# Patent

## Title
MCM6 and MCM7 monoclonal antibodies and methods for their use in the detection of cervical disease

## Abstract

Compositions and methods for diagnosing high-grade cervical disease in a patient sample are provided. The compositions include novel monoclonal antibodies, and variants and fragments thereof, that specifically bind to MCM6 or MCM7. Monoclonal antibodies having the binding characteristics of an MCM6 or MCM7 antibody of the invention are further provided. Hybridoma cell lines that produce an MCM6 or MCM7 monoclonal antibody of the invention are also disclosed herein. The compositions find use in practicing methods for diagnosing high-grade cervical disease comprising detecting overexpression of MCM6, MCM7, or both MCM6 and MCM7 in a cervical sample from a patient. Kits for practicing the methods of the invention are further provided. Polypeptides comprising the amino acid sequence for an MCM6 or an MCM7 epitope and methods of using these polypeptides in the production of antibodies are also encompassed by the present invention.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application claims the benefit of U.S. Provisional Application Ser. No. 60/751,495, filed Dec. 19, 2005, which is incorporated herein by reference in its entirety.


FIELD OF THE INVENTION
The invention relates to antibodies capable of binding to MCM6 or MCM7 and methods of using these antibodies, particularly in the diagnosis of cervical disease.
BACKGROUND OF THE INVENTION
Carcinoma of the cervix is the second most common neoplasm in women, accounting for approximately 12% of all female cancers and causing approximately 250,000 deaths per year. Baldwin et al. (2003) Nature Reviews Cancer 3:1-10. In many developing countries where mass screening programs are not available, the clinical problem is more serious. Cervical cancer in these countries is the number one cause of cancer deaths in women.
The majority of cases of cervical cancer represent squamous cell carcinoma, although adenocarcinoma is also seen. Cervical cancer can be prevented by population screening as it evolves through well-defined noninvasive intraepithelial stages, which can be distinguished morphologically. Williams et al. (1998) Proc. Natl. Acad. Sci. USA 95:14932-14937. While it is not understood how normal cells become transformed, the concept of a continuous spectrum of histopathological change from normal, stratified epithelium through cervical intraepithelial neoplasia (CIN) to invasive cancer has been widely accepted for years. The precursor to cervical cancer is dysplasia, also known in the art as CIN or squamous intraepithelial lesions (SIL). Squamous intraepithelial abnormalities may be classified by using the three-tiered (CIN) or two-tiered (Bethesda) system. Under the Bethesda system, low-grade squamous intraepithelial lesions (LSIL), corresponding to CINI and HPV infection, generally represent productive HPV infections with a relatively low risk of progression to invasive disease. High-grade squamous intraepithelial lesions (HSIL), corresponding to CINII and CINIII in the three-tiered system, show a higher risk of progression to cervical cancer than do LSIL, although both LSIL and HSIL are viewed as potential precursors of malignancy. Patient samples may also be classified as ASCUS (atypical squamous cells of unknown significance) or AGUS (atypical glandular cells of unknown significance) under this system.
A strong association of cervical cancer and infection by high-risk types of human papilloma virus (HPV), such as types 16, 18, and 31, has been established. In fact, a large body of epidemiological and molecular biological evidence has established HPV infection as a causative factor in cervical cancer. Moreover, HPV is found in 85% or more of the cases of high-grade cervical disease. However, HPV infection is very common, possibly occurring in 5-15% of women over the age of 30, but few HPV-positive women will ever develop high-grade cervical disease or cancer. The presence of HPV alone is indicative only of infection, not of high-grade cervical disease, and, therefore, testing for HPV infection alone results in many false positives. See, for example, Wright et al. (2004) Obstet. Gynecol. 103:304-309.
Current literature suggests that HPV infects the basal stem cells within the underlying tissue of the uterine-cervix. Differentiation of the stem cells into mature keratinocytes, with resulting migration of the cells to the stratified cervical epithelium, is associated with HPV viral replication and re-infection of cells. During this viral replication process, a number of cellular changes occur that include cell-cycle de-regulation, active proliferation, DNA replication, transcriptional activation and genomic instability (Crum (2000) Modern Pathology 13:243-251; Middleton et al. (2003) J. Virol. 77:10186-10201; Pett et al. (2004) Cancer Res. 64:1359-1368).
Most HPV infections are transient in nature, with the viral infection resolving itself within a 12-month period. For those individuals who develop persistent infections with one or more oncogenic subtypes of HPV, there is a risk for the development of neoplasia in comparison to patients without an HPV infection. Given the importance of HPV in the development of cervical neoplasia, the clinical detection of HPV has become an important diagnostic tool in the identification of patients at risk for cervical neoplasia development. The clinical utility of HPV-based screening for cervical disease is in its negative predictive value. An HPV negative result in combination with a history of normal Pap smears is an excellent indicator of a disease-free condition and a low risk of cervical neoplasia development during the subsequent 1-3 years. However, a positive HPV result is not diagnostic of cervical disease; rather it is an indication of infection. Although the majority of HPV infections is transient and will spontaneously clear within a 12-month period, a persistent infection with a high-risk HPV viral subtype indicates a higher risk for the development of cervical neoplasia. To supplement HPV testing, the identification of molecular markers associated with cervical neoplasia is expected to improve the clinical specificity for cervical disease diagnosis.
