Classifications

• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
  • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
  • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
  • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
  • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
  • G01N33/57407—Specifically defined cancers
  • G01N33/57449—Specifically defined cancers of ovaries
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
  • G01N2333/435—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans
  • G01N2333/46—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans from vertebrates
  • G01N2333/47—Assays involving proteins of known structure or function as defined in the subgroups
  • G01N2333/4701—Details
  • G01N2333/4703—Regulators; Modulating activity
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2800/00—Detection or diagnosis of diseases
  • G01N2800/50—Determining the risk of developing a disease
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N2800/00—Detection or diagnosis of diseases
  • G01N2800/52—Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis

Definitions

• the invention relates generally to diagnosing ovarian cancer in women.
• Ovarian cancer is one of the foremost causes of cancer deaths among women in the U.S.
• One reason for the relatively high mortality rate among ovarian cancer patients is that the disease is often not diagnosed until it reaches an advanced phase.
• An ovarian tumor can be classified by the cell type from which the tumor arose, by the morphology of cells of the tumor, and by the stage to which the tumor has progressed.
• Ovarian tumors can arise from any of three ovarian cell types - epithelial, germ cells, and stromal cells.
• Epithelial ovarian tumors are the most common type of ovarian tumor, accounting for 85 percent or more of all ovarian tumors. EOTs arise from the epithelial cells that cover the outer surface of the ovary. Some EOTs are benign and cause relatively little medical harm. However, malignant EOTs can grow uncontrollably, invade nearby tissues, or metastasize to distant body locations.
• Germ cell ovarian tumors arise from ova-producing cells and can also be either benign or malignant.
• Stromal ovarian tumors arise from ovary connective tissue cells and are relatively rare.
• EOTs are further characterized by the type of cells that make up the EOT. Recognized cell types include serous, mucinous, endometrioid, and clear cell types. Some EOTs are not clearly differentiated among these cell types, and these non-differentiated EOTs tend to grow and spread more quickly than more clearly differentiated types of EOTs. [0007] EOTs are also classified by grade and stage. The grade of a tumor describes its macroscopic appearance. Grade 1 tumors tend to closely resemble normal ovarian tissue, and also tend to have a better prognosis. Grade 3 tumors tend to have an abnormal appearance, and usually have a worse prognosis. Grade 2 tumors are intermediate between Grades 1 and 3.
• Stage I ovarian tumors are limited to one or both ovaries. Gradations within Stage I describe tumors limited to the interior of one (Stage IA) or both ovaries (Stage IB) and tumors (Stage IC) which appear on the surface of one or both ovaries, in one or more ovaries having a ruptured capsule, or in association with tumor cells present in ascites or detected in a peritoneal wash. Stage II ovarian tumors have extended within the pelvis beyond the ovaries. Gradations within Stage II describe tumors that have extended to one or both of the uterus and the fallopian tubes (Stage LTA), to other pelvic organs (Stage HB).
• Stage LTA fallopian tubes
• Stage III ovarian tumors have spread beyond the pelvis, to the lymph nodes, or both.
• Stage IN ovarian tumors have spread to organs beyond the peritoneal cavity.
• Markers that have been used by others to diagnose ovarian cancer include CA 125 (Halila et al., 1987, Br. J. Cancer 56(2):153-156), carcmoembryonic antigen (CEA; Juweid et al, 1997, Gynecol. Oncol. 67(3):259-271), vascular endothelial growth factor (NEGF; Candido Dos Reis et al., 2002, Gynecol. Obstet. Invest. 54(3): 132- 136), urinary gonadotropin peptide (UGP; Schutter et al., 1999, Anticancer Res.
• Mesothelin is a protein which is expressed on the surface of at least mesothelial cells, mesotheliomas, some squamous cell carcinomas, and ovarian cancers (Chang et al., 1996, Proc. Natl. Acad. Sci. USA 93:136-140). Mesothelin has been described in the literature (e.g., U.S. Patent No. 6,083,502). Antibodies that bind with mesothelin have also been described. For example, a monoclonal antibody designated Kl is described in U.S. Patent No.
• a useful diagnostic test should not only be able to detect occurrence of ovarian cancer in a patient, it is also preferably inexpensive, non-invasive, and easy to use. Diagnostic tests that use blood or serum as a testing substrate require that blood be drawn from a patient to be screened, and sometimes require further separation, purification, or other treatment of the withdrawn blood sample. Drawing blood must be perfo ⁇ ned by a trained health care worker, is painful and invasive for the patient, requires specialized equipment and reagents for storage and transportation of blood samples, and carries the risk of transmission of blood-borne pathogens.
• the present invention provides an ovarian cancer diagnostic test that can be performed using urine samples and that can be used to detect ovarian cancer at an early phase of disease progression.
