Abstract:
The present invention is directed to diagnostic methods based upon the expression of the protein prostasin. In particular, it is concerned with assays performed on women to determine their risk of ovarian cancer.

Description:
CROSS REFERENCE TO RELATED APPLICATIONS 
     The present application is a division of U.S. Ser. No. 09/948, 094, (now U.S Pat. No 6,846,642), which was filed on Sep. 7, 2001. The &#39;094 application claims the benefit of U.S. provisional application No. 60/231,166, filed on Sep. 7, 2000 (now abandoned). 
    
    
     FIELD OF THE INVENTION  
     The present invention is in the field of tumor cell markers and is particularly concerned with methods of detecting cancer by assaying samples for prostasin. In its most preferred embodiment, the invention is directed to methods in which serum or plasma samples obtained from a woman are assayed to assess her risk of developing ovarian cancer. 
     BACKGROUND OF THE INVENTION  
     Ovarian cancer is the fifth leading cause of death from cancer in U.S. women. In most instances, a diagnosis is not made until the cancer is in an advanced state; at a time when the five year survival rate of patients is only about 28% (Ries, et al., SEERC Cancer Stat. Rev. 1973–1995 (1998)). In contrast, the five year survival rate for women diagnosed with localized disease is about 95%. These statistics provide an incentive to search for tests that can be used to identify ovarian cancer at an early stage. 
     The protein prostasin was originally isolated from human seminal fluid and is present at high levels in the prostate gland (Yu, et al.,  J. Biol. Chem.  270:13483–13489 (1995); Heid, et al.,  Genome Res.  6:986–994 (1996)). It is expressed to a lesser extent in the kidney, liver, pancreas, salivary gland, lung and colon (Yu, et al.)  J. Biol.  270:13483–13489 (1995); Yu, et al.,  J. Biol. Chem.  269:18843–18848 (1994)). Its function in these tissues has not yet been determined and a clear association between prostasin and cancer has not been established. 
     SUMMARY OF THE INVENTION  
     The present invention is based upon the discovery that prostasin can be used as a marker for identifying patients who have, or are likely to develop, certain types of cancer. In particular, it has been found that prostasin is elevated in the serum of women with ovarian cancer. 
     In its first aspect, the invention is directed to a method of determining whether a human subject has, or is likely to develop, a malignant growth. A biological sample is obtained from the subject and then assayed to determine the concentration of prostasin protein or mRNA present. The results obtained from this assay are then compared with the results obtained using one or more comparable biological control samples. In general, control samples will be of the same type as test samples but will be obtained from a population not believed to have a malignant growth. Alternatively, controls may simply be the normal concentration range of prostasin in comparable samples from the general population. Once assays have been completed, a conclusion may be drawn that the subject being examined has or is likely to develop a malignant growth if the prostasin concentration present in the test sample is significantly higher than in the control sample. As used herein, the term “significantly higher” means that a difference meets the criteria for significance accepted in the art using standard statistical methods. A significantly higher risk in this context means a probability of having cancer which is greater than that of the population as a whole and which warrants further diagnostic testing. 
     In general, biological samples will be samples of either serum or plasma and prostasin levels will be determined using an ELISA type assay. An example of a specific assay that can be used is set forth in the Examples section below. Most preferably, tests are performed on women for the purpose of determining whether they are at increased risk of having ovarian cancer. It is expected however that the assay will also be applied to other types of cancers such as cancer of the breast, prostate, lung, colon and pancreas. In another embodiment, assays are performed using tissue samples obtained by biopsy. The prostasin levels present in the tissue may be evaluated by ELISA or prostasin mRNA levels may be determined by reverse transcription PCR. 
     In a more specific aspect, the invention is directed to a method of determining the likelihood that a woman has or is likely to develop ovarian cancer by obtaining a test sample of plasma or serum from the woman and determining the concentration of prostasin present in the sample. The results obtained are compared with results from a control sample and a conclusion is drawn that the woman has or is likely to develop ovarian cancer if the concentration determined for the test sample is significantly higher than the concentration in the controls. Most preferably, the test will be performed using the ELSA discussed above. This same method can also be carried out by assaying a test sample of serum or plasma and concluding that an increased likelihood of ovarian cancer exists if the concentration of prostasin is greater than 10 micrograms per ml. or, in a more stringent test, if the concentration is greater than 12 micrograms per ml. 
     The assays of prostasin discussed above may either be used alone or in conjunction with other diagnostic tests. In particular, the assays may be used in conjunction with other methods in which the concentration of a tumor marker is determined. Such markers may include, for example, prostate specific antigen, CEA, alpha-fetoprotein and, in the case of tests for ovarian cancer, CA 125. 
    
    
     DETAILED DESCRIPTION OF THE INVENTION  
     The discovery of a correlation between prostasin concentration and ovarian cancer is an outgrowth of more extensive studies on genes that are either over- or underexpressed in cancerous ovarian epithelial cells. Numerous genes were identified which may also be used as markers and which are listed in the tables found in the Examples section below. Nevertheless, the strongest correlation has been found for prostasin which also has the advantage of being detectable in biological samples that can be readily obtained, i.e., samples of plasma or serum. The other genes that have been correlated with the transformation of ovarian cells have all been described in the literature and methods are known for assaying the concentration of each. 
     In the case of prostasin, the full length amino acid and nucleotide sequence of the human protein and gene are known in the art. These may be found as GenBank accession number L41351. The full length cDNA is 1834 nucleotides long, with the coding sequence running from nucleotide 229 to 1260. The sequence is also disclosed herein as SEQ ID NO:1 (DNA sequence) and SEQ ID NO:2, amino acid sequence). The protein may be purified using procedures described in the art or, alternatively, it can be chemically synthesized. 
     Assays for prostasin expression may be determined by RT-PCR using primers selected from the known gene sequence. Specific examples of primers that can be used for successfully carrying out RT-PCR are described in detail in the Examples section. ELISA assays are also disclosed in which the antibody described by Yu, et al. is used. However, other types of immunoassays can also be successfully used and antibodies may be produced using standard methods. 
     Antibodies that bind specifically to prostasin are defined for the purposes of the present invention as those that have at least a 100 fold greater affinity for prostasin then for any other similar undenatured protein. The process for producing such antibodies may involve either injecting the prostasin protein itself into an appropriate animal or injecting short peptides made to correspond to different regions of prostasin. The peptides injected should be a minimum of 5 amino acids in length and should be selected from regions believed to be unique to the protein. Methods for making and detecting antibodies are well known to those of skill in the art has evidenced by standard reference works such as: Harlow, et al.,  Antibodies, Laboratory Manual , Cold Spring Harbor Laboratory, N.Y. (1988); Klein,  Immunology: The Science of Self-Nonself Discrimination  (1982); Kennett, et al.,  Monoclonal Antibodies and Hybridomas: A New Dimension in Biological Analyses  (1980); and Campbell, “Monoclonal Antibody Technology,” in:  Laboratory Techniques in Biochemistry and Molecular Biology  (1984). 
     “Antibody,” as used herein is meant to include intact molecules as well as fragments which retained the ability to bind antigen (e.g., Fab and F(ab′) 2  fragments). These fragments are typically produced by proteolytically cleaving intact antibodies using enzymes such as a papain (to produce Fab fragments) or pepsin (to produce F(ab′) 2  fragments). The term “antibody” also refers to both monoclonal antibodies and polyclonal antibodies. Polyclonal antibodies are derived from the sera of animals immunized with the antigen. Monoclonal antibodies can be prepared using hybridoma technology (Kohler, et al.,  Nature  256:495 (1975). In general, this technology involves immunizing an animal, usually a mouse, with either intact prostasin or a fragment derived from prostasin. The splenocytes of the immunized animals are extracted and fused with suitable myeloma cells, e.g. SP 2 O cells. After fusion, the resulting hybridoma cells are selectively maintained in HAT medium and then cloned by limiting dilution (Wands, et al.,  Gastroenterology  80:225–232 (1981)). The cells obtained through such selection are then assayed to identify clones which secrete antibodies capable of binding to prostasin. 
     The antibodies or fragments of antibodies of the present invention may be used to detect to the presence of the prostasin protein in any of a variety of immunoassays. For example, antibodies may be used in radioimmunoassays or immunometric assays, also known as “two-site” or “sandwich assays” (see Chard, “Introduction to Radioimmune Assay and Related Techniques,” in:  Laboratory Techniques in Biochemistry and Molecular Biology,  North Holland Publishing Co., N.Y. (1978)). In a typical immunometric assay, a quantity of unlabelled antibody is bound to a solid support that is insoluble in the fluid being tested, e.g., blood lymph, cellular extracts, etc. After the initial binding of antigen to immobilized antibody, a quantity of detectably labeled second antibody (which may or may not be the same as the first) is added to permit the detection and/or quantitation of bound antigen (see e.g.,  Radioimmune Assay Method , Kirkham, et al., ed. pp. 199–206, E&amp;S Livingston, Edinburgh (1970)). Many variations of these types of assays are known in the art and may be employed for the detection of prostasin. 
     If desired, antibodies to prostasin may also be used in the purification of the protein (see generally, Dean, et al.,  Affinity Chromatography, A Practical Approach , IRL Press (1986)). Typically, antibody is immobilized on a chromatographic matrix such as Sepharose 4B. The matrix is then packed into a column and the preparation containing prostasin is passed through under conditions that promote binding, e.g., under conditions of low salt. The column is then washed and bound prostasin is eluted using a buffer that promotes disassociation of antibody, e.g., a buffer having an altered pH or salt concentration. The eluted prostasin may be transferred into a buffer of choice, e.g., by dialysis, and either stored or used directly. 
     The same basic techniques described above in connection with prostasin may also be adapted to any of the other genes or proteins identified herein as being associated with ovarian cancer. Also, it should be readily apparent that the same assays may be used in connection with other types of cancer as well, especially those of the pancreas, prostate, kidney, and lungs. 
     EXAMPLES 
     Example 1  
     Differentially Exposed Genes from Ovarian Cancer Cells 
     A. Materials and Methods 
     Cell Culture 
     Cultures of normal human ovarian surface epithelial cells (HOSE) were established by scraping the HOSE cells from the ovary and growing them in a mixture of Medium 199 and MCDB105 supplemented with 10% fetal calf serum (Mok, et al.,  Gynecol. Oncol.  52:247–52, (1994)). The seven HOSE cells used were HOSE17, HOSE636, HOSE642, HOSE695, HOSE697, HOSE713, and HOSE726. Ovarian cancer cell lines used were OVCA3, OVCA420, OVCA432, OVCA433, OVCA633, SKOV3, and ALST. 
     Microarray Probe and Hybridization 
     MICROMAX™ human cDNA microarray system I (NEN Life Science Products, Inc., Boston, Mass.), which contains 2400 known human cDNAs on a 1×3″ slide, was used in this study. Microarray probe and hybridization were performed as described in the instruction manual. In brief, biotin-labeled cDNA was generated from 3 μg total RNA, which was pooled from HOSE17,HOSE636 and HOSE642. Dinitrophenyl (DNP)-labeled cDNA was generated from 3 μg total RNA that was pooled from ovarian cancer cell lines OVCA420, OVCA433 and SKOV3. Before the cDNA reaction, an equal amount of RNA control was added to each batch of the RNA samples for normalization during data analysis. Biotin-labeled and DNP-labeled cDNA were mixed, dried and resuspended in 20 μl hybridization buffer, which was added to the cDNA microarray and covered with a coverslip. Hybridization was carried out overnight at 65° C. inside a hybridization cassette. 
     Post hybridization and Cyanine-3 (Cy3™) and Cyanine-5 (Cy5™) Tyramide Signal Amplification (TSA) 
     After hybridization, microarrays were washed with 30 ml 0.5×SSC, 0.01% SDS, and then 30 ml 0.06×SSC, 0.01% SDS. Finally the microarray was washed with 0.06×SSC. Hybridization signal from biotin-labeled cDNA was amplified with streptavidin-horseradish peroxidase and Cy5™-tyramide, while hybridization signal from DNP-labeled cDNA was amplified with anti-DNP-horseradish peroxidase and Cy3™-tyramide. After signal amplification and post-hybridization wash, cDNA microarray was air-dried and detected with a laser scanner. 
     Image Acquisition and Data Analysis 
     Cy3 signal was derived from ovarian cancer cells and Cy5 signal was derived from HOSE cells. Laser detection of the Cy3 and Cy5 signal on the microarray was acquired with a confocal laser reader, ScanArray3000 (GSI Lumonics, Watertown, Mass.). Separate scans were taken for each fluor at a pixel size of 10μ. cDNA derived from the control RNA hybridized to 12 specific spots within the microarray. Cy3 and Cy5 signals from these 12 spots should theoretically be equal and were used to normalize the different efficiencies in labeling and detection with the two fluors. The fluorescence signal intensities and the Cy3/Cy5 ratios for each of the 2400 cDNAs were analyzed by the software Imagene 3.0 (Biodiscovery Inc, Los Angeles, Calif.). 
     Real-Time Quantitative RT-PCR 
     Real-time PCR was performed in duplicate using primer sets specific to GA733-2, osteopontin, prostasin, creatine kinase B, CEA, KOC and a housekeeping gene, cyclosporin, in an ABI PRISM 5700 Sequence Detector. RNA was first extracted form normal ovarian epithelial cell cultures (HOSE695, 697, 713, and 726) and six ovarian carcinoma cell lines (OVCA3, OVCA432, OVCA433, OVCA633, SKOV3 and ALST). cDNA were generated from 1 μg total RNA using the TaqMan reverse transcription reagents containing 1× TaqMan RT buffer, 5.5 mM MgCl 2 , 500 μM dNTP, 2.5 μM random hexamer, 0.4 U/μl RNase inhibitor, 1.25 U/μl MultiScribe reverse transcriptase (PE Applied Biosystems, Foster City, Calif.) in 100 μl. The reaction was incubated at 25° C. for 10 min, 48° C. for 30 min and finally at 95° C. for 5 min. 0.5 μl of cDNA was used in a 20 μl PCR mix containing 1×SYBR PCR buffer, 3 mM MgCl 2 , 0.8 mM dNTP, and 0.025 U/μl AmpliTaq Gold (PE Applied Biosystems, Foster City, Calif.). Amplification was then performed with denaturation for 10 min at 95° C., followed by 40 PCR cycles of denaturation at 95° C. for 15 sec and annealing/extension at 60° C. for 1 min. The changes in fluorescence of SYBR Green I dye in every cycle was monitored by the ABI5700 system software, and the threshold cycle (C T ) for each reaction was calculated. The relative amount of PCR products generated from each primer set was determined based on the threshold-cycle or C T  value. Cyclosporin was used for the normalization of quantity of RNA used. Its C T  value was then subtracted from that of each target gene to obtain a ΔCT value. The difference (ΔΔC T ) between the ΔC T  values of the samples for each gene target and the ΔC T  value of the calibrator (HOSE726) was determined. The relative quantitative value was expressed as 2 −ΔΔCT . 
     B. Results and Discussion 
     The MICROMAX System 
     The MICROMAX system allows the simultaneous analysis of the expression level of 2400 known genes. The use of TSA signal amplification in the system after hybridization reduces the amount of total RNA needed to a few micrograms which is about 20–100 times less than currently used methods. The details of TSA have been described previously for chromosome mapping of PCR-labeled probes less than 1 kb by FISH (Schriml, et al.,  Biotechniques  27:608–611, (1999)). In this study, 30 putative differentially over-expressed genes (excluding 9 ribosomal genes) were identified in ovarian cancer cell lines (Table 1). Using high density cDNA array on membranes, Schummer et al. (Schummer, et al.,  Gene  238:375–385, (1999)) has identified 32 known genes that exhibit a tumor-to-HOSE ratios of more than 2.5-fold. Fourteen of these 32 genes were present in the MICROMAX cDNA microarray but only five of them were present at more than 3-fold. 
     Biotin-labeled cDNA was made from ovarian cancer cell lines, while DNP-labeled cDNA was made from HOSE cells. The differential TSA amplification of the hybridization signal depends on the use of a Steptavidin-HRP conjugate or anti-DNP-HRP conjugate in a sequential step. At each step, cyanine-5-Tyramide or cyanine-3-Tyramide can be added and the HRP will then catalyze the deposit of Cy3 or Cy5 onto the hybridized cDNA nonspecifically. As a result, either Cy3 or Cy5 signals can be used for the cDNA derived from ovarian cancer cell lines, and vice versa for HOSE cells. Thus, it is not necessary to make two different sets of probes to compare the effect of Cy3 or Cy5 fluorescence as a result of their differences in extinction coefficients and quantum yields. Cy3 and Cy5 signals on the processed slides were stable for more than 6 months. 
     Normalization of Signals 
     The MICROMAX system has 3 nonhuman genes as internal controls. Each of the control genes is spotted 4 times on the microarray. Equal amounts of polyA RNA derived from these control genes were spiked into the total RNA samples derived from both HOSE and ovarian cancer cell lines during cDNA synthesis. Thus, hybridization signals from these control genes in two RNA samples should theoretically be the same. The Cy3 to Cy5 ratios for these control genes varied from 0.4 to 4.0 and the average ratio was 1.5±1.1. From a prior microarray analysis of human cancer cells, 88 genes have been identified to express at relatively constant levels in many cell types (DeRisi, et al.,  Nat. Genet.  14:457–60, (1996)). The MICROMAX microarray also contains 58 of these 88 genes and 21 of these genes with signal to background ratio more than 3-fold were analyzed (Table 2). The ratios varied from 0.23 to 5.22. The average ratio is 1.6±1.5. Thus, the result of internal control RNA for normalizing signal was similar to that of genes that express at a relatively constant level in different cell types. 
     Effect of Background Signal on the Identification of Differentially Expressed Genes 
     In the present study, 1357 of the 2400 genes on the microarray have Cy3 signals (from ovarian cancer cell lines) that were at least two-fold higher than the background, and 740 genes have Cy3 signals that were at least three-fold higher than the background. After post-hybridization washes, there was still significant background intensity for the Cy3 signal but very low background for Cy5. Subsequently, the microarray was washed again in 30 ml TNT buffer at 42° C. for 20 minutes instead of at room temperature, followed by 30 ml of 0.006×SSC for 1 minute. The washed microarray was then dried and re-scanned. This process was repeated several times until the number of genes with signal to background ratios at least 3-fold remained the same. The extensive washing steps decreased the background intensity significantly, but there was no obvious changes in the signal intensity. As a result, the number of genes with at least 3-fold signal to background ratios increased from 740 to 791 genes. Moreover, the differential expression ratios, in general, also increased (Table 1 to Table 2). More importantly, after the extensive washing, we were able to detect the differential expression of two weakly expressed genes, thiol-specific antioxidant protein (4.5-fold) and elongation factor-1-β (9.7-fold), which were previously identified by Schummer et al. Thus, the extensive post-hybridization washing and re-scanning of signals may be necessary to decrease background signal especially in the case of differentially expressed genes with low expression levels. 
     Confirmation of Differential Expression by Real-Time Quantitative PCR 
     To further validate differential expression, five interesting genes were chosen, GA733-2, osteopontin, koc, prostasin, and creatine kinase B, for real-time PCR analysis. All these genes are either surface antigens or secreted proteins. Thus, they may be useful as tumor markers for ovarian cancer. GA733-2 is a cell surface 40-kDa glycoprotein associated with human carcinomas of various origins (Szala, et al.,  Proc. Natl. Acad. Sci. USA  87:3542–6, (1990)). Osteopontin is a secreted glycoprotein with a conserved Arg-Gly-Asp (RGD) integrin-binding motif and is expressed predominantly in bone, but has also been found in breast cancer and thyroid carcinoma with enhanced invasiveness (Sharp, et al.,  Lab. Investigat.  79:869–877, (1999), Tuck, et al.,  Oncogene  18:4237–4246, (1999)). Prostasin is a novel secreted serine proteinase which was originally identified in seminal fluid (Yu, et al.,  J. Biol. Chem.  269:18843–8, (1994)). The koc transcript is highly over-expressed in pancreatic cancer cell lines as well as in pancreatic cancer. It is speculated that koc may assume a role in the regulation of tumor cell proliferation by interfering with transcriptional and or posttranscriptional processes (Mueller-Pillasch, et al.,  Oncogene  14:2729–33, (1997)). Creatine kinase B is a serum marker associated with renal carcinoma and lung cancer (Kurtz, et al.,  Cancer  56:562–6, (1985), Takashi, et al.,  Urologia Internationalis  48:144–8, (1992)). Two randomly selected genes, CEA and RGS, were used as negative controls. 
     The results showed that all the tested ovarian cancer cell lines expressed higher levels of GA733-2. However, osteopontin, prostasin, KOC and creatine kinase B were over-expressed in only some of the cancer cell lines. Since we were using pools of RNA, the differential expression that was observed is an average of the gene expression from 3 independent HOSE cells or 3 different cancer cell lines. This strategy allows us to capture genes that overexpress in either some or all of the cell lines. Genes that only overexpress in some of the ovarian cancer cell lines may be useful for molecular classification of ovarian cancer cells. Since as little as 10 pg cDNA is enough for real-time quantitative RT-PCR reaction, RNA extracted from microdissected tissue would be enough for thousands of such real-time quantitative RT PCR analyses. 
     
       
         
               
             
               
               
               
               
               
             
               
               
               
               
               
             
           
               
                 TABLE 1 
               
             
             
               
                   
               
               
                 List of genes differentially over-expressed in ovarian cancer cells more 
               
               
                 than 10-fold. 
               
             
          
           
               
                   
                   
                 Before 
                 After 
                   
               
               
                   
                   
                 extensive 
                 extensive 
               
               
                   
                   
                 washing 
                 washing 
                 Cy3 signal 
               
               
                 Accession # 
                 Description 
                 (Cy3/Cy5) 
                 (Cy3/Cy5) 
                 intensity 
               
               
                   
               
             
          
           
               
                 M33011 
                 carcinoma-associated antigen 
                 472 
                 444 
                 1249 
               
               
                   
                 GA733-2 
               
               
                 J04765 
                 Osteopontin 
                 156 
                 184 
                 11851 
               
               
                 L41351 
                 Prostasin 
                 44 
                 170 
                 3172 
               
               
                 L19783 
                 GPI-H 
                 4 
                 88 
                 916 
               
               
                 U96759 
                 Von Hippel-Lindau binding protein 
                 60 
                 59 
                 1377 
               
               
                   
                 (VBP-1) 
               
               
                 M57730 
                 B61 
                 20 
                 49 
                 5514 
               
               
                 L33930 
                 CD24 signal transducer and 3′ 
                 24 
                 47 
                 26722 
               
               
                   
                 region 
               
               
                 D55672 
                 hnRNP D 
                 45 
                 44 
                 950 
               
               
                 U97188 
                 Putative RNA binding protein KOC 
                 223 
                 38 
                 3599 
               
               
                 L19871 
                 ATF3 
                 9 
                 37 
                 3507 
               
               
                 J04991 
                 p18 
                 15 
                 34 
                 9914 
               
               
                 D00762 
                 mRNA for proteasome subunit HC8 
                 17 
                 29 
                 4703 
               
               
                 U17989 
                 Nuclear autoantigen GS2NA 
                 5 
                 28 
                 721 
               
               
                 U43148 
                 Patched homolog (PTC) 
                 10 
                 28 
                 4155 
               
               
                 AF010312 
                 Pig7(PIG7) 
                 13 
                 23 
                 17379 
               
               
                 M80244 
                 E16 
                 18 
                 21 
                 4180 
               
               
                 X99802 
                 mRNA for ZYG homologue 
                 14 
                 21 
                 2086 
               
               
                 U05598 
                 Dihydrodioldehydrogenase 
                 10 
                 18 
                 21595 
               
               
                 L47647 
                 Creatine kinase B. 
                 7 
                 18 
                 787 
               
               
                 M55284 
                 Protein kinase C-L (PRKCL) 
                 7 
                 16 
                 863 
               
               
                 X15722 
                 mRNA for glutathione reductase 
                 23 
                 14 
                 794 
               
               
                 554005 
                 Thymosin beta-10 
                 6 
                 13 
                 1476 
               
               
                 AB006965 
                 mRNA for Dnmlp/Vpslp-like 
                 7 
                 13 
                 4183 
               
               
                   
                 protein 
               
               
                 M83653 
                 Cytoplasmic phosphotyrosyl protein 
                 6 
                 13 
                 2156 
               
               
                   
                 Phosphatase 
               
               
                 X12597 
                 mRNA for high mobility group-1 
                 7 
                 12 
                 2785 
               
               
                   
                 protein 
               
               
                   
                 (HMG-1) 
               
               
                 M18112 
                 poly(ADP-ribose) polymerase 
                 6 
                 12 
                 9277 
               
               
                 U56816 
                 Kinase Mytl (Mytl) 
                 4 
                 11 
                 1773 
               
               
                 X06233 
                 mRNA for calcium-binding protein 
                 7 
                 11 
                 3007 
               
               
                   
                 In macrophages (MRP-14) 
               
               
                 D85181 
                 mRNA for fungal sterol-C5- 
                 6 
                 11 
                 3571 
               
               
                   
                 desaturase 
               
               
                   
                 homolog 
               
               
                 M31627 
                 X box binding protein-1 (XBP-1) 
                 5 
                 10 
                 12151 
               
               
                   
               
             
          
         
       
     
     
       
         
               
             
               
               
               
               
             
               
               
               
               
             
           
               
                 TABLE 2 
               
             
             
               
                   
               
               
                 Cy3 versus Cy5 ratio for a set of genes that are previously 
               
               
                 shown to express at relative constant level (2) 
               
             
          
           
               
                   
                   
                 Before 
                 After 
               
               
                   
                   
                 extensive 
                 extensive 
               
               
                 Accession 
                   
                 washing 
                 washing 
               
               
                 # 
                 Description 
                 (Cy3/Cy5) 
                 (Cy3/Cy5) 
               
               
                   
               
             
          
           
               
                 X06323 
                 MRL3 mRNA for ribosomal 
                 3.31 
                 5.22 
               
               
                   
                 protein L3 homologue 
               
               
                 AF006043 
                 3-phosphoglycerate dehydrogenase 
                 3.81 
                 4.8 
               
               
                 M37400 
                 Cytosolic aspartate aminotransferase 
                 3.03 
                 3.66 
               
               
                 D30655 
                 mRNA for eukaryotic initiation factor 
                 4.17 
                 3.48 
               
               
                   
                 4A11 
               
               
                 J04208 
                 inosine-5′-monophosphate 
                 1.13 
                 2.15 
               
               
                   
                 dehydrogenase (IMP) 
               
               
                 M17885 
                 Acidic ribosomal phosphoprotein PO 
                 2.74 
                 2.09 
               
               
                 X54326 
                 mRNA for glutaminyl-tRNA 
                 1.17 
                 2.01 
               
               
                   
                 synthetase 
               
               
                 J04973 
                 Cytochrome bc-1 complex core 
                 0.98 
                 1.6 
               
               
                   
                 protein II 
               
               
                 D13900 
                 mitochondrial short-chain. enoyl-CoA 
                 0.91 
                 1.52 
               
               
                   
                 hydratase 
               
               
                 Z1531 
                 mRNA for elongation factor 
                 0.76 
                 0.89 
               
               
                   
                 1-gamma 
               
               
                 D78361 
                 mRNA for ornithine decarboxylase 
                 0.51 
                 0.82 
               
               
                   
                 antizyme 
               
               
                 U13261 
                 e1F-2 associated p67 homolog 
                 0.41 
                 0.82 
               
               
                 X15183 
                 mRNA for 90-kDa heat-shock protein 
                 0.8 
                 0.75 
               
               
                 M36340 
                 ADP-ribosylation factor 1 (ARF1) 
                 0.5 
                 0.66 
               
               
                 X91257 
                 mRNA for seryl-tRNA synthetase 
                 0.75 
                 0.52 
               
               
                 AF047470 
                 Malate dehydrogenase precursor 
                 0.41 
                 0.51 
               
               
                   
                 (MDH) mRNA 
               
               
                 D13748 
                 mRNA for eukaryotic initiation factor 
                 0.33 
                 0.43 
               
               
                   
                 4A1 
               
               
                 L36151 
                 Phosphatidylinosito14-kinase 
                 0.26 
                 0.38 
               
               
                 X04297 
                 mRNA for Na, K-ATPase 
                 0.27 
                 0.34 
               
               
                   
                 alpha-subunit 
               
               
                 X79535 
                 mRNA for beta tubulin, clone 
                 0.18 
                 0.28 
               
               
                   
                 nuk_278 
               
               
                 J04173 
                 Phosphogylcerate mutase (PGAM-B) 
                 0.14 
                 0.23 
               
               
                   
               
             
          
         
       
     
     
       
         
               
             
               
               
               
               
               
               
               
               
             
               
               
               
               
               
               
               
               
             
           
               
                 TABLE 3 
               
             
             
               
                   
               
               
                 Real-time quantitative RT-PCR analysis of a few selected genes a . 
               
             
          
           
               
                   
                   
                   
                   
                   
                 Creatin 
                   
                   
               
               
                   
                 GA733-2 
                 Osteopontin 
                 KOC 
                 Prostasin 
                 Kinase B 
                 CEA 
                 RGS 
               
               
                   
                   
               
             
          
           
               
                 Normal ovarian cells 
                   
                   
                   
                   
                   
                   
                   
               
               
                 HOSE695 
                 4 
                 21 
                 5 
                 28 
                 0.4 
                 5 
                 32 
               
               
                 HOSE697 
                 1 
                 1 
                 2 
                 4 
                 0.4 
                 3 
                 18 
               
               
                 HOSE713 
                 1 
                 20 
                 7 
                 5 
                 1 
                 16 
                 25 
               
               
                 HOSE726 
                 1 
                 1 
                 1 
                 1 
                 1 
                 1 
                 1 
               
               
                 Average (HOSE) 
                 2 
                 11 
                 4 
                 9 
                 1 
                 6 
                 19 
               
               
                 Ovarian cancer cell lines 
               
               
                 OVCA3 
                 419 
                 6 
                 4 
                 61 
                 393 
                 1 
                 4 
               
               
                 OVCA432 
                 136 
                 0 
                 0 
                 17 
                 8 
                 0 
                 1 
               
               
                 OVAC433 
                 2048 
                 0 
                 52 
                 57 
                 12 
                 1 
                 4 
               
               
                 OVCA633 
                 2917 
                 13777 
                 3 
                 228 
                 4 
                 15 
                 27 
               
               
                 SKOV3 
                 2856 
                 265 
                 10 
                 2 
                 31 
                 6 
                 13 
               
               
                 ALST 
                 3875 
                 6081 
                 78 
                 10 
                 1 
                 2 
                 5 
               
               
                 Average 
                 2042 
                 3355 
                 24 
                 62 
                 75 
                 4 
                 9 
               
               
                 (OVCA) 
               
               
                 OVCA/HOSE 
                 1361 
                 310 
                 6 
                 7 
                 103 
                 1 
                 0.5 
               
               
                 (average) 
               
               
                   
               
               
                   a Each gene was analyzed using an identical panel of 10 cDNA samples that comprised of 4 normal ovarian surface epithelial cells and 6 ovarian cancer cell lines. The expression of each gene for each cDNA sample was normalized against cyclosporin. Duplicated reactions were performed for each of the genes and similar results were obtained. 
               
             
          
         
       
     
     Example 2 
     Differentially Expressed Genes 
     A. Choice of Samples and the Identification of Differentially Expressed Genes 
     We compared the expression of 2400 genes between primary human ovarian surface epithelial (HOSE) cells and ovarian cancer (OVCA) cells using the MICROMAX™ cDNA microarray system (NEN Life Science Products, Boston, Mass., USA). Three primary HOSE cells from different individuals were pooled together as a normal sample. The use of pooled normal samples has two advantages—(1) fluctuations in gene expression among normal HOSE cells due to the individual difference in age or physiological states may be minimized, and (2) a sufficient amount of RNA for direct labelling can be obtained from the precious primary cell cultures. Similarly, three different cancer cell lines were pooled together as an ovarian cancer sample for the analysis. 
     47 genes over-expressed (Table 4 and Table 5), and 58 genes down-regulated in ovarian cancer cells (Table 6) were identified from a single microarry experiment. However, the list of genes described here is different from two similar studies reported previously (Schummer, et al.,  Gene  238:375 (1999), Wang, et al.,  Gene  229:101, (1999)). Only a few differentially expressed genes were shared by these studies. The differences in the list of differentially expressed genes may be due to the use of different samples in the analysis. We compared the gene expression of primary normal ovarian surface epithelial cells and ovarian cancer cell lines. In one of the previous studies, gene expression of normal ovary was compared with tumor tissues, while gene expression of low passage, ovarian surface epithelial cells were compared with tumor tissues in another study. Apparently, the choice of samples for analysis would account for the different set of genes identified. 
     B. Background Hybridization Signal and the Identification of Weakly Expressed Genes 
     Gene expression from OVCA samples was detected as a Cy3 signal while gene expression from HOSE samples was detected as Cy5 signal. After completion of the recommended procedures, significant background signal was still observed in the Cy3 signal that derived from OVCA sample. A series of additional, stringent post-hybridization washes reduced the background signal. While the Cy3 to Cy5 ratios for most of the genes increased slightly after stringent post-hybridization washes, the ratios, for some genes increased significantly. More importantly, after the stringent post-hybridization washes, we were able to detect the weakly expressed genes that are differentially over-expressed in ovarian cancer cells (Table 5). 
     C. Genes Over-Expressed in Ovarian Cancer Cells 
     From the list of over-expressed genes, several putative mechanisms may be involved in the pathogenesis of ovarian cancer—(1) inactivation of a tumor suppressor, (2) altered expression of transcription factors, (3) overexpression of oncogenes, (4) overexpression of glycosylphosphatidylinositol (GPI) anchor associated proteins, and (5) altered cell cycle control. According to this list of genes, VBP1 interacts with the product of the von Hippel-Lindau gene and is expected to participate in pathways by inactivation of this tumor suppressor gene. RNA binding proteins, Koc and hnRNP D, may assume a role in the regulation of tumor cell proliferation by interfering with transcriptional and/or posttranscriptional processes of tumor suppressor genes. However, the precise role of these RNA binding proteins in human tumor cells remains to be elucidated. ATF3 and XBP-1 are transcription factors which may play an important role in the regulation of gene expression by cAMP-dependent intracellular signaling pathways and be essential for hepatocyte growth respectively. Also related to gene transcription, HMG-I protein has been implicated as a potential marker for thyroid carcinoma. p18 and E16 are two oncogenes that have been found to be over-expressed in acute leukemia cells and various human cancers respectively. The glycosylphosphatidylinositol (GPI) anchor, potentially capable of generating a number of second messengers, such as diacylglycerol, phosphatidic acid, and inositol phosphate glycan, has been postulated to be involved in signal transduction in various cell types, including T-cells. Genes encoding GPI anchored proteins. (GPI-H, B61 and CD24) were found to be over-expressed in ovarian cancer cells. Mytl activity is temporally regulated during the cell cycle and is suggested to play a role in mitotic control. CD24, a GPI anchored protein, is also involved in cell cycle control. 
     The differential expression of five interesting genes, GA733-2, osteopontin, koc; prostasin, and creatine kinase B, has previously been confirmed by real-time RT-PCR. All these genes are either surface antigens or secreted proteins, which may be potential serum markers. In fact, we have found that prostasin is significantly higher in the plasma of an ovarian cancer patient. GA733-2 is known as epithelial cell surface antigen (EPG) or adenocarcinoma-associated antigen (KSA). These proteins may function as growth factor receptors. Osteopontin is an acidic phosphorylated glycoprotein of about 40 Kd which is abundant in the mineral matrix of bones and possibly functions as a cell attachment factor involved in tumor invasion and metastasis. Prostasin is a serine proteinase expressed in prostate and prostate carcinoma. Creatine kinase has been shown to be at an elevated level in the blood of patients with renal cell carcinoma or small lung carcinoma. 
     D. Genes Down-Regulated in Ovarian Cancer Cells 
     More than 50 genes down-regulated in ovarian cancer cells were identified in this study. In this list of genes (Table 6), SPARC/osteonectin has been previously identified as a down-regulated gene. SPARC is an extracellular matrix (ECM) protein with tumor-suppressing activity in human ovarian epithelial cells (Mok, et al.,  Oncogene  12:1895, (1996)). Other ECM or ECM related proteins such as fibronectin, tenascin, OB-cadherin-1, HXB, matrix metalloproteinase, and ICAM-1 were also found to be down-regulated. Tenascin has been suggested to be a prognostic marker for colon cancer. Patients with more tenascin expression have better long-term survival than patients with no or weak expression. 
     Several other genes involved in responding to growth factors or mitogens were also down-regulated. These genes were Shps-1, phosphorylase-kinase, phosphoinositide 3-kinase, NDP kinase, ZIP-kinase, signal transducing guanine nucleotide-binding regulatory protein, IGFBP2, TGF-beta, and TNFα receptor. SHPS-1, a novel glycoprotein, binds the Sh2-domain-containing protein tyrosine phosphatase SHP-2 in response to mitogens and cell adhesion. Suppression of SHPS-1 expression by v-Src via the Ras-MAP kinase pathway has been shown to promote the oncogenic growth of cells. NDP kinase gene located on chromosome 17q has been proposed as a metastasis suppressor gene in a variety of tumor types. ZIP kinase is a novel serine/threonine kinase and has been shown to mediate apoptosis through its catalytic activities. Previous work suggests that the TGF-beta receptor complex and its downstream signaling intermediates constitute a tumor suppressor pathway. The stabilization of TNF-alpha receptors on the surface of human colon carcinoma cells is necessary for TNFα induced cell death. Besides these two major groups of genes, other genes encoding proteases and complement C1 components were also down-regulated. Some of these down-regulated genes, such as testican and osteoblast specific factor 2, have not yet been associated with carcinogenesis. 
     
       
         
               
               
               
               
             
               
               
               
               
             
           
               
                 TABLE 4 
               
               
                   
               
               
                   
                   
                   
                 OVCA 
               
               
                 Accession 
                   
                 (OVCA/ 
                 signal 
               
               
                 # 
                 Description 
                 HOSE) 
                 intensity 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
                 M33011 
                 carcinoma-associated antigen 
                 444 
                 1249 
               
               
                   
                 GA733-2 
               
               
                 704765 
                 Osteopontin 
                 184 
                 11851 
               
               
                 L41351 
                 Prostasin 
                 170 
                 3172 
               
               
                 L19783 
                 GPI-H 
                 88 
                 916 
               
               
                 U96759 
                 Von Hippel-Lindau binding protein 
                 59 
                 1377 
               
               
                   
                 (VBP-1) 
               
               
                 M57730 
                 B61 
                 49 
                 5514 
               
               
                 L33930 
                 CD24 signal transducer and 3′ region 
                 47 
                 26722 
               
               
                 D55672 
                 hnRNP D 
                 44 
                 950 
               
               
                 U97188 
                 Putative RNA binding protein KOC 
                 38 
                 3599 
               
               
                 L19871 
                 ATF3 
                 37 
                 3507 
               
               
                 704991 
                 p18 
                 34 
                 9914 
               
               
                 D00762 
                 proteasome subunit HC8 
                 29 
                 4703 
               
               
                 U17989 
                 Nuclear autoantigen GS2NA 
                 28 
                 721 
               
               
                 U43148 
                 Patched homolog (PTC) 
                 28 
                 4155 
               
               
                 AF010312 
                 Pig7 (PIG7) 
                 23 
                 17379 
               
               
                 M80244 
                 E16 
                 21 
                 4180 
               
               
                 X99802 
                 ZYG homologue 
                 21 
                 2086 
               
               
                 U05598 
                 Dihydrodiol dehydrogenase 
                 18 
                 21595 
               
               
                 L47647 
                 Creatine kinase B. 
                 18 
                 787 
               
               
                 M55284 
                 Protein kinase C-L (PRKCL) 
                 16 
                 863 
               
               
                 X15722 
                 glutathione reductase 
                 14 
                 794 
               
               
                 554005 
                 Thymosin beta-10 
                 13 
                 1476 
               
               
                 AB006965 
                 Dnmlp/Vpslp-like protein 
                 13 
                 4183 
               
               
                 M83653 
                 Cytoplasmic phosphotyrosyl protein 
                 13 
                 2156 
               
               
                   
                 phosphatase 
               
               
                 X12597 
                 high mobility group-1 protein 
                 12 
                 2785 
               
               
                   
                 (HMG-1) 
               
               
                 M18112 
                 poly(ADP-ribose) polymerise 
                 12 
                 9277 
               
               
                 U56816 
                 Kinase Mytl (Mytl) 
                 11 
                 1773 
               
               
                 X06233 
                 calcium-binding protein in 
                 11 
                 3007 
               
               
                   
                 macrophages (MRP-14) 
               
               
                 D85181 
                 fungal sterol-C5-desaturase homolog 
                 11 
                 3571 
               
               
                 M31627 
                 X box binding protein-1 (XBP-1) 
                 10 
                 12151 
               
               
                   
               
             
          
         
       
     
     
       
         
               
             
               
               
               
               
             
           
               
                 TABLE 5 
               
               
                   
               
               
                 Weakly expressed genes identified after stringent washes. 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
                 AF005654 
                 Actin-binding double-zinc-finger protein 
                 18770 
                 751 
               
               
                   
                 (abLIM). 
               
               
                 L10844 
                 Cellular growth-regulating protein. 
                 33 
                 725 
               
               
                 M88163 
                 Global transcription activator homologous 
                 18 
                 642 
               
               
                   
                 sequence. 
               
               
                 U02882 
                 Rolipram-sensitive 3′, 5′-cyclic AMP 
                 27 
                 636 
               
               
                   
                 phosphodiesterase. 
               
               
                 X12517 
                 U1 small nuclear RNP-specific C protein. 
                 112 
                 550 
               
               
                 D29833 
                 Salivary proline rich peptide P-B. 
                 10 
                 492 
               
               
                 AF020918 
                 Glutathione transferase GSTA4 
                 47 
                 475 
               
               
                 J05262. 
                 Farnesyl pyrophosphate synthetase 
                 95 
                 469 
               
               
                 L08424 
                 Achaete scute homologous protein 
                 57 
                 457 
               
               
                   
                 (ASH1). 
               
               
                 M84526. 
                 Adipsin/complement factor D 
                 65 
                 441 
               
               
                 U35113 
                 Metastasis-associated mtal. 
                 13 
                 367 
               
               
                 D28468 
                 DNA-binding protein TAXREB302. 
                 268 
                 357 
               
               
                 AF012126 
                 Zinc finger protein (ZNF198). 
                 15 
                 342 
               
               
                 ABOO0714 
                 RVP1. 
                 11 
                 314 
               
               
                 AF029750 
                 Tapasin (NGS-17). 
                 118 
                 305 
               
               
                 X60489 
                 Elongation factor-1-beta. 
                 10 
                 282 
               
               
                 L36645 
                 Receptor protein-tyrosine kinase (HEK8). 
                 71 
                 273 
               
               
                   
               
             
          
         
       
     
     
       
         
               
             
               
               
               
               
             
               
               
               
               
             
           
               
                 TABLE 6 
               
             
             
               
                   
               
               
                 List of genes down-regulated in ovarian cancer cells more than 10-fold. 
               
             
          
           
               
                 Accession 
                   
                 (HOSE/ 
                 HOSE 
               
               
                 # 
                 Description 
                 OVCA) 
                 signal 
               
               
                   
               
             
          
           
               
                 D45421 
                 phosphodiesterase I alpha 
                 ∞ 
                 667 
               
               
                 M35410 
                 Insulin-like growth factor binding 
                 ∞ 
                 1517 
               
               
                   
                 protein 2 (IGFBP2) 
               
               
                 X81334 
                 collagenase-3 protein 
                 ∞ 
                 5146 
               
               
                 D13665 
                 osteoblast specific factor 2 (OSF-2pl) 
                 ∞ 
                 24300 
               
               
                 J03040 
                 SPARC/osteonectin 
                 ∞ 
                 28711 
               
               
                 D86043 
                 SHPS-1 
                 681  
                 9450 
               
               
                 U89942 
                 Lysyl oxidase-related protein (WS9-14) 
                 454  
                 25055 
               
               
                 M59807 
                 NK4 
                 118  
                 22438 
               
               
                 Z74616 
                 Prepro-alpha2(I) collagen 
                 101  
                 2281 
               
               
                 Z74615 
                 Prepro-alpha1(I) collagen 
                 81 
                 24323 
               
               
                 X06596 
                 Complement component Cls 
                 76 
                 22672 
               
               
                 M95787 
                 22 kDa smooth muscle protein (SM22) 
                 71 
                 31581 
               
               
                 X06256 
                 Fibronectin receptor alpha subunit 
                 66 
                 27901 
               
               
                 M36981 
                 Putative NDP kinase (nm23 H2S) 
                 60 
                 15411 
               
               
                 AJ001838 
                 Maleylacetoacetate isomerase 
                 59 
                 304 
               
               
                 X56160 
                 Tenascin 
                 42 
                 36062 
               
               
                 D21254 
                 OB-cadherin-1 
                 40 
                 20621 
               
               
                 Y07921 
                 Serine protease 
                 37 
                 2247 
               
               
                 Y10032 
                 Putative serine/threonine protein kinase 
                 36 
                 8510 
               
               
                 X04526 
                 Beta-subunit signal transducing 
                 36 
                 13321 
               
               
                   
                 proteins Gs/Gi (beta-G) 
               
               
                 L31409 
                 Creatine transporter 
                 35 
                 8677 
               
               
                 X04701 
                 Complement component Clr 
                 33 
                 10299 
               
               
                 X13839 
                 Vascular smooth muscle alpha-actin 
                 32 
                 27311 
               
               
                 X84908 
                 Phosphorylase-kinase, beta subunit. 
                 30 
                 11341 
               
               
                 L14595 
                 Alanine/serine/cysteine/threonine 
                 27 
                 2234 
               
               
                   
                 transporter (ASCTI) 
               
               
                 M97796 
                 Helix-loop-helix protein (Id-2) 
                 25 
                 3187 
               
               
                 X04741 
                 Protein gene product (PGP) 9.5 
                 25 
                 13138 
               
               
                 Y10055 
                 Phosphoinositide 3-kinase 
                 23 
                 614 
               
               
                 X83535 
                 Membrane-type matrix 
                 20 
                 6464 
               
               
                   
                 metalloproteinase 
               
               
                 U69546 
                 RNA binding protein Etr-3 
                 18 
                 2714 
               
               
                 U16268 
                 AMP deaminase isoform L, 
                 18 
                 3512 
               
               
                   
                 alternatively spliced (AMPD2) mRNA, 
               
               
                   
                 exons 1B, 2 and 3. 
               
               
                 S59749 
                 5E10 antigen 
                 18 
                 1249 
               
               
                 U03057 
                 Actin bundling protein (HSN) 
                 17 
                 9285 
               
               
                 J02854 
                 20-kDa myosin light chain (MLC-2) 
                 16 
                 8323 
               
               
                 X16940 
                 Enteric smooth muscle gamma-actin 
                 16 
                 18776 
               
               
                 X13223 
                 N-acetylglucosamide-(beta 1-4)- 
                 16 
                 3357 
               
               
                   
                 galactosyltransferase 
               
               
                 M69181 
                 Nonmuscle myosin heavy chain-B 
                 16 
                 11126 
               
               
                   
                 (MYH10) 
               
               
                 X06990 
                 ICAM-1 
                 16 
                 25605 
               
               
                 M13656 
                 Plasma protease (C1) inhibitor 
                 I5 
                 1091 
               
               
                 X73608 
                 Testican 
                 15 
                 2977 
               
               
                 M96803 
                 General beta-spectrin (SPTBNI) 
                 15 
                 13359 
               
               
                 D00632 
                 Glutathione peroxidase 
                 15 
                 4951 
               
               
                 X03445 
                 Nuclear envelope protein lamin C 
                 13 
                 17451 
               
               
                   
                 precursor 
               
               
                 L06419 
                 Lysyl hydroxylase (PLOD) 
                 13 
                 9288 
               
               
                 M12125 
                 Fibroblast muscle-type tropomyosin 
                 12 
                 34379 
               
               
                 S45630 
                 Alpha B-crystallin, Rosenthal fiber 
                 12 
                 1536 
               
               
                   
                 component. 
               
               
                 AB005298 
                 BAI2 
                 11 
                 3839 
               
               
                 L77864 
                 Stat-like protein (Fe65) 
                 11 
                 1914 
               
               
                 AB007144 
                 ZIP-kinase 
                 11 
                 4277 
               
               
                 M16538 
                 Signal-transducing guanine nucleotide- 
                 11 
                 2793 
               
               
                   
                 binding regulatory (G) protein beta 
               
               
                   
                 subunit 
               
               
                 L35545 
                 Endothelial cell protein C/APC 
                 11 
                 1002 
               
               
                   
                 receptor (EPCR) 
               
               
                 M75161 
                 Granulin 
                 11 
                 13289 
               
               
                 X69910 
                 p63 
                 11 
                 16460 
               
               
                 D12686 
                 eIF-4 gamma 
                 11 
                 21555 
               
               
                 L07594 
                 Transforming growth factor-beta type 
                 11 
                 672 
               
               
                   
                 III receptor (TGF-beta) 
               
               
                 M33294 
                 Tumor necrosis factor receptor 
                 10 
                 6592 
               
               
                 U18121 
                 136-kDa double-stranded RNA binding 
                 10 
                 1619 
               
               
                   
                 protein p136 (K88dsRBP) 
               
               
                 M55618 
                 Hexabrachion (HXB) 
                 10 
                 3866 
               
               
                   
               
             
          
         
       
     
     Example 3  
     Prostasin as a Serum Marker for Ovarian Cancer  
     I. Materials and Methods 
     Biological Specimens 
     Ovarian tissue and cells were freshly collected from women undergoing surgery at the Brigham and Women&#39;s Hospital for diagnosis of primary ovarian cancer or from control subjects having a hysterectomy and ophorectomy for benign disease. Cultures of normal ovarian surface epithelial (HOSE) cells were established by scraping the surface of the ovary and growing recovered cells in a mixture of medium 199 and MCDB 105 medium supplemented with 10% fetal calf serum. The following seven normal HOSE cells were used: HOSE17, HOSE636, HOSE642, HOSE697, HOSE713, HOSE726 and HOSE730. Ovarian cell lines were established by recovery from ascites fluid or explanted from solid tumors. The following ten ovarian cancer cell lines were used: OVCA3, OVCA420, OVCA429, OVCA432, OVCA433, OVCA633, CAOV3, DOV13, ALST and SKOV3. 
     Serum specimens from women with ovarian cancer, other gynecologic cancers and benign gynecologic disorders requiring hysterectomy and from non-diseased normal women were obtained from discarded specimens, from discarded specimens that were archived during the period from 1983 through 1988 or from specimens collected under more recent protocols since 1996. The archived samples were collected from several studies assessing the performance of CA 125 in a variety of diagnostic circumstances, including gynecologically normal subjects as well as subjects having exploratory surgery for pelvic masses that proved to be ovarian, cervical or endometrial cancer for a benign disease such as a fibroid tumor. The archived specimens were stored at −70° C. However, thawing was known to have occurred once for some of the archived specimens. More recent specimens were obtained within the past five years and were stored at −70° C. without any incident of thawing. In both specimen banks, serum from case patients with ovarian cancer and serum from control patients were collected concurrently. 
     Microarray Probe and Hybridization 
     The MICROMAX™ Human cDNA Microarray System I(NEN Life Science Products, Inc. Boston, Mass.) was used in this study. Biotin-labeled cDNA was generated-from 3 micrograms of total RNA that was pooled from HOSE17, HOSE636 and HOSE642 cells. Dinitrophenyl-labelled cDNA was generated from 3 micrograms of total RNA that was pooled from ovarian cancer cell lines OVCA420, OVCA433, and SKOV3. Before the cDNA reaction, 5 ng of Arabidopsis control RNA were added to each batch of the RNA samples for the normalization of hybridization signals. The biotin-labelled cDNA and the dinitrophenyl-labelled cDNA were mixed, dried and resuspended in 20 microliters of hybridization buffer 5× standard saline citrate (SSC), 0.1% sodium dodecyl sulfate (SDS) and salmon sperm DNA at 0.1 mg/ml (1×SSC=0.15 M NaCl, 0.15 M sodium citrate, pH 7). This mixture was added to the cDNA microarray and was covered with a coverslip. Hybridization was carried out overnight at 65° C. inside a hybridization cassette. 
     After hybridization, the microarray was washed with 30 ml of 0.5×SSC-0.01% SDS, with 30 ml of 0.06×SSC-0.01% SDS and then with 30 ml of 0.06×SSC alone. The hybridization signal from biotin-labelled cDNA was amplified with streptavidin-horseradish peroxidase and fluorescent dye, Cy5-tyramide. The hybridization signal from the dinitrophenyl-labelled cDNA was amplified with anti-dinitrophenyl-horseradish peroxidase and another fluorescent dye, Cy3-tyramide. After signal amplification and post-hybridization wash in TNT buffer (i.e., 0.1 M Tris-HCl (pH 7.5)-0.15 M NaCl-0.15% Tween20), the microarray was air-dried and signal amplification was detected with a laser scanner. 
     Laser detection of the Cy3 signal (derived from ovarian cancer cells) and the Cy5 signal (derived from HOSE cells) on the microarray was acquired with a confocal laser reader. Separate scans were taken for each fluor at a pixel size of 10 micrometers. cDNA derived from the added  Arabidopsis  RNA hybridized to 12 specific spots on the microarray, which were composed of DNA sequences obtained from four different  Arabidopsis  expressed sequence tags in triplicate. Cy3 and Cy5 signals from these 12 spots should theoretically be equal and were used to normalize the different efficiencies in labeling and detection with the two fluors. The fluorescence signal intensity and the ratio of the signals from Cy3 and Cy5 for each of the 2400 cDNAs were analyzed by the software Imagene 3.0 (Biodiscovery Inc., Los Angeles, Calif.). 
     Real-Time Quantitative Reverse Transcription-Polymerase Chain Reaction 
     Real-time reverse transcription-polymerase chain reaction (RT-PCR) was performed in duplicate by using primer sets specific for the overexpressed gene encoding the secretory protein prostasin (forward primer=5′-ACTTGAGCCACTCCTTCCTTCAG-3′ (SEQ ID NO:3); reverse primer=5′-CTGATGGTCCCAAAAAGCACAC-3′ (SEQ ID NO:4)) and a housekeeping gene, GADPH. RNA was first extracted from normal ovarian epithelial cell cultures (HOSE697, HOSE713, HOSE726, and HOSE730) and from 10 ovarian carcinoma cell lines (OVCA3, OVCA420, OVCA429, OVCA432, OVCA433, OVCA633, CAOV3, DOV13, SKOV3, and ALST). cDNA was generated from 1 microgram of total RNA using the TaqMan RT reagents containing 1× TaqMan reverse transcriptase buffer, 5.5 mM MgCl 2 , all four deoxyribonucleoside triphosphates (each at 500 μM), 2.5 μM random hexamers, MultiScribe reverse transcriptase at 1.25 U/μl, and RNasin at 0.4 U/μl in 100 μl. The reaction was incubated at 25° C. for ten minutes at 48° C. for thirty minutes and finally at 95° C. for five minutes. A total of one microgram of cDNA was used in 20 μl PCR mixture containing 1×SYBR PCR buffer, 3 mM MgCl 2 , all for deoxyribonucleoside triphosphates (each at 0.8 mM) and AmpliTaq Gold. The cDNAs were then amplified by denaturation for ten minutes at 95° C., followed by 40 PCR cycles of denaturation at 95° C. for 15 seconds and annealing-extension at 60° C. for one minute. The changes in fluorescence of the SYBR Green I dye in every cycle were monitored by ABI 5700 system software and the threshhold cycle, which represents the PCR cycle at which an increase in reporter fluorescence above a baseline signal can first be detected for each reaction, was calculated. The relative amount of PCR products generated from each primer set was determined on the basis of the threshhold cycle (C T ) value. GAPDH was used to normalize the quantity of RNA used. Its C T  value was then subtracted from each target gene to obtain a ΔC T  value. The difference between the ΔC T  values of the samples for each gene target and the ΔC T  value of a calibrator which served as a physiologic reference was determined. For confirmation of the specificity of the PCR, PCR products were subjected to electrophoresis on a 1.2% agrose gel. A single PCR product with the expected size should be observed in samples that express the gene of interest. 
     Immunohistochemical Localization of Prostasin 
     Immunostaining with anti-prostasin antibody was performed on sections prepared from two normal ovaries, from two serous borderline ovarian tumors, and from two grade 1, two grade 2, and two grade 3 serous ovarian adenocarcinomas. This rapid polyclonal antibody, also used in the serum assay was prepared from prostasin purified from human seminal fluid as described previously (Yu, et al.,  J. Biol. Chem.  269:18843–18848 (1994)). Tissues were fixed in 4% paraformaldehyde and embedded in paraffin. Sections (5 μm) were cut, mounted on microscopic slides and incubated at 50° C. overnight. They were then transferred to Tris-buffered saline (TBS) and quenched in 0.2% H 2 O 2  for 20 minutes. After quenching, the sections Were washed in TBS for 20 minutes, incubated with normal horse serum for 20 minutes, and then incubated with anti-prostasin polyclonal antibody (diluted 1:400) at room temperature for one hour. The slides were then washed in TBS for 10 minutes, incubated with diluted biotinylated secondary horse anti-rabbit antibody solution for 30 minutes, washed again in TBS for 10 minutes, incubated with avidin-biotin complex reagent for 30 minutes and washed in TBS for 10 minutes. Stain development was performed for 5 minutes using a diaminobenzidine kit. Finally, the sections were washed in water for 10 minutes. They were then counterstained with hemanoxylin, dehydrated with an ascending series of alcohol solutions, cleared in xylene and mounted. The specificity of the staining was confirmed by using preimmunization rabbit serum and by preabsorbing the antibody with the purified peptide (60 mg/ml) or prostasin for 2 hours at 37° C. before applying the adsorbed antiserum to the sections. 
     Measurement of Prostasin and CA 125 in Sera 
     Sera were available from a total of 201 subjects (64 case patients with ovarian cancer and 137 control subjects, including 34 with other gynecologic cancers, 42 with benign gynecologic diseases, and 71 with no known gynecologic diseases). In all of the case patients and in the 68 control subjects who had surgery, preoperative specimens were available. Serum levels of immunoreactive human prostasin were determined by the enzyme-linked immunosorbent assay (ELICA) prepared with the previously described antibody to human prostasin. Microtiter plates (96 well) were coated with anti-prostasin immunoglobulin G (IgG) (1 μg/ml, 100 μl per well) overnight at 4° C. Purified prostasin standards or samples were added to individual wells in a total volume of 100 μl of phosphate-buffered saline containing 0.05% Tween 20 and 0.5% gelatin (dilution buffer) and incubated at 37° C. for 90 minutes. Biotin labeled anti-human prostasin IgG was added to each well at a concentration of 1 μg/ml in a total of 100 μl and incubated at 37° C. for 60 minutes. Peroxidase-avidin at a concentration of 1 μl/ml in a total volume of 100 μl was added and incubated at 37° C. for 30 minutes. The color reaction was performed by adding to each well 100 μl of freshly prepared substrate solution and 0.03% H 2 O 2  in 0.1 M sodium citrate (pH 4.3) and incubating the mixture at room temperature for 30 minutes. The plates were read at 405 nm with a plate reader. 
     For 37 case patients with ovarian cancers and for 100 control subjects (about 70% of all subjects) a CA 125 level had been determined previously (from the same specimens) and was available for comparison. These measurements had been performed with the original CA 125 radioimmunoassay from Centocor and the assays were not repeated for this study. 
     Statistical Analysis 
     Univariate comparisons for quantitative variables between normal and cancer cell lines or between case and control sera were made using Student&#39;s t test. For analysis of serum levels, adjustment for potential confounding variables such as the subject&#39;s age, year of collection and whether the specimen had undergone freezing and thawing was carried out using general linear modeling. Logistic regression analysis was used to determine the statistical significance of both prostasin and CA 125 as a predictor of case status. Paired Student&#39;s t test was used to compare the change in postoperative prostasin levels from preoperative levels. Pearson correlation coefficients were calculated between CA 125 and prostasin. Because the distributions of prostasin and CA 125 were skewed positively, log-transformed values were used in statistical tests. Analyses with a P value of 0.05 or less were considered to be statistically significant. All statistical tests were two sided and all confidence intervals are 95%. 
     II. Results 
     Microarray analysis of pooled RNA isolated from three normal HOSE cell lines and from three ovarian cancer cell lines was performed. Thirty genes with Cy3/Cy5 signal ratios ranging from 5 to 444 were identified, suggesting that these genes were overexpressed in ovarian cancer cells compared with normal HOSE cells. Among them, both prostasin and osteopontin encode secretory proteins which may be potential serum markers. Another gene, creatine kinase B has been shown to produce a serum marker associated with renal carcinoma and lung cancer. Prostasin was selected for further study because this gene had an available antibody assay. 
     To evaluate the differential expression of prostasin in individual normal and malignant ovarian epithelial cell lines derived from normal and neoplastic ovaries, we performed quantitative PCR analysis on four normal HOSE cultures and on ten ovarian cancer cell lines. The relative prostasin gene expression ranged from 120.3-fold to 410.1-fold greater for seven of the ten ovarian cancer cell lines compared with that for HOSE 697 cells but was only marginally greater for three other ovarian cell lines. Overall, there was a highly statistically significant difference between expression for the four normal cell lines compared to the ten ovarian cancer cell lines P&lt;0.001. 
     For further validation of the expression of prostasin in actual tumor tissue, sections from two normal ovaries, from two serous borderline ovarian tumors and from two grade 1, two grade 2 and two grade 3 serous ovarian cystadenocarcinomas were immunostained with an anti-prostasin polyclonal antibody. Stronger cytoplasmic staining was detected in cancer cells than in normal HOSE cells, suggesting that prostasin is overexpressed by the ovarian cancer cells. Prostasin was, however, also detected in normal ovarian tissue by immunostaining. We next examined prostasin levels detected by ELISA in sera from case patients and control subjects. The mean prostasin level for all of the case patients was 13.7 μg/ml compared with 7.5 μg/ml in all of the control subjects. Based on log-transformed values, this difference was statistically significant (P&lt;0.001) and persisted after adjustment for the subject&#39;s age, year of collection, and quality of specimen (possible freeze-thaw damage). Among case patients, there was considerable variability by stage; however, notably-women with stage II disease had the highest levels of prostasin, suggesting that prostasin may be of use for early-stage detection. It also appeared that women with mucinous-type ovarian tumors had lower levels of prostasin than women with ovarian tumors of other epithelial types. Among control subjects, there was a statistically significant tendency for the archived specimens to have lower prostasin levels than the current specimens (P&lt;0.001), but there was no evidence for an effect of age or diagnostic category (i.e., normal tissue, benign gynecologic disease, or other gynecologic cancer). In addition, 60.5% of the archived case specimens and 66.2% of the control specimens had been in the freezer in which freezing and thawing had occurred. There was no evidence of a tendency for these samples to have lower prostasin levels. 
     In sixteen women with nonmucinous epithelial ovarian cancers, preoperative and postoperative specimens were available for comparison. For fourteen of these women, a decreased prostasin level was observed after surgery, and, in the entire group of sixteen, postoperative P levels were statistically lower when compared with preoperative levels using a pair T test on the log-transformed values (P=0.004). 
     A bivariate plot of prostasin versus CA 125 performed for the 37 case patients with nonmucinous ovarian cancers and for the 100 control subjects who had both measurements available failed to show a statistically significant correlation. This lack of correlation suggests that the two markers may provide complementary information. The combined markers had a sensitivity of 34/37 (92%) and a specificity of 94/100 (94%). In contrast, the sensitivity of CA 125 alone at the same specificity was 24/37 (64.9%) and the sensitivity of prostasin alone at the same specificity was 19/37 (51.4%). 
     III. Discussion 
     The present study demonstrates prostasin&#39;s potential as a biomarker through real-time PCR in cancer and normal epithelial cell lines and by differential staining in cancer tissue compared with normal tissue. Higher levels of serum prostasin were found to be present in case patients with ovarian cancer when compared to control subjects and a declining level of prostasin was observed after surgery for ovarian cancer. Results also suggest that assays with prostasin may be combined with those for other markers such as CA 125 to improve the reliability of procedures for the detection of ovarian cancer.