REFERENCE TO A SEQUENCE LISTING SUBMITTED AS A TEXT FILE VIA EFS-WEB

The official copy of the sequence listing is submitted concurrently with the specification as a text file via EFS-Web, in compliance with the American Standard Code for Information Interchange (ASCII), with a file name of 386567SEQLIST.txt, a creation date of March 4, 2010, and a size of 7.56 KB. The sequence listing filed via EFS-Web is part of the specification and is hereby incorporated in its entirety by reference herein.

FIELD OF THE INVENTION The invention relates to monoclonal antibodies capable of binding to matrix metalloproteinase-7 protein (MMP-7) and methods of using these antibodies, particularly in methods for diagnosing ovarian cancer and for identifying patients with an increased likelihood of having ovarian cancer. Hybridoma cell lines that produce these monoclonal antibodies are further disclosed.

BACKGROUND OF THE INVENTION

Ovarian cancer represents a heterogeneous group of diseases that affect women on a global basis. There are several forms of ovarian cancer which include epithelial cancer, germ- line cancer of the ovaries and ovarian stromal cancer. Epithelial ovarian cancer represents the most common form of the disease. Approximately 5-10% of epithelial ovarian cancer represents a hereditary form of the disease and three common patterns are recognized: ovarian cancer alone; ovarian and breast cancer linked to BRCAl and BRC A2 genetic linkage on chromosomes 17q21 and 13ql2 respectively; and ovarian and colon cancer. The most important risk factor for ovarian cancer is a first degree relative with the disease (e.g., a mother, sister or daughter with ovarian cancer). See, for example, Patridge et al. (1999) CA-A Cancer Journal for Clinicians 49:297-320. In 2005, there were an estimated 22,000 new cases of ovarian cancer diagnoses and 16,000 deaths from ovarian cancer. Ovarian cancer is the fifth leading cause of death of women and the leading cause of death from gynecological cancers. See generally American Cancer Society website cancer.org available on the world wide web; National Cancer Institute website cancer.gov available on the world wide web. Ovarian cancer is a disease that primarily affects post-menopausal women with the median age for diagnosis at 63 years of age. However, the disease can affect women of all age groups. See generally National Cancer Institute Surveillance, Epidemiology, and End Results (SEER) Program website seer.cancer.gov available on the world wide web.

The classification of ovarian cancer stage is based upon the extent of localization versus spread of the disease beyond the ovaries. Stage 1 ovarian cancer is confined to one or both of the ovaries. Stage 2 disease involves a tumor in one or both ovaries with pelvic extension. In Stage 3 ovarian cancer, a tumor is present in one or both ovaries with microscopically confirmed peritoneal metastasis outside the pelvis and/or regional lymph node metastasis. Stage 4 ovarian cancer is characterized by distant metastasis beyond the peritoneal cavity. Ovarian cancer is generally diagnosed in an advance stage of the disease due to the lack of specific clinical symptoms that would indicate the presence of small tumors. For women under the age of 50, less than 40% of ovarian cancers are detected when tumors are localized to one or both ovaries and when disease prognosis is best. For women over the age of 50, that number drops to less than 15%. Approximately 68% of women of all age groups afflicted with ovarian cancer are not diagnosed until distant metastasis is present. See generally National Cancer Institute Surveillance, Epidemiology, and End Results (SEER) Program website seer.cancer.gov available on the world wide web.

Ovarian cancer spreads via local shedding from the ovarian epithelium into the peritoneal cavity followed by implantation on the peritoneum and local invasion of the bowel and bladder. The presence of lymph node involvement in ovarian cancer is evident in all stages of diagnosed ovarian cancer. The percentage of positive lymph nodes increases significantly with progression of the disease (i.e., Stage 1, 24%; Stage 2, 50%, Stage 3, 74%; Stage 4, 73%). Id. The survival of patients with ovarian cancer is a function of the stage at which the disease is diagnosed, with the 5-year survival rate decreasing with advanced disease. More than 90% of women diagnosed with ovarian cancer in Stage 1 survive for at least 5 years following diagnosis. The 5-year survival rate drops to less than 30% when the disease is not diagnosed until Stage 4 (i.e., distant metastasis). Id.

Epithelial ovarian cancer is the most common form of the disease. There are four recognized major histological classes of epithelial ovarian cancer and these include serous, endometrioid, clear cell, and mucinous subtypes. The pathogenesis of ovarian cancer is poorly understood but it is believed to arise from ovarian surface epithelium. See Bell (2005) Mod. PatholΛS (Suppl. 2):S19-32. Life factors that provide the greatest reduction in risk of ovarian cancer include multiparity, use of oral contraceptives, and breast feeding, all of which prevent ovulation. Because ovulation results in epithelial damage, followed by repair and possible inflammatory responses, repetition of this process throughout a woman's reproductive life without interruption appears to lead to cell damage and to increase the risk of ovarian cancer. See, for example, Ness et al. (1999) J. Natl. Cancer Inst. 91 :1459-1467. However, there is no recognized, stepwise progression of ovarian cancer through defined precursor lesions, such as those recognized for both cervical carcinoma and colon cancer. Hence, considerable research has been directed at understanding the molecular basis for ovarian cancer and the basic differences between the various histological subtypes of ovarian cancer. Gene expression analyses have been utilized to provide this understanding and have identified a series of potential biomarkers for evaluation in diagnostic applications. See for example Ono et al. (2000) Cancer Res. 60:5007-11; Welsh et al. (2001) Proc. Natl. Acad. Sci. USA 98:1176-1181; Donninger et al. (2004) Oncogene 23:8065-8077; and Lee et al. (2004) Int. J. Oncol. 24(4):847-851.

Ovarian cancer is often detected with the presentation of overt clinical symptoms, most notably the presentation of abdominal pain, an adnexal mass, abdominal bloating, and urinary urgency. As such, the detection of ovarian cancer is often detected at an advanced stage, where the prognosis and clinical outcome is poor. Detection of ovarian cancer at an early stage (i.e., Stage 1) results in an approximately 90% cure rate using standard surgery and chemotherapy; hence there is a clinical need to detect ovarian cancer at an early stage where treatment will be most effective. Unfortunately, current screening methods to detect early stage ovarian cancer are insufficient. The current practice for ovarian cancer screening employs the use of CA125 and transvaginal ultrasound (sonography). Rising serum levels of CAl 25 are sometimes associated with ovarian cancer and subsequent utilization of transvaginal ultrasound helps detect the presence of ovarian cancer. Confirmation of ovarian disease is based upon invasive procedures such as laparotomy.

CAl 25 serum testing is ineffective for general population screening due to issues of limited sensitivity, limited specificity, and a poor positive predictive value of <3%. Bast (2003) J Clin Oncol. 21(10 Suppl.):200-205. CA125 is a well characterized tumor marker normally expressed on the surface of epithelial cells and is generally detected in the serum of normal patients at 35 U/mL. Elevated serum levels of CAl 25 (>35 U/mL) are detected in approximately 85% of ovarian cancer patients. The remaining 15% of patients suffering from ovarian cancer, however, have normal serum levels of CAl 25. Furthermore, CAl 25 is elevated in only 50% of stage 1 ovarian cancer patients, thereby limiting its clinical utility in the early detection of ovarian cancer. As a result, there is no consensus on the recommendations for generally screening for ovarian cancer in the asymptomatic patient population. See National Cancer Institute website at cancer.gov available on the world wide web. For high risk patients, the generally accepted procedures for the detection of ovarian cancer include the use of pelvic examinations, the use of CAl 25 serum testing, and transvaginal ultrasound (sonography). Patridge et al. (1999) CA-A Cancer Journal for Clinicians 49:297-320.

The low prevalence rates of ovarian cancer in the general population create additional challenges for the development of methods and screening tests that would promote early detection of the disease. Screening methods for diseases with low prevalence rates such as ovarian cancer often result in a high ratio of false positives to true positives, which limits the clinical utility of such screening programs. Given the significant risks associated with surgical exploration for possible ovarian cancer, a clinically useful screening test should refer to surgery no more than 10 women for every woman who actually has ovarian cancer (i.e., a positive predictive value (PPV) of at least 10%). Skates et al. (2004) J. Clin. Oncol. 22:4059-4066. PPV is highly dependent upon the prevalence rates for a particular disease or condition and will shift dramatically as a result of differences in disease prevalence. Therefore, with low-prevalence diseases, such as ovarian cancer, screening diagnostic tests with a relatively low PPV still have significant clinical utility. Potential ovarian cancer screening programs must be adjusted for the low prevalence of ovarian cancer and assessed for biomarker performance and clinical need. See, for example, Skates et al. (2004) J. Clin. Oncol. 22:4059-4066; Bast et al. (2005) Int. J. Gynecol. Cancer 15:274-281; and Rosen et al. (2005) Gyn. Oncol. 99:267-277 '. Despite efforts to identify a biomarker or panel of biomarkers for the detection, particularly early detection, of ovarian cancer, no adequate screening or diagnostic test that satisfies clinical needs currently exists. Currently available methods, such as detection of CAl 25, exhibit unacceptably high false-positive rates.