• the invention relates to a method of diagnosing an ovarian cancer (i.e., one or more of an epithelial, stromal, and germ cell ovarian cancer) in a woman.
• the method comprises assessing occurrence of a mesothelin/megakaryocyte potentiating factor family (MMPFF) peptide in urine obtained from the woman. Occurrence of the MMPFF peptide in the urine is an indication that the woman is afflicted with an ovarian cancer.
• MMPFF mesothelin/megakaryocyte potentiating factor family
• the MMPFF peptide is assessed in the woman's urine by contacting the urine (or centrifuged urine) with a first antibody that binds specifically with the MMPFF peptide.
• a first antibody that binds specifically with the MMPFF peptide.
• the first antibody can be bound to a substrate, such as a plastic multi- well plate of the type adapted for automated analysis in a robotic apparatus. Binding of the MMPFF peptide and the first antibody can, for example, be assessed by contacting the first antibody with a second antibody that binds specifically with the MMPFF peptide and assessing co- localization of the first and second antibodies.
• the second antibody can be detectably labeled, such as with a compound selected from the group consisting of an enzyme, a radionuclide, a fluorophore, and a chromophore.
• the method can comprise contacting a plate having an anti- MMPFF peptide 'capture' antibody bound thereto with urine obtained from a woman.
• the urine can, optionally, be incubated with the plate for a period such as 10 minutes or an hour.
• the plate can then be contacted with a biotinylated second antibody that binds with an epitope of the MMPFF peptide than does the capture antibody.
• a streptavidin-linked enzyme can be bound to the biotinylated antibody to enable its detection in the presence of a chromogenic substrate (e.g., 3,3',5,5'-tetramethylbenzidine, which is a chromogenic substrate of horseradish peroxidase).
• the second antibody could instead be fluorescently labeled, radiolabeled, or otherwise detectably labeled.
• the first antibody can be contacted with a labeled substrate thereof contacting the first antibody with the urine.
• the amount of labeled ligand that binds with the first antibody that has been contacted with the urine with the amount of labeled ligand that binds with an equivalent amount of the first antibody that has not been contacted with the urine, one can assess how much of MMPFF from the urine has bound with the first antibody.
• kits and methods described herein can be used to detect a variety of MMPFF peptides, including naturally occurring MMPFF peptides (i.e., both full length proteins such as mesothelin and fragments of such proteins that are naturally produced in the bodies of ovarian cancer patients) and synthetically produced MMPFF peptides.
• the amino acid sequence of the MMPFF peptide should comprise at least 10 (20, 50, or 200) consecutive residues of a sequence selected from the group consisting of SEQ ID NOs: 1-5.
• the MMPFF peptide can comprise a portion of at least 20 consecutive amino acid residues, wherein the amino acid sequence of the portion is at least 90% (or 95%) identical to 20 consecutive residues of a sequence selected from the group consisting of SEQ ID NOs: 1-5.
• the kits and methods disclosed herein can be used in conjunction with known or hereafter developed kits and methods for assessing occurrence (e.g., in urine or serum) other ovarian cancer markers.
• ovarian cancer markers known to occur in urine include urinary gonadotropin peptide, cysteine proteinase, neopterin, and tumor- associated trypsin inhibitor.
• CA 125 Known serum ovarian cancer markers include CA 125, carcinoembryonic antigen, vascular endothelial growth factor, tumor-associated trypsin inhibitor, a CD44 splice variant, anti-malignin antibody, lactate dehydrogenase, alpha- hydroxybutyrate dehydrogenase, CA19-9, tissue polypeptide antigen, and sialyl TN.
• CA 125 is known to be a surrogate marker for ovarian cancer occurrence and progression. Assessment of occurrence of MMPFF peptide in a woman's urine can likewise be performed in conjunction with assessment of the MMPFF peptide in the woman's serum.
• kits and methods can be used to assess the likelihood that a woman will develop an ovarian cancer. That is, occurrence of an MMPFF peptide in urine obtained from a woman is an indication that the woman is more likely to develop an ovarian cancer than an otherwise identical woman in whose urine the MMPFF does not occur.
• Substantially the same kits and methods can also be used to assess the efficacy of a therapy for an ovarian cancer in a woman.
• the amount of an MMPFF peptide in urine obtained from the woman following the therapy can be compared with the amount of the MMPFF in her urine before the therapy. A lower amount of the MMPFF peptide in the urine following the therapy is an indication that the therapy is efficacious.
• a greater amount of the MMPFF peptide in the urine following the therapy is an indication that the therapy is not efficacious.
• Such kits and methods can be used to compare the efficacy of various therapeutic agents or regimens.
• the invention in another aspect, relates to a kit for assessing occurrence of an MMPFF peptide in urine obtained from a woman.
