Pro-angiogenic genes in ovarian tumor endothelial cell isolates

This is a continuation-in-part application of International Patent Application PCT/US2008/054014, filed Feb. 14, 2008, designating the United States and published in English as WO 2008/101118, which claims the benefit of U.S. Provisional Application No. 60/901,455, filed on Feb. 14, 2007. The entire contents of these prior applications are incorporated herein by reference.

This invention was made with government support under contract CA083639 awarded by the National Institutes of Health. The government has certain rights in the invention.

This disclosure relates to the field of ovarian cancer and in particular, to methods for treating ovarian cancer by targeting ovarian endothelial cell tumor-associated molecules identified by an ovarian tumor endothelial cell gene expression profile and methods for identifying therapeutic agents.

Ovarian cancer is the fifth most common form of cancer in women in the United States, accounting for three percent of the total number of cancer cases and twenty-six percent of those occurring in the female genital tract. The American Cancer Society estimated that 15,310 deaths would be caused in women living in the United States in 2006. A large majority of women who die of ovarian cancer will have had serous carcinoma of the ovarian epithelium, a condition which occurs in sixty percent of all cases of ovarian cancer (Boring et al., Cancer J. Clin. 44: 7-26, 1994).

Women with ovarian cancer are typically asymptomatic until the cancer has metastasized. As a result, most women with ovarian cancer are not diagnosed until the cancer has progressed to an advanced and usually incurable stage (Boente et al., Curr. Probl. Cancer 20: 83-137, 1996). Survival rates are much better in women diagnosed with early-stage ovarian cancers, about ninety percent of these women are still alive five years after diagnosis.

Treatment of ovarian cancer typically involves a variety of treatment modalities. Generally, surgical intervention serves as the basis for treatment (Dennis S Chi & William J. Hoskins, Primary Surgical Management of Advanced Epithelial Ovarian Cancer , in Ovarian Cancer 241, Stephen C. Rubin & Gregory P. Sutton eds., 2d ed. 2001). Treatment of serous carcinoma often involves cytoreductive surgery (hysterectomy, bilateral salpingo-oophorectomy, omentectomy, and lymphadenectomy) followed by adjuvant chemotherapy with paclitaxel and either cisplatin or carboplatin (Eltabbakh, G. H. & Awtrey, C. S., Expert Op. Pharmacother. 2(10): 109-24, 2001).

Despite a clinical response rate of 80% to primary treatment with surgery and chemotherapy, most subjects experience tumor recurrence within two years of treatment. The overwhelming majority of subjects will eventually develop chemoresistance and die as a result of their cancer. Thus, a need exists to identify alternative treatments for ovarian cancer.

A gene profiling signature is disclosed herein that can be used to predict clinical outcome and develop therapeutics for treating ovarian cancer in a subject. For example, the ovarian endothelial cell tumor-associated molecules identified by the gene profile signature can serve as prognostic indicators as well as targets for specific therapeutic molecules that can reduce or eliminate ovarian cancer. Thus, methods of identifying an agent for treating an ovarian tumor are provided. In some examples, the methods include contacting a cell, such as an ovarian tumor cell or an ovarian tumor endothelial cell, with one or more test agents under conditions sufficient for the one or more test agents to alter the activity of at least one ovarian endothelial cell tumor-associated molecule listed in any of Tables 1-5. The method includes detecting the activity of the at least one ovarian endothelial cell tumor-associated molecule in the presence and absence of the one or more test agents. The activity of the at least one ovarian endothelial cell tumor-associated molecule in the presence of the one or more test agents is then compared to the activity in the absence of such agents to determine if there is differential expression of the at least one ovarian endothelial cell tumor associated molecule. Differential expression of the ovarian endothelial cell tumor-associated molecule in the presence of the test agent(s) indicates that the one or more test agents can be used to treat an ovarian tumor.

Methods are also provided for treating an ovarian tumor. In some examples, the method includes administering to the subject a therapeutically effective treatment to inhibit ovarian tumor growth. In an example, the treatment includes administering a therapeutically effective amount of a specific binding agent that binds with high specificity to one of the ovarian endothelial cell tumor-associated molecules listed in Tables 1, 2, 4 or 5 and alters expression or activity of the molecules, thereby treating the ovarian tumor in the subject (for example, by decreasing tumor vascular growth, tumor growth or tumor volume). In particular examples, the specific binding agent preferentially binds to and inhibits expression or activity of one of the ovarian endothelial cell tumor-associated molecules that is upregulated in an ovarian tumor endothelial cell, such as Zeste homologue 2 (EZH2), EGF-like domain, multiple 6 (EGFL6), tumor necrosis factor, alpha-induced protein 6 (TNFAIP6), Twist homologue 1 (TWIST1), stanniocalcin 1 (STC1), homeodomain-only protein (HOP), chondroitin sulfate proteoglycan 2 (CSPG2), and plexin domain containing 1 (PLXDC1). In other particular examples, ovarian tumor growth is inhibited by the specific binding agent preferentially binding to and inhibiting expression of one of the ovarian endothelial cell tumor-associated molecules listed in any of Tables 1, 2, 4 or 5 which are involved in angiogenesis, such as molecules involved in cell proliferation, tube formation or cell motility and are upregulated in ovarian tumor endothelial cells.

Methods are also provided for determining the effectiveness of an agent for the treatment of an ovarian tumor in a subject with the ovarian tumor. In an example, the method includes detecting expression of an ovarian endothelial cell tumor-associated molecule in a sample from the subject following administration of the agent. The expression of the ovarian endothelial cell tumor-associated molecule following administration is compared to a control, such as specific binding agents that bind to and inhibit one of the ovarian endothelial cell tumor-associated molecules listed in any of Tables 1, 2, 4 or 5 that is upregulated in ovarian endothelial tumor cells. An alteration in the expression of the ovarian endothelial cell tumor-associated molecule (such as a decrease in expression of a molecule upregulated in ovarian tumor endothelial cells or an increase in expression of a molecule downregulated in such cells) following treatment indicates that the agent is effective for the treatment of the ovarian cancer in the subject. In a specific example, the method includes detecting and comparing the protein expression levels of the ovarian endothelial cell tumor-associated molecules. In other examples, the method includes detecting and comparing the mRNA expression levels of the ovarian endothelial cell tumor-associated molecules.

Methods of diagnosing and prognosing an ovarian tumor (such as a tumor that overexpresses at least one of the disclosed ovarian endothelial cell tumor-associated molecules) are provided. In some examples, such methods are performed prior to the treatment methods described herein. However, such methods can also be used independently of the disclosed treatment methods. In particular examples, the method includes determining the metastatic potential of an ovarian tumor in a subject by detecting expression of at least one ovarian endothelial cell tumor-associated molecule in a sample obtained from a subject with an ovarian tumor. The at least one ovarian endothelial cell tumor-associated molecule is involved in promoting angiogenesis, such as cell proliferation, cell motility or tube formation, such as EZH2. The method further includes comparing expression of the at least one ovarian endothelial cell tumor-associated molecule in the sample obtained from the subject with the ovarian tumor to a control. An alteration in the expression of the at least one ovarian endothelial cell tumor-associated molecule involved in promoting angiogenesis indicates that the subject has an ovarian tumor with increased metastatic potential.

In additional examples, methods are disclosed for predicting a clinical outcome in a subject with an ovarian tumor, such as advanced stage epithelial ovarian cancer. In an example, the methods include detecting expression of at least one ovarian endothelial cell tumor-associated molecules listed in Tables 1-5 or combinations thereof (such as at least 1, at least 3, at least 5 or at least 10 of such molecules) in a sample obtained from the subject with the ovarian tumor. The methods also can include comparing expression of the at least one ovarian endothelial cell tumor-associated molecule in the sample obtained from the subject with the ovarian tumor to a control (such as a normal sample or value representing such expression expected in a normal sample), wherein an alteration in the expression of the at least one ovarian endothelial cell tumor-associated molecule indicates that the subject has a decreased chance of survival. For example, an alteration in the expression, such as an increase in the expression of EZH2 indicates a poor prognosis, such as a decreased chance of survival. In one example, a decreased chance of survival includes a survival time of equal to or less than a year. Alterations in the expression can be measured using methods known in the art, and this disclosure is not limited to particular methods. For example, expression can be measured at the nucleic acid level (such as by real time quantitative polymerase chain reaction or microarray analysis) or at the protein level (such as by Western blot analysis).

The foregoing and other features of the disclosure will become more apparent from the following detailed description of several embodiments which proceeds with reference to the accompanying figures.

FIG. 1 is a graph illustrating the comparative fold change in relative expression levels between microarray data and real-time quantitative RT-PCR data of selected genes from the pro-angiogenic gene signature provided in Table 1.

FIG. 2 is a graph illustrating protein expression in ovarian endothelial cells for a subset of the proteins detected following staining of samples with immunofluorescently-labeled PTK2, Fyn, MMP-9, β2-arrestin, Jagged1 and PLXDC1.

FIGS. 3A , 3 B and 3 C are digital images of siRNA-mediated silencing of ( FIG. 3A ) EZH2, ( FIG. 3B ) Jagged1 and ( FIG. 3C ) protein tyrosine kinase 2 (PTK2), as assessed using Western blot analyses.

FIG. 3D is a graph illustrating the effect of EZH2, Jagged1 or PTK2 silencing on human umbilical vein endothelial cell (HUVEC) tube formation.

FIG. 3E is a graph illustrating the effect of EZH2 silencing on HUVEC migration.

FIG. 3F is a graph illustrating the effect of Jagged1 silencing on HUVEC migration.

FIG. 3G is a graph illustrating the effect of PTK2 silencing on HUVEC migration.

FIG. 4 is a digital image illustrating down regulation of EZH2 by mouse EZH2 siRNA in mouse ovarian endothelial cells.

FIGS. 5A , 5 B and 6 provide graphs illustrating the therapeutic effects of siRNA-mediated EZH2 down regulation on HeyA8 ( FIG. 5A ) and SKOV3ip1 ( FIGS. 5B and 6 ) ovarian tumors.

FIGS. 7A-7H illustrate EZH2 expression in human ovarian carcinoma. FIG. 7A provides digital images representative of human tumors with low and high EZH2 expression based on immunohistochemical staining. FIG. 7B provides Kaplan-Meier curves of disease-specific mortality for patients whose ovarian tumors expressed high and low levels of EZH2 (EZH2-T). The log-rank test (two-sided) was used to compare differences between the two groups. Increased EZH2-T was significantly associated with decreased overall survival (p<0.001). FIG. 7C provides digital images representative of human ovarian tumor vasculature (arrowheads point to endothelial cells) with low and high immunohistochemical staining for EZH2. FIG. 7D provides Kaplan-Meier curves of disease-specific mortality of patients whose ovarian vasculature expressed low versus high EZH2 (EZH2-Endo) EZH2-Endo was predictive of poor overall survival. FIG. 7E provides digital images representative of human ovarian tumors with low or high immunohistochemical staining for VEGF. FIG. 7F provides a bar graph VEGF expression was strongly associated with high EZH2-Endo (*p<0.01). FIG. 7G provides digital images representative of human ovarian tumors with low or high immunohistochemical staining for microvessel density (MVD). FIG. 7H provides a bar graph illustrating high MVD counts in a tumor were significantly associated with high EZH2-Endo expression (*p<0.001). Images in panels A, C, and E were taken at original magnification ×200, and in panel g at original magnification ×200.

FIGS. 8A-8C are graphs illustrating VEGF-increased EZH2 expression in endothelial cells. Results in FIGS. 8A and 8B are in response to 6-hour treatments with EGF (25 ng/μL), VEGF (50 ng/μL), conditioned medium (CM) from the non-cancerous ovarian epithelial cell line IOSE120, two ovarian cancer cell lines OVCA420 and SKOV3, and complete medium with either 10% serum (A) or 2% serum (B). Percent fold changes represent the mean+/−s.d. of triplicate experiments compared to untreated control cells. *p<0.05; **p<0.01; ***p<0.001. FIG. 8A illustrates that EZH2 promoter activity is increased in an endothelial cell line in response to EGF, VEGF, and conditioned media from ovarian cancer cell lines. EAhy926 hybridoma endothelial cell line was cotransfected with the Renilla luciferase plasmid and firefly luciferase plasmid either with or without the EZH2 promoter construct followed by treatment with EGF, VEGF and conditioned medium and promoter activity was determined. FIG. 8B illustrates that EZH2 mRNA levels are increased in HUVEC in response to EGF, VEGF, and conditioned media from ovarian cancer cell lines. Cells were treated as indicated and purified RNA was used in real-time quantitative RT-PCR. Control values were normalized using 3 housekeeping genes. FIG. 8C Pearson's analysis shows significant correlation between EZH2 and VEGF expression values (Log 2 ) from 29 microdissected high-grade serous papillary ovarian adenocarcinomas.

FIGS. 9A-9E show EZH2 gene silencing increases VASH1 mRNA expression in endothelial cells. FIG. 9A is a digital image of a polyacrylamide gel illustrating PCR products generated by as ChIP assay of EZH2 binding to human VASH1 promoter in response to VEGF in HUVEC. Cross-linked chromatin from HUVEC was treated with (+) or without (−) VEGF and immunoprecipitated (IP) using EZH2 or mouse IgG antibodies. The input and immunoprecipitated DNA were subjected to PCR using primers corresponding to the 3800 to 3584 base pairs upstream of VASH1 transcription start site. PCR products were examined on ethidium bromide-stained agarose gel. FIG. 9B is a bar graph illustrating EZH2 mRNA levels in cells transfected with control or mouse EZH2 siRNA and harvested after 72 hours. RNA was isolated and subjected to real-time quantitative RT-PCR. The fold difference in levels of EZH2 mRNA represents the mean of triplicate experiments compared to control siRNA treated cells. Error bars represent s.e.m. *p<0.05. FIG. 9C is a bar graph illustrating the fold difference in levels of VASH1 mRNA as compared to control siRNA treated cells. Error bars represent s.e.m. *p<0.01. FIG. 9D illustrates the effect of EZH2 gene silencing on methylation status of VASH1 in VEGF-treated MOECs as detected by methylation specific PCR. The inhibitory units of methylated VASH1 were normalized by that of the un-methylated VASH1 and represent the mean of triplicate experiments. FIG. 9E is a digital image of a Western blot of lysate collected 48 hours after transfection of MOEC with control, VEGF treated and mouse EZH2 siRNA treated cells.

FIGS. 10A-10C show E2F transcription factors increases upon VEGF treatment in MOEC. FIG. 10A is a bar graph illustrating expression levels of E2F transcription factors in MOEC. Cells were treated with VEGF for 6 hours and subjected to Q-RT-PCR. FIG. 10 B provides a pair of bar graphs illustrating silencing of E2F1, E2F3 and E2F5 transcription factors by targeted siRNA in MOEC. Cells were transfected with corresponding siRNAs. After 24 hours and 48 hours, cells were collected; RNA was isolated and was subjected to real-time Q-RT-PCR. E2F3 and E2F5 gene silencing decreases EZH2 expression levels. EZH2 expression levels were analyzed in E2F1, E2F3 and E2F5 silenced samples using Q-RT-PCR. The fold difference in levels of mRNA expression represents the mean of triplicate experiments compared to cells (A) and VEGF treated cells (B). Error bars represent s.e.m. *p<0.01. FIG. 10C is a bar graph illustrating the effect of VASH1 gene silencing on tube formation in endothelial cells. HUVECs were plated on Matrigel after transfecting the cells with either control or human VASH1 siRNA. Vascular tube formation was evaluated by microscopic observation.

FIGS. 11A-11E illustrate the physical characteristics of siRNA/CH nanoparticles. FIG. 11A is a table providing the composition of CH/TPP/siRNAs. FIG. 11B is a graph illustrating the mean particle size of siRNA/CH particles as measured using light scattering with a particle analyzer, showing that nanoparticles maintained 100-200 nm size up to 7:1 ratio (CH:TPP). FIG. 11C is a graph illustrating that zeta potential of siRNA/CH nanoparticles showed slight positive charge. FIG. 11D is a graph illustrating incorporation efficiency of siRNA into CH nanoparticles with 3:1 ratio of CH:TPP resulting in >75% incorporation efficiency. FIG. 11E is a digital image following atomic force microscopy (AFM) demonstrating that siRNA/CH nanoparticles were spherical and <150 nm in size.

FIGS. 12A-12E illustrate incorporation, stability and intracellular uptake of siRNA/CH nanoparticles. FIG. 12A is a digital image illustrating electrophoretic migration of naked siRNA and siRNA/CH nanoparticles. SiRNA/CH nanoparticles (open arrow) remained at top of the gel compared to naked siRNA (solid arrow), which migrated downward. FIG. 12B is a digital image illustrating electrophoretic migration of siRNA/CH nanoparticles in the presence of 50% serum. SiRNA/CH nanoparticles were collected at different time points of incubation at 37° C. (Lane 1; naked siRNA, Lanes 2 to 5; siRNA/CH nanoparticles). Naked siRNA (solid arrow) was degraded over 12 to 24 hours in serum containing media; whereas CH nanoparticles (open arrow) protected the siRNA from degradation in serum. Increased binding efficiency of siRNA/CH nanoparticles was noted compared to naked siRNA. FIG. 12C is a fluorescence microscopy digital image of HeyA8 cells after incubating either with siRNA alone or with siRNA/CH nanoparticles at 4° C. for 20 minutes in PBS. FIG. 12D is a series of tracings from a flow cytometry analysis demonstrating that uptake efficiency of nanoparticles into cells was increased by 72-fold after incubating cells in PBS at 4° C. for 20 minutes. FIG. 12E is graphical representation of percentage of uptake of Alexa-555 siRNA by cells by flow cytometry analysis.

FIGS. 13A-13E illustrate in vivo siRNA delivery using CH nanoparticles and the distribution of siRNA following single intravenous injection of Alexa-555 siRNA/CH nanoparticles in orthotopic HeyA8 tumor bearing nude mice. FIG. 13A provides a pair of digital images illustrating fluorescent siRNA distribution in tumor tissue of hematoxylin and eosin, original magnification ×200 (left); stained with anti-CD31 (green) antibody to detect endothelial cells (right). FIG. 13B provides a pair of digital images of 50-μm sections stained with Cytox Green and examined with confocal microscopy (original magnification ×400) (left); lateral view (right) Images taken every 1 μm were stacked and examined from the lateral view. Nuclei were labeled green and fluorescent siRNA (red) was seen throughout the section. At all time points, punctated emissions of the siRNA were noted in the perinuclear regions of individual cells, and siRNA was seen in >80% of fields examined. (c) Western blot of lysates from orthotopic tumors collected 24, 48, 72 and 96 hours after a single injection of control siRNA/CH or human (EZH2 Hs siRNA/CH). FIG. 13D provides multiple digital images illustrating EZH2 gene silencing in HeyA8 tumor as well as tumor endothelial cells. Tumors were collected after 48 hours of single injection of control siRNA/CH, or EZH2 Hs siRNA/CH, or EZH2 Mm siRNA/CH and stained for EZH2 (green) and CD31 (red). Images were taken at original magnification, ×200. FIG. 13E is a pair of graphs illustrating the effects of EZH2 Hs siRNA/CH or EZH2 Mm siRNA/CH on tumor weight in mouse orthotopic tumor models. Nude mice were injected with HeyA8 or SKOV3ip1 ovarian cancer cells and 1 week later, were randomly assigned (10 mice per group) to receive therapy: (1) control siRNA/CH, (2) EZH2 Hs siRNA/CH, (3) EZH2 Mm siRNA/CH, and (4) combination of EZH2 Hs siRNA/CH plus EZH2 Mm siRNA/CH. Mice were sacrificed when any animals in control or a treatment group became moribund (after 3 to 4 weeks of therapy) and mouse weight, tumor weight and tumor location were recorded. Error bars represent s.e.m. *p<0.05; **p<0.001.

FIG. 14 provides a series of digital images of Western blots of lysate collected 72 hours after transfection of HeyA8 cells or MOEC with control, human EZH2, or mouse EZH2 siRNA.

FIG. 15 is a pair of graphs illustrating the weight distribution of HeyA8 and SKOV3ip1 tumors. Seven days following tumor cell injection, mice were randomly divided into 4 groups (10 mice per group) to receive therapy: (1) control siRNA/CH, (2) EZH2 Hs siRNA/CH, (3) EZH2 Mm siRNA/CH, and (4) combination of EZH2 Hs siRNA/CH plus EZH2 Mm siRNA/CH. Mice were sacrificed when any animals in control or a treatment group became moribund (after 3 to 4 weeks of therapy) and tumor weight was recorded.

