome analysis protocols:
Methods in Molecular Biology: 112, 1999).

HPLC fractionation Human amniotic fluid samples after removal of albumin and IgG (1-l5mg protein) were dissolved in 20mM Tris-HCI, pH 7.5. Anion-exchange chromatography was performed using TSK gel DEAF-SPW column on a Waters 1525 HPLC equipped with an auto sampler and a UV absorbance detector. A linear salt elution gradient was used to fractionate the proteins. Fractions were collected at one minute intervals. Fractions were pooled, digested with trypsin and peptide mixtures were analyzed using the mass spectrometer (Q-Tof 2).
Mass SpectrometryAnalysis (1) Q-Tof 2 Samples after in-gel digestion were analyzed on a Micromass Q-Tof 2 mass spectrometer connected to a Micromass CapLC. The Q-Tof 2 was equipped with a regular Z-spray or nanospray source and connected to a Integrafrit C18 75um ~ x l5cm fused silica capillary column. The instrument was controlled by, and data were acquired on, a Compaq workstation with Windows NT and MassLynx 3.5 software. The Q-Tof 2 was calibrated using GlulFibrinopeptide B by direct infusion or injection into the CapLC. A
MS/MSMS
survey method was used to acquire MS/MSMS spectra. Masses 400 to 1500 were scanned for MS survey and masses 50 to 1900 for MSMS. Primary data analysis was performed on a PC with Windows 2000 and SEQUEST (version 1.3) and/or LUTEFISK. Peak lists were generated, using the built-in automatic functions for peak-picking and applying centroid-fitting to each peals.
(2) LCQ-MS
Protein spots from dried Coomassie blue stained gels were excised and rehydrated/washed for 30 min. in 0.5 ml of 20 mM ammouum bicarbonate, 50°/~ acetonitrile solution. The gel regions were then dried by vacuum centrifugation and digested insitu by rehydrating in 20 nM sequencing grade modified trypsin (ProMega, Madison, WI, USA) using the method of Courchesne and Patterson, Identification of proteins by matrix-assisted laser desorption/ionization masses, Methods Mol. Biol. 112:487-511 (1999).
Tryptic digests were then concentrated by vacuum centrifugation, separated by reverse phase chromatography, and peptides analyzed by a model LCQ ion trap mass spectrometer (ThermoFinnigan, San Jose, CA). Samples were separated with Zorbax C-18 0.5 mm x 150 mm microbore column using a 10 ~,L miri 1 flow rate and a gradient of 0 to 40%
B (75 Acetonitrile in water) over one hour with an 1100 Capillary LC System (Agilent Technologies, Foster City, CA). Peptides were introduced directly into the standard ThermoFinnigan electrospray source. MSfi~IS spectra were acquired in an automated fashion using standard LCQ software and then analyzed further using SEQUEST
(ThermoFinnigan).
For further details see, Courchesne, P.L. and Patterson, S.D., supra.
Data Ana~sis (1) Sequest and DTASelect Automated analysis of tandem mass spectra (MS/MS) was performed using SEQUEST software (ThermoFinnigan) as described by Yates et al., Methods Mol.
Biol.
112:553-69 (1999). SEQUEST matches uninterrupted tandem mass spectra to database peptide sequences. Searches were run with the default parameters using a combined indexed non-redundant database of protein sequences obtained from the Protein Information Resource (release date) and SwissProt (release date). The database was constructed using the Xcalibur Database Manager (ThermoFinnigan). S-Carboxyamidated cysteine was the only considered modification.
Sequest results were further analyzed using DTASelect (The Scripps Research Institute, Tabb, 2002). DTASelect organizes and filters SEQUEST
identifications. The default parameters were used except as follows: 1) any database matches including the string "keratin" in the protein description were excluded and 2) spectra from the LCQ
mass spectrometer were filtered with a cross correlation score cut-off of 2.4 for the doubly charged ions. Each spectra and proposed sequence pair selected by DTASelect were visually inspected and the final results were input into a spreadsheet (Microsoft Excel) or a database (Microsoft Access) for management.
For further details, see also: Tabb DL, et al., DTASelect and Contrast: Tools for Assembling and Comparing Protein Identifications from Shotgun Proteomics.
J.1'r~teo3Yl.e Res. 1:21-26 (2002).
(2) Lutefisk Automated de novo sequencing of all spectra was performed using a computer program, Lutefisk 1900 v1.2.5 (Taylor JA, Johnson RS. Implementation and uses of automated de novo peptide sequencing by tandem mass spectrometry. Anal Chem 73(11):2594-604 (2001). Lutefisk generates peptide sequences for spectra of which some are sufficiently detailed for homology-based sequence searches. Modifications, acrylamide, carbamidomethylation, and phosphorylation, were considered.

MALDI Detection protocol and parameters MALDI mass spectrometry was performed on a custom-built time-of flight reflector mass spectrometer (Jensen ON, et al., Direct observation of UV-crosslinked protein-nucleic acid complexes by matrix-assisted laser desorption ionization mass spectrometry. Rapid Comnaun Mass Spectf~om 7(6):496-501 (1993)) equipped with a two-stage delayed extraction source. Approximately 1 ~.L of sample solution was mixed with 1 ~,L SA
(Sinapinic acid in 60:40 waterlacetonitrile 0.1% TFA final cone) A 1.0 ~L droplet of this analyte/matrix solution was deposited onto a matrix pre-crystallized sample probe and allowed to dry in air.
Mass spectra were produced by radiating the sample with a (355nm) Nd:YAG laser (Spectra Physics) and operating the ion source at 23 kV with a 700ns/l.OkV delay. Every mass spectrum was recorded as the sum of 20 consecutive spectra, each produced by a single pulse of photons. Ions from an added standard were used for mass calibration.
SELDI analysis of amniotic fluid A total of 0.5 - 3.0 ug protein from amniotic fluid samples was spotted on a Normal Phase NP20 (SiO2 surface), Reverse Phase H4 (hydrophobic surface: C-16 (long chain aliphatic), or immobilized nickel (IMAC) SELDI ProteinChip~ array (Ciphergen Biosystems, Inc. Fremont, CA). After incubation at room temperature for 1 hour, NP1 and H4 chips were subjected to a 5 u1 water wash to remove unbound proteins and interfering substances (ie buffers, salts, detergents). After air-drying for 2-3 minutes, tv~o 0.5 u1 applications of a saturated solution of sinapinic acid in 50% acetonitrile (v/v), 0.5%
trifluoroacetic acid (v/v) was added and mass analysis was performed by time-of flight mass spectrometry in a Ciphergen Protein Biology System II (PBS II), Issaq, J.H, et al. : The SELDI-TOF MS Approach to proteomics : Protein Profiling and Biomarker Identification.
Biochem Biophys Res Commun. 5;292(3):587-92, 2000.
Polyclonal Antibodies and Western Immunoblotting Immunogenic peptides from corresponding proteins were used to generate rabbit polyclonal antibodies (DSL Laboratories, Webster, TX). Affinity-purified antibodies were then used for Western blots. One hundred ~,g of AF protein was resolved on 4-20% SDS-PAGE and transferred to PVDF membranes. From maternal serum, 300 ~,g of protein was used for immunoprecipitation using IGFBP 1 monoclonal antibody (DSLLaboratories) and products were western blotted. For detection of calgranulin B in maternal serum 150 ~,g of albumin depleted maternal serum was used for western blot. The membranes were blocked with 5% fat-free milk in PBST for 45 minutes at room temperature and incubated with 1 ~,g/ml primary antibody (IGFBP-1, azurocidin, vitamin-D binding protein and calgranulin-B
from DSL 11c., Santa Cruz, CA) overnights at 4 °C. After three washes with TBST, the membrane was incubated with IgG-HRP secondary antibody (Sigma) and visualized with enhanced chemiluminescence.
Example 2 Identification of Proteins and Polypeptides Expressed in the Amniotic Fluid Using the materials and methods described in Example 1, proteins and polypeptides expressed in normal and infected amniotic fluid were identified. Human and primate amniotic fluid samples (pooled and individual) were subjected to protein separation techniques (1-D, 2-D and HPLC fractionation) as described in Example 1. The separated proteins (gel bands, spots and fractions) were digested with trypsin to generate peptide pools.
The peptide pools were analyzed using tandem IVIS to decipher their amino acid sequence and composition.
Five thousand ~S spectra were selected using spectral verification programs.
These spectral files were analyzed using de raovo sequencing programs (Lutefisk, Peaks) to generate the amino acid sequence corresponding to each peptide. The de fa~v~ sequences generated from the peptide pool were used to search protein and DllTA databases as described in Example 1.
Using homology maps and sequence verification, expression of a variety of proteins was discovered in the amniotic fluid. The detected proteins were analyzed for potential function based on known structural similarities (sequence homology maps).
Proteins belonging to important functional classes involved in a wide range of diseases were discovered. Proteins and polypeptides discovered for the first time in the human amniotic fluid are listed in the following Table 2 under these potential functional categories.
Proteins shown to be differentially expressed by immunoassays also, and proteins more abundantly or uniquely represented in the infected amniotic fluid are separately marked.
In this context, relative abundance is defined as the amount of the peptides representing a certain polypeptide or protein in a test sample, relative to a reference sample. Accordingly, a protein is more abundantly represented in infected amniotic fluid if more peptides derived from the same protein are present in infected amniotic fluid than in a non-infected reference sample of amniotic fluid.
Table 3 lists proteins and polypeptides previously known to be present in amniotic fluid, the presence of which was reaffirmed by the present assays. Proteins which are known markers for infection related events are separately marked.
Table 2. Proteins and polypeptides discovered for the first time in the human amniotic fluid.
GenBank Acc. No protein ID Protein Name Immune response related genes U12026 CAPG HUMAN Macrophage capping protein #