Cytological examination of Papanicolaou-stained cervical smears (Pap smears) currently is the method of choice for detecting cervical cancer. The Pap test is a subjective method that has remained substantially unchanged for 60 years. There are several concerns, however, regarding its performance. The reported sensitivity of a single Pap test (the proportion of disease positives that are test-positive) is low and shows wide variation (30-87%). The specificity of a single Pap test (the proportion of disease negatives that are test-negative) might be as low as 86% in a screening population and considerably lower in the ASCUS PLUS population for the determination of underlying high-grade disease. See, Baldwin et al., supra. A significant percentage of Pap smears characterized as LSIL or CINI are actually positive for high-grade lesions. Furthermore, up to 10% of Pap smears are classified as ASCUS (atypical squamous cells of undetermined significance), i.e., it is not possible to make a clear categorization as normal, moderate or severe lesion, or tumor. However, experience shows that up to 10% of this ASCUS population has high-grade lesions, which are consequently overlooked. See, for example, Manos et al. (1999) JAMA 281:1605-1610. Therefore, molecular biomarkers that are selectively overexpressed in high-grade cervical disease and compositions for the detection of these biomarkers are needed to practice reliable methods for diagnosing high-grade cervical disease.
Minichromosome maintenance (MCM) proteins play an essential part in eukaryotic DNA replication. The minichromosome maintenance (MCM) proteins function in the early stages of DNA replication through loading of the prereplication complex onto DNA and functioning as a helicase to help unwind the duplex DNA during de novo synthesis of the duplicate DNA strand. Each of the MCM proteins has DNA-dependent ATPase motifs in their highly conserved central domain. Levels of MCM proteins generally increase in a variable manner as normal cells progress from G0 into the G1/S phase of the cell cycle. In the G0 phase, MCM2 and MCM5 proteins are much less abundant than are the MCM7 and MCM3 proteins. MCM6 forms a complex with MCM2, MCM4, and MCM7, which binds histone H3. In addition, the subcomplex of MCM4, MCM6, and MCM7 has helicase activity, which is mediated by the ATP-binding activity of MCM6 and the DNA-binding activity of MCM4. See, for example, Freeman et al. (1999) Clin. Cancer Res. 5:2121-2132; Lei et al. (2001) J. Cell Sci. 114:1447-1454; Ishimi et al. (2003) Eur. J. Biochem. 270:1089-1101, all of which are herein incorporated by reference in their entirety.
Early publications have shown that the MCM proteins, and in particular, MCM5, are useful for the detection of cervical disease (Williams et al. (1998) Proc Natl Acad Sci U.S.A. 95:14932-14937), as well as other cancers (Freeman et al. (1999) Clin Cancer Res. 5:2121-2132). The published literature indicates that antibodies to MCM5 are capable of detecting cervical neoplastic cells. The specificity for detection of high-grade cervical disease has not been demonstrated for MCM5 (Williams et al. (1998) Proc Natl Acad Sci U.S.A. 95:14932-14937). The detection of MCM5 expression is not restricted to high-grade cervical disease but is also detected in identified low-grade dysplasia and proliferative cells that have re-entered the cell cycle following infection with high-risk HPV. The detection of cervical neoplasia with antibodies to MCM5 is shown in FIG. 4. In addition to MCM5, other members from the MCM family, including MCM2 and MCM7 have been shown to be potentially useful markers for the detection of cervical neoplasia in tissue samples (Freeman et al. (1999) Clin Cancer Res. 5:2121-2132; Brake et al. (2003) Cancer Res. 63:8173-8180). Recent results have shown that MCM7 appears to be a specific marker for the detection of high-grade cervical disease using immunochemistry formats (Brake et al. (2003) Cancer Res. 63:8173-8180; Malinowski et al. (2004) Acta Cytol. 43:696).
Therefore, there is a need in the art for antibodies that are capable of detecting expression of a biomarker that is selectively overexpressed in high-grade cervical disease. Such antibodies could be used in methods for differentiating high-grade disease from conditions that are not considered clinical disease, such as early-stage HPV infection and mild dysplasia.
SUMMARY OF THE INVENTION
Compositions and methods for diagnosing high-grade cervical disease are provided. Compositions include monoclonal antibodies capable of binding to nuclear biomarker proteins of the invention, particularly MCM proteins, more particularly MCM6 and MCM7. Antigen-binding fragments and variants of these monoclonal antibodies, hybridoma cell lines capable of producing these antibodies, and kits comprising the monoclonal antibodies of the invention are also encompassed herein.
The compositions of the invention find use in methods for diagnosing high-grade cervical disease. The methods comprise detecting expression of at least one nuclear biomarker, wherein overexpression of the nuclear biomarker is indicative of high-grade cervical disease. Specifically, the methods comprise using the antibodies of the invention to detect overexpression of MCM6 or MCM7 in a cervical sample.
Compositions of the invention further include isolated polypeptides that comprise an epitope capable of binding an MCM6 or MCM7 monoclonal antibody. These polypeptides find use in methods for producing MCM6 or MCM7 antibodies. Isolated nucleic acid molecules encoding the amino acid sequences of the MCM6 or MCM7 epitopes are also provided.