FIGS. 16A-16B (A) Effect of tumor (EZH2 Hs siRNA/CH) or endothelial (EZH2 Mm siRNA/CH) targeted EZH2 siRNA on MVD and pericyte coverage. Tumors harvested following 3 to 4 weeks of therapy were stained for CD31 (MVD; red) and desmin (pericyte coverage; green). All pictures were taken at original magnification ×200. The bars in the graphs correspond sequentially to the labeled columns of images at left. Error bars represent s.e.m. *p<0.05; **p<0.001. (B) Effects of VASH1 gene silencing on tumor growth in vivo. Nude mice were injected with SKOV3ip1 ovarian cancer cells and 1 week later, were randomly divided into 5 groups (10 mice per group): (1) control siRNA/CH, (2) EZH2 Mm siRNA1/CH, (3) EZH2 Mm siRNA2/CH (4) EZH2 Mm siRNA3/CH (5) VASH1 Mm siRNA1/CH and (6) combination of EZH2 Mm siRNA1/CH plus VASH1 Mm siRNA/CH.

FIG. 16B is a bar graph illustrating the number of cells that migrated in the presence and absence of VASH1 siRNA. Mice were sacrificed when any animals in control or a treatment group became moribund (after 3 to 4 weeks of therapy) and mouse weight, tumor weight and tumor location were recorded. Error bars represent s.e.m. *p<0.05.

FIG. 17 illustrates the effects of EZH2 Hs siRNA/CH or EZH2 Mm siRNA/CH on proliferation. Tumors were harvested following 3-4 weeks of therapy and then stained for proliferating cell nuclear antigen (PCNA). All images were taken at original magnification ×100. The bars in the graphs correspond sequentially to the labeled columns of images at left. Error bars represent s.e.m. *p<0.05.

The nucleic and amino acid sequences listed in the accompanying sequence listing are shown using standard letter abbreviations for nucleotide bases, and three letter code for amino acids, as defined in 37 C.F.R. 1.822. Only one strand of each nucleic acid sequence is shown, but the complementary strand is understood as included by any reference to the displayed strand. In the accompanying sequence listing:

SEQ ID NOS: 1, 6-27, and 44-47 are nucleic acid sequences of exemplary primers.

SEQ ID NOS: 2-5 and 28-43 are nucleic acid sequences of exemplary siRNAs.

Despite improvements in surgery and chemotherapy, mortality rates in women with advanced ovarian carcinoma have remained largely unchanged (Cannistra, N. Engl. J. Med. 329: 1550-1559, 1993). Therefore, novel therapeutic strategies are needed. Growth of tumors, both at the primary and metastatic sites, requires a blood supply for expansion beyond 1-2 mm (Folkman, J. Nat. Canc. Inst. 82: 4-6, 1990). Targeting tumor angiogenesis by inhibiting endothelial cells that support tumor growth is particularly promising because of their presumed genetic stability. The recent success of a humanized monoclonal antibody bevacizumab (trade name Avastin®) against vascular endothelial growth factor in prolonging the lives of patients with advanced colon and breast carcinoma demonstrates the promise of such approaches (Hurwitz et al., N. Engl. J. Med. 350: 2335-2342, 2004 and Jain et al., Nat. Clin. Pract. Oncol. 3: 24-40, 2006). However, the full spectrum of differences in the tumor vasculature compared to its normal counterpart is not known. Identification of additional targets on tumor endothelium may allow opportunities for developing new therapeutic approaches to inhibit angiogenesis in a tumor-specific manner.

In recent years, whole genome expression profiling of cancer using methods such as microarray and serial analysis of gene expression (SAGE) have provided insight into the molecular pathways involved in cancer onset and progression. While selected genes in ovarian cancer vasculature have been characterized, there is little information regarding global gene expression alterations in ovarian cancer endothelium.

Disclosed herein is a gene expression signature identifying endothelial cell tumor-associated molecules in ovarian tumor endothelial cell isolates. Endothelial cells were purified from human ovarian tissues and invasive ovarian epithelial cancers, and a gene expression profile was established for ovarian tumor endothelial cells using microarray analyses. The gene expression profile disclosed herein identifies genes whose expression is differentially regulated in tumor versus normal endothelial cells. This profile reveals distinct expression profiles for tumor endothelial cell isolates as compared to non-tumor endothelial isolates.

The disclosed gene expression profile also reveals genes and collections or sets of genes that serve as effective molecular markers for angiogenesis in ovarian cancer, predict clinical outcome as well as such genes or gene sets that can provide clinically effective therapeutic targets for ovarian cancer. This has significant implications for the treatment of ovarian cancer. For example, methods are disclosed for treating ovarian cancer (for example, reducing or inhibiting ovarian cancer growth by targeting ovarian endothelial cell tumor-associated molecules, such as molecules believed to be involved in angiogenesis). For example, molecules involved in cell motility, tube formation or cell proliferation can be identified by the gene profile signature. In an example, a therapeutically effective amount of a specific binding agent is administered to a subject. For example, the specific binding agent preferentially binds to one or more of the identified ovarian endothelial cell tumor-associated molecules listed in any of Tables 1, 2, 4, 5 or a combination thereof to alter the expression or activity of such molecule (e.g., increase expression or activity of a molecule that is downregulated in ovarian endothelial tumor cells or decrease expression or activity of a molecule that is upregulated in such cells). In one example, the specific binding agent preferentially binds to one or more of the identified ovarian endothelial cell tumor-associated molecules listed in any of Tables 1, 2, 4, 5 or a combination thereof that are upregulated in ovarian endothelial tumor cells (as indicated by a positive fold change in Table 1) to decrease expression or activity of the one or more molecules. As a result, ovarian cancer in the subject is thereby reduced or eliminated. In a particular example, the specific binding agent is an inhibitor, such as a siRNA, of one or more of the disclosed ovarian endothelial cell tumor-associated molecules described in any of Table 1, 2, 4 or 5 whose expression is upregulated in ovarian endothelial tumor cells, such as EZH2. In some examples, the specific binding agent preferentially binds to one or more of the identified ovarian endothelial cell tumor-associated molecules listed in any of Tables 1, 2, 4, 5 or a combination thereof that are downregulated in ovarian endothelial tumor cells (as indicated by a negative fold change in Table 1) to increase expression or activity of the one or more molecules. As a result, ovarian cancer in the subject is thereby reduced or eliminated.

Terms

The following explanations of terms and methods are provided to better describe the present disclosure and to guide those of ordinary skill in the art in the practice of the present disclosure. The singular forms “a,” “an,” and “the” refer to one or more than one, unless the context clearly dictates otherwise. For example, the term “comprising a nucleic acid molecule” includes single or plural nucleic acid molecules and is considered equivalent to the phrase “comprising at least one nucleic acid molecule.” The term “or” refers to a single element of stated alternative elements or a combination of two or more elements, unless the context clearly indicates otherwise. As used herein, “comprises” means “includes.” Thus, “comprising A or B,” means “including A, B, or A and B,” without excluding additional elements.

Unless explained otherwise, all technical and scientific terms used herein have the same meaning as commonly understood to one of ordinary skill in the art to which this disclosure belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present disclosure, suitable methods and materials are described below. The materials, methods, and examples are illustrative only and not intended to be limiting.

Administration:

To provide or give a subject an agent, such as a chemotherapeutic agent, by any effective route. Exemplary routes of administration include, but are not limited to, injection (such as subcutaneous, intramuscular, intradermal, intraperitoneal, and intravenous), oral, sublingual, rectal, transdermal, intranasal, vaginal and inhalation routes.

Agent:

Any protein, nucleic acid molecule, compound, small molecule, organic compound, inorganic compound, or other molecule of interest. Agent can include a therapeutic agent, a diagnostic agent or a pharmaceutical agent. A therapeutic or pharmaceutical agent is one that alone or together with an additional compound induces the desired response (such as inducing a therapeutic or prophylactic effect when administered to a subject). In a particular example, a pharmaceutical agent (such as a siRNA to any of the genes listed in Tables 2 and Table 4) significantly reduces angiogenesis. A test agent is any substance, including, but not limited to, a protein (such as an antibody), nucleic acid molecule (such as a siRNA), organic compound, inorganic compound, or other molecule of interest. In particular examples, a test agent can permeate a cell membrane (alone or in the presence of a carrier).

Amplifying a Nucleic Acid Molecule:

To increase the number of copies of a nucleic acid molecule, such as a gene or fragment of a gene, for example a region of an ovarian endothelial cell tumor-associated gene. The resulting products are called amplification products.

An example of in vitro amplification is the polymerase chain reaction (PCR), in which a biological sample obtained from a subject (such as a sample containing ovarian cancer cells) is contacted with a pair of oligonucleotide primers, under conditions that allow for hybridization of the primers to a nucleic acid molecule in the sample. The primers are extended under suitable conditions, dissociated from the template, and then re-annealed, extended, and dissociated to amplify the number of copies of the nucleic acid molecule. Other examples of in vitro amplification techniques include quantitative real-time PCR, strand displacement amplification (see U.S. Pat. No. 5,744,311); transcription-free isothermal amplification (see U.S. Pat. No. 6,033,881); repair chain reaction amplification (see WO 90/01069); ligase chain reaction amplification (see EP-A-320 308); gap filling ligase chain reaction amplification (see U.S. Pat. No. 5,427,930); coupled ligase detection and PCR (see U.S. Pat. No. 6,027,889); and NASBA™ RNA transcription-free amplification (see U.S. Pat. No. 6,025,134).

A commonly used method for real-time quantitative polymerase chain reaction involves the use of a double stranded DNA dye (such as SYBR Green I dye). For example, as the amount of PCR product increases, more SYBR Green I dye binds to DNA, resulting in a steady increase in fluorescence. Another commonly used method is real-time quantitative TaqMan PCR (Applied Biosystems). The 5′ nuclease assay provides a real-time method for detecting only specific amplification products. The use of fluorogenic probes makes it possible to eliminate post-PCR processing for the analysis of probe degradation. The probe is an oligonucleotide with both a reporter fluorescent dye and a quencher dye attached. While the probe is intact, the proximity of the quencher greatly reduces the fluorescence emitted by the reporter dye by Förster resonance energy transfer (FRET) through space. Probe design and synthesis has been simplified by the finding that adequate quenching is observed for probes with the reporter at the 5′ end and the quencher at the 3′ end.

Angiogenesis:

A physiological process involving the growth of new blood vessels from pre-existing vessels. Angiogenesis can occur under normal physiological conditions such as during growth and development or wound healing (known as physiological angiogenesis) as well as pathological conditions such as in the transition of tumors from a dormant state to a malignant state (known as pathological angiogenesis). As used herein, pro-angiogenic genes are genes that facilitate angiogenesis, such as angiogenesis in an ovarian tumor.

The complex phenomenon of angiogenesis begins with degradation of the basement membrane by cellular proteases. This allows endothelial cells to penetrate and migrate (process known as cell motility) into the extracellular matrix and then proliferate. In the final stages of this process, the endothelial cells align themselves to form capillary or tubelike structures (process known as tube formation). These new structures then form a network that undergoes significant remodeling and rearrangement before fully functioning capillaries exist. Therefore, angiogenesis can be studied or identified by monitoring tube formation, cell motility, and/or cell proliferation.

Antibody:

A polypeptide ligand including at least a light chain or heavy chain immunoglobulin variable region which specifically recognizes and binds an epitope of an antigen, such as an ovarian endothelial cell tumor-associated molecule or a fragment thereof. Antibodies are composed of a heavy and a light chain, each of which has a variable region, termed the variable heavy (V H ) region and the variable light (V L ) region. Together, the V H region and the V L region are responsible for binding the antigen recognized by the antibody. In one example, an antibody specifically binds to one of the proteins listed in Tables 8 and 9.

This includes intact immunoglobulins and the variants and portions of them well known in the art, such as Fab′ fragments, F(ab)′ 2 fragments, single chain Fv proteins (“scFv”), and disulfide stabilized Fv proteins (“dsFv”). A scFv protein is a fusion protein in which a light chain variable region of an immunoglobulin and a heavy chain variable region of an immunoglobulin are bound by a linker, while in dsFvs, the chains have been mutated to introduce a disulfide bond to stabilize the association of the chains. The term also includes genetically engineered forms such as chimeric antibodies (for example, humanized murine antibodies), heteroconjugate antibodies (such as, bispecific antibodies). See also, Pierce Catalog and Handbook, 1994-1995 (Pierce Chemical Co., Rockford, Ill.); Kuby, J., Immunology, 3 rd Ed., W.H. Freeman & Co., New York, 1997.

Typically, a naturally occurring immunoglobulin has heavy (H) chains and light (L) chains interconnected by disulfide bonds. There are two types of light chain, lambda and kappa. There are five main heavy chain classes (or isotypes) which determine the functional activity of an antibody molecule: IgM, IgD, IgG, IgA and IgE.

Each heavy and light chain contains a constant region and a variable region, (the regions are also known as “domains”). In combination, the heavy and the light chain variable regions specifically bind the antigen. Light and heavy chain variable regions contain a “framework” region interrupted by three hypervariable regions, also called “complementarity-determining regions” or “CDRs”. The extent of the framework region and CDRs have been defined (see, Kabat et al., Sequences of Proteins of Immunological Interest , U.S. Department of Health and Human Services, 1991, which is hereby incorporated by reference). The Kabat database is now maintained online. The sequences of the framework regions of different light or heavy chains are relatively conserved within a species. The framework region of an antibody, that is the combined framework regions of the constituent light and heavy chains, serves to position and align the CDRs in three-dimensional space.

The CDRs are primarily responsible for binding to an epitope of an antigen. The CDRs of each chain are typically referred to as CDR1, CDR2, and CDR3, numbered sequentially starting from the N-terminus, and are also typically identified by the chain in which the particular CDR is located. Thus, a V H CDR3 is located in the variable domain of the heavy chain of the antibody in which it is found, whereas a V L CDR1 is the CDR1 from the variable domain of the light chain of the antibody in which it is found. An antibody that binds RET will have a specific V H region and the V L region sequence, and thus specific CDR sequences. Antibodies with different specificities (such as different combining sites for different antigens) have different CDRs. Although it is the CDRs that vary from antibody to antibody, only a limited number of amino acid positions within the CDRs are directly involved in antigen binding. These positions within the CDRs are called specificity determining residues (SDRs).

References to “V H ” or “VH” refer to the variable region of an immunoglobulin heavy chain, including that of an Fv, scFv, dsFv or Fab. References to “V L ” or “VL” refer to the variable region of an immunoglobulin light chain, including that of an Fv, scFv, dsFv or Fab.

A “monoclonal antibody” is an antibody produced by a single clone of B-lymphocytes or by a cell into which the light and heavy chain genes of a single antibody have been transfected. Monoclonal antibodies are produced by methods known to those of skill in the art, for instance by making hybrid antibody-forming cells from a fusion of myeloma cells with immune spleen cells. Monoclonal antibodies include humanized monoclonal antibodies.

A “polyclonal antibody” is an antibody that is derived from different B-cell lines. Polyclonal antibodies are a mixture of immunoglobulin molecules secreted against a specific antigen, each recognizing a different epitope. These antibodies are produced by methods known to those of skill in the art, for instance, by injection of an antigen into a suitable mammal (such as a mouse, rabbit or goat) that induces the B-lymphocytes to produce IgG immunoglobulins specific for the antigen which are then purified from the mammal's serum.

A “chimeric antibody” has framework residues from one species, such as human, and CDRs (which generally confer antigen binding) from another species, such as a murine antibody that specifically binds an ovarian endothelial cell tumor-associated molecule.

A “humanized” immunoglobulin is an immunoglobulin including a human framework region and one or more CDRs from a non-human (for example a mouse, rat, or synthetic) immunoglobulin. The non-human immunoglobulin providing the CDRs is termed a “donor,” and the human immunoglobulin providing the framework is termed an “acceptor.” In one embodiment, all the CDRs are from the donor immunoglobulin in a humanized immunoglobulin. Constant regions need not be present, but if they are, they must be substantially identical to human immunoglobulin constant regions, e.g., at least about 85-90%, such as about 95% or more identical. Hence, all parts of a humanized immunoglobulin, except possibly the CDRs, are substantially identical to corresponding parts of natural human immunoglobulin sequences. Humanized immunoglobulins can be constructed by means of genetic engineering (see for example, U.S. Pat. No. 5,585,089).

Array:

An arrangement of molecules, such as biological macromolecules (such as peptides or nucleic acid molecules) or biological samples (such as tissue sections), in addressable locations on or in a substrate. A “microarray” is an array that is miniaturized so as to require or be aided by microscopic examination for evaluation or analysis.

The array of molecules (“features”) makes it possible to carry out a very large number of analyses on a sample at one time. In certain example arrays, one or more molecules (such as an oligonucleotide probe) will occur on the array a plurality of times (such as twice), for instance to provide internal controls. The number of addressable locations on the array can vary, for example from at least one, to at least 2, to at least 5, to at least 10, at least 20, at least 30, at least 50, at least 75, at least 100, at least 150, at least 200, at least 300, at least 500, least 550, at least 600, at least 800, at least 1000, at least 10,000, or more. In particular examples, an array includes nucleic acid molecules, such as oligonucleotide sequences that are at least 15 nucleotides in length, such as about 15-40 nucleotides in length. In particular examples, an array includes oligonucleotide probes or primers which can be used to detect sensitive to ovarian endothelial cell tumor-associated molecule sequences, such as at least one of those listed in Table 1, such as at least 5, at least 7, at least 10, at least 20, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 600, at least 700, at least 800, at least 900, at least 1000, or at least 1100 sequences listed in Table 1 (for example, 2, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 120, 130, 140, 150, 175, 225, 275, 325, 350, 375, 450, 550, 650, 750, 850, 950, 1050 or 1149 of those listed). In an example, the array is a commercially available such as a U133 Plus 2.0 oligonucleotide array from Affymetrix (Affymetrix, Santa Clara, Calif.).

Within an array, each arrayed sample is addressable, in that its location can be reliably and consistently determined within at least two dimensions of the array. The feature application location on an array can assume different shapes. For example, the array can be regular (such as arranged in uniform rows and columns) or irregular. Thus, in ordered arrays the location of each sample is assigned to the sample at the time when it is applied to the array, and a key may be provided in order to correlate each location with the appropriate target or feature position. Often, ordered arrays are arranged in a symmetrical grid pattern, but samples could be arranged in other patterns (such as in radially distributed lines, spiral lines, or ordered clusters). Addressable arrays usually are computer readable, in that a computer can be programmed to correlate a particular address on the array with information about the sample at that position (such as hybridization or binding data, including for instance signal intensity). In some examples of computer readable formats, the individual features in the array are arranged regularly, for instance in a Cartesian grid pattern, which can be correlated to address information by a computer.

Protein-based arrays include probe molecules that are or include proteins, or where the target molecules are or include proteins, and arrays including nucleic acids to which proteins are bound, or vice versa. In some examples, an array contains antibodies to ovarian endothelial cell tumor-associated proteins, such as any combination of those listed in Table 1, such as at least 2, least 5, at least 7, at least 10, at least 20, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 600, at least 700, at least 800, at least 900, at least 1000, or at least 1100 sequences listed in Table 1 (for example, 2, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 120, 130, 140, 150, 175, 225, 275, 325, 350, 375, 450, 550, 650, 750, 850, 950, 1050 or 1149 of those listed).

Binding or Stable Binding:

An association between two substances or molecules, such as the hybridization of one nucleic acid molecule to another (or itself), the association of an antibody with a peptide, or the association of a protein with another protein or nucleic acid molecule. An oligonucleotide molecule binds or stably binds to a target nucleic acid molecule if a sufficient amount of the oligonucleotide molecule forms base pairs or is hybridized to its target nucleic acid molecule, to permit detection of that binding. “Preferentially binds” indicates that one molecule binds to another with high affinity, and binds to heterologous molecules at a low affinity.

Binding can be detected by any procedure known to one skilled in the art, such as by physical or functional properties of a target:oligonucleotide complex or a protein:antibody complex. For example, binding can be detected functionally by determining whether binding has an observable effect upon a biosynthetic process such as expression of a gene, DNA replication, transcription, translation, and the like.

Physical methods of detecting the binding of complementary strands of nucleic acid molecules, include but are not limited to, such methods as DNase I or chemical footprinting, gel shift and affinity cleavage assays, Northern blotting, dot blotting and light absorption detection procedures. For example, one method involves observing a change in light absorption of a solution containing an oligonucleotide (or an analog) and a target nucleic acid at 220 to 300 nm as the temperature is slowly increased. If the oligonucleotide or analog has bound to its target, there is a sudden increase in absorption at a characteristic temperature as the oligonucleotide (or analog) and target disassociate from each other, or melt. In another example, the method involves detecting a signal, such as a detectable label, present on one or both nucleic acid molecules (or antibody or protein as appropriate).

The binding between an oligomer and its target nucleic acid is frequently characterized by the temperature (T m ) at which 50% of the oligomer is melted from its target. A higher (T m ) means a stronger or more stable complex relative to a complex with a lower (T m ).

Biological Activity:

An expression describing the beneficial or adverse effects of an agent on living matter. When the agent is a complex chemical mixture, this activity is exerted by the substance's active ingredient or pharmacophore, but can be modified by the other constituents. Activity is generally dosage-dependent and it is not uncommon to have effects ranging from beneficial to adverse for one substance when going from low to high doses. In one example, a specific binding agent significantly reduces the biological activity of the one or more ovarian endothelial cell tumor-associated molecules that is upregulated in ovarian endothelial tumor cells (such as those listed in Tables 2 and 4) which reduces or eliminates ovarian cancer, such as by reducing or inhibiting angiogenesis. In some examples, a specific binding agent significantly increases the biological activity of one or more ovarian endothelial cell tumor-associated molecules that is downregulated in ovarian endothelial tumor cells (such as those listed in Table 3).