X83006 NGAL HUMAN Neutrophil gelatinase-associated lipocalin #

M19507 PERM HUMAN Myeloperoxidase precursor #

M22300 PLSL HUMAN L-plastin (Lymphocyte cytosolic protein 1) NM001700 A~Ul HUMAN Azurocidin #

X38026 FA39 HUMAN Antibacterial protein FALL-39 precursor AF159456 Q9UKJ4 Gp-340 variant protein AL355392 Novel protein similar to mouse von ~9H4~6 Ebner salivary gland protein, isoform 2 M93056 ILEU HUMAN Leukocyte elastase inhibitor #

x'00278 S 108 HUMAN Calgranulin A ~ #

X06233 5109 HUMAN Calgranulin B

Structural proteins D00682 COF1 HUMAN Cofilin, non-muscle isoform M69066 Moesin (Membrane-organizing extension MOES_HUMAN spike protein) J03191 PRO1 HUMAN Profilin I* #
D44497 COlA HCJMAN Coronin-like protein p57 (Coronin 1A) D00017 ANX2 HUMAN Annexin II (Lipocortin II) M15801 F1NC HUMAN Fibronectin precursor M17783 GDN HUMAN Glia derived nexin precursor #

Proteases and protease inhibitors M21642 ANT3 HUMAN Antithrombin-III precursor 566896 SCC1 HUMAN Squamous cell carcinoma antigen 1 U19576 SCC2 HUMAN Squamous cell carcinoma antigen 2 AB006423 SPI2 HUMAN Serpin I2 precursor #

X05978 CYTA HUMAN Cystatin A (Stefin A) (Cystatin AS) #

U46692 CYTB HUMAN Cystatin B (Liver thiol proteinase inhibitor) X05607 CYTC HUMAN Cystatin C precursor Transporters and binding proteins Y00856 Insulin-like growth factor binding IBP 1 HUMAN protein 1-Proteolytic fragment (only) L10641 VTDB HUMAN Vitamin D-binding protein precursor J00098 APAl HUMAN Apolipoprotein A-I precursor (Apo-AI) X57348 1435 HUMAN 14-3-3 protein sigma (Stratifm) M864.00 14.3 HUMAN 14-3-3 protein ~eta/delta X04412 GELS HUMAN Gelsolin precursor, plasma X53961 TRFL HUMAN Lactotransferrin precursor (Lactoferrin) Enzymes and other molecules V00572 PGI~1 HUMAN Phosphoglycerate kinase 1 J04.173 PMG1 HUMAN Phosphoglycerate mutase 1 X67688 TKT HCTMAN Transketolase ~ Proteins shown to be differentially expressed by immunoassays also.
# Peptides representing these proteins are more abundantly or uniquely detected in the infected amniotic fluid.

Table 3. Proteins and polypeptides, previously known to be present in the amniotic fluid, identified using de novo sequencing.
GenBank Acc. No protein ID Protein Name K02765 C03 HUMAN Complement C3 precursor *
J00241 KAC HUMAN Ig kappa chain C region J00253 LAC HUMAN Ig lambda chain C regions J00228 GC1 HCJMAN Ig gamma-1 chain C region X57127 H2BF HUMAN Histone H2B.f X00038 H4 HUMAN Histone H4*

HBA HUMAN Hemoglobin alpha chain U01317 HBB HUMAN Hemoglobin beta chain U01317 HBI~ HUMAN Hemoglobin delta chain M91036 HBG HUMAN Hemoglobin gamma-A and gamma-G chains 283742 H2AC HUMAN Histone H2A

M22919 MLEN HUMAN Myosin light chain alkali, non-muscle isofonn J05070 MM09 HUMAN type I~ collagenase precursor ~

V00496 AlAT HUMAN Alpha-1-antitrypsin precursor '' KO1500 AACT HUMAN Alpha-1-antichymotrypsin precursor*

M12530 TRFE HUMAN Serotransferrin precursor M11714 TTHY HUMAN Transthyretin precursor (Prealbumin) M13699 CERU HUMAN Ceruloplasmin precursor *

X02544 AlAH HUMAN Alpha-1-acid glycoprotein 2 precursor *

X06675 AlAG HUMAN Alpha-1-acid glycoprotein 1 precursor *

M12523 ALBU HUMAN Serum albumin precursor J00098 APAl HUMAN Apolipoprotein A-I precursor (Apo-AI) * Known markers for infection related events.

Additional proteins discovered the first time in amniotic fluid are provided in the following Table 4.
Table 4 GenBank Protein ID
Description BC001440143E HUMAN 14-3-3 PROTEIN EPSILON.

MONOOXYGENASE ACTIVATION PROTEIN, GAMMA

POLYPEPTIDE.

M86400 1432 HUMAN 14-3-3 PROTEIN ZETA/DELTA.

X02544 A1AG_HUMAN ALPHA-1-ACID GLYCOPROTEIN 1 PRECURSOR.

AV661485A1AH_HUMAN ALPHA-1-ACID GLYCOPROTEIN 2 PRECURSOR.

BC011991A1AT_HUMAN ALPHA-1-ANTITRYPSIN PRECURSOR.

AF414429A1 HUMAN ALPHA-1 B-GLYCOPROTEIN PRECURSOR.
BG_ D00174 A2AP_HUMAN ALPHA-2-ANTIPLASMIN PRECURSOR.

AF403428A2GL_HUMAN LEUCINE-RICH ALPHA-2-GLYCOPROTEIN PRECURSOR.

M16961 A2HS_HUMAN ALPHA-2-HS-GLYCOPROTEIN PRECURSOR.

A1678968ZA2G_HUMAN ALPHA-2-GLYCOPROTEIN 1, ZINC ALPHA-2-GLYCOPROTEIN 1, ZINC.

M11313 A2MG _HUMAN ALPHA-2-MACROGLOBULIN PRECURSOR.

AH002551AACT HUMAN ALPHA-1-ANTICHYMOTRYPSIN PRECURSOR.

HUMAN
ACTIN, AORTIC
SMOOTH
MUSCLE.

X00351 ACT~ _HUMAN ACTIN, CYTOPLASM IC 1.

M19283 ACTG _HUMAN ACTIN, CYTOPLASMIC 2.

J00068 ACTS _HUMAN ACTIN, ALPHA SKELETAL MUSCLE.

U5124.3 AFAM _HUMAN AFAMIN PRECURSOR.

M12523 ALBU _HUMAN SERUM ALBUMIN PRECURSOR.

M86826 ALS _HUMAP~ INSULIN-LIKE GROWTH FACTOR BINDING
PROTEIN

COMPLEX ACID LABILE CHAIN PRECURSOR.

BC041593AMBP _HUMAN AMBP PROTEIN PRECURSOR [Contains:

MICROGLOBULIN (PROTEIN HC) (COMPLEX-FORMING

GLYCOPROTEIN HETEROGENEOUS IN CHARGE) (ALPHA-1 MICROGLYCOPROTEIN) INTER-ALPHA-TRYPSIN INHIBITOR LIGHT CHAIN (ITI-LC) (BIKUNIN) (HI-30)].

M22324 AMPN HUMAN MEMBRANE ALANINE AMINOPEPTIDASE PRECURSOR.

102215 ANGT _HUMAN ANGIOTENSINOGEN PRECURSOR [Contains:

ANGIOTENSIN I (ANG I) ANGIOTENSIN II (ANG
II) ANGIOTENSIN III (ANG III) (DES-ASP[1]- ANGIOTENSIN
II

)].
X68793 ANT3 _HUMAN Antithrombin-III precursor X05908 ANX1 _HUMAN ANNEXIN I.

D00017 ANX2 _HUMAN ANNEXIN A2. (Lipocortin II) D78152 ANX4 _HUMAN ANNEXIN IV.

X02162 APA1 _HUMAN APOLIPOPROTEIN A-I PRECURSOR.

X02619 APA2 _HUMAN APOLIPOPROTEIN A-II PRECURSOR.

J02758 APA4 _HUMAN APOLIPOPROTEIN A-IV PRECURSOR.

X53595 APOH _HUMAN BETA-2-GLYCOPROTEIN I PRECURSOR.

AF207664ATS1 _HUMAN ADAMTS-1 PRECURSOR.

A1686916B2MG _HUMAN BETA-2-MICROGLOBULIN PRECURSOR.

_ PROTEIN IG-H3 PRECURSOR.

U03274 BTD _HUMAN BIOTINIDASE PRECURSOR

Y08374 C3L1 HUMAN CHITINASE-3 LIKE PROTEIN 1 PRECURSOR.

274615 CA11 _ _HUMAN COLLAGEN ALPHA 1(I) CHAIN PRECURSOR.

A1755052CA13 _HUMAN COLLAGEN ALPHA 1 (III) CHAIN PRECURSOR.

D90279 CA15 _HUMAN COLLAGEN ALPHA 1.

274616 CA21_ HUMANCOLLAGEN ALPHA 2(I) CHAIN PRECURSOR.

BC015705CA25_ HUMANCOLLAGEN ALPHA 2(V) CHAIN PRECURSOR.

A1890107CAD1_ HUMANEPITHELIAL-CADHERIN PRECURSOR.

SEG_AB001CADD_ HUMANCADHERIN-13 PRECURSOR.

J03037 CAH2_ HUMANCARBONIC ANHYDRASE II.

J02943 CBG_ HUMANCORTICOSTEROID-BINDING GLOBULIN PRECURSOR.

X13334 CD14_ HUMANMONOCYTE DIFFERENTIATION ANTIGEN CD14 PRECURSOR.

M13699 CERU_ HUMANCeruloplasmin precursor AL701961CFAB_ HUMANSPLICE ISOFORM 1 OF P00751 COMPLEMENT
FACTOR B

PRECURSOR.P

AL701961CFAB_ HUMANSPLICE ISOFORM 2 OF P00751 COMPLEMENT
FACTOR B

PRECURSOR.P

BC051001CFAD_ HUMANCOMPLEMENT FACTOR D PRECURSOR.