DETAILED DESCRIPTION OF THE INVENTION
Compositions and methods for diagnosing high-grade cervical disease are provided. Compositions include monoclonal antibodies that are capable of binding to nuclear biomarker proteins that are selectively overexpressed in high-grade cervical disease, particularly MCM proteins, more particularly MCM6 and MCM7. 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 present compositions find use in methods for diagnosing high-grade cervical disease in a patient.
The compositions of the invention include monoclonal antibodies that specifically bind to MCM6 or MCM7, or to a variant or fragment thereof. The amino acid and nucleotide sequences for MCM6 are set forth in SEQ ID NO:3 (Accession No. NP—005906) and SEQ ID NO:4 (Accession No. NM—005915), respectively. The amino acid and nucleotide sequences for MCM7 are set forth in SEQ ID NO:1 (Accession No. NP—005907) and SEQ ID NO:2 (Accession No. NM—005916), respectively. In particular embodiments, the MCM6 monoclonal antibody designated as 9D4.3 and the MCM7 monoclonal antibody designated as 2E6.2 are provided. A hybridoma cell line that produces MCM7 monoclonal antibody 2E6.2 was deposited with the Patent Depository of the American Type Culture Collection (ATCC), Manassas, Va., 20110-2209 on Apr. 14, 2005 and assigned Patent Deposit No. PTA-6669. A hybridoma cell line that produces MCM6 monoclonal antibody 9D4.3 was deposited with the Patent Depository of the American Type Culture Collection (ATCC), Manassas, Va., 20110-2209 on Aug. 9, 2005 and assigned Patent Deposit No. PTA-6911. 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. 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 9D4.3 and 2E6.2 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 monoclonal antibody 9D4.3 or 2E6.2. Variants and fragments of monoclonal antibody 9D4.3 and 2E6.2 that retain the ability to specifically bind to MCM6 or MCM7, respectively, 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, “MCM6 antibody” or “MCM7 antibody” refers to any antibody that specifically binds to MCM6 (SEQ ID NO:3) or MCM7 (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 MCM6 and MCM7 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 15 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 effecter 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 (L1), 50-56 (L2) and 89-97 (L3) in the light chain variable domain and 31-35 (H1), 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 (L1), 50-52 (L2) and 91-96 (L3) in the light chain variable domain and 2632 (H1), 53-55 (H2) and 96-101 (H3) in the heavy chain variable domain; Clothia and Lesk, J. Mol. 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 multispecific 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 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 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 VH-VL 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 (CH1) 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 CH1 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 MCM6 and MCM7 antibodies are encompassed by the invention so long as they retain the desired affinity of the full-length antibody. Thus, for example, a fragment of an MCM6 antibody will retain the ability to bind to an MCM6 antigen. Similarly, a fragment of an MCM7 antibody will retain the ability to bind to an MCM7 antigen. Such fragments are characterized by properties similar to the corresponding full-length antibody, that is, the fragments will specifically bind MCM6 or MCM7. 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 VH and VL domains of an antibody, wherein these domains are present in a single polypeptide chain. See, for example, U.S. Pat. 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 VH and VL 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. Pat. No. 5,514,548. Clackson et al. (1991) Nature 352:624-628 and Marks et al. (1991) J. Mol. 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.
Preferably 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 MCM6 or MCM7 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. Pat. 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. (1991) J. Mol. Biol. 222:581-597; and U.S. Pat. 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. Pat. 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 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 Nos. WO 92/18619; WO 91/17271; WO 92/20791; WO 92/15679; 93/01288; WO 92/01047; 92/09690; and 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.
In some aspects of the invention, antibodies may be selected on the basis of desirable staining of cytological, rather than histological, samples. That is, in particular embodiments the antibodies are selected with the end sample type (e.g., cytology preparations) in mind and for binding specificity. Antibodies directed to specific biomarkers of interest, such as MCM6 or MCM7, are selected and purified via a multi-step screening process. Such methods for antibody selection are described in pending U.S. application Ser. No. 11/087,227, entitled “Methods and Compositions for the Detection of Cervical Disease,” filed Mar. 23, 2005, which is herein incorporated by reference in its entirety.
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 “MCM6 epitope” comprises the part of the MCM6 protein to which an MCM6 monoclonal antibody binds. An “MCM7 epitope” comprises the part of the MCM7 protein to which an MCM7 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”; 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-specific 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 MCM6 or MCM7 monoclonal antibody. These polypeptides correspond to a portion of the antigen (i.e., MCM6 or MCM7) that binds to a monoclonal antibody. Such polypeptides find use in methods for producing antibodies that bind selectively to MCM6 or MCM7. 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:5 (corresponding to residues 760-772 in the MCM6 amino acid sequence set forth in SEQ ID NO:3) comprise an epitope recognized by an MCM6 monoclonal antibody, more particularly monoclonal antibody 9D4.3. The amino acid sequence set forth in SEQ ID NO:6 (corresponding to residues 127-138 in the MCM7 amino acid sequence set forth in SEQ ID NO:1) comprise an epitope recognized by an MCM7 monoclonal antibody, more particularly monoclonal antibody 2E6.2. Variants and fragments of the MCM6 and MCM7 epitope sequences set forth in SEQ ID NOs:5 and 6 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 MCM6 or MCM7 epitopes, and variants and fragments thereof.
The polypeptides of the invention comprising MCM6 or MCM7 epitopes can be used in methods for producing monoclonal antibodies that specifically bind to MCM6 or MCM7, as described herein above. Such polypeptides can also be used in the production of polyclonal MCM6 or MCM7 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 MCM6 or MCM7 epitope (i.e., 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 biomarker protein. 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, N.Y.), 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, N.Y.); 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) Yale J. Biol. Med., 54:387-402).
Amino acid sequence variants of a monoclonal antibody or a polypeptide comprising an MCM6 or MCM7 epitope described herein are also encompassed by the present invention. Variants can be prepared by mutations in the cloned DNA sequence encoding the antibody 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, N.Y.); U.S. Pat. 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, GlyAla, ValIleLeu, AspGlu, LysArg, AsnGln, and PheTrpTyr.
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.
Preferably, variants of a reference polypeptide have amino acid sequences that have at least 70% or 75% sequence identity, preferably at least 80% or 85% sequence identity, more preferably 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. More preferably, the molecules share at least 96%, 97%, 98% or 99% 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 amino acid residues. Corrections for sequence identity associated with conservative residue substitutions or gaps can be made (see Smith-Waterman homology search algorithm).
The MCM6 and MCM7 monoclonal antibodies of the invention may be labeled with a detectable substance as described below to facilitate biomarker protein detection in the 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, bioluminescent materials, and radioactive materials. Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, β-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 125I, 131I, 35S, or 3H.
Kits comprising at least one MCM6 or one MCM7 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 MCM6 or MCM7. The kit may be promoted, distributed, or sold as a unit for performing the methods of the present invention. Additionally, the kits may contain a package insert describing the kit and methods for its use.
Kits of the invention generally comprise at least one monoclonal antibody directed to MCM6 or MCM7, 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. In some embodiments, the detection chemicals comprise a labeled polymer conjugated to a secondary antibody. 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. In one embodiment, the kit comprises a secondary antibody that is conjugated to an HRP-labeled polymer. 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. In other embodiments, antibody binding to a biomarker protein is detected through the use of a mouse probe reagent that binds to monoclonal antibodies, followed by addition of a dextran polymer conjugated with HRP that binds to the mouse probe reagent. Such detection reagents are commercially available from, for example, Biocare Medical.
