# Patent

## Title
Monoclonal antibodies against PCBP-1 antigens, and uses therefor

## Abstract

The present invention provides and includes monoclonal antibodies specific or preferentially selective for PCBP-1 antigens, as well as methods utilizing these antibodies to determine the severity of breast cancer in a patient.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application, filed under 35 U.S.C. §111(a), is a continuation of U.S. application Ser. No. 13/739,931, filed Jan. 11, 2013, which is a national stage entry under 35 U.S.C. §371 based on PCT of International Application PCT/US2011/044080, filed Jul. 14, 2011, which claims priority to U.S. Provisional Application No. 61/364,362, filed on Jul. 14, 2010, all of which are incorporated herein by reference in their entirety.


BACKGROUND OF THE INVENTION
1. Field of the Invention
The present invention provides and includes monoclonal antibodies (MoAbs or mAbs) specific or preferentially selective for a PCBP-1 antigen, hybridoma lines that secrete these PCBP-1 antibodies or antibody fragments, and the use of such antibodies and antibody fragments to detect PCBP-1 antigens, particularly those expressed by cancer cells. The present invention also includes antibodies that are specific for or show preferential binding to a soluble form of PCBP-1 (sPCBP-1). The present invention further includes chimeric and humanized antibodies, processes for producing monoclonal, chimeric, and humanized antibodies using recombinant DNA technology, and therapeutic uses of these antibodies, particularly in the treatment of cancer. The present invention further includes methods and kits for the immunodetection and immunotherapy of cells for samples which express a PCBP-1 antigen of the present invention.
2. Background
One human carcinoma tumor antigen is PCBP-1 (poly(rC) binding protein-1). Pcbp-1 is an intronless human gene reported to have been generated by retrotransposition of a fully processed PCBP-2 mRNA. It is also reported to be located on chromosome 2 (70.17-70.17 Mb). The protein encoded by the Pcbp-1 gene is a reported multifunctional protein. PCBP-1, along with PCBP-2 and hnRNPK, are reported to form the major cellular poly(rC)-binding proteins. Pcbp-1 has been sequenced. See UniProt Q15365, Q53SS8, Q14975; OMIM 601209; NCBI Gene 5093; NCBI RefSeq NP_006187; NCBI RefSeq NM_006196, NP_006187; NCBI UniGene 5093; and NCBI Accession AK130439, AAA91317. Homologues of Pcbp-1 are also reported, including, but not limited to, homologues of Pcbp-1 in the mouse (see NCBI UniGene 23983; UniProt P60335; and NCBI RefSeq NM_011865, NP_035995), dog, and rat.
PCBP-1 has also been reported to regulate transcription for a few individual promoters, to be important for the metabolism and gene expression of HIV-1 and poliovirus, and to stimulate IRES-mediated translation initiation in vitro and in vivo (Mitchell et al., 2003). It has also been reported to be modestly increased in the epidermis of elderly individuals (Gromov et al., Mol Cell Proteomics 2(2):70-84, 2003).
The breast cancer-specific survival rates of women with one or two positive nodes were found to have similar likelihoods of long-term survival; however, women with three positive nodes experienced significantly reduced survival compared to those with one or two involved nodes. (Tai, P., et al., Prognostic Significance of Number of Positive Nodes: A Long-Term Study of One to Two Nodes Versus Three Nodes in Breast Cancer Patients, International Journal of Radiation Oncology; 77 (1) p. 180-187 (May 2010)). Accordingly, there is a need for an additional molecular marker, more than just lymph node status, of overall survival, particularly for women with three or more positive nodes. There is also a need for a molecular marker to determine metastatic status of a ductal breast cancer in women with any lymph node involvement.
SUMMARY OF THE INVENTION
The present invention includes a method of determining a metastatic status of a breast cell or tissue in a sample comprising contacting the sample from a patient in need thereof with an antibody capable of detecting nuclear and cytoplasmic PCBP-1 and determining the subcellular location of said PCBP-1, where localization of said PCBP-1 in a cell cytoplasm of the sample is indicative of cellular metastasis.
In another aspect, the present invention includes a method of determining a metastatic status of a breast cell or tissue in a sample comprising contacting the sample from a patient in need thereof with an antibody capable of detecting nuclear and cytoplasmic PCBP-1 and determining the subcellular location of said PCBP-1, where the absence of subcellular co-localization of PCBP-1 and estrogen receptor (ER), progesterone receptor (PR), or ER and PR, is inversely correlated with overall survival. In this aspect, the absence of co-localization can include a lack of ER or PR staining where PCBP-1 staining is present in a ductal breast cancer cell cytoplasm.
The present invention includes a method of determining a likelihood of survival for a patient of breast cancer comprising contacting the sample from the patient in need thereof with an antibody capable of detecting nuclear and cytoplasmic PCBP-1; and determining the expression level of PCBP-1, where greater expression of said PCBP-1 in the sample is inversely correlated with overall survival.
The present invention includes a method of determining likelihood of survival for a patient of breast cancer comprising contacting the sample from the patient in need thereof with an DNA probe capable of detecting pcbp-1; and determining the chromosome localization of pcbp-1, wherein detection of more than two copies of said pcbp-1 in the sample is correlated with overall survival.
The present invention also provides a method for determining the likelihood of survival of a patient suffering from a disease characterized by the expression of gene products of Pcbp-1 and homologues thereof, comprising the steps of contacting a tissue specimen from a subject in need thereof with a PCBP-1 antibody of the present invention or an antibody fragment thereof, and staining said tissue specimens with an immunohistochemical staining.
The present invention also provides a method of determining the status of a cell in a sample comprising: (a) contacting a sample from a patient in need thereof with an antibody capable of preferentially detecting a soluble form of PCBP-1 antigen; and (b) determining the quantity of said antigen.
The present invention also provides a method of determining the status of a cell in a sample comprising: (a) contacting a sample from a patient in need thereof with an antibody or a fragment thereof capable of preferentially detecting a soluble form of PCBP-1 antigen; and (b) determining the localization of said antigen.
The present invention also provides a method for diagnosing breast cancer in a patient in need thereof, comprising: (a) determining the level, localization, or both of PCBP-1 in a sample obtained from said patient; (b) determining whether said breast cancer is ductal carcinoma or lobular carcinoma; (c) determining whether said breast cancer is HER2-positive or HER2-negative; (d) determining whether said breast cancer is estrogen receptor-positive or estrogen receptor-negative; and (e) determining whether said breast cancer is progesterone receptor-positive or progesterone receptor-negative.
The present invention also provides a method for determining the cytopathology of a breast cancer in a patient in need thereof comprising: (a) contacting a specimen from said patient with a monoclonal antibody having one or more of the heavy chain CDR antigen binding site sequences selected from the group consisting of SEQ ID NO: 45, SEQ ID NO: 46 and SEQ ID NO: 47, and one or more of the light chain CDR antigen binding site sequences selected from the group consisting of SEQ ID NO: 48, SEQ ID NO: 49 and SEQ ID NO: 50, thereby forming antigen-antibody complexes in said specimen; labeling the specimen with a label specific for the antigen-antibody complex; and (d) detecting the level, localization, or both of the antigen-antibody complex.
The present invention also provides a method for determining whether a breast cancer specimen is from a ductal breast carcinoma or a lobular breast carcinoma comprising: (a) contacting the specimen with a monoclonal antibody having one or more of the heavy chain CDR antigen binding site sequences selected from the group consisting of SEQ ID NO: 45, SEQ ID NO: 46 and SEQ ID NO: 47, and one or more of the light chain CDR antigen binding site sequences selected from the group consisting of SEQ ID NO: 48, SEQ ID NO: 49 and SEQ ID NO: 50, thereby forming antigen-antibody complexes in said specimen; labeling the specimen with a label specific for the antigen-antibody complex; (b) detecting the level, localization or both of the antigen-antibody complex; and (c) correlating the level, localization, or both of the antigen-antibody complex with the type of breast cancer present in said patient.