Y00716 CFAH_ HUMANSPLICE ISOFORM 1 OF P08603 COMPLEMENT
FACTOR

H PRECURSOR. P

J02770 CFAI_ HUMANCOMPLEMENT FACTOR I PRECURSOR.

L00974 CLUS_ HUMANCLUSTERIN PRECURSOR.

X04481 CO2 HUMANCOMPLEMENT C2 PRECURSOR.

K02765 C03_ HUMANCOMPLEMENT COMPONENT 3 PRECUROR [C3A

ANAPHYLATOXIN]

AH002623CO4._ HUMANCOMPLEMENT C4 PRECURSOR [Contains: C4A

ANAPHYLATOXIN].

J03507 C07_ HUMANCOMPLEMENT COMPONENT C7 PRECURSOR.

BC020721C09_ HUMANCOMPLEMENT COMPONENT C9 PRECURSOR.

AU120397COMP_ HUMANCARTILAGE OLIGOMERIC MATRIX PROTEIN

PRECURSOR.

M32294 CRTC_ HUMANCALRETICULIN PRECURSOR.

SEG_AB008CYTA_HUMAN CYSTATIN A.

AF208234~CYTB_ HUMAi~CYSTATIN B.

BC013083CYTC_ HUMANCYSTATIN C PRECURSOR.

AF319564CYTT_ HUMANCYSTATIN SA PRECURSOR.

L19711 DAG1 HUMANDYSTROGLYCAN PRECURSOR (DYSTROPHIN-ASSOCIATED GLYCOPROTEIN 1 ) [Contains:
ALPHA-DYSTROGLYCAN (ALPHA-DG) BETA-DYSTROGLYCAN

(BETA- DG)].

X14088 EMBP_ HUMANEOSINOPHIL GRANULE MAJOR BASIC PROTEIN

PRECURSOR.

AH005292FA12_ HUMANCOAGULATION FACTOR XII PRECURSOR.

D87120 FA3C_ HUMANPROTEIN FAM3C PRECURSOR.

AF217999FBL1_ HUMANSPLICE ISOFORM B OF P23142 FIBULIN-1 PRECURSOR.

P

AF217999FBL1_ HUMANSPLICE ISOFORM C OF P23142 FIBULIN-1 PRECURSOR.

P

_ PRECURSOR.

P

V01514 FETA_ HUMANALPHA-FETOPROTEIN PRECURSOR.

AJ242928FETB_ HUMANFETUIN-B PRECURSOR.

M65292 FHR1_ HUMANCOMPLEMENT FACTOR H-RELATED PROTEIN

PRECURSOR.

M64982 FIBA _HUMANSPLICE ISOFORM ALPHA OF P02671 FIBRINOGEN

ALPHA/ALPHA-E CHAIN PRECURSOR [Contains:

FIBRINOPEPTIDE A]. P

J00129 FIBB HUMANFIBRINOGEN BETA CHAIN PRECURSOR [Contains:

F IBRINOPEPTIDE B].

M15801 FINC _HUMANSPLICE ISOFORM 2 OF P02751 FIBRONECTIN

PRECURSOR.P

BC000055FSL1 HUMANFOLLISTATIN-RELATED PROTEIN 1 PRECURSOR.

AI742454GELS_HUMAN GELSOLIN PRECURSOR, PLASMA.

X60069 GGT1_HUMAN SPLICE ISOFORM 1 OF P19440 GAMMA-GLUTAMYLTRANSPEPTIDASE 1 PRECURSOR.
P

D16360 GSHP_HUMAN PLASMA GLUTATHIONE PEROXIDASE PRECURSOR.

AH005275HBA_HUMAN HEMOGLOBIN ALPHA CHAIN.

L48217 HBB_HUMAN BETA GLOBIN.

AH002827HUMAN HEMOPEXIN PRECURSOR.
HEMO

M12849 _ HEPARIN COFACTOR II PRECURSOR.

HUMAN

X00442 _ HAPTOGLOBIN-1 PRECURSOR HAPTOGLOBIN-1 HPT1_HUMAN

PRECURSOR.

X00442 HPT2_HUMAN HAPTOGLOBIN-2 PRECURSOR HAPTOGLOBIN-2 PRECURSOR.

AH003344HPTR_HUMAN HAPTOGLOBIN-RELATED PROTEIN PRECURSOR.

AB005803HRG_HUMAN HISTIDINE-RICH GLYCOPROTEIN PRECURSOR.

M59316 IBP1_HUMAN INSULIN-LIKE GROWTH FACTOR BINDING

PRECURSOR.

X16302 IBP2_HUMAN INSULIN-LIKE GROWTH FACTOR BINDING

PRECURSOR.

S75725 IBP7_HUMAN INSULIN LIKE GROWTH FACTOR BINDING

M13656 IC1_HUMAN PLASMA PROTEASE C1 INHIBITOR PRECURSOR.

#N/A IP100000513E CADHERIN

#N/A IP100001037PRO2275 similar to A1AT_HUMAN alpha-1-antitrypsin [[120 AA 13097 MW]]

#N/A IP100003269SIMILAR TO CYTOPLASMIC BETA-ACTIN.

#N/A IP100003799SOUL PROTEIN.

#N/A IP100010852FIBRONECTIN.

#N/A IP100018348SPONDIN 2.

#N/A IP10002364.8ISLR PRECURSOR.

#N/A IP100023673MAC-2 BINDING PROTEIN PRECURSOR.

#N/A IP100025785CHORIONIC SOMATOMAMMOTROPIN CS-2.

#f~/A IP100027227SIMILAR TO OMEGA PROTEIN.

#N/A IP100033238SIMILAR TO RII<EN CDNA 2610528605 GENE.

#N/A IP10006096199% similar to ALC1_HUMAN IG alpha-1 C chain region HYPOTHETICAL PROTEIN FLJ25298.

#N/A IP100064689FIBRONECTIN.

#N/A IP100065351HYPOTHETICAL PROTEIN FLJ25008 locuslink 117608:

~NF354B: zinc fiinger protein 354.8 #N/A IP10007044.2FIBRONECTIN.

#N/A IP100093987GAMMA-GLUTAMYLTRANSFERASE-LIKE 4.

#N/A IP100098026GAMMA-GLUTAMYLTRANSFERASE GAMMA-GLUTAMYLTRANSFERASE.

#N/A IP100103602SNC66 PROTEIN.

#N/A IP100104074M130 ANTIGEN CYTOPLASMIC VARIANT 2 PRECURSOR.

#N/A IP100151989HYPOTHETICAL PROTEIN KIAA1628. [[980 AA, 105361 MW]]

#N/A IP100151992HYPOTHETICAL PROTEIN FLJ31320. [[634 AA, 67970 MW]]

#N/A IP100160257Hypothetical [[100 AA, 10654 MW]]

#N/A IP100160384SPLICE ISOFORM LONG OF P80370 DELTA-LIKE

PROTEIN PRECURSOR (DLK) (P62) [Contains:
FETAL

ANTIGEN 1 (FA1 )].

#N/A IP100164623SIMILAR TO PROSTATE CANCER ANTIGEN-1.
[[187,235 MW]]

#N/A IP100164713E-CADHERIN.

#N/A IP100164755PREPRO-ALPHA2(I) COLLAGEN PRECURSOR.

#N/A IP100165421SIMILAR TO SERINE (OR CYSTEINE) PROTEINASE

INHIBITOR, CLADE C (ANTITHROMBIN), MEMBER 1.

#N/A IP100167087SIMILAR TO COLLAGEN, TYPE III, ALPHA
1.

#N/A IP100168679HYPOTHETICAL PROTEIN. [[236 AA, 25024 MW]]

#N/A IP100168728FLJ00385 PROTEIN. [[56111]]