The kits of the present invention may further 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.
In another embodiment, the kits of the invention comprise at least two monoclonal antibodies. In certain aspects of the invention, the kits comprise an MCM6 and an MCM7 antibody, more particularly the MCM6 monoclonal antibody 9D4.3 and the MCM7 antibody 2E6.2. When multiple antibodies are present in the kit, each antibody may be provided as an individual reagent or, alternatively, as an antibody cocktail comprising all of the antibodies of interest. 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 of the invention are useful in the diagnosis of high-grade cervical disease and may further include reagents for Pap staining (e.g., EA50 and Orange G).
The compositions of the invention find use in methods for diagnosing high-grade cervical disease in a patient such as those disclosed in pending U.S. application Ser. No. 11/087,227, entitled “Methods and Compositions for the Detection of Cervical Disease,” filed Mar. 23, 2005, which is herein incorporated by reference in its entirety. “Diagnosing high-grade cervical disease” is intended to include, for example, diagnosing or detecting the presence of cervical disease, monitoring the progression of the disease, and identifying or detecting cells or samples that are indicative of high-grade cervical disease. The terms diagnosing, detecting, and identifying high-grade cervical disease are used interchangeably herein. By “high-grade cervical disease” is intended those conditions classified by colposcopy as premalignant pathology, malignant pathology, moderate to severe dysplasia, and cervical cancer. Underlying high-grade cervical disease includes histological identification of CINII, CINIII, HSIL, carcinoma in situ, adenocarcinoma, and cancer (FIGO stages I-IV).
The methods of the invention comprise detecting overexpression of at least one nuclear biomarker that is selectively overexpressed in high-grade cervical disease. By “nuclear biomarker” is intended any gene of protein that is predominantly expressed in the nucleus of the cell. A nuclear biomarker may be expressed to a lesser degree in other parts of the cell. By “selectively overexpressed in high-grade cervical disease” is intended that the nuclear biomarker of interest is overexpressed in high-grade cervical disease but is not overexpressed in conditions classified as LSIL, CINI, HPV-infected samples without any dysplasia present, immature metaplastic cells, and other conditions that are not considered to be clinical disease. Thus, detection of the nuclear biomarkers of the invention permits the differentiation of samples indicative of underlying high-grade cervical disease from samples that are indicative of benign proliferation, early-stage HPV infection, or mild dysplasia. Nuclear biomarkers of particular interest include MCM proteins, particularly MCM6 and MCM7.
In a particular aspect of the invention, the methods comprise obtaining a cervical sample from a patient, contacting the sample with at least one MCM6 or MCM7 monoclonal antibody of the invention, and detecting binding of the antibody to the MCM protein. In other embodiments, the sample is contacted with at least two monoclonal antibodies, a first antibody that specifically binds to MCM6, particularly monoclonal antibody 9D4.3, and a second antibody that specifically binds to MCM7, particularly monoclonal antibody 2E6.2. Techniques for detecting antibody binding are well known in the art. Antibody binding to a biomarker of interest may be detected 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 binding may used to practice the methods of the invention.
As used herein, “cervical sample” refers to any sampling of cells, tissues, or bodily fluids from the cervix in which expression of a biomarker can be detected. Examples of such body samples include but are not limited to gynecological fluids, biopsies, and smears. Cervical samples may be obtained from a patient by a variety of techniques including, for example, by scraping or swabbing an area or by using a needle to aspirate bodily fluids. Methods for collecting cervical samples are well known in the art. In particular embodiments, the cervical sample comprises cervical cells, particularly in a liquid-based preparation. In one embodiment, cervical samples are collected according to liquid-based cytology specimen preparation guidelines such as, for example, the SUREPATH® (TriPath Imaging, Inc.) or the THINPREP® preparation (CYTYC, Inc.). Cervical samples may be transferred to a glass slide for viewing under magnification. Fixative and staining solutions may be applied to the cells on the glass slide for preserving the specimen and for facilitating examination. In one embodiment the cervical sample will be collected and processed to provide a monolayer sample, as set forth in U.S. Pat. No. 5,346,831, herein incorporated by reference.
One of skill in the art will appreciate 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 cervical sample preparation, antibody, and detection of antibody binding may be automated. The methods of the invention may also be combined with conventional Pap staining techniques to permit a more accurate diagnosis of high-grade cervical disease.
The following examples are offered by way of illustration and not by way of limitation:
EXPERIMENTAL
Example 1
Production of Mouse Monoclonal Antibodies to MCM7
Mouse monoclonal antibodies specific for MCM7 were generated. The antigen (an immunogenic polypeptide) was a recombinant hexahistidine-tagged N-terminal fragment of the MCM7 protein. The antigen was expressed using a baculovirus expression system in Tni cells. Specifically, the coding sequence for the hexahistidine-tagged MCM7 N-terminal fragment (SEQ ID NO:7) was cloned into the pFastBac1 plasmid (Invitrogen) for expression in Tni cells. Methods for producing recombinant proteins using baculovirus expression systems are well known in the art. The tagged MCM7 fragment was purified using a chelating agarose charged with Ni+2 ions (Ni—NTA from Qiagen) and used as an immunogen. The amino acid sequence of the immunogenic MCM7 N-terminal polypeptide fragment is provided in SEQ ID NO:8.
Mouse immunizations and hybridoma fusions were performed essentially as described in Kohler et al. (1975) Nature 256:495-496. Mice were immunized with the immunogenic tagged-MCM7 fragment in solution. Antibody-producing cells were isolated from the immunized mice and fused with myeloma cells to form monoclonal antibody-producing hybridomas. The hybridomas were cultured in a selective medium. The resulting cells were plated by serial dilution and assayed for the production of antibodies that specifically bind MCM7 (and that do not bind to unrelated antigens). To confirm that the monoclonal antibodies of interest reacted with the MCM7 protein only and not with the hexahistidine tag, selected hybridomas were screened against an MCM7-FLAG-tagged protein. Selected monoclonal antibody (mAb)-secreting hybridomas were then cultured.
Antibodies were purified from the culture media supernatants of “exhausted” hybridoma cells (i.e., cells grown until viability drops to between 0-15%) using recombinant Protein A-coated resin (STREAMLINE®, Amersham, Inc.). Antibodies were eluted using low pH followed by immediate neutralization of pH. Fractions with significant absorbances at 280 nM were pooled. The resultant pool was dialyzed against PBS. Purified antibodies were subjected to further characterization. MCM7 monoclonal antibody 2E6.2 was determined to be an IgG1 isotype. Details of the epitope mapping of this antibody are described below.
Example 2
Production of Mouse Monoclonal Antibodies to MCM6
Mouse monoclonal antibodies specific for MCM6 were generated. The antigen (an immunogenic polypeptide) was a recombinant FLAG-tagged MCM6 protein. The antigen was expressed using a proprietary expression vector from Cell & Molecular Technology, Inc. in HEK293 cells or alternatively expressed using a baculovirus expression system in Tni cells. The coding sequence for the FLAG-tagged MCM6 is set forth in SEQ ID NO:9. FLAG-tagged MCM6 was purified from cell lysates using the anti-FLAG M2 Affinity Gel matrix and the FLAG peptide for elution (Sigma Chemical Co., St. Louis, Mo.). The FLAG-tagged MCM6 protein used as an immunogen. The amino acid sequence of the immunogenic FLAG-tagged MCM6 polypeptide is provided in SEQ ID NO:10.
Mouse immunizations and lymphocyte fusion were performed by RIMMS technology, essentially as described in Kilpatrick et al. (1997) Hybridoma 16(4):381-389. Mice were immunized with the immunogenic FLAG-tagged-MCM6. Primary screening of uncloned hybridoma supernatants was performed using recombinant MCM6 protein. Secondary screening and screening of cloned hybridoma supernatants was performed using a separate batch of recombinant MCM6 protein. Selected monoclonal antibody (mAb)-secreting hybridomas were then cultured.
Antibodies were purified from the culture media supernatants of “exhausted” hybridoma cells (i.e., cells grown until viability drops to between 0-15%) using recombinant Protein A-coated resin (STREAMLINE®, Amersham, Inc.). Antibodies were eluted using low pH followed by immediate neutralization of pH. Fractions with significant absorbances at 280 nM were pooled. The resultant pool was dialyzed against PBS. Purified antibodies were subjected to further characterization. MCM6 monoclonal antibody 9D4.3 was determined to be an IgG2a isotype. Details of the epitope mapping of this antibody are described below.
Example 3
Isolation of Monoclonal Antibodies from Hybridoma Cells
The following procedure is used to isolate monoclonal antibodies from hybridoma cells:
Media Preparation