• the kit comprises a first agent (e.g., an antibody) for binding the MMPFF peptide and an instructional material that describes contacting urine with the first agent.
• the format of the kit is not critical - many standard formats can be used, such as ELISA, latex bead aggregation, and surface plasmon resonance formats.
• the kit can include an MMPFF peptide for use as a positive control.
• the kit can also include reagents for assessing other known markers of ovarian cancer.
• Figure 1 is the amino acid sequence (SEQ ID NO: 1) of mesothelin precursor protein. This sequence is the same as that listed in GENBANK® accession number 2207386A and reported in Chang et al., 1996, Proc. Natl. Acad. Sci. USA 93(1): 136-140.
• Figure 2 is the amino acid sequence (SEQ ID NO: 2) of megakaryocyte potentiating factor (MPF) precursor protein. This sequence is the same as that listed in GENBANK® accession number NP_005814 and reported in Yamaguchi et al., 1994, J. Biol. Chem. 269(2):805-808.
• Figure 3 is a partial amino acid sequence (SEQ ID NO: 3) of a soluble variant form of MPF precursor protein listed in GENBANK® accession number AFl 80951 and reported in Scholler et al, 1999, Proc. Natl. Acad. Sci. USA 96(20):11531-11536.
• Figure 4 comprising Figures 4A and 4B, is a comparison of residues 294-628 of SEQ ID NO: 1 and a nearly identical portion of SEQ ID NO: 2. Residue numbers are listed in the right margin.
• MST means mesothelin.
• MPF means megakaryocyte potentiating factor.
• Figure 5 is a comparison of similar portions of SEQ ID NOs: 1-3. Residue numbers are listed in the right margin.
• MST means mesothelin.
• MPF means megakaryocyte potentiating factor.
• SMR means the soluble variant form of MPF for which the sequence is listed in Fig. 3.
• Figure 6 comprises Figures 6 A and 6B.
• Figure 6 A is an amino acid sequence (SEQ ID NO: 4) that includes preferred epitopes for generation of antibodies described herein.
• Figure 6B is another amino acid sequence (SEQ ID NO: 5) that includes preferred epitopes for generation of antibodies described herein.
• the underlined, bold X represents any amino acid residue, preferably being either aspartate or asparagine.
• Other underlined, bold residues in Figure 6A represent residues that are not present in the sequence shown in Figure 6B.
• Figure 7 is a bar graph that indicates serum levels of CA125II antigen (bars with stripes slanting downward from left to right) and urine levels of an MMPFF peptide (bars with stripes slanting upward from left to right), assayed as disclosed herein. Assays were performed for four patients, designated 1-4, both at the time of ovarian cancer diagnosis ("a") and approximately one month after the onset of therapy ("b").
• the invention relates to the discovery that one or more polypeptides having significant amino acid sequence similarity with a family of proteins that includes mesothelin, megakaryocyte potentiating factor (MPF), and a soluble variant of MPF occurs in the urine of women afflicted with ovarian cancer.
• These urine polypeptides bind specifically with antibodies that are raised against proteins of that family. Occurrence of these polypeptides in a patient's urine is diagnostic that the patient is afflicted with ovarian cancer. The amount of the polypeptides decreases with effective treatment of the ovarian cancer. Thus, the urine polypeptides can also be used to assess the efficacy of anti-ovarian cancer therapy.
• MMPFF peptide is a polypeptide that has an amino acid sequence that either (i) comprises at least 10 consecutive residues of a sequence selected from the group consisting of SEQ ID NOs: 1-5 or (ii) comprises a portion of at least 20 consecutive amino acid residues wherein the amino acid sequence of the portion is at least 90% (preferably at least 95% or 100%) identical to 20 consecutive residues of a sequence selected from the group consisting of SEQ ID NOs: 1-5.
• an "antibody” refers collectively and individually to immunoglobulin molecules and immunologically active portions of immunoglobulin molecules, i.e., molecules that contain an antigen binding site which specifically binds an MMPFF peptide.
• a molecule which specifically binds with an MMPFF peptide is a molecule which binds the peptide, but does not substantially bind other molecules in a sample (e.g., a urine sample) which naturally contains the polypeptide.
• immunologically active portions of immunoglobulin molecules include F(ab) and F(ab')2 fragments which can be generated by treating the antibody with an enzyme such as papain or pepsin, respectively. Either or both of polyclonal and monoclonal antibodies can be used in the methods and kits described herein.
• the term "monoclonal antibody” refers to a population of antibody molecules that contain only one species of an antigen binding site capable of immunoreacting with a particular epitope.