The current recommendations from the National Cancer Institute state that "there is insufficient evidence to establish that routine screening for ovarian cancer with serum markers such as CAl 25, transvaginal ultrasound or pelvic examinations would result in a decrease in mortality from ovarian cancer" {NCI Summary of Evidence (Level 4, 5); dated February 2005). In light of the serious risk of false-positives with currently available screening techniques, the NCI has not supported the institution of general screening procedures for ovarian cancer. As such, no standardized screening test exists for ovarian cancer, despite the fact that early diagnosis significantly improves 5-year survival rates. As the 5-year survival rate for ovarian cancer depends greatly on the stage of the disease at the time of diagnosis, with increased survival associated with early detection (i.e., Stage 1 or 2), there is a need to identify more ovarian cancers at an earlier stage. The identification and characterization of biomarkers that permit earlier identification of ovarian cancers have the potential to improve the clinical outcome for many patients.

One candidate biomarker for ovarian cancer screening is matrix metalloproteinase- 7 (MMP-7). Matrix metalloproteinases (MMPs) are a family of zinc and calcium dependent endopeptidases with the combined ability to degrade all of the components of the extracellular matrix. MMP-7 (also referred to in the literature as "matrilysin") is expressed in epithelial cells of normal and diseased tissues, and is capable of digesting a large series of proteins located in the extracellular matrix. These include collagen IV and X, gelatin, casein, laminin, aggrecan, entactin, elastin and versican. MMP-7 appears to play a role in the activation of other proteinases such as plasminogen, MMP-I, MMP-2, and MMP9. In addition to its role in connective tissue remodeling, MMP-7 has been shown to be expressed in some malignant tumors and may play an important role in tumor invasion and metastasis. Structurally, MMP-7 is the smallest of the MMPs and consists of two domains: a pro-domain that is cleaved upon activation and a catalytic domain containing the zinc-binding site. Several publications, have shown that the IvIMP proteins, and in particular MMP-7. have been implicated in ovarian and other cancers. Sec, for example, Wang ei «./. (2005) Int. J. Cancer 114(1):19-31; Wang ei «./. (2006) Int. J. Cancer 118(4):879-88; Maurel et ui. (2007) Int. J. Cancer 121(5): 1066-1071; and Sarkissian et al. (2008) Clin. Chem. 54(3): 574-581.

Therefore, a significant need exists in the art for reliable compositions (e.g., monoclonal antibodies) and methods that are capable of specifically identifying women that have ovarian cancer or an increased likelihood of having ovarian cancer. Women identified as having an increased likelihood of having ovarian cancer could be selected for more aggressive diagnostic methods to definitively determine if they presently have the disease. Moreover, such screening methods could be performed in the general female patient population on a routine basis to facilitate the detection of ovarian cancer in the earliest stages of the disease when prognosis and disease outcome are most favorable. Compositions and methods for monitoring efficacy of treatments and potential relapse of ovarian cancer are also needed.

SUMMARY OF THE INVENTION

Compositions and methods for detecting or diagnosing ovarian cancer in a patient or for identifying a patient with an increased likelihood of having ovarian cancer are provided. Compositions include monoclonal antibodies capable of binding to an ovarian cancer biomarker protein of interest, particularly MMP-7. Antigen-binding fragments and variants of the disclosed monoclonal antibodies, hybridoma cell lines capable of producing these antibodies, and kits comprising the monoclonal antibodies of the invention are also described herein.

The compositions of the invention find use in any method involving the detection of MMP-7, particularly methods for diagnosing ovarian cancer or identifying a patient with an increased likelihood of having ovarian cancer. The methods generally comprise detecting expression of at least one biomarker (e.g., MMP-7) in a patient body sample, wherein overexpression of the biomarker or a plurality of biomarkers is indicative of ovarian cancer or an increased likelihood of the patient having ovarian cancer. In particular, the methods comprise using one or more of the antibodies of the invention to detect expression of MMP-7 in a patient body sample. Methods for assessing the efficacy of a particular therapy for ovarian cancer in a patient and for monitoring the regression or progression of ovarian cancer in a patient are also disclosed herein.

The methods for diagnosing ovarian cancer in a patient or identifying a patient with an increased likelihood of having ovarian cancer may comprise, for example, detecting overexpression of MMP-7 protein in a patient body sample via a two-antibody or "sandwich" ELISA (enzyme-linked immunosorbent assay) technique, as described herein. Such screening methods generally comprise detecting in a patient body sample expression of one or a plurality of biomarkers that are selectively overexpressed in ovarian cancer. Overexpression of the one or more biomarkers is indicative of an increased likelihood that the patient has ovarian cancer.

The methods of the invention may comprise, for example, a "two-step" analysis, wherein a first assay step is performed to detect the expression of a first biomarker (e.g., MMP-7) or a panel of biomarkers. If the first biomarker or panel of biomarkers is overexpressed, a second assay step is performed to detect the expression of a second biomarker or panel of biomarkers. Overexpression of the first and second biomarkers or panels of biomarkers is indicative of an increased likelihood that the patient has ovarian cancer. The methods of the invention may utilize the disclosed MMP-7 antibodies to detect expression of MMP-7 in a patient sample. The compositions and methods of the invention may be further utilized in the diagnosis or detection of other types of cancer.

Compositions of the invention further include isolated polypeptides that comprise an epitope capable of binding an MMP-7 monoclonal antibody of the invention. These polypeptides find use in methods for producing MMP-7 antibodies. Isolated nucleic acid molecules encoding the amino acid sequences of the MMP-7 epitopes are also provided.

BRIEF DESCRIPTION OF THE DRAWING

Figure 1 provides a schematic representation of the protein fragments used in the general epitope mapping procedure described in Example 2. Linear expression fragments are generated by an initial PCR followed by sub-cloning into pSCREEN®-GFP. The overlap regions added to the gene of interest during the first PCR have restriction sites to permit cloning. See Example 2 for further experimental details.

DETAILED DESCRIPTION OF THE INVENTION

Compositions and methods for diagnosing ovarian cancer or identifying a patient having an increased likelihood of having ovarian cancer are provided. Compositions include monoclonal antibodies that are capable of binding to the biomarker protein MMP- 7, which is selectively overexpressed in ovarian cancer. By "selectively overexpressed in ovarian cancer" is intended that the biomarker of interest is overexpressed in ovarian cancer but is not overexpressed in conditions classified as nonmalignant, benign, and other conditions that are not considered to be clinical disease. Hybridoma cell lines that produce the monoclonal antibodies of the present invention are also disclosed. Kits comprising the monoclonal antibodies described herein are further provided.

The compositions of the invention include monoclonal antibodies that specifically bind to MMP-7, or to a variant or fragment thereof. The amino acid and nucleotide sequences for MMP-7 are set forth in SEQ ID NO:1 (Accession No. NP 002414.1) and SEQ ID NO:2 (Accession No. NM_002423.3), respectively. In particular embodiments, the MMP-7 monoclonal antibodies designated as 5Gl 1.9 and 15H8.12 are provided. A hybridoma cell line that produces MMP-7 monoclonal antibody 5Gl 1.9 was deposited with the Patent Depository of the American Type Culture Collection (ATCC), Manassas, Virginia, 20110-2209 on January 7, 2009 and assigned Patent Deposit No. PTA-9682. A hybridoma cell line that produces MMP-7 monoclonal antibody 15H8.12 was deposited with the Patent Depository of the American Type Culture Collection (ATCC), Manassas, Virginia, 20110-2209 on January 7, 2009 and assigned Patent Deposit No. PTA-9683. These deposits will be maintained under the terms of the Budapest Treaty on the

International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure. Access to these deposits will be available during the pendency of the application to the Commissioner of Patents and Trademarks and persons determined by the Commissioner to be entitled thereto upon request. Upon allowance of any claims in the application, the Applicants will make available to the public, pursuant to 37 C. F. R. § 1.808, sample(s) of the deposits with the ATCC. This deposit was made merely as a convenience for those of skill in the art and are not an admission that a deposit is required under 35 U.S.C. § 112.