Cancer:

The “pathology” of cancer includes all phenomena that compromise the well-being of the subject. This includes, without limitation, abnormal or uncontrollable cell growth, metastasis, interference with the normal functioning of neighboring cells, release of cytokines or other secretory products at abnormal levels, suppression or aggravation of inflammatory or immunological response, neoplasia, premalignancy, malignancy, invasion of surrounding or distant tissues or organs, such as lymph nodes, etc. “Metastatic disease” refers to cancer cells that have left the original tumor site and migrate to other parts of the body for example via the bloodstream or lymph system.

Chemotherapeutic Agent or Chemotherapy:

Any chemical agent with therapeutic usefulness in the treatment of diseases characterized by abnormal cell growth. Such diseases include tumors, neoplasms, and cancer as well as diseases characterized by hyperplastic growth such as psoriasis. In one embodiment, a chemotherapeutic agent is an agent of use in treating ovarian cancer, such as papillary serous ovarian cancer. In one example, a chemotherapeutic agent is a radioactive compound. One of skill in the art can readily identify a chemotherapeutic agent of use (see for example, Slapak and Kufe, Principles of Cancer Therapy, Chapter 86 in Harrison's Principles of Internal Medicine, 14th edition; Perry et al., Chemotherapy, Ch. 17 in Abeloff, Clinical Oncology 2nd ed., 2000 Churchill Livingstone, Inc; Baltzer and Berkery. (eds): Oncology Pocket Guide to Chemotherapy, 2nd ed. St. Louis, Mosby-Year Book, 1995; Fischer Knobf, and Durivage (eds): The Cancer Chemotherapy Handbook, 4th ed. St. Louis, Mosby-Year Book, 1993). Chemotherapeutic agents used for treating ovarian cancer include, but are not limited to, carboplatin, cisplatin, paclitaxel, docetaxel, doxorubicin, epirubicin, topotecan, irinotecan, gemcitabine, iazofurine, gemcitabine, etoposide, vinorelbine, tamoxifen, valspodar, cyclophosphamide, methotrexate, fluorouracil, mitoxantrone and vinorelbine. Combination chemotherapy is the administration of more than one agent (such as more than one chemotherapeutic agent) to treat cancer.

Chrondroitin Sulfate Proteoglycan 2 (CSPG2):

An extracellular matrix component of the vitreous gel that has been reported to be an anti-cell adhesive. In particular examples, expression of CSPG2 is increased in ovarian cancer endothelial cells. The term CSPG2 includes any CSPG2 gene, cDNA, mRNA, or protein from any organism and that is CSPG2 and is expressed and in some examples overexpressed in ovarian cancer endothelial cells.

Nucleic acid and protein sequences for CSPG2 are publicly available. For example, GenBank Accession Nos.: NM — 004385 and BC096495 disclose CSPG2 nucleic acid sequences, and GenBank Accession Nos.: AAH50524, NP — 004376, and AAH96495 disclose CSPG2 protein sequences, all of which are incorporated by reference as provided by GenBank on Feb. 14, 2007.

In one example, CSPG2 includes a full-length wild-type (or native) sequence, as well as CSPG2 allelic variants that retain the ability to be expressed in ovarian tumor endothelial cells and/or modulate ovarian tumor endothelial cells, such as increase vascular growth. In certain examples, CSPG2 has at least 80% sequence identity, for example at least 85%, 90%, 95%, or 98% sequence identity to GenBank Accession No. AAH50524, NP — 004376, or AAH96495. In other examples, CSPG2 has a sequence that hybridizes to AFFYMETRIX® Probe ID No. 204619_s_at and 221731_x_a and retains CSPG2 activity (such as the capability to be expressed in ovarian tumor endothelial cells and/or modulate tumor and/or vascular growth).

Complementarity and Percentage Complementarity:

Molecules with complementary nucleic acids form a stable duplex or triplex when the strands bind, (hybridize), to each other by forming Watson-Crick, Hoogsteen or reverse Hoogsteen base pairs. Stable binding occurs when an oligonucleotide molecule remains detectably bound to a target nucleic acid sequence (such as an ovarian endothelial cell tumor-associated molecule) under the required conditions.

Complementarity is the degree to which bases in one nucleic acid strand base pair with the bases in a second nucleic acid strand. Complementarity is conveniently described by percentage, that is, the proportion of nucleotides that form base pairs between two strands or within a specific region or domain of two strands. For example, if 10 nucleotides of a 15-nucleotide oligonucleotide form base pairs with a targeted region of a DNA molecule, that oligonucleotide is said to have 66.67% complementarity to the region of DNA targeted.

In the present disclosure, “sufficient complementarity” means that a sufficient number of base pairs exist between an oligonucleotide molecule and a target nucleic acid sequence (such as a ovarian endothelial cell tumor-associated molecule, for example any of the genes listed in Table 1) to achieve detectable binding. When expressed or measured by percentage of base pairs formed, the percentage complementarity that fulfills this goal can range from as little as about 50% complementarity to full (100%) complementary. In general, sufficient complementarity is at least about 50%, for example at least about 75% complementarity, at least about 90% complementarity, at least about 95% complementarity, at least about 98% complementarity, or even at least about 100% complementarity.

A thorough treatment of the qualitative and quantitative considerations involved in establishing binding conditions that allow one skilled in the art to design appropriate oligonucleotides for use under the desired conditions is provided by Beltz et al. Methods Enzymol. 100:266-285, 1983, and by Sambrook et al. (ed.), Molecular Cloning: A Laboratory Manual, 2nd ed., vol. 1-3, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989.

Contacting:

Placement in direct physical association, including both a solid and liquid form. Contacting can occur in vitro, for example, with isolated cells or in vivo by administering to a subject.

Decrease:

To reduce the quality, amount, or strength of something. In one example, a therapy decreases a tumor (such as the size of a tumor, the growth of a tumor, number of tumors, the metastasis of a tumor, or combinations thereof), or one or more symptoms associated with a tumor, for example as compared to the response in the absence of the therapy (such as a therapy administered to affect tumor size by inhibiting angiogenesis via administration of a binding agent capable of binding to one or more of the ovarian endothelial cell tumor-associated markers listed in Tables 1 through 5 that is involved in promoting angiogenesis, such as by inhibiting an ovarian endothelial cell tumor-associated marker that is upregulated in ovarian endothelial tumor cells or by increasing activity of an ovarian endothelial cell tumor-associated marker that is downregulated in ovarian endothelial tumor cells). In a particular example, a therapy decreases the size of a tumor, the growth of a tumor, the number of tumors, the metastasis of a tumor, or combinations thereof, subsequent to the therapy, such as a decrease of at least 10%, at least 20%, at least 50%, or even at least 90%. Such decreases can be measured using the methods disclosed herein.

Determining Expression of a Gene Product:

Detection of a level expression in either a qualitative or quantitative manner.

Diagnosis:

The process of identifying a disease by its signs, symptoms and results of various tests. The conclusion reached through that process is also called “a diagnosis.” Forms of testing commonly performed include blood tests, medical imaging, urinalysis, and biopsy.

DNA (Deoxyribonucleic Acid):

A long chain polymer which includes the genetic material of most living organisms (some viruses have genes including ribonucleic acid, RNA). The repeating units in DNA polymers are four different nucleotides, each of which includes one of the four bases, adenine, guanine, cytosine and thymine bound to a deoxyribose sugar to which a phosphate group is attached. Triplets of nucleotides, referred to as codons, in DNA molecules code for amino acid in a polypeptide. The term codon is also used for the corresponding (and complementary) sequences of three nucleotides in the mRNA into which the DNA sequence is transcribed.

Differential Expression:

A difference, such as an increase or decrease, in the conversion of the information encoded in a gene (such as an ovarian endothelial cell tumor-associated molecule) into messenger RNA, the conversion of mRNA to a protein, or both. In some examples, the difference is relative to a control or reference value, such as an amount of gene expression that is expected in a subject who does not have ovarian cancer or in a normal (non-cancerous) endothelial cell sample. Detecting differential expression can include measuring a change in gene expression.

Downregulated or Inactivation:

When used in reference to the expression of a nucleic acid molecule, such as a gene, refers to any process which results in a decrease in production of a gene product. A gene product can be RNA (such as mRNA, rRNA, tRNA, and structural RNA) or protein. Therefore, gene downregulation or deactivation includes processes that decrease transcription of a gene or translation of mRNA. Examples of genes whose expression is downregulated in ovarian tumor endothelial cells can be found in Table 1 (indicated by a negative fold change, such as TLOC1 and HS6ST2) and Table 3 (such as PLN, SELE, GREB1, OGN and LCXD3).

Examples of processes that decrease transcription include those that facilitate degradation of a transcription initiation complex, those that decrease transcription initiation rate, those that decrease transcription elongation rate, those that decrease processivity of transcription and those that increase transcriptional repression. Gene downregulation can include reduction of expression above an existing level. Examples of processes that decrease translation include those that decrease translational initiation, those that decrease translational elongation and those that decrease mRNA stability.

Gene downregulation includes any detectable decrease in the production of a gene product. In certain examples, production of a gene product decreases by at least 2-fold, for example at least 3-fold or at least 4-fold, as compared to a control (such an amount of gene expression in a normal endothelial cell). In one example, a control is a relative amount of gene expression or protein expression in a biological sample taken from a subject who does not have ovarian cancer.

Endothelial Cell:

Cells that line the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall. For example, endothelial cells line the entire circulatory system. Further, both blood and lymphatic capillaries are composed of a single layer of endothelial cells.

Epidermal Growth Factor-like Domain Multiple 6 (EGFL6):

A member of the epidermal growth factor (EGF) repeat superfamily of genes known to encode proteins that govern cellular proliferative responses. EGFL6 has been identified as a possible regulator of cell cycle and oncogenesis.

In particular examples, expression of EGFL6 is increased in ovarian cancer endothelial cells. The term EGFL6 includes any EGFL6 gene, cDNA, mRNA, or protein from any organism and that is EGFL6 and is expressed and in some examples overexpressed in ovarian cancer endothelial cells.

Nucleic acid and protein sequences for EGFL6 are publicly available. For example, GenBank Accession Nos.: NM — 015507, NM — 019397 and BC038587 disclose EGFL6 nucleic acid sequences, and GenBank Accession Nos.: AAQ88699, CAM23572, and AAF27812 disclose EGFL6 protein sequences, all of which are incorporated by reference as provided by GenBank on Feb. 14, 2007.

In one example, EGFL6 includes a full-length wild-type (or native) sequence, as well as EGFL6 allelic variants that retain the ability to be expressed in ovarian tumor endothelial cells and/or modulate ovarian tumor endothelial cells, such as increase vascular growth. In certain examples, EGFL6 has at least 80% sequence identity, for example at least 85%, 90%, 95%, or 98% sequence identity to GenBank Accession No. AAQ88699, CAM23572, or AAF27812. In other examples, EGFL6 has a sequence that hybridizes to Affymetrix Probe ID No. 219454_at and retains EGFL6 activity (such as the capability to be expressed in ovarian tumor endothelial cells and/or modulate tumor and/or vascular growth).

Expression:

The process by which the coded information of a gene is converted into an operational, non-operational, or structural part of a cell, such as the synthesis of a protein. Gene expression can be influenced by external signals. For instance, exposure of a cell to a hormone may stimulate expression of a hormone-induced gene. Different types of cells can respond differently to an identical signal. Expression of a gene also can be regulated anywhere in the pathway from DNA to RNA to protein. Regulation can include controls on transcription, translation, RNA transport and processing, degradation of intermediary molecules such as mRNA, or through activation, inactivation, compartmentalization or degradation of specific protein molecules after they are produced.

The expression of a nucleic acid molecule can be altered relative to a normal (wild type) nucleic acid molecule. Alterations in gene expression, such as differential expression, include but are not limited to: (1) overexpression; (2) underexpression; or (3) suppression of expression. Alternations in the expression of a nucleic acid molecule can be associated with, and in fact cause, a change in expression of the corresponding protein. Specific examples of ovarian endothelial cell tumor-associated molecules that are up-regulated in ovarian tumor endothelial cells are provided in Tables 2 and 4. Specific examples of ovarian endothelial cell tumor-associated molecules that are down-regulated in ovarian tumor endothelial cells are listed in Table 3. For example, EZH2, EGFL6, TNFAIP6, TWIST1, STC1, HOP, CSPG2, and PLXDC1 are upregulated or increased in expression in ovarian tumor endothelial cells, while TLOC1 and HS6ST2 are downregulated or decreased in expression in such cells.

Protein expression can also be altered in some manner to be different from the expression of the protein in a normal (wild type) situation. This includes but is not necessarily limited to: (1) a mutation in the protein such that one or more of the amino acid residues is different; (2) a short deletion or addition of one or a few (such as no more than 10-20) amino acid residues to the sequence of the protein; (3) a longer deletion or addition of amino acid residues (such as at least 20 residues), such that an entire protein domain or sub-domain is removed or added; (4) expression of an increased amount of the protein compared to a control or standard amount; (5) expression of a decreased amount of the protein compared to a control or standard amount; (6) alteration of the subcellular localization or targeting of the protein; (7) alteration of the temporally regulated expression of the protein (such that the protein is expressed when it normally would not be, or alternatively is not expressed when it normally would be); (8) alteration in stability of a protein through increased longevity in the time that the protein remains localized in a cell; and (9) alteration of the localized (such as organ or tissue specific or subcellular localization) expression of the protein (such that the protein is not expressed where it would normally be expressed or is expressed where it normally would not be expressed), each compared to a control or standard.

Controls or standards for comparison to a sample, for the determination of differential expression, include samples believed to be normal (in that they are not altered for the desired characteristic, for example a sample from a subject who does not have cancer, such as ovarian cancer) as well as laboratory values, even though possibly arbitrarily set, keeping in mind that such values can vary from laboratory to laboratory.

Laboratory standards and values may be set based on a known or determined population value and can be supplied in the format of a graph or table that permits comparison of measured, experimentally determined values.

Gene Expression Profile (or Fingerprint):

Differential or altered gene expression can be detected by changes in the detectable amount of gene expression (such as cDNA or mRNA) or by changes in the detectable amount of proteins expressed by those genes. A distinct or identifiable pattern of gene expression, for instance a pattern of high and low expression of a defined set of genes or gene-indicative nucleic acids such as ESTs; in some examples, as few as one or two genes provides a profile, but more genes can be used in a profile, for example at least 3, at least 4, at least 5, at least 6, at least 10, at least 20, at least 25, at least 30, at least 50, at least 80, at least 100, at least 190, at least 200, at least 300, at least 400, at least 500, at least 550, at least 600, at least 700, at least 800, at least 900, at least 1000, at least 1100 or more of those listed in any of Tables 1-5. A gene expression profile (also referred to as a fingerprint) can be linked to a tissue or cell type (such as ovarian cancer cell), to a particular stage of normal tissue growth or disease progression (such as advanced ovarian cancer), or to any other distinct or identifiable condition that influences gene expression in a predictable way. Gene expression profiles can include relative as well as absolute expression levels of specific genes, and can be viewed in the context of a test sample compared to a baseline or control sample profile (such as a sample from a subject who does not have ovarian cancer or normal endothelial cells). In one example, a gene expression profile in a subject is read on an array (such as a nucleic acid or protein array). For example, a gene expression profile is performed using a commercially available array such as a Human Genome U133 2.0 Plus Microarray from AFFYMETRIX® (AFFYMETRIX®, Santa Clara, Calif.).

Homeodomain-Only Protein, Transcript Variant 2 (HOP):

A transcriptional repressor that modulates serum response factor-dependent cardiac-specific gene expression and cardiac development. In particular examples, expression of HOP is increased in ovarian cancer endothelial cells. The term HOP includes any HOP gene, cDNA, mRNA, or protein from any organism and that is HOP and is expressed and in some examples overexpressed in ovarian cancer endothelial cells.

Nucleic acid and protein sequences for HOP are publicly available. For example, GenBank Accession Nos.: NM — 139211, XM — 001083738, and XM — 001137349 disclose HOP nucleic acid sequences, and GenBank Accession Nos.: AAH14225, NP — 631958, and NP — 631957 disclose HOP protein sequences, all of which are incorporated by reference as provided by GenBank on Feb. 14, 2007.

In one example, HOP includes a full-length wild-type (or native) sequence, as well as HOP allelic variants that retain the ability to be expressed in ovarian tumor endothelial cells and/or modulate ovarian tumor endothelial cells, such as increase vascular growth. In certain examples, HOP has at least 80% sequence identity, for example at least 85%, 90%, 95%, or 98% sequence identity to GenBank Accession No.: AAH14225, NP — 631958, or NP — 631957. In other examples, HOP has a sequence that hybridizes to AFFYMETRIX® Probe ID No. 211597_s_at and retains HOP activity (such as the capability to be expressed in ovarian tumor endothelial cells and/or modulate tumor and/or vascular growth).

Hybridization:

To form base pairs between complementary regions of two strands of DNA, RNA, or between DNA and RNA, thereby forming a duplex molecule. Hybridization conditions resulting in particular degrees of stringency will vary depending upon the nature of the hybridization method and the composition and length of the hybridizing nucleic acid sequences. Generally, the temperature of hybridization and the ionic strength (such as the Na + concentration) of the hybridization buffer will determine the stringency of hybridization. Calculations regarding hybridization conditions for attaining particular degrees of stringency are discussed in Sambrook et al., (1989) Molecular Cloning, second edition, Cold Spring Harbor Laboratory, Plainview, N.Y. (chapters 9 and 11). The following is an exemplary set of hybridization conditions and is not limiting:

Very High Stringency (Detects Sequences that Share at Least 90% Identity)

Hybridization: 5×SSC at 65° C. for 16 hours

Wash twice: 2×SSC at room temperature (RT) for 15 minutes each

Wash twice: 0.5×SSC at 65° C. for 20 minutes each

High Stringency (Detects Sequences that Share at Least 80% Identity)

Hybridization: 5×-6×SSC at 65° C.-70° C. for 16-20 hours

Wash twice: 2×SSC at RT for 5-20 minutes each

Wash twice: 1×SSC at 55° C.-70° C. for 30 minutes each

Low Stringency (Detects Sequences that Share Greater than 50% Identity)

Hybridization: 6×SSC at RT to 55° C. for 16-20 hours

Wash at least twice: 2×-3×SSC at RT to 55° C. for 20-30 minutes each.

Inhibitor:

Any chemical compound, nucleic acid molecule, peptide or polypeptide such as an antibody or RNAi that can reduce activity of a gene product or interfere with expression of a gene, respectively. In some examples, an inhibitor can reduce or inhibit the activity of a protein that is encoded by a gene either directly or indirectly. Direct inhibition can be accomplished, for example, by binding to a protein and thereby preventing the protein from binding an intended target, such as a receptor. Indirect inhibition can be accomplished, for example, by binding to a protein's intended target, such as a receptor or binding partner, thereby blocking or reducing activity of the protein. In some examples, an inhibitor of the disclosure can inhibit a gene by reducing or inhibiting expression of the gene, inter alia by interfering with gene expression (transcription, processing, translation, post-translational modification), for example, by interfering with the gene's mRNA and blocking translation of the gene product or by post-translational modification of a gene product, or by causing changes in intracellular localization.

Isolated:

An “isolated” biological component (such as a nucleic acid molecule, protein, or cell) has been substantially separated or purified away from other biological components in the cell of the organism, or the organism itself, in which the component naturally occurs, such as other chromosomal and extra-chromosomal DNA and RNA, proteins and cells. Nucleic acid molecules and proteins that have been “isolated” include nucleic acid molecules and proteins purified by standard purification methods. The term also embraces nucleic acid molecules and proteins prepared by recombinant expression in a host cell as well as chemically synthesized nucleic acid molecules and proteins. For example, an isolated serous papillary ovarian cancer cell is one that is substantially separated from other ovarian cell subtypes, such as endometrioid, clear cell or mucinous subtypes.

Label:

An agent capable of detection, for example by ELISA, spectrophotometry, flow cytometry, or microscopy. For example, a label can be attached to a nucleic acid molecule or protein, thereby permitting detection of the nucleic acid molecule or protein. Examples of labels include, but are not limited to, radioactive isotopes, enzyme substrates, co-factors, ligands, chemiluminescent agents, fluorophores, haptens, enzymes, and combinations thereof. Methods for labeling and guidance in the choice of labels appropriate for various purposes are discussed for example in Sambrook et al. (Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, N.Y., 1989) and Ausubel et al. (In Current Protocols in Molecular Biology, John Wiley & Sons, New York, 1998). In a particular example, a label is conjugated to a binding agent that specifically binds to one or more of the ovarian endothelial cell tumor-associated molecules disclosed in Tables 1 through 5 to allow for the detection/screening for angiogenesis and/or the presence of a tumor in a subject.

Malignant:

Cells that have the properties of anaplasia invasion and metastasis.