• labeled with regard to an antibody or a peptide, includes direct labeling of the peptide or antibody by coupling (i.e., physically linking) a detectable substance to the peptide or antibody, as well as indirect labeling of the peptide or antibody by coupling it with another reagent that is directly labeled. Examples of indirect labeling include detection of a primary antibody using a fluorescently labeled secondary antibody and end-labeling of a peptide with biotin such that it can be detected with fluorescently labeled streptavidin.
• An "instructional material” is a publication, a recording, a diagram, or any other medium of expression which can be used to communicate how to use a kit described herein, information for interpreting occurrence of an MMPFF in urine as it relates to an ovarian cancer, or both.
• the instructional material of the kit of the invention can, for example, be affixed to a container which contains a kit of the invention or be shipped together with a container which contains the kit. Alternatively, the instructional material can be shipped separately from the container with the intention that the instructional material and the kit be used cooperatively by the recipient.
• MMPFF mesothelin/megakaryocyte potentiating factor family
• MMPFF peptides Owing to the variety of ovarian cancer types, the genetic variability among individuals, and other factors, MMPFF peptides will likely not appear in the urine of all patients afflicted with ovarian cancer, and the peptides will likely appear in differing amounts in individuals afflicted with ovarian cancers of substantially the same type. Even taking these variations into account, occurrence of one or more MMPFF peptides in the urine of a woman is an indication that the woman is afflicted with ovarian cancer.
• occurrence of MMPFF peptides in the urine of women afflicted with ovarian cancer does not appear to depend on the stage by which the ovarian cancer is characterized. For this reason, urinary occurrence of MMPFF peptides can be used to diagnose ovarian cancer at an early stage, facilitating efficacious treatment of the cancer before it has reached a phase of the disease at which therapy is futile or nearly so.
• kits and methods disclosed herein are indicative of the state of the tumor. For this reason, assessment of urinary MMPFF peptide occurrence can be used to assess the efficacy of an ovarian cancer therapeutic regimen. To the extent the regimen induces tumor shrinkage or regression, urinary concentration of MMPFF peptide can be expected to decrease. Similarly, gradual or unimpeded increase in urinary MMPFF peptide concentration during ovarian cancer therapy is indicative of a therapeutic regimen that is not inhibiting tumor growth.
• kits and methods described herein can be used to assess occurrence or progression of various ovarian cancer types.
• the kits and methods are used to assess occurrence or progi-ession of an epithelial ovarian cancer, which are among the most common ovarian cancers.
• the kits and methods are used to assess occurrence of progression of stromal ovarian tumors or germ cell ovarian tumors.
• the invention includes a method of diagnosing an ovarian cancer in a woman.
• the method comprises assessing occurrence of a mesothelin/megakaryocyte potentiating factor family (MMPFF) peptide in urine obtained from the woman.
• MMPFF mesothelin/megakaryocyte potentiating factor family
• Occurrence of the MMPFF peptide in the urine is an indication that the woman is afflicted with an ovarian cancer.
• Ovarian cancers of various type e.g., epithelial ovarian cancer
• grade, and stage can be diagnosed using this method.
• the method can also be used to diagnose ovarian cancers characterized by various cell types (e.g., serous, mucinous, endometrioid, clear, and non-differentiated ovarian tumors).
• the method used to assess occurrence of the MMPFF peptide in the woman's urine is not critical. Any method that can be used to assess whether the peptide is present or absent is suitable. Methods capable of assessing the quantity (e.g., concentration) of the MMPFF peptide in the urine are preferable in some embodiments, particularly when assessments made over a period of time are to be compared (e.g., as when assessing the efficacy of a regimen of anti-cancer therapy). [0046] In one embodiment, occurrence of the MMPFF peptide in the patient's urine is assessed by contacting the urine with an antibody that binds specifically with the MMPFF peptide and assessing whether the MMPFF peptide has bound with the first antibody.
• MMPFF-binding antibodies are known in the art.
• the antibody described in U.S. Patent No. 5,320,956 and secreted by the hybridoma deposited with the ATCC as accession no. HB 10570 can be used. That antibody binds specifically with an approximately 40 kilodalton portion of mesothelin protein, as described by Chang et al. (1996, Proc. Natl. Acad. Sci. USA 93(1): 136-140).
• Other suitable antibodies have been described by Scholler et al. (1999, Proc. Natl., Acad. Sci. USA 96(20):11531-11536) and in PCT publication number WO 00/50900, wherein such antibodies are designated OV569, 4H3, 3G3, and 1A6.
• the two antibodies preferably do not compete to bind the same epitope.
• the antibody designated OV569 by Scholler et al. binds at an epitope which is independent of the epitopes bound by the antibodies designated 4H3, 3G3, and 1 A6.