Antibodies that have the binding characteristics of monoclonal antibody 5Gl 1.9 and 15H8.12 are also disclosed herein. Such antibodies include, but are not limited to, antibodies that compete in competitive binding assays with these antibodies, as well as antibodies that bind to an epitope capable of binding MMP-7 monoclonal antibody 5Gl 1.9 or 15H8.12. Methods for assessing whether antibodies have the same or similar binding characteristics include traditional quantitative methods such as, for example, determining and comparing antibody affinity or avidity for the antigen (e.g., MMP-7). See, for example, Roitt et ah, eds. (1989) Immunology (Glower Medical Publishing, London) and Kuby (1992) Immunology (W.H. Freeman and Company, New York). Other exemplary methods for comparing the binding characteristics of antibodies include western blotting, enzyme immunoassays, ELISA, and flow cytometry. Methods for assessing and comparing antibody-antigen binding characteristics are well known in the art. Variants and fragments of monoclonal antibodies 5G11.9 and 15H8.12 that retain the ability to specifically bind to MMP-7 are also provided. Compositions further include hybridoma cell lines that produce the monoclonal antibodies of the present invention and kits comprising at least one monoclonal antibody disclosed herein. "Antibodies" and "immunoglobulins" (Igs) are glycoproteins having the same structural characteristics. While antibodies exhibit binding specificity to an antigen, immunoglobulins include both antibodies and other antibody-like molecules that lack antigen specificity. Polypeptides of the latter kind are, for example, produced at low levels by the lymph system and at increased levels by myelomas. The terms "antibody" and "antibodies" broadly encompass naturally occurring forms of antibodies and recombinant antibodies such as single-chain antibodies, chimeric and humanized antibodies and multi-specific antibodies as well as fragments and derivatives of all of the foregoing, which fragments and derivatives have at least an antigenic binding site. Antibody derivatives may comprise a protein or chemical moiety conjugated to the antibody. The term "antibody" is used in the broadest sense and covers fully assembled antibodies, antibody fragments that can bind antigen (e.g., Fab', F'(ab)2, Fv, single chain antibodies, diabodies), and recombinant peptides comprising the foregoing. As used herein, "MMP-7 antibody" refers to any antibody that specifically binds to MMP-7 (SEQ ID NO: 1), or to a variant or fragment thereof, and includes monoclonal antibodies, polyclonal antibodies, single-chain antibodies, and fragments thereof which retain the antigen binding function of the parent antibody.

The MMP-7 antibodies of the invention are optimally monoclonal antibodies. The term "monoclonal antibody" as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally-occurring mutations that may be present in minor amounts.

"Native antibodies" and "native immunoglobulins" are usually heterotetrameric glycoproteins of about 150,000 daltons, composed of two identical light (L) chains and two identical heavy (H) chains. Each light chain is linked to a heavy chain by one covalent disulfide bond, while the number of disulfide linkages varies among the heavy chains of different immunoglobulin isotypes. Each heavy and light chain also has regularly spaced intrachain disulfide bridges. Each heavy chain has at one end a variable domain (VH) followed by a number of constant domains. Each light chain has a variable domain at one end (V,) and a constant domain at its other end; the constant domain of the light chain is aligned with the first constant domain of the heavy chain, and the light chain variable domain is aligned with the variable domain of the heavy chain. Particular amino acid residues are believed to form an interface between the light and heavy-chain variable domains. The term "variable" refers to the fact that certain portions of the variable domains differ extensively in sequence among antibodies and are used in the binding and specificity of each particular antibody for its particular antigen. However, the variability is not evenly distributed throughout the variable domains of antibodies. It is concentrated in three segments called complementarity determining regions (CDRs) or hypervariable regions both in the light chain and the heavy-chain variable domains. The more highly conserved portions of variable domains are called the framework (FR) regions. The variable domains of native heavy and light chains each comprise four FR regions, largely adopting a p-sheet configuration, connected by three CDRs, which form loops connecting, and in some cases forming part of, the p-sheet structure. The CDRs in each chain are held together in close proximity by the FR regions and, with the CDRs from the other chain, contribute to the formation of the antigen-binding site of antibodies (see Kabat et al., NIH Publ. No. 91-3242, Vol. I, pages 647-669 (1991)).

The constant domains are not involved directly in binding an antibody to an antigen, but exhibit various effector functions, such as participation of the antibody in antibody-dependent cellular toxicity.

The term "hypervariable region" when used herein refers to the amino acid residues of an antibody which are responsible for antigen-binding. The hypervariable region comprises amino acid residues from a "complementarily determining region" or "CDR" (i.e., residues 24-34 (Ll), 50-56 (L2) and 89-97 (L3) in the light chain variable domain and 31-35 (Hl), 50-65 (H2) and 95-102 (H3) in the heavy chain variable domain; Kabat et al. , Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institute of Health, 25 Bethesda, MD. [1991]) and/or those residues from a "hypervariable loop" (i.e., residues 26-32(Ll), 50-52 (L2) and 91-96 (L3) in the light chain variable domain and 26-32(Hl), 53-55 (H2) and 96-101 (H3) in the heavy chain variable domain; Clothia and Lesk, J. MoI. Biol, 196:901 -917 [1987]). Framework" or "FR" residues are those variable domain residues other than the hypervariable region residues as herein deemed.

"Antibody fragments" comprise a portion of an intact antibody, preferably the antigen-binding or variable region of the intact antibody. Examples of antibody fragments include Fab, Fab', F(ab')2, and Fv fragments; diabodies; linear antibodies (Zapata et al. (1995) Protein Eng. 8(10): 1057-1062); single-chain antibody molecules; and multispecifϊc antibodies formed from antibody fragments. Papain digestion of antibodies produces two identical antigen-binding fragments, called "Fab" fragments, each with a single antigen- binding site, and a residual "Fc" fragment, whose name reflects its ability to crystallize readily. Pepsin treatment of antibodies yields an F(ab')2 fragment that has two antigen- combining sites and is still capable of cross-linking antigen. "Fv" is the minimum antibody fragment that contains a complete antigen recognition and binding site. In a two-chain Fv species, this region consists of a dimer of one heavy- and one light-chain variable domain in tight, non-covalent association. In a single-chain Fv species, one heavy- and one light-chain variable domain can be covalently linked by a flexible peptide linker such that the light and heavy chains can associate in a "dimeric" structure analogous to that in a two-chain Fv species. It is in this configuration that the three CDRs of each variable domain interact to define an antigen-binding site on the surface of the V _H -V _L dimer. Collectively, the six CDRs confer antigen-binding specificity to the antibody. However, even a single variable domain (or half of an Fv comprising only three CDRs specific for an antigen) has the ability to recognize and bind antigen, although at a lower affinity than the entire binding site.

The Fab fragment also contains the constant domain of the light chain and the first constant domain (C _H 1) of the heavy chain. Fab fragments differ from Fab' fragments by the addition of a few residues at the carboxy terminus of the heavy-chain C _H I domain including one or more cysteines from the antibody hinge region. Fab'-SH is the designation herein for Fab' in which the cysteine residue(s) of the constant domains bear a free thiol group. F(ab')2 antibody fragments originally were produced as pairs of Fab' fragments that have hinge cysteines between them.

Fragments of the claimed MMP-7 monoclonal antibodies are encompassed by the invention so long as they retain the desired function of the full-length antibody (i.e., the ability to selectively bind to MMP-7). Thus, for example, a fragment of an MMP-7 monoclonal antibody of the invention will retain the ability to bind to an MMP-7 antigen. Such fragments are characterized by properties similar to the corresponding full-length antibody, that is, the fragments will specifically bind MMP-7. Such fragments are referred to herein as "antigen-binding" fragments.

Suitable antigen-binding fragments of an antibody comprise a portion of a full- length antibody, generally the antigen-binding or variable region thereof. Examples of antibody fragments include, but are not limited to, Fab, F(ab')2, and Fv fragments and single-chain antibody molecules. By "Fab" is intended a monovalent antigen-binding fragment of an immunoglobulin that is composed of the light chain and part of the heavy chain. By "F(ab') ₂ " is intended a bivalent antigen-binding fragment of an immunoglobulin that contains both light chains and part of both heavy chains. By "single-chain Fv" or "sFv" antibody fragments is intended fragments comprising the V _H and V _L domains of an antibody, wherein these domains are present in a single polypeptide chain. See, for example, U.S. Patent Nos. 4,946,778, 5,260,203, 5,455,030, and 5,856,456, herein incorporated by reference. Generally, the Fv polypeptide further comprises a polypeptide linker between the V _H and V _L domains that enables the sFv to form the desired structure for antigen binding. For a review of sFv see Pluckthun (1994) in The Pharmacology of Monoclonal Antibodies, Vol. 113, ed. Rosenburg and Moore (Springer- Verlag, New York), pp. 269-315.

Antibodies or antibody fragments can be isolated from antibody phage libraries generated using the techniques described in, for example, McCafferty et al. (1990) Nature 348:552-554 (1990) and U.S. Patent No. 5,514,548. Clackson et al. (1991) Nature 352:624-628 and Marks et al. (1991) J. MoI. Biol. 222:581-597 describe the isolation of murine and human antibodies, respectively, using phage libraries. Subsequent publications describe the production of high affinity (nM range) human antibodies by chain shuffling (Marks et al. (1992) Bio/Technology 10:779-783), as well as combinatorial infection and in vivo recombination as a strategy for constructing very large phage libraries (Waterhouse et al. (1993) Nucleic. Acids Res. 21 :2265-2266). Thus, these techniques are viable alternatives to traditional monoclonal antibody hybridoma techniques for isolation of monoclonal antibodies.

