Patent Publication Number: US-2006014221-A1

Title: Detection of urinary mesothelin-/megakaryocyte potentiating factor-related peptides for assessment of mesothelioma

Description:
CROSS-REFERENCES TO RELATED APPLICATIONS  
      This application is entitled to priority pursuant to 35 U.S.C. §119(e) to U.S. provisional patent application 60/537,987, which was filed on 21 Jan. 2004. 
    
    
     BACKGROUND OF THE INVENTION  
      The invention relates generally to diagnosing mesothelioma in humans.  
      Mesothelioma is a relatively uncommon in which malignant cells are found on, in, or adhered to an internal membrane, such as the sac (the pleura) lining the chest, the lining (the peritoneum) of the abdominal cavity, or the lining (the pericardium) around the heart. Mesothelioma is more common among individuals exposed to airborne asbestos particles and other respiratory irritants.  
      Mesothelioma can be difficult to diagnose, especially at an early stage of the cancer, owing to the lack of specific symptoms which definitively indicate mesothelioma. Common symptoms of mesothelioma include shortness of breath, pleural effusion, and chest or abdominal pain. Reliable diagnosis has previously required fluid drainage, biopsy, and pathologist confirmation of cancer occurrence. As a result, many mesothelioma patients have been diagnosed only at a relatively late stage in the progression of the disease. Earlier diagnosis permits earlier, and potentially more effective and/or less morbid, intervention.  
      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. Pat. No. 6,083,502). Antibodies that bind with mesothelin have also been described. For example, a monoclonal antibody designated K1 is described in U.S. Pat. No. 5,320,956, and is secreted by the hybridoma that was deposited by others with the American Type Culture Collection (ATCC; 10801 University Boulevard; Manassas, Va. 20110-2209; USA) as accession number HB 10570. Antibody K1 was found to bind with an approximately 40 kilodalton protein found on the surface of ovarian cancer and other cells (Chang et al., 1996, Proc. Natl. Acad. Sci. USA 93(1):136-140). That protein, designated mesothelin, is derived from a larger (approximately 69 kilodalton) precursor protein for which the sequence is shown in  FIG. 1 . Scholler et al. (1999, Proc. Natl. Acad. Sci. USA 96(20):11531-11536) recognized that an antigen having an amino acid sequence highly similar to the amino terminal sequences of mesothelin and of megakaryocyte potentiating factor (MPF) occurs in the serum of many patients afflicted with ovarian carcinoma. Scholler proposed that this antigen could be a useful serum marker for diagnosing ovarian carcinoma.  
      A useful diagnostic test should not only be able to detect occurrence of mesothelioma 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 performed 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. By contrast, urine samples can be collected with little or no specialized equipment, do not require substantial oversight by a healthcare worker, are produced as a part of a patient&#39;s normal physiological processes, and generally are not significant sources of transmissible diseases. For these reasons, diagnostic testing using urine samples as a testing substrate can be preferable to comparable testing done with blood samples.  
     BRIEF SUMMARY OF THE INVENTION  
      The present invention provides a mesothelioma diagnostic test that can be performed using urine samples and that can be used to detect mesothelioma at an early phase of disease progression.  
      The invention relates to a method of diagnosing mesothelioma in a human patient. The method comprises assessing occurrence of a mesothelin/megakaryocyte potentiating factor family (MMPFF) peptide in urine obtained from the patient. Occurrence of the MMPFF peptide in the urine is an indication that the patient is afflicted with mesothelioma.  
      In one embodiment, the MMPFF peptide is assessed in the patient&#39;s urine by contacting the urine (or centrifuged urine) with a first antibody that binds specifically with the MMPFF peptide. By assessing whether the MMPFF peptide has bound with the first antibody, occurrence of the MMPFF peptide in the patient&#39;s urine can be assessed. For example, 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.  
      By way of example, the method can comprise contacting a plate having an anti-MMPFF peptide ‘capture’ antibody bound thereto with urine obtained from a patient. 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). Of course, the second antibody could instead be fluorescently labeled, radiolabeled, or otherwise detectably labeled.  
      In another embodiment of the method of diagnosing mesothelioma, the first antibody can be contacted with a labeled substrate thereof contacting the first antibody with the urine. By comparing 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.  