• OV569 can be bound to a substrate and used as a 'capture' antibody to bind MMPFF peptide present in a patient's urine under appropriate antibody-binding conditions, and one of antibodies 4H3, 3G3, and 1 A6 can be detectably labeled and contacted with the 'capture' antibody after contacting the 'capture' antibody with the patient's urine. Binding of the detectably labeled antibody with the 'capture' antibody indicates that the MMPFF peptide was present in the patient's urine. Analysis of the amount of detectable label co-localized with the 'capture' antibody can indicate the quantity of the peptide that was present.
• Figs. 1-3 show at least portions of the amino acid sequences of three MMPFF proteins.
• Figure 4 and 5 show alignments of those sequences, indicating the regions of greatest sequence homology among these proteins. From these figures, it is apparent that the sequences shown in Figs. 6A and 6B (SEQ ID NOs: 4 and 5, respectively) represent useful portions of MMPFF peptides.
• Antibodies raised against all or a portion (e.g., 10, 20, 50, or 200 consecutive residues) of either of these sequences can be expected to bind specifically with a broad range of MMPFF peptides, including those that occur in the urine of ovarian cancer patients.
• An MMPFF (e.g., one described herein or in the prior art), or a fragment thereof, can be used as an immunogen to generate antibodies using standard techniques for polyclonal and monoclonal antibody preparation.
• a fragment of a full-length MMPFF, when used as an immunogen, should comprise at least 10 (preferably 12, 15, 20, 50, 100, or 20 or more) amino acid residues of the amino acid sequence of any of SEQ ID NOs: 1-5 or the amino acid sequence of another MMPFF member.
• Appropriate MMPFF peptides for generation of antibodies useful in the kits and methods described herein comprise a portion of at least 20 consecutive amino acid residues that is at least 90% (preferably at least 95% or 100%) identical to 20 consecutive residues of a sequence selected from the group consisting of SEQ ID NOs: 1-5 (preferably either SEQ ID NO: 4 or SEQ ID NO: 5).
• An immunogen typically is used to prepare antibodies by immunizing a suitable (i.e., immunocompetent) subject such as a rabbit, goat, mouse, or other mammal or vertebrate.
• An appropriate immunogenic preparation can contain, for example, recombinantly- expressed or chemically-synthesized polypeptide.
• the preparation can further include an adjuvant, such as Freund's complete or incomplete adjuvant, or a similar i munostimulatory agent.
• Polyclonal antibodies can be prepared as described above by immunizing a suitable subject with a polypeptide of the invention as an immunogen.
• the antibody titer in the immunized subject can be monitored over time by standard techniques, such as with an enzyme linked immunosorbent assay (ELISA) using immobilized polypeptide.
• ELISA enzyme linked immunosorbent assay
• the antibody molecules can be harvested or isolated from the subject (e.g., from the blood or serum of the subj ect) and further purified by well-known techniques, such as protein A chromatography to obtain the IgG fraction.
• 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), Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, hie, pp. 77- 96) or trioma techniques.
• Hybridoma cells producing a monoclonal antibody of the invention are detected by screening the hybridoma culture supernatants for antibodies that bind the polypeptide of interest, e.g., using a standard ELISA assay.
• a monoclonal antibody directed against a polypeptide of the invention can be identified and isolated by screening a recombinant combinatorial immunoglobulin library (e.g., an antibody phage display library) with the polypeptide of interest.
• 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 SURFZAPTM Phage Display Kit, Catalog No. 240612). Additionally, examples of methods and reagents particularly amenable for use in generating and screening antibody display library can be found in, for example, U.S. Patent No. 5,223,409; PCT Publication No. WO 92/18619; PCT Publication No. WO 91/17271; PCT Publication No. WO 92/20791; PCT Publication No. WO 92/15679; PCT Publication No. WO 93/01288; PCT Publication No.
• Recombinant antibodies such as chimeric and humanized monoclonal antibodies, comprising both human and non-human portions, which can be made using standard recombinant DNA techniques, are within the scope of the invention.
• Such chimeric and humanized monoclonal antibodies can be produced by recombinant DNA techniques known in the art, for example using methods described in PCT Publication No. WO 87/02671; European Patent Application 184,187; European Patent Application 171,496; European Patent Application 173,494; PCT Publication No. WO 86/01533; U.S. Patent No. 4,816,567; European Patent Application 125,023; Better et al. (1988) Science 240:1041-1043; Liu et al.
• Patent 5,225,539 Jones et al. (1986) Nature 321:552-525; Verhoeyan et al. (1988) Science 239:1534; and Beidler et al. (1988) J. Immunol. 141:4053-4060.
• the urine can be used in its naturally-expressed state or it can be partially purified or clarified prior to use.
• urine can be centrifuged using standard methods to substantially remove any sediment therefrom prior to contacting the urine with the antibody.
• the urine can be filtered or ultrafiltered to reduce its volume or to remove large contaminants. Because MMPFF peptides that occur in urine can be expected to be polypeptides having molecular weights in the range 10,000 - 100,000 Daltons, selection of an appropriate filtration/ultrafiltration is necessary to prevent removal of the MMPFF peptide prior to its detection.
• a relatively large pore filter e.g., one that permits passage of globular particles having molecular weights of 250,000 to 1 million Daltons can be used to remove particulate material from urine and an ultrafiltration device equipped with a membrane that excludes passage of proteins having molecular weights greater than about 5,000 Daltons can be used to concentrate the filtrate.
• occurrence of the MMPFF can be assessed in the retentate in the ultrafiltration device.
• concentration of urine is usually not necessary to detect occurrence of MMPFF peptides in urine of ovarian cancer patients. In situations in which clarification of urine is desired, centrifugation can be preferable, since the potential that MMPFF peptides present in the urine will become bound with or enmeshed within the filter medium is not present.
• One preferred method for assessing occurrence of an MMPFF peptide in urine of a woman is the procedure commonly known as a "sandwich ELISA" assay.
• ELISA is an abbreviation for enzyme-linked immunosorbent assay.
• an antibody is bound to a substrate, such as a glass bead or the bottom surface of a plastic multi-well assay plate. This antibody is designated a 'capture' antibody.
• Raw, clarified, or purified urine from the woman is contacted with the substrate under conditions (e.g., low concentrations of salt and detergents and non-protein-denaturing conditions), so that any MMPFF peptide present in the urine binds specifically with the capture antibody.
• the substrate is optionally rinsed with a fluid that does not comprise the MMPFF peptide to remove residual urine and any non-bound MMPFF.
• the substrate is then contacted with a second antibody that specifically binds with the MMPFF peptide at an epitope independent of the epitope at which the capture antibody binds.
• the second antibody is either detectably labeled or linked with either a ligand or a receptor of the ligand. Either way, binding of the second antibody is detected (and, optionally, quantitated) after rinsing the substrate with a fluid that does not comprise the second antibody. Detection of the second antibody is indicative of the presence in the urine of the MMPFF peptide.
• the amount of the second antibody is quantitated, then the amount of the MMPFF peptide in the urine can be quantitated, for example, by comparison of the amount of second antibody detected with measurements made using control samples containing known amounts of the MMPFF.
• Detection an antibody can be facilitated by coupling the antibody to a detectable substance. Examples of detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, and radioactive materials.
• suitable enzymes include horseradish peroxidase, alkaline phosphatase, beta-galactosidase, or acetylcholinesterase;
• suitable prosthetic group complexes include streptavidin / biotin and avidin / biotin;
• suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin;
• an example of a luminescent material includes luminol;
• bioluminescent materials include luciferase, luciferin, and aequorin, and examples of suitable radioactive material
• 125 131 35 3 include I, I, S or H.
• standardized assay apparatus permits automation of the method described herein.
• many different standardized assay containers are known, such as 24-, 48-, 96-, and 384-well plastic plates. Where these containers are adapted to fit a robotic apparatus, automated analysis of samples can be achieved, permitting high-throughput screening of many samples in a relatively short time.
• Automated assay apparatus and containers adapted for their use in computer-controlled assays are known in the art and readily adapted for the kits and methods described herein.
• Another type of immunological assay that can be used to assess occurrence of an MMPFF peptide in urine obtained from a woman is commonly designated a 'competition' assay.
• an antibody that binds specifically with the MMPFF peptide is fixed to a substrate.
• Raw, clarified, or purified urine is contacted with the substrate (preferably for a period of minutes or hours), so that any MMPFF peptide present in the urine binds with the antibody.
• a labeled ligand e.g., a labeled version of the same MMPFF peptide or another MMPFF peptide
• the substrate preferably for a period of minutes or hours
• the amount of labeled ligand bound with the substrate is assessed after rinsing the substrate with a fluid that does not comprise the label or the labeled ligand.
• the amount of label bound with the substrate is compared with the amount of label bound with an otherwise identically treated substrate that is not contacted with the patient's urine.
• the difference between the two amounts of bound label represents the amount of MMPFF peptide bound to the substrate, and is indicative of the amount of the MMPFF peptide that was present in the urine sample applied to the substrate.
• the labeled ligand of the antibody bound with the substrate should be as nearly identical to the MMPFF peptide known or expected to be present in the patient's urine as possible.
• the ligand and the MMPFF peptide should have or comprise the same amino acid sequence.
• the MMPFF peptide that may occur in the patient's urine is expected to by glycosylated, then the ligand should be glycosylated in the same way, at the same position, and to the same extent. In this way, affinity differences of the antibody for the ligand and for the MMPFF peptide can be minimized and the accuracy of the competition assay can be improved.
• kits and methods described herein can be used alone to assess occurrence of an MMPFF peptide in urine of a human patient, and such occurrence is indicative that the woman is afflicted with ovarian cancer.
• a greater number of ovarian cancers can be detected and greater confidence in the diagnosis of ovarian cancer can be achieved if occurrence of more than one marker of ovarian cancer is assessed in the woman.
• Any additional ovarian cancer marker(s) can be a marker normally found in urine, a marker normally found in blood, or a marker normally found in both urine an blood.
• MMPFF peptides are normally found in the serum of patients afflicted with ovarian cancer (Scholler et al., 1999, Proc. Natl. Acad. Sci. USA 96(20): 11531-11536).
• kits and methods described herein for assessing occurrence of MMPFF peptides in urine can be used in conjunction with kits and methods of detecting the same or other MMPFF peptides in serum.
• Other ovarian cancer markers known to occur in urine include urinary gonadotropin peptide (UGP; Schutter et al., 1999, Anticancer Res. 19(6C):5551-5557), cysteine proteinase (UCP; Gao et al., 1996, Hua Xi Yi Ke Da Xue Xue Bao 27(3):291-294), neopterin (Szarka et al., 1988, Acta Chir. Hung.
• TATI tumor-associated trypsin inhibitor
• Other ovarian cancer markers known to occur in serum include CA 125 (Halila et al., 1987, Br. J. Cancer 56(2):153-156), carcinoembryonic antigen (CEA; Juweid et al., 1997, Gynecol. Oncol. 67(3):259-271), vascular endothelial growth factor (VEGF; Candido Dos Reis et al., 2002, Gynecol. Obstet.
• TATI tumor-associated trypsin inhibitor
• CD44 splice variants
• anti-malignin antibody Bogoch et al., 1991, Lancet 337:927
• LDH lactate dehydrogenase
• aHBDH alpha-hydroxybutyrate dehydrogenase
• TPA tissue polypeptide antigen
• STN sialyl TN
• kits and methods for assessing any combination of these known markers in blood and/or urine so long as the kits and methods include assessing occurrence of at least MMPFF peptide in urine.
• the kits and methods described herein for assessing occurrence of a MMPFF peptide in urine obtained from a woman can be used to assess the likelihood that the woman will develop an ovarian cancer. Detection of occurrence of an MMPFF peptide in a woman's urine is an indication that the woman is more likely to develop an ovarian cancer than an otherwise identical woman in whose urine the MMPFF does not occur.
• Anti-MMPFF peptide antibodies can be used diagnostically or prognostically to monitor MMPFF levels in urine as part of a clinical testing procedure, e.g., to, for example, determine the efficacy of a given ovarian cancer treatment regimen.
• the kits and methods described herein can be used to determine whether an agent (e.g., an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate) can be administered to a subject in order to alleviate, inhibit, reverse, or prevent ovarian cancer. For example, such methods can be used to determine whether an ovarian cancer patient can be effectively treated using a specific agent or class of agents.
• kits for Assessing Occurrence of Urinary MMPFF Peptides also encompasses kits for detecting occurrence of an MMPFF in a urine sample obtained from a mammal (e.g., a woman).
• the kit comprises a first agent for binding the MMPFF peptide, a second agent for assessing binding of the MMPFF peptide with the agent, and an instructional material that describes contacting urine with the first agent.
• kits can be used to determine if a subject is suffering from or is at increased risk of developing ovarian cancer.
• the kit can comprise a labeled compound or agent capable of detecting the MMPFF peptide in a urine sample.
• kits can also, or alternatively, contain means for determining the amount of the MMPFF peptide in the sample.
• Kits can include instructions for assessing whether the tested subject is suffering from or is at risk of developing ovarian cancer if the amount of the MMPFF peptide is above or below a normal level (e.g., an absorbance measurement of at least 0.2 at 450 nanometers using the methodology set forth in Example 1).
• the kit can comprise, for example: (1) a first antibody (e.g., attached to a solid support) which specifically binds with an MMPFF peptide and, optionally, (2) a second, different antibody which specifically binds with either the MMPFF peptide (e.g., at a epitope distinct from the epitope at which the first antibody binds) or the first antibody and is conjugated with a detectable agent.
• the kit can comprise the first antibody and a labeled ligand of the first antibody. After contacting the first antibody with a woman's urine sample, binding of the labeled ligand with the first antibody can be assessed in a competition-type assay, as described herein.
• the kits can further comprise reagents and/or instructions for assessing occurrence in urine or serum of the woman another marker indicative of occurrence of ovarian cancer in the woman.