#NlA IP100175228 SIMILAR TO TYROSINE 3 TRYPTOP
#N/A IP100177988 COMPLEMENT FACTOR B PREPROPROTEIN.
#N/A IP100178198 NUCLEAR FACTOR IA.
#N/A IP100178229 LAMRLS.
#N/A IP100178276 BPOZ SPLICE VARIANT TYPE3 BPOZ SPLICE VARIANT
TYP E3.
#N/A IP100180776 Hypothetical [[245 AA, 27742]]
#N/A IP100181399 Hypothetical [[1267 AA, 121210 MW]]
#N/A IP100182059 similar to CA11_HUMAN Collagen alpha 1 (I) chain #N/A IP100182398 97% similar to B2MG_HUMAN beta-2-microgloblin HYPOTHETICAL PROTEIN FLJ40785.
#N/A IP100184715 96% similar to KV2E_HUMAN IG Kappa V-II
#N/A IP100185882 SIMILAR TO CHROMOSOME 21 OPEN READING FRAME
70.
#N/A IP100186312 Hypothetical ([330 AA, 37651 MW]]
#N/A IP100216722 ALPHA 1B-GLYCOPROTEIN.
#N/A IP100216773 SIMILAR TO SERUM ALBUMIN PRECURSOR.
#N/A IP100218585 SPLICE ISOFORM OSF-2P1 OF Q15063 OSTEOBLAST
SPECIFIC FACTOR 2 PRECURSOR.
#N/A IP100219083 GAMMA-GLUTAMYL TRANSPEPTIDASE.
#N/A IP100220706 SIMILAR TO HEMOGLOBIN, GAMMA A.
#N/A IP100233308 SIMILAR TO HYPOTHETICAL PROTEIN.
#N/A IP100238312 SIMILAR TO GAMMA-GLUTAMYLTRANSFERASE.
#N/A IP100247616 COLLECTIN PLACENTA 1.
#N/A IP100249952 HYPOTHETICAL PROTEIN XP 294667 weakly similar to IRF5_HUMAN Interferon regulatory factor 5 #N/A IP100290898 ANNEXIN A2.
#N/A IP100297382 SIMILAR TO CG12393 GENE PRODUCT.
#N/A IP100305975 SPONDIN 2 EXTRACELLULAR MATR
#N/A IP100328111 FACTOR VII ACTIVE SITE MUTANT IMMUNOCONJUGATE.
#N/A IP100328609 HUMAN FULL-LENGTH CDNA 5-PRIME END OF CLONE
CSODM009YC13 OF FETAL LIVER OF HOMO SAPIENS.
#N/A IP100329204 SIMILAR TO NIDOGEN.
#N/A IP100329377 SIMILAR TO ALPHA-FETOPROTEIN.
#N/A IP100332595 Hypothetical [[783 AA, 79471 MW]]
#N/A IP100333038 Hypothetical [[213 AA, 23900 MW]]
#N/A IP100333150 Hypothetical [[469 AA, 51143 MW]]
#N/A IP100333611 Hypothetical [[1744 AA, 19275 MW]]
#N/A IP100333629 Hypothetical [[537 AA, 60416 MW]]
#N/A IP100333717 Hypothetical [[172 AA, 19385 MW]]
#N/A IP100333905 COMPLEMENT COMPONENT 4B PROPROTEIN.
#N/A IP100333917 Hypothetical [[587 AA, 65429 MW]]
#N/A IP100333960 83% simliar to PGBM_HUMAN basement membrane specific heparon sulfate proteoglycan core protein #N/A IP100333982 98% similar to GC3_HUMAN IG gamma 3 chain C.
#N/A IP100334249 Hypothetical [[241 AA, 25335 MW]]
#N/A IP100334282 Hypothetical [[232 AA, 25218 MW]]
#N/A IP100334423 Hypothetical [[241 AA, 25389 MW]]
#N/A IP100334432 Hypothetical [[141 AA, 15396 MW]]
#N/A IP100334465 Hypothetical [[373 AA, 42146 MW]]
#N/A IP100334477 Hypothetical [[345 AA, 38576 MW]]
#N/A IP100334645 81 % similar to K2C8_HUMAN keratin [[419 AA 46536 MW]]
#N/A IP100334832 Hypothetical [[177 AA, 20495 MW]]
#N/A IP100334857 Hypothetical [[120 AA, 13710 MW]]
#N/A IP100335176 similar to PGBM_HUMAN basement membrane-specific heparan sulfate proteoglycan core protein #N/A IP100335256 Hypothetical [[420 AA, 47163 MW]]
#N/A IP100335743 FIBRONECTIN.
#N/A IP100335852 Hypothetical ([731 AA, 81417 MW]]

PRECURSOR.
A1217735 ITH4_HUMAN SPLICE ISOFORM 2 OF Q14624 INTER-ALPHA-TRYPSIN
INHIBITOR HEAVY CHAIN H4 PRECURSOR (1T1 HEAVY
CHAIN H4) (INTER-ALPHA-INHIBITOR HEAVY CHAIN 4) (INTER-ALPHA-TRYPSIN INHIBITOR FAMILY HEAVY
CHAIN-RELATED PROTEIN) (IHRP) (PLASMA KALLIKREIN
SENSITIVE GLYCOPROTEIN 120) (PK-120) (GP120) (PR01851) [Contains: GP57]. Q14624-2 AI217735 ITH4_HUMAN SPLICE ISOFORM 1 OF Q14624 INTER-ALPHA-TRYPSIN
INHIBITOR HEAVY CHAIN H4 PRECURSOR (1T1 HEAVY
CHAIN H4) (INTER-ALPHA-INHIBITOR HEAVY CHAIN 4) (INTER-ALPHA-TRYPSIN INHIBITOR FAMILY HEAVY
CHAIN-RELATED PROTEIN) (IHRP) (PLASMA KALLIKREIN
SENSITIVE GLYCOPROTEIN 120) (PK-120) (GP120) (PR01851 ) [Contains: GP57]. Q14624-1 NT_022184 KAC_HUMAN IG KAPPA CHAIN C REGION.
X03663 KFMS_HUMAN MACROPHAGE COLONY STIMULATING FACTOR I
RECEPTOR PRECURSOR.
A1133186 KNG_HUMAN SPLICE ISOFORM HMW OF P01042 KININOGEN
PRECURSOR.P
A1133186 KNG_HUMAN SPLICE ISOFORM LMW OF P01042 KININOGEN
PRECURSOR.P
J04456 LEG1_HUMAN BETA-GALACTOSIDASE BINDING LECTIN PRECURSOR.
#N/A LTBL_HUMAN LATENT TRANSFORMING GROWTH FACTOR BETA
BINDING PROTEIN, ISOFORM 1 L PRECURSOR.
BC007038 LUM_HUMAN LUMICAN PRECURSOR.
Y09926 MAS2_HUMAN SPLICE ISOFORM 1 OF 000187 MANNAN-BINDING
LECTIN SERINE PROTEASE 2 PRECURSOR. 000187-1 Y09926 MAS2_HUMAN SPLICE ISOFORM 2 OF 000187 MANNAN-BINDING
LECTIN SERINE PROTEASE 2 PRECURSOR. 000187-2 M82962 MEPA_HUMAN MEPRIN A ALPHA-SUBUNIT PRECURSOR.
J05026 MLE3_HUMAN MYOSIN LIGHT CHAIi~ 3, SKELET~4L MUSCLE ISOFORM.
AH002654 MM02_HUMAN 72 KDA TYPE IV COLLAGENASE PRECURSOR.
AW778875 NGAL_HUMAN NEUTROPHIL GELATINASE ASSOCIA
AJ223500 NID2_HUMAN NIDOGEN-2 PRECURSOR.
M30269 NIDO_HUMAN NIDOGEN PRECURSOR
J04129 PAEP_HUMAN SPLICE ISOFORM 1 OF P094~65 GLYCODELIN
PRECURSOR.
J04129 PAEP_HUMAN SPLICE ISOFORM 2 OF P09466 GLYCODELIN
PRECURSOR.
J04129 PAEP_HUMAN SPLICE ISOFORM 3 OF P09466 GLYCODELIN
PRECURSOR.
AF083655 PC01_HUMAN PROCOLLAGEN C-PROTEINASE ENHANCER PROTEIN
PRECURSOR.
AA351026 PEDF_HUMAN PIGMENT EPITHELIUM-DERIVED FACTOR PRECURSOR.
AA621632 PGHD_HUMAN PROSTAGLANDIN-H2 D-ISOMERASE PRECURSOR.
AH002681 PGS2_HUMAN SPLICE ISOFORM A OF P07585 DECORIN PRECURSOR.
AH002681 PGS2_HUMAN SPLICE ISOFORM B OF P07585 DECORIN PRECURSOR.
AH002681 PGS2_HUMAN SPLICE ISOFORM D OF P07585 DECORIN PRECURSOR.
J03071 PLL_HUMAN LACTOGEN PRECURSOR.
X05199 PLMN HUMAN PLASMINOGEN PRECURSOR (EC 3.4.21.7) [Contains:
ANGIOSTATIN].
AH002870 PLSL_HUMAN L-plastin (Lymphocyte cytosolic protein 1 ) AF052157 PLTP_HUMAN SPLICE ISOFORM 1 OF P55058 PHOSPHOLIPID
TRANSFER PROTEIN PRECURSOR. P
AF052157 PLTP_HUMAN SPLICE ISOFORM 2 OF P55058 PHOSPHOLIPID
TRANSFER PROTEIN PRECURSOR. P
BC012549 PLUN_HUMAN PROTEIN PLUNC PRECURSOR.
BC010038 PMG1_HUMAN Phosphoglycerate mutase 1 BC005379 PRGB HUMAN PLASMINOGEN-RELATED PROTEIN B PRECURSOR.

BC015850 PRL _HUMANPROLACTIN PRECURSOR.

X00129 RETB _HUMANPLASMA RETINOL-BINDING PROTEIN PRECURSOR.

BC009273 SAP3 _HUMANGANGLIOSIDE GM2 ACTIVATOR PRECURSOR.

X16349 SHBG _HUMANSPLICE ISOFORM 1 OF P04278 SEX HORMONE-BINDING

GLOBULIN PRECURSOR. P

X16349 SHBG _HUMANSPLICE ISOFORM 2 OF P04278 SEX HORMONE-BINDING

GLOBULIN PRECURSOR. P

U10116 SODE _HUMANEXTRACELLULAR SUPEROXIDE DISMUTASE [CU-ZN]

P RECURSOR.

J03040 SPRC _HUMANSPARC PRECURSOR.

X94912 STN1 _HUMANSTATHMIN 1.

X64559 TETN _HUMANTETRANECTIN PRECURSOR.

M14091 THBG _HUMANTHYROXINE-BINDING GLOBULIN PRECURSOR.

M17262 THRB _HUMANPROTHROMBIN PRECURSOR.

X03124 TIM1 _HUMANMETALLOPROTEINASE INHIBITOR 1 PRECURSOR.

BC009329 TPIS _HUMANTRIOSEPHOSPHATE ISOMERASE 1.

S95936 TRFE _HUMANSEROTRANSFERRIN PRECURSOR.

A1290070 TSP1 _HUMANTHROMBOSPONDIN 1 PRECURSOR.

K02091 TTHY_HUMAN TRANSTHYRETIN PRECURSOR.

BC000379 UBIQ _HUMANUBIQUITIN.

U10362 VP36 _HUMANVESICULAR INTEGRAL-MEMBRANE PROTEIN VIP36 PRECURSOR.

BC022310 VTDB _HUMANVITAMIN D-BINDING PROTEIN PRECURSOR.

A1352496 VTNC _HUMANVITRONECTIN PRECURSOR.