      The 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 mesothelioma 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. Alternatively, 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 mesothelioma markers. Assessment of occurrence of MMPFF peptide in a patient&#39;s urine can likewise be performed in conjunction with assessment of the MMPFF peptide in the patient&#39;s serum.  
      Substantially the same kits and methods can be used to assess the likelihood that a patient will develop mesothelioma. That is, occurrence of an MMPFF peptide in urine obtained from a patient is an indication that the patient is more likely to develop mesothelioma than an otherwise identical patient 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 mesothelioma in a patient. The amount of an MMPFF peptide in urine obtained from the patient 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. Similarly, 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.  
      In another aspect, the invention relates to a kit for assessing occurrence of an MMPFF peptide in urine obtained from a patient. 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. Of course, the kit can also include reagents for assessing other known markers of mesothelioma.  
    
    
     BRIEF SUMMARY OF THE SEVERAL VIEWS OF THE DRAWINGS  
      In all figures comprising amino acid sequences, standard single-letter amino acid codes are used to represent amino acid residues.  
       FIG. 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.  
       FIG. 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.  
       FIG. 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 AF180951 and reported in Scholler et al., 1999, Proc. Natl. Acad. Sci. USA 96(20):11531-11536.  
       FIG. 4 , comprising  FIGS. 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. In this alignment, identical amino acid residues are indicated by a vertical line, a conservative amino acid substitution is indicated by a cross (+), and dashes (−) indicate a gap inserted into SEQ ID NO: 2 for the purpose of aligning the sequences.  
       FIG. 5 , comprising  FIGS. 5A and 5B , 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 . In this alignment, residues that are identical in all three sequences are represented by upper case single-letter codes, residues that are not identical in all three sequences are represented by lower case single-letter codes, and gaps inserted for the purpose of aligning the sequences are represented by dashes (−).  
       FIG. 6  comprises  FIGS. 6A and 6B .  FIG. 6A  is an amino acid sequence (SEQ ID NO: 4) that includes preferred epitopes for generation of antibodies described herein.  FIG. 6B  is another amino acid sequence (SEQ ID NO: 5) that includes preferred epitopes for generation of antibodies described herein. In each of SEQ ID NOs: 4 and  5 , the underlined, bold X represents any amino acid residue, preferably being either aspartate or asparagine. Other underlined, bold residues in  FIG. 6A  represent residues that are not present in the sequence shown in  FIG. 6B .  
       FIG. 7  is a graph that indicates urinary MMPFF peptide levels in mesothelioma patients described in Example 2.  
       FIG. 8  is a graph that indicates the correlation between urinary MMPFF peptide levels and serum MMPFF peptide levels in mesothelioma patients described in Examples 2 and 3.  
       FIG. 9  is a graph that indicates MMPFF peptide levels in pleural effusion samples obtained from mesothelioma patients described in Example 4. 
    
    
     DETAILED DESCRIPTION OF THE INVENTION  
      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 patients afflicted with mesothelioma. These urine polypeptides bind specifically with antibodies that are raised against proteins of that family. Occurrence of these polypeptides in a patient&#39;s urine is diagnostic that the patient is afflicted with mesothelioma. The amount of the polypeptides decreases with effective treatment of the mesothelioma. Thus, the urine polypeptides can also be used to assess the efficacy of anti-mesothelioma therapy.  
      Definitions  
      As used herein, each of the following terms has the meaning associated with it in this section.  
      A mesothelin/megakaryocyte potentiating factor family peptide (“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. Examples of 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.  
      The term “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 mesothelioma, 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.  
      Detailed Description  
      Soluble mesothelin-related peptides (SMRP) were first described as a serum marker for ovarian cancer and more generally as a serum marker for mesothelial cell related cancers. Indeed, recent reports indicate elevated levels of SMRP in serum samples taken from mesothelioma patients. The present invention demonstrates that SMRP can be detected in pleural effusions and urines of mesothelioma patients and further, the presence of elevated levels of SMRP in these bodily fluids (in addition to serum) is diagnostic for mesothelioma.  