The present invention also provides an immunoassay for determining whether a breast cancer specimen is from a ductal breast carcinoma or a lobular breast carcinoma comprising: (a) contacting the specimen with a monoclonal antibody having one or more of the heavy chain CDR antigen binding site sequences selected from the group consisting of SEQ ID NO: 45, SEQ ID NO: 46 and SEQ ID NO: 47, and one or more of the light chain CDR antigen binding site sequences selected from the group consisting of SEQ ID NO: 48, SEQ ID NO: 49 and SEQ ID NO: 50, thereby forming antigen-antibody complexes in said specimen; labeling the specimen with a label specific for the antigen-antibody complex; and (b) detecting the level, localization, or both of the antigen-antibody complex.
The present invention also provides a method of determining whether a breast cancer sample is a ductal breast carcinoma or a lobular breast carcinoma, comprising: (a) contacting said sample with an antibody capable of preferentially detecting a soluble form of PCBP-1 antigen; (b) determining the localization of said antigen; and (c) correlating the localization of said antigen with ductal breast carcinoma or lobular breast carcinoma.
The present invention also provides a method of determining whether a breast cancer sample is a ductal breast carcinoma or a lobular breast carcinoma, comprising: (a) contacting said sample with an antibody capable of preferentially detecting a soluble form of PCBP-1 antigen; (b) determining the level of said antigen; and (c) correlating the level of said antigen with ductal breast carcinoma or lobular breast carcinoma.
The present invention also provides a method for treating breast cancer in a patient in need thereof, comprising: (a) determining the level, localization, or both of PCBP-1 in a sample obtained from said patient; (b) determining whether said breast cancer is ductal carcinoma or lobular carcinoma; (c) determining whether said breast cancer is HER2-positive or HER2-negative; (d) determining whether said breast cancer is estrogen receptor-positive or estrogen receptor-negative; (e) determining whether said breast cancer is progesterone receptor-positive or progesterone receptor-negative; and (f) administering one or more chemotherapeutic agents to said patient.
The present invention also provides a method of selecting a treatment for a patient in need thereof, comprising: (a) determining whether a breast cancer is ductal or lobular; and (b) selecting an appropriate treatment based on whether said breast cancer is ductal or lobular.
The present invention also provides a method of identifying pre-metastic tumor cells in a tissue sample comprising: a) contacting said sample from a patient in need thereof with an antibody capable of detecting nuclear and cytoplasmic PCBP-1; and b) determining the subcellular location of said PCBP-1 in cells of said sample, wherein localization of said PCBP-1 in a cell cytoplasm of said cells is indicative of the presence of pre-metastic tumor cells.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1. Plasma filamin-A levels are measured with an enzyme-linked immunosorbent enzyme assay. The figures represent optical density (OD) values of plasma readings for filamin-A levels. P-values are derived using the Mann Whitney Test and show a significant difference between the control and non-metastatic groups, and between the control and metastatic groups (p<0.001). P values are determined by comparison with controls by ANOVA. Data are representative of four independent experiments performed in triplicate.
FIGS. 2A and 2B. Plasma samples from breast cancer patients are subjected to ELISA analysis using an anti-PCBP-1 monoclonal antibody. The figures represent optical density (OD) values of plasma readings for PCBP-1 levels. P-values are derived using the Mann Whitney Test. Control and metastatic group showed a significant difference (p<0.001). Control and non-metastatic groups did not show a significant difference. There is a significant difference between non-metastatic and metastatic groups (p<0.001). P values are determined by comparison with controls by ANOVA. Data are representative of four independent experiments performed in triplicate. FIG. 2A is a bar graph of duplicate ELISA results. FIG. 2B is a box plot of averaged ELISA results.
FIGS. 3A, 3B, and 3C. Human normal mammary epithelial cells (HMECs), SKBR3 cells (human non-metastatic breast cancer cells) and MDA-MB-231 cells (human metastatic breast cancer cells) are seeded and grown on glass slides. The cells are fixed with formalin (10% with 0.1% Triton-X), washed with PBS and stained with anti-PCBP-1 mouse monoclonal antibody. Cells are then labeled with a FITC-labeled secondary goat-anti-mouse antibody and subjected to laser confocal microscopy. Indirect immunofluorescent staining is observed in the cytoplasm of HMECs (FIG. 3A). SKBR3 cells exhibit cytoplasmic and nuclear staining (FIG. 3B). MDA-MB-231 cells exhibit cytoplasmic staining (FIG. 3C).
FIGS. 4A and 4B. Cervical cells obtained from pap smears of healthy and cervical cancer patients are seeded and grown on glass slides. The cells are fixed with formalin (10% with 0.1% Triton-X), washed with PBS and stained with anti-PCBP-1 mouse monoclonal antibody. Cells are then labeled with a FITC-labeled secondary goat-anti-mouse antibody and subjected to laser confocal microscopy. Indirect immunofluorescent staining is observed in the cytoplasm and nucleus of normal cervical cells (FIG. 4A). Cervical cancer cells (CIN III) display cytoplasmic staining only (FIG. 4B).
FIGS. 5A and 5B. Approximately 2 μg of purified Alper PCBP-1 mouse mAb (identified as 7SK) is suspended in PBS, and is applied under reducing (boiled 3 minutes in sample buffer with beta-mercaptoethanol and 10% SDS) and non-reducing (not boiled, and without beta-mercaptoethanol) conditions to 8 and 6% Tris-glycine gels, respectively, and run at 120 volts. The gels are then stained with Coomassie Blue (0.1% (w/v) Coomassie blue R350, 20% (v/v) methanol, and 10% (v/v) acetic acid), destained in 50% (v/v) methanol in water with 10% (v/v) acetic acid, and images of the gels are taken. Molecular weight markers are shown on the right. The 6% Tris-glycine gel shows the Alper PCBP-1 mouse IgG1 antibody (7SK) at  ̃150 kDa under non-reduced conditions (FIG. 5A). The 8% Tris-glycine gel shows the heavy chain of the Alper PCBP-1 mouse IgG1 antibody (7SK) at  ̃50 kDa (FIG. 5B).
FIG. 6. Approximately 1 μg of purified Alper PCBP-1 mouse mAb (identified as 7SK) is suspended in PBS, and is applied under reducing (boiled 3 minutes in sample buffer with beta-mercaptoethanol and 10% SDS) and non-reducing (not boiled, and without beta-mercaptoethanol) conditions to 8% Tris-glycine gels and run at 120 volts. The gels are then stained with Coomassie Blue (0.1% (w/v) Coomassie blue R350, 20% (v/v) methanol, and 10% (v/v) acetic acid), destained in 50% (v/v) methanol in water with 10% (v/v) acetic acid, and images of the gels are taken. Molecular weight markers are shown on the left. Under denatured conditions, the heavy chain of Alper PCBP-1 mouse IgG1 Ab (7SK) is detected at  ̃50 kDa and light chain of Alper PCBP-1 mouse IgG1 (7SK) is detected at  ̃25 kDa. In a non-reducing gel, intact Alper PCBP-1 mouse IgG1 (7SK) is detected at 150 kDa.
FIGS. 7A and 7B. SKBR3 cells are fixed with 10% gluteraldehyde, permeabilized with 0.1% Triton-X100. PCBP-1 expression is then visualized with the Alper PCBP-1 mouse mAb (7SK) and secondary FITC-labeled anti-mouse antibodies (Jackson ImmunoResearch, West Grove, Pa.). Nuclei are visualized by DAPI staining (Molecular Probes, Eugene, Oreg.). The images are analyzed using an Olympus microscope equipped with 63× objective lens. FIG. 7A shows PCBP-1 staining only, and FIG. 7B shows both PCBP-1 and nuclei staining.