    
    
        To a sterile 1,000 ml storage bottle, add 100 ml Hyclone Fetal Bovine Serum (FBS).
        Add 10 ml of MEM Non-Essential Amino Acids Solution.
        Add 10 ml of Penicillin-Streptomycin-L-Glutamine Solution.
        QS to approximately 1000 ml with ExCell 610-HSF media.
        Place sterile cap on bottle and secure tightly. Swirl gently to mix.
        Connect a 1000 ml sterile acetate vacuum filter unit (0.2 μm) to a vacuum pump system.
        Gently pour approximately half of the media solution into sterile acetate vacuum filter unit and turn on the vacuum.
        Once the first half of the media has been filtered, pour the remaining media into the filter unit and continue filtering.
        After all the media has been filtered, disconnect the vacuum hose from the vacuum filter unit and turn off the vacuum pump. Remove the receiver portion of the filter unit from the filter bottle. Place a new sterile bottle cap on the bottle.
        Store at 2° C. to 10° C. Protect from light.

Initial Hybridoma Cell Culture

        Thaw vial of stock hybridoma frozen culture in a pre-warmed 37° C. H2O bath.
        Spray the outside of the freeze vial with 70% ethanol.
        Move the thawed vial into the Biological Safety Cabinet.
        Remove the cells from the freeze vial and transfer the cells to a 15 ml centrifuge tube.
        Add 7 ml of cell culture media drop-wise to the 15 ml centrifuge tube containing the thawed cells.
        Centrifuge the 15 ml centrifuge tube containing the thawed cells and culture media for 5 minutes at 200 g force.
        While the cells are in the centrifuge, add 45 ml of cell culture media to a sterile T-225 flask.
        After centrifugation, visually inspect the tube for the presence of a cell pellet.
        Remove the media from the centrifuge tube being careful not to dislodge the cell pellet. Note: If the cell pellet is disturbed, repeat the centrifugation step.
        Add 5 ml of cell culture media to the 15 ml centrifuge tube containing the pelleted cells. Pipette to re-suspend the cell pellet into the media.
        Transfer the entire contents of the resuspended cells and culture media into the T-225 flask containing the 45 ml of media.
        Cap the T-225 flask.
        Observe for presence of intact cells under the microscope. Place the T-225 flask immediately into a CO2 incubator and allow the cells to incubate overnight.

Expansion of Hybridoma Cell Line

        Continue to monitor the cell culture for viability, concentration, and presence of contamination.
        Monitor and adjust the cell suspension from the initial T-225 flask until the concentration is approximately 600,000 cells/ml to 800,000 cells/ml and a total of 200 to 250 ml of media.
        Dislodge cells and add additional media as needed to meet minimum cell density requirements. Divide and transfer cell suspension into one new sterile T-225 flask. Place the 2×T-225 flasks into the CO2 incubator.
        Monitor the cells from the 2×T-225 flasks until the concentration is approximately 600,000 cells/ml to 800,000 cells/ml, and a total of between 200 to 250 ml of media for each flask.
        Dislodge cells and add additional media as needed to meet minimum cell density requirements. Divide and transfer the cell suspensions into 2 additional new sterile T-225 flasks for a total of 4×T-225 flasks. Return all flasks to the CO2 incubator.
        Monitor the cells, and adjust volume in the 4×T-225 flasks until the cell concentration is approximately 600,000 cells/ml to 800,000 cells/ml with a total volume of approximately 250 ml per T-225 flask (or approximately 1000 ml total).
        Continue to monitor the cells from the 4×T-225 flasks until the cells have grown to exhaustion, with a final viability of 0%-15%. The cell culture supernatant is now ready for the Clarification Process.

Clarification of Supernatant

        Turn on the tabletop centrifuge. Place the 500 ml tube adapters into the rotor buckets, close the lid and set the temperature to 4° C. (+/−) 4° C.
        Using aseptic technique, pour the media from all four of the now exhausted T-225 flasks into 2×500 ml conical centrifuge tubes.
        Make sure the 2×500 ml tubes are balanced. Transfer supernatant from one tube to the other as necessary to balance them.
        Centrifuge the exhausted supernatant at 1350 g (+/−40 g) for 15 minutes at 2° C. to 10° C.
        After centrifugation is complete, aseptically decant the supernatant into a sterile 1000 ml storage bottle and secure with a sterile cap.
        Aseptically transfer 1 ml to the microfuge tube. Store microfuge tube with sample at 2° C. to 10° C. (Protect from light).
        The clarified supernatant sample is ready for IgG evaluation using the Easy-Titer® Assay.

Buffer Preparation

Binding Buffer:

        Add approximately 600 ml of DI H2O to a clean beaker.
        Add 77.28 ml of Boric Acid solution (4% W/V). Stir at room temperature with a clean stir bar.
        Weigh out 233.76 g of Sodium Chloride and place into the solution while continuing to stir.
        Bring solution up to approximately 950 ml with DI H2O and continue to stir.
        When the Sodium Chloride has dissolved and the solution is clear, adjust the pH to 9.0±0.2 with Sodium Hydroxide.
        Remove the solution to a clean 1000 ml graduated cylinder and QS to 1000 ml with DI H2O.
        Transfer the completed buffer to an appropriate storage bottle. This buffer may be stored for up to 7 days before use.
        Repeat this entire process to prepare an additional 0.2 liters to 1.0 liter of Binding Buffer.

Elution Buffer

        Weigh out 1.725 g of sodium phosphate, monobasic and place into a clean 250 ml beaker with a clean stir bar.
        Weigh out 3.676 g of sodium citrate and place into the same clean 250 ml beaker.
        Add approximately 175 ml of DI H2O and stir at room temperature until dissolved.
        Weigh out 4.38 g of Sodium Chloride and place into the solution while continuing to stir.
        Bring solution up to approximately 225 ml with DI H2O and continue to stir.
        When the Sodium Chloride has dissolved and the solution is clear, adjust the pH to 3.5±0.2 with Hydrochloric Acid.
        Remove the solution to a clean 250 ml graduated cylinder and QS to 250 ml with DI H2O.
        Connect a 500 ml sterile acetate vacuum filter unit (0.2 μm) to a vacuum pump system and filter sterilize the solution.
        Remove the filter and close the container with a sterile cap.

Antibody Adsorption

        Pour the Clarified Supernatant ( ̃1 L) into a clean 4000 ml plastic beaker with a clean stir bar.
        Add an approximately equal amount ( ̃1 L) of the Binding Buffer to the clean 4000 ml plastic beaker containing the clarified supernatant. Add a clean stir bar.
        Cover the beaker with clean plastic wrap and label “Antibody Binding.”
        Calculate the approximate amount of STREAMLINE® Protein A that will be needed using the data in Table 1.
    