      It has been discovered that one or more polypeptides having significant amino acid sequence similarity with a family of proteins (the mesothelin/megakaryocyte potentiating factor family; “MMPFF”) occurs in the urine of patients afflicted with mesothelioma. These urine peptides can be detected, for example with an antibody raised against a protein of the MMPFF. Occurrence of such peptides in a patient&#39;s urine is an indication that the patient is afflicted with mesothelioma. Owing to the variety of mesothelioma types, the genetic variability among individuals, and other factors, MMPFF peptides will likely not appear in the urine of all patients afflicted with mesothelioma, and the peptides will likely appear in differing amounts in individuals afflicted with mesotheliomas of substantially the same type. Even taking these variations into account, occurrence of one or more MMPFF peptides in the urine of a patient is an indication that the patient is afflicted with mesothelioma.  
      Advantageously, occurrence of MMPFF peptides in the urine of patients afflicted with mesothelioma does not appear to depend on the stage by which the mesothelioma is characterized. For this reason, urinary occurrence of MMPFF peptides can be used to diagnose mesothelioma 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.  
      Another advantage of the kits and methods disclosed herein is that the amount and concentration of MMPFF peptide in the urine of a mesothelioma patient is indicative of the state of the tumor. For this reason, assessment of urinary MMPFF peptide occurrence can be used to assess the efficacy of a mesothelioma 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 mesothelioma therapy is indicative of a therapeutic regimen that is not inhibiting tumor growth.  
      The kits and methods described herein can be used to assess occurrence or progression of various mesothelioma types.  
      Diagnostic Methods  
      The invention includes a method of diagnosing mesothelioma in a patient. The method comprises assessing occurrence of a mesothelin/megakaryocyte potentiating factor family (MMPFF) peptide in urine obtained from the patient. Occurrence of the MMPFF peptide in the urine is an indication that the patient is afflicted with mesothelioma. Mesotheliomas of various type, grade, recurrence, and stage can be diagnosed using this method. The method can also be used to diagnose mesothelioma characterized by various cell types (e.g., pleural, peritoneal, and pericardial mesotheliomas).  
      The method used to assess occurrence of the MMPFF peptide in the patient&#39;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).  
      In one embodiment, occurrence of the MMPFF peptide in the patient&#39;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.  
      Numerous MMPFF-binding antibodies are known in the art. For example, the antibody described in U.S. Pat. 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.  
      In diagnostic kits and methods that use two anti-MMPFF peptide antibodies, the two antibodies preferably do not compete to bind the same epitope. By way of example, 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 1A6. Thus, for example, OV569 can be bound to a substrate and used as a ‘capture’ antibody to bind MMPFF peptide present in a patient&#39;s urine under appropriate antibody-binding conditions, and one of antibodies 4H3, 3G3, and 1A6 can be detectably labeled and contacted with the ‘capture’ antibody after contacting the ‘capture’ antibody with the patient&#39;s urine. Binding of the detectably labeled antibody with the ‘capture’ antibody indicates that the MMPFF peptide was present in the patient&#39;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.  
      As described herein, portions of MMPFF proteins share significant amino acid sequence homology.  FIGS. 1-3  show at least portions of the amino acid sequences of three MMPFF proteins.  FIG. 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 mesothelioma 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).  
      Methods of generating antibodies are well known and only briefly summarized here.  
      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&#39;s complete or incomplete adjuvant, or a similar immunostimulatory 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. If desired, the antibody molecules can be harvested or isolated from the subject (e.g., from the blood or serum of the subject) and further purified by well-known techniques, such as protein A chromatography to obtain the IgG fraction.  
      At an appropriate time after immunization, e.g., when the specific 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), Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96) or trioma techniques. The technology for producing hybridomas is well known (see generally Current Protocols in Immunology (1994) Coligan et al. (Eds.) John Wiley &amp; Sons, Inc., New York, N.Y.). 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.  
      Alternative to preparing monoclonal antibody-secreting hybridomas, 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 SURFZAP™ 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. Pat. 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. WO 92/01047; PCT Publication No. WO 92/09690; PCT Publication No. 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.  