FIGS. 8A, 8B, and 8C. Plasma samples (C: control breast blood sample, NM: non-metastatic breast blood sample, M: metastatic breast blood sample) obtained from control and patient groups are diluted with PBS at a ratio of 1:100. Plasma PCBP-1 levels are measured with an enzyme-linked immunosorbent enzyme assay. The ELISA plates (Nalge NUNC International, Rochester, N.Y.) are coated with 100 μl/well of diluted plasma and incubated at 4° C. overnight. The blood plasma samples are analyzed in a blinded fashion. The wells are washed with PBS and incubated at room temperature for one hour with blocking buffer (5% BSA in PBS). After washing with PBS, the primary antibody, 7SK (clone name: Alper-pCBP-1) is added in dilution buffer (45 μg/ml) (PBS buffer, 1% BSA, 0.01% Tween-20). The wells are washed with PBS/0.03% Tween-20 and incubated at room temperature for one hour with 100 μl/well secondary antibody (HRP-Donkey anti-mouse IgG, Jackson ImmunoResearch, West Grove, Pa.) diluted 1:3000. After washing the wells, 100 μl Immunopure TMB substrate solution (Pierce, Rockford, Ill.) is added. Color reaction is stopped by the addition of 100 μl/well 1N H2SO4 and the analysis is performed with an ELISA Reader. FIG. 8A represents the measured optical density (OD) values of plasma readings for PCBP-1 levels for each patient; FIG. 8B is the bar chart of the OD values of plasma readings for PCBP-1 levels; FIG. 8C is the bar chart of the average OD values of plasma readings for PCBP-1 levels for the controls and each patient group.
FIGS. 9A, 9B, 9C, and 9D. Plasma samples (C: control breast blood sample, NM: non-metastatic breast blood sample, M: metastatic breast blood sample) obtained from control and patient groups are diluted with PBS at a ratio of 1:100. Plasma PCBP-1 levels are measured with an enzyme-linked immunosorbent enzyme assay. The ELISA plates (Nalge NUNC International, Rochester, N.Y.) are coated with 100 μl/well of diluted plasma and incubated at 4° C. overnight. The plasma samples are analyzed in a blinded fashion. The wells are washed with PBS and incubated at room temperature for one hour with blocking buffer (5% BSA in PBS). After washing with PBS, the primary antibody, Alper PCBP-1 mouse mAB (7SK) (clone name: Alper-pCBP-1) is added in dilution buffer (45 μg/ml) (PBS buffer, 1% BSA, 0.01% Tween-20). The wells are washed with PBS/0.03% Tween-20 and incubated at room temperature for one hour with 100 μl/well secondary antibody (HRP-Donkey anti-mouse IgG, Jackson ImmunoResearch, West Grove, Pa.) diluted 1:3000. After washing the wells, 100 μl Immunopure TMB substrate solution (Pierce, Rockford, Ill.) is added. Color reaction is stopped by the addition of 100 μl/well 1N H2SO4 and the analysis is performed with an ELISA Reader. FIG. 9A represents the measured OD values for PCBP-1 levels in the plasma of controls (C) and patients suffering from non-metastatic cancer (NM) and patients suffering from metastatic cancer (M). FIG. 9B is the vertical bar chart of the OD values for PCBP-1 plasma levels, in which series 1-2 represent control plasma samples, series 3-4 represent nonmetastatic plasma samples and series 5-6 represent metastatic plasma samples. FIG. 9C represents the horizontal bar chart (top) of the average OD values for the controls and patient groups. FIG. 9D shows the vertical bar chart of the overall average OD values of the controls and patient groups, in which 1 represents metastatic plasma samples, 3 represents nonmetastatic plasma samples, and 6 represents control plasma samples.
FIGS. 10A, 10B, 10C, 10D, 10E, and 10F. Multiple Sequence Alignment. FIG. 10A summarizes the BLAST search results of the heavy chain sequence of a PCBP-1 mAb (7SK). FIGS. 10B, 10C, 10D, 10E, and 10F show the FWRs and CDRs of the heavy chain of a PCBP-1 mAb (7SK), in which the polypeptide sequence provided in the top line (SEQ ID NO: 16) corresponds to the sequence of a PCBP-1 mAb (SEQ ID NO:15). The figures also disclose the following sequences, in order of appearance: J558.18 (SEQ ID NO: 17); VMU-3.2 (SEQ ID NO: 19); J558.85.191 (SEQ ID NO: 20); JH3 (SEQ ID NO: 21); JE2 (SEQ ID NO: 22); J558.83.189 (SEQ ID NO: 23); J558.29 (SEQ ID NO: 24); J558.27 (SEQ ID NO: 25); J558.87.193 (SEQ ID NO: 26); VEA1 (SEQ ID NO: 27); J558.30 (SEQ ID NO: 28); and J558.18A (SEQ ID NO: 29). Amino acid residues are numbered using the convention of Kabat et al., (1991) Sequences of Proteins of Immunological Interest, 5th Edition, Department of Health and Human Services, Public Health Service, National Institutes of Health, Bethesda (NIH Publication No. 91-3242). Bold residues set forth in underlined text indicate specificity determining residues (SDRs) (SEQ ID NO: 18).
FIGS. 11A, 11B, 11C, 11D, and 11F. Multiple Sequence Alignment. FIG. 11A summarizes the BLAST search results of the light heavy chain sequence of a PCBP-1 mAb (7SK). FIGS. 11B, 11C, 11D, 11E, and 11F show the FWRs and CDRs of the light chain of a PCBP-1 mAb (7SK), in which the polypeptide sequence provided in the top line (SEQ ID NO: 31) corresponds to the nucleotide sequence of a PCBP-1 mAb (SEQ ID NO: 30). The figures also disclose the following sequences, in order of appearance: 21-12 SEQ ID NO: 32); 21-7 (SEQ ID NO: 34); 21-4 (SEQ ID NO: 35); JK2 (SEQ ID NO: 36); JK1 (SEQ ID NO: 37); 21-10 (SEQ ID NO: 38); 21-8 (SEQ ID NO: 39); 21-3 (SEQ ID NO: 40); 21-5 (SEQ ID NO: 41); 21-2 (SEQ ID NO: 42); 21-9 (SEQ ID NO: 43); 21-1 (SEQ ID NO: 44). Amino acid residues are numbered using the convention of Kabat et al. Bold residues set forth in underlined text indicate the specificity determining residues (SDRs) (SEQ ID NO: 33).
FIG. 12. Experimental mass, calculated mass and sequence of PCBP-1 regions (SEQ ID NOs. 1-14).
FIG. 13. Chart of PCBP-1 expression as detected by immunohistochemistry using Alper PCBP-1 mouse monoclonal antibody in normal vs. cancer tissues.
FIGS. 14A and 14B Immunohistochemical staining of samples from lobular and ductal carcinoma patients. The YTMA 49-10 node-positive/node-negative invasive breast carcinoma tissue micro array (obtained from Yale Cancer Center Department of Pathology Tissue Microarray Facility) is stained with Alper PCBP-1 mouse monoclonal antibody. Samples are then labeled with a FITC-labeled secondary goat-anti-mouse antibody and subjected to laser confocal microscopy. Samples are assigned a value (0, 1+, 2+ or 3+) based on amount of staining with Alper PCBP-1 mouse monoclonal antibody. High (2+ or 3+) indirect immunofluorescent staining is observed in about 50% of patients with lobular carcinoma. High indirect immunofluorescent staining is observed in about 70% of patients with ductal carcinoma. FIG. 14A shows the staining of a sample from a lobular carcinoma patient, and FIG. 14B shows the staining of a sample from a ductal carcinoma patient.
FIG. 15. Chart A of FIG. 15 is the number of ductal and lobular carcinoma samples displaying negative (0), low (1+) and high (2+ or 3+) immunohistochemical staining with Alper PCBP-1 mouse monoclonal antibody. Chart B of FIG. 15 is a graph of the number of ductal and lobular carcinoma samples displaying negative, low and high immunohistochemical staining with Alper PCBP-1 mouse monoclonal antibody. A higher percentage of ductal carcinoma patients expressed high levels of PCBP-1 than in lobular carcinoma patients.
FIG. 16. An example of a bladder tissue sample displaying negative (0) immunohistochemical staining with Alper anti-PCBP-1 mouse monoclonal antibody.
FIGS. 17A, 17B, and 17C. FIGS. 17A, 17B, and 17C are examples of lobular carcinoma samples displaying low (1+) (FIG. 17A) and high (2+ or 3+) (FIGS. 17B and 17C, respectively) immunohistochemical staining with Alper anti-PCBP-1 mouse monoclonal antibody.
FIGS. 18A, 18B, and 18C. FIGS. 18A, 18B, and 18C are examples of ductal carcinoma samples displaying low (1+) (FIG. 18A) and high (2+ or 3+) (FIGS. 18B and 18C, respectfully) immunohistochemical staining with Alper anti-PCBP-1 mouse monoclonal antibody.
FIGS. 19A, 19B, 19C. FIGS. 19A, 19B, and 19C are FISH analyses for PCBP-1 in the human breast cancer cell lines: metastatic MDA 231 cell line (FIG. 19A), metastatic C2T2 cell line (FIG. 19B), and nonmetastatic SK-BR 3 cell line (FIG. 19C).
FIG. 20. Higher PCBP-1 expression levels correlate with a decrease in overall survival of ductal breast cancer patients.
FIG. 21. Higher PCBP-1 expression levels from patients with more than three positive lymph nodes correlate with a decrease in overall survival of those ductal breast cancer patients.
FIGS. 22A, 22B, 22C, and 22D. FIGS. 22A, 22B, 22C, and 22D show nuclear subcellular localization of ER and PCBP-1 from whole tissues samples from ductal invasive breast carcinoma patients. White bars are 50 μm (20×) and 10 μm (60×). FIGS. 22A and 22C show PCBP-1 expression at 20× and 63× magnification, respectively. FIGS. 22B and 22D show ER expression at 20× and 63× magnification, respectively.