Mammal:

This term includes both human and non-human mammals. Examples of mammals include, but are not limited to: humans and veterinary and laboratory animals, such as pigs, cows, goats, cats, dogs, rabbits and mice.

Neoplasm:

Abnormal growth of cells.

Normal Cell:

Non-tumor cell, non-malignant, uninfected cell.

Nucleic Acid Array:

An arrangement of nucleic acids (such as DNA or RNA) in assigned locations on a matrix, such as that found in cDNA arrays, or oligonucleotide arrays, such as those listed in Tables 1-5.

Nucleic Acid Molecules Representing Genes:

Any nucleic acid, for example DNA (intron or exon or both), cDNA, or RNA (such as mRNA), of any length suitable for use as a probe or other indicator molecule, and that is informative about the corresponding gene.

Nucleic Acid Molecules:

A deoxyribonucleotide or ribonucleotide polymer including, without limitation, cDNA, mRNA, genomic DNA, and synthetic (such as chemically synthesized) DNA. The nucleic acid molecule can be double-stranded or single-stranded. Where single-stranded, the nucleic acid molecule can be the sense strand or the antisense strand. In addition, nucleic acid molecule can be circular or linear.

The disclosure includes isolated nucleic acid molecules that include specified lengths of an ovarian endothelial cell tumor-associated molecule nucleotide sequence, for sequences for genes listed in Tables 1 through 4. Such molecules can include at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45 or at least 50 consecutive nucleotides of these sequences or more, and can be obtained from any region of a ovarian endothelial cell tumor-associated molecule.

Oligonucleotide:

A plurality of joined nucleotides joined by native phosphodiester bonds, between about 6 and about 300 nucleotides in length. An oligonucleotide analog refers to moieties that function similarly to oligonucleotides but have non-naturally occurring portions. For example, oligonucleotide analogs can contain non-naturally occurring portions, such as altered sugar moieties or inter-sugar linkages, such as a phosphorothioate oligodeoxynucleotide.

Particular oligonucleotides and oligonucleotide analogs can include linear sequences up to about 200 nucleotides in length, for example a sequence (such as DNA or RNA) that is at least 6 nucleotides, for example at least 8, at least 10, at least 15, at least 20, at least 21, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 100 or even at least 200 nucleotides long, or from about 6 to about 50 nucleotides, for example about 10-25 nucleotides, such as 12, 15 or 20 nucleotides.

Oligonucleotide Probe:

A short sequence of nucleotides, such as at least 8, at least 10, at least 15, at least 20, at least 21, at least 25, or at least 30 nucleotides in length, used to detect the presence of a complementary sequence by molecular hybridization. In particular examples, oligonucleotide probes include a label that permits detection of oligonucleotide probe:target sequence hybridization complexes, such as with an ovarian endothelial cell tumor-associated molecule listed in Tables 1-5.

Ovarian Cancer: A

malignant ovarian neoplasm (an abnormal growth located on the ovaries). Cancer of the ovaries includes ovarian carcinoma, papillary serous cystadenocarcinoma, mucinous cystadenocarcinoma, endometrioid tumors, celioblastoma, clear cell carcinoma, unclassified carcinoma, granulosa-thecal cell tumors, Sertoli-Leydig cell tumors, dysgerminoma, and malignant teratoma. The most common type of ovarian cancer is papillary serous carcinoma.

Surgery is an exemplary treatment for ovarian cancer and can be necessary for diagnosis. The type of surgery depends upon how widespread the cancer is when diagnosed (the cancer stage), as well as the type and grade of cancer. The surgeon may remove one (unilateral oophorectomy) or both ovaries (bilateral oophorectomy), the fallopian tubes (salpingectomy), and the uterus (hysterectomy). For some very early tumors (stage 1, low grade or low-risk disease), only the involved ovary and fallopian tube will be removed (called a “unilateral salpingo-oophorectomy,” USO), especially in young females who wish to preserve their fertility. In advanced disease as much tumor as possible is removed (debulking surgery). In cases where this type of surgery is successful, the prognosis is improved compared to subjects where large tumor masses (more than 1 cm in diameter) are left behind.

Chemotherapy is often used after surgery to treat any residual disease. At present systemic chemotherapy often includes a platinum derivative with a taxane as a method of treating advanced ovarian cancer. Chemotherapy is also used to treat subjects who have a recurrence.

Ovarian Endothelial Cell Tumor-Associated (or Related) Molecule:

A molecule whose expression is altered in ovarian tumor endothelial cells. Such molecules include, for instance, nucleic acid sequences (such as DNA, cDNA, or mRNAs) and proteins. Specific genes include those listed in Tables 1 through 5. Thus, the presence of the respective ovarian endothelial cell tumor-associated molecules can be used to diagnose, or determine the prognosis of, an ovarian tumor in a subject.

In an example, an ovarian endothelial cell tumor-associated molecule is any molecule listed in Tables 1 through 5. Specific examples of ovarian endothelial cell tumor-associated molecules that are up-regulated in ovarian tumor endothelial cells are provided in Tables 2 and 4. Specific examples of ovarian endothelial cell tumor-associated molecules that are down-regulated in ovarian tumor endothelial cells are listed in Table 3. As illustrated in Table 4, a number of the identified ovarian cell tumor-associated molecules are related to cell proliferation, tube formation and cell motility.

Ovarian endothelial cell tumor-associated molecules can be involved in or influenced by cancer in different ways, including causative (in that a change in a ovarian endothelial cell tumor-associated molecule leads to development of or progression of ovarian cancer) or resultive (in that development of or progression of ovarian cancer causes or results in a change in the ovarian endothelial cell tumor-associated molecule).

Pharmaceutically Acceptable Carriers:

The pharmaceutically acceptable carriers (vehicles) useful in this disclosure are conventional. Remington's Pharmaceutical Sciences, by E. W. Martin, Mack Publishing Co., Easton, Pa., 15th Edition (1975), describes compositions and formulations suitable for pharmaceutical delivery of one or more therapeutic agents, such as one or more compositions that include a binding agent that specifically binds to at least one of the disclosed ovarian endothelial cell tumor-associated molecules.

In general, the nature of the carrier will depend on the particular mode of administration being employed. For instance, parenteral formulations can include injectable fluids that include pharmaceutically and physiologically acceptable fluids such as water, physiological saline, balanced salt solutions, aqueous dextrose, glycerol or the like as a vehicle. In addition to biologically-neutral carriers, pharmaceutical compositions to be administered can contain minor amounts of non-toxic auxiliary substances, such as wetting or emulsifying agents, preservatives, and pH buffering agents and the like, for example sodium acetate or sorbitan monolaurate, sodium lactate, potassium chloride, calcium chloride, and triethanolamine oleate.

Plexin Domain Containing 1 (PLXDC1):

A large transmembrane receptor. In vitro, plexin-C1 has been shown to bind the GPI-anchored semaphorin Sema7A and the soluble viral semaphorins SemaVA (A39R) and SemaVB (AHV). Plexin C1 engagement by SemaVA inhibits integrin-mediated dendritic cell adhesion and chemotaxis in vitro, suggesting a role for plexin C1 in dendritic cell migration.

In an example, expression of PLXDL1 is increased in ovarian tumor endothelial cells. The term PLXDC1 includes any plexin C1 gene, cDNA, mRNA, or protein from any organism and that is a PLXDC1 and is expressed and in some examples overexpressed in ovarian tumor endothelial cells.

Exemplary nucleic acid and protein sequences for PLXDC1 are publicly available. For example, GenBank Accession Nos.: NM — 018797, XM — 622776, AB208934, and NM — 005761 disclose PLXDC1 nucleic acid sequences and GenBank Accession Nos.: NP — 061267, XP — 622776, BAD92171, and NP — 005752 disclose PLXDC1 protein sequences, all of which are incorporated by reference as provided by GenBank on Feb. 14, 2007.

In one example, a PLXDC1 sequence includes a full-length wild-type (or native) sequence, as well as PLXDC1 allelic variants, fragments, homologs or fusion sequences that retain the ability to be expressed in ovarian tumor endothelial cells and/or modulate ovarian tumor endothelial cells, such as increase vascular growth. In certain examples, PLXDC1 has at least 80% sequence identity, for example at least 85%, 90%, 95%, or 98% sequence identity to GenBank Accession No.: NP — 061267, XP — 622776, BAD92171, or NP — 005752. In other examples, a PLXDC1 has a sequence that hybridizes to AFFYMETRIX® Probe ID No. 214081_at and retains PLXDC1 activity (such as the capability to be expressed in ovarian tumor endothelial cells and/or modulate tumor and/or vascular growth).

Polymerase Chain Reaction (PCR):

An in vitro amplification technique that increases the number of copies of a nucleic acid molecule (for example, a nucleic acid molecule in a sample or specimen). In an example, a biological sample collected from a subject (e.g., with ovarian cancer) is contacted with a pair of oligonucleotide primers, under conditions that allow for the hybridization of the primers to nucleic acid template in the sample. The primers are extended under suitable conditions, dissociated from the template, and then re-annealed, extended, and dissociated to amplify the number of copies of the nucleic acid. The product of a PCR can be characterized by methods known in the art such as electrophoresis, restriction endonuclease cleavage patterns, oligonucleotide hybridization or ligation, and/or nucleic acid sequencing, using standard techniques.

Primers:

Short nucleic acid molecules, for instance DNA oligonucleotides 10-100 nucleotides in length, such as about 15, 20, 25, 30 or 50 nucleotides or more in length. Primers can be annealed to a complementary target DNA strand (such as a gene listed in Table 1) by nucleic acid hybridization to form a hybrid between the primer and the target DNA strand. Primer pairs can be used for amplification of a nucleic acid sequence, such as by PCR or other nucleic acid amplification methods known in the art.

Methods for preparing and using nucleic acid primers are described, for example, in Sambrook et al. (In Molecular Cloning: A Laboratory Manual , CSHL, New York, 1989), Ausubel et al. (ed.) (In Current Protocols in Molecular Biology , John Wiley & Sons, New York, 1998), and Innis et al. ( PCR Protocols, A Guide to Methods and Applications , Academic Press, Inc., San Diego, Calif., 1990). PCR primer pairs can be derived from a known sequence, for example, by using computer programs intended for that purpose such as Primer (Version 0.5, © 1991, Whitehead Institute for Biomedical Research, Cambridge, Mass.). One of ordinary skill in the art will appreciate that the specificity of a particular primer increases with its length. Thus, for example, a primer including 30 consecutive nucleotides of an ovarian endothelial cell tumor-associated molecule will anneal to a target sequence, such as another homolog of the designated endothelial cell tumor-associated protein, with a higher specificity than a corresponding primer of only 15 nucleotides. Thus, in order to obtain greater specificity, primers can be selected that include at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50 or more consecutive nucleotides of an ovarian endothelial cell tumor-associated nucleotide sequence.

Prognosis:

A prediction of the course of a disease, such as ovarian cancer. The prediction can include determining the likelihood of a subject to develop aggressive, recurrent disease, to survive a particular amount of time (e.g., determine the likelihood that a subject will survive 1, 2, 3 or 5 years), to respond to a particular therapy (e.g., chemotherapy), or combinations thereof.

Purified:

The term “purified” does not require absolute purity; rather, it is intended as a relative term. Thus, for example, a purified protein preparation is one in which the protein referred to is more pure than the protein in its natural environment within a cell. For example, a preparation of a protein is purified such that the protein represents at least 50% of the total protein content of the preparation. Similarly, a purified oligonucleotide preparation is one in which the oligonucleotide is more pure than in an environment including a complex mixture of oligonucleotides.

Recombinant:

A recombinant nucleic acid molecule is one that has a sequence that is not naturally occurring or has a sequence that is made by an artificial combination of two otherwise separated segments of sequence. This artificial combination can be accomplished for example, by chemical synthesis or by the artificial manipulation of isolated segments of nucleic acid molecules, such as by genetic engineering techniques.

Sample (or Biological Sample):

A biological specimen containing genomic DNA, RNA (including mRNA), protein, or combinations thereof, obtained from a subject. Examples include, but are not limited to, peripheral blood, urine, saliva, tissue biopsy, surgical specimen, amniocentesis samples and autopsy material. In one example, a sample includes an ovarian cancer tissue biopsy.

Sensitivity:

A measurement of activity, such as biological activity, of a molecule or a collection of molecules in a given condition. In an example, sensitivity refers to the activity of an agent, such as a binding agent that preferentially binds to one or more ovarian endothelial cell tumor-associated molecules, to alter the growth, development or progression of a disease, such as ovarian cancer. In certain examples, sensitivity or responsiveness can be assessed using any endpoint indicating a benefit to the subject, including, without limitation, (1) inhibition, to some extent, of tumor growth, including slowing down and complete growth arrest; (2) reduction in the number of tumor cells; (3) reduction in tumor size; (4) inhibition (such as reduction, slowing down or complete stopping) of tumor cell infiltration into adjacent peripheral organs and/or tissues; (5) inhibition (such as reduction, slowing down or complete stopping) of metastasis; (6) enhancement of anti-tumor immune response, which may, but does not have to, result in the regression or rejection of the tumor; (7) relief, to some extent, of one or more symptoms associated with the tumor; (8) increase in the length of survival following treatment; (9) decreased mortality at a given point of time following treatment; and/or (10) reducing or inhibiting angiogenesis.

Sequence Identity/Similarity:

The identity/similarity between two or more nucleic acid sequences, or two or more amino acid sequences, is expressed in terms of the identity or similarity between the sequences. Sequence identity can be measured in terms of percentage identity; the higher the percentage, the more identical the sequences are. Sequence similarity can be measured in terms of percentage similarity (which takes into account conservative amino acid substitutions); the higher the percentage, the more similar the sequences are. Homologs or orthologs of nucleic acid or amino acid sequences possess a relatively high degree of sequence identity/similarity when aligned using standard methods. This homology is more significant when the orthologous proteins or cDNAs are derived from species which are more closely related (such as human and mouse sequences), compared to species more distantly related (such as human and C. elegans sequences).

Methods of alignment of sequences for comparison are well known in the art. Various programs and alignment algorithms are described in: Smith & Waterman, Adv. Appl. Math. 2:482, 1981; Needleman & Wunsch, J. Mol. Biol. 48:443, 1970; Pearson & Lipman, Proc. Natl. Acad. Sci. USA 85:2444, 1988; Higgins & Sharp, Gene, 73:237-44, 1988; Higgins & Sharp, CABIOS 5:151-3, 1989; Corpet et al., Nuc. Acids Res. 16:10881-90, 1988; Huang et al. Computer Appls. in the Biosciences 8, 155-65, 1992; and Pearson et al., Meth. Mol. Bio. 24:307-31, 1994. Altschul et al., J. Mol. Biol. 215:403-10, 1990, presents a detailed consideration of sequence alignment methods and homology calculations.

The NCBI Basic Local Alignment Search Tool (BLAST) (Altschul et al., J. Mol. Biol. 215:403-10, 1990) is available from several sources, including the National Center for Biological Information (NCBI, National Library of Medicine, Building 38A, Room 8N805, Bethesda, Md. 20894) and on the Internet, for use in connection with the sequence analysis programs blastp, blastn, blastx, tblastn and tblastx. Additional information can be found at the NCBI web site.

BLASTN is used to compare nucleic acid sequences, while BLASTP is used to compare amino acid sequences. If the two compared sequences share homology, then the designated output file will present those regions of homology as aligned sequences. If the two compared sequences do not share homology, then the designated output file will not present aligned sequences.

Once aligned, the number of matches is determined by counting the number of positions where an identical nucleotide or amino acid residue is presented in both sequences. The percent sequence identity is determined by dividing the number of matches either by the length of the sequence set forth in the identified sequence, or by an articulated length (such as 100 consecutive nucleotides or amino acid residues from a sequence set forth in an identified sequence), followed by multiplying the resulting value by 100. For example, a nucleic acid sequence that has 1166 matches when aligned with a test sequence having 1154 nucleotides is 75.0 percent identical to the test sequence (1166÷1554*100=75.0). The percent sequence identity value is rounded to the nearest tenth. For example, 75.11, 75.12, 75.13, and 75.14 are rounded down to 75.1, while 75.15, 75.16, 75.17, 75.18, and 75.19 are rounded up to 75.2. The length value will always be an integer. In another example, a target sequence containing a 20-nucleotide region that aligns with 20 consecutive nucleotides from an identified sequence as follows contains a region that shares 75 percent sequence identity to that identified sequence (that is, 15÷20*100=75).

For comparisons of amino acid sequences of greater than about 30 amino acids, the Blast 2 sequences function is employed using the default BLOSUM62 matrix set to default parameters, (gap existence cost of 11, and a per residue gap cost of 1). Homologs are typically characterized by possession of at least 70% sequence identity counted over the full-length alignment with an amino acid sequence using the NCBI Basic Blast 2.0, gapped blastp with databases such as the nr or swissprot database. Queries searched with the blastn program are filtered with DUST (Hancock and Armstrong, 1994 , Comput. Appl. Biosci. 10:67-70). Other programs use SEG. In addition, a manual alignment can be performed. Proteins with even greater similarity will show increasing percentage identities when assessed by this method, such as at least about 75%, 80%, 85%, 90%, 95%, 98%, or 99% sequence identity with the proteins listed in Table 1.

When aligning short peptides (fewer than around 30 amino acids), the alignment is be performed using the Blast 2 sequences function, employing the PAM30 matrix set to default parameters (open gap 9, extension gap 1 penalties). Proteins with even greater similarity to the reference sequence will show increasing percentage identities when assessed by this method, such as at least about 60%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% sequence identity with the proteins listed in Table 1. When less than the entire sequence is being compared for sequence identity, homologs will typically possess at least 75% sequence identity over short windows of 10-20 amino acids, and can possess sequence identities of at least 85%, 90%, 95% or 98% depending on their identity to the reference sequence. Methods for determining sequence identity over such short windows are described at the NCBI web site.

One indication that two nucleic acid molecules are closely related is that the two molecules hybridize to each other under stringent conditions, as described above. Nucleic acid sequences that do not show a high degree of identity may nevertheless encode identical or similar (conserved) amino acid sequences, due to the degeneracy of the genetic code. Changes in a nucleic acid sequence can be made using this degeneracy to produce multiple nucleic acid molecules that all encode substantially the same protein. Such homologous nucleic acid sequences can, for example, possess at least about 60%, 70%, 80%, 90%, 95%, 98%, or 99% sequence identity with the genes listed in Table 1 as determined by this method. An alternative (and not necessarily cumulative) indication that two nucleic acid sequences are substantially identical is that the polypeptide which the first nucleic acid encodes is immunologically cross reactive with the polypeptide encoded by the second nucleic acid.

One of skill in the art will appreciate that the particular sequence identity ranges are provided for guidance only; it is possible that strongly significant homologs could be obtained that fall outside the ranges provided.

Short interfering RNA (siRNA):

A double stranded nucleic acid molecule capable of RNA interference or “RNAi.” (See, for example, Bass Nature 411: 428-429, 2001; Elbashir et al., Nature 411: 494-498, 2001; and Kreutzer et al., International PCT Publication No. WO 00/44895; Zernicka-Goetz et al., International PCT Publication No. WO 01/36646; Fire, International PCT Publication No. WO 99/32619; Plaetinck et al., International PCT Publication No. WO 00/01846; Mello and Fire, International PCT Publication No. WO 01/29058; Deschamps-Depaillette, International PCT Publication No. WO 99/07409; and Li et al., International PCT Publication No. WO 00/44914.) As used herein, siRNA molecules need not be limited to those molecules containing only RNA, but further encompasses chemically modified nucleotides and non-nucleotides having RNAi capacity or activity. In an example, an siRNA molecule is one that reduces or inhibits the biological activity or expression of one or more ovarian endothelial cell tumor-associated molecules disclosed in Tables 1, 2, 4 or 5 that are upregulated in ovarian tumor endothelial cells, such as EGFL6, TNFAIP6, TWIST1, STC1, HOP, CSPG2, PLXDC1, EZH2, the Notch ligand Jagged1 or PTK2.

Specific Binding Agent:

An agent that binds substantially or preferentially only to a defined target (for example, those listed in Table 1), such as a protein, enzyme, polysaccharide, oligonucleotide, DNA, RNA, recombinant vector or a small molecule. In an example, a “specific binding agent” is capable of binding to at least one of the disclosed ovarian endothelial cell tumor-associated molecules. Thus, a RNA-specific binding agent binds substantially only to the defined RNA, or to a specific region within the RNA. For example, a “specific binding agent” includes a siRNA that binds substantially to a specified RNA.

A protein-specific binding agent binds substantially only the defined protein, or to a specific region within the protein. For example, a “specific binding agent” includes antibodies and other agents that bind substantially to a specified polypeptide. The antibodies can be monoclonal or polyclonal antibodies that are specific for the polypeptide, as well as immunologically effective portions (“fragments”) thereof. The determination that a particular agent binds substantially only to a specific polypeptide may readily be made by using or adapting routine procedures. One suitable in vitro assay makes use of the Western blotting procedure (described in many standard texts, including Harlow and Lane, Using Antibodies: A Laboratory Manual, CSHL, New York, 1999).