      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. Pat. No. 4,816,567; European Patent Application 125,023; Better et al. (1988) Science 240:1041-1043; Liu et al. (1987) Proc. Natl. Acad. Sci. USA 84:3439-3443; Liu et al. (1987) J. Immunol. 139:3521-3526; Sun et al. (1987) Proc. Natl. Acad. Sci. USA 84:214-218; Nishimura et al. (1987) Cancer Res. 47:999-1005; Wood et al. (1985) Nature 314:446-449; and Shaw et al. (1988) J. Natl. Cancer Inst. 80:1553-1559); Morrison (1985) Science 229:1202-1207; Oi et al. (1986) Bio/Techniques 4:214; U.S. Pat. No. 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.  
      In embodiments in which an anti-MMPFF peptide antibody is contacted with urine obtained from a patient, the urine can be used in its naturally-expressed state or it can be partially purified or clarified prior to use. For example, urine can be centrifuged using standard methods to substantially remove any sediment therefrom prior to contacting the urine with the antibody. Alternatively, 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. By way of example, 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. In this example, occurrence of the MMPFF can be assessed in the retentate in the ultrafiltration device.  
      Because MMPFF peptides are often relatively abundant in urine of mesothelioma patients and because many of the methods (e.g., the immunological methods) described herein are relatively sensitive, concentration of urine is usually not necessary to detect occurrence of MMPFF peptides in urine of mesothelioma 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 patient is the procedure commonly known as a “sandwich ELISA” assay. (ELISA is an abbreviation for enzyme-linked immunosorbent assay.) In this method, 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 patient 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. If 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. Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, beta-galactosidase, or acetylcholinesterase; examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin; examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; an example of a luminescent material includes luminol; examples of bioluminescent materials include luciferase, luciferin, and aequorin, and examples of suitable radioactive material include  125 I,  131 I,  35 S  3 H.  
      Use of standardized assay apparatus permits automation of the method described herein. For example, 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 patient is commonly designated a ‘competition’ assay. In this 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) that binds specifically with the antibody is then contacted with 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&#39;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.  
      When an immunological competition assay is used, 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&#39;s urine as possible. For example, the ligand and the MMPFF peptide should have or comprise the same amino acid sequence. Similarly, if the MMPFF peptide that may occur in the patient&#39;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.  
      The 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 patient is afflicted with mesothelioma. However, a greater number of mesothelioma can be detected and greater confidence in the diagnosis of mesothelioma can be achieved if occurrence of more than one marker of mesothelioma is assessed in the patient. Any additional mesothelioma marker(s) can be a marker normally found in urine, a marker normally found in blood, or a marker normally found in both urine and blood. Thus, the 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.  
      The kits and methods described herein for assessing occurrence of a MMPFF peptide in urine obtained from a patient can be used to assess the likelihood that the patient will develop mesothelioma. Detection of occurrence of an MMPFF peptide in a patient&#39;s urine is an indication that the patient is more likely to develop mesothelioma than an otherwise identical patient in whose urine the MMPFF does not occur. It is recognized that the difference between being afflicted with mesothelioma, the earliest stages of tumor growth, the onset of tumorigenesis, and enhanced susceptibility to mesothelioma may be substantially indistinguishable. Nonetheless, the outcome of each of these processes is development of mesothelioma to the detriment of the patient&#39;s health. For this reason, assessment of any of these states using the kits and methods disclosed herein is useful.  
      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 mesothelioma 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 mesothelioma. For example, such methods can be used to determine whether a mesothelioma patient can be effectively treated using a specific agent or class of agents.  
      Kits for Assessing Occurrence of Urinary MMPFF Peptides  
      The invention also encompasses kits for detecting occurrence of an MMPFF in a urine sample obtained from a mammal (e.g., a human patient). 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. These kits can be used to determine if a subject is suffering from or is at increased risk of developing mesothelioma. For example, the kit can comprise a labeled compound or agent capable of detecting the MMPFF peptide in a urine sample. The kit 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 mesothelioma 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).  
      For antibody-based kits, 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. Alternatively, the kit can comprise the first antibody and a labeled ligand of the first antibody. After contacting the first antibody with a patient&#39;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 patient another marker indicative of occurrence of mesothelioma in the patient.  
     EXAMPLES  
      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.  