DETAILED DESCRIPTION
1. Definitions
Antibody: This refers to single chain, two-chain, and multi-chain proteins and glycoproteins belonging to the classes of polyclonal, monoclonal, chimeric and hetero immunoglobulins (monoclonal antibodies being preferred); it also includes synthetic and genetically engineered variants of these immunoglobulins. “Antibody fragment” includes Fab, Fab′, F(ab′)2, and Fv fragments, as well as any portion of an antibody having specificity toward a desired target epitope or epitopes.
Monoclonal Antibody: This refers to antibodies that are identical because they are produced by one type of immune cell that are all clones of a single parent cell. The monoclonal antibodies of the present invention can include intact monoclonal antibodies, antibody fragments, conjugates, or fusion proteins, which contain a VH-VL pair where the CDRs form the antigen binding site.
Chimeric Antibody: This refers to an antibody which includes sequences derived from two different antibodies, which typically are of different species. Most typically, chimeric antibodies include human and non-human antibody fragments, generally human constant and non-human variable regions.
Humanized Antibody: This refers to an antibody derived from a non-human antibody, and a human antibody which retains or substantially retains the antigen-binding properties of the parent antibody but which is less immunogenic in humans.
Antibody Conjugates, Fusion Proteins, and Bispecific Antibodies: These refer to monoclonal antibodies conjugated by chemical methods with radionuclides, drugs, macromolecules, or other agents.
Antigen: This refers to a molecule or a portion of a molecule capable of being bound by an antibody which is additionally capable of inducing an animal to produce an antibody capable of binding to an epitope of that antigen. An antigen can have one or more than one epitope. The specific reaction referred to above is meant to indicate that the antigen will react, in a highly selective manner, with its corresponding antibody and not with the multitude of other antibodies which can be evoked by other antigens.
Epitope: This refers to that portion of any molecule capable of being recognized by, and bound by, an antibody. In general, epitopes consist of chemically active surface groupings of molecules, for example, amino acids or sugar side chains, and have specific three-dimensional structural characteristics as well as specific charge characteristics. The present invention includes epitopes that are comprising amino acids.
Complementarity Determining Region, or CDR: This refers to amino acid sequences which together define the binding affinity and specificity of the natural Fv region of a native immunoglobulin binding site. The light and heavy chains of an immunoglobulin each have three CDRs. By definition, the CDRs of the light chain are bounded by the residues at positions 30 and 34 (CDR1), 49 and 65 (CDR2), 75 and 88 (CDR3); the CDRs of the heavy chain are bounded by the residues at positions 22 and 36 (CDR1), 52 and 58 (CDR2), and 70 and 77 (CDR3), using the numbering convention delineated by Kabat et al., (1991) Sequences of Proteins of Immunological Interest, 5th Edition, Department of Health and Human Services, Public Health Service, National Institutes of Health, Bethesda (NIH Publication No. 91-3242).
Framework Region or FWR: This refers to amino acid sequences interposed between CDRs. These portions of the antibody serve to hold the CDRs in an appropriate orientation for antigen binding.
Specificity Determining Residue, or SDR: This refers to amino acid residues of an immunoglobulin that are directly involved in antigen contact.
Constant Region: This refers to the portion of the antibody molecule which confers effector functions. The heavy chain constant region can be selected from any of five isotypes: alpha, delta, epsilon, gamma or mu. Heavy chains of various subclasses (such as the IgG subclass of heavy chains) are responsible for different effector functions. Thus, by choosing the desired heavy chain constant region, humanized antibodies with the desired effector function can be produced. The light chain constant region can be of the kappa or lambda type, preferably the kappa type.
Immunogenicity: A measure of the ability of a targeting protein or therapeutic moiety to elicit an immune response (humoral or cellular) when administered to a recipient. The present invention is concerned with the immunogenicity of antibodies to PCBP-1.
Immunoreactivity: A measure of the ability of an immunoglobulin to recognize and bind to a specific antigen.
PCBP-1 Antibodies or PCBP-1 mAbs: This refers to antibodies specific to expression products of the PCBP-1 gene and homologues of the PCBP-1 gene, which can include antibodies specific to modified forms of the expression product that are produced by cancer cells. Antibodies of the present invention can include variants, such as chimeric, humanized, and other variants known to those skilled in the art. PCBP-1 antibodies are said to be specific for the PCBP-1 antigen if they exhibit preferential binding to the PCBP-1 antigen at least 85% of the time, at least 90% of the time, or, in a preferred aspect, at least 95% of the time. An example of such an antibody is Alper PCBP-1 mouse monoclonal antibody (7SK).
PCBP-1 antibodies of the present invention are specific for a PCBP-1 antigen and can comprise the heavy chain CDR antigen binding site sequences CDR1 (SEQ ID NO: 45), CDR2 (SEQ ID NO: 46), and CDR3 (SEQ ID NO: 47) as set forth in FIG. 10, and the light chain CDR antigen binding site sequences CDR1 (SEQ ID NO: 48), CDR2 (SEQ ID NO: 49), and CDR3 (SEQ ID NO: 50) as set forth in FIG. 11.
PCBP-1 antibodies of the present invention can also comprise one or more of the heavy chain CDR antigen binding site sequences set forth in FIG. 10 (SEQ ID NOs: 45-47), and one or more of the light chain CDR antigen binding site sequences set forth in FIG. 11 (SEQ ID NOs: 48-50).
The present invention also includes nucleic acid molecules that may comprise an isolated DNA sequence which encodes the heavy chain of an antibody molecule, wherein said antibody molecule has specificity for PCBP-1 and wherein the variable domain of said heavy chain comprises a CDR having the antigen binding site sequences CDR1 (SEQ ID NO: 45), CDR2 (SEQ ID NO: 46), and CDR3 (SEQ ID NO: 47) set forth in FIG. 10.
The present invention also includes nucleic acid molecules that may also comprise an isolated DNA sequence which encodes the light chain of an antibody molecule, wherein said antibody molecule has specificity for PCBP-1 and further wherein the variable domain of said light chain comprises a CDR having the antigen binding site sequences CDR1 (SEQ ID NO: 48), CDR2 (SEQ ID NO: 49), and CDR3 (SEQ ID NO: 50) set forth in FIG. 11.
PCBP-1 Antigens: This refers to expression products generated by PCBP-1, which can be used as antigens, target molecules, biomarkers, or any combination thereof, for a PCBP-1 antibody. The PCBP-1 antigens can be produced by the PCBP-1 gene or homologues of the PCBP-1 gene, and can include various modifications introduced by the cells expressing the PCBP-1 antigens, such as cancer cells.
Substantially Similar Binding Properties: This refers to a chimeric or humanized antibody or antibody fragment which retains the ability to specifically bind the antigen recognized by the parent PCBP-1 antibody used to produce the chimeric antibody, humanized antibody, or antibody fragment. Preferably, the affinity of a chimeric antibody, humanized antibody, or antibody fragment is at least about 10% of the affinity of the parent PCBP-1 antibody, more preferably at least about 25%, even more preferably at least about 50%. Most preferably, the chimeric antibody, humanized antibody, or antibody fragment exhibits antigen-binding affinity that is at least about 75% of the affinity of the parent PCBP-1 antibody. Methods for assaying antigen-binding affinity are known in the art and include half-maximal binding assays, competition assays, and Scatchard analysis. In a preferred aspect, antigen-binding affinity is assayed using a competition assay. Such a comparison can be relative to Alper PCBP-1 mouse monoclonal antibody (7SK).
Substantially Homologous Refers to immunoglobulin sequences that exhibit at least about 85% identity, more preferably about 90% identity, most preferably about 95% identity with a reference immunoglobulin, wherein % identity is determined by comparing the number identical of amino acid residues between the two immunoglobulins, wherein the positions of the amino acid residues are indicated using the Kabat numbering scheme.
Sameness for Monoclonal Antibody Products: For the purpose of determining sameness of monoclonal antibodies, and products thereof, the complementarity determining regions of the heavy and light chain variable regions are the principal molecular structural feature of a monoclonal antibody product. Two monoclonal antibodies can be considered the same if the amino acid sequences of the CDRs are the same, or if there are only minor amino acid differences between them. Whether differences in the amino acid sequences are minor can be determined by factors that include (but are not limited to) whether any particular residues have been established to be important for antigen binding. Amino acid differences outside the CDRs, or differences due to glycosylation patterns or post translational modifications do not result in different monoclonal antibodies. Changes in antibody structure that do not constitute differences between two monoclonal antibody products with the same CDRs include changes in the FWRs (i.e., humanizing a non-human derived monoclonal antibody or engineering certain framework residues that are important for antigen contact or for stabilizing the binding site, or changes in the constant region (i.e., changing the class or subclass of the constant region, changing specific amino acid residues which might alter an effector function, or changing the species from which the constant region is derived).