IPI =
International Protein Index I~ia.~rt~stie fo>~
mat~kers Irttrauterivte a~nditi~ras:

The proteins listed in the foregoing tables are promising candidates for detecting and monitoring tions. A few examples of such conditions intrauterine and the corresponding condi protein below in greater detail.
markers are discussed Aetih-ttaodulatirt~ artd related,~ar~tei>zs as frtaa~kev~s ~ devel~darrteh,tal defects:
Moesin (Membrane-organizing extension spike protein), listed among the structural proteins in Table 2, is known to be responsible for linking transmembrane proteins to the actin cytoskeleton and implicated in various cell signaling pathways (Speck ~, et al.: Moesin functions antagonistically to the Rho pathway to maintain epithelial integrity. Natut~e 2;421(6918):83-7, 2003). It was shown that Rho-family GTPases and their effectors to modulate the activities of actin modifying molecules such as Cofilin and Profilin (also listed as a structural protein in Table 2), resulting in cytoskeletal changes associated with growth cone extension or retraction (Tang BL. Inhibitors of neuronal regeneration:
mediators and signaling mechanisms. Neurochem Int , 42(3):189-203, 2003). Coronin-like protein p57 (yet another structural protein listed in Table 2) is also involved in actin cross-linking and capping (Weitzdoerfer R et al. : Reduction of actin-related protein complex 2/3 in fetal Down syndrome. Biochem Biophys res Commun. 293:836, 2002) and are dysregulated in known developmental defects. Gelsolin (see, the Gelsolin precursor listed an a transporter/binding protein in Table 2), another actin-modulating protein is also known to be developmentally regulated and important in organ systems (Arai M, Kwiatkowski DJ. Differential developmentally regulated expression of gelsolin family members in the mouse.
Dev Dyn, 215, 297, 1999). 14-3-3 proteins are also known epithelial markers which participate in signal transduction and differentiation pathways and are essential for normal development of brain and other vital organs (Wu C, Muslin AJ. Role of 14-3-3 proteins in early Xenopus development. Mech Dev, 119, 45, 2002).
Accordingly, the listed actin-modulating proteins and other related molecules with important roles during development, that were identified for the first time in human amniotic fluid, could be used to detect developmental defects of various organ systems such as, central nervous system, cardiovascular system and other musculoskeletal deformities, which can, for example, result from chromosomal aneuploides. This is particularly true for Profiling I, which has been shown to be differentially expressed in infected amniotic fluid, and the differential expression of which has been confirmed by immunoassay.
lVlec~ke~s o iyafecti~n afad inamu~t.e-~esla~fase t~elec~ed dis~v~de~s:
The present detection of macrophage capping protein, leukocyte elastase, neutrophil gelatenase-associated lipocalicn, myleoperoxidase, L-plastin (lymphocyte cytosolic protein) and calgranulins (see the list of immune response related genes in Table 2) infected axmliotic fluid is the first demonstration of the presence and regulation of these proteins in intraamniotic infection. Several of these proteins are known responders of immune cells in response to infection, inflammation and stress. Macrophage capping protein (MCP) is a Ca(2+)-sensitive protein which modulates actin filaments and involved in inflammatory process (Dabiri GA, Molecular cloning of human macrophage capping protein cDNA. A
unique member of the gelsolin/villin family expressed primarily in macrophages J Biol Chem 15;267(23):16545-52, 1992). Similarly, Calgranulins are calcium binding proteins known to play a role in injury and wound healing (Thorey IS. et al. The Ca2+-binding proteins S 1 OOA8 and S 100A9 are encoded by novel injury-regulated genes. J Biol Chem 21;276(38):35818-25, 2001). Leukocyte elastase and neutrophil gelatinase-associated lipocalcin (NGAL) are involved in bacteriostatic and baceterolysis mechanisms (Goetz DH. et al. The neutrophil lipocalin NGAL is a bacteriostatic agent that interferes with siderophore-mediated iron acquisition. : Mol Cell 10(5):1033-43, 2002).

In addition to the above immunomodulators we also discovered, for the first time, two antibacterial proteins Fall-39 and azurocidin in the infected amniotic fluid.
Antibacterial protein Fall-39 (LL-37) binds to bacterial lipopolysaccharides (lps), and is expressed in bone marrow, testis and neutrophils. Fall-39 stimulates the degranulation of mast cells, and is a potent chemotactic factor for mast cells. Besides its antibacterial activities, Fall-39 may have the potential to recruit mast cells to inflammation foci. In the presence of the basal medium E, synthetic FALL-39 was highly active against Escherichia coli D21 and Bacillus megaterium Bml 1. A protective role for Fall 39 has been proposed, when the integrity of the skin barrier is damaged, participating in the first line of defense, and preventing local infection and systemic invasion of microbes (Agerberth B, et al. : FALL-39, a putative human peptide antibiotic, is cysteine-free and expressed in bone marrow and testis. Proc Natl Acad Sci U S
A, 3;92(1):195-9, 1995).
Azurocidin (CAP37) is a cationic antimicrobial protein isolated from human neutrophils and has important implications in host defense and inflammation. It is released during inflammation and regulates monocyte/macrophage functions, such as chemotaxis, increased sur~rival, and differentiation (Perelra HA. CAP37, a neutrophil-derived multifunctional inflammatory mediator. J Leukoc Biol ;57(6):~OS-12, 1995).
Proteases and protease il~llibitors play a key role in protein regulation and thus control several key physiological mechanisms. We have identified the expression of Serpin family of proteases (Serpin, squamous cell carcinoma antigen 1 8i 2, glia derived nexin) for the first time in human amniotic fluid, including intraamniotic infection. The serpin superfamily of serine proteinase inhibitors has a central role in controlling proteinases in many biological pathways and implicated in conformational diseases, such as the amyloidoses, the prion encephalopathies and Huntington and Alzheimer disease (Lomas DA, Carrell RW, Serpinopathies and the conformational dementias. Nat Rev Genet; 3:759, 2002).
Additionally, in intraamniotic infection we identified the expression of Cystatins, well known proteinase inhibitors involved in immunomodulation (Vray B, Hartmann S, Hoebeke J. Immunomodulatory properties of cystatins. Cell Mol Life Sci ;59(9):1503-12,2002).
The listed proteins are promising markers of infection and/or immune-response related disorders.
It is noteworthy that peptides representing macrophage capping protein, neutrophil gelatinase-associated lipocalin, myeloperoxidase precursor, L-plastin, azurocidin, antibacterial protein Fall-39, calgranulin A, profilin I, glia-derived nexin, serpin I2, and cystatin A were more abundantly or uniquely detected in infected amniotic fluid relative to normal amniotic fluid, and/or showed differential expression in immunoassays.
Accordingly, these proteins are particularly important as markers of infra-amniotic infection and/or immune-response related disorders.
Other disease~infection) speci ac proteins detected in human amniotic uid Gp-340 variant protein listed in Table 2, which has been detected in human infected amniotic fluid, is a scavenger receptor previously identified in lung. This protein is known to bind to bacteria (streptococcus and variants ) The detection of this protein in infected amniotic fluid complements the sensitive proteomic approach of the present invention to identify biomarkers for IAI. Thus, Gp-340 variant protein identified in the infected amniotic fluid lends itself for the detection of neonatal sepsis).
IGFBP-1 p~oteolytic ra nit) As shown in Table 2, IGFBP-1 has been shown to be differentially expressed in infected annaiotic fluid. The insulin-like growth factor (IGF) systems is critically involved in fetal and placental growth and modulates steroid hormone actions in the endometrium through autocuine/paracrine mechanisms. IGF-I and IGF-II stimulated proliferation and differentiation, and maintain differentiated cell functions in several cell types in vitro.
Endometrial stromal cells produce IGF-I and IGF-II as well as the high affinity IGF-binding proteins (IGFBPs). The mI~TA of six high affinity IGFBPs, which can modulate IGF
actions, are expressed in human endometrium. The most abundant IGFBP in human endometrium is IGFBP-1, which is secreted by predecidualized/
decidualized endometrial stromal cells in late secretory phase and during pregnancy. This has implications for clinical obstetrics and gynecology, where there is evidence for a pathophysiological role for IGFBP-1 in pre-eclampsia, intrauterine growth restriction, polycystic ovarian syndrome and trophoblast and endometrial neoplasms.
The presence and regulation of an IGFBP-1 proteolytic fragment in human amniotic fluid and maternal serum opens a new way for monitoring intrauterine and maternal conditions associated with pregnancy.
For further details see, also Example 12 below.
Example 3 Protein Expression Profiles of Primate and Human Amniotic Fluid Following Intrauterine Infection Whole-spectrum SELDI-TOF MS analyses collected at 235 laser intensity of AF
extracts bound to chemically defined normal-phase chip arrays revealed several peak intensity differences in 3-5 kDa and 11-12 kDa regions between infected and non-infected primate and human AF.
Protein expression profiles of primate amniotic fluid following intrauterine infection, compaxed with the corresponding normal expression profiles, are shown in Figures lA-C. As illustrated in Figures lA-C, the global protein expression profiles of control and infected amniotic fluid are distinct. A detailed spectra of amniotic fluid profiles in a smaller mass range (Figures 1B and 1C), shows distinct and characteristic differences between the protein expression profiles of control and infected samples approximately in the 3-5 I~Da and 10-12 I~Da range. This illustrates global regulation of protein expression in response to intrauterine infection and the ability to detect a unique expression signature diagnostic of intrauterine infection.
Figure 2 shows the time course analyses of the primate armliotic fluid in response to infection (GBS). Amniotic fluid was collected before the inoculation of bacteria and serially after infection and subjected to SELDI-TOF analysis as described in Example 1.
Figure 2A
shows the protein expression profile before infection, Figure 2B 12 hours after infection, and Figure 2C 36 hours after infection.
As shown in Figure 2C, one of the diagnostic peaks (10-11 I~Da) of intrauterine infections clearly reaches high levels of expression within 36 hours of acute infection. This demonstrates that diagnostic protein profiles can be used for monitoring the disease state and response to treatment.
Figure 3 shows the results of SELDI-TOF analysis of human amniotic fluid extracts bound to chemically defined normal phase chip arrays. Figure 3A shows the whole spectrum at 235 laser intensity. Figure 3B is a detailed spectrum showing the differences between infected and control samples in the 10-12 kDa region. Figure 3 is a detailed spectrum showing the characteristic differences between infected and control samples in the 3-5 kDa region.
As shown in Figures 3A-C, the global protein expression profiles of control and infected amniotic fluid are distinct. A detailed spectra of amniotic fluid profiles in a smaller mass range (Figures 3B and C), shows distinct over expressed proteins (3-5 KDa and 10-12 KDa range) between control and infected samples. Analysis of protein peaks relative intensities suggests the presence of two distinct diagnostic clusters (10-12 kDa and 3-5 kDa ranges). This illustrates global regulation of protein expression in response to intrauterine infection and the ability to detect a unique expression signature diagnostic of intrauterine infection both in human and primate models.
It is noteworthy that the diagnostic pattern of human amniotic fluid is in good agreement with the diagnostic pattern of primate amniotic fluid (Examples 3 and 4).
Example 4 Generation of Diamostic Profiles Using Different Mass Spectrometers The diagnostic protein expression profile can be detected using different types of mass spectrometers. It has been examined whether different mass spectrometers produce similar diagnostic profiles. If the diagnostic profiles are substantially independent on the type of mass spectrometer, the detected differential protein expression in the amniotic fluid can provide a diagnostic signature for intrauterine infection.
Figure 4~ shows mass spectra acquired on a generic MALDI-T~F mass spectrometer (Jensen ~N, et czl., Direct observation of UV-crosslinked protein-nucleic acid complexes by matrix-assisted laser desorption ionisation mass spectrometry. t~ezpi~' G'~~rafnufr llr~~s~
Spectf~om 7(6):496-501 (1993)) using amniotic fluid from human control (A), without intrauterine infection, and a sample (E) with intrauterine infection.
As shown in Figures 4A and E, the diagnostic profile of intrauterine infection in the 10-12 I~Da range is detected using the alternate mass spectrometer is similar to the profile detected using the SELDI-T~F machine. This indicates that differential protein expression profiles are robust and can be detected using a wide range of current mass spectrometers.
In summary, it has been discovered that amniotic fluid proteins and polypeptides exhibit differential expression patterns diagnostic of disease state. The results presented here demonstrate that disease-specific diagnostic patterns can be detected using multiple mass spectrometry approaches. The patterns or protein expression profiles are comparable between humans and primates. The profiles can be used to monitor a time-course (infection or treatment) effect.