     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 (Nunc) that had been previously coated with 100 microliters of capture antibody (MAb, 4H3 as described in Scholler et al., 1999, Proc. Natl. Acad. Sci. USA 96(12):11531-11536 and in PCT publication WO 00/50900) at a concentration of 5 micrograms per milliliter in carbonate-bicarbonate buffer, pH 9.6 overnight at 4° C. Each well was then blocked by filling it with a 3% (w/v) suspension of bovine serum albumin (BSA) for 2 hours at room temperature, after which time the BSA suspension was removed from the wells.  
      Standard curves were prepared using a fusion protein comprising a portion of the mesothelin amino acid sequence (i.e., residues 294-628) fused to an immunoglobulin (Ig) constant region using a described vector encoding a human Ig sequence (as described in PCT publication number WO 00/50900 and in Hollenbaugh et al., 1995, J. Immunol. Meth. 188:1-7). This fusion protein was designated hIgG. Antigen was diluted to 10, 5, 2.5, 1.0, and 0.5 nanograms per milliliter. Sample diluent used for standard dilutions as well as detection antibodies was a 7% (w/v) suspension of BSA.  
      To perform the assay, 100 microliters of each standard dilution, controls, 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 thereafter washed with tris-buffered saline (pH 7.8 to 8) containing 0.05% (v/v) TWEEN® 20 surfactant. 100 microliters of a 200 nanogram per milliliter suspension of biotinylated monoclonal antibody OV569 (as described in Scholler et al., 1999, Proc. Natl. Acad. Sci. USA 96(20):11531-11536 and in PCT publication number WO 00/50900) was added to each well at a concentration of 1 microgram per milliliter. After incubating the plate for 1 hour at room temperature and thereafter washing each well with tris-buffered saline (pH 7.8 to 8) containing 0.05% (v/v) TWEEN® 20 surfactant, 50 microliters of a 1:5000 dilution of Streptavidin-horseradish peroxidase (obtained from Southern Biotechnology Associates, Inc., Birmingham, Ala., catalog no. 7100-05) at was added to each well, and the plate was incubated for 1 hour at room temperature. 100 Microliters of 3,3′,5,5′-tetramethylbenzidine (TMB; a chromogenic substrate for horseradish peroxidase; obtained from Kirkegaard &amp; Perry Laboratories, Inc., Gaithersburg, Md.) was added to each well to generate signal. The plate was incubated for 15 minutes at room temperature before adding 100 microliters of TMB Stop solution (0.1 normal sulfuric acid; obtained from Kirkegaard &amp; Perry Laboratories, Inc., Gaithersburg, Md.) to halt the peroxidase reaction. 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.  
     Example 2  
      Detection of an MMPFF in Urine Samples Obtained from Mesothelioma Patients  
      25 Paired serum/urine samples were obtained from mesothelioma patients. 10 Urine samples from normal, healthy adults were run as negative controls. Urine samples were centrifuged briefly to remove debris. Samples were diluted with a 7% BSA solution as needed to fall into the range of the assay&#39;s standard curve. 100 Microliters of each sample dilution was tested in the assay described in Example 1. The results, displayed in  FIG. 7 , indicate that MMPFF peptide is useful as a urine marker of mesothelioma.  
     Example 3  
      Detection of an MMPFF in Serum Samples Obtained from Mesothelioma Patients  
      Serum samples obtained from all 25 mesothelioma patients described in Example 2, as well as 10 samples from normal, healthy adults, were run at a dilution of 1:50. Correlation of these data is shown in  FIG. 8 .  
     Example 4  
      Detection of an MMPFF in Pleural Effusion Samples Obtained from Mesothelioma Patients  
      46 pleural effusion samples obtained from mesothelioma patients, as well as 93 samples from non-mesothelioma lung cancer patients, were tested using the assay format described in Example 1. The results, displayed in  FIG. 9 , indicate that MMPFF peptide is useful as a pleural effusion marker of mesothelioma.  
      The disclosure of every patent, patent application, and publication cited herein is hereby incorporated herein by reference in its entirety.  
      While this invention has been disclosed with reference to specific embodiments, it is apparent that other embodiments and variations of this invention can be devised by others skilled in the art without departing from the true spirit and scope of the invention. The appended claims include all such embodiments and equivalent variations.