Various techniques have been developed for the production of antibody fragments. Traditionally, these fragments were derived via proteolytic digestion of intact antibodies (see, e.g., Morimoto et al. (1992) Journal of Biochemical and Biophysical Methods

24:107-117 (1992) and Brennan et al. (1985) Science 229:81). However, these fragments can now be produced directly by recombinant host cells. For example, the antibody fragments can be isolated from the antibody phage libraries discussed above. Alternatively, Fab'-SH fragments can be directly recovered from E. coli and chemically coupled to form F(ab') ₂ fragments (Carter et al. (1992) Bio/Technology 10:163-167). According to another approach, F(ab') ₂ fragments can be isolated directly from recombinant host cell culture. Other techniques for the production of antibody fragments will be apparent to the skilled practitioner.

In some embodiments, antibodies of the invention are monoclonal in nature. As indicated above, "monoclonal antibody" is intended an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts. The term is not limited regarding the species or source of the antibody. The term encompasses whole immunoglobulins as well as fragments such as Fab, F(ab')2, Fv, and others which retain the antigen binding function of the antibody. Monoclonal antibodies are highly specific, being directed against a single antigenic site, i.e., a particular epitope within the MMP-7 protein, as defined herein below. Furthermore, in contrast to conventional (polyclonal) antibody preparations that typically include different antibodies directed against different determinants (epitopes), each monoclonal antibody is directed against a single determinant on the antigen. The modifier "monoclonal" indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method. For example, the monoclonal antibodies to be used in accordance with the present invention may be made by the hybridoma method first described by Kohler et al. (1975) Nature 256:495, or may be made by recombinant DNA methods (see, e.g., U.S. Patent No. 4,816,567). The "monoclonal antibodies" may also be isolated from phage antibody libraries using the techniques described in, for example, Clackson et al. (1991) Nature 352:624-628; Marks et al. (199I) J. MoI. Biol. 222:581-597; and U.S. Patent No. 5,514,548.

Monoclonal antibodies can be prepared using the method of Kohler et al. (1975) Nature 256:495-496, or a modification thereof. Typically, a mouse is immunized with a solution containing an antigen. Immunization can be performed by mixing or emulsifying the antigen-containing solution in saline, preferably in an adjuvant such as Freund's complete adjuvant, and injecting the mixture or emulsion parenterally. Any method of immunization known in the art may be used to obtain the monoclonal antibodies of the invention. After immunization of the animal, the spleen (and optionally, several large lymph nodes) are removed and dissociated into single cells. The spleen cells may be screened by applying a cell suspension to a plate or well coated with the antigen of interest. The B cells expressing membrane bound immunoglobulin specific for the antigen (i.e., antibody-producing cells) bind to the plate and are not rinsed away. Resulting B cells, or all dissociated spleen cells, are then induced to fuse with myeloma cells to form monoclonal antibody-producing hybridomas, and are cultured in a selective medium. The resulting cells are plated by serial dilution and are assayed for the production of antibodies that specifically bind the antigen of interest (and that do not bind to unrelated antigens). The selected monoclonal antibody (mAb)-secreting hybridomas are then cultured either in vitro (e.g., in tissue culture bottles or hollow fiber reactors), or in vivo (as ascites in mice). Monoclonal antibodies can also be produced using Repetitive Immunizations Multiple

Sites technology (RIMMS). See, for example, Kilpatrick et al. (1997) Hybridoma 16(4):381-389; Wring et al. (1999) J. Pharm. Biomed. Anal. 19(5):695-707; and Bynum et al. (1999) Hybridoma 18(5):407-411, all of which are herein incorporated by reference in their entirety.

As an alternative to the use of hybridomas, antibody can be produced in a cell line such as a CHO cell line, as disclosed in U.S. Patent Nos. 5,545,403; 5,545,405; and 5,998,144; incorporated herein by reference. Briefly, the cell line is transfected with vectors capable of expressing a light chain and a heavy chain, respectively. By transfecting the two proteins on separate vectors, chimeric antibodies can be produced. Another advantage is the correct glycosylation of the antibody. A monoclonal antibody can also be identified and isolated by screening a recombinant combinatorial immunoglobulin library (e.g., an antibody phage display library) with a biomarker protein to thereby isolate immunoglobulin library members that bind the biomarker protein. Kits for generating and screening phage display libraries are commercially available (e.g., the Pharmacia Recombinant Phage Antibody System, Catalog No. 27-9400-01; and the Stratagene SurfZAPQ Phage Display Kit, Catalog No. 240612). Additionally, examples of methods and reagents particularly amenable for use in generating and screening an antibody display library can be found in, for example, U.S. Patent No. 5,223,409; PCT Publication Nos. WO 92/18619; WO 91/17271; WO 92/20791; WO 92/15679; 93/01288; WO 92/01047; WO 92/09690; and WO 90/02809; Fuchs et al. (1991) Bio/Technology 9:1370-1372; Hay et al. (1992) Hum. Antibod. Hybridomas 3:81-85; Huse et al. (1989) Science 246:1275-1281; Griffiths et al. (1993) EMBO J. 12:725-734. The methods utilized in the production of MMP-7 monoclonal antibodies 5Gl 1.9 and 15H8.12 are set forth in Example 1 below.

In some aspects of the invention, antibodies may be selected on the basis of desirable staining of cyto logical or histological samples. That is, in particular embodiments the antibodies are selected with the end sample type (e.g., cytology preparations; tissue samples) in mind and for binding specificity. Antibodies directed to MMP-7 are selected and purified via a multi-step screening process. Such methods for antibody selection are described in U.S. Patent No. 7,157,233, which is herein incorporated by reference in its entirety. Moreover, particular MMP-7 antibody pairings or larger groupings may be chosen for use in a certain assay format for optimal results (e.g., sandwich ELISA, etc.; see Example 4). Antibodies having the binding characteristics of a monoclonal antibody of the invention are also provided. "Binding characteristics" or "binding specificity" when used in reference to an antibody means that the antibody recognizes the same or similar antigenic epitope as a comparison antibody. Examples of such antibodies include, for example, an antibody that competes with a monoclonal antibody of the invention in a competitive binding assay. One of skill in the art could determine whether an antibody competitively interferes with another antibody using standard methods.

By "epitope" is intended the part of an antigenic molecule to which an antibody is produced and to which the antibody will bind. An "MMP-7 epitope" comprises the part of the MMP-7 protein to which an MMP-7 monoclonal antibody binds. Epitopes can comprise linear amino acid residues (i.e., residues within the epitope are arranged sequentially one after another in a linear fashion), nonlinear amino acid residues (referred to herein as "nonlinear epitopes" or "conformational epitopes"; these epitopes are not arranged sequentially), or both linear and nonlinear amino acid residues. Typically epitopes are short amino acid sequences, e.g. about five amino acids in length. Systematic techniques for identifying epitopes are known in the art and are described, for example, in U.S. Pat. No. 4,708,871 and in the examples set forth below. Briefly, in one method, a set of overlapping oligopeptides derived from the antigen may be synthesized and bound to a solid phase array of pins, with a unique oligopeptide on each pin. The array of pins may comprise a 96-well microtiter plate, permitting one to assay all 96 oligopeptides simultaneously, e.g., for binding to a biomarker-specifϊc monoclonal antibody. Alternatively, phage display peptide library kits (New England BioLabs) are currently commercially available for epitope mapping. Using these methods, the binding affinity for every possible subset of consecutive amino acids may be determined in order to identify the epitope that a given antibody binds. Epitopes may also be identified by inference when epitope length peptide sequences are used to immunize animals from which antibodies are obtained.

The invention also encompasses isolated polypeptides comprising an epitope for binding an MMP-7 monoclonal antibody of the invention. These polypeptides correspond to a portion of the MMP-7 antigen that binds to monoclonal antibody 5Gl 1.9 or 15H8.12. Such polypeptides find use in methods for producing antibodies that selectively bind to MMP-7. The ability of a polypeptide to be used in the production of antibodies is referred to herein as "antigenic activity." For example, the amino acid sequence set forth in SEQ