Substantially pure: For the purpose of the present invention, substantially pure refers to a homogeneous preparation preferably of PCBP-1 antibody or antibody fragment, or other chemical or biological agents. Substantially pure immunoglobulins of at least 80% homogeneity are preferred, with about 90% to about 95% homogeneity being more preferred, and 98% to 99% or more homogeneity is most preferred, and is generally considered acceptable for pharmaceutical uses.
2. Antibodies and Antibody Fragments
The present invention provides antibodies and antibody fragments specific for PCBP-1 antigens, including an antibody or antibody fragment capable of binding to a soluble form of PCBP-1 with a specific affinity of between 10−8 M and 10−11 M; an antibody or antibody fragment capable of binding to a soluble form of PCBP-1 in a cell; an antibody or antibody fragment capable of selectively reducing the activity of a soluble PCBP-1 in a cell; and an antibody or antibody fragment capable of preferentially binding to a soluble form of a PCBP-1.
A soluble form of PCBP-1 can be found in the cytoplasm of a ductal cancer cell with a PCBP-1 antibody of the present invention. PCBP-1 can be localized and expressed in high amounts in the nucleus in healthy breast tissue epithelial cells. As a cell undergoes transformation, PCBP-1 expression can become more cytoplasmic with some nuclear expression as well, and overall increased expression than in the healthy cells. As the ductal carcinoma cells become metastatic, PCBP-1 expression is entirely in the cytoplasm of the cells with no staining in the nucleus. While not limited to any particular mechanism, PCBP-1 protein moves from the nucleus in normal ductal epithelial cells, and as the cells are transformed, PCBP-1 becomes more cytoplasmic with some nuclear expression. As the ductal epithelial cancer cells become metastatic, the PCBP-1 can localize entirely in the cytoplasm of the cells.
The present invention includes a method of determining a likelihood of survival for a patient of breast cancer comprising contacting the sample from the patient in need thereof with an antibody capable of detecting nuclear and cytoplasmic PCBP-1; and determining the expression level of PCBP-1, where greater expression of said PCBP-1 in the sample is inversely correlated with overall survival. In an aspect, normal, non-metastatic and metastatic breast cancer ductal epithelial cellular sample images be scored 0 to 3+ according to normal pathological methods. In a particular aspect, a PCBP-1 stained assay is sent to an independent pathology laboratory to blindly score samples.
In one aspect, a score of “0” can be directed to no staining observed in invasive tumor cells. A score of “1+” can be directed to Weak, nuclear staining observed in any proportion of invasive tumor cells, or weak, cytoplasmic staining observed in less than 30% of cells in the sample. A score of “2+” can be weak cytoplasmic observed in 50% or more cells or strong cytoplasmic staining of more than 30% is observed in invasive tumor cells. A score of “3+” can be strong cytoplasmic staining observed that is in more than 50% of tumor cells. In a preferred aspect, the difference between 0/+1 and +2/+3 in ductal breast cancer samples can be particularly apparent in the higher amount of cytoplasmic staining of arrayed tissue samples scored +2 or +3. In a preferred aspect, intense staining can be easily visualized with a 10× objective, and weak staining can require 40× objective for visualization.
In an aspect of the present invention, higher levels of PCBP-1 expression (PCBP-1 score of +2 or +3) can be correlated with a decrease in a ductal breast cancer patient's overall prognosis or survival relative to ductal breast cancer patients with a lower level of PCBP-1 expression (PCBP-1 score of 0 or +1). Correspondingly, low levels of PCBP-1 expression indicate a better prognosis for a ductal breast cancer patient than high levels of PCBP-1 expression in ductal breast cancer samples.
In another aspect, higher levels of PCBP-1 expression can be correlated with a decrease in the overall prognosis of a ductal breast cancer patient with three or more positive lymph nodes. The breast cancer-specific survival rates of women with one or two positive nodes were found to have similar long-term survival; however, women with three positive nodes experienced significantly reduced survival compared to those with one or two involved nodes. (Tai, P., et al., supra). Accordingly, detection of PCBP-1 expression levels can be used to estimate overall survival of a ductal breast cancer patient.
The present invention includes a method of determining metastatic status of a breast cell or tissue in a sample comprising contacting the sample from a patient in need thereof with an antibody capable of detecting nuclear and cytoplasmic PCBP-1 and determining the subcellular location of said PCBP-1, where localization of said PCBP-1 in a cell cytoplasm of the sample is indicative of cellular metastasis. In an aspect, an antibody capable of detecting nuclear and cytoplasmic PCBP-1 is a monoclonal antibody having one or more of the heavy chain CDR antigen binding site sequences selected from the group consisting of SEQ ID NO: 45, SEQ ID NO: 46 and SEQ ID NO: 47, and one or more of the light chain CDR antigen binding site sequences selected from the group consisting of SEQ ID NO: 48, SEQ ID NO: 49 and SEQ ID NO: 50.
In another aspect, the present invention includes a method of determining a metastatic status of a breast cell or tissue in a sample comprising contacting the sample from a patient in need thereof with an antibody capable of detecting nuclear and cytoplasmic PCBP-1 and determining the subcellular location of said PCBP-1 and estrogen receptor (ER), progesterone receptor (PR), or ER and PR, where greater expression of said PCBP-1 in the sample is inversely correlated with overall survival.
In another aspect, the present invention includes a method of determining a metastatic status of a breast cell or tissue in a sample comprising contacting the sample from a patient in need thereof with an antibody capable of detecting nuclear and cytoplasmic PCBP-1 and determining the subcellular location of said PCBP-1 and estrogen receptor (ER), progesterone receptor (PR), or ER and PR, where similar subcellular localization of PCBP-1 and estrogen receptor (ER), progesterone receptor (PR), or ER and PR, is positively correlated with overall survival, non-metastasis, or overall survival and non-metastasis. In these aspects, the absence of similar localization pattern, i.e. co-localization, can include a lack of ER or PR staining where PCBP-1 staining is present in a ductal breast cancer cell cytoplasm.
An antibody or antibody fragment can be any antibody or antibody fragment of a PCBP-1 antibody of the present invention and, without limitation, can be a monoclonal antibody, a chimeric antibody, a humanized antibody, or an antibody conjugate thereof.
In an aspect, an antibody or antibody fragment can be any gamma globulin protein found in blood or other bodily fluids of vertebrates, and used by the host immune system to identify and neutralize foreign objects, such as bacteria and viruses. In one aspect, the antibody or antibody fragment can be selected from an antibody, a monoclonal antibody, a chimeric antibody, a humanized antibody, or an antibody conjugate. In an aspect, an antibody or antibody fragment can be any type of immunoglobulin protein, such as IgA, IgD, IgE, IgG or IgM.
In one aspect, an antibody or antibody fragment is capable of reducing the activity of PCBP-1. PCBP-1 activity is determined by measuring the poly(rC) binding of a sample. In an aspect, the poly(rC)-binding assay is carried out using a gel-shift assay as described in Ausubel F M, (1994). Current Protocols in Molecular Biology. Chichester: John Wiley and Sons (“Ausubel”).
Antibodies or antibody fragments include those that are specific or preferentially selective for PCBP-1, and can be used to detect a soluble form of the PCBP-1 protein. A soluble PCBP-1 protein has a molecular weight of about 35-40 kDa, as measured by gradient polyacrylamide gel electrophoresis.
In one aspect of the present invention, an antibody or antibody fragment is capable of preferentially binding to a soluble form of PCBP-1 protein. In this aspect, such preferential binding PCBP-1 can be relative to any protein. In a particular aspect, such preferential binding to PCBP-1 is relative to PCBP-1 that is membrane bound or associated. In another particular aspect, such preferential binding to PCBP-1 is relative to PCBP-1 that is nuclear membrane bound or associated.
As used herein, a membrane associated protein is a protein that can be found localized with a membrane upon examination of cell. A membrane bound protein is one that interfaces at least in part with the lipid bilayer. In one aspect, it is bound to the membrane via ionic interactions. In another aspect, a membrane bound protein is bound to the membrane via covalent interactions. In a preferred aspect, a membrane bound protein is bound to the membrane via hydrogen bonds.
In an aspect of the present invention, the preferential binding is at least 2-fold, 3-fold, 4-fold, 5-fold, 10-fold, 100-fold, 1,000-fold, 10,000-fold or 1,000,000-fold. In another aspect, an antibody of the present invention preferentially binds a soluble form of PCBP-1 compared to a membrane form of PCBP-1. In a particular aspect, an antibody of the present invention preferentially binds a soluble form of PCBP-1 compared to a nuclear membrane form of PCBP-1, or the reverse, in another aspect. A binding of the antibody can be measured in any way, and a preferred methodology is a gel-shift assay, set forth in Ausubel.
In an aspect, an antibody or antibody fragment binds PCBP-1 or a particular form of PCBP-1 such as a soluble form or a membrane bound form with a specific affinity of greater than 10−7 M, 10−8 M, 10−9 M, 10−10 M, or 10−11 M, between 10−8 M-10−11 M, 10−9 M-10−10 M, and 10−10 M-10−11 M. In a preferred aspect, specific activity is measured using a competitive binding assay as set forth in Ausubel.