    









TABLE 1







Volume of Protein A Resin Required











Volume of Protein A



Quantity IgG (μg/ml)
Resin Required in



in Supernatant
Milliliters (ml)














>180-≦200
12.0



>160-≦180
11.0



>140-≦160
10.0



>120-≦140
9.0



>100-≦120
8.0



 >80-≦100
7.0



>60-≦80
6.0



>40-≦60
4.5



>20-≦40
3.5



≦20
2.0










    
    
        Secure a clean Disposable Column and stopcock assembly to a ring stand and clamp. Close the stopcock.
        Mix appropriate amount of STREAMLINE Protein A beads by inverting the bottle several times. Withdraw the required volume and place into the Disposable Column.
        Wash the STREAMLINE Protein A beads with 10 ml of DI H2O. Open the stopcock and allow the DI H2O to drain. Close the stopcock. Repeat with an additional 10 ml of DI H2O.
        Wash the STREAMLINE Protein A beads with 10 ml of Binding Buffer. Open the stopcock and allow the Binding Buffer to drain. Close the stopcock. Repeat with an additional 10 ml of Binding Buffer.
        Resuspend the STREAMLINE Protein A beads in  ̃10 ml of the Clarified Supernatant and Binding Buffer solution (from the 4000 ml beaker) and transfer the beads into the 4000 ml beaker containing the Clarified Supernatant and Binding Buffer solution. Repeat as required to transfer any remaining beads. When completed, discard the column and stopcock.
        Allow the mixture to mix vigorously at 2° C. to 10° C. for approximately 18 hours.
        When mixing is complete, turn off the stir plate and remove the “Antibody Binding” beaker with the buffered supernatant and bead suspension back to the lab bench area. Allow the STREAMLINE Protein A beads to settle to the bottom of the beaker (approximately 5 minutes).
        Secure a clean Disposable Column and stopcock assembly to a ring stand and clamp. Close the stopcock.
        Label a clean, 250 ml bottle or suitable container “Column Wash-Post Binding.”
        Label a clean plastic beaker “Supernatant-Post Binding.”
        Decant the supernatant from the 4000 ml beaker into the clean, labeled, 2 liter plastic beaker, leaving the beads in the bottom of the 4000 ml beaker. Cover the 2000 ml beaker containing the “Supernatant-Post Binding” solution with clean plastic wrap and store at 2° C. to 10° C.
        Add approximately 15 ml of Binding Buffer into the decanted 4000 ml “Antibody Binding” beaker. Resuspend the STREAMLINE Protein A beads and transfer them to the column. Open the stopcock and allow the Binding Buffer to drain into the “Column Wash-Post binding” container. Close the stopcock when drained.
        Transfer any remaining STREAMLINE Protein A beads in the “Antibody Binding” beaker by adding additional Binding Buffer, mixing, and transferring to the column as in the preceding steps. Close the stopcock when drained.
        Calculate the approximate amount of Binding Buffer needed to wash the STREAMLINE Protein A beads in the column using the data in Table 2.
    
    









TABLE 2







Binding Buffer Volume for Column Wash









Volume of Binding


Quantity IgG (μg/ml)
Buffer Required in


in Supernatant
Milliliters (ml)





>180-≦200
5 column washes total



with 15.0 ml each


>160-≦180
5 column washes total



with 15.0 ml each


>140-≦160
5 column washes total



with 12.5 ml each


>120-≦140
5 column washes total



with 12.5 ml each


>100-≦120
5 column washes total



with 12.5 ml each


>80-≦100
5 column washes total



with 10.0 ml each


>60-≦80
5 column washes total



with 10.0 ml each


>40-≦60
5 column washes total



with 7.5 ml each


>20-≦40
5 column washes total



with 5.0 ml each


≦20
5 column washes total



with 5.0 ml each









    
    
        Wash the STREAMLINE Protein A beads in the column with the appropriate volume of Binding Buffer for the appropriate number of washes, continuing to collect the efluent into the “Column Wash-Post Binding” container.
        When completed, close the stopcock. Store the “Column Wash-Post Binding” container at 2° C. to 10° C.
        Determine the Total Volumes of Elution Buffer and Neutralization Buffer needed to elute the STREAMLINE Protein A beads in the column from Table 3.
    
    









TABLE 3







Determination of Amount of Elution Buffer and Neutralization Buffer












Total


Volume of



Volume of
Total
Volume of
Neutralization



Elution
Volume of
Elution
Buffer


Quantity IgG
Buffer
Neutralization
Buffer
Required


(μg/ml) in
Required
Buffer
Required per
per fraction


Supernatant
(ml)
Required (ml)
fraction (ml)
(ml)














>180-≦200
72
7.2
12
1.2


>160-≦180
66
6.6
11
1.1


>140-≦160
60
6.0
10
1.0


>120-≦140
54
5.4
9
0.9


>100-≦120
48
4.8
8
0.8


 >80-≦100
42
4.2
7
0.7


>60-≦80
36
3.6
6
0.6


>40-≦60
27
2.7
4.5
0.45


>20-≦40
21
2.1
3.5
0.35


≦20
12
1.2
2
0.2









    
    
        Label 9 sterile conical centrifuge tubes “Eluted Antibody”, Fraction # (1 through 9).
        Place the appropriate volume of Neutralization Buffer required per fraction (as determined from Table “C” above) into each of the 9 “Eluted Antibody” fraction tubes and place securely under the column stopcock outlet.
        Elute the STREAMLINE Protein A beads in the column fraction by fraction with the appropriate volume of Elution Buffer required per fraction (as determined from Table 3 above) while collecting the eluate into each of the “Eluted Antibody” tubes containing Neutralization Buffer.
        When the elutions are complete, mix each “Eluted Antibody” fraction tube gently by swirling several times. Remove approximately 50 μl of fraction # 3 and place on a pH test paper strip to ensure that the eluate has been neutralized to an approximate pH between 6.5 to 8.5. If required, add additional Neutralizing Buffer or Elution Buffer as needed to bring pH into range.
        When pH evaluation is completed, perform an Absorbance Scan of a sample from each fraction at 280 nm-400 nm to determine the approximate concentration of IgG in the eluate prior to proceeding to the Dialysis Process.
        
            Accept fractions as part of the Eluate Pool if the A280-A400 value is ≧0.200.
            Reject fractions as part of the Eluate Pool if the A280-A400 value is <0.200.
        