ID NO:3 (corresponding to residues 115 to 134 in the MMP-7 amino acid sequence set forth in SEQ ID NO:1) comprises the epitope recognized by an MMP-7 monoclonal antibody, more particularly monoclonal antibody 5Gl 1.9. The amino acid sequence set forth in SEQ ID NO:4 (corresponding to residues 45 to 108 in the MMP-7 amino acid sequence set forth in SEQ ID NO:1) comprises the epitope recognized by an MMP-7 monoclonal antibody, more particularly monoclonal antibody 15H8.12. Variants and fragments of the MMP-7 epitope sequences set forth in SEQ ID NOs: 3 and 4 that retain the antigenic activity of the original polypeptide are also provided. The invention further includes isolated nucleic acid molecules that encode polypeptides that comprise the MMP- 7 epitopes set forth in SEQ ID NOs:3 and 4, and variants and fragments thereof. The polypeptides of the invention comprising MMP-7 epitopes can be used in methods for producing monoclonal antibodies that specifically bind to MMP-7, as described herein above. Such polypeptides can also be used in the production of polyclonal MMP-7 antibodies. For example, polyclonal antibodies can be prepared by immunizing a suitable subject (e.g., rabbit, goat, mouse, or other mammal) with a polypeptide comprising an MMP-7 epitope (i.e., an immunogen). The antibody titer in the immunized subject can be monitored over time by standard techniques, such as with an ELISA using an immobilized biomarker protein (e.g., MMP-7). At an appropriate time after immunization, e.g., when the antibody titers are highest, antibody-producing cells can be obtained from the subject and used to prepare monoclonal antibodies by standard techniques, such as the hybridoma technique originally described by Kohler and Milstein (1975) Nature 256:495-497, the human B cell hybridoma technique (Kozbor et al. (1983) Immunol. Today 4:72), the EBV -hybridoma technique (Cole et al. (1985) in Monoclonal Antibodies and Cancer Therapy, ed. Reisfeld and Sell (Alan R. Liss, Inc., New York, NY), pp. 77-96) or trioma techniques. The technology for producing hybridomas is well known {see generally Coligan et al., eds. (1994) Current Protocols in Immunology (John Wiley & Sons, Inc., New York, NY); Galfre et al. (1977) Nature 266:550-52; Kenneth ( 1980) in Monoclonal Antibodies: A New Dimension In Biological Analyses (Plenum Publishing Corp., NY; and Lerner (1981) YaIe J. Biol. Med, 54:387 - 402).

Amino acid sequence variants of a monoclonal antibody or a polypeptide comprising an MMP-7 epitope described herein are also encompassed by the present invention. Variants can be prepared by mutations in the cloned DNA sequence encoding the antibody or polypeptide of interest. Methods for mutagenesis and nucleotide sequence alterations are well known in the art. See, for example, Walker and Gaastra, eds. (1983)

Techniques in Molecular Biology (MacMillan Publishing Company, New York); Kunkel (1985) Proc. Natl. Acad. Sci. USA 82:488-492; Kunkel et al. (1987) Methods Enzymol. 154:367-382; Sambrook et al. (1989) Molecular Cloning: A Laboratory Manual (Cold Spring Harbor, New York); U.S. Patent No. 4,873,192; and the references cited therein; herein incorporated by reference. Guidance as to appropriate amino acid substitutions that do not affect biological activity of the polypeptide of interest may be found in the model of Dayhoff et al. (1978) in Atlas of Protein Sequence and Structure (Natl. Biomed. Res. Found., Washington, D. C), herein incorporated by reference. Conservative substitutions, such as exchanging one amino acid with another having similar properties, may be preferred. Examples of conservative substitutions include, but are not limited to, Gly<t>Ala, Val<t>Ile<t>Leu, Asp<t>Glu, Lys<t>Arg, Asn<t>Gln, and Phe<t>Trp<t>Tyr.

In constructing variants of the polypeptide of interest, modifications are made such that variants continue to possess the desired activity, i.e., similar binding affinity to the biomarker. Obviously, any mutations made in the DNA encoding the variant polypeptide must not place the sequence out of reading frame and preferably will not create complementary regions that could produce secondary mRNA structure. See EP Patent Application Publication No. 75,444.

The variants of a reference polypeptide generally have amino acid sequences that have at least 70% or 75% sequence identity, particularly at least 80% or 85% sequence identity, more particularly at least 90%, 91%, 92%, 93%, 94% or 95% sequence identity to the amino acid sequence for the reference antibody molecule, or to a shorter portion of the reference antibody molecule. Optimally, the molecules share at least 96%, 97%, 98%, 99%, or more sequence identity. For purposes of the present invention, percent sequence identity is determined using the Smith- Waterman homology search algorithm using an affine gap search with a gap open penalty of 12 and a gap extension penalty of 2, BLOSUM matrix of 62. The Smith- Waterman homology search algorithm is taught in Smith and Waterman (1981) Adv. Appl. Math. 2:482-489. A variant may, for example, differ from the reference antibody by as few as 1 to 15 amino acid residues, as few as 1 to 10 amino acid residues, such as 6-10, as few as 5, as few as 4, 3, 2, or even 1 amino acid residue. With respect to optimal alignment of two amino acid sequences, the contiguous segment of the variant amino acid sequence may have additional amino acid residues or deleted amino acid residues with respect to the reference amino acid sequence. The contiguous segment used for comparison to the reference amino acid sequence will include at least 20 contiguous amino acid residues, and may be 30, 40, 50, or more contiguous amino acid residues. Corrections for sequence identity associated with conservative residue substitutions or gaps can be made (see Smith-Waterman homology search algorithm). The MMP-7 monoclonal antibodies of the invention may be labeled with a detectable substance as described below to facilitate MMP-7 biomarker protein detection in a sample. Such antibodies find use in practicing the methods of the invention. The antibodies and antibody fragments of the invention can be coupled to a detectable substance to facilitate detection of antibody binding. The word "label" when used herein refers to a detectable compound or composition that is conjugated directly or indirectly to the antibody so as to generate a "labeled" antibody. The label may be detectable by itself (e.g., radioisotope labels or fluorescent labels) or, in the case of an enzymatic label, may catalyze chemical alteration of a substrate compound or composition that is detectable. Examples of detectable substances for purposes of labeling antibodies include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bio luminescent materials, and radioactive materials. Examples of suitable enzymes include but are not limited to horseradish peroxidase, alkaline phosphatase, β-galactosidase, or acetylcholinesterase; examples of suitable prosthetic group complexes include but are not limited to streptavidin/biotin and avidin/biotin; examples of suitable fluorescent materials include but are not limited to umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; an example of a luminescent material includes but is not limited to luminol; examples of bioluminescent materials include but are not limited to luciferase, luciferin, and aequorin; and examples of suitable radioactive material include ¹²⁵ I, ¹³¹ 1, ³⁵ S, or ³ H. Other exemplary detectable labels for use in the practice of the instant invention include digoxigenin and quantum dots.

Although the MMP-7 monoclonal antibodies disclosed herein may be used in any method in which detection of MMP-7 protein is desirable, the MMP-7 monoclonal antibody compositions of the invention find particular use in methods for detecting, diagnosing ovarian cancer or identifying patients with an increased likelihood of having ovarian cancer, such as those disclosed in U.S. Patent Application Publication No. 2007/0212721, which is herein incorporated by reference in its entirety. By "ovarian cancer" is intended those conditions classified by post-exploratory laparotomy as premalignant pathology, malignant pathology, and cancer (FIGO Stages 1-4). Staging and classification of ovarian cancer are described in detail above. "Early-stage ovarian cancer" refers to those disease states classified as Stage 1 or Stage 2 carcinoma. Early detection of ovarian cancer significantly increases 5 -year survival rates. As used herein, "identifying patients with an increased likelihood of having ovarian cancer" is intended methods for classifying those females that are more likely to have ovarian cancer so that additional tests and monitoring can be performed, particularly to detect ovarian cancer at an early stage during which prognosis is most favorable. An "increased likelihood of having ovarian cancer" is intended to mean that patients who are determined in accordance with the present methods to exhibit overexpression of particular biomarkers are more likely to have ovarian cancer than those patients who do not. As used herein, "patient" or "subject" is intended an animal, including a mammal, particularly a human. The patient or subject may or may not be suspected of having ovarian cancer (e.g., exhibiting symptoms, tested positive for another ovarian cancer biomarker). "Diagnosing ovarian cancer" is intended to include, for example, diagnosing or detecting the presence of ovarian cancer, monitoring the progression of the disease, and identifying or detecting cells or samples that are indicative of ovarian cancer. The terms diagnosing, detecting, and identifying ovarian cancer are used interchangeably herein. Although the methods of the invention can identify patients more likely to have to ovarian cancer and to aid in the diagnosis of this disease, particularly at an early stage, a

"definitive" diagnosis of ovarian cancer will generally comprise performing a biopsy on a tissue sample from the subset of patients identified by the methods of the invention.

The term "screening method" refers to strategies to identify patients that have an increased likelihood of having ovarian cancer so that such patients can be selected for more aggressive diagnostic methods to definitively determine if the patients have ovarian cancer. The "screening methods" of the invention are generally not intended to definitively diagnose a patient as having (or not having) ovarian cancer. Rather, such methods are intended to identify women having an increased likelihood of having ovarian cancer so that these women may undergo additional diagnostic methods to obtain a definitive diagnosis. That is, a patient that is identified as having ovarian cancer or an increased likelihood of having ovarian cancer in accordance with the disclosed methods may be subjected to further diagnostic testing to definitively determine if the patient has ovarian cancer. "Further diagnostic testing" includes but is not limited to pelvic examination, transvaginal ultrasound, CT scan, MRI, laparotomy, laparoscopy, and biopsy. Such diagnostic methods are well known in the art. Moreover, patients classified as having an increased likelihood of having ovarian cancer that are determined by further diagnostic testing not to currently have ovarian cancer may be closely monitored on a regular basis for the development of ovarian cancer. Monitoring of such patients may include but is not limited to periodic pelvic examination, transvaginal ultrasound, CT scan, and MRI. A physician of ordinary skill in the art will appreciate appropriate techniques for monitoring patients for the development of ovarian cancer. The screening methods of the invention may be performed on a case-by-case basis or as a periodic routine screening test for the general female population. In some embodiments, the screening methods for identifying patients with an increased likelihood of having ovarian cancer may be viewed as comparable to Pap smears for the identification of patients having an increased likelihood of having cervical cancer.