Example 5 Quantification of Protein and Polypeptide Expression in Amniotic Fluid for Diva ,nostic and Prognostic Monitoring SDS-PAGE:
Proteins from human amniotic fluid (AF) containing high salt was precipitated with acetone. 100 ~g of amniotic fluid proteins was run on a 15% SDS-PAGE. The gel was stained with Coomassie Blue R-250. The gel image was scanned by Bio-Rad gel Scanner.
Figure 5 shows the SDS-Coomassie Blue stained gel of A) 4 human control AF
samples pooled; B) individual control AF sample; C) 4 human infected AF
samples pooled;
and D) individual infected AF sample.
Figure 5 shows significant differences between the control and infected protein expression levels in the 10-15 KDa range. It has been concluded that some of the proteins and proteolytic fragments in this mass detected using the mass spectrometers are responsible for the diagnostic profiles reflective of the protein expression levels, and have diagnostic and prognostic utility.
Example 6 Western Blot Analysis of Anmiotic Fluid from Intrauterine Infection 100 ~.g of AF proteins were run on 4-20% SDS-PAGE at 200 V for 60 minutes and transferred to PVDF membrane at 90 mM for 75 minutes. The membrane was blocked with 5°/~ milk PBST for 45 min at RT and incubated with 1 ~,g/ml primary antibody (Santa Cruz and Dako) overnight at 4 C. After wash with TBST 3 times, the membrane was incubated with secondary antibody IgG-HRP (Sigma) for 90 min at RT and visualized with ECL
(Pierce).
The results are shown in Figure 6: A) Control AF sample (pooled); B) Infected AF
sample (pooled). Figure 6 shows that IGFBP1 (11 KDa), profilin and ceruloplasmin (130 KDa) are expressed at a higher level in infected AF compared to non-infected AF. L-Plastin levels were lower in the infected sample compared to control AF sample. These proteins were also identified from the human infected samples using MS approaches (de novo sequencing) and are listed in Example 2 above.

Example 7 Immunoprecipitation Analysis of Amniotic Fluid from Intrauterine Infection Two micrograms of primary antibody was mixed with 600 ~.g of AF protein and incubated at 4 °C overnight. 15 ~,l of protein G Sepharose beads was added and incubated on a shaker for 60 minutes at room temperature. The beads were washed with IP
buffer for 6 times.
The results 'are shown in Figure 7, where (A) shows the control amniotic fluid sample (pooled), and (B) shows the infected amniotic fluid sample. Figure 7 shows that ceruloplasmin 0130 KDa) and calgranulin (~16I~Da) are expressed at a higher level in the infected amniotic fluid than control amniotic fluid.
Example 8 Detection of Differential Protein Expression in the Human Anmiotic Fluid and Maternal Serum It has been examined if the differentially expressed proteins in the amniotic fluid can be used as a lead to measure similar proteins in the maternal serum. This will enable to develop rapid and non-invasive testing for diagnoses and monitoring. The results are shown in Figure 8, where (A) is the control sample (pooled), and (B) is the infected sample (pooled).
Figure 8 shows that an IGFBP-1 smaller proteolytic fragment is consistently differentially expressed both in AF and maternal serum in response to intrauterine infection.
Example 9 Protein Microarra.~ysis of Amniotic Fluid from W trauterine Infection Antibodies: IGFBP-1( DSL); complement C3, Desmin, neutrophil elastase, NSE
antibody (DAIS~); calgranulin, ceruloplasmin, TIMP-1, plastin and profiling (Santa Cruz).
Antibody spotting: antibodies were dissolved in 40% glycerol, 60% PBS, pH 7.5 at a concentration of 100 ~,g/ml and were spotted on aldehyde slides using a Arrayer (Cartesian).
Following a 3 hr incubation in a humid chamber at room temperature, the slides were incubated for one hour in a solution of PBS, pH 7.5 containing 1 % BSA (w/v at room temperature with gentle agitation.

Biotinylation of proteins: Biotin-NHS was dissolved in DD water at 50 mg/1. 10 u1 of this solution was added into maternal serum protein solution ( 5 mg/ml in 10 mM PB, pH~.S) and incubated for 3 hours on a shaker. 5 u1 of ethanolamine was added to stop the reaction.
Biotinylated proteins were diluted in 200 u1 of TNB buffer and added to antibody arrays arid incubated overnight at 4 C. Following three washes in TNT buffer, streptavidin-HRP was added and incubated for 30 minutes at room temperature. Antigen-Antibody interaction was detected using Cy5-tyramide fluorescence. Slides were scanned on a PE
fluorescent scanner for quantification. Images of control and infected slides were overlayed using a image analysis program to generate a pseudocolor representation for relative abundance. The results are shown in Figure 9, which is a pseudocolor image of the protein array showing the binding of corresponding proteins with their antibodies. Green color represents infected sample, red color represents control sample. Part II is an enlarged area of the array showing that calgranulin expression (green) is higher in the infected serum sample. Part III is a western blot of calgranulin IP showing similar increased expression in the infected amniotic fluid sample.
Example 10 Further Analysis of Proteins Represented in the Unique Diagnostic Signature of Infected Amniotic Fluid It has been demonstrated that the SELDI-TOF profiles of control and infected amniotic fluid show a unique signature in the mass range of 10-12 I~Da (Figures 1, 2 and 3), representative of positively infected sample. The control and infected amniotic fluid resolved on a 1-D gel (Figure 5) also shows bands in the mass range of 10-12 KDa that are more abundant in the pooled or independent infected amniotic fluid samples.
Isolation of these 1-D
gel bands and further analysis using LCQ-MS as shown in Figure 13, identified peptides representative of IGF-BR-1 and S-100 calcium binding proteins.
Western blot analysis of control and infected amniotic fluid using an anti-IGF-BPl antibody as shown in Figure ~, also demonstrates the differential expression of a proteolytic fragment (~11 I~IDa) in infection.
Sequencing of the amniotic fluid polypeptides also identified the presence of IGF-BPl and calgranulins in the infected amniotic fluid (Table 3).
The sequence of the identified novel proteolytic fragment of IGFBP-1 is shown in Figure 12 (SEQ ID NO:1). In the Figure, the peptide sequences found in samples "0426seq_HI 12" and "0425se~HI-113" following 1-D gel electrophoresis, trypsin digestion and MS/MS analysis of infected amniotic fluid are shown in lower case (SEQ ID
NOs: 2 and 3). The proteolytic fragment of IGF-BP-1 detected inl-D gels (low molecular weight range, Figure 5), Western blots (Figure 6), and MS/MS analysis (Figure 13) of trypsin digested 10.5-12 KDa band from infected amniotic fluid, is represented in the region of the underlined sequence (SEQ ID NO: 4).
Indeed, MS/MS analysis and sequence search results demonstrated that the parent ion 434.89 in the mass spectrum shown in Figure 13 represents an IGF-BP-1 sequence (RSPGSPEIR), which is also shown in the Figure 12 sequence map of the IGF-BP-1 proteolytic fragment. The parent ion 1082.97 represents S-100 calcium binding proteins (i.e., Calgranulins A and B), also independently identified by de novo sequencing of AF (Tables 2 and 3).
Figure 14 shows mass spectrum for the 17.55-18.21 minute retention time peak shown in Figure 13. It is apparent that the dominate peak appears at mass 434.9.
Figure 15 shows the MS/MS spectrum for the parent ion of the 434.9 peak shown in Figure 14. Based on database search, the parent ion corresponds to a partial sequence of IGFBP-1.
Ez~ample 11 Immunodetection of IAI Biomarkers To validate the differential expression of proteins identified in IAI, two markers were selected from the 11-kDa SEI,DI-TOF MS profile (calgranulin B and IGFBP-1), one irmnunoregulatory molecule (azurocidin), and an unregulated protein (Vitamin D
binding protein) identified in global protein expression analysis. As shown in Figure 16, western blot analysis confirmed all three biomarkers showing differential expression that is consistent with the protein identification experiments performed on IAI amniotic fluid.
Utilizing specific antibodies developed against IGFBP-1 amd calgranulin B it was investigated whether differentially expressed proteins in amniotic fluid could be identified in pooled maternal serum from a limited number of. patients (n=5) where sera were available. In this limited analysis, the 11 kDa proteolytic fragment of IGFBP-1 and calgranulin B, corresponding to the 11-kDa peak that was differentially present in infected versus control amniotic fluid, was also detected in maternal serum in response to IAI
(Figures 16d and e).
Azurocidin was not detected in maternal serum.