Antibodies and antibody fragments can optionally be immobilized on a solid phase, detectably labeled, or conjugated to a cytotoxic radionuclide, a cytotoxic drug, or a cytotoxic protein and the like.
Antibodies and antibody fragments of the present invention can target expression of soluble PCBP-1 antigen by cells, preferably human cells, more preferably human cancer cells, and most preferably human breast, ovary, cervix, prostate, colon, stomach, kidney, liver, head, neck, lung, blood, pancreas, skin, testicle, thyroid and brain cancer cells. In one aspect of the present invention, the human breast cells can be lobular breast carcinoma cells. In another aspect of the present invention, the human breast cells can be ductal breast carcinoma cells. Expressed PCBP-1 antigens can include any form of the gene product, although particularly preferred aspects relate to the detection of the soluble or secreted form of PCBP-1. Such antigens can also include gene produced homologues of the Pcbp-1 gene and modified PCBP-1 antigens expressed by cancer cells.
In one aspect, antibodies or antibody fragments of the present invention may be used to correlate PCBP-1 expression or localization status with prognosis of survival or to determine an appropriate treatment of a patient in need thereof. In one aspect, high cytoplasmic staining of PCBP-1 relative to healthy controls using the antibodies or antibody fragments of the present invention may indicate a low likelihood of patient survival. In another aspect, nuclear PCBP-1 staining that is normal (similar to that seen in healthy controls) using the antibodies or antibody fragments of the present invention may indicate a higher likelihood of patient survival.
In another aspect of the present invention, PCBP-1 antibodies or antibody fragments of the present invention may be used to correlate PCBP-1 expression or localization status with type of disease or to determine an appropriate treatment of a patient in need thereof. In one aspect, high (2+ or 3+) cytoplasmic immunohistochemical staining of breast cancer tissues with an antibodies or antibody fragment of the present invention may be indicative of ductal breast carcinoma, while negative (0) or low (1+) cytoplasmic staining of breast cancer tissues with the antibodies or antibody fragments of the present invention may be indicative of lobular breast carcinoma.
In one aspect of the present invention, immunohistochemical staining may be high or increased relative to a suitable control. In one aspect, high or increased immunohistochemical staining is assigned a value of 2+ or 3+ for purposes of quantitation of staining. In an aspect, the suitable control may be a cell line of the same tissue type, a sample from a healthy individual or a patient having a different cytopathology, or a healthy sample from a patient having a disease, where the healthy sample is unstained on the same sample slide. In one aspect, the disease may be cancer. In another aspect, the disease may be breast cancer. In yet another aspect, the disease may be lobular or ductal breast cancer. In one aspect, the increase relative to a suitable control is two-, four-, ten- or twenty-fold or more. In another aspect, the increase relative to a suitable control is greater than 10, 20, 30, 40, 50, 60, 70, 80, 90, 95 or 99%. In another aspect, the increase is in cytoplasmic levels of the PCBP-1 antigen-antibody complex. In an aspect, an increase in the cytoplasmic levels of the PCBP-1 antigen-antibody complex is associated with ductal breast carcinoma.
In one aspect of the present invention, immunohistochemical staining may be low or reduced relative to a suitable control. In one aspect, low or reduced immunohistochemical staining is assigned a value of 0 or 1+ for purposes of quantitation of staining. In one aspect, low or reduced immunohistochemical staining means that the cytoplasm of less than 10% of cells is stained. In a preferred aspect, a score of 2+ means that the cytoplasm of greater than 50% of cancer cells in a tissue sample is not stained, while the cytoplasm of less than 50% of cancer cells in the tissue sample is stained. In another aspect, a score of 2+ is associated with ductal breast cancer.
In a preferred aspect, a score of 3+ means that the cytoplasm of greater than 90% of cancer cells in a tissue sample is stained, while the cytoplasm of less than 10% of cancer cells in the tissue sample is not stained. In another aspect, a score of 3+ is associated with ductal breast cancer. In another aspect, tissue samples assigned a score of 3+ will have a higher number of stained cells, and the cells will be stained at a higher intensity than that seen in a tissue sample assigned a score of 2+.
In an aspect, the suitable control may be a normal commercial cell line of the same type (such as SKBR3 cells or MDA-MB-231 cells), a sample from a healthy individual, or a healthy sample from a patient having a disease. In one aspect, the disease may be cancer. In another aspect, the disease may be breast cancer. In yet another aspect, the disease may be lobular or ductal breast cancer. In one aspect, the reduction relative to a suitable control is two-, four-, ten- or twenty-fold or more. In another aspect, the reduction relative to a suitable control is greater than 10, 20, 30, 40, 50, 60, 70, 80, 90, 95 or 99%. In another aspect, the reduction is in cytoplasmic levels of the PCBP-1 antigen-antibody complex. In an aspect, a reduction in the cytoplasmic levels of the PCBP-1 antigen-antibody complex is associated with lobular breast carcinoma. In an aspect, the present invention provides an antibody or antibody fragment specific for a PCBP-1 antigen, including the heavy chain CDR antigen binding site amino acid sequences CDR1 (SEQ ID NO: 45), CDR2 (SEQ ID NO: 46), and CDR3 (SEQ ID NO: 47) as set forth in FIG. 10, and the light chain CDR antigen binding site amino acid sequences CDR1 (SEQ ID NO: 48), CDR2 (SEQ ID NO: 49), and CDR3 (SEQ ID NO: 50) as set forth in FIG. 11. The present invention also provides an antibody specific for a PCBP-1 antigen, comprising one or more of the heavy chain CDR antigen binding site amino acid sequences set forth in FIG. 10 (SEQ ID NOs: 45-47), and one or more of the light chain CDR antigen binding site amino acid sequences set forth in FIG. 11 (SEQ ID NOs: 48-50).
The present invention includes PCBP-1 antibodies or antibody fragments having antigen binding sites CDR1 (SEQ ID NO: 45), CDR2 (SEQ ID NO: 46), and CDR3 (SEQ ID NO: 47), both heavy and light chains, as described in FIGS. 10 and 11. The invention also includes antibodies and antibody fragments specific to PCBP-1 expression products that contain antigen binding sites that are substantially homologous to these, or that result in substantially similar binding properties. The present invention also includes new hybridoma lines, and the monoclonal antibody molecules that they secrete, which are specific to PCBP-1 antigen expressed by normal or cancer cells. The present invention also includes chimeric and humanized antibodies and antibody fragments and also includes other modified antibodies and antibody fragments.
In addition to the specific amino acid sequences of the antigen binding sites of the heavy and light chains set forth in FIGS. 10 and 11, the present invention also encompasses antibodies and antibody fragments that are specific to PCBP-1 but which have FWR and/or CDR antigen binding site nucleotide sequences that are not identical to those set forth in FIGS. 10 and 11 (SEQ ID NOs: 19-29 and 34-44). Such antibodies and antibody fragments are preferred if they are specific or preferentially selective for the PCBP-1 antigen, preferably at least 85% as specific, more preferably at least 90% as specific, and most preferably at least 95% as specific for the PCBP-1 antigen as the antibody or antibody fragment of the present invention. According to a preferred aspect, a variant of an antibody or antibody fragment of the present invention can be as specific for the PCBP-1 antigen as a non-variant antibody or antibody fragment of the present invention, or can be more specific.
Antibodies and antibody fragments that are specific to PCBP-1 but which have FWR and/or CDR antigen binding site amino acid sequences that are not identical to those set forth in FIGS. 10 and 11 can possess the same or different specificity determining regions (SDRs) as the FWRs and/or CDRs of FIGS. 10 and 11 (SEQ ID NOs: 17 and 32) are included (set forth in bold, underlined text in these figures).
Modifications to the amino acid sequences of the antigen binding sites CDR1 (SEQ ID NO: 45 and 48, respectively), CDR2 (SEQ ID NO: 46 and 49, respectively), and CDR3 (SEQ ID NO: 47 and 50, respectively) set forth in FIG. 10 (heavy chain) and FIG. 11 (light chain) can occur in either or both of the FWR and CDR sequences. According to certain aspects of the invention, variations in antibodies or antibody fragments can occur where they have substantially homologous amino acid sequences, antibodies having substantially similar binding properties, or both.
Humanized variants of the antibodies or antibody fragments of the invention can contain a reduced murine content, and potentially, reduced immunogenicity, when compared to the murine antibodies or antibody fragments. Humanized variants include those that retain a binding affinity that is substantially similar to that of the original antibody or antibody fragment. An aspect of the invention provides CDR variants of humanized PCBP-1 antibodies or antibody fragments in which 1, 2, 3, 4, 5, or 6 (three heavy chain and three light chain) CDRs are humanized. A second aspect of the invention provides SDR variants of humanized PCBP-1 antibodies and antibody fragments in which only Specificity Determining Regions (SDRs) of at least one CDR from the PCBP-1 antibodies and antibody fragments are present in the humanized antibodies. The SDRs are selected from Table 1 or Table 2.