        
        Label a sterile conical centrifuge tube “Eluted Antibody,” “Eluate Pool,” and combine all fractions that were Accepted as part of the pool.
        Perform an Absorbance Scan of a sample of the Eluate Pool to determine the approximate concentration of IgG in the eluate prior to proceeding to the Dialysis Process.
        Estimate the volume of the Eluate Pool and calculate the approximate total mgs of IgG.
        Volume of Eluate Pool: ______mls×______IgG mg/ml=______Total mgs of IgG

Antibody Dialysis

        Remove the “Eluted Antibody” tube from 2° C. to 10° C.
        Calculate the approximate length of Dialysis Tubing that will be needed to dialyze the antibody eluate using the approximate volume of eluate and the data in Table 4.
    
    









TABLE 4







Calculation of Length of Dialysis Tubing Needed

















Approximate








Length
Approximate




Approximate

Needed for
Length
Approximate


Approximate
Volume/length
Length Needed
Head Space
Sample plus
Needed for
Total Length of


Volume of
Ratio of Dialysis
for Eluent
of 20%
Headspace
Tie Off of
Dialysis Tubing


Eluent (ml)
Tubing
Sample (cm)
(cm)
(cm)
Tubing (cm)
Needed (cm)
















39.6
2
20
4
24
15
63


36.3
2
18
4
22
15
59


33.0
2
17
3
20
15
55


29.7
2
15
3
18
15
51


26.4
2
13
3
16
15
47


23.1
2
12
2
14
15
43


19.8
2
10
2
12
15
39


14.85
2
7
1
9
15
33


11.55
2
6
1
7
15
29


6.6
2
3
1
4
15
23









    
    
        Cut the appropriate length of dialysis tubing required. SPECTRA/POR® 2Regenerated Cellulose Membrane, 12,000-14,000 Dalton Molecular Weight Cutoff (MWCO), 16 mm Diameter, Spectrum Laboratories Inc., Cat. No. 132678).
        Hydrate the dialysis membrane tubing in 1000 ml of DIH2O for >30 minutes.
        Calculate the approximate volume of Dialysis Buffer needed to dialyze the antibody eluate using the data in Table 5.
    
    









TABLE 5







Volume of Dialysis Buffer Required












Length of



Quantity IgG
Final Volume of
Dialysis
Volume of Dialysis


(μg/ml) in
Eluted Antibody in
Tubing Needed
Buffer (1 × PBS)


Supernatant
Milliliters (ml)
(cm)
Needed in Liters





>180-≦200
39.6 ml
63 cm
3 complete changes





of 4.0 Liters


>160-≦180
36.3 ml
59 cm
3 complete changes





of 3.6 Liters


>140-≦160
33.0 ml
55 cm
3 complete changes





of 3.3 Liters


>120-≦140
29.7 ml
51 cm
3 complete changes





of 3.0 Liters


>100-≦120
26.4 ml
47 cm
3 complete changes





of 2.6 Liters


 >80-≦100
23.1 ml
43 cm
3 complete changes





of 2.3 Liters


>60-≦80
19.8 ml
39 cm
3 complete changes





of 1.9 Liters


>40-≦60
14.85 ml 
33 cm
3 complete changes





of 1.5 Liters


>20-≦40
11.55 ml 
29 cm
3 complete changes





of 1.2 Liters


≦20
 6.6 ml
23 cm
3 complete changes





of 0.7 Liters









    
    
        Place the appropriate amount of Dialysis Buffer into a suitable sized plastic beaker. Label the beaker “Dialyzed Antibody.” Add a clean stir bar and place the beaker on a stir plate inside a refrigerator or cold room at 2° C. to 10° C.
        Rinse the dialysis tubing thoroughly in DI—H2O. Tie two end knots approximately 7 cm from one end of the dialysis tubing and secure tightly.
        Add approximately 5 ml of DI—H2O into the dialysis tubing.
        Fill the dialysis tubing with the eluted antibody from the “Eluted Antibody” collection tube.
        Tie two end knots approximately 7 cm from the remaining open end of the dialysis tubing and secure tightly. Ensure that the headspace is approximately that as derived from Table 4.
        Place the filled and closed dialysis tubing into the dialysis reservoir with the appropriate volume of 1×PBS (from Table 5).
        Cover the beaker with clean plastic wrap. Adjust the speed on the stir plate such that the dialysis sample spins freely, but is not pulled down into the vortex of the dialysate. Dialysis should take place at 2° C. to 10° C. with 3 buffer exchanges in total within a 24 hour period.

Antibody Filtration

        Label a sterile collection tube “Dialyzed Antibody.”
        Remove the dialyzed sample tubing from the dialysis beaker. Cut the dialysis tubing open at one end and transfer the dialyzed sample into the “Dialyzed Antibody” centrifuge tube.
        Label another sterile collection tube “Dialyzed Antibody.”
        Select a sterile Luer Lok syringe with adequate capacity to hold the final dialyszed volume.
        Attach an Acrodisc® Syringe Filter to the opening of the syringe (0.2 μm HT Tuffryn® Membrane, Low Protein binding, Gelman Laboratories, Cat. No. 4192). Remove the plunger from the syringe and while holding the syringe upright, transfer the dialyszed monoclonal antibody from the “Dialyzed Antibody” tube into the syringe. Replace the plunger.
        Hold the Acrodisc® Syringe Filter over the opened, sterile, labeled “Purified Antibody” collection tube, and depress the syringe plunger to filter the purified antibody into the “Purified Antibody” tube.
        When filtration is complete, cap the “Purified Antibody” tube and store at 2° C. to 10° C.
        Determine concentration of purified monoclonal antibody using A280 procedure.
    
    


Example 4
General Method for Epitope Mapping
General Approach
Epitope mapping is performed to identify the linear amino acid sequence within an antigenic protein (i.e., the epitope) 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 8-15 amino acid sequence. An epitope can be a continuous linear sequence of 8-15 amino acids or it can be discontinuous with the antibody binding to a site on the protein composed of different sections of the peptide chain. Discontinuous epitopes generally cannot be mapped.
Construct Design and Creation
The first step in epitope mapping is the design of nested gene truncations. Frequently, the gene is divided into four equal parts for further analysis.
Gene Cloning Strategy
The general cloning strategy begins with PCR-based generation of the cloned gene fragments. In order to efficiently express the cloned fragment, especially when using small amino acid regions, the cloned fragment is expressed as a fusion protein, i.e. fused to another carrier protein that is stably expressed in the system. Green fluorescent protein (GFP) is frequently used as the carrier protein. GFP is included as a fusion partner to stabilize the truncation fragments and improve expression during the subsequent in vitro protein expression step. GFP also permits the tracking of fusion-protein expression using anti-GFP antibodies.
Cloning to create the GFP-protein construct is performed using either the mega-priming approach or through the use of plasmid cloning into the pScreen-GFP vector. Generally, the truncation fragments are fused to GFP and control sequences necessary for protein expression using a technique called megapriming.
Megapriming is the joining of two or more DNA fragments by annealing homologous regions at the end of the respective fragments and extending the annealed single-stranded DNA with a thermostable DNA polymerase. This process creates one large DNA fragment from two or more smaller fragments, linking them by their shared sequence. This large fragment is then amplified using standard PCR.
If megapriming cannot be used successfully, the truncation fragments can be cloned into a plasmid containing GFP and protein-expression control sequences. This cloning creates the GFP/fragment fusions necessary for epitope mapping. The remainder of the protocol can then proceed as described below.
Protein Expression
The expression constructs created by, for example, megapriming are then introduced into the Rapid Translation System (RTS). RTS is a cell-free protein expression system derived from E. coli lysates. This system permits rapid (3-4 hour) expression of proteins from DNA templates.
If RTS does not produce adequate levels of protein expression, then the truncation fragments will be cloned into the GFP protein-expression plasmid. These fusion plasmids are then transformed into an E. coli strain optimized for protein expression. Protein expression is induced in a growing culture of bacteria and, following outgrowth, the cells are lysed. The proteins in the complex cell lysate are then separated by polyacrylamide gel electrophoresis (PAGE), and the remainder of the protocol is the same as below.
Protein Detection and Epitope Mapping
Protein fragments produced by RTS are separated using PAGE and transferred onto nitrocellulose membranes. The membrane-bound proteins are then exposed to the antibody under investigation in solution. Antibody/protein binding is identified using colorimetric techniques known in the art.
Antibody binding of the full-length protein and some subset of the truncated protein fragments constitutes a positive result. If the absence of a particular section of the protein eliminates antibody binding, then the epitope lies on this fragment.
If the antibody to be mapped does not recognize protein bound to nitrocellulose membranes, then alternative methods for detecting antibody/protein interactions, such as, for example, ELISA or immunoprecipitation are used. Methods for detecting antibody/protein interactions are well known in the art.
Refining the Epitope Location
Since the above-described protocol will only narrow the location of the epitope down to approximately one-quarter of the protein, it is necessary to repeat the process on the quarter of the protein determined to contain the epitope in order to further resolve the location of the epitope. For a very large protein, it may be necessary to repeat this process two to three times to narrow the epitope down to 8-15 amino acids.
Example 5
Characterization of Epitope for MCM6 Monoclonal Antibody 9D4.3
Epitope mapping for MCM6 monoclonal antibody 9D4.3 was carried out essentially as described above in Example 4. Specifically, PCR was used to create four MCM6 gene truncations of the full-length MCM6 protein, followed by RTS to generate recombinant MCM6 protein fragments as GFP fusion proteins, and finally western blotting to detect antibody binding to specific MCM6 fragments. GFP was joined with the MCM6 gene truncations in a second round of PCR to ensure robust and stable expression in RTS.
The MCM6 protein fragments were analyzed by western blotting to identify fragment(s) that bind the 9D4.3 antibody. The western blot was probed directly with the 9D4.3 monoclonal antibody and a GFP antibody. A positive band was detected with the MCM6 truncation product designated as fragment 4. Fragment 4 was divided into five smaller fragments and the above process repeated to narrow the epitope.
The second set of MCM6 protein fragments was also analyzed by western blotting to identify fragment(s) that bind the 9D4.3 antibody. The western blot was probed directly with the 9D4.3 monoclonal antibody and a GFP antibody. Monoclonal antibody 9D4.3 was shown to bind to the region of MCM6 designated as 4-4. This fragment was again divided into six smaller fragments and the above process repeated to narrow the epitope.
The MCM6 protein fragments were again analyzed by western blotting as before. The western blot was probed directly with the 9D4.3 monoclonal antibody and a GFP antibody. A positive band was detected with the MCM6 fragment designated as 4-4-1. Additional fragments were generated to narrow the epitope region. Western blot analysis indicated that the epitope for the MCM6 antibody 9D4.3 comprises the amino acid sequence IDSEEELINKKRI (SEQ ID NO:5).
Results
Initial results showed that the epitope for the MCM6 monoclonal antibody 9D4.3 is located within the C-terminal region of the MCM6 protein. Continued truncations of the MCM6 protein showed that the epitope recognized by 9D4.3 is located within a thirteen amino acid region, specifically corresponding to amino acid residues 760-772 of SEQ ID NO:3 (IDSEEELINKKRI (SEQ ID NO:5)). Additional rounds of RTS may be able to refine the epitope location further.
Example 6
Characterization of Epitope for MCM7 Monoclonal Antibody 2E6.2
Epitope mapping for MCM7 monoclonal antibody 2E6.2 was performed essentially as described above in Example 5. The full-length MCM7 gene sequence (SEQ ID NO:1) was used as the starting sequence for designing gene fragments.
Results
The epitope for MCM7 monoclonal antibody 2E6.2 was determined to be located within the protein region comprising amino acid residues 127-138 of SEQ ID NO:1 (PAELMRRFELYF (SEQ ID NO:6)). Additional rounds of RTS may be able to refine the epitope location further.

## Claims

1. A monoclonal antibody that is capable of specifically binding to MCM7, wherein the antibody is selected from the group consisting of:
(a) the monoclonal antibody produced by the hybridoma cell line 2E6.2, deposited with the ATCC as Patent Deposit No. PTA-6669;
(b) a monoclonal antibody that binds to an MCM7 epitope consisting of the amino acid sequence of SEQ ID NO:6; and
(c) an antigen binding fragment of a monoclonal antibody of (a) or (b), wherein the fragment retains the capability of specifically binding to MCM7.

2. The hybridoma cell line 2E6.2, deposited with the ATCC as Patent Deposit No. PTA-6669.

3. A hybridoma cell line capable of producing a monoclonal antibody of claim 1(a) or claim 1(b).

4. A kit for diagnosing high-grade cervical disease comprising at least one monoclonal antibody or an antigen binding fragment according to claim 1.

5. The kit of claim 4, wherein the monoclonal antibody is the monoclonal antibody produced by the hybridoma cell line 2E6.2, deposited with the ATCC as Patent Deposit No. PTA-6669.

6. The kit according to claim 4, wherein said kit further comprises a peroxidase blocking reagent, a protein blocking reagent, chemicals for the detection of antibody binding to a biomarker protein, a counterstain, a bluing agent, and instructions for diagnosing high-grade cervical disease.

7. The kit according to claim 4 further comprising reagents for Papanicolaou (Pap) staining.