Example 12 Diagnostic Prbfiles Characteristic of Chromosomal Aneuploidies The utility of proteomic profiling was examined to identify trisomy-21 more accurately using maternal serum screening. This study was performed with a panel of (control (n=6), trisomy-21 (n=6) and trisomy-18 (n=4), well-characterized maternal serum samples (matching amniotic fluid samples for the same cases were tested by standard chromosomal mapping method and positively confirmed the presence of trisomies) and analyzed using SELDI-TOF methodology as described above for the intrauterine infection model.
Figure 10 shows differential protein expression patterns in the maternal serum with unique profiles to distinguish trisomies. One microgram of maternal serum (after removal of albumin and immunoglobulins using protein separation columns, BioRad technologies) was used to perfomn SELDI-TOF analysis of maternal serum extracts bound to chemically defined Normal Phase chip arrays as described earlier. Whole spectrum collected at 235-laser intensity showing the differences in the peak intensities. A) Control serum;
B) trisomy-21 (Down's) serum; C) trisomy-18 serum. Detailed spectrum showing the differences in the 4.-15 KDa region unique for each case. Arrows indicate diagnostic peaks that can be used in a combination to fornmlate an algorithm to develop diagnostic screening tests.
This further illustrates detection of protein expression patterns in various biological fluids (such as maternal serum) could identify fetal-maternal conditions more accurately and in a non-invasive approach.
The detection of a significantly over-expressed 11-kDa peak in SELDI-TOF MS in the setting of IAI in the experimental primate model which utilized clinically relevant microorganisms and in women infected with different microorganisms confirms the specificity of this signature for IAI caused by a broad range of pathogens.
This over-expressed cluster may represent a basic intrauterine immune response to infection since one set of proteins identified in this unique cluster, i.e., the calgranulins, are members of the 5-100 calcium binding protein family, expressed by macrophages and by epithelial cells in acutely inflamed tissues. The second candidate from this cluster, a specific proteolytic fragment of IGFBP-1, indicates a potential protease-related mechanism in response to infection. Intact IGFBP-1 is the major IGFBP found in AF, and is synthesized by both fetal membranes and maternal decidua. Although the proteolytic cleavage of IGFBP's is a well-characterized phenomenon (Maile et al. IGF binding protein hydrolysis in various clinical states. In: The IGF System, In: Rosenfeld CR, Roberts C, Jr., eds. Totowa, NJ:
Humana Press, 1999), the particular fragment described in the current study has not been previously described.
In the second approach, characterization of proteins expressed in AF in control and IAI using LC-MS/MS identified a significant number of infection and immune-response-related molecules in IAI for the first time. Macrophage capping protein (MCP) is a Ca+2-sensitive protein that modulates actin filaments and is involved in inflammatory processes (Dabri et al.. J Biol Chem 267:16545-52 (1992)). Leukocyte elastase and neutrophil gelatinase-associated lipocalcin (NGAL) are involved in bacteriostatic and baceterolysis mechanisms (Goetz et al., Mol Cell 1):1033-43 (2002)).
In addition to the above immunomodulators, the detection of antibacterial proteins Fall-39 and azurocidin in AF in response to infection provides new insights into intrauterine immune responses. Antibacterial protein Fall-39 (LL-37) binds to bacterial lipopolysaccharides, is a potent chemotactic factor for mast cells, and serves as a first line defense to prevent local infection and systemic invasion of microbes (Agerberth et al., Proc Natl Acad sCI usa 92:195-9 (1995)). Azurocidin (CAP37) is a cationic antimicrobial protein isolated from human neutrophils with important implications in host defense and inflammation (pEREIRA, j. IELJI~f~C bI~L 57:X05-12 (1995)). Gp-340 variant protein is a scavenger receptor previously identified in lung which binds to bacteria (Prakobhol et al., J
Biol Chem 275:3960-6 (2000)). Identification of these proteins complements the sensitive proteomic approaches used to identify biomarkers for IAI.
Currently available laboratory tests utilized to confirm the diagnosis of IAI, include the measurements of maternal C-reactive protein, direct examination of AF for leukocytes or bacteria on Gram stain, AF microbial culture or PCR, measurement of AF glucose and IL-6 concentrations, and detection of AF leukocyte esterase. ~nly microbial cultures and broad-spectrum bacterial rDNA poymerase chain reaction of amniotic fluid appears to be sensitive and specific for IAI. However, microbial cultures for genital mycoplasmas or PCR-based tests are not widely available and amniocentesis is required to obtain amniotic fluid. One advantage of a proteomics based approach is that candidate peptide biomarkers lend themselves to the development of rapid point-of service and cost-effective diagnostic immunoassays. By analogy with other AF and serum screening tests (e.g., alpha-fetoprotein for neural tube defects), peptides identified within infected amniotic fluid could also be detected in maternal serum and find utility in non-invasive diagnostic tests.
The data presented in the foregoing examples, especially those utilizing pooled maternal sera, demonstrate the feasibility of this approach in that IGFBP-1 restrictive fragment and calgranulin B are two such biomarkers that appear in both AF and maternal blood during IAI
but not in the absence of infection.
In summary, .a proteomics-based analysis of AF has been employed to identify biomarkers for IAI in both an experimental non-human primate model and in a cohort of women with preterm labor and occult IAI. Diagnostic protein expression profiles were identified by SELDI-TOF MS profiling that were both sensitive and specific in detecting IAI.
High-throughput analysis of expressed proteins in AF identified expression of several immunoregulatory molecules for the first time. Immunodetection of proteins detected in the diagnostic 11-kDa peak (IGFBP-1 and calgranulin B) confirmed the presence and differential expression of these biomarkers in amniotic fluid and in maternal blood during IAI. The data presented herein serve as the basis for rapid and non-invasive assays to detect occult IAI
during pregnancy. This is an important breakthrough since it allows clinicians and investigators to target a particular subgroup of women at high risk for premature delivery, for specific interventions and in therapeutic trials. Finally, these studies demonstrate the utility of proteomics-based approaches to identify specific biomarkers and diagnostic profiles for infectious and inflammatory processes and in pathophysiologic conditions of pregnancy in general. Accordingly, the data presented herein demonstrate that differential expression of proteins in the amniotic fluid as well as other biological fluids, such as serum, represents a valid approach for a rapid, non-invasive and accurate diagnosis, prognosis, and monitoring of various maternal/fetal conditions and chrolllosomal aneuploidies.
Throughout the foregoing description the invention has been discussed with reference to certain embodiments, but it is not so limited. Indeed, various modifications of the invention in addition to those shown and described herein will become apparent to those skilled in the art from the foregoing description and fall within the scope of the appended claims.
All references cited throughout the description, and the references cited therein, are hereby expressly incorporated by reference in their entirety.

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Claims (71)

1. A method for determining the state of a maternal or fetal condition, comprising comparing the proteomic profile of a test sample of a biological fluid obtained from a mammalian subject with the proteomic profile of a normal sample, or a reference proteomic profile comprising at least one unique expression signature characteristic of said condition and determining the state of said maternal or fetal condition.

2. The method of claim 1 wherein said mammalian subject is a pregnant female.

3. The method of claim 2 wherein said pregnant female is human.

4. The method of claim 3 wherein said maternal condition is selected from the group consisting of intraamniotic infection, preeclampsia, and preterm labor.

5. The method of claim 3 wherein said fetal condition is selected from the group consisting of chromosomal aneuploidies, congenital malformation, gestational age and fetal maturity.

6. The method of claim 1 wherein said biological fluid is selected from the group consisting of amniotic fluid, serum, plasma, urine, cerebrospinal fluid, breast milk, mucus, and saliva.

7. The method of claim 3 wherein said biological fluid is amniotic fluid or maternal serum.

8. The method of claim 1 wherein the proteomic profile of the test sample comprises information of at least 2 proteins.

9. The method of claim 1 wherein the proteomic profile is a mass spectrum.

10. The method of claim 9 wherein the proteomic profile comprises at least one unique expression signature in the 3 to 5 kDa range of the mass spectrum.

11. The method of claim 9 wherein the proteomic profile comprises at least one unique expression signature in the 10 to 12 kDa range of the mass spectnun.

12. The method of claim 9 wherein the maternal condition is intra-amniotic infection, and the unique expression signature is an extra peak in the 10 to 12 kDa molecular weight range in the test sample, which is indicative of intra-amniotic infection.

13. The method of claim 12 wherein the biological fluid is amniotic fluid or maternal serum.

14. The method of claim 1 wherein the proteomic profile is produced by Western blot analysis.

15. The method of claim 1 wherein the biological fluid is that of a human, and proteomic profile includes information of the expression of one or more of the proteins selected from the group consisting of: macrophage capping protein, neutrophil gelatinase-associated lipocalin, myeloperoxidase; L-plastin;
azurocidin;
antibacterial protein FALL-39; Gp340 variant protein; Ebner salivary gland protein homolog (GenBank Accession No. 355392); leukocyte elastase inhibitor;
calgranulin A; calgranulin B; cofilin; moesin; profilin I, cronin-like protein p57;
annexin II, fibronectin; glia-derived nexin; antithrombin-III; squamous cell carcinoma antigen 1, squamous cell carcinoma antigen 2; serpin 12; cystatin A; cystatin B; cystatin C;
IGFBP-1; Vitamin D-binding protein; apolipoprotein A-I; 14-3-3 protein sigma;

3 protein zeta/delta; gelsolin; lactotransferrin; phosphoglycerate kinase 1;
phosphoglycerate mutase 1; and transketolase; or a fragment, precursor, or naturally occurring variant thereof.