TABLE 1







Specificity-Determining Residues in Alper PCBP-1 Mouse


Monoclonal Antibody Heavy Chain (SEQ ID NO: 17)










Position
Residue














−1
Q



4
Q



5
Q



23
A



30
S

















TABLE 2







Specificity-Determining Residues in Alper PCBP-1 Mouse


Monoclonal Antibody Light Chain (SEQ ID NO: 32)










Position
Residue














−2
D



−1
I



1
V



2
L



21
C



38
Y



47
K



53
A



93
S










CDR variants can be formed by replacing at least one CDR of humanized PCBP-1 antibodies and antibody fragments with a corresponding CDR from a human antibody. CDR variants in which one, two, three, four, five, or six CDRs are replaced by a corresponding CDR from a human antibody and retain biological activity that is substantially similar to the binding affinity of the parental PCBP-1 mAb. CDR variants of the invention can have a binding affinity that is at least 25% of the binding affinity of the parental PCBP-1 antibody or antibody fragment, more preferably at least 50%, most preferably at least 75% or 90%.
CDR variants that have altered immunogenicity when compared to PCBP-1 antibodies and antibody fragments can be formed by grafting all six (three heavy chain and three light chain) CDRs from the PCBP-1 antibodies and antibody fragments of the present invention onto the variable light (VL) and variable heavy (VH) frameworks of human antibodies and antibody fragments. However, less than all six of the CDRs of the PCBP-1 antibodies and antibody fragments of the present invention can be present, while still permitting the humanized antibody to retain activity. Residues that are directly involved in antigen contact, the Specificity Determining Residues (SDRs), can be refined. SDR variants are formed by replacing at least one SDR of the PCBP-1 antibody or antibody fragment with a residue at a corresponding position from a human antibody. It should be noted that not all CDRs include SDRs.
In a preferred aspect, the variants of the present antibodies and antibody fragments include a combination of CDR and/or SDR substitutions to generate variants having reduced immunogenicity and a binding affinity that is substantially similar to that of the parental antibody or antibody fragment to PCBP-1.
In addition to variants specifically described herein, other “substantially homologous” modified immunoglobulins can be readily designed and manufactured using various recombinant DNA techniques. For example, the framework regions (FWRs) can be varied at the primary structure level. Moreover, a variety of different human framework regions can be used singly or in combination as a basis for the variant. In general, modifications of the genes can be readily accomplished by a variety of techniques, such as site-directed mutagenesis.
Alternatively, polypeptide fragments comprising only a portion of the primary antibody structure can be produced wherein the fragment substantially retains the immunoreactivity properties of the variant. Such polypeptide fragments include fragments produced by proteolytic cleavage of intact antibodies or fragments produced by inserting stop codons at the desired locations nucleotide sequence using site-directed mutagenesis. Single chain antibodies and fusion proteins which include at least an immunoreactivity fragment of the variant are also included within the scope of the invention.
The antibodies and their variants in accordance with the present invention can be directly or indirectly attached to effector moieties having therapeutic activity. Suitable effector moieties include cytokines, cytotoxins, radionuclides, drugs, immunomodulators, therapeutic enzymes, anti-proliferative agents, etc. Methods for attaching antibodies to such effectors are known in the art. These conjugated antibodies can be incorporated into any composition, including pharmaceutical compositions for use in treating diseases characterized by the expression of PCBP-1, including cancer, such as cancer of the breast, ovary, cervix, prostate, colon, stomach, kidney, liver, head, neck, lung, blood, pancreas, skin, testicle, thyroid and brain. The pharmaceutical compositions are preferably administered to a mammal, more preferably a human patient in need of such treatment, in order to treat the disease.
Antibodies and antibody fragments can either be labeled or unlabeled. Unlabeled antibodies can be used in combination with other labeled antibodies (second antibodies) that are reactive with the humanized antibody, such as antibodies specific for human immunoglobulin constant regions. Alternatively, the antibodies can be directly labeled. A wide variety of labels can be employed, such as radionuclides, fluors, enzymes, enzyme substrates, enzyme cofactors, enzyme inhibitors, ligands (particularly haptens), etc. Numerous types of immunoassays are available.
3. Nucleic Acid Molecules and Host Cells
Any of the antibodies or antibody fragments of the present invention can be encoded by nucleic acids. The present invention includes such molecules, fragments of such molecules and such molecules included in vectors and the like. Nucleic acid molecules also include the complement of such nucleic acid molecules. Both DNA and RNA molecules are examples of nucleic acid molecules.
In another aspect, the present invention provides an isolated DNA sequence which encodes the heavy chain of an antibody molecule, wherein said antibody molecule has specificity for PCBP-1 antigens and wherein the variable domain of said heavy chain comprises a CDR having the antigen binding site amino acid sequences CDR1, CDR2, and CDR3 set forth in FIG. 10.
In yet another aspect, the present invention provides an isolated DNA sequence which encodes the light chain of an antibody molecule, wherein said antibody molecule has specificity for PCBP-1 antigens and further wherein the variable domain of said light chain comprises a CDR having the antigen binding site amino acid sequences CDR1, CDR2, and CDR3 set forth in FIG. 11.
In another aspect, the present invention includes and provides a nucleic acid molecule in a host cell. Such nucleic acid molecule can be integrated into the genome of the host cell or can be present on a vector such as a plasmid or viral vector. A nucleic acid molecule may be transiently present in such a host cell. In one aspect, a host cell is selected from the group E. coli; Bacilli, including Bacillus subtilis; enterobacteriacae, including Salmonella, Serratia and Psesudomonas, yeast, including Saccharomyces; Pichia pastoris; Sf9 insect cells; Sp2/0, VERO and HeLa cells, Chinese hamster ovary (CHO) cell lines; W138, BHK, COS-7 and MDCK cell lines. In one aspect, a host cell is selected from a breast cancer cell line such as SKBR3, MCF-7, MDA-MB-231, MDA-MB-435, and ZR75B cells. In another aspect, a host cell is selected from a prostate cancer cell line such as PC3, DU145 and LNCap cells.
4. Methods of Making PCBP-1 Antibodies or Antibody Fragments
PCBP-1 antibodies or antibody fragments of the present invention can be developed, for example, using the human breast cancer cell line SKBR3 (available from the American Type Culture Collection as ATCC No. HTB30).
The present invention includes processes for producing monoclonal, chimeric, including humanized antibodies using recombinant DNA technology. See, for example, Antibodies, A Laboratory Manual (Harlow & Lane Eds., Cold Spring Harbor Press, 1988).
PCBP-1 antibodies or antibody fragments of the present invention can be produced by any known method including, without limitation, generating murine hybridomas which produce antibodies or antibody fragments specific for PCBP-1. Hybridomas can be formed, for example, by the fusion of a mouse fusion partner cell and spleen cells from mice immunized against PCBP-1. Mice can be immunized with crude or semi-purified preparations containing the antigens of interest. To immunize the mice, a variety of different conventional protocols can be followed. For example, mice can receive primary and boosting immunizations of antigenic preparations.
Cell fusions can be accomplished by any procedures known to those skilled in the field of immunology. Fusion partner cell lines and methods for fusing and selecting hybridomas and screening for antibodies or antibody fragments are known.
Antibodies or antibody fragments of the present invention can be produced in large quantities, for example, by injecting hybridoma cells secreting the antibody into the peritoneal cavity of mice and, after appropriate time, harvesting the ascites fluid which contains a high titer of the antibody or antibody fragment, and isolating the antibody or antibody fragment therefrom. Alternatively, the antibodies and antibody fragments can be produced by culturing hybridoma cells in vitro and isolating the secreted antibody or antibody fragment from the cell culture medium.
PCBP-1 antibodies or antibody fragments of the present invention can also be produced by expressing the appropriate DNA sequence in a host after the sequence has been operably linked to an expression control sequence. Such expression vectors are often replicable in a host organism either as episomes or as an integral part of the host chromosomal DNA. Expression vectors often contain expression control sequences compatible with the host cell, such as an origin of replication. In addition, an expression vector can include a promoter to control expression of the gene, optionally, with operator sequences, and have ribosome binding site sequences and the like for initiating and completing transcription and translation. Suitable promoters include, without limitation, the polyhedrin promoter, lactose promoter system, a tryptophan promoter system, a beta-lactamase promoter system, or a promoter system from phage lambda. Expression vectors can also contain selection markers. DNA sequences encoding the light chain and heavy chain of the PCBP-1 antibodies and antibody fragments can be inserted into separate expression vectors, or into the same expression vector.
Suitable hosts include, without limitation, prokaryotic strains such as E. coli; Bacilli, including Bacillus subtilis; enterobacteriacae, including Salmonella, Serratia and Psuedomonas. Suitable hosts also include eukaryotic hosts such as yeast, including Saccharomyces; Pichia pastoris; Sf9 insect cells; Sp2/0, VERO and HeLa cells, Chinese hamster ovary (CHO) cell lines; W138, BHK, COS-7 and MDCK cell lines. Other suitable hosts can also be used in accordance with known expression techniques.
The vectors containing the DNA segments of interest can be transferred into the host cell by any method, which varies depending on the type of cellular host. For example, calcium chloride transfection, calcium phosphate treatment, electroporation or cationic liposome mediated transfection (such as DOTAP). Successfully transformed cells, can be identified by a variety of techniques for detecting the binding of a receptor to a ligand.
Expressed gene products can be purified according to any method, including, without limitation, ammonium sulfate precipitation, affinity columns, column chromatography, and gel electrophoresis. Substantially pure immunoglobulins of at least 80% homogeneity are preferred, with about 90% to about 95% homogeneity being more preferred, and 98% to 99% or more homogeneity is most preferred, and is generally considered acceptable for pharmaceutical uses.
Isolated or purified DNA sequences can be incorporated into a cloning or expression vector, which can in turn be used to transform a host cell. The transformed host cells can be used in a process for the production of an antibody molecule having specificity for PCBP-1 antigens, including culturing the host cells and isolating the antibody molecules they produce.
5. Diagnostic Methods, Assays, and Kits
In a further aspect, the present invention provides an immunoassay for detecting a PCBP-1 antigen comprising an antibody or antibody fragment of the present invention.
The present invention also provides an immunoassay for detecting a PCBP-1 antigen which binds to a monoclonal antibody having one or more of the heavy chain CDR antigen binding site amino acid sequences set forth in FIG. 10 (SEQ ID NOs: 45-47), and one or more of the light chain CDR antigen binding site amino acid sequences set forth in FIG. 11 (SEQ ID NOs: 48-50).
The present invention also provides an immunoassay for detecting a PCBP-1 antigen which binds to a monoclonal antibody having the one or more of the heavy chain CDR antigen binding site sequences set forth in FIG. 10 (SEQ ID NOs: 45-47), and one or more of the light chain CDR antigen binding site sequences set forth in FIG. 11 (SEQ ID NOs: 48-50), comprising: (a) contacting said sample with an effective binding amount of an antibody specific for a PCBP-1 antigen, comprising the heavy chain CDR antigen binding site sequences CDR1, CDR2, and CDR3, selected from the group consisting of SEQ ID NO: 45, SEQ ID NO: 46, and SEQ ID NO: 47, and the light chain CDR antigen binding site sequences CDR1, CDR2, and CDR3, selected from the group consisting of SEQ ID NO: 48, SEQ ID NO: 49, and SEQ ID NO: 50; and (b) detecting said antigen by detecting the binding of the antibody to the PCBP-1 antigen. The present invention also provides an immunoassay for detecting a PCBP-1 antigen which binds to a monoclonal antibody having the one or more of the heavy chain CDR antigen binding site sequences set forth in FIG. 10 (SEQ ID NOs: 45-47), and one or more of the light chain CDR antigen binding site sequences set forth in FIG. 11 (SEQ ID NOs: 48-50), comprising: (a) contacting said sample with an effective binding amount of an antibody specific for a PCBP-1 antigen, comprising one or more of the heavy chain CDR antigen binding site sequences selected from the group consisting of SEQ ID NO: 45, SEQ ID NO: 46, and SEQ ID NO: 47, and one or more of the light chain CDR antigen binding site sequences selected from the group consisting of SEQ ID NO: 48, SEQ ID NO: 49, and SEQ ID NO: 50; and (b) detecting said antigen by detecting the binding of the antibody to the PCBP-1 antigen. In one aspect of the invention, an immunoassay of the present invention is used to determine an appropriate treatment of a patient in need thereof where said patient has symptoms of a disease characterized by the expression of gene products of Pcbp-1 and its homologues. In vitro analysis can be performed on a tissue specimen obtained from patients in need thereof in order to predict the likelihood of patient survival.