Stanniocalcin 1 (STC1):

A hormone that plays a role in calcium regulation, phosphate homeostasis and cell metabolism. In particular examples, expression of STC1 is increased in ovarian tumor endothelial cells. The term STC1 includes any STC1 gene, cDNA, mRNA, or protein from any organism and that is STC1 and is expressed or overexpressed in some examples in ovarian tumor endothelial cells.

Nucleic acid and protein sequences for STC1 are publicly available. For example, GenBank Accession Nos.: NM — 009285, NM — 00003155, and NM — 031123 disclose STC1 nucleic acid sequences, and GenBank Accession Nos.: AAH21425, NP — 112385, and NP — 033311 disclose STC1 protein sequences, all of which are incorporated by reference as provided by GenBank on Feb. 14, 2007.

In one example, STC1 includes a full-length wild-type (or native) sequence, as well as STC1 allelic variants that retain the ability to be expressed in ovarian tumor endothelial cells and/or modulate ovarian tumor endothelial cells, such as increase vascular growth. In certain examples, STC1 has at least 80% sequence identity, for example at least 85%, 90%, 95%, or 98% sequence identity to GenBank Accession No.: AAH21425, NP — 112385, or NP — 033311. In other examples, STC1 has a sequence that hybridizes to AFFYMETRIX® Probe ID No. 230746_s_at, 204595_s_at, and 204597_x_at and retains STC1 activity (such as the capability to be expressed in ovarian tumor endothelial cells and/or modulate tumor and/or vascular growth).

Subject:

Living multi-cellular vertebrate organisms, a category that includes human and non-human mammals.

Target Sequence:

A sequence of nucleotides located in a particular region in the human genome that corresponds to a desired sequence, such as an ovarian endothelial cell tumor-associated sequence. The target can be for instance a coding sequence; it can also be the non-coding strand that corresponds to a coding sequence. Examples of target sequences include those sequences associated with ovarian tumor endothelial cells, such as any of those listed in Tables 1 through 5.

Therapeutically Effective Amount:

An amount of a composition that alone, or together with an additional therapeutic agent(s) (for example a chemotherapeutic agent), induces the desired response (e.g., treatment of a tumor). The preparations disclosed herein are administered in therapeutically effective amounts.

In one example, a desired response is to decrease ovarian tumor size or metastasis in a subject to whom the therapy is administered. Tumor metastasis does not need to be completely eliminated for the composition to be effective. For example, a composition can decrease metastasis by a desired amount, for example by at least 20%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or even at least 100% (elimination of the tumor), as compared to metastasis in the absence of the composition.

In particular examples, it is an amount of the therapeutic agent conjugated to the specific binding agent effective to decrease a number of ovarian cancer cells, such as in a subject to whom it is administered, for example a subject having one or more ovarian carcinomas. The cancer cells do not need to be completely eliminated for the composition to be effective. For example, a composition can decrease the number of cancer cells or growth of such cells by a desired amount, for example by at least 20%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or even at least 100% (elimination of detectable cancer cells), as compared to the number of cancer cells in the absence of the composition.

In other examples, it is an amount of the specific binding agent for one or more of the disclosed ovarian endothelial cell tumor-associated molecules capable of reducing angiogenesis by least 20%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, or even at least 100% (elimination of detectable angiogenesis) by the specific binding agent, or both, effective to decrease the metastasis of a tumor.

A therapeutically effective amount of a specific binding agent for at least one of the disclosed ovarian endothelial cell tumor-associated molecules, or cancer cells lysed by a therapeutic molecule conjugated to the agent, can be administered in a single dose, or in several doses, for example daily, during a course of treatment. However, the therapeutically effective amount can depend on the subject being treated, the severity and type of the condition being treated, and the manner of administration. For example, a therapeutically effective amount of such agent can vary from about 1 μg-10 mg per 70 kg body weight if administered intravenously and about 10 μg-100 mg per 70 kg body weight if administered intratumorally.

Tissue:

A plurality of functionally related cells. A tissue can be a suspension, a semi-solid, or solid. Tissue includes cells collected from a subject such as the ovaries.

Treating a Disease:

“Treatment” refers to a therapeutic intervention that ameliorates a sign or symptom of a disease or pathological condition, such as a sign or symptom of ovarian cancer. Treatment can also induce remission or cure of a condition, such as ovarian cancer. In particular examples, treatment includes preventing a disease, for example by inhibiting the full development of a disease. Prevention of a disease does not require a total absence of disease. For example, a decrease of at least 50% can be sufficient.

Tumor:

All neoplastic cell growth and proliferation, whether malignant or benign, and all pre-cancerous and cancerous cells and tissues. In an example, a tumor is an ovarian tumor.

Tumor-Necrosis Factor, Alpha-Induced Protein 6 (TNFAIP6):

A protein capable of regulating the expression of various molecules involved in the control of inflammation. In particular examples, expression of TNFAIP6 is increased in ovarian cancer endothelial cells. The term TNFAIP6 includes any TNFAIP6 gene, cDNA, mRNA, or protein from any organism and that is TNFAIP6 and is expressed or overexpressed in some examples in ovarian cancer endothelial cells.

Nucleic acid and protein sequences for TNFAIP6 are publicly available. For example, GenBank Accession Nos.: NM — 007115, BC021155 and NM — 009398 disclose TNFAIP6 nucleic acid sequences, and GenBank Accession Nos.: AAH21155, NP — 009046 and NP — 033424 disclose TNFAIP6 protein sequences, all of which are incorporated by reference as provided by GenBank on Feb. 14, 2007.

In one example, TNFAIP6 includes a full-length wild-type (or native) sequence, as well as TNFAIP6 allelic variants that retain the ability to be expressed in ovarian tumor endothelial cells and/or modulate ovarian tumor endothelial cells, such as suppression of vascular growth. In certain examples, TNFAIP6 has at least 80% sequence identity, for example, at least 85%, 90%, 95%, or 98% sequence identity to GenBank Accession No.: AAH21155, NP — 009046 or NP — 033424. In other examples, TNFAIP6 has a sequence that hybridizes to AFFYMETRIX® Probe ID No. 206026_s_at and retains TNFAIP6 activity (such as the capability to be expressed in ovarian tumor endothelial cells and/or modulate tumor and/or vascular growth).

Twist Homologue 1 (TWIST1):

Overexpression of TWIST1 has been reported to play a role in destabilizing the genome, thus promoting chromosomal instability. For example, TWIST1 is capable of inhibiting chrondrogenesis. TWIST1 protein has also been noted to be involved in the regulation of tumor necrosis factor alpha production by antiinflammatory factors and pathways. In particular examples, expression of TWIST1 is increased in ovarian cancer endothelial cells. The term TWIST1 includes any TWIST1 gene, cDNA, mRNA, or protein from any organism and that is TWIST1 and is expressed or overexpressed in some examples in ovarian cancer endothelial cells.

Nucleic acid and protein sequences for TWIST1 are publicly available. For example, GenBank Accession Nos.: NM — 000474, NM — 053530 and XM — 001076553 and disclose TWIST1 nucleic acid sequences, and GenBank Accession Nos.: NP — 000465 and ABM87769 disclose TWIST1 protein sequences, all of which are incorporated by reference as provided by GenBank on Feb. 14, 2007.

In one example, TWIST1 includes a full-length wild-type (or native) sequence, as well as TWIST1 allelic variants that retain the ability to be expressed in ovarian tumor endothelial cells and/or modulate ovarian tumor endothelial cells, such as increase vascular growth. In certain examples, TWIST1 has at least 80% sequence identity, for example at least 85%, 90%, 95%, or 98% sequence identity to GenBank Accession No.: NP — 000465 or ABM87769. In other examples, TWIST1 has a sequence that hybridizes to AFFYMETRIX® Probe ID No. 206026_s_at and retains TWIST1 activity (such as the capability to be expressed in ovarian tumor endothelial cells and/or modulate tumor and/or vascular growth).

Under Conditions Sufficient for:

A phrase that is used to describe any environment that permits the desired activity. In one example, includes administering a test agent to an ovarian cancer cell or a subject sufficient to allow the desired activity. In particular examples, the desired activity is altering the activity (such as the expression) of an ovarian endothelial cell tumor-associated molecule.

Unit Dose:

A physically discrete unit containing a predetermined quantity of an active material calculated to individually or collectively produce a desired effect, such as a therapeutic effect. A single unit dose or a plurality of unit doses can be used to provide the desired effect, such as treatment of a tumor, for example a metastatic tumor. In one example, a unit dose includes a desired amount of an agent that decreases or inhibits angiogenesis.

Upregulated or Activation:

When used in reference to the expression of a nucleic acid molecule, such as a gene, refers to any process which results in an increase in production of a gene product. A gene product can be RNA (such as mRNA, rRNA, tRNA, and structural RNA) or protein. Therefore, gene upregulation or activation includes processes that increase transcription of a gene or translation of mRNA. Specific examples of ovarian endothelial cell tumor-associated molecules that are up-regulated in ovarian tumor endothelial cells are provided in Tables 2 and 4. For example, EZH2, EGFL6, TNFAIP6, TWIST1, STC1, HOP, CSPG2, and PLXDC1 are upregulated or increased in expression in ovarian tumor endothelial cells.

Examples of processes that increase transcription include those that facilitate formation of a transcription initiation complex, those that increase transcription initiation rate, those that increase transcription elongation rate, those that increase processivity of transcription and those that relieve transcriptional repression (for example by blocking the binding of a transcriptional repressor). Gene upregulation can include inhibition of repression as well as stimulation of expression above an existing level. Examples of processes that increase translation include those that increase translational initiation, those that increase translational elongation and those that increase mRNA stability.

Gene upregulation includes any detectable increase in the production of a gene product. In certain examples, production of a gene product increases by at least 2-fold, for example at least 3-fold or at least 4-fold, as compared to a control (such an amount of gene expression in a normal endothelial cell). In one example, a control is a relative amount of gene expression in a biological sample, such as in an ovarian tissue biopsy obtained from a subject that does not have ovarian cancer.

Vasohibin 1 (VASH1):

a protein that is expressed in a variety of tissues and inhibits functions relevant to neovascularization (migration, proliferation, and network formation by endothelial cells). Vasohibin also inhibits angiogenesis in vivo. The unglycosylated protein (42 kDa) does not contain a classical secretory secretion sequence and appears in the medium as a protein of 30 kDa, suggesting proteolytic processing during secretion. In particular examples, VASH1 is regulated by EZH2 wherein EZH2 binds to the VASH1 promoter and decreases or inhibits VASH1 anti-angiogenesis activity. The term VASH1 includes any VASH1 gene, cDNA, mRNA, or protein from any organism and that is VASH1 and is expressed or overexpressed in some examples in ovarian cancer endothelial cells.

Nucleic acid and protein sequences for VASH1 are publicly available. For example, GenBank Accession Nos.: NP — 055724 (human); NP — 796328 (mouse); and NP — 659128 disclose VASH1 amino acid sequences which are incorporated by reference as provided by GenBank on Aug. 14, 2009. Further, GenBank Accession Nos.: NM — 014909 (human) and NM — 177354 (mouse) disclose nucleic acid sequences which are incorporated by reference as provided by GenBank on Aug. 14, 2009.

In one example, vasohibin includes a full-length wild-type (or native) sequence, as well as VASH1 allelic variants that retain the ability to be expressed in ovarian tumor endothelial cells and/or modulate ovarian tumor endothelial cells, such as increase vascular growth. In certain examples, VASH1 has at least 80% sequence identity, for example at least 85%, 90%, 95%, or 98% sequence identity to GenBank Accession No.: NP — 055724; NP — 796328 or NP — 659128 and retains VASH1 activity (such as the capability to be expressed in ovarian tumor endothelial cells and/or modulate tumor and/or vascular growth).

Zeste Homologue 2 (EZH2):

A member of the polycomb group of genes that has been reported to be involved in cell cycle regulation EZH2, a component of the polycomb repressive complex 2 (PRC2), has intrinsic histone methyl transferase (HMTase) activity and has been implicated in the progression and metastasis of several cancers. EZH2 is also a transcriptional repressor that has multiple targets, including anti-angiogenic, pro-apoptotic, and tumor suppressor genes. In particular examples, expression of EZH2 is increased in ovarian cancer endothelial cells. In one example, expression of EZH2 is an indicator of poor prognosis. The term EZH2 includes any EZH2 gene, cDNA, mRNA, or protein from any organism and that is EZH2 and is expressed or overexpressed in some examples in ovarian cancer endothelial cells.

Nucleic acid and protein sequences for EZH2 are publicly available. For example, GenBank Accession Nos.: NM — 004456 and AY519465.1 disclose EZH2 nucleic acid sequences, and GenBank Accession No. AAS09975 discloses a EZH2 protein sequence, which are incorporated by reference as provided by GenBank on Feb. 14, 2007.

In one example, EZH2 includes a full-length wild-type (or native) sequence, as well as EZH2 allelic variants, fragments, homologs or fusion sequences that retain the ability to be expressed in ovarian tumor endothelial cells and/or modulate ovarian tumor endothelial cells, such as increase vascular growth. In certain examples, EZH2 has at least 80% sequence identity, for example at least 85%, 90%, 95%, or 98% sequence identity to AAS09975. In other examples, EZH2 has a sequence that hybridizes to AFFYMETRIX® Probe ID No. 203358_s_at and retains EZH2 activity (such as the capability to be expressed in ovarian tumor endothelial cells and/or modulate tumor and/or vascular growth).

Additional terms commonly used in molecular genetics can be found in Benjamin Lewin, Genes V published by Oxford University Press, 1994 (ISBN 0-19-854287-9); Kendrew et al. (eds.), The Encyclopedia of Molecular Biology, published by Blackwell Science Ltd., 1994 (ISBN 0-632-02182-9); and Robert A. Meyers (ed.), Molecular Biology and Biotechnology: a Comprehensive Desk Reference, published by VCH Publishers, Inc., 1995 (ISBN 1-56081-569-8).

Methods of Treatment

It is shown herein that ovarian cancer is associated with differential expression of ovarian endothelial cell tumor-associated molecules. For example, the disclosed gene expression profile has identified ovarian endothelial cell tumor-associated molecules. Based on these observations, methods of treatment to reduce or eliminate ovarian cancer are disclosed. For example, the method can include inhibiting the expression or biological activity of at least one of the ovarian endothelial cell tumor associated molecules from Tables 1, 2, 4, and/or 5 that are upregulated in ovarian tumor cells or increasing the expression or biological activity of at least one of the ovarian endothelial cell tumor associated molecules from Tables 1, 3 and/or 5 that are downregulated in ovarian tumor cells or combinations thereof. As used herein, “inhibit” does not require 100% inhibition of expression or activity. For example, a substantial reduction may be adequate, such as reduction in expression or activity of at least 20%, at least 30%, at least 50%, at least 75%, or at least 95% may be sufficient to obtain desired therapeutic results. In some examples, an “increase” in expression or activity is an increase of at least 20%, at least 30%, at least 50%, at least 75%, or at least 95%. In some embodiments, the subject is a human, but the subject can alternatively be a veterinary or laboratory subject. In some embodiments, the ovarian cancer is papillary serous ovarian cancer.

Methods are disclosed herein for treating an ovarian tumor, such as ovarian cancer. In one example, the method includes administering a therapeutically effective amount of a composition to a subject. The composition can include a binding agent that is specific for one of the ovarian endothelial cell tumor-associated molecules listed in any of Tables 1, 2, 4 or 5 that are upregulated in ovarian tumor cells. Administration of such compounds decreases the expression or activity of the molecule that is undesirably upregulated in ovarian cancer cells. The molecules in Tables 1, 2, 4, or 5 include, for instance, nucleic acid sequences (such as DNA, cDNA, or mRNAs) and proteins. Specific genes include those listed in Tables 1, 2, 4 or 5 as well as fragments of the full-length genes, cDNAs, or mRNAs (and proteins encoded thereby) whose expression is upregulated in response to an ovarian tumor, such as ovarian cancer.

In particular examples, the specific binding agent is an inhibitor such as a siRNA or an antibody to one of the disclosed ovarian endothelial cell tumor-associated molecules that is upregulated in ovarian tumor cells. For example, the specific binding agent can be a siRNA that interferes with mRNA expression of one of the disclosed ovarian endothelial cell tumor-associated molecules that are involved in angiogenesis, such as a molecule involved in regulating cell motility, cell proliferation or tube formation, thereby inhibiting cell motility, cell proliferation or tube formation. For example, the specific binding agent can be a siRNA that inhibits the expression of PTK2, EZH2 or Jagged1. In other particular examples, ovarian tumor growth is reduced or inhibited by administering a specific binding agent to inhibit or reduce the expression or production of EZH2, EGFL6, TNFAIP6, TWIST1, STC1, HOP, CSPG2, and PLXDC1. In additional examples, a composition includes at least two specific binding agents such as two specific siRNAs that each bind to their respective ovarian endothelial cell tumor-associated nucleotide sequences and inhibit ovarian tumor growth in a subject. In some examples, the composition includes at least 2, 3, 4, 5, 5, 8 or 10 different siRNA molecules. For example, the composition can include PTK2, EZH2 and Jagged1 siRNAs.

Treating Ovarian Cancer by Altering Activity of an Ovarian Endothelial Cell Tumor-Associated Molecule

Methods are provided to inhibit ovarian endothelial cell tumor-associated molecule activity or expression to treat an ovarian tumor. Treatment of tumors by reducing the number of ovarian endothelial cell tumor-associated molecules can include delaying the development of the tumor in a subject (such as preventing metastasis of a tumor). Treatment of a tumor also includes reducing signs or symptoms associated with the presence of such a tumor (for example by reducing the size, growth or volume of the tumor or a metastasis thereof). Such reduced growth can in some examples decrease or slow metastasis of the tumor, or reduce the size or volume of the tumor by at least 10%, at least 20%, at least 50%, or at least 75%, such as by inhibiting angiogenesis by at least 10%, at least 20%, at least 50%, or at least 75%. For example, ovarian endothelial cell tumor-associated molecules involved in angiogenesis, such as molecules involved in promoting cell proliferation, cell motility or tube formation can be inhibited to treat an ovarian tumor, such as those provided in any of Tables 1, 2, 4 or 5 that are upregulated in ovarian endothelial tumor cells. In other examples, ovarian tumor growth is reduced or inhibited by inhibiting the expression or biological activity ovarian endothelial cell tumor-associated molecules provided in any of Tables 1, 2, 4 or 5 that are upregulated in ovarian tumor endothelial cells. In further examples, inhibition of ovarian endothelial cell tumor-associated molecules includes reducing the invasive activity of the tumor in the subject. In some examples, treatment using the methods disclosed herein prolongs the time of survival of the subject.

Specific Binding Agents

Specific binding agents are agents that selectively bind with higher affinity to a molecule of interest, than to other molecules. For example, a specific binding agent can be one that binds with high affinity to one of the genes or gene products of the ovarian endothelial cell tumor-associated molecules listed in any of Tables 1, 2, 4 or 5 that are upregulated in ovarian tumor endothelial cells, but does not substantially bind to another gene or gene product. In a specific example, a specific binding agent binds to one gene listed in Tables 1, 2, 4 or 5 that is upregulated in ovarian tumor endothelial cells thereby reducing or inhibiting expression of the gene, but does not bind to the other genes (or gene product) listed in such Tables under similar conditions. For example, the agent can interfere with gene expression (transcription, processing, translation, post-translational modification), such as, by interfering with the gene's mRNA and blocking translation of the gene product or by post-translational modification of a gene product, or by causing changes in intracellular localization. In another specific example, a specific binding agent binds to a protein encoded by of one of the genes listed in Table 1, 2, 4 or 5 that is upregulated in ovarian tumor endothelial cells with a binding affinity in the range of 0.1 to 20 nM and reduces or inhibits the activity of such protein.

Examples of specific binding agents include, but are not limited to, siRNAs, antibodies, ligands, recombinant proteins, peptide mimetics, and soluble receptor fragments. One example of a specific binding agent is a siRNA. Methods of making siRNA that can be used clinically are known in the art. Particular siRNAs and methods that can be used to produce and administer them are described in detail below. In some examples, the siRNA is incorporated into a chitosan (CH) nanoparticle, such as chitosan obtained from shellfish or fungi.

Another specific example of a specific binding agent is an antibody, such as a monoclonal or polyclonal antibody. Methods of making antibodies that can be used clinically are known in the art. Particular antibodies and methods that can be used to produce them are described in detail below.

In a further example, small molecular weight inhibitors or antagonists of the receptor protein can be used to regulate activity such as the expression or production of ovarian endothelial cell tumor-associated molecules. In a particular example, small molecular weight inhibitors or antagonists of the proteins encoded by the genes listed in Tables 2 and/or 4 are employed.

Specific binding agents can be therapeutic, for example by reducing or inhibiting the biological activity of a nucleic acid or protein. Complete inhibition is not required. For example, a reduction by at least 10%, at least 20%, at least 30%, at least 50%, at least 70%, or even at least 90% can be sufficient. For example, a specific binding agent that binds with high affinity to a gene listed in Tables 1, 2, 4 and/or 5 that are upregulated in ovarian tumor endothelial cells, may substantially reduce the biological function of the gene or gene product (for example, the ability of the gene or gene product to facilitate angiogenesis). In other examples, a specific binding agent that binds with high affinity to one of the proteins encoded by the genes listed in Tables 1, 2, 4 and/or 5 that are upregulated in ovarian tumor endothelial cells, may substantially reduce the biological function of the protein (for example, the ability of the protein to promote angiogenesis). Such agents can be administered in therapeutically effective amounts to subjects in need thereof, such as a subject having ovarian cancer, such as papillary serous ovarian cancer.

Pre-Screening Subjects

In some examples, subjects are initially screened to determine if they have ovarian cancer. In an example, subjects are initially screened for ovarian cancer by using one of the disclosed gene expression profiles (as discussed in detail below). In some examples, if one or more of the disclosed endothelial cell tumor-associated molecules upregulated in ovarian endothelial cells (such as those listed in Tables 2 and 4) is detected, a specific binding agent capable of reducing or inhibiting ovarian cancer is adminstered.

Pre-Screening Specific Binding Agents

In some examples, specific binding agents are initially screened for treating ovarian cancer by use of the disclosed gene expression profile (see below). For example, the disclosed gene expression profile can be used to identify specific binding agents capable of reducing or inhibiting ovarian cancer. In an example, the disclosed gene expression profile is used to identify compositions that can be employed to reduce or inhibit angiogenesis in ovarian tumors.

Exemplary Tumors

A tumor is an abnormal growth of tissue that results from excessive cell division. A particular example of a tumor is cancer. For example, the current application provides methods for the treatment (such as the prevention or reduction of metastasis) of tumors (such as cancers) by altering the expression/production of one or more disclosed ovarian endothelial cell tumor-associated molecules. In some examples, the tumor is treated in vivo, for example in a mammalian subject, such as a human subject. Exemplary tumors that can be treated using the disclosed methods include, but are not limited to ovarian cancer, including metastases of such tumors to other organs. Generally, the tumor is an ovarian cancer, such as papillary serous ovarian cancer.

Administration

Methods of administrating the disclosed compositions are routine, and can be determined by a skilled clinician. For example, the disclosed therapies (such as those that include a binding agent specific for one of the disclosed ovarian endothelial cell tumor-associated molecules listed in Tables 1, 2, 4 or 5 whose expression is increased in ovarian endothelial tumor-associated cells) can be administered via injection, intratumorally, orally, topically, transdermally, parenterally, or via inhalation or spray. In a particular example, a composition is administered intravenously to a mammalian subject, such as a human.

The therapeutically effective amount of the agents administered can vary depending upon the desired effects and the subject to be treated. In one example, the method includes daily administration of at least 1 μg of the composition to the subject (such as a human subject). For example, a human can be administered at least 1 μg or at least 1 mg of the composition daily, such as 10 μg to 100 μg daily, 100 μg to 1000 μg daily, for example 10 μg daily, 100 μg daily, or 1000 μg daily. In one example, the subject is administered at least 1 μg (such as 1-100 μg) intravenously of the composition including a binding agent that specifically binds to one of the disclosed ovarian endothelial cell tumor-associated molecules provided herein. In one example, the subject is administered at least 1 mg intramuscularly (for example in an extremity) of such composition. In a specific example, the dose is 50 to 350 μg/kg twice weekly, such as 150 μg/kg twice weekly (for example via iv injection). The dosage can be administered in divided doses (such as 2, 3, or 4 divided doses per day), or in a single dosage daily.

In particular examples, the subject is administered the therapeutic composition that includes a binding agent specific for one of the disclosed ovarian endothelial cell tumor-associated molecules on a multiple daily dosing schedule, such as at least two consecutive days, 10 consecutive days, and so forth, for example for a period of weeks, months, or years. In one example, the subject is administered the therapeutic composition that a binding agent specific for one of the disclosed ovarian endothelial cell tumor-associated molecules daily for a period of at least 30 days, such as at least 2 months, at least 4 months, at least 6 months, at least 12 months, at least 24 months, or at least 36 months.

The therapeutic compositions, such as those that include a binding agent specific for one of the ovarian endothelial cell tumor-associated molecules, can further include one or more biologically active or inactive compounds (or both), such as anti-neoplastic agents and conventional non-toxic pharmaceutically acceptable carriers, respectively.

In a particular example, a therapeutic composition that includes a therapeutically effective amount of a binding agent specific for one of the disclosed ovarian endothelial cell tumor-associated molecules further includes one or more biologically inactive compounds. Examples of such biologically inactive compounds include, but are not limited to: carriers, thickeners, diluents, buffers, preservatives, and carriers. The pharmaceutically acceptable carriers useful for these formulations are conventional (see Remington's Pharmaceutical Sciences, by E. W. Martin, Mack Publishing Co., Easton, Pa., 19th Edition (1995)). For solid compositions (for example, powder, pill, tablet, or capsule forms), conventional non-toxic solid carriers can include, for example, pharmaceutical grades of mannitol, lactose, starch, or magnesium stearate. In addition to biologically-neutral carriers, pharmaceutical compositions to be administered can include minor amounts of non-toxic auxiliary substances, such as wetting or emulsifying agents, preservatives, and pH buffering agents and the like, for example sodium acetate or sorbitan monolaurate.

Additional Treatments

In particular examples, prior to, during, or following administration of a therapeutic amount of an agent that reduces or inhibits ovarian cancer due to the interaction of a binding agent with one of the disclosed ovarian endothelial cell tumor-associated molecules, the subject can receive one or more other therapies. In one example, the subject receives one or more treatments to remove or reduce the tumor prior to administration of a therapeutic amount of a composition including a binding agent specific for one of the disclosed ovarian endothelial cell tumor-associated molecules.

Examples of such therapies include, but are not limited to, surgical treatment for removal or reduction of the tumor (such as surgical resection, cryotherapy, or chemoembolization), as well as anti-tumor pharmaceutical treatments which can include radiotherapeutic agents, anti-neoplastic chemotherapeutic agents, antibiotics, alkylating agents and antioxidants, kinase inhibitors, and other agents. Particular examples of additional therapeutic agents that can be used include microtubule binding agents, DNA intercalators or cross-linkers, DNA synthesis inhibitors, DNA and/or RNA transcription inhibitors, antibodies, enzymes, enzyme inhibitors, and gene regulators. These agents (which are administered at a therapeutically effective amount) and treatments can be used alone or in combination. Methods and therapeutic dosages of such agents are known to those skilled in the art, and can be determined by a skilled clinician.

“Microtubule binding agent” refers to an agent that interacts with tubulin to stabilize or destabilize microtubule formation thereby inhibiting cell division. Examples of microtubule binding agents that can be used in conjunction with the disclosed therapy include, without limitation, paclitaxel, docetaxel, vinblastine, vindesine, vinorelbine (navelbine), the epothilones, colchicine, dolastatin 15, nocodazole, podophyllotoxin and rhizoxin. Analogs and derivatives of such compounds also can be used and are known to those of ordinary skill in the art. For example, suitable epothilones and epothilone analogs are described in International Publication No. WO 2004/018478. Taxoids, such as paclitaxel and docetaxel, as well as the analogs of paclitaxel taught by U.S. Pat. Nos. 6,610,860; 5,530,020; and 5,912,264 can be used.

The following classes of compounds are of use in the methods disclosed herein: Suitable DNA and/or RNA transcription regulators, including, without limitation, actinomycin D, daunorubicin, doxorubicin and derivatives and analogs thereof also are suitable for use in combination with the disclosed therapies. DNA intercalators and cross-linking agents that can be administered to a subject include, without limitation, cisplatin, carboplatin, oxaliplatin, mitomycins, such as mitomycin C, bleomycin, chlorambucil, cyclophosphamide and derivatives and analogs thereof. DNA synthesis inhibitors suitable for use as therapeutic agents include, without limitation, methotrexate, 5-fluoro-5′-deoxyuridine, 5-fluorouracil and analogs thereof. Examples of suitable enzyme inhibitors include, without limitation, camptothecin, etoposide, formestane, trichostatin and derivatives and analogs thereof. Suitable compounds that affect gene regulation include agents that result in increased or decreased expression of one or more genes, such as raloxifene, 5-azacytidine, 5-aza-2′-deoxycytidine, tamoxifen, 4-hydroxytamoxifen, mifepristone and derivatives and analogs thereof. Kinase inhibitors include Gleevac, Iressa, and Tarceva that prevent phosphorylation and activation of growth factors.

Other therapeutic agents, for example anti-tumor agents, that may or may not fall under one or more of the classifications above, also are suitable for administration in combination with the disclosed therapies. By way of example, such agents include adriamycin, apigenin, rapamycin, zebularine, cimetidine, and derivatives and analogs thereof.

In one example, the therapeutic composition (such as one including a binding agent specific for one or more of the disclosed ovarian endothelial cell tumor-associated molecules) is injected into the subject in the presence of an adjuvant. An adjuvant is an agent that when used in combination with an immunogenic agent augments or otherwise alters or modifies a resultant immune response. In some examples, an adjuvant increases the titer of antibodies induced in a subject by the immunogenic agent. In one example, the one or more peptides are administered to the subject as an emulsion with an adjuvant and sterile water for injection (for example an intravenous or intramuscular injection). Incomplete Freund's Adjuvant (Seppic, Inc.) can be used as the Freund's Incomplete Adjuvant (IFA) (Fairfield, N.J.). In some examples, IFA is provided in 3 ml of a mineral oil solution based on mannide oleate (Montanide ISA-51). At the time of injection, the peptide(s) is mixed with the Montanide ISA.51 and then administered to the subject. Other adjuvants can be used, for example, Freund's complete adjuvant, B30-MDP, LA-15-PH, montanide, saponin, aluminum hydroxide, alum, lipids, keyhole lympet protein, hemocyanin, a mycobacterial antigen, and combinations thereof.

In some examples, the subject receiving the therapeutic peptide composition (such as one including a binding agent specific for one of the disclosed ovarian endothelial cell tumor-associated molecules) is also administered interleukin-2 (IL-2), for example via intravenous administration. In particular examples, IL-2 (Chiron Corp., Emeryville, Calif.) is administered at a dose of at least 500,000 IU/kg as an intravenous bolus over a 15 minute period every eight hours beginning on the day after administration of the peptides and continuing for up to 5 days. Doses can be skipped depending on subject tolerance.

In some examples, the disclosed compositions can be co-administered with a fully human antibody to cytotoxic T-lymphocyte antigen-4 (anti-CTLA-4). In some example subjects receive at least 1 mg/kg anti-CTLA-4 (such as 3 mg/kg every 3 weeks or 3 mg/kg as the initial dose with subsequent doses reduced to 1 mg/kg every 3 weeks).

In one example, at least a portion of the ovarian tumor (such as a metastatic tumor) is surgically removed (for example via cryotherapy), irradiated, chemically treated (for example via chemoembolization) or combinations thereof, prior to administration of the disclosed therapies (such as administration of a binding agent specific for one of the disclosed ovarian endothelial cell tumor-associated molecules). For example, a subject having a metastatic tumor can have all or part of the tumor surgically excised prior to administration of the disclosed therapies (such as one including a binding agent specific for one of the disclosed ovarian endothelial cell tumor-associated molecules). In an example, one or more chemotherapeutic agents is administered following treatment with a binding agent specific for one of the disclosed ovarian endothelial cell tumor-associated molecules. In another particular example, the subject has a metastatic tumor and is administered radiation therapy, chemoembolization therapy, or both concurrently with the administration of the disclosed therapies (such as one including a binding agent specific for one of the disclosed ovarian endothelial cell tumor-associated molecules).

Generation and Administration of siRNA

In an example, certain inhibitors provided by this disclosure are species of siRNAs. One of ordinary skill in the art can readily generate siRNAs which specifically bind to one of the disclosed ovarian endothelial cell tumor-associated molecules that are upregulated in ovarian endothelial cell tumor cells. In an example, commercially available kits, such as siRNA molecule synthesizing kits from PROMEGA® (Madison, Wis.) or AMBION® (Austin, Tex.) may be used to synthesize siRNA molecules. In another example, siRNAs are obtained from commercial sources, such as from QIAGEN® Inc (Germantown, Md.), INVITROGEN® (Carlsbad, Calif.), AMBION (Austin, Tex.), DHARMACON® (Lafayette, Colo.) or OPENBIOSYSTEMS® (Huntsville, Ala.).

In certain examples, expression vectors are employed to express the at least one siRNA molecule. For example, an expression vector can include a nucleic acid sequence encoding at least one siRNA molecule corresponding to at least one of the disclosed ovarian endothelial cell tumor-associated molecules listed in Tables 1, 2, 4 and/or Table 5 that are upregulated in ovarian endothelial cell tumor cells. For example, siRNA specific for EZH2 can be generated using publicly available EZH2 nucleic acid sequences, such as those described above. In a particular example, the vector contains a sequence(s) encoding both strands of a siRNA molecule comprising a duplex. In another example, the vector also contains sequence(s) encoding a single nucleic acid molecule that is self-complementary and thus forms a siRNA molecule. Non-limiting examples of such expression vectors are described in Paul et al., Nature Biotechnology 19:505, 2002; Miyagishi and Taira, Nature Biotechnology 19:497, 2002; Lee et al., Nature Biotechnology 19:500, 2002; and Novina et al., Nature Medicine , online publication Jun. 3, 2003.

In other examples, siRNA molecules include a delivery vehicle, including inter alia liposomes, for administration to a subject, carriers and diluents and their salts, and can be present in pharmaceutical compositions. Nucleic acid molecules can be administered to cells by a variety of methods known to those of skill in the art, including, but not restricted to, encapsulation in liposomes, by iontophoresis, or by incorporation into other delivery vehicles, such as hydrogels, cyclodextrins, biodegradable nanocapsules, and bioadhesive microspheres, or by proteinaceous vectors (see, for example, O'Hare and Normand, International PCT Publication No. WO 00/53722). In one specific example, siRNAs are administered at according to the teachings of Soutschek et al. (Nature Vol. 432: 173-178, 2004) or Karpilow et al. (Pharma Genomics 32-40, 2004) both of which are herein incorporated by reference in their entireties.

In some examples, siRNAs are incorporated into neutral liposomes, such as DOPC or chitosan, and injected intraperitoneal or intravenously. For example, a siRNA can be administered at least 1 μg/kg twice weekly, such as at least 50 μg/kg twice weekly, at least 100 μg/kg twice weekly, at least 125 μg/kg twice weekly, at least 150 μg/kg twice weekly, at least 200 μg/kg twice weekly for at least 1 week, such as at least 2 weeks, at least 3 weeks, at least 4 weeks, at least 6 weeks, at least 12 weeks, or at least 24 weeks. In one example, about at least 1-500 μg/kg, such 10-250 μg/kg, is adminstered at least twice weekly for at least 1 week, such as at least 2 weeks, at least 3 weeks, at least 4 weeks, at least 6 weeks, at least 12 weeks, or at least 24 weeks. In a certain example, approximately 150 μg/kg is administered twice weekly, for 2 to 3 weeks. In other examples, approximately 1 ug/kg daily for 3 weeks or 50 ug/kg every other day for 3 weeks is administered.

Alternatively, the nucleic acid/vehicle combination can be locally delivered by direct injection or by use of an infusion pump. Direct injection of the nucleic acid molecules of the disclosure, whether subcutaneous, intramuscular, or intradermal, can take place using standard needle and syringe methodologies, or by needle-free technologies such as those described by Barry et al., International PCT Publication No. WO 99/31262. Other delivery routes, but are not limited to, oral delivery (such as in tablet or pill form), intrathecal or intraperitoneal delivery. For example, intraperitoneal delivery can take place by injecting the treatment into the peritoneal cavity of the subject in order to directly deliver the molecules to the tumor site. More detailed descriptions of nucleic acid delivery and administration are provided in Sullivan et al., PCT WO 94/02595, Draper et al., PCT WO93/23569, Beigelman et al., PCT WO99/05094, and Klimuk et al., PCT WO99/04819, all of which are incorporated by reference herein.

Alternatively, certain siRNA molecules can be expressed within cells from eukaryotic promoters. Those skilled in the art will recognize that any nucleic acid can be expressed in eukaryotic cells using the appropriate DNA/RNA vector. The activity of such nucleic acids can be augmented by their release from the primary transcript by an enzymatic nucleic acid (Draper et al., PCT WO 93/23569, and Sullivan et al., PCT WO 94/02595).

In other examples, siRNA molecules can be expressed from transcription units (see for example, Couture et al., 1996, TIG 12:510) inserted into DNA or RNA vectors. The recombinant vectors can be DNA plasmids or viral vectors. siRNA expressing viral vectors can be constructed based on, for example, but not limited to, adeno-associated virus, retrovirus, adenovirus, lentivirus or alphavirus. In another example, pol III based constructs are used to express nucleic acid molecules (see for example, Thompson, U.S. Pat. Nos. 5,902,880 and 6,146,886).

The recombinant vectors capable of expressing the siRNA molecules can be delivered as described above, and persist in target cells. Alternatively, viral vectors can be used that provide for transient expression of nucleic acid molecules. Such vectors can be repeatedly administered as necessary. Once expressed, the siRNA molecule interacts with the target mRNA and generates an RNAi response. Delivery of siRNA molecule expressing vectors can be systemic, such as by intravenous or intramuscular administration, by administration to target cells ex-planted from a subject followed by reintroduction into the subject, or by any other means that would allow for introduction into the desired target cell.

Generation of Antibodies

One of ordinary skill in the art can readily generate antibodies which specifically bind to the disclosed ovarian endothelial cell tumor-associated molecules. These antibodies can be monoclonal or polyclonal. They can be chimeric or humanized. Any functional fragment or derivative of an antibody can be used including Fab, Fab′, Fab2, Fab′2, and single chain variable regions. So long as the fragment or derivative retains specificity of binding for the ovarian endothelial cell tumor-associated molecule it can be used in the methods provided herein. Antibodies can be tested for specificity of binding by comparing binding to appropriate antigen to binding to irrelevant antigen or antigen mixture under a given set of conditions. If the antibody binds to appropriate antigen at least 2, at least 5, at least 7 or 10 times more than to irrelevant antigen or antigen mixture, then it is considered to be specific.

In an example, monoclonal antibodies are generated to the ovarian endothelial cell tumor-associated molecules disclosed in Tables 1, 2, 4 or 5 that are upregulated in ovarian endothelial cell tumor cells. These monoclonal antibodies each include a variable heavy (V H ) and a variable light (V L ) chain and specifically bind to the specific ovarian endothelial cell tumor-associated molecules. For example, the antibody can bind the specific ovarian endothelial cell tumor-associated molecules with an affinity constant of at least 10 6 M −1 , such as at least 10 7 M −1 , at least 10 8 M −1 , at least 5×10 8 M −1 , or at least 10 9 M −1 .

The specific antibodies can include a V L polypeptide having amino acid sequences of the complementarity determining regions (CDRs) that are at least about 90% identical, such as at least about 95%, at least about 98%, or at least about 99% identical to the amino acid sequences of the specific ovarian endothelial cell tumor-associated molecules and a V H polypeptide having amino acid sequences of the CDRs that are at least about 90% identical, such as at least about 95%, at least about 98%, or at least about 99% identical to the amino acid sequences of the specific ovarian endothelial cell tumor-associated molecules.

In one example, the sequence of the specificity determining regions of each CDR is determined Residues that are outside the SDR (non-ligand contacting sites) are substituted. For example, in any of the CDR sequences, at most one, two or three amino acids can be substituted. The production of chimeric antibodies, which include a framework region from one antibody and the CDRs from a different antibody, is well known in the art. For example, humanized antibodies can be routinely produced. The antibody or antibody fragment can be a humanized immunoglobulin having CDRs from a donor monoclonal antibody that binds one of the disclosed ovarian endothelial cell tumor-associated molecules and immunoglobulin and heavy and light chain variable region frameworks from human acceptor immunoglobulin heavy and light chain frameworks. Generally, the humanized immunoglobulin specifically binds to one of the disclosed ovarian endothelial cell tumor-associated molecules with an affinity constant of at least 10 7 M −1 , such as at least 10 8 M −1 at least 5×10 8 M −1 or at least 10 9 M −1 .

In another example, human monoclonal antibodies to the disclosed ovarian endothelial cell tumor-associated molecules in Tables 1, 2, 4 and 5 that are upregulated in ovarian endothelial tumor cells are produced. Human monoclonal antibodies can be produced by transferring donor complementarity determining regions (CDRs) from heavy and light variable chains of the donor mouse immunoglobulin into a human variable domain, and then substituting human residues in the framework regions when required to retain affinity. The use of antibody components derived from humanized monoclonal antibodies obviates potential problems associated with the immunogenicity of the constant regions of the donor antibody. For example, when mouse monoclonal antibodies are used therapeutically, the development of human anti-mouse antibodies (HAMA) leads to clearance of the murine monoclonal antibodies and other possible adverse events. Chimeric monoclonal antibodies, with human constant regions, humanized monoclonal antibodies, retaining only murine CDRs, and “fully human” monoclonal antibodies made from phage libraries or transgenic mice have all been used to reduce or eliminate the murine content of therapeutic monoclonal antibodies.

Techniques for producing humanized monoclonal antibodies are described, for example, by Jones et al., Nature 321:522, 1986; Riechmann et al., Nature 332:323, 1988; Verhoeyen et al., Science 239:1534, 1988; Carter et al., Proc. Natl. Acad. Sci. U.S.A. 89:4285, 1992; Sandhu, Crit. Rev. Biotech. 12:437, 1992; and Singer et al., J. Immunol. 150:2844, 1993. The antibody may be of any isotype, but in several embodiments the antibody is an IgG, including but not limited to, IgG 1 , IgG 2 , IgG 3 and IgG 4 .

In one example, the sequence of the humanized immunoglobulin heavy chain variable region framework can be at least about 65% identical to the sequence of the donor immunoglobulin heavy chain variable region framework. Thus, the sequence of the humanized immunoglobulin heavy chain variable region framework can be at least about 75%, at least about 85%, at least about 99% or at least about 95%, identical to the sequence of the donor immunoglobulin heavy chain variable region framework. Human framework regions, and mutations that can be made in a humanized antibody framework regions, are known in the art (see, for example, in U.S. Pat. No. 5,585,089).

Antibodies, such as murine monoclonal antibodies, chimeric antibodies, and humanized antibodies, include full length molecules as well as fragments thereof, such as Fab, F(ab′) 2 , and Fv, which include a heavy chain and light chain variable region and are capable of binding the epitopic determinant. These antibody fragments retain some ability to selectively bind with their epitope. These fragments include: (1) Fab, the fragment which contains a monovalent antigen-binding fragment of an antibody molecule, can be produced by digestion of whole antibody with the enzyme papain to yield an intact light chain and a portion of one heavy chain; (2) Fab′, the fragment of an antibody molecule can be obtained by treating whole antibody with pepsin, followed by reduction, to yield an intact light chain and a portion of the heavy chain; two Fab′ fragments are obtained per antibody molecule; (3) (Fab′) 2 , the fragment of the antibody that can be obtained by treating whole antibody with the enzyme pepsin without subsequent reduction; F(ab′) 2 is a dimer of two Fab′ fragments held together by two disulfide bonds; (4) Fv, a genetically engineered fragment containing the variable region of the light chain and the variable region of the heavy chain expressed as two chains; and (5) Single chain antibody (such as scFv), defined as a genetically engineered molecule containing the variable region of the light chain, the variable region of the heavy chain, linked by a suitable polypeptide linker as a genetically fused single chain molecule. Methods of making these fragments are known in the art (see for example, Harlow and Lane, Antibodies: A Laboratory Manual , Cold Spring Harbor Laboratory, New York, 1988. Fv antibodies are typically about 25 kDa and contain a complete antigen-binding site with three CDRs per each heavy chain and each light chain. To produce these antibodies, the V H and the V L can be expressed from two individual nucleic acid constructs in a host cell. If the V H and the V L are expressed non-contiguously, the chains of the Fv antibody are typically held together by noncovalent interactions. However, these chains tend to dissociate upon dilution, so methods have been developed to crosslink the chains through glutaraldehyde, intermolecular disulfides, or a peptide linker. Thus, in one example, the Fv can be a disulfide stabilized Fv (dsFv), wherein the heavy chain variable region and the light chain variable region are chemically linked by disulfide bonds.

In an additional example, the Fv fragments include V H and V L chains connected by a peptide linker. These single-chain antigen binding proteins (scFv) are prepared by constructing a structural gene comprising DNA sequences encoding the V H and V L domains connected by an oligonucleotide. The structural gene is inserted into an expression vector, which is subsequently introduced into a host cell such as E. coli . The recombinant host cells synthesize a single polypeptide chain with a linker peptide bridging the two V domains. Methods for producing scFvs are known in the art (see Whitlow et al., Methods: a Companion to Methods in Enzymology , Vol. 2, page 97, 1991; Bird et al., Science 242:423, 1988; U.S. Pat. No. 4,946,778; Pack et al., Bio/Technology 11:1271, 1993; and Sandhu, supra).

Antibody fragments can be prepared by proteolytic hydrolysis of the antibody or by expression in E. coli of DNA encoding the fragment. Antibody fragments can be obtained by pepsin or papain digestion of whole antibodies by conventional methods. For example, antibody fragments can be produced by enzymatic cleavage of antibodies with pepsin to provide a 5S fragment denoted F(ab′) 2 . This fragment can be further cleaved using a thiol reducing agent, and optionally a blocking group for the sulfhydryl groups resulting from cleavage of disulfide linkages, to produce 3.5S Fab′ monovalent fragments. Alternatively, an enzymatic cleavage using pepsin produces two monovalent Fab′ fragments and an Fc fragment directly (see U.S. Pat. No. 4,036,945 and U.S. Pat. No. 4,331,647, and references contained therein; Nisonhoff et al., Arch. Biochem. Biophys. 89:230, 1960; Porter, Biochem. J. 73:119, 1959; Edelman et al., Methods in Enzymology , Vol. 1, page 422, Academic Press, 1967; and Coligan et al. at sections 2.8.1-2.8.10 and 2.10.1-2.10.4).

Other methods of cleaving antibodies, such as separation of heavy chains to form monovalent light-heavy chain fragments, further cleavage of fragments, or other enzymatic, chemical, or genetic techniques may also be used, so long as the fragments bind to the antigen that is recognized by the intact antibody.

One of skill will realize that conservative variants of the antibodies can be produced. Such conservative variants employed in antibody fragments, such as dsFv fragments or in scFv fragments, will retain critical amino acid residues necessary for correct folding and stabilizing between the V H and the V L regions, and will retain the charge characteristics of the residues in order to preserve the low pI and low toxicity of the molecules Amino acid substitutions (such as at most one, at most two, at most three, at most four, or at most five amino acid substitutions) can be made in the V H and the V L regions to increase yield. Conservative amino acid substitution tables providing functionally similar amino acids are well known to one of ordinary skill in the art. The following six groups are examples of amino acids that are considered to be conservative substitutions for one another: 1) Alanine (A), Serine (S), Threonine (T); 2) Aspartic acid (D), Glutamic acid (E); 3) Asparagine (N), Glutamine (Q); 4) Arginine (R), Lysine (K); 5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); and 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W).

In some examples, naked antibodies can be administered at least 5 mg per kg every two weeks, such as at least 10 mg per kg, at least 25 mg per kg, at least 30 mg per kg, at least 50 mg per kg (for example, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50 mg per kg), at least once a week, at least once every 2 weeks, at least once every 3 weeks, or at least once every month depending upon the ovarian cancer. In an example, the antibodies are administered continuously. In another example, antibodies or antibody fragments conjugated to cytotoxic agents (immunotoxins) are administered at least 10 μg per kg, such as at least 20, at least 30, at least 50, at least 70, at least 100 μg per kg, at least twice a week, at least once a week, at least once every two weeks, at least once every month depending upon the ovarian cancer. In one example, 50 μg per kg is administered twice a week for 2 to 3 weeks. In other examples, the subject is administered the therapeutic composition that a binding agent specific for one or more of the disclosed ovarian endothelial cell tumor-associated molecules daily for a period of at least 30 days, such as at least 2 months, at least 4 months, at least 6 months, at least 12 months, at least 24 months, or at least 36 months. Subjects can be monitored by methods known to those skilled in the art to determine ovarian tumor responsiveness to the antibody treatment. The subject can be monitored by non invasive techniques such as CT or MRI imaging to assess tumor response. It is contemplated that additional agents can be administered, such as antineoplastic agents in combination with or following treatment with the antibodies.

Methods of Evaluating the Effectiveness of an Ovarian Tumor Treatment

Methods are disclosed herein for determining the effectiveness of a binding agent specific for one of the disclosed ovarian endothelial cell tumor-associated molecules) for the treatment of an ovarian tumor in a subject with the ovarian tumor. In an example, the method includes detecting expression of an ovarian endothelial cell tumor-associated molecule in a sample from the subject following administration of the binding agent (such as an siRNA), for example at least 24 hours, at least 1 week, at least 2 weeks, or at least 4 weeks following administration of the agent. The expression of the ovarian endothelial cell tumor-associated molecule following administration can be compared to a control, such as a reference value. An alteration in the expression of the ovarian endothelial cell tumor-associated molecule relative to the control following administration indicates that the agent is effective for the treatment of the ovarian cancer in the subject.

In a specific example, the method includes detecting and comparing the protein expression levels of the ovarian endothelial cell tumor-associated molecules. In other examples, the method includes detecting and comparing the mRNA expression levels of the ovarian endothelial cell tumor-associated molecules. In certain examples, the treatment is considered effective if the expression levels are altered by at least 2-fold, such as by at least 3-fold, at least 4-fold, at least 6-fold or at least 10-fold relative to the control.

In one example, the specific ovarian endothelial cell tumor-associated molecule is detected in a biological sample. In a particular example, the biological sample is a tumor biopsy. In another example, the ovarian endothelial cell tumor-associated molecule is detected in a serum sample. For example, the ovarian endothelial cell tumor-associated molecule is detected in a serum sample if the specific molecule is known to be secreted or located on a cell surface susceptible to enzymatic cleavage.

Altering Ovarian Endothelial Cell Tumor-Associated Molecules' Activity Such as Expression

In an example, an alteration in the expression of one or more of the disclosed ovarian endothelial cell tumor-associated molecules following administration includes an increase or decrease in production of a gene product/expression, such as RNA or protein. For example, an alteration can include processes that downregulate or decrease transcription of a gene or translation of mRNA whose expression or activity is increased in ovarian endothelial tumor cells. Gene downregulation includes any detectable decrease in the production of a gene product. In certain examples, production/expression of a gene product decreases by at least 2-fold, for example at least 3-fold, at least 4-fold, at least 6-fold, or at least 10-fold as compared to a control. Exemplary ovarian endothelial cell tumor-associated molecules that are up-regulated in ovarian tumor endothelial cells are presented in Tables 1, 2, 4 and 5. Thus, a decrease in the expression of one or more of the molecules listed in Tables 1, 2, 4 or 5 that is noted as being up-regulated in ovarian tumor endothelial cells following treatment indicates that the agent is of use for treating the ovarian cancer.

Exemplary ovarian endothelial cell tumor-associated molecules that are down-regulated in ovarian tumor endothelial cells are presented in Table 1 with specific examples provided in Table 3. Thus, an increase in the expression of one or more of the molecules listed in Table 3 following administration indicates that the agent is effective for the treatment of ovarian cancer.

In another example, an alteration can include processes that increase transcription of a gene or translation of mRNA. Gene up-regulation includes any detectable increase in the production of a gene product. In certain examples, production/expression of a gene product increases by at least 2-fold, for example at least 3-fold or at least 4-fold, at least 6-fold, at least 10-fold or at least 28-fold following treatment as compared to a control.

Detection of Ovarian Endothelial Cell Tumor-Associated Nucleic Acids

Nucleic acids can be detected by any method known in the art. In some examples, nucleic acids are isolated, amplified, or both, prior to detection. In an example, the biological sample can be incubated with primers that permit the amplification of one or more of the disclosed ovarian endothelial cell tumor-associated mRNAs, under conditions sufficient to permit amplification of such products. For example, the biological sample is incubated with probes that can bind to one or more of the disclosed ovarian endothelial cell tumor-associated nucleic acid sequences (such as cDNA, genomic DNA, or RNA (such as mRNA)) under high stringency conditions. The resulting hybridization can then be detected using methods known in the art. In one example, the effectiveness of an ovarian tumor treatment is identified by applying isolated nucleic acid molecules to an array in which the isolated nucleic acid molecules are obtained from a biological sample including ovarian endothelial cancer cells following treatment with the ovarian tumor treatment. In such example, the array includes oligonucleotides complementary to all ovarian endothelial cell tumor-associated genes listed in Table 1. In a particular example, the array is a commercially available array such as a U133 Plus 2.0 oligonucleotide array from AFFYMETRIX® (AFFYMETRIX®, Santa Clara, Calif.).

In an example, the isolated nucleic acid molecules are incubated with the array including oligonucleotides complementary to the ovarian endothelial cell tumor-associated molecules that are up-regulated in ovarian tumor endothelial cells, such as those listed in Table 2, Table 3, Table 4 and/or Table 5 for a time sufficient to allow hybridization between the isolated nucleic acid molecules and oligonucleotide probes, thereby forming isolated nucleic acid molecule:oligonucleotide complexes. The isolated nucleic acid molecule:oligonucleotide complexes are then analyzed to determine if expression of the isolated nucleic acid molecules is altered. In such example, an ovarian tumor treatment is effective if a decrease in the expression of ovarian endothelial tumor-associated molecules is observed as compared to a control (such as a normal endothelial cell) or reference value. In an additional example, the array includes oligonucleotides complementary to the ovarian endothelial cell tumor-associated molecules that down-regulated in ovarian tumor endothelial cells, such as those listed in Table 3. In this example, an ovarian tumor treatment is effective if an increase in the expression of one or more ovarian endothelial tumor-associated molecules is observed.

Gene Expression Profile

A gene expression profile is disclosed herein that can be used to identify the effectiveness of an ovarian tumor treatment. In an example, the gene expression profile includes at least two of the ovarian endothelial cell tumor-associated molecules listed in Table 1, such as at least 5, at least 7, at least 10, at least 20, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 600, at least 700, at least 800, at least 900, at least 1000, or at least 1100 molecules (for example, 2, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 120, 130, 140, 150, 175, 225, 275, 325, 350, 375, 450, 550, 650, 750, 850, 950, 1050 or 1149 of those listed).

In a particular example, the gene expression profile includes at least 2, at least 5, at least 7, at least 10, at least 20, at least 25, at least 27 molecules (for example, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 24, 25, 26, 27, 28 or 29 molecules) listed in Table 2, Table 4 and/or Table 5 that are associated with an at least six-fold increase in expression in tumor endothelial cells. In a particular example, the at least two molecules include EGFL6 and TNFAIP6. In other particular examples, the at least two ovarian endothelial cell tumor-associated molecules include EGFL6, TNFAIP6, TWIST1, STC1, HOP, CSPG2, and PLXDC1.

In other particular examples, the gene expression profile includes at least 2, at least 5, at least 7, at least 10, at least 13, or at least 15 molecules (for example, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 or 17 molecules) that are down-regulated in ovarian tumor endothelial cells as listed in Table 3. For example, the profile includes the seventeen ovarian endothelial cell tumor-associated molecules listed in Table 3.

Detecting Ovarian Endothelial Cell Tumor-Associated Proteins

As an alternative to analyzing the sample for the presence of nucleic acids, the presence of proteins can be determined. Proteins can be detected by any method known in the art. In some examples, proteins are purified prior to detection. For example, the effect of an ovarian tumor treatment can be determined by incubating the biological sample with one or more antibodies that specifically binds to one of the disclosed ovarian endothelial cell tumor-associated proteins encoded by the genes listed in Tables 1, Table 2, Table 3, Table 4 or Table 5 to detect expression. The primary antibody can include a detectable label. For example, the primary antibody can be directly labeled, or the sample can be subsequently incubated with a secondary antibody that is labeled (for example with a fluorescent label). The label can then be detected, for example by microscopy, ELISA, flow cytometry, or spectrophotometry. In another example, the biological sample is analyzed by Western blotting for the presence or absence of the specific ovarian endothelial cell tumor-associated molecule. In other examples, the biological sample is analyzed by mass spectrometry for the presence or absence of the specific ovarian endothelial cell tumor-associated molecule.

In one example, the antibody that specifically binds an ovarian endothelial cell tumor-associated molecule (such as those listed in Table 1) is directly labeled with a detectable label. In another example, each antibody that specifically binds an ovarian endothelial cell tumor-associated molecule (the first antibody) is unlabeled and a second antibody or other molecule that can bind the human antibody that specifically binds the respective ovarian endothelial cell tumor-associated molecule is labeled. As is well known to one of skill in the art, a second antibody is chosen that is able to specifically bind the specific species and class of the first antibody. For example, if the first antibody is a human IgG, then the secondary antibody can be an anti-human-IgG. Other molecules that can bind to antibodies include, without limitation, Protein A and Protein G, both of which are available commercially.

Suitable labels for the antibody or secondary antibody include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, magnetic agents and radioactive materials. Non-limiting examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, beta-galactosidase, or acetylcholinesterase. Non-limiting examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin. Non-limiting examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin A non-limiting exemplary luminescent material is luminol; a non-limiting exemplary magnetic agent is gadolinium, and non-limiting exemplary radioactive labels include 125 I, 131 I, 35 S or 3 H.

In an alternative example, ovarian endothelial cell tumor-associated molecules can be assayed in a biological sample by a competition immunoassay utilizing ovarian endothelial cell tumor-associated molecule standards labeled with a detectable substance and unlabeled antibody that specifically bind to the desired ovarian endothelial cell tumor-associated molecule. In this assay, the biological sample (such as serum, tissue biopsy, or cells isolated from a tissue biopsy), the labeled ovarian endothelial cell tumor-associated molecule standards and the antibody that specifically binds to ovarian endothelial cell tumor-associated molecule are combined and the amount of labeled ovarian endothelial cell tumor-associated molecule standard bound to the unlabeled antibody is determined. The amount of ovarian endothelial cell tumor-associated molecule in the biological sample is inversely proportional to the amount of labeled ovarian endothelial cell tumor-associated molecule standard bound to the antibody that specifically binds the ovarian endothelial cell tumor-associated molecule.

Identifying Agents to Treat Ovarian Cancer

Methods are provided herein for identifying agents to treat an ovarian cancer. For example, agents that decrease expression or activity of a gene that is upregulated in ovarian endothelial tumor cells (such as those listed in Tables 2 and 4), as well as agents that increase activity of a gene that is downregulated in ovarian endothelial tumor cells (such as those listed in Table 3), can be identified using these methods. In an example, the method includes contacting an ovarian tumor endothelial cell with one or more test agents under conditions sufficient for the one or more test agents to alter the activity of at least one ovarian endothelial cell tumor-associated molecule listed in any of Tables 1-5. It is contemplated that several doses of the agent can be tested and then expression levels of nucleic acids or proteins can be determined. The method also includes detecting the activity or expression of the at least one ovarian endothelial cell tumor-associated molecule in the presence and absence of the one or more test agents. The activity or expression of the at least one ovarian endothelial cell tumor-associated molecule in the presence of the one or more test agents is then compared to the activity or expression of the at least one ovarian endothelial cell tumor-associated molecule in the absence of such agents to determine if there is differential expression of the at least one ovarian endothelial cell tumor associated molecule. In several examples, differential expression of the ovarian endothelial cell tumor-associated molecule in the presence of the agent (as compared to expression in the absence of the agent) indicates that the one or more test agents is of use to treat the ovarian tumor.

In an example, determining whether there is differential expression of one or more ovarian endothelial cell tumor-associated molecules includes generating a gene expression profile for the subject. For example, a gene expression profile for the subject can be generated by using an array of molecules including an ovarian endothelial cell tumor-associated expression profile.

Ovarian Endothelial Cell Tumor-Associated Molecules

Ovarian endothelial cell tumor-associated molecules can include nucleic acid sequences (such as DNA, cDNA, or mRNAs) and proteins. In a specific example, detecting differential expression of the ovarian endothelial cell tumor-associated molecules includes detecting differential mRNA expression of the disclosed ovarian endothelial cell tumor-associated molecules. For example, such differential expression can be measured by real time quantitative polymerase chain reaction or microarray analysis or other methods known in the art. In another example, detecting differential expression of the ovarian endothelial cell tumor-associated molecules includes detecting differential protein expression of the disclosed ovarian endothelial cell tumor-associated molecules. For example, protein differential expression is measured by Western blot analysis or a protein microarray.

The one or more test agents can be any substance, including, but not limited to, a protein (such as an antibody), a nucleic acid molecule (such as a siRNA), an organic compound, an inorganic compound, a small molecule or any other molecule of interest. In a particular example, the test agent is a siRNA that reduces or inhibits the activity (such as the expression) of one of the ovarian endothelial cell tumor-associated molecules listed in Tables 2, 4 or 5. For example, the siRNA is directed to an ovarian endothelial cell tumor-associated molecule listed in Table 2, 4 or 5 which is involved in angiogenesis, such as a molecule that is involved in at least one of cell proliferation, tube formation or cell motility.

In other examples, the test agent is an antibody. For example, the antibody is directed to specifically bind to an ovarian endothelial cell tumor-associated protein encoded by one of the genes listed in any of Tables 1, 2, 4 or 5 that are upregulated in ovarian endothelial tumor cells. In a particular example, the antibody is directed to an ovarian endothelial cell tumor-associated protein encoded by one of the genes listed in Tables 2, 4 or 5 that is upregulated in ovarian endothelial tumor cells and which is involved in angiogenesis, such as a gene that is involved in at least one of cell proliferation, tube formation or cell motility. In another example, the test agent is a nucleic acid encoding one or more of the proteins listed in Table 3. For example, the nucleic acid can be part of a vector suitable for gene therapy.

Altering Ovarian Endothelial Cell Tumor-Associated Molecules' Activity

In an example, an alteration in the activity of one or more of the disclosed ovarian endothelial cell tumor-associated molecules includes an increase or decrease in production of a gene product, such as RNA or protein. For example, an alteration can include processes that downregulate or decrease transcription of a gene or translation of mRNA. Gene downregulation includes any detectable decrease in the production of a gene product. In certain examples, production/expression of a gene product decreases by at least 2-fold, for example at least 3-fold, at least 4-fold, at least 6-fold, or at least 10-fold as compared to a control (such as a reference value or a normal endothelial cell). For example, a decrease in one or more of the disclosed ovarian endothelial cell tumor-associated molecules up-regulated in ovarian tumor endothelial cells (such as those listed in Tables 2, 4 and 5), is indicative of an agent that is effective at treating ovarian cancer.

In another example, an alteration can include processes that increase transcription of a gene or translation of mRNA. Gene up-regulation includes any detectable increase in the production of a gene product. In certain examples, production/expression of a gene product increases by at least 2-fold, for example at least 3-fold or at least 4-fold, at least 6-fold, at least 10-fold or at least 28-fold as compared to a control. For example, an increase in one or more of the disclosed ovarian endothelial cell tumor-associated molecules down-regulated in ovarian tumor endothelial cells (such as those listed in Table 3) is indicative of an agent that is effective at treating ovarian cancer.

Detection of Ovarian Endothelial Cell Tumor-Associated Nucleic Acids

Nucleic acids can be detected by any method known in the art, such as those described above. In one example, a therapeutic agent is identified by applying isolated nucleic acid molecules to an array in which the isolated nucleic acid molecules are obtained from a biological sample including ovarian endothelial cancer cells following treatment with the one or more test agents. In such example, the array includes oligonucleotides complementary to all ovarian endothelial cell tumor-associated genes listed in Table 1. In a particular example, the array is a commercially available array such as a U133 Plus 2.0 oligonucleotide array from AFFYMETRIX® (AFFYMETRIX®, Santa Clara, Calif.).

In an example, the isolated nucleic acid molecules are incubated with the array including oligonucleotides complementary to the ovarian endothelial cell tumor-associated molecules listed in Table 2, 4 and/or 5 for a time sufficient to allow hybridization between the isolated nucleic acid molecules and oligonucleotide probes, thereby forming isolated nucleic acid molecule:oligonucleotide complexes. The isolated nucleic acid molecule:oligonucleotide complexes are then analyzed to determine if expression of the isolated nucleic acid molecules is altered. In such example, an agent is considered is effective if the test agent decreases expression of ovarian endothelial tumor-associated molecules upregulated in ovarian endothelial cell tumors relative to the absence of the agent (such as a decrease of at least 2-, 3-, 4-, 5- or 10-fold). Similarly, an agent is considered is effective if the test agent increases expression of ovarian endothelial tumor-associated molecules downregulated in ovarian endothelial cell tumors relative to the absence of the agent (such as an increase of at least 2-, 3-, 4-, 5- or 10-fold).

Gene Expression Profile

The disclosed gene profile (as described above) can also be used to identify agents to treat an ovarian tumor, such as a cancer, in a subject. In an example, the gene expression profile includes at least two of the ovarian endothelial cell tumor-associated molecules listed in Table 1, such as at least 5, at least 7, at least 10, at least 20, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 600, at least 700, at least 800, at least 900, at least 1000, or at least 1100 molecules (for example, 2, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 120, 130, 140, 150, 175, 225, 275, 325, 350, 375, 450, 550, 650, 750, 850, 950, 1050 or 1149 of those listed).

In a particular example, the gene expression profile includes at least 2, at least 5, at least 7, at least 10, at least 20, at least 25, or at least 27 molecules (for example, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 24, 25, 26, 27, 28 or 29 molecules) listed in Table 2, 4 and/or 5 that are associated with an at least six-fold increase in expression in tumor endothelial cells. In a particular example, the at least two molecules include EGFL6 and TNFAIP6. In other particular examples, the at least two ovarian endothelial cell tumor-associated molecules include EGFL6, TNFAIP6, TWIST1, STC1, HOP, CSPG2, and PLXDC1.

In other particular examples, the gene expression profile includes at least 2, at least 5, at least 7, at least 10, at least 13, or at least 15 molecules (for example, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 or 17 molecules) that are down-regulated in ovarian tumor endothelial cells as listed in Table 3. For example, the profile includes the seventeen ovarian endothelial cell tumor-associated molecules listed in Table 3.

Detecting Ovarian Endothelial Cell Tumor-Associated Proteins

As an alternative to analyzing the sample for the presence of nucleic acids, the presence of proteins can be determined using any method known in the art. In some examples, proteins are purified before detection. For example, the effect of one or more test agents on an ovarian tumor can be determined by incubating the biological sample with an antibody that specifically binds to one of the disclosed ovarian endothelial cell tumor-associated proteins encoded by the genes listed in Tables 1-5. The primary antibody can include a detectable label. For example, the primary antibody can be directly labeled, or the sample can be subsequently incubated with a secondary antibody that is labeled (for example with a fluorescent label). The label can then be detected, for example by microscopy, ELISA, flow cytometry, or spectrophotometry. In another example, the biological sample is analyzed by Western blotting for the presence or absence of the specific ovarian endothelial cell tumor-associated molecule. In some examples, the biological sample is analyzed by mass spectrometry.

In one example, the antibody that specifically binds an ovarian endothelial cell tumor-associated molecule (such as those listed in Table 1) is directly labeled with a detectable label. In another example, each antibody that specifically binds an ovarian endothelial cell tumor-associated molecule (the first antibody) is unlabeled and a second antibody or other molecule that can bind the human antibody that specifically binds the respective ovarian endothelial cell tumor-associated molecule is labeled. As is well known to one of skill in the art, a second antibody is chosen that is able to specifically bind the specific species and class of the first antibody. For example, if the first antibody is a human IgG, then the secondary antibody can be an anti-human-IgG. Other molecules that can bind to antibodies include, without limitation, Protein A and Protein G, both of which are available commercially.

Suitable labels for the antibody or secondary antibody include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, magnetic agents and radioactive materials. Non-limiting examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, beta-galactosidase, or acetylcholinesterase. Non-limiting examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin. Non-limiting examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin A non-limiting exemplary luminescent material is luminol; a non-limiting exemplary magnetic agent is gadolinium, and non-limiting exemplary radioactive labels include 125 I, 131 I, 35 S or 3 H.

In an alternative example, ovarian endothelial cell tumor-associated molecules can be assayed in a biological sample by a competition immunoassay utilizing ovarian endothelial cell tumor-associated molecule standards labeled with a detectable substance and an unlabeled antibody that specifically binds the desired ovarian endothelial cell tumor-associated molecule. In this assay, the biological sample (such as serum, tissue biopsy, or cells isolated from a tissue biopsy), the labeled ovarian endothelial cell tumor-associated molecule standards and the antibody that specifically binds the desired ovarian endothelial cell tumor-associated molecule are combined and the amount of labeled ovarian endothelial cell tumor-associated molecule standard bound to the unlabeled antibody is determined. The amount of ovarian endothelial cell tumor-associated molecule in the biological sample is inversely proportional to the amount of labeled ovarian endothelial cell tumor-associated molecule standard bound to the antibody that specifically binds the ovarian endothelial cell tumor-associated molecule.

Methods of Diagnosing and Prognosing an Ovarian Tumor

Metastasis is a major complication in the pathogenesis of tumors, such as ovarian cancer, and is typically indicative of poor prognosis. It is also known that angiogenesis is a crucial factor in the progression of solid tumors and metastases, including ovarian cancer. The formation of the vascular stroma plays an important role in the pathophysiology of malignancy. For instance, in the absence of vascular support tumors may become necrotic, or even apoptotic. In contrast, the onset of angiogenesis marks a phase of rapid proliferation, local invasion, and ultimately metastasis.

Without wishing to be bound to a particular theory, it is proposed that an alteration in the expression of the disclosed ovarian endothelial tumor-associated molecules associated with angiogenesis, such as molecules involved in cell proliferation, cell motility or tube formation, including those disclosed in FIG. 5 (such as EZH2), is related to enhanced ovarian tumor cell metastasis and a poor clinical outcome. Thus, methods of diagnosing or prognosing an ovarian tumor that overexpresses at least one pro-angiogenic ovarian endothelial cell tumor-associated molecule (such as those listed in Tables 1, 2, 4 and 5 that are upregulated in ovarian endothelial tumor cells; e.g., EZH2) or underexpresses at least one proangiogenic ovarian endothelial cell tumor associated molecule (such as those listed in Tables 1 and 3 that are downregulated in ovarian endothelial tumor cells), are disclosed. In some examples, such methods can be used to identify those subjects that will benefit from the disclosed treatment methods. For example, such diagnostic methods can be performed prior to the subject undergoing the treatments described above. In other examples, these methods are utilized to predict the metastatic potential of the ovarian cancer, a poor prognosis, or combinations thereof. In one particular example, these methods are utilized to predict a poor prognosis, such as to indicate a decreased survival time.

In an example, the method includes detecting expression of at least one angiogenic ovarian endothelial cell tumor-associated molecule listed in Tables 1-5, such as at least two, at least 5, at least 7, at least 10, at least 20, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200 ovarian endothelial cell tumor-associated molecules related to angiogenesis (for example, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 15, 17, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 100, 125, 150, 175, 200, or 250 listed in Tables 1-5) in a sample from the subject exhibiting one or more symptoms associated with ovarian cancer.

In an example, the specific angiogenic ovarian endothelial cell tumor-associated molecule, such as EZH2, is detected in a biological sample. In a particular example, the biological sample is a sample taken from a subject with ovarian epithelial cancer. In a particular example, the biological sample is a tumor biopsy. In another example, the angiogenic ovarian endothelial cell tumor-associated molecule is detected in a serum sample. For example, the ovarian endothelial cell tumor-associated molecule is detected in a serum sample if the specific molecule is secreted or located on a cell surface susceptible to enzymatic cleavage.

In one example, detection of at least one angiogenic ovarian endothelial cell tumor-associated molecule listed in any of Tables 1, 2, 3, 4 or 5, such as detection of EZH2, in a biological sample from the subject is used to diagnose or prognose an ovarian tumor. Methods of detecting such molecules in a sample are known in the art and are routine. In some examples, the relative amount of pro-angiogenic ovarian endothelial cell tumor-associated molecules present is determined, for example by quantitating the expression level of such molecules. For example, the relative or absolute quantity of the at least one angiogenic ovarian endothelial cell tumor-associated molecule in a sample can be determined.

The activity such as the expression level of the disclosed pro-angiogenic ovarian endothelial cell tumor-associated molecules in a sample obtained from a subject is compared to a control. In one example, an increase in expression of one or more of the angiogenic ovarian endothelial cell tumor-associated molecules upregulated in ovarian tumor endothelial cells (such as those listed in Table 2) as compared to a non-tumor control or reference value indicates the presence of an ovarian tumor, the ovarian tumor is metastatic, the ovarian tumor is likely to become metastatic, a poor prognosis or a combination thereof. In some examples, a decrease in expression of one or more of the angiogenic ovarian endothelial cell tumor-associated molecules that is downregulated in ovarian tumor endothelial cells (such as those listed in Table 3 or VASH1) as compared to a non-tumor control or reference value indicates the presence of an ovarian tumor, the ovarian tumor is metastatic, the ovarian tumor is likely to become metastatic, a poor prognosis or a combination thereof.

For example, the level of the angiogenic ovarian endothelial cell tumor-associated molecules, such as the level of EZH2, detected can be compared to a non-tumor control or reference value, such as a value that represents a level of angiogenic ovarian endothelial cell tumor-associated molecules expected if an ovarian tumor is or is not metastatic or is a low grade tumor or early stage tumor. In one example, the angiogenic ovarian endothelial cell tumor-associated molecules detected in a tumor sample are compared to the level of such molecules detected in a sample obtained from a subject that does not have an ovarian tumor or has a non-metastatic ovarian tumor. In certain examples, detection of at least a 2-fold, such as by at least 3-fold, at least 4-fold, at least 6-fold or at least 10-fold alteration in the relative amount of the pro-angiogenic ovarian endothelial cell tumor-associated molecules in a tumor sample, as compared to the relative amount of such molecules in a control indicates that the subject has a tumor with metastatic potential, has a tumor that has metastasized, has a poor prognosis, or combinations thereof. In some examples, detection of statistically similar relative amounts of pro-angiogenic ovarian endothelial cell tumor-associated molecules observed in a tumor sample, as compared to the relative amount of such molecules in a control sample that is not metastatic, indicates that that subject does not have a tumor with metastatic potential, does not have a tumor that has metastasized, has a good prognosis, or combinations thereof.

In a specific example, the method includes detecting and comparing the nucleic acid expression levels of the pro-angiogenic ovarian endothelial cell tumor-associated molecules such as DNA, cDNA, or mRNAs. In a specific example, the method includes detecting and comparing the mRNA expression levels of the pro-angiogenic ovarian endothelial cell tumor-associated molecules. For example, such expression can be measured by real time quantitative polymerase chain reaction or microarray analysis. In a particular example, the disclosed gene expression profile is utilized to diagnosis and/or prognosis an ovarian tumor.

Detection of Ovarian Endothelial Cell Tumor-Associated Nucleic Acids

Nucleic acids can be detected by any method known in the art. In some examples, nucleic acids are isolated, amplified, or both, prior to detection. In an example, the biological sample can be incubated with primers that permit the amplification of one or more of the disclosed ovarian endothelial cell tumor-associated mRNAs, under conditions sufficient to permit amplification of such products. For example, the biological sample is incubated with probes that can bind to one or more of the disclosed ovarian endothelial cell tumor-associated nucleic acid sequences (such as cDNA, genomic DNA, or RNA (such as mRNA)) under high stringency conditions. The resulting hybridization can then be detected using methods known in the art. In one example, a therapeutic agent is identified by applying isolated nucleic acid molecules to an array in which the isolated nucleic acid molecules are obtained from a biological sample including ovarian endothelial cancer cells for example following treatment with the one or more test agents. In such example, the array includes oligonucleotides complementary to all ovarian endothelial cell tumor-associated genes listed in Table 1. In a particular example, the array is a commercially available array such as a U133 Plus 2.0 oligonucleotide array from AFFYMETRIX® (AFFYMETRIX®, Santa Clara, Calif.).

In an example, the isolated nucleic acid molecules are incubated with the array including oligonucleotides complementary to the ovarian endothelial cell tumor-associated molecules listed in Tables 2, 3, 4 and/or 5 for a time sufficient to allow hybridization between the isolated nucleic acid molecules and oligonucleotide probes, thereby forming isolated nucleic acid molecule:oligonucleotide complexes. In a particular example, the isolated nucleic acid molecules are incubated with the array including oligonucleotides complementary to at least EZH2. The isolated nucleic acid molecule:oligonucleotide complexes are then analyzed to determine if expression of the isolated nucleic acid molecules is altered.

Gene Expression Profile

The disclosed gene profile (as described above) can also be used in the diagnosis and prognosis of an ovarian tumor in a subject. In an example, the gene expression profile includes at least two of the ovarian endothelial cell tumor-associated molecules listed in Table 1, such as at least 5, at least 7, at least 10, at least 20, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400, at least 500, at least 600, at least 700, at least 800, at least 900, at least 1000, or at least 1100 molecules (for example, 2, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 120, 130, 140, 150, 175, 225, 275, 325, 350, 375, 450, 550, 650, 750, 850, 950, 1050 or 1149 of those listed).

In a particular example, the gene expression profile includes at least 1, at least 3, at least 5, at least 7, at least 10, at least 20, at least 25, or at least 27 molecules (for example, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 24, 25, 26, 27, 28 or 29 molecules) listed in Table 2, 4 and/or 5 that are associated with angiogenesis, such as molecules involved in cell proliferation, cell motility and/or tube formation. In a particular example, the at least one molecule includes EZH2

In other particular examples, the gene expression profile includes at least 2, at least 5, at least 7, at least 10, at least 13, or at least 15 molecules (for example, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 or 17 molecules) that are down-regulated in ovarian tumor endothelial cells as listed in Table 3. For example, the profile includes the seventeen ovarian endothelial cell tumor-associated molecules listed in Table 3.

Detecting Ovarian Endothelial Cell Tumor-Associated Proteins

As an alternative to analyzing the sample for the presence of nucleic acids, alterations in protein expression can be measured by methods known in the art such as Western blot analysis, mass spectrometry, immunoassay or a protein microarray (as described above). For example, the metastatic potential of an ovarian tumor can be determined by using a protein array that includes one or more capture agents, such as antibodies that are specific for the one or more disclosed ovarian endothelial tumor-associated molecules that are related to angiogenesis, such as molecules that play a role in cell proliferation, cell motility or tube formation, such as EZH2.

The disclosure is further illustrated by the following non-limiting Examples.

The present results provide a new understanding of the regulation of tumor angiogenesis. A novel mechanism by which VEGF increases EZH2 levels in the tumor vasculature was disclosed, which contributes to tumor angiogenesis by inactivating the anti-angiogenic factor, VASH1 via methylation of VASH1 gene and Histone 3 (Lys 27) (H3K27). Moreover, a novel and highly efficient method of gene silencing in the tumor cells as well as in the blood vessels that support their growth was developed and characterized. This approach was highly effective for EZH2 silencing in both compartments.

PcG proteins play a role in determining cell fate during both normal and pathologic processes. Two separate subsets of PcG complexes (PRC1 and PRC2) have been described in humans. PRC1 may be involved in maintenance of repression, whereas PRC2 plays a role in initiating repression. The PRC2 complex includes the EZH2, EED, and SUZ proteins. Altered expression of these proteins has been implicated in cancer pathogenesis. Increased EZH2 levels have been related to cancer cell proliferation and invasion. However, prior to the disclosed work, the role of EZH2 in angiogenesis was not known.

Angiogenesis is regulated by the balance of various pro-angiogenic stimulators, such as VEGF, and several angiogenesis inhibitors, such as angiostatin, endostatin, and antithrombin. On the basis of findings from genomic profiling of endothelial cells from ovarian cancer versus those from normal ovaries, it was discovered that EZH2 expression is significantly increased in tumor-associated endothelial cells. VEGF is well recognized as a pro-angiogenic factor in ovarian and other cancers. In the current study, it was shown for the first time that VEGF can directly increase EZH2 levels in endothelial cells, which in turn inactivating a potent anti-angiogenic factor, VASH1, via methylating VASH1 gene and H3K27. Silencing EZH2 gene resulted in demethylation of VASH1 gene and H3K27 in endothelial cells, which is consistent with other report indicating EZH2 directly controls DNA methylation of EZH2-targeted genes, concomitant with reducing H3K27. Therefore, through this study, a novel mechanism by which tumor angiogenesis is regulated was discovered and a rationale for pursuing EZH2 as a therapeutic target was provided.

While a number of attractive targets in tumor and endothelial cells have been identified, many of these are difficult to target with small molecule inhibitors and monoclonal antibodies. Therefore, RNA interference was employed as a means to target EZH2. Due to limited delivery of siRNA into the tumor-associated endothelial cells with this approach, additional nanoparticles were developed that would allow siRNA delivery into both tumor and tumor-associated endothelial cells. Chitosan (CH) is a naturally occurring polysaccharide with low immunogenicity and low toxicity. Here, CH was used because of its advantageous biological properties such as biodegradability, biocompatibility, and slight positive charge. These properties make use of CH for systemic in vivo siRNA delivery highly attractive. Indeed, the disclosed data demonstrate highly efficient delivery of siRNA incorporated into CH nanoparticles into both tumor and tumor-associated endothelial cells. Therefore, the present work provides an attractive method for systemic delivery of siRNA that could be developed for clinical applications.

Molecular and genetic manipulations have identified EZH2 as a key regulator of tumor angiogenesis here, but these effects do not rule out the possibility that EZH2 has oncogenic functions in the tumor cells. For example, EZH2 has been implicated in cellular transformation, proliferation, and avoidance of apoptosis. Such results imply that multiple signaling pathways likely convey the net effects of EZH2 in promoting tumor growth. However, to the extent that targeting tumor endothelial cells provides therapeutic benefit, interfering with EZH2 in the tumor and endothelial cells represents a novel strategy for treatment of ovarian and other cancers.

In summary, these studies illustrate that increased EZH2 expression in either tumor cells or in tumor vasculature is predictive of poor clinical outcome. The increase in endothelial EZH2 is a direct result of VEGF stimulation and indicates the presence of a paracrine circuit that promotes angiogenesis by methylating (histone H3; lysine 27) and silencing VASH1 EZH2 silencing in tumor cells and in the tumor-associated endothelial cells resulted in inhibition of angiogenesis and ovarian cancer growth. The anti-angiogenic effect was mediated by reactivating VASH1. Thus, these data support the potential for targeting EZH2 as a novel therapeutic approach