16. The method of claim 15 wherein the proteomic profile includes information of the expression of two or more of said proteins.

17. The method of claim 15 wherein the proteomic profile includes information of the expression of all of said proteins.

18. The method of claim 15 wherein the biological fluid is amniotic fluid.

19. The method of claim 15 wherein the proteomic profile is that of the normal sample.

20. The method of claim 15 wherein the proteomic profile is that of the test sample or reference sample.

21. The method of claim 15 wherein one or more of said proteins are differentially expressed in said test sample relative to said normal sample.

22. The method of claim 21 wherein the proteomic profile includes information of the expression of one or more of the proteins selected from the group consisting of macrophage capping protein; neutrophil gelatinase-associated lipocalin;
myeloperoxidase; L-plastin; azurocidin; antibacterial protein FALL-39;
leukocyte elastase inhibitor; calgranulin A; calgranulin B; profilin I, glia-derived nexin; serpin 12; cystatin A; and IGFBP-1; or a fragment, precursor, or naturally occurring variant thereof.

23. The method of claim 22 wherein the proteomic profile includes information of the expression of two or more of said proteins.

24. The method of claim 22 wherein the proteomic profile includes information of the expression of all of said proteins.

25. The method of claim 22 wherein said subject is diagnosed with intra-amniotic infection.

26. The method of claim 22 wherein said patient is diagnosed with a developmental defect.

27. The method of claim 26 wherein said developmental defect is a defect in the development of an organ system.

28. The method of claim 27 wherein said organ system is the central nervous system or the cardiovascular system.

29. The method of claim 28 wherein said developmental defect is a musculoskeletal deformity.

30. The method of claim 28 wherein said developmental defect is results from a chromosomal aneuploidy.

31. The method of claim 22 wherein the proteomic profile of the test sample is essentially the same as the proteomic profile of the normal sample, and the subject is determined to be free of said maternal or fetal condition.

32. The method of claim 22 wherein the proteomic profile includes information of the expression of one or more of the proteins selected from the group consisting of the proteins listed in Tables 3 and 4.

33. The method of claim 22 wherein the proteomic profile contains the same unique expression signature as the reference sample.

34. The method of claim 32 wherein the unique expression signature is characteristic of intra-amniotic infection.

35. The method of claim 34 wherein said subject is diagnosed with intra-amniotic infection.

36. A method for the diagnosis of intra-amniotic infection, comprising (a) comparing the proteomic profile of a test sample of a biological fluid obtained from a pregnant female mammal with the proteomic profile of a normal sample, or a reference proteomic profile, wherein said proteomic profiles provide information of the mass of the proteins present in said samples, or the proteolytic fragments thereof; and (b) diagnosing said mammal with intra-amniotic infection if the proteomic profile of the test sample shows a unique expression signature in the 3-5 and/or 10-12 KDa molecular weight range.

37. The method of claim 36 wherein the proteomic profiles are represented in the form of mass spectra.

38. The method of claim 37 wherein said mammal is a primate.

39. The method of claim 38 wherein said primate is human.

40. The method of claim 39 further comprising the step of monitoring the course of said intra-amniotic infection.

41. The method of claim 39 wherein the biological fluid is amniotic fluid or maternal serum.

42. A method for the diagnosis of intra-amniotic infection, comprising:
(a) comparing the proteomic profile of a test sample of a biological fluid obtained from a pregnant female mammal with the proteomic profile of a normal sample; and (b) diagnosing said mammal with intra-amniotic infection if at least one protein selected from the group consisting of IGFB-1, calgranulin, azurocidin, profilin, ceruloplasmin, and L-plastin, or a fragment, precursor or naturally occurring variant thereof, is differentially expressed in said test sample relative to said normal sample.

43. The method of claim 42 wherein said mammal is a primate.

44. The method of claim 43 wherein said primate is human.

45. The method of claim 44 wherein said biological fluid is amniotic fluid or maternal serum.

46. The method of claim 42 wherein at least one of IGFBP-1, calgranulin, azurocidin, profilin, and ceruloplasmin, or a fragment, precursor, or naturally-occurring variant thereof, is overexpressed in said test sample relative to said normal sample.

47. The method of claim 42 wherein L-plastin is underexpressed in said test sample relative to said normal sample.

48. The method of claim 46 wherein the presence of IGFBP-1 is detected by identifying the proteolytic fragment shown in Figure 12, or a fragment thereof.

49. The method of claim 48 further comprising the step of monitoring the state of said intra-amniotic infection.

50. A method for the diagnosis of a chromosomal aneuploidy, comprising:
(a) comparing the proteomic profile of a test sample of a biological fluid obtained from a pregnant female mammal with the proteomic profile of a normal sample, or a reference proteomic profile, wherein said proteomic profiles provide information of the mass of the proteins present in said samples, or the proteolytic fragments thereof; and (b) diagnosing said mammal with said chromosomal aneuploidy if the proteomic profile of the test sample shows a unique expression signature in the 4 to 15 KDa molecular weight range.

51. The method of claim 50 wherein the chromosomal aneuploidy is Down syndrome.

52. A method for the diagnosis of a developmental defect of a fetus, comprising:
(a) comparing the proteomic profile of a test sample of a biological fluid obtained from a pregnant female mammal with the proteomic profile of a normal sample, or a reference proteomic profile; and (b) confirming the presence of said developmental defect if at least one actin-modulating protein, or a fragment, precursor, or naturally occurring variant thereof, is differentially expressed in said test sample relative to said normal sample.

53. The method of claim 52 wherein said actin-modulating protein is selected from the group consisting of moesin, p57, gelsolin, and a 14-3-3 protein.

54. A method for the diagnosis of a maternal or fetal infection or immune-response related disorder, comprising (a) comparing the proteomic profile of a test sample of a biological fluid obtained from a pregnant female mammal with the proteomic profile of a normal sample, or a reference proteomic profile; and (b) confirming the presence of said maternal or fetal infection or immune-response related disorder, if at least one protein selected from the group consisting of macrophage capping protein (MCP), leukocyte elastase, neutrophil gelatinase-associated lipcalcin (NGAL), myeloperoxidase, L-plastin, calgranulin, FALL-39, azyrocidin (CAF37), proteases and protease inhibitors, is differentially expressed in said test sample relative to said normal sample.

55. A method for the diagnosis of neonatal sepsis, comprising detecting in the proteomic profile of a biological fluid obtained from a pregnant females mammal the presence of Gp-340.

56. A proteomic profile of a biological fluid comprising information of one or more proteins selected from the group consisting of macrophage capping protein, neutrophil gelatinase-associated lipocalin, myeloperoxidase; L-plastin;
azurocidin;
antibacterial protein FALL-39; Gp340 variant protein; Ebner salivary gland protein homolog (GenBank Accession No. 355392); leukocyte elastase inhibitor;
calgranulin A; calgranulin B; cofilin; moesin; profilin I, cronin-like protein p57;
annexin II, fibronectin; glia-derived nexin; antithrombin-III; squamous cell carcinoma antigen 1, squamous cell carcinoma antigen 2; serpin 12; cystatin A; cystatin B; cystatin C;
IGFBP-1; Vitamin D-binding protein; apolipoprotein A-I; 14-3-3 protein sigma;

3 protein zeta/delta; gelsolin; lactotransferrin; phosphoglycerate kinase 1;
phosphoglycerate mutase 1; and transketolase; or a fragment, precursor, or naturally occurring variant thereof.

57. A proteomic profile of a biological fluid comprising information of one or more proteins selected from the group consisting of macrophage capping protein;
neutrophil gelatinase-associated lipocalin; myeloperoxidase; L-plastin;
azurocidin;
antibacterial protein FALL-39; leukocyte elastase inhibitor; calgranulin A;
calgranulin B; profilin I, glia-derived nexin; serpin 12; cystatin A; and IGFBP-1; or a fragment, precursor, or naturally occurring variant thereof.

58. A proteomic profile of a biological sample comprising information of one or more proteins selected from the group consisting of the proteins listed in Tables 3 and 4.

59. The proteomic profile of claim any one of claims 56-58 confirming the presence of one or more of said proteins, or a fragment, precursor, or naturally occurring variant thereof.

60. A proteomic profile of a biological fluid characteristic of intra-amniotic infection, comprising information confirming the presence of a protein selected from the group consisting of IGFB-1, profilin, ceruloplasmin, L-plastin, and calgranulin.

61. A proteomic profile of a biological fluid characteristic of intra-amniotic infection represented in a form providing information of the molecular weight of proteins present in said biological fluid, or the proteolytic fragments thereof, comprising a unique expression signature in the 3-5 KDa and/or 10-12 KDa molecular weight range.

62 62. The proteomic profile of claim 60 represented as a mass spectrum.

63. The proteomic profile of claim 61 wherein the biological fluid is amniotic fluid or maternal serum.

64. A proteomic profile essentially as shown in any one of Figures 1A-1C.

65. A proteomic profile essentially as shown in any one of Figures 2A-C.

66. A proteomic profile essentially as shown in any one of Figures 3A-C.

67. A proteomic profile essentially as shown in Figure 4A or 4B.

68. A proteomic profile essentially as shown in any one of Figures 6-10.

69. A proteomic profile of any one of claims 63-67, analyzed in a microarray format.

70. A protein array comprising one or more proteins selected from the proteins listed in Tables 2-4 immobilized on a solid support.

71. An antibody array comprising antibodies specifically binding one or more of the proteins listed in Tables 2-4 immobilized on a solid support.