Such immunoassays can be used in any suitable manner, including, without limitation, by comprising: (a) contacting said sample with an effective binding amount of one of the antibodies or antibody fragments of the invention; and (b) detecting said antigen by detecting the binding of the antibody to the PCBP-1 antigen. Immunoassays of the present invention can be used to detect cancer cells expressing a PCBP-1 antigen, particularly cancer, tumor, carcinoma cells or neoplastic disease cells selected from the group consisting of breast, ovarian, cervical, prostate, colon, stomach, kidney, liver, head, neck, lung, blood, pancreatic, skin, testicular, thyroid and brain cancers.
In a further aspect, the present invention provides a kit for the immunohistochemical detection of carcinoma comprising: (a) an antibody or antibody fragment of the present invention; and (b) a secondary antibody conjugated to a detectable label. In a further aspect, a kit of the present invention further comprises an antibody or antibody fragment capable of recognizing the estrogren receptor (ER).
In a further aspect, the present invention provides a kit for making a prognosis regarding the likelihood of survival of a carcinoma patient in need thereof, or for determining appropriate treatment options for a patient in need thereof, comprising: (a) an antibody or antibody fragment of the present invention; and (b) a secondary antibody conjugated to a detectable label. In a further aspect, a kit of the present invention further comprises an antibody or antibody fragment capable of recognizing the estrogen receptor (ER).
In a further aspect, the present invention provides a kit for making a prognosis regarding the status of disease in a breast carcinoma patient in need thereof comprising: (a) an antibody or antibody fragment of the present invention; and (b) a secondary antibody conjugated to a detectable label. In one aspect, the kit may differentiate between ductal and lobular breast carcinoma. In a further aspect, a kit of the present invention further comprises an antibody or antibody fragment capable of recognizing the estrogen receptor (ER).
In a further aspect, the present invention provides a kit for the immunohistochemical detection of carcinoma comprising: (a) a monoclonal antibody having one or more of the heavy chain CDR antigen binding site amino acid sequences set forth in FIG. 10, and one or more of the light chain CDR antigen binding site amino acid sequences set forth in FIG. 11; and (b) a secondary antibody conjugated to a detectable label. In a further aspect, a kit of the present invention further comprises an antibody or antibody fragment capable of recognizing the estrogen receptor (ER).
In one aspect, the immunohistochemical analysis can be performed on a glass slide. In another aspect, the immunohistochemical analysis can be performed on a plastic slide. In another aspect, the immunohistochemical analysis can be performed on a slide made from a material other than glass or plastic.
In a further aspect, the present invention provides for Fluorescence In Situ Hybridization (FISH) of the pcbp-1 gene to determine the copy number of pcbp-1 gene sequences in a normal cells, non-metastic cancer cells and metastatic cancer cells. In one aspect, increased expression of PCBP-1 protein as determined using the methods of the present invention can be accompanied by duplication/amplification of the pcbp-1 gene. In another aspect, duplication of the pcbp-1 gene may precede the changes of expression of PCBP-1 protein as provided in the present invention. FISH is a method to analyze genes at the chromosome level and is capable of detecting and characterizing genetic changes such as gene/chromosome amplification/duplication, deletion, translocation, rearrangement and other abnormalities associated with genes and/or chromosomes. The term “in situ hybridization” generally refers to hybridization of a nucleic acid probe to a nucleic acid target that is part of a cytological or histological preparation. Typically, FISH methods involve the following steps: (a) fixing the tissue, cells from a culture or other biological material under investigation to a support (e.g., glass slide or wall of a micro titer well), (b) treatment of the tissue or material to increase accessibility of probe DNA to target DNA (e.g., permeabilizing the cell, denaturing the target DNA, and blocking repetitive sequences in the target DNA) (c) contacting the tissue or material containing target DNA with probes to form specific hybridization complexes, (d) post hybridization washes of the complexes to selectively remove probes that are not specifically hybridized to the target, and (e) detection of probes that have formed hybridization complexes with target DNA molecules (e.g., by directly visualizing a fluorescently labeled DNA probe or by using a secondary fluorescent probe). An advantage of FISH is that one can analyze individual cells and visualize the location on chromosomes. FISH can determine both the number of copies of a given DNA probe sequence in a cell as well as identify duplications, translocations and deletions of target DNA sequences. Methods for FISH are known in the art and are described in a number of sources, including: Gall and Pardue, (1981) Methods of Enzymology 21:470-480; Henderson, (1982) International Review of Cytology, 76:1-46; and Angerer, et al., (1985) in Genetic Engineering: Principles and Methods (Setlow and Hollaender, Eds.) vol. 7, pp. 43-65, Plenum Press, New York.
The FISH method is performed on a chromosome spread of a sample. In one aspect, a FISH sample may be a histological preparation obtained from a breast cell or tissue from a sample obtained from a patient. In one aspect, the chromosome spread is obtained from a culture of cells including primary cultures prepared from a sample of a patient or from established cell lines known to one of ordinary skill in the art. A chromosomal spread may be an interphase or metaphase spread or the sample can have cells at a variety of stages of the cell cycle.
Probe size is important because longer probes hybridize less specifically than shorter probes. The overlap defines the resolution of detectable features. For example, if the goal of an experiment is to detect the breakpoint of a translocation, then the overlap of the probes—the degree to which one DNA sequence is contained in the adjacent probes—defines the minimum window in which the breakpoint may be detected.
The mixture of probe sequences determines the type of features the probe can detect. Probes that hybridize along an entire chromosome are used to count the number of a certain chromosome, show translocations, or identify extra-chromosomal fragments of chromatin. This is often called “whole-chromosome painting.” If every possible probe is used, every chromosome, (the whole genome) would be marked fluorescently, which would not be particularly useful for determining features of individual sequences. However, a mixture of smaller probes can be created that is specific to a particular region (locus) of DNA; these mixtures are used to detect deletion mutations. When combined with a specific color, a locus-specific probe mixture is used to detect very specific translocations.
A variety of other techniques use mixtures of differently-colored probes. A range of colors in mixtures of fluorescent dyes can be detected, so each human chromosome can be identified by a characteristic color using whole-chromosome probe mixtures and a variety of ratios of colors. Although there are more chromosomes than easily-distinguishable fluorescent dye colors, ratios of probe mixtures can be used to create secondary colors. Similar to comparative genomic hybridization, the probe mixture for the secondary colors is created by mixing the correct ratio of two sets of differently-colored probes for the same chromosome. This technique is sometimes called M-FISH. The same physics that make a variety of colors possible for M-FISH can be used In the opposite situation—where the absence of the secondary color is pathological—is illustrated by an assay used to investigate translocations where only one of the breakpoints is known or constant. Locus-specific probes are made for one side of the breakpoint and the other intact chromosome. In normal cells, the secondary color is observed, but only the primary color is observed when the translocation occurs. This technique is sometimes called “break-apart FISH”.
In one aspect of the present invention, bacterial artificial chromosome (BAC) clone number RP11-175A7 (Genbank No. AC016700, 177995 bp, SEQ ID NO: 55) can be used to detect the presence, copy number and chromosomal location of the pcbp-1 gene in a sample using FISH. In one aspect, an increased number of copies can be detected by FISH that correlates with the increased expression of PCBP-1 protein detected using the immunological techniques of the present invention. In another aspect, the changes in copy number or chromosomal location can correspond with the change in cellular location of PCBP-1 protein (e.g., nuclear vs. cytoplasmic). In yet another aspect, an increased copy number of the pcbp-1 gene may be used to identify cells in tissue samples that have an increased likelihood of becoming metastatic.
In a further aspect, DNA probes for FISH analysis of the pcbp-1 gene can be prepared by one of ordinary skill in the art. In one aspect, additional probes may comprise cDNA sequences of the pcbp-1 gene. In another aspect nucleic acid sequences obtainable from the group consisting of UniProt Q15365, Q53SS8, Q14975; OMIM 601209; NCBI Gene 5093; NCBI RefSeq NP_006187; NCBI RefSeq NM_006196, NP_006187; NCBI UniGene 5093; and NCBI Accession AK130439, AAA91317 can be used.
In an aspect of the present invention, FISH probes (e.g., DNA probes containing a detectable label) of the nucleic acid sequences capable of detecting the pcbp-1 gene can be prepared by nick translation. Nick translation is well known to one of ordinary skill in the art. Briefly, nick translation is a tagging technique in molecular biology in which DNA Polymerase I is used to replace some of the nucleotides of a DNA sequence with their labeled analogues, creating a tagged DNA sequence which can be used as a probe in FISH or other hybridization techniques. This process is called nick translation because the DNA to be processed is treated with DNase to produce single-stranded “nicks.” This is followed by replacement in nicked sites by DNA polymerase I, which elongates the 3′ hydroxyl terminus, removing nucleotides by 5′-3′ exonuclease activity, replacing them with dNTPs. To radioactively label a DNA fragment for use as a probe in blotting procedures, one of the incorporated nucleotides provided in the reaction is radiolabeled in the alpha phosphate position. Similarly, a fluorophore can be attached instead for fluorescent labeling, or an antigen for immunodetection. When DNA polymerase I eventually detaches from the DNA, it leaves another nick in the phosphate backbone. The nick has “translated” some distance depending on the processivity of the polymerase. This nick could be sealed by DNA ligase, or its 3′ hydroxyl group could serve as the template for further DNA polymerase I activity. Proprietary enzyme mixes are available commercially to perform all steps in the procedure in a single incubation. Nick translation may cause double-stranded DNA breaks but this does not influence the performance of the labeled probe in in situ hybridization.
In one aspect, the DNA sequence can be tagged directly with a fluorescently labeled nucleotide. In a further aspect, the DNA sequence can be indirectly labeled with a nucleotide incorporating a modified nucleotide. In an aspect, a detectable label can be introduced by polymerization using nucleotides that include at least some modified nucleotides, such as nucleotides modified to include biotin, digoxygenin, fluorescein, or cyanine. In another aspect, the detectable label is introduced by random-priming and polymerization. Other examples include nick translation (Roche Applied Science, Indianapolis Ind.; Invitrogen, Carlsbad Calif.) and chemical labeling (Kreatech ULS, Amsterdam NL). Detectable labeling of nucleic acids is well known in the art and any labeling method appropriate for labeling DNA can be used.
First, a probe is constructed. The probe must be large enough to hybridize specifically with its target but not so large as to impede the hybridization process. The probe is tagged directly with fluorophores, with targets for antibodies or with biotin. Tagging can be done in various ways, such as nick translation, or PCR using tagged nucleotides.
Then, an interphase or metaphase chromosome preparation is produced. The chromosomes are firmly attached to a substrate, usually glass. Repetitive DNA sequences must be blocked by adding short fragments of DNA to the sample. The probe is then applied to the chromosome DNA and incubated for approximately 12 hours while hybridizing. Several wash steps remove all unhybridized or partially-hybridized probes. The results are then visualized and quantified using a microscope that is capable of exciting the dye and recording images.
In an aspect, if the fluorescent signal is weak, amplification of the signal can be used in order to exceed the detection threshold of the microscope. Fluorescent signal strength depