Patent Publication Number: US-2013244900-A1

Title: Gene Expression Profiling in Primary Ovarian Serous Papiliary Tumors and Normal Ovarian Epithelum

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS 
     This application is a divisional under 35 U.S.C. §120 of pending application U.S. Ser. No. 13/066,004, filed Apr. 4, 2011, which is a divisional under 35 U.S.C. §120 of application U.S. Ser. No. 10/862,517, filed Jun. 7, 2004, now U.S. Pat. No. 7,927,795, which is a nonprovisional under 35 U.S.C. §119(e) of provisional patent application U.S. Ser. No. 60/476,934, filed Jun. 9, 2003, now abandoned, the entirety of all of which are hereby incorporated by reference. 
    
    
     BACKGROUND OF THE INVENTION 
     1. Field of the Invention 
     The present invention relates generally to the field of cancer research. More specifically, the present invention relates to gene expression profiling between primary ovarian serous papillary tumors and normal ovarian epithelium. 
     2. Description of the Related Art 
     Ovarian carcinoma remains the cancer with the highest mortality rate among gynecological malignancies with 25,400 new cancer cases estimated in 2003 in the United 
     States alone. Ovarian serous papillary cancer (OSPC) represents the most common histological type of ovarian carcinoma ranging from 45 to 60% of all epithelial ovarian tumors. Because of the insidious onset of the disease and the lack of reliable screening tests, two thirds of patients have advanced disease when diagnosed, and although many patients with disseminated tumors respond initially to standard combinations of surgical and cytotoxic therapy, nearly 90 percent will develop recurrence and inevitably succumb to their disease. Understanding the molecular basis of ovarian serous papillary cancer may have the potential to significantly refine diagnosis and management of these serous tumors, and may eventually lead to the development of novel, more specific and more effective treatment modalities. 
     cDNA microarray technology has recently been used to identify genes involved in ovarian carcinogenesis. Gene expression fingerprints representing large numbers of genes may allow precise and accurate grouping of human tumors and may have the potential to identify patients who are unlikely to be cured by conventional therapy. Consistent with this view, evidence has been provided to support the notion that poor prognosis B cell lymphomas and biologically aggressive breast and ovarian carcinomas can be readily separated into different groups based on gene expression profiles. In addition, large scale gene expression analysis have the potential to identify a number of differentially expressed genes in ovarian serous papillary tumor cells compare to normal ovarian epithelial cells and may therefore lay the groundwork for future studies testing some of these markers for clinical utility in the diagnosis and, eventually, the treatment of ovarian serous papillary cancer. 
     Because of the lack of an effective ovarian cancer screening program and the common development of chemotherapy resistant disease after an initial response to cytotoxic agents (i.e., platinum based regimen), ovarian cancer remains the most lethal among the gynecologic malignancies. Thus, the identification of novel ovarian tumor markers to be used for early detection of the disease as well as the development of effective therapy against chemotherapy resistant/recurrent ovarian cancer remains a high priority. 
     The prior art is deficient in understanding the molecular differences between ovarian serous papillary cancer cells and normal ovarian epithelium. The present invention fulfills this need in the art by providing gene expression profiling for these two types of tissues. 
     SUMMARY OF THE INVENTION 
     The present invention identifies genes with a differential pattern of expression between ovarian serous papillary carcinomas (OSPC) and normal ovarian epithelium and uses this knowledge to develop novel diagnostic and therapeutic marker for the treatment of this disease. Oligonucleotide microarrays with probe sets complementary to 12,533 genes were used to analyze gene expression profiles of ten primary ovarian serous papillary carcinomas cell lines, two established ovarian serous papillary cancer cell lines (i.e., UCI-101, UCI-107) and five primary normal ovarian epithelium cultures (NOVA). Unsupervised analysis of gene expression data identified 129 and 170 genes that exhibited &gt;5-fold up-regulation and down-regulation respectively in primary ovarian serous papillary carcinomas compared to normal ovarian epithelium. Genes overexpressed in established ovarian serous papillary carcinomas cell lines were found to have little correlation to those overexpressed in primary ovarian serous papillary carcinomas, highligthing the divergence of gene expression that occur as the result of long-term in vitro growth. 
     Hierarchial clustering of the expression data readily distinguished normal tissue from primary ovarian serous papillary carcinomas. Laminin, claudin 3 and claudin 4, tumor-associated calcium signal transducer 1 and 2 (TROP-1/Ep-CAM; TROP-2), ladinin 1, S100A2, SERPIN2 (PAI-2), CD24, lipocalin 2, osteopontin, kallikrein 6 (protease M) and kallikrein 10, matriptase (TADG-15) and stratifin were found among the most highly overexpressed gene in ovarian serous papillary carcinomas compared to normal ovarian epithelium. Down-regulated genes in ovarian serous papillary carcinomas included transforming growth factor beta receptor III, platelet-derived growth factor receptor alpha, SEMACAP3, ras homolog gene family member I (ARHI), thrombospondin 2 and disabled-2/differentially expressed in ovarian carcinoma 2 (Dab2/DOC2). Differential expression of some of these genes including claudin 3 and claudin 4, TROP-1 and CD24 was validated by quantitative RT-PCR as well as by flow cytometry. Immunohistochemical staining of formalin fixed paraffin embedded tumor specimens from which primary ovarian serous papillary carcinomas cultures were derived further confirmed differential expression of CD24 and TROP-1/Ep-CAM markers on ovarian serous papillary carcinomas vs normal ovarian epithelium. These results, obtained from highly purified primary cultures of ovarian cancer, highlight important molecular features of ovarian serous papillary carcinomas and provide a foundation for the development of new type-specific therapies against this disease. For example, a therapeutic strategy targeting TROP-1/Ep-CAM by monoclonal chimeric/humanized antibodies may be beneficial in patients harboring chemotherapy-resistant ovarian serous papillary carcinomas. 
     The present invention is drawn to a method of detecting ovarian serous papillary carcinoma based on overexpression of a group of genes listed in Table 2. 
     In another embodiment, the present invention provides a method of detecting ovarian serous papillary carcinoma based on down-regulation of a group of genes listed in Table 3. 
     In another embodiment, the present invention provides a method of treating ovarian serous papillary carcinoma by inhibiting the expression and function of tumor-associated calcium signal transducer 1 (TROP-1/Ep-CAM) gene. 
     In another embodiment, the present invention provides a method of treating ovarian serous papillary carcinoma by delivering Clostridium perfringens enterotoxins to ovarian tumor cells overexpressing claudin 3 or claudin 4 protein. 
     Other and further aspects, features, and advantages of the present invention will be apparent from the following description of the presently preferred embodiments of the invention. These embodiments are given for the purpose of disclosure. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
         FIG. 1  shows hierarchical clustering of 15 primary ovarian cell lines (i.e., 10 ovarian serous papillary carcinomas lines and 5 normal ovarian epithelial cell lines) and two established ovarian serous papillary carcinomas cell lines (i.e., UCI-101 and UCI-107). 
         FIG. 2  shows molecular profile of 10 primary ovarian serous papillary carcinomas cell lines and 5 normal ovarian epithelial cell lines. Hierarchical clustering of 299 genes uses a 5-fold threshold (P&lt;0.05). The cluster is color coded using red for up-regulation, green for down-regulation, and black for median expression. Agglomerative clustering of genes was illustrated with dendrograms. 
         FIGS. 3A-3H  show quantitative real-time PCR and microarray expression analysis of TROP-1 ( FIGS. 3A-3B ), CD24 ( FIGS. 3C-3D ), claudin-3 ( FIGS. 3E-3F ), and claudin-4 ( FIGS. 3G-3H ), genes differentially expressed between ovarian serous papillary carcinomas cells and normal ovarian epithelial cells. 
         FIGS. 4A-4F  show representative FACS analysis of CD24 staining ( FIGS. 4A-4C ) and TROP-1/Ep-CAM staining ( FIGS. 4D-4F ) of 2 primary ovarian serous papillary carcinomas cell lines and 1 normal ovarian epithelial cell lines. Data with CD24 and TROP-1/Ep-CAM are shown in solid black while isotype control mAb profiles are shown in white. Both CD24 and TROP-1/Ep-CAM expression were significantly higher on ovarian serous papillary carcinomas cell lines compared to normal ovarian epithelial cell lines (p&lt;0.001 by student t test). 
         FIGS. 5A-5F  show representative immunohistochemical staining for Trop-1/Ep-CAM ( FIGS. 5A-5C ) and CD24 ( FIGS. 5D-5F ) on 2 paraffin-embedded ovarian serous papillary carcinomas (OSPC) cell lines and 1 normal ovarian epithelial cell (NOVA) specimen. NOVA1 ( FIGS. 5A ,  5 D) showed negative or light (1+) staining for both Trop-1/Ep-CAM and CD24 while OSPC 1 and OSPC 3 showed strong membranous staining for TROP-1/Ep-CAM ( FIGS. 5B-5C ) and heavy apical membranous staining for CD24 ( FIGS. 5E-5F ). Original magnification 400×. 
     
    
    
     DETAILED DESCRIPTION OF THE INVENTION 
     High-throughput technologies for assaying gene expression, such as high-density oligonucleotide and cDNA microarrays, may offer the potential to identify clinically relevant gene highly differentially expressed between ovarian tumors and normal control ovarian epithelial cells. This report discloses a genome-wide examination of differential gene expression between primary ovarian serous papillary carcinomas and normal ovarian epithelial cells (NOVA). Short-term primary ovarian serous papillary carcinomas and normal ovarian epithelial cells cultures were used to minimize the risk of a selection bias inherent in any long term in vitro growth. In the present invention, only the cancer cells derived from papillary serous histology tumors, which is the most common histological type of ovarian cancer, were included to limit the complexity of gene expression analysis. 
     Hierarchical clustering of the samples and gene expression levels within the samples led to the unambiguous separation of ovarian serous papillary carcinomas from normal ovarian epithelial cells. Of interest, the expression patterns detected in primary ovarian serous papillary carcinomas cells were consistently different from those seen in established serous papillary ovarian carcinoma cell lines (i.e., UCI-101 and UCI-107). These data thus highlight the divergence of gene expression that occur as a result of long-term in vitro growth. Furthermore, these data emphasize that although established ovarian cancer cell lines provide a relatively simple model to examine gene expression, primary ovarian serous papillary carcinomas and normal ovarian epithelial cells cultures represent better model systems for comparative gene expression analysis. Because of these results, the present invention was limited to analysis of differential gene expression between the two homogeneous groups of primary ovarian serous papillary carcinomas and normal ovarian epithelial cells. 
     The present invention detected 298 genes that have at least five-fold difference in expression levels between ovarian serous papillary carcinomas and normal ovarian epithelial cells. The known function of some of these genes may provide insight into the biology of serous ovarian tumors while others may prove to be useful diagnostic and therapeutic markers against ovarian serous papillary carcinomas. 
     Laminin Gamma 2 
     Laminin gamma 2 gene was found to be the most highly differentially expressed gene in ovarian serous papillary carcinomas with over 46-fold up-regulation relative to normal ovarian epithelial cells. Cell migration of ovarian tumor cells is considered essential for cell dissemination and invasion of the submesothelial extracellular matrix commonly seen in ovarian cancer. The laminin gamma 2 isoform has been previously suggested to play an important role in tumor cell adhesion, migration, and scattering of ovarian carcinoma cells. Thus, in agreement with recent reports in other human tumor, it is likely that high laminin expression by ovarian tumor cells may be a marker correlated with the invasive potential of ovarian serous papillary carcinomas. Consistent with this view, increased cell surface expression of laminin was found in highly metastatic tumors cells compared to cells of low metastatic potential. Importantly, previous work has shown that attachment and metastases of tumor cells can be inhibited by incubation with anti-laminin antibodies or synthetic laminin peptides. 
     TROP-1/ED-CAM 
     TROP-1/Ep-CAM (also called 17-1A, ESA, EGP40) is a 40 kDa epithelial transmemebrane glycoprotein found to be overexpressed in normal epithelia cells and in various carcinomas including colorectal and breast cancer. In most adult epithelial tissues, enhanced expression of Ep-CAM is closely associated with either benign or malignant proliferation. Because among mammals Ep-CAM is an evolutionary highly conserved molecule, this seem to suggest an important biologic function of this molecule in epithelial cells and tissue. In this regard, Ep-CAM is known to function as an intercellular adhesion molecule and could have a role in tumor metastasis. Because a randomized phase II trial with mAb C017-1A in colorectal carcinoma patients has demonstrated a significant decrease in recurrence and mortality in mAb-treated patients versus control patients, TROP-1/Ep-CAM antigen has attracted substantial attention as a target for immunotherapy for treating human carcinomas. Importantly, data disclosed herein showed that TROP-1/Ep-CAM was overexpressed 39-folds in ovarian serous papillary carcinomas compared to normal ovarian epithelial cells. These data provide support for the notion that anti-Ep-CAM antibody therapy may be a novel, and potentially effective treatment option for ovarian serous papillary carcinomas patients with residual/resistant disease after surgical and cytotoxic therapy. Protein expression data obtained by flow cytometry on primary ovarian serous papillary carcinomas cell lines and by immunohistochemistry on uncultured ovarian serous papillary carcinomas blocks support this view. 
     Claudin 3 And Claudin 4 
     Claudin 3 and claudin 4, two members of claudin family of tight junction proteins, were two of the top five differentially expressed genes in ovarian serous papillary carcinomas. These results are consistent with a previous report on gene expression in ovarian cancer. Although the function of claudin proteins in ovarian cancer is still unclear, these proteins likely represent a transmembrane receptor. Of interest, claudin-3 and claudin 4 are homologous to CPE-R, the low and high-affinity intestinal epthelial receptor for  Clostridium Perfringens  enterotoxin (CPE), respectively, and are sufficient to mediate  Clostridium Perfringens  enterotoxin binding and trigger subsequent toxin-mediated cytolysis. These known functions of claudin-3 and claudin-4, combined with their extremely high level of expression in ovarian serous papillary carcinomas suggest a potential use of  Clostridium Perfringens  enterotoxin as a novel therapeutic strategy for the treatment of chemotherapy resistant disease in ovarian cancer patients. Supporting this view, functional cytotoxicity of  Clostridium Perfringens  enterotoxin in metastatic androgen-independent prostate cancer overexpressing claudin-3 has recently been reported. 
     Plasminogen Activator Inhibitor-2 (PAI-2) 
     Plasminogen activator inhibitor-2 (PAI-2), a gene whose expression has been linked to cell invasion in several human malignancies as well as to protection from tumor necrosis factor-a (TNF-a)-mediated apoptosis, was overexpressed 12-folds in ovarian serous papillary carcinomas compared to normal ovarian epithelial cells. Previous studies have shown that elevated levels of plasminogen activator inhibitor-2 are detectable in the ascites of ovarian cancer patients and that high plasminogen activator inhibitor-2 levels are independently predictive of a poor disease-free survial. Interestingly, in some of these studies, a 7-fold increase in plasminogen activator inhibitor-2 content was found in the omentum of ovarian cancer patients compared to the primary disease suggesting that metastatic tumors may overexpressed plasminogen activator inhibitor-2. Other studies, however, have identified plasminogen activator inhibitor-2 production as a favorable prognostic factor in epithelial ovarian cancer. Indeed, high PAI-2 expression in invasive ovarian tumors was limited to a group of ovarian serous papillary carcinomas patients who experience a more prolonged disease free and overall survival. The reason of these differences are not clear, but, as previously suggested, they may be related at least in part to the actions of macrophage colony stimulating factor-1 (CSF-1), a cytokine which has been shown to stimulate the release of PAI-2 by ovarian cancer cells. 
     CD24 
     CD24 is a small heavily glycosylated glycosylphosphatidylinositol-linked cell surface protein expressed in hematological malignancies as well as in a large variety of solid tumors. However, it is only recently that CD24 expression has been reported at RNA level in ovarian cancer. Consistent with this recent report, the present study shows that CD24 gene was overexpressed 14-folds in ovarian serous papillary carcinomas compared to normal ovarian epithelial cells. Because CD24 is a ligand of P-selectin, an adhesion receptor on activated endothelial cells and platelets, its expression may contribute to the metastatic capacities of CD24-expressing ovarian tumor cells. Importantly, because CD24 expression has been reported as an independent prognostic marker for ovarian cancer patients survival, it is likely that this marker delineating aggressive ovarian cancer disease may have therapeutic and/or diagnostic potential. 
     Lipocalin-2  
     Among the overexpressed genes identified herein, lipocalin 2 has not been previously linked to ovarian cancer. Lipocalin-2 represents a particularly interesting marker because of several features. Lipocalins are extracellular carriers of lipophilic molecules such as retinoids, steroids, and fatty acid, all of which may play important roles in the regulation of epithelial cells growth. In addition, because lipocalin is a secreted protein, it may play a role in the regulation of cell proliferation and survival. Of interest, two recent publications on gene expression profile of breast and pancreatic cancer have proposed lipocalin-2 as a novel therapeutic and diagnostic marker for prevention and treatment of these diseases. On the basis of the data disclosed herein, lipocalin 2 may be added to the known markers for ovarian cancer. 
     Osteopontin (SPP1) 
     Osteopontin (SPP1) is an acidic, calcium-binding glycophosphoprotein that has recently been linked to tumorigeneis in several experimental animal models and human patients studies. Because of its integrin-binding arginine-glycine-aspartate (RDG) domain and adhesive properties, osteopontin has been reported to play a crucial role in the metastatic process of several human tumors. However, it is only recently that upregulated expression of osteopontin in ovarian cancer has been identified. Importantly, because of the secreted nature of this protein, osteopontin has been proposed as a novel biomarkers for the early recognition of ovarian cancer. In the data disclosed herein, SPP1 gene was overexpressed 10-folds in ovarian serous papillary carcinomas compared to normal ovarian epithelial cells. Taken together, these data confirm a high expression of osteopontin in ovarian serous papillary carcinomas and it is of interest to further assess its clinical usefulness in ovarian cancer. 
     Kallikreins 
     The organization of kallikreins, a gene family consisting of 15 genes that all encode for trypsin-like or chymotrypsin-like serine proteases, has been recently elucidated. Serine proteases have well characterized roles in diverse cellular activities, including blood coagulation, wound healing, digestion, and immune responses, as well as tumor invasion and metastasis. Importantly, because of the secreted nature of some of these enzymes, prostate-specific antigen (PSA) and kallikrein 2 have already found important clinical application as prostate cancer biomarkers. Of interest, kallikrein 10, kallikrein 6 (also known as zyme/protease M/neurosin), and matriptase (TADG-15/MT-SP1) were all found highly expressed in ovarian serous papillary carcinomas compared to normal ovarian epithelial cells. These data confirm previous results showing high expression of several kallikrein genes and proteins in ovarian neoplasms. Moreover, these results obtained by high-throughput technologies for assaying gene expression further emphasize the view that some members of the kallikrein family have the potential to become novel ovarian cancer markers for ovarian cancer early diagnosis as well as targets for novel therapies against recurrent/refractory ovarian disease. 
     Other highly overexpressed genes in ovarian serous papillary carcinomas include stratifin, desmoplakin, S100A2, cytokeratins 6 and 7, MUC-1, and MMP12. 
     Down-Regulated Genes 
     The present invention also identified a large number of down-regulated (at least 5-fold) genes in ovarian serous papillary carcinomas such as transforming growth factor beta receptor III, platelet-derived growth factor receptor alpha, SEMACAP3, ras homolog gene family member I (ARHI), thrombospondin 2 and disabled-2/differentially expressed in ovarian carcinoma 2 (Dab2/DOC2) (Table 3). Some of these genes encode well-known tumor suppressor genes such as SEMACAP3, ARHI, and Dab2/DOC2, while others encode for proteins important for ovarian tissue homeostasis or that have been previously implicated in apoptosis, proliferation, adhesion or tissue maintenance. 
     In conclusion, several ovarian serous papillary carcinomas restricted markers have been identified herein. Some of these genes have been previously reported to be highly expressed in ovarian cancer while others have not been previously linked with this disease. Identification of TROP-1/Ep-CAM as the second most highly overexpressed gene in ovarian serous papillary carcinomas suggests that a therapeutic strategy targeting TROP-1/Ep-CAM by monoclonal antibodies, an approach that has previously been shown to increase survival in patients harboring stage III colon cancer, may be also beneficial in patients harboring chemotherapy-resistant ovarian serous papillary carcinomas. Targeting claudin 3 and claudin 4 by local and/or systemic administration of  Clostridium Perfringens  enterotoxin may represent another novel therapeutic modalities in patients harboring ovarian serous papillary carcinomas refractory to standard treatment. 
     Thus, the present invention is drawn to a method of detecting ovarian serous papillary carcinoma. The method involves performing statistical analysis on the expression levels of a group of genes listed in Table 2. Examples of such genes include laminin, tumor-associated calcium signal transducer 1 (TROP-1/Ep-CAM), tumor-associated calcium signal transducer 2 (TROP-2), claudin 3, claudin 4, ladinin 1, S100A2, SERPIN2 (PAI-2), CD24, lipocalin 2, osteopontin, kallikrein 6 (protease M), kallikrein 10, matriptase and stratifin. Over-expression of these genes would indicate that such individual has ovarian serous papillary carcinoma. In general, gene expression can be examined at the protein or RNA level. Preferably, the examined genes have at least a 5-fold over-expression compared to expression in normal individuals. In one embodiment, gene expression is examined by DNA microarray and the data are analyzed by the method of hierarchical cluster analysis. In another embodiment, gene expression is determined by flow cytometric analysis or immunohistochemical staining. 
     The present invention also provides a method of detecting ovarian serous papillary carcinoma based on down-regulation of a group of genes listed in Table 3. Examples of such genes include transforming growth factor beta receptor III, platelet-derived growth factor receptor alpha, SEMACAP3, ras homolog gene family, member I (ARHI), thrombospondin 2 and disabled-2/differentially expressed in ovarian carcinoma 2 (Dab2/DOC2). In general, gene expression can be examined at the protein or RNA level. Preferably, the examined genes have at least a 5-fold down-regulation compared to expression in normal individuals. In one embodiment, gene expression is examined by DNA microarray and the data are analyzed by the method of hierarchical cluster analysis. In another embodiment, gene expression is determined by flow cytometric analysis or immunohistochemical staining. 
     In another aspect of the present invention, there is provided a method of treating ovarian serous papillary carcinoma by inhibiting the expression and function of tumor-associated calcium signal transducer 1 (TROP-1/Ep-CAM) gene. In general, inhibition of gene expression can be obtained using anti-TROP-1/Ep-CAM antibody or anti-sense oligonucleotide according to protocols well known in the art. For example, monoclonal anti-TROP-1/Ep-CAM (chimeric/humanized) antibody can be used in antibody-directed therapy that has improved survival of patients described previously (1). 
     In another embodiment, there is provided a method of treating ovarian serous papillary carcinoma by delivering  Clostridium perfringens  enterotoxins to ovarian tumor cells overexpressing claudin 3 or claudin 4 protein. Preferably, the enterotoxins are delivered by systemic administration, intraperitoneal administration or intratumoral injection. 
     The following examples are given for the purpose of illustrating various embodiments of the invention and are not meant to limit the present invention in any fashion. One skilled in the art will appreciate readily that the present invention is well adapted to carry out the objects and obtain the ends and advantages mentioned, as well as those objects, ends and advantages inherent herein. Changes therein and other uses which are encompassed within the spirit of the invention as defined by the scope of the claims will occur to those skilled in the art. 
     EXAMPLE 1  
     Establishment of Primary Ovarian Serous Papillary Carcinoma and Normal Ovarian Epithelial Cell Lines 
     A total of 15 primary cell lines (i.e., 10 ovarian serous papillary carcinomas cell lines and 5 normal ovarian epithelial cell lines) were established after sterile processing of the tumor samples from surgical biopsies as previously described for ovarian carcinoma specimens (2-4 Ismail et al., 2000; Hough et al., 2000; Santin et al., 2000). UCI-101 and UCI-107, two previously characterized ovarian serous papillary carcinomas cell lines (5-6) were also included in the analysis. Tumors were staged according to the F.I.G.O. operative staging system. Radical tumor debulking, including a total abdominal hysterectomy and omentectomy, was performed in all ovarian carcinoma patients while normal ovarian tissue was obtained from consenting donors who undergo surgery for benign pathology scraping epithelial cells from the ovarian surface. No patient received chemotherapy before surgical therapy. The patient and donors characteristics are described in Table 1. 
     Briefly, normal tissue was obtained by scraping epithelial cells from the ovarian surface and placing cells in RPMI 1640 medium (Sigma Chemical Co., St. Louis, Mo.) containing 10% fetal bovine serum (FBS, Invitrogen, Grand Island, N.Y.), 200 U/ml penicillin, and 200 μg/ml streptomycin. The epithelial explants were then allowed to attach and proliferate. Once the epithelial cells reached confluency, explants were trypsinized and subcultured for 3 to 4 passages before being collected for RNA extraction. 
     Viable tumor tissue was mechanically minced in RPMI 1640 to portions no larger than 1-3 mm 3  and washed twice with RPMI 1640. The portions of minced tumor were then placed into 250 ml flasks containing 30 ml of RPMI 1640 enzyme solution containing 0.14% collagenase Type I (Sigma, St. Louis, Mo.) and 0.01% DNAse (Sigma, 2000 KU/mg), and incubated on a magnetic stirring apparatus overnight at 4° C. Enzymatically dissociated tumor was then filtered through 150 mm nylon mesh to generate single cell suspension. The resultant cell suspension was then washed twice in RPMI 1640 plus 10% fetal bovine serum (FBS, Invitrogen, Grand Island, N.Y.). Primary cell lines were maintained in RPMI 1640 supplemented with 10% FBS, 200 U/ml penicillin, and 200 μg/ml streptomycin at 37° C., 5% CO 2  in 75-150 cm 2  tissue culture flasks (Corning Inc., Corning, N.Y.). Tumor cells were collected for RNA extraction at a confluence of 50% to 80% after a minimum of two to a maximum of twelve passages in vitro. The epithelial nature and the purity of ovarian serous papillary carcinomas and normal ovarian epithelial cells cultures were verified by immunohistochemical staining and flow cytometric analysis with antibodies against cytokeratin as previously described (2,4). Only primary cultures which had at least 90% viability and contained &gt;99% epithelial cells were used for total RNA extraction. 
     
       
         
           
               
             
               
                 TABLE 1 
               
             
            
               
                   
               
               
                 Characteristics of The Patients 
               
            
           
           
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                 Chemotherapy 
                   
               
               
                 Patient 
                 Age 
                 Race 
                 Grade 
                 regimen 
                 Stage 
               
               
                   
               
               
                 OSPC 1 
                 42 
                 White 
                 G2/3 
                 TAX + CARB 
                 IV A 
               
               
                 OSPC 2 
                 67 
                 White 
                 G3 
                 TAX + CARB 
                 III B 
               
               
                 OSPC 3 
                 61 
                 White 
                 G3 
                 TAX + CARB 
                 III C 
               
               
                 OSPC 4 
                 60 
                 White 
                 G3 
                 TAX + CARB 
                 III C 
               
               
                 OSPC 5 
                 59 
                 Afro-American 
                 G2/3 
                 TAX + CARB 
                 III C 
               
               
                 OSPC 6 
                 72 
                 White 
                 G3 
                 TAX + CARB 
                 IV A 
               
               
                 OSPC 7 
                 63 
                 White 
                 G3 
                 TAX + CARB 
                 III C 
               
               
                 OSPC 8 
                 74 
                 Afro-American 
                 G2/3 
                 TAX + CARB 
                 III C 
               
               
                 OSPC 9 
                 68 
                 White 
                 G3 
                 TAX + CARB 
                 III B 
               
               
                   
               
               
                 OSPC, ovarian serous papillary carcinoma. 
               
            
           
         
       
     
     EXAMPLE 2  
     Microarray Hybridization and Statistical Analysis 
     RNA purification, cDNA synthesis, cRNA preparation, and hybridization to the Affymetrix Human U95Av2 GeneChip microarray were performed according to the manufacturer&#39;s protocols and as reported (7). 
     All data used in the analyses were derived from Affymetrix 5.0 software. GeneChip 5.0 output files are given as a signal that represents the difference between the intensities of the sequence-specific perfect match probe set and the mismatch probe set, or as a detection of present, marginal, or absent signals as determined by the GeneChip 5.0 algorithm. Gene arrays were scaled to an average signal of 1500 and then analyzed independently. Signal calls were transformed by the log base 2 and each sample was normalized to give a mean of 0 and variance of 1. 
     Statistical analyses of the data were performed with the software packages SPSS10.0 (SPSS, Chicago, Ill.) and the significance analysis of microarrays (SAM) method (8). Genes were selected for analysis based on detection and fold change. In each comparison, genes having “present” detection calls in more than half of the samples in the overexpressed gene group were retained for statistical analysis if they showed &gt;2-fold change between groups. Retained genes were subjected to SAM to establish a false discovery rate (FDR), then further filtered via the Wilcoxon rank sum (WRS) test at alpha=0.05. The false discovery rate (FDR) obtained from the initial SAM analysis was assumed to characterize genes found significant via WRS. 
     The hierarchical clustering of average-linkage method with the centered correlation metric was used (9). The dendrogram was constructed with a subset of genes from 12,533 probe sets present on the microarray, whose expression levels vary the most among the 11 samples, and thus most informative. For the hierarchical clustering shown in  FIGS. 1-2 , only genes significantly expressed and whose average change in expression level was at least two-fold were chosen. The expression value of each selected gene was re-normalized to have a mean of zero. 
     EXAMPLE 3  
     Gene Expression Profiles Distinguish Ovarian Serous Papillary Carcinoma Cells from Normal Ovarian Epithelial Cells and Identify Differentially Expressed Genes 
     Flash frozen biopsies from ovarian tumor tissue are known to contain significant numbers of contaminant stromal cells as well as a variety of host derived immune cells (e.g., monocytes, dendritic cells, lymphocytes). In addition, because ovarian epithelial cells represent a small proportion of the total cells found in the normal ovary, it is difficult to collect primary material that is free of contaminating ovarian stromal cells in sufficient quantities to conduct comparative gene expression analyses. Ovarian epithelial cells, however, can be isolated and expanded in culture for about 15 passages (2-3) while the majority of primary ovarian carcinomas can be expanded in vitro for at least a few weeks (4). Thus, short-term primary ovarian serous papillary carcinomas and normal ovarian epithelial cell cultures were used in the following studies. 
     Comprehensive gene expression profiles of 10 primary ovarian serous papillary carcinomas cell lines and 5 primary normal ovarian epithelial cell lines were generated using high-density oligonucleotide arrays with 12,533 probe sets, which in total interrogated some 10,000 genes. In addition, gene expression profiles derived from two established and previously characterized cell lines (UCI-101 and UCI-107) were also analyzed. By combining the detection levels of genes significantly expressed in primary and established ovarian serous papillary carcinomas cell lines, very little correlation between the two groups of cells was found. Indeed, as shown in  FIG. 1 , UCI-101 and UCI-107 established cell lines grouped together in the dendrogram while all 10 primary ovarian serous papillary carcinomas cell lines clustered tightly together in the rightmost columns separately by the 5 normal ovarian epithelial cell line controls. Because of these results, gene expression profile analysis was focused on the two homogeneous groups of primary ovarian serous papillary carcinomas cells and normal ovarian epithelial cells. 
     Using the nonparametric WRS test (p&lt;0.05) that readily distinguished between the two groups of primary cultures, 1,546 genes were found to be differentially expressed between ovarian serous papillary carcinomas cells and normal ovarian epithelial cells. There were 365 genes showing &gt;5-fold change along with “present” detection calls in more than half the samples in the overexpressed group. Of these, 350 were found significant by SAM, with a median FDR of 0.35% and a 90 th  percentile FDR of 0.59%. Of the 365 aforementioned genes, 299 yielded p&lt;0.05 via WRS, and 298 were among the genes found significant by SAM. 
       FIG. 2  describes the cluster analysis performed on hybridization intensity values for 298 gene segments whose average change in expression level was at least five-fold and which were found significant with both WRS test and SAM analysis. All 10 ovarian serous papillary carcinomas were grouped together in the rightmost columns. Similarly, in the leftmost columns all 5 normal ovarian epithelial cell cultures were found to cluster tightly together. The tight clustering of ovarian serous papillary carcinomas from normal ovarian epithelial cells was “driven” by two distinct profiles of gene expression. The first was represented by a group of 129 genes that were highly expressed in ovarian serous papillary carcinomas and underexpressed in normal ovarian epithelial cells (Table 2). Many genes shown previously to be involved in ovarian carcinogenesis are present on these lists, while others are novel in ovarian carcinogeneis. Included in this group of genes are laminin, claudin 3 and claudin 4, tumor-associated calcium signal transducer 1 and 2 (TROP-1/Ep-CAM; TROP-2), ladinin 1, S100A2, SERPIN2 (PAI-2), CD24, lipocalin 2, osteopontin, kallikrein 6 (protease M), kallikrein 10, matriptase (TADG-15) and stratifin (Table 2). Importantly, TROP-1/Ep-CAM gene, which encodes for a transmembrane glycoprotein previously found to be overexpressed in various carcinoma types including colorectal and breast and where antibody-directed therapy has resulted in improved survival of patients, was 39-fold differentially expressed in ovarian serous papillary carcinomas when compared to normal ovarian epithelial cells (Table 2). 
     The second profile was represented by 170 genes that were highly expressed in normal ovarian epithelial cells and underexpressed in ovarian serous papillary carcinomas (Table 3). Included in this group of genes are transforming growth factor beta receptor III, platelet-derived growth factor receptor alpha, SEMACAP3, ras homolog gene family, member I (ARHI), thrombospondin 2 and disabled-2/differentially expressed in ovarian carcinoma 2 (Dab2/DOC2) (Table 3). 
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                 Upregulated Genes Expressed At Least 5 Fold Higher In Ovarian Serous 
               
               
                 Papillary Carcinoma Compared With Normal Ovarian Epithelial Cells 
               
            
           
           
               
               
               
               
            
               
                 Probe Set 
                 Gene Symbol 
                 Score(d)(SAM) 
                 Ratio OVA/NOVA 
               
               
                   
               
            
           
           
               
               
               
               
            
               
                 35280_at 
                 LAMC2 
                 1.68927386 
                 0.006 
               
               
                 35276_at 
                 CLDN4 
                 1.734410451 
                 0.015 
               
               
                 33904_at 
                 CLDN3 
                 1.650076713 
                 0.02 
               
               
                 575_s_at 
                 TACSTD1 
                 1.705816336 
                 0.02 
               
               
                 32154_at 
                 TFAP2A 
                 1.667038647 
                 0.002 
               
               
                 39015_f_at 
                 KRT6E 
                 1.062629117 
                 0.047 
               
               
                 1713_s_at 
                 CDKN2A 
                 1.137682905 
                 0.015 
               
               
                 41376_i_at 
                 UGT2B7 
                 0.939735032 
                 0.047 
               
               
                 38551_at 
                 L1CAM 
                 1.151935363 
                 0.008 
               
               
                 291_s_at 
                 TACSTD2 
                 1.249487388 
                 0.047 
               
               
                 33282_at 
                 LAD1 
                 1.422481563 
                 0.006 
               
               
                 34213_at 
                 KIBRA 
                 1.533570321 
                 0.002 
               
               
                 38489_at 
                 HBP17 
                 1.522882814 
                 0.004 
               
               
                 36869_at 
                 PAX8 
                 1.43906836 
                 0.004 
               
               
                 38482_at 
                 CLDN7 
                 1.307716566 
                 0.027 
               
               
                 37909_at 
                 LAMA3 
                 1.121654521 
                 0.027 
               
               
                 34674_at 
                 S100A1 
                 1.219106334 
                 0.008 
               
               
                 1620_at 
                 CDH6 
                 0.908193479 
                 0.036 
               
               
                 32821_at 
                 LCN2 
                 1.99990601 
                 0.008 
               
               
                 522_s_at 
                 FOLR3 
                 1.113781518 
                 0.02 
               
               
                 39660_at 
                 DEFB1 
                 0.837612681 
                 0.036 
               
               
                 2011_s_at 
                 BIK 
                 1.594057668 
                 0.006 
               
               
                 41587_g_at 
                 FGF18 
                 0.965726983 
                 0.02 
               
               
                 36929_at 
                 LAMB3 
                 1.115590892 
                 0.047 
               
               
                 35726_at 
                 S100A2 
                 1.036576352 
                 0.004 
               
               
                 1887_g_at 
                 WNT7A 
                 1.186990893 
                 0.004 
               
               
                 35879_at 
                 GAL 
                 1.223278825 
                 0.002 
               
               
                 266_s_at 
                 CD24 
                 1.756569076 
                 0.004 
               
               
                 1108_s_at 
                 EPHA1 
                 1.242309171 
                 0.006 
               
               
                 37483_at 
                 HDAC9 
                 1.406744957 
                 0.006 
               
               
                 31887_at 
                 — 
                 1.311220827 
                 0.011 
               
               
                 1788_s_at 
                 DUSP4 
                 1.22421987 
                 0.003 
               
               
                 32787_at 
                 ERBB3 
                 0.996784565 
                 0.02 
               
               
                 41660_at 
                 CELSR1 
                 1.634286803 
                 0.004 
               
               
                 33483_at 
                 NMU 
                 1.100849065 
                 0.004 
               
               
                 31792_at 
                 ANXA3 
                 0.896090153 
                 0.011 
               
               
                 36838_at 
                 KLK10 
                 1.026306829 
                 0.02 
               
               
                 1585_at 
                 ERBB3 
                 1.102058608 
                 0.011 
               
               
                 1898_at 
                 TRIM29 
                 1.071987353 
                 0.002 
               
               
                 37185_at 
                 SERPINB2 
                 0.815945986 
                 0.027 
               
               
                 406_at 
                 ITGB4 
                 1.296194559 
                 0.006 
               
               
                 1914_at 
                 CCNA1 
                 0.936342778 
                 0.011 
               
               
                 977_s_at 
                 CDH1 
                 0.93637461 
                 0.036 
               
               
                 37603_at 
                 IL1RN 
                 1.103624942 
                 0.015 
               
               
                 35977_at 
                 DKK1 
                 1.123240701 
                 0.006 
               
               
                 36133_at 
                 DSP 
                 1.280269127 
                 0.002 
               
               
                 36113_s_at 
                 TNNT1 
                 1.269558595 
                 0.002 
               
               
                 1802_s_at 
                 ERBB2 
                 0.787465706 
                 0.006 
               
               
                 2092_s_at 
                 SPP1 
                 1.34315986 
                 0.02 
               
               
                 35699_at 
                 BUB1B 
                 1.026388835 
                 0.006 
               
               
                 37554_at 
                 KLK6 
                 0.895036336 
                 0.027 
               
               
                 38515_at 
                 BMP7 
                 0.945367 
                 0.027 
               
               
                 34775_at 
                 TSPAN-1 
                 1.001195829 
                 0.02 
               
               
                 37558_at 
                 IMP-3 
                 1.023799379 
                 0.011 
               
               
                 38324_at 
                 LISCH7 
                 1.308000521 
                 0.006 
               
               
                 39610_at 
                 HOXB2 
                 1.355268631 
                 0.006 
               
               
                 572_at 
                 TTK 
                 1.122796615 
                 0.006 
               
               
                 1970_s_at 
                 FGFR2 
                 1.022708001 
                 0.02 
               
               
                 160025_at 
                 TGFA 
                 1.065272755 
                 0.015 
               
               
                 41812_s_at 
                 NUP210 
                 1.39287031 
                 0.006 
               
               
                 34282_at 
                 NFE2L3 
                 1.165273649 
                 0.008 
               
               
                 2017_s_at 
                 CCND1 
                 1.114984456 
                 0.002 
               
               
                 33323_r_at 
                 SFN 
                 1.202433185 
                 0.008 
               
               
                 38766_at 
                 SRCAP 
                 1.131917941 
                 0.008 
               
               
                 41060_at 
                 CCNE1 
                 1.151246634 
                 0.006 
               
               
                 39016_r_at 
                 KRT6E 
                 0.973486831 
                 0.008 
               
               
                 31610_at 
                 MAP17 
                 1.0156502 
                 0.027 
               
               
                 2027_at 
                 S100A2 
                 0.941919001 
                 0.008 
               
               
                 418_at 
                 MKI67 
                 0.826426448 
                 0.011 
               
               
                 1536_at 
                 CDC6 
                 1.08868941 
                 0.017 
               
               
                 634_at 
                 PRSS8 
                 0.899891713 
                 0.02 
               
               
                 34342_s_at 
                 SPP1 
                 1.318723271 
                 0.02 
               
               
                 182_at 
                 ITPR3 
                 1.107167336 
                 0.006 
               
               
                 32382_at 
                 UPK1B 
                 0.731294678 
                 0.047 
               
               
                 863_g_at 
                 SERPINB5 
                 0.783530451 
                 0.015 
               
               
                 904_s_at 
                 TOP2A 
                 0.971648429 
                 0.02 
               
               
                 40095_at 
                 CA2 
                 0.798857154 
                 0.027 
               
               
                 41294_at 
                 KRT7 
                 1.082553892 
                 0.011 
               
               
                 39951_at 
                 PLS1 
                 0.995091449 
                 0.006 
               
               
                 38051_at 
                 MAL 
                 0.819842532 
                 0.036 
               
               
                 40726_at 
                 KIF11 
                 0.803689697 
                 0.036 
               
               
                 1148_s_at 
                 — 
                 0.683569558 
                 0.047 
               
               
                 37920_at 
                 PITX1 
                 0.996497645 
                 0.015 
               
               
                 37117_at 
                 ARHGAP8 
                 1.129131077 
                 0.002 
               
               
                 38881_i_at 
                 TRIM16 
                 0.721698355 
                 0.047 
               
               
                 34251_at 
                 HOXB5 
                 1.219463307 
                 0.002 
               
               
                 41359_at 
                 PKP3 
                 1.047269618 
                 0.004 
               
               
                 40145_at 
                 TOP2A 
                 0.961173129 
                 0.02 
               
               
                 37534_at 
                 CXADR 
                 0.888147605 
                 0.006 
               
               
                 40303_at 
                 TFAP2C 
                 0.948734146 
                 0.004 
               
               
                 31805_at 
                 FGFR3 
                 0.969764101 
                 0.011 
               
               
                 33245_at 
                 MAPK13 
                 0.877514586 
                 0.011 
               
               
                 885_g_at 
                 ITGA3 
                 0.702747685 
                 0.036 
               
               
                 34693_at 
                 STHM 
                 0.872525584 
                 0.008 
               
               
                 38555_at 
                 DUSP10 
                 0.880305317 
                 0.008 
               
               
                 38418_at 
                 CCND1 
                 1.071102249 
                 0.002 
               
               
                 33730_at 
                 RAI3 
                 0.813298748 
                 0.011 
               
               
                 39109_at 
                 TPX2 
                 1.040973216 
                 0.011 
               
               
                 36658_at 
                 DHCR24 
                 1.122129795 
                 0.004 
               
               
                 35281_at 
                 LAMC2 
                 0.747766326 
                 0.047 
               
               
                 38749_at 
                 MGC29643 
                 0.683275086 
                 0.036 
               
               
                 1083_s_at 
                 MUC1 
                 0.746980491 
                 0.027 
               
               
                 40079_at 
                 RAI3 
                 0.709840659 
                 0.02 
               
               
                 2047_s_at 
                 JUP 
                 0.815282235 
                 0.011 
               
               
                 32275_at 
                 SLPI 
                 0.940625784 
                 0.02 
               
               
                 2020_at 
                 CCND1 
                 0.926408163 
                 0.002 
               
               
                 33324_s_at 
                 CDC2 
                 1.026683994 
                 0.008 
               
               
                 36863_at 
                 HMMR 
                 0.96343264 
                 0.006 
               
               
                 1657_at 
                 PTPRR 
                 0.764510362 
                 0.02 
               
               
                 37985_at 
                 LMNB1 
                 0.895475347 
                 0.008 
               
               
                 36497_at 
                 C14orf78 
                 0.942921564 
                 0.008 
               
               
                 2021_s_at 
                 CCNE1 
                 0.893228297 
                 0.006 
               
               
                 37890_at 
                 CD47 
                 0.775908217 
                 0.015 
               
               
                 40799_at 
                 C16orf34 
                 0.852774782 
                 0.008 
               
               
                 35309_at 
                 ST14 
                 0.852534105 
                 0.008 
               
               
                 1599_at 
                 CDKN3 
                 0.925527261 
                 0.02 
               
               
                 981_at 
                 MCM4 
                 1.058558782 
                 0.006 
               
               
                 32715_at 
                 VAMP8 
                 0.938171642 
                 0.006 
               
               
                 38631_at 
                 TNFAIP2 
                 0.72369235 
                 0.015 
               
               
                 34715_at 
                 FOXM1 
                 1.31035831 
                 0.008 
               
               
                 33448_at 
                 SPINT1 
                 0.924028022 
                 0.015 
               
               
                 419_at 
                 MKI67 
                 0.938133197 
                 0.015 
               
               
                 1651_at 
                 UBE2C 
                 1.436239741 
                 0.008 
               
               
                 35769_at 
                 GPR56 
                 0.937347548 
                 0.015 
               
               
                 37310_at 
                 PLAU 
                 0.885110741 
                 0.036 
               
               
                 36761_at 
                 ZNF339 
                 0.937123503 
                 0.011 
               
               
                 37343_at 
                 ITPR3 
                 1.001079303 
                 0.003 
               
               
                 40425_at 
                 EFNA1 
                 0.813414458 
                 0.047 
               
               
                 1803_at 
                 CDC2 
                 0.732852195 
                 0.027 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 3 
               
             
            
               
                   
               
               
                 Upregulated Genes Expressed At Least 5 Fold Higher In Normal Ovarian 
               
               
                 Epithelial Cells Compared With Ovarian Serous Papillary Carcinoma 
               
            
           
           
               
               
               
               
               
            
               
                   
                   
                   
                 p 
                 Ratio 
               
               
                 Probe Set 
                 Gene Symbol 
                 Score(d)(SAM) 
                 of WRS 
                 NOVA/OVA 
               
               
                   
               
            
           
           
               
               
               
               
               
            
               
                 39701_at 
                 PEG3 
                 1.991111245 
                 0.006 
                 113.32 
               
               
                 32582_at 
                 MYH11 
                 1.921434447 
                 0.002 
                 67.31 
               
               
                 39673_i_at 
                 ECM2 
                 1.740409609 
                 0.011 
                 53.54 
               
               
                 37394_at 
                 C7 
                 1.597329897 
                 0.02 
                 50.45 
               
               
                 37247_at 
                 TCF21 
                 2.261979734 
                 0.002 
                 39.29 
               
               
                 1897_at 
                 TGFBR3 
                 1.648143277 
                 0.003 
                 38.12 
               
               
                 36627_at 
                 SPARCL1 
                 1.610346382 
                 0.008 
                 37.84 
               
               
                 37015_at 
                 ALDH1A1 
                 1.886579474 
                 0.002 
                 35.18 
               
               
                 38469_at 
                 TM4SF3 
                 1.620821878 
                 0.003 
                 34.43 
               
               
                 35717_at 
                 ABCA8 
                 1.709820793 
                 0.008 
                 33.92 
               
               
                 32664_at 
                 RNASE4 
                 1.720857082 
                 0.003 
                 32.94 
               
               
                 40775_at 
                 ITM2A 
                 1.393751125 
                 0.006 
                 31.35 
               
               
                 38519_at 
                 NR1H4 
                 1.431579641 
                 0.004 
                 27.02 
               
               
                 37017_at 
                 PLA2G2A 
                 1.263990266 
                 0.011 
                 26.68 
               
               
                 36681_at 
                 APOD 
                 1.44030134 
                 0.008 
                 26.04 
               
               
                 34193_at 
                 CHL1 
                 1.738491852 
                 0.006 
                 25.97 
               
               
                 34363_at 
                 SEPP1 
                 1.490374268 
                 0.015 
                 25.93 
               
               
                 1501_at 
                 IGF1 
                 1.116943817 
                 0.027 
                 25.87 
               
               
                 33240_at 
                 SEMACAP3 
                 1.818843975 
                 0.003 
                 25.54 
               
               
                 36939_at 
                 GPM6A 
                 0.924236354 
                 0.047 
                 25.47 
               
               
                 614_at 
                 PLA2G2A 
                 1.391395227 
                 0.003 
                 23.15 
               
               
                 37407_s_at 
                 MYH11 
                 1.72766007 
                 0.002 
                 22.73 
               
               
                 39325_at 
                 EBAF 
                 1.248164036 
                 0.02 
                 22.49 
               
               
                 767_at 
                 — 
                 1.688001805 
                 0.002 
                 21.90 
               
               
                 37595_at 
                 — 
                 1.582101386 
                 0.004 
                 20.94 
               
               
                 1290_g_at 
                 GSTM5 
                 1.383630361 
                 0.003 
                 20.84 
               
               
                 34388_at 
                 COL14A1 
                 1.400078214 
                 0.015 
                 20.39 
               
               
                 607_s_at 
                 VWF 
                 1.314435559 
                 0.002 
                 19.05 
               
               
                 37599_at 
                 AOX1 
                 1.669903577 
                 0.003 
                 17.61 
               
               
                 41504_s_at 
                 MAF 
                 1.463988429 
                 0.008 
                 16.40 
               
               
                 41412_at 
                 PIPPIN 
                 1.799353403 
                 0.002 
                 16.08 
               
               
                 279_at 
                 NR4A1 
                 1.194733065 
                 0.008 
                 15.42 
               
               
                 38427_at 
                 COL15A1 
                 1.570514035 
                 0.002 
                 15.38 
               
               
                 41405_at 
                 SFRP4 
                 1.478603828 
                 0.002 
                 14.44 
               
               
                 39066_at 
                 MFAP4 
                 1.91469237 
                 0.004 
                 14.26 
               
               
                 1731_at 
                 PDGFRA 
                 1.791307012 
                 0.003 
                 13.91 
               
               
                 36595_s_at 
                 GATM 
                 1.382271028 
                 0.004 
                 13.86 
               
               
                 34343_at 
                 STAR 
                 2.080476608 
                 0.003 
                 13.67 
               
               
                 36917_at 
                 LAMA2 
                 1.359731285 
                 0.006 
                 13.51 
               
               
                 38430_at 
                 FABP4 
                 1.054221974 
                 0.02 
                 13.05 
               
               
                 36596_r_at 
                 GATM 
                 1.22177547 
                 0.008 
                 12.67 
               
               
                 35898_at 
                 WISP2 
                 1.276226302 
                 0.004 
                 12.55 
               
               
                 36606_at 
                 CPE 
                 1.608244463 
                 0.003 
                 12.30 
               
               
                 32057_at 
                 LRRC17 
                 1.345223643 
                 0.011 
                 12.22 
               
               
                 33431_at 
                 FMOD 
                 1.516795166 
                 0.003 
                 12.17 
               
               
                 34985_at 
                 CILP 
                 0.905018335 
                 0.02 
                 11.53 
               
               
                 755_at 
                 ITPR1 
                 1.433938835 
                 0.002 
                 11.06 
               
               
                 1466_s_at 
                 FGF7 
                 1.184028604 
                 0.027 
                 11.00 
               
               
                 36727_at 
                 — 
                 0.98132702 
                 0.036 
                 10.96 
               
               
                 1103_at 
                 RNASE4 
                 1.456068199 
                 0.002 
                 10.88 
               
               
                 32666_at 
                 CXCL12 
                 1.342426238 
                 0.006 
                 10.72 
               
               
                 914_g_at 
                 ERG 
                 1.264721284 
                 0.002 
                 10.54 
               
               
                 40698_at 
                 CLECSF2 
                 1.325237675 
                 0.002 
                 10.46 
               
               
                 36873_at 
                 VLDLR 
                 1.344197327 
                 0.004 
                 10.45 
               
               
                 1090_f_at 
                 — 
                 0.914708216 
                 0.027 
                 10.34 
               
               
                 36042_at 
                 NTRK2 
                 0.950553444 
                 0.02 
                 10.32 
               
               
                 36311_at 
                 PDE1A 
                 1.356950738 
                 0.004 
                 10.21 
               
               
                 41685_at 
                 NY-REN-7 
                 0.8848466 
                 0.036 
                 10.08 
               
               
                 32847_at 
                 MYLK 
                 1.545610138 
                 0.002 
                 10.00 
               
               
                 35358_at 
                 TENC1 
                 1.539140855 
                 0.003 
                 9.97 
               
               
                 32249_at 
                 HFL1 
                 1.257702238 
                 0.02 
                 9.86 
               
               
                 36695_at 
                 Na 
                 1.452847153 
                 0.003 
                 9.82 
               
               
                 1987_at 
                 PDGFRA 
                 1.50655467 
                 0.002 
                 9.76 
               
               
                 37446_at 
                 GASP 
                 1.219014593 
                 0.004 
                 9.76 
               
               
                 35752_s_at 
                 PROS1 
                 1.211272096 
                 0.008 
                 9.66 
               
               
                 36533_at 
                 PTGIS 
                 1.882348646 
                 0.004 
                 9.62 
               
               
                 38886_i_at 
                 ARHI 
                 1.127672988 
                 0.02 
                 9.59 
               
               
                 36733_at 
                 FLJ32389 
                 1.420588897 
                 0.011 
                 9.57 
               
               
                 38717_at 
                 DKFZP586A0522 
                 1.158933663 
                 0.015 
                 9.50 
               
               
                 32551_at 
                 EFEMP1 
                 1.385495033 
                 0.004 
                 9.38 
               
               
                 1968_g_at 
                 PDGFRA 
                 1.364848071 
                 0.003 
                 9.31 
               
               
                 33910_at 
                 PTPRD 
                 1.129963902 
                 0.008 
                 9.20 
               
               
                 32778_at 
                 ITPR1 
                 1.370809534 
                 0.002 
                 9.08 
               
               
                 280_g_at 
                 NR4A1 
                 1.074894321 
                 0.006 
                 8.79 
               
               
                 35389_s_at 
                 ABCA6 
                 1.209294071 
                 0.011 
                 8.79 
               
               
                 32889_at 
                 RPIB9 
                 1.145333813 
                 0.003 
                 8.74 
               
               
                 37248_at 
                 CPZ 
                 1.238797022 
                 0.002 
                 8.69 
               
               
                 39674_r_at 
                 ECM2 
                 0.874009817 
                 0.027 
                 8.67 
               
               
                 33911_at 
                 PTPRD 
                 1.099609918 
                 0.02 
                 8.66 
               
               
                 35234_at 
                 RECK 
                 1.407865518 
                 0.008 
                 8.58 
               
               
                 32119_at 
                 — 
                 1.153957574 
                 0.011 
                 8.57 
               
               
                 35998_at 
                 LOC284244 
                 1.104281231 
                 0.008 
                 8.54 
               
               
                 37279_at 
                 GEM 
                 1.012760866 
                 0.008 
                 8.31 
               
               
                 35702_at 
                 HSD11B1 
                 1.164189513 
                 0.004 
                 8.28 
               
               
                 32126_at 
                 FGF7 
                 1.336918337 
                 0.008 
                 8.22 
               
               
                 36867_at 
                 — 
                 1.273166453 
                 0.008 
                 8.21 
               
               
                 38653_at 
                 PMP22 
                 1.422063697 
                 0.002 
                 8.19 
               
               
                 38875_r_at 
                 GREB1 
                 1.026886865 
                 0.015 
                 8.10 
               
               
                 35366_at 
                 NID 
                 1.483421362 
                 0.002 
                 8.10 
               
               
                 34417_at 
                 FLJ36166 
                 0.783978445 
                 0.047 
                 7.98 
               
               
                 37221_at 
                 PRKAR2B 
                 0.927090765 
                 0.036 
                 7.91 
               
               
                 39031_at 
                 COX7A1 
                 1.564725491 
                 0.004 
                 7.89 
               
               
                 39757_at 
                 SDC2 
                 1.288106392 
                 0.002 
                 7.80 
               
               
                 36629_at 
                 DSIPI 
                 0.981563882 
                 0.008 
                 7.79 
               
               
                 35390_at 
                 ABCA6 
                 1.026714913 
                 0.036 
                 7.79 
               
               
                 39629_at 
                 PLA2G5 
                 1.405181995 
                 0.002 
                 7.70 
               
               
                 40961_at 
                 SMARCA2 
                 0.996692724 
                 0.015 
                 7.68 
               
               
                 719_g_at 
                 PRSS11 
                 1.399043078 
                 0.002 
                 7.65 
               
               
                 40856_at 
                 SERPINF1 
                 1.077533093 
                 0.008 
                 7.55 
               
               
                 37008_r_at 
                 SERPINA3 
                 1.134224016 
                 0.002 
                 7.53 
               
               
                 33834_at 
                 CXCL12 
                 1.060878451 
                 0.002 
                 7.51 
               
               
                 31880_at 
                 D8S2298E 
                 1.177864913 
                 0.002 
                 7.45 
               
               
                 37628_at 
                 MAOB 
                 1.194963489 
                 0.004 
                 7.43 
               
               
                 34853_at 
                 FLRT2 
                 1.250330254 
                 0.027 
                 7.41 
               
               
                 38887_r_at 
                 ARHI 
                 1.169953614 
                 0.015 
                 7.32 
               
               
                 38220_at 
                 DPYD 
                 1.024334451 
                 0.02 
                 7.26 
               
               
                 1327_s_at 
                 MAP3K5 
                 0.891703475 
                 0.02 
                 7.23 
               
               
                 1380_at 
                 FGF7 
                 1.096254206 
                 0.004 
                 7.14 
               
               
                 37573_at 
                 ANGPTL2 
                 1.052539345 
                 0.002 
                 7.08 
               
               
                 718_at 
                 PRSS11 
                 1.381205346 
                 0.002 
                 6.99 
               
               
                 36712_at 
                 — 
                 1.15195149 
                 0.005 
                 6.88 
               
               
                 1709_g_at 
                 MAPK10 
                 1.160327795 
                 0.002 
                 6.85 
               
               
                 39123_s_at 
                 TRPC1 
                 1.060327922 
                 0.015 
                 6.79 
               
               
                 38627_at 
                 HLF 
                 0.911787462 
                 0.036 
                 6.79 
               
               
                 32076_at 
                 DSCR1L1 
                 1.127515982 
                 0.002 
                 6.77 
               
               
                 36669_at 
                 FOSB 
                 1.023057503 
                 0.011 
                 6.65 
               
               
                 38194_s_at 
                 IGKC 
                 1.239936045 
                 0.015 
                 6.64 
               
               
                 39545_at 
                 CDKN1C 
                 1.040717569 
                 0.004 
                 6.62 
               
               
                 36993_at 
                 PDGFRB 
                 1.384657766 
                 0.004 
                 6.60 
               
               
                 35837_at 
                 SCRG1 
                 1.023840456 
                 0.036 
                 6.48 
               
               
                 1507_s_at 
                 EDNRA 
                 1.23933124 
                 0.004 
                 6.48 
               
               
                 40488_at 
                 DMD 
                 1.291791538 
                 0.002 
                 6.42 
               
               
                 38364_at 
                 — 
                 1.030881108 
                 0.004 
                 6.35 
               
               
                 41424_at 
                 PON3 
                 0.946224951 
                 0.036 
                 6.32 
               
               
                 32109_at 
                 FXYD1 
                 1.005577422 
                 0.004 
                 6.19 
               
               
                 1182_at 
                 PLCL1 
                 1.097390316 
                 0.002 
                 6.17 
               
               
                 31897_at 
                 DOC1 
                 1.533672652 
                 0.003 
                 6.13 
               
               
                 37208_at 
                 PSPHL 
                 1.007759699 
                 0.015 
                 6.08 
               
               
                 36396_at 
                 — 
                 1.009684807 
                 0.015 
                 6.07 
               
               
                 41505_r_at 
                 MAF 
                 1.116101319 
                 0.006 
                 6.06 
               
               
                 37765_at 
                 LMOD1 
                 1.127716375 
                 0.003 
                 6.00 
               
               
                 37398_at 
                 PECAM1 
                 0.970664041 
                 0.008 
                 5.98 
               
               
                 41013_at 
                 FLJ31737 
                 1.036561659 
                 0.003 
                 5.98 
               
               
                 39279_at 
                 BMP6 
                 1.106724571 
                 0.002 
                 5.93 
               
               
                 1527_s_at 
                 CG018 
                 0.804755548 
                 0.047 
                 5.91 
               
               
                 39038_at 
                 FBLN5 
                 1.279283798 
                 0.004 
                 5.89 
               
               
                 32542_at 
                 FHL1 
                 1.134214637 
                 0.002 
                 5.88 
               
               
                 38508_s_at 
                 TNXB 
                 0.878513741 
                 0.011 
                 5.74 
               
               
                 32696_at 
                 PBX3 
                 0.888011703 
                 0.027 
                 5.69 
               
               
                 41796_at 
                 PLCL2 
                 0.857601993 
                 0.02 
                 5.68 
               
               
                 34473_at 
                 TLR5 
                 0.871815246 
                 0.027 
                 5.67 
               
               
                 661_at 
                 GAS1 
                 1.267909476 
                 0.004 
                 5.66 
               
               
                 41449_at 
                 SGCE 
                 1.050056933 
                 0.004 
                 5.65 
               
               
                 35740_at 
                 EMILIN1 
                 1.366368794 
                 0.011 
                 5.58 
               
               
                 37908_at 
                 GNG11 
                 0.989043327 
                 0.004 
                 5.43 
               
               
                 37406_at 
                 MAPRE2 
                 1.265872665 
                 0.002 
                 5.41 
               
               
                 33802_at 
                 HMOX1 
                 1.034088234 
                 0.015 
                 5.41 
               
               
                 39106_at 
                 APOA1 
                 1.266005754 
                 0.008 
                 5.40 
               
               
                 1771_s_at 
                 PDGFRB 
                 1.336082701 
                 0.006 
                 5.39 
               
               
                 39409_at 
                 C1R 
                 1.05784087 
                 0.011 
                 5.39 
               
               
                 32535_at 
                 FBN1 
                 1.422415283 
                 0.006 
                 5.35 
               
               
                 37710_at 
                 MEF2C 
                 0.98149558 
                 0.011 
                 5.35 
               
               
                 37958_at 
                 TM4SF10 
                 1.293658009 
                 0.003 
                 5.35 
               
               
                 33756_at 
                 AOC3 
                 0.829203515 
                 0.02 
                 5.29 
               
               
                 36569_at 
                 TNA 
                 0.926096917 
                 0.006 
                 5.25 
               
               
                 39771_at 
                 RHOBTB1 
                 1.048906896 
                 0.008 
                 5.20 
               
               
                 39852_at 
                 SPG20 
                 0.82401517 
                 0.027 
                 5.20 
               
               
                 35168_f_at 
                 COL16A1 
                 1.509830282 
                 0.011 
                 5.18 
               
               
                 33244_at 
                 CHN2 
                 0.92878389 
                 0.015 
                 5.18 
               
               
                 35681_r_at 
                 ZFHX1B 
                 1.170745794 
                 0.006 
                 5.14 
               
               
                 2087_s_at 
                 CDH11 
                 1.656534188 
                 0.008 
                 5.12 
               
               
                 40496_at 
                 C1S 
                 0.973175912 
                 0.011 
                 5.10 
               
               
                 41137_at 
                 PPP1R12B 
                 1.12885067 
                 0.008 
                 5.07 
               
               
                 39698_at 
                 HOP 
                 0.797252583 
                 0.011 
                 5.05 
               
               
                 38211_at 
                 ZNF288 
                 0.926263264 
                 0.015 
                 5.04 
               
               
                 41839_at 
                 GAS1 
                 1.127093791 
                 0.006 
                 5.03 
               
               
                 39979_at 
                 F10 
                 0.890787173 
                 0.002 
                 5.02 
               
               
                 1135_at 
                 GPRK5 
                 1.150554994 
                 0.002 
                 5.01 
               
               
                 479_at 
                 DAB2 
                 1.255638531 
                 0.006 
                 5.01 
               
               
                   
               
            
           
         
       
     
     EXAMPLE 4  
     Validation of the Microarray Data by Quantitative Real-Time PCR 
     Quantitative real time PCR assays were used to validate the microarray data. Four highly differentially expressed genes between normal ovarian epithelial cells and ovarian serous papillary carcinoma (i.e., TROP-1, CD24, Claudin-3 and Claudin-4) were selected for the analysis. 
     Quantitative real time PCR was performed with an ABI Prism 7000 Sequence Analyzer using the manufacturer&#39;s recommended protocol (Applied Biosystems, Foster City, Calif.). Each reaction was run in triplicate. The comparative threshold cycle (C T ) method was used for the calculation of amplification fold as specified by the manufacturer. Briefly, five mg of total RNA from each sample was reverse transcribed using SuperScript II Rnase H Reverse Transcriptase (Invitrogen, Carlsbad, Calif.). Ten ml of reverse transcribed RNA samples (from 500 ml of total volume) were amplified by using the TaqMan Universal PCR Master Mix (Applied Biosystems) to produce PCR products specific for TROP-1, CD24, Claudin-3 and Claudin-4. Primers specific for 18s ribosomal RNA and empirically determined ratios of 18 s competimers (Applied Biosystems) were used to control for the amounts of cDNA generated from each sample. 
     Primers for TROP-1, claudin-3 and claudin-4 were obtained from Applied Biosystems as assay on demand products. Assays ID were Hs00158980_ml (TROP-1), Hs00265816_s1 (claudin-3), and Hs00533616_s1 (claudin-4). CD24 primers sequences were as following: forward, 5′-CCCAGGTGTTACTGTAATTCCTCAA (SEQ ID NO: 1); reverse, 5′-GAACAGCAATAGCTCAACAATGTAAAC (SEQ ID NO: 2). Amplification was carried out by using 1 unit of polymerase in a final volume of 20 μl containing 2.5 mM MgCl 2 . TaqGold was activated by incubation at 96° C. for 12 min, and the reactions were cycled 26-30 times at 95° C. for 1 min, 55° C. for 1 min, and 72° C. for 1 min, followed by a final extension at 72° C. for 10 min. PCR products were visualized on 2% agarose gels stained with ethidium bromide, and images were captured by an Ultraviolet Products Image Analysis System. Differences among ovarian serous papillary carcinoma and normal ovarian epithelial cells in the quantitative real time PCR expression data were tested using the Kruskal-Wallis nonparametric test. Pearson product-moment correlations were used to estimate the degree of association between the microarray and quantitative real time PCR data. 
     A comparison of the microarray and quantitative real time PCR data for these genes is shown in  FIG. 3 . Expression differences between ovarian serous papillary carcinoma and normal ovarian epithelial cells for TROP-1 (p=0.02) ( FIGS. 3A-3B ), CD24 (p =0.004)  FIGS. 3C-3D ), claudin-3 (p=0.02)  FIGS. 3E-3F ), and claudin-4 (p=0.01)  FIGS. 3G-3H ) were readily apparent (Table 2). Moreover, for all four genes tested, the quantitative real time PCR data were highly correlated to the microarray data (p&lt;0.001) (r=0.81, 0.90, 0.80 and 0.85, respectively). Thus, quantitative real time PCR data suggest that most array probe sets are likely to accurately measure the levels of the intended transcript within a complex mixture of transcripts. 
     EXAMPLE 5  
     Flow Cytometry Analysis of TROP-1 and CD24 Expression 
     An important issue is whether differences in gene expression result in meaningful differences in protein expression. Because TROP-1/Ep-CAM gene encodes the target for the anti-Ep-CAM antibody (17-1A), Edrecolomab (Panorex), that has previously been shown to increase survival in patients harboring stage III colon cancer, expression of Ep-CAM protein by 
     FACS analysis was analyzed on 13 primary cell lines (i.e., 10 ovarian serous papillary carcinoma cell lines and 3 normal ovarian epithelial cell lines). As positive controls, breast cancer cell lines (i.e., B7-474 and SK-BR-3, American Type Culture Collection) known to overexpress TROP-1/Ep-CAM were also studied. 
     Unconjugated anti-TROP-1/EP-CAM (IgG2a), anti-CD24 (IgG2a) and isotype control antibodies (mouse IgG2a) were all obtained from BD PharMingen (San Diego, Calif.). Goat anti-murine FITC labeled mouse Ig was purchased from Becton Dickinson (San Jose, Calif.). Flow cytometry was conducted with a FACScan, utilizing cell Quest software (Becton Dickinson). High TROP-1/Ep-CAM expression was found on all ten primary ovarian serous papillary carcinoma cell lines tested (100% positive) with mean fluorescence intensity (MFI) ranging from 116 to 280 ( FIG. 4 ). In contrast, primary normal ovarian epithelial cell lines were negative for TROP-1/Ep-CAM surface expression (p&lt;0.001) ( FIGS. 4D-4F ). Similarly, CD24 expression was found on all primary ovarian serous papillary carcinoma cell lines tested (100% positive) with mean fluorescence intensity (MFI) ranging from 26 to 55 ( FIGS. 4D-4F ). In contrast, primary normal ovarian epithelial cell lines were negative for CD24 surface expression (p &lt;0.005). These results show that high expression of the TROP-1/Ep-CAM and CD24 genes by ovarian serous papillary carcinoma correlate tightly with high protein expression by the tumor cells. Breast cancer positive controls were found to express high levels of TROP-1/Ep-CAM (data not shown). 
     EXAMPLE 6  
     Immunohistochemical Analysis of TROP-1 and CD24 Expression 
     To determine whether the high or low gene expression and Ep-CAM and CD24 protein expression detected by microarray and flow cytometry are the result of a selection of a subpopulation of cancer cells present in the original tumor, or whether in vitro expansion conditions may have modified gene expression, immunohistochemical analysis of TROP-1/Ep-CAM and CD24 protein expression was performed on formalin-fixed tumor tissue from all uncultured primary surgical specimens. Study blocks were selected after histopathologic review by a surgical pathologist. The most representative hematoxylin and eosin-stained block sections were used for each specimen. Briefly, immunohistochemical stains were performed on 4 mm-thick sections of formalin-fixed, paraffin-embedded tissue. After pretreatment with 10 mM citrate buffer at pH 6.0 using a steamer, they were incubated with anti-Ep-CAM mAb (PharMingen) or anti-CD24 antibody (Neo Markers, Fremont, Calif.) at 1: 2000 dilution. Slides were subsequently labelled with streptavidin-biotin (DAKO, Glostrup, Denmark), stained with diaminobenzidine and counterstained with hematoxylin. The intensity of staining was graded as 0 (staining not greater than negative control), 1+ (light staining), 2+ (moderate staining), or 3+ (heavy staining). 
     As shown in the  FIGS. 5E-5F , heavy apical membranous staining for CD24 protein expression was noted in all ovarian serous papillary carcinoma specimens that also overexpressed the CD24 gene and its gene product as determined by microarray and flow cytometry, respectively. In contrast, negative or low (i.e., score 0 or 1+) staining was found in all normal ovarian epithelial cell samples tested by immunohistochemistry ( FIGS. 5A ,  5 D). Similarly, as shown in  FIGS. 5B-5C , heavy membranous staining for TROP-1/Ep-CAM protein expression (i.e., score 3+) was noted in all ovarian serous papillary carcinoma specimens that also overexpressed the TROP-1/Ep-CAM gene and its gene product as determined by microarray and flow cytometry, respectively. In contrast, negative or low (i.e., score 0 or 1+) staining was found in all normal ovarian epithelial cell samples tested by immunohistochemistry. 
     The following references were cited herein:
     1. Riethmuller et al., J Clin. Oncol. 16:1788-1794 (1998).   2. Ismail et al., Cancer Res. 60:6744-6749 (2000).   3. Hough et al., Cancer Res. 60:6281-6287 (2000).   4. Santin et al., Obstet. Gynecol. 96:422-430 (2000).   5. Fuchtner et al., Gynecol. Oncol. 48: 203-209 (1993).   6. Gamboa et al., Gynecol. Oncol. 58:336-343 (1995).   7. Zhan et al., Blood 99:1745-1757 (2002).   8. Tusher et al., Proc Natl. Acad. Sci. USA. 98:5116-5121 (2001).   9. Eisen et al., Proc Natl. Acad. Sci. USA 95:14863-14868 (1998).