• Example 1 The invention is now described with reference to the following Examples. These Examples are provided for the purpose of illustration only, and the invention is not limited to these Examples, but rather encompasses all variations which are evident as a result of the teaching provided herein. [0076] Example 1
• Sandwich ELISA Assay for Assessing MMPFF in a Sample A typical assay used to detect an MMPFF in a urine sample is now described. Assays were performed in a 96-well clear, flat-bottom microtiter plate that had been previously coated with monoclonal antibody 4H3 (as described in Scholler et al., 1999, Proc. Natl. Acad. Sci. USA 96(12):11531-11536 and in PCT publication WO 00/50900). The bottom of the wells were coated with the antibody by adding to individual wells 50 microliters of a suspension comprising 3 micrograms of antibody per milliliter in carbonate- bicarbonate buffer (pH 9.6).
• Standard curves were prepared using a fusion protein (as described in Scholler et al., 1999, Proc. Natl. Acad. Sci.
• the diluent used was a 7% (w/v) suspension of BSA.
• 50 microliters of an hlgG fusion protein dilution, a control, or a urine sample, or a diluted urine sample was added to individual wells. The plate was incubated for 1 hour at room temperature and the wells were washed with tris- buffered saline (pH 7.8 to 8) containing 0.05% (v/v) TWEEN® 20 surfactant.
• 50 microliters of a 200 nanogram per milliliter suspension of biotinylated monoclonal antibody OV569 as described in Scholler et al, 1999, Proc. Natl. Acad. Sci.
• TMB 3,3',5,5'-tetramethylbenzidine
• TMB Stop solution 0.1 normal sulfuric acid; obtained from Kirkegaard & Perry Laboratories, Inc., Gaithersburg, MD
• Blue color generated by the action of the peroxidase on TMB was assessed using a Molecular Devices SpectraMax® Plus 384 spectrophotometric plate reader (model number 02523) to measure the absorbance at 450 nanometers.
• Urine samples were obtained from 25 patients known to be afflicted with ovarian cancer. Individual urine samples were centrifuged for 15 minutes at 13,000 rpm (ca. 15,700 x g) to remove sediment. Individual 50 microliter aliquots of urine sample supernatants were tested using the assay described in Example 1.
• Example 2 In order to rule out non-specific binding that may have mimicked signal corresponding to occurrence of MMPFF in a urine sample described in Example 2, urine samples for which relatively high absorbance values were obtained in Example 2 were selected. An assay plate was prepared as described in Example 1, except that the plate had not been coated with antibody 4H3. Individual urine samples were prepared and added to the plate as described in Example 2. [0088] No signal above the background level was detected in any of the samples tested in this Example.
• Example 2 In a separate experiment, the urine samples described in Example 2 were tested using a plate prepared as described in Example 1. The 569 monoclonal antibody used in this experiment was not biotinylated, however. Otherwise, the assay was as described in Example 1. No signal above background level was detected for any of the samples tested. [0090] hi another separate experiment, the assay was performed as described in Example 1, except that a biotinylated antibody that has no relation to the MMPFF was used in place of biotinylated monoclonal antibody 569. Assays of the urine samples described in Example 2 by this method yielded no signal above background when tested in this manner. [0091] These data indicate that the increased absorbance signal at 450 nanometers observed in the sandwich ELISA assay using urine obtained from ovarian cancer patients is a true response indicating the presence of the MMPFF peptide in the patients' urine.
• Urine samples obtained from 31 patients who had been diagnosed with bladder cancer, from 3 women who were afflicted with benign gynecological diseases, and from 22 urine samples obtained from normal, healthy adults were tested using the assay described in Example 1.
• the data demonstrate that urine obtained from normal, healthy patients has very- low levels of MMPFF peptide.
• urine from 22 of 25 ovarian cancer patients (88%) exhibited significantly elevated MMPFF peptide levels.
• Urine samples obtained from bladder cancer patients i.e., another genitourinary disease
• MMPFF peptides could be detected in both urine and serum samples from all patients, albeit at very low levels in some instances. Using a cut-off value of 0.2 absorbance units (at 450 nanometers) for the test of urinary samples, 22 out of 25 urine samples (88%) tested positive for MMPFF. Using a cut-off value of 0.1 absorbance units (at 450 nanometers) for the test of serum samples, only 16 of the 25 (64%) tested positive for MMPFF. These data demonstrate that MMPFF peptide level is elevated in both the serum and urine of ovarian cancer patients. However, detection of MMPFF peptide in urine appears to be more sensitive and may therefore have greater diagnostic value.
• CA 125 level was assessed in each of the 25 urine samples described in Example 2 using the CA125IITM test kit. None of the urine samples yielded results above the assay's background level. These results indicate that CA 125 is not present in the urine of these patients. These data also confirm that serum tumor markers such as CA 125 are not necessarily present in the urine of patients in whose serum they occur.

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