In another embodiment of the invention, a two antibody or ELISA format is used to diagnose ovarian cancer or to identify a patient with an increased likelihood of having ovarian cancer by detecting overexpression of MMP-7 in a patient body sample. Such sandwich or "two-site" immunoassays are known in the art. See, for example, Current Protocols in Immunology. Indirect Antibody Sandwich ELISA to Detect Soluble Antigens, John Wiley & Sons, 1991. In the certain sandwich ELISA methods encompassed by the invention, two antibodies specific to two distinct antigenic sites on MMP-7 are used, such as, for example, the MMP-7 monoclonal antibodies designated as 5Gl 1.9 and 15H8.12. By "distinct antigenic site" is intended that the antibodies are specific for different sites on the biomarker protein of interest (i.e., MMP-7) such that binding of one antibody does not significantly interfere with binding of the other antibody to the biomarker protein. Sandwich ELISA techniques utilize two antibodies: a "capture" antibody and a "detector" antibody. The first antibody, the "capture antibody," is generally immobilized on or bound to a solid support. For example, a capture antibody may be covalently or noncovalently attached to a cell culture plate, microtiter cell culture plate well, a bead (e.g., MAGPLEX® magnetic microbeads), a cuvette, nanoparticle, or other reaction vessel. In certain aspects of the invention, the capture antibody is bound to a microtiter plate well. Methods for attaching an antibody to a solid support are routine in the art. The patient body sample, particularly a blood sample, more particularly a serum sample, is then contacted with the capture antibody-bound solid support and allowed to form a complex with the capture antibody. Unbound sample is removed, and a second antibody, the "detector" or "tag" antibody, is exposed to the solid support containing the capture antibody-antigen complex. The detector antibody is specific for a distinct antigenic site on the biomarker of interest (e.g., MMP-7) and is coupled to or labeled with a detectable substance, as described herein. Such antibody labels are well known in the art and include various enzymes, prosthetic groups, fluorescent materials (e.g., enzymes (e.g., horseradish peroxidase (HRP)), phycoerythrin, luminescent materials, bioluminescent materials, and radioactive materials). Following incubation with the detector antibody, unbound sample is removed, and MMP-7 expression levels are determined by quantitating the level of labeled detector antibody bound to the solid support, which in turn directly correlates with the level of MMP-7 present in the sample. This quantitation step can be performed by a number of known techniques and will vary depending on the specific detectable substance coupled to the detector antibody, as would be appreciated by those of skill in the art.

The methods of the invention generally comprise detecting overexpression of at least one biomarker, more particularly a plurality of biomarkers, that is selectively overexpressed in ovarian cancer in a patient body sample. Thus, detection of the biomarkers permits the differentiation of samples indicative of an increased likelihood of having ovarian cancer or the presence of ovarian cancer from normal samples (i.e., samples from patients that are ovarian-cancer free) and samples that are indicative of nonmalignant and benign proliferation. A biomarker of particular interest in the detection, diagnosis, or monitoring of ovarian cancer is MMP-7. One of skill in the art will appreciate that in addition to the detection of MMP-7 expression, the methods of the invention for detecting ovarian cancer and for identifying a patient with an increased likelihood of having ovarian cancer further encompass the detection of a plurality of biomarkers that are selectively expressed in ovarian cancer. For example, other biomarkers of interest, include but are not limited to HE4, CA125, glycodelin, Muc-1, PAI- 1 , CTHRC 1 , inhibin, PLAU-R, prolactin, KLK- 10, KLK-6, and SLPI, alpha- 1 antitrypsin (AAT), Imp-2, FLJ10546, FLJ23499, MGC13057, SPONl, SlOOAl, SLC39A4, TACSTD2, MBG2, HETKL27 (MAL2), Cox-1, protein kinase C-iota, cadherin-6, ADPRT, matriptase, folate receptor, claudin 4, mesothelin, aquaporin 5, cofϊlin 1, gelsolin, clusterin, alpha tetranectin, vitronectin, pregnancy-associated plasma protein-A (PAPP-A), folistatin, B7-H4, YKL-40, claudin 3, and KOP. Biomarkers of particular interest include HE4, CA125, glycodelin, Muc-1, PAI-I, CTHRCl, inhibin, PLAU-R, prolactin, KLK-IO, KLK-6, SLPI, and alpha- 1 anti-trypsin. Antibodies for the detection of these exemplary ovarian cancer biomarkers are known in the art or can be produced in accordance with routine methods. As used herein, "body sample" refers to any sampling of cells, tissues, or bodily fluids from a patient in which expression of a biomarker can be detected. Examples of such body samples include but are not limited to blood (e.g., whole blood, blood serum, blood having platelets removed, etc.), lymph, ascitic fluids, urine, gynecological fluids (e.g., ovarian, fallopian, uterine secretion, menses, etc.), biopsies, and fluids obtained during laparoscopy. Body samples may be obtained from a patient by a variety of techniques including, for example, by venipuncture, by scraping or swabbing an area, or by using a needle to aspirate bodily fluids or tissues. Methods for collecting various body samples are well known in the art. In particular embodiments, the body sample comprises blood or serum.

In a particular aspect of the invention, the methods comprise obtaining a sample (e.g., blood or serum) from a patient, contacting the sample with at least one MMP-7 monoclonal antibody of the invention, and detecting binding of the antibody to the MMP- 7 protein. In other embodiments, the sample is contacted with at least two monoclonal antibodies that bind to MMP-7. Techniques for detecting antigen (e.g., MMP-7)-antibody binding are well known in the art. Antibody binding to a biomarker of interest may be detected, for example, through the use of chemical reagents that generate a detectable signal that corresponds to the level of antibody binding and, accordingly, to the level of biomarker protein expression. Any method for detecting antibody-antigen (e.g., MMP-7) binding may be used to practice the methods of the invention. Such methods include but are not limited to traditional enzyme immunoassays (EIA), sandwich ELISA techniques (as described herein below), western blotting, immunocytochemistry, immunohistochemistry, immunoprecipitation, flow cytometry, Raman spectroscopy of nanoparticles, multiplex bead-based assays (e.g., using MAGPLEX® magnetic beads and a fluorescent tag such as phycoerythrin or utilizing the LUMINEX® platform).

The methods of the invention for diagnosing ovarian cancer in a patient or for identifying patients with an increased likelihood of having ovarian cancer, such as the sandwich ELISA, may further comprise comparing the level of MMP-7 protein in a patient body sample to a threshold level to determine if the patient has ovarian cancer or has an increased likelihood of having ovarian cancer. As used herein, "threshold level" refers to a level of MMP-7 expression above which a patient sample is deemed "positive" and below which the sample is classified as "negative" for ovarian cancer or an increased likelihood of having ovarian cancer. A threshold expression level for a particular biomarker (e.g., MMP-7) may be based on one or more compilations of data from "normal" patient samples (i.e., a patient population of females who do not have ovarian cancer). For example, the threshold expression level may be established as the value within two standard deviations of the mean MMP-7 expression level, based on the analysis of "normal" samples from patients who do not have ovarian cancer. One of skill in the art will appreciate that a variety of statistical and mathematical methods for establishing the threshold level of expression are known in the art.

The skilled artisan in the art would further recognize that the capture and detector antibodies can be contacted with the body sample sequentially, as described above, or simultaneously. Furthermore, the detector antibody can be incubated with the body sample first, prior to contacting the sample with the immobilized capture antibody. When the MMP-7 monoclonal antibodies of the present invention are used in the sandwich ELISA methods disclosed herein, either the 5Gl 1.9 or 15H8.12 antibody may be used as the capture or detector antibody. In one particular embodiment, the capture antibody is MMP-7 monoclonal antibody 5Gl 1.9 and the detector antibody is the 15H8.12 antibody. The antibodies of the invention may be used in any assay format to detect MMP-7, including but not limited to multiplex bead-based assays, using the LUMINEX 200® platform or MAGPLEX® magnetic microbeads.

With respect to the sandwich ELISA format described above in which two antibodies for the same biomarker (i.e., MMP-7) are used, multi-step analyses may be performed to identify particular antibody combinations or pairings and concentrations of these antibodies that produce the best results with respect to complementarity of the antibodies and signal-to-noise ratios achieved with a particular combinations of antibodies. See Example 4. In order to obtain optimal results in a sandwich ELISA format, the capture and detector antibodies should have distinct antigenic sites, as discussed above. The methods of the invention find further use in monitoring the progression or regression of ovarian cancer. In one embodiment of the invention for monitoring the progression/regression of ovarian cancer, the method comprises testing a sample from the patient to determine the level of MMP-7 in the patient body sample, determining the level of MMP-7 in another sample from the patient at a later point in time, and comparing the MMP-7 expression level at the earlier time point with that at the later time point, wherein a change in the level of MMP-7 is indicative of the progression of the cancer in the patient. A decrease in MMP-7 expression would be consistent with an improvement in the patient's condition. Similarly, the methods disclosed herein may be used to assess the efficacy of a particular ovarian cancer therapy or therapeutic regimen. For example, the method comprises testing a sample from the patient to determine the level of MMP-7 in the patient body sample prior to initiation of an ovarian cancer therapy, administering the ovarian cancer therapy, determining the level of MMP-7 in another sample from the patient during the time period of the therapy and/or following the completion of the therapy, and comparing the MMP-7 expression level prior to initiation of the therapy and after therapy has started or has been completed, wherein a change in the level of MMP-7 is indicative of the efficacy of the ovarian cancer therapy. A decrease in MMP-7 expression would be consistent with the therapy being efficacious.

The efficacy of the methods disclosed herein may be assessed by calculating such values as sensitivity, specificity, positive predictive (PPV), and negative predictive value (NPV). As used herein, "specificity" refers to the proportion of disease negatives that are test-negative. In a clinical study, specificity is calculated by dividing the number of true negatives by the sum of true negatives and false positives. By "sensitivity" is intended the level at which a method of the invention can accurately identify samples that have been confirmed as positive (i.e., true positives). Thus, sensitivity is the proportion of disease positives that are test-positive. Sensitivity is calculated in a clinical study by dividing the number of true positives by the sum of true positives and false negatives. In some embodiments, the sensitivity of the disclosed methods for diagnosing ovarian cancer or for identifying patients with an increased likelihood of having ovarian cancer is at least about 70%, in other embodiments at least about 80%, and in still other embodiments at least about 90, 91, 92, 93, 94, 95, 96, 97, 98, 99% or more. Furthermore, the specificity of the present methods in some embodiments is at least about 70%, in other embodiments at least about 80%, and in still other embodiments at least about 90, 91, 92, 93, 94, 95, 96, 97, 98, 99% or more. The term "positive predictive value" or "PPV" refers to the probability that a patient has the disease of interest (e.g., ovarian cancer) restricted to those patients who are classified as positive using a method of the invention. PPV is calculated in a clinical study by dividing the number of true positives by the sum of true positives and false positives. The "negative predictive value" or "NPV" of a test is the probability that the patient will not have the disease when restricted to all patients who test negative. NPV is calculated in a clinical study by dividing the number of true negatives by the sum of true negatives and false negatives. Kits comprising at least one MMP-7 monoclonal antibody of the invention are further provided. By "kit" is intended any manufacture (e.g., a package or a container) comprising at least one reagent, i.e., an antibody, for specifically detecting the expression of MMP-7. The kit may be promoted, distributed, or sold as a unit for performing the methods of the present invention. Furthermore, any or all of the kit reagents may be provided within containers that protect them from the external environment, such as in sealed containers. The kits may also contain a package insert describing the kit and or instructions for its use.

Kits for performing methods for detecting ovarian cancer and for identifying a patient with an increased likelihood of having ovarian cancer generally comprise at least one monoclonal antibody directed to MMP-7, chemicals for the detection of antibody binding, a counterstain, and, optionally, a bluing agent to facilitate identification of positive staining cells. Any chemicals that detect antigen-antibody binding may be used in the kits of the invention. For example, a secondary antibody that is conjugated to an enzyme that catalyzes the deposition of a chromogen at the antigen-antibody binding site may be provided. Such enzymes and techniques for using them in the detection of antibody binding are well known in the art. Chromogens compatible with the conjugated enzyme (e.g., DAB in the case of an HRP-labeled secondary antibody) and solutions, such as hydrogen peroxide, for blocking non-specific staining may be further provided. The kits may additionally comprise a peroxidase blocking reagent (e.g., hydrogen peroxide), a protein blocking reagent (e.g., purified casein), and a counterstain (e.g., hematoxylin). A bluing agent (e.g., ammonium hydroxide or TBS, pH 7.4, with Tween-20 and sodium azide) may be further provided in the kit to facilitate detection of positive staining cells. Kits may also comprise positive and negative control samples for quality control purposes. Development of appropriate positive and negative controls is well within the routine capabilities of those of ordinary skill in the art.

Other kits of the invention for performing the sandwich ELISA methods described herein generally comprise a capture antibody, optionally immobilized on a solid support (e.g., a microtiter plate), and a detector antibody coupled with a detectable substance, examples of which are set forth herein above. In certain embodiments, the capture antibody and the detector antibody are monoclonal antibodies, particularly MMP-7 monoclonal antibodies, more particularly the MMP-7 monoclonal antibodies designated 5Gl 1.9 and 15H8.12. In one kit of the invention for practicing the sandwich ELISA method, the capture antibody is MMP-7 monoclonal antibody 5Gl 1.9, immobilized on a microtiter plate, and the detector antibody is HRP-labeled 15H8.12. Chemicals for detecting and quantitating the level of detector antibody bound to the solid support (which directly correlates with the level of MMP-7 in the sample) may be optionally included in the kit. Purified MMP-7 may also be provided as an antigen standard.

In another embodiment, the kits of the invention comprise at least two MMP-7 monoclonal antibodies, more particularly monoclonal antibodies 5Gl 1.9 and 15H8.12. Without intending to be limited to any particular assay format or methodology, as described below in the Experimental Section, MMP-7 monoclonal antibodies 5Gl 1.9 and 15H8.12 have been shown to be a particularly useful combination of MMP-7 monoclonal antibodies for the detection of purified MMP-7 and ovarian cancer samples, more particularly in sandwich ELISA methods wherein the 5Gl 1.9 antibody serves as the capture antibody and the 15H8.12 antibody serves as the detector antibody. One of skill in the art will recognize that the capture and detector antibody may be "switched" in the sandwich ELISA format or that other antibodies may be used in the methods and kits of the invention, in addition to one or more of the MMP-7 monoclonal antibodies disclosed herein. For example, antibodies to other biomarkers selectively overexpressed in ovarian cancer, including but not limited to HE4, CA125, glycodelin, Muc-1, PAI-I, CTHRCl, inhibin, PLAU-R, prolactin, KLK-IO, KLK-6, and SLPI, alpha- 1 anti-trypsin (AAT), Imp- 2, FLJ10546, FLJ23499, MGC13057, SPONl, SlOOAl, SLC39A4, TACSTD2, MBG2, HETKL27 (MAL2), Cox-1, protein kinase C-iota, cadherin-6, ADPRT, matriptase, folate receptor, claudin 4, mesothelin, aquaporin 5, cofϊlin 1, gelsolin, clusterin, alpha tetranectin, vitronectin, pregnancy-associated plasma protein-A (PAPP-A), and folistatin. Biomarkers of particular interest include but are not limited to HE4, CA125, glycodelin, Muc- 1 , PAI- 1 , CTHRC 1 , inhibin, PLAU-R, prolactin, KLK- 10, KLK-6, SLPI, and alpha- 1 anti-trypsin. When multiple antibodies are present in a kit of the invention, each antibody may be provided as an individual reagent or, alternatively, as an antibody cocktail comprising all of the antibodies of interest.

Although the above methods, antibodies, and kits for diagnosing ovarian cancer and for identifying patients with an increased likelihood of having ovarian cancer have been described herein in some detail, one of skill in the art will recognize that the disclosed methods and compositions could be similarly applied to other cancers or diseases in which MMP-7 is overexpressed. One of skill in the art will further recognize that any or all of the steps in the methods of the invention could be implemented by personnel in a manual or automated fashion. Thus, the steps of sample preparation, antibody incubation, and detection of antibody binding may be automated.

The article "a" and "an" are used herein to refer to one or more than one (i.e., to at least one) of the grammatical object of the article. By way of example, "an element" means one or more element.

Throughout the specification the word "comprising," or variations such as "comprises" or "comprising," will be understood to imply the inclusion of a stated element, integer or step, or group of elements, integers or steps, but not the exclusion of any other element, integer or step, or group of elements, integers or steps.

The following examples are offered by way of illustration and not by way of limitation:

EXPERIMENTAL Example 1 : Production of Mouse Monoclonal Antibodies to MMP-7

Recombinant antigen immunization strategies were undertaken to generate mouse monoclonal antibodies specific for MMP-7. The immunogenic polypeptide used to produce the mouse MMP-7 monoclonal antibodies comprised the MMP-7 sequence (SEQ ID NO:1) fused to a small polypeptide linker and a carboxy-terminal hexahistidine tag. The sequence of the MMP-7 immunogenic polypeptide is set forth in SEQ ID NO:5. The immunogenic MMP-7 polypeptide was overexpressed in a HEK (human embryonic kidney) cell line that contains the nucleic acid encoding the Epstein-Barr Nuclear Antigen, and the hexahistidine-tagged MMP-7 protein was purified from the media fraction using a chelating agarose charged with Ni+2 ions (Ni-NTA, Qiagen Inc.). Mice were then immunized with the purified MMP-7 protein and lymphocyte fusions were accomplished by performing Repetitive Immunizations Multiple Sites technology (RIMMS), essentially as described in Kilpatrick et al (1997) Hybridoma 16(4):381-389; Wring et al. (1999) J. Pharm. Biomed. Anal. 19(5):695-707; and Bynum et al. (1999) Hybridoma 18(5):407-411. Antibody-producing cells were isolated from the immunized mice and fused with myeloma cells to form monoclonal antibody-producing hybridomas. Primary screening of hybridoma supernatants was performed using recombinant MMP-7 protein and routine ELISA and Western blot techniques well known in the art to confirm binding to MMP-7. Specific MMP-7 monoclonal antibodies of interest were selected and purified from the culture media supernatants of the hybridoma cells using recombinant Protein A-coated resin (MABSELECT SURE®, GE Healthcare). Purified antibodies were subjected to further characterization. MMP-7 monoclonal antibodies 5Gl 1.9 and 15H8.12 were determined to be of the IgG ₁ isotype. Details of the epitope mapping of these antibodies are described below.

Example 2: General Method for Epitope Mapping General Approach Epitope mapping was performed essentially as described in U.S. Patent

Application Publication No. 2006/0252106 to identify the linear or non-linear, discontiguous amino acid sequence within an antigenic protein (i.e., the epitope in, for example, MMP-7) that is recognized by a particular monoclonal antibody. A general approach for epitope mapping requires the expression of the full-length protein, as well as various fragments (i.e., truncated forms) of the protein, generally in a heterologous expression system. These various recombinant proteins are then used to determine if the specific monoclonal antibody is capable of binding one or more of the truncated forms of the target protein. Through the use of reiterative truncation and the generation of recombinant proteins with overlapping amino acid regions, it is possible to identify the region that is recognized by the monoclonal antibody under investigation. Western blot analysis or ELISA is employed to determine if the specific monoclonal antibody under investigation is capable of binding one or more of the recombinant protein fragments. This approach can ultimately identify the peptide regions that contains the epitope and, in some cases, to refine the epitope precisely to an approximately 5-15 amino acid sequence. An epitope can be a continuous linear sequence approximately 5-15 amino acids in length, nonlinear (e.g., discontinuous with the antibody binding to a site on the protein composed of different sections of the peptide chain), or both linear and nonlinear epitope.

Systematic techniques for identifying epitopes are known in the art, and one general approach requires expression of the full length protein as well as various fragments (i.e., truncated forms) of the protein, generally in a heterologous expression system (e.g., RTS System, "Rapid Translation System" Roche Applied Science). The recombinant proteins, fused with an N-terminal protein (e.g., GFP), are then used to determine if the specific monoclonal antibody is capable of binding one or more of the truncated forms of the MMP-7 protein. Through the use of reiterative truncation and generation of recombinant proteins with overlapping amino acid regions, and by Western blot, ELISA, and/or immunoprecipitation methods, it is possible to identify the region that is recognized by the monoclonal antibody under investigation. A schematic of the MMP- 7/GFP construct and the various regions of the MMP-7 used to identify the epitopes of the 5Gl 1.9 and 15H8.12 MMP-7 monoclonal antibodies of the present invention are set forth in Figure 1.

Characterization of the epitopes of MMP-7 Monoclonal Antibodies 5G11.9 and 15H8.12 Epitope mapping for MMP-7 monoclonal antibodies 5Gl 1.9 and 15H8.12 was carried out essentially via the iterative process described above. The analyses revealed that the epitope for the MMP-7 monoclonal antibody designated as 5Gl 1.9 is linear and is all or a portion of the amino acid sequence S YTRDLPHIT VDRLVSKALN (SEQ ID NO:3; corresponding to residues 115 through 134 of the full-length MMP-7 amino acid sequence set forth in SEQ ID NO:1). The epitope for the MMP-7 monoclonal antibody designated as 15H8.12, however, was determined to be a non- linear, conformational epitope containing all or a portion of the amino acid sequence

DSETKNANSLEAKLKEMQKFFGLPITGMLNSRVIEIMQKPRCGVPDVAEYSLFPNS PKWTSKV (SEQ ID NO:4; corresponding to residues 45 through 108 of the full-length MMP-7 amino acid sequence set forth in SEQ ID NO:1). Additional rounds of RTS may be able to refine the epitopes further.

Example 3: Sandwich ELISA Assay Utilizing MMP-7 Monoclonal Antibodies 5Gl 1.9 and 15H8.12 to Detect MMP-7 in Ovarian Cancer in Patient Serum Samples

The sandwich ELISA immunoassay was used to detect MMP-7 in sera from ovarian cancer patents and ovarian cancer-free patients. The capture antibody used in this set of experiments, the 5Gl 1.9 MMP-7 antibody, was bound to a microtiter plate well by passive absorption, as is known in the art. The 15H8.12 antibody was used as the detector antibody and was labeled with horseradish peroxidase (HRP; the detectable substance) for detection of antigen-antibody binding using the chromagen tetramethylbenzidine (TMB). The "readout" for antigen-antibody binding was optical density (OD) at 450 nM and was measured using standard methods in the art. The patient sera samples were analyzed using the sandwich ELISA technique, essentially as described above, to measure MMP-7 levels in sera from a patient cohort of 91 ovarian cancer patients, at various stages of the disease, and 89 "normal" patients not suffering from ovarian cancer. A cut-off threshold of MMP- 7 expression of two standard deviations from the mean MMP-7 expression level was obtained from the cohort of 89 non-cancerous patient serum samples. MMP-7 levels above the threshold value were deemed "positive," whereas those below the threshold level were considered "negative."

Results

Overall, analysis of MMP-7 expression using the sandwich ELISA demonstrated a high specificity of 91% and a sensitivity of 35% in differentiating ovarian cancer samples from the normal, non-cancerous samples. Specifically within each stage of ovarian cancer, this method resulted in sensitivities of 24% (Stage 1; 6/25), 29% (Stage 2; 6/21), 44% (Stage 3; 17/39), and 50% (Stage 4; 3/6).

Example 4: Assay to Identify Preferred Pairs of Monoclonal MMP-7 Antibodies for Use in the Sandwich ELISA Format

Analyses were performed to identify preferred complementary pairings of MMP-7 monoclonal antibodies for use in sandwich ELISA immunoassays. Specifically, each of the various MMP-7 monoclonal antibodies (i.e., 5Gl 1.9, 15H8.12, and various other MMP-7 monoclonal antibodies designated only as, for example, "Clone A") was assayed at various concentrations and alternately used as the "capture" or "detector" antibody in the sandwich ELISA. The detector antibodies were labeled with HRP as above for detection of antibody-antigen binding using the chromagen TMB. In certain aspects of the experiment, normal serum samples (i.e., from patients not suffering from ovarian cancer) were spiked with 250 ng of recombinant MMP-7. The results obtained in the sandwich ELISA with these spiked samples were compared to those observed with buffer only samples (i.e., negative control), as described above. The results obtained with the various pairings are set forth below in Table 1. As described above, the values presented are the optical density (OD) of the samples at 450 nm. The column titled "MMP-7/Buffer only Signal" refers to the result obtained with the MMP-7 spiked samples divided by the buffer only, negative control samples. Table 1 clearly shows that the best MMP-7 monoclonal antibody pairing of those tested with the MMP-7 spiked serum samples was achieved with the use of 5Gl 1.9 as the capture antibody and 15H8.12 as the detector antibody. Table 1 : Results with Serum Samples Spiked with Purified MMP-7

In another aspect of this experiment, the sandwich ELISA was performed as described above with serum samples pooled from patients with ovarian cancer and buffer only, negative control samples. The results obtained with the various antibody pairings are set forth below in Table 2. Again, the values presented are the optical density (OD) of the samples at 450 nm. The column titled "Pooled Ovarian Cancer Serum Samples /Buffer only" refers to the signal obtained with the pooled ovarian cancer serum samples divided by that obtained with the buffer only samples. Table 2 clearly shows that the best MMP-7 monoclonal antibody pairing of those tested with the pooled ovarian cancer serum samples was achieved with the use of 5Gl 1.9 as the capture antibody and 15H8.12 as the detector antibody. Table 2: Results with Pooled Ovarian Cancer Serum Samples

All publications and patent applications mentioned in the specification are indicative of the level of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.

Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be obvious that certain changes and modifications may be practiced within the scope of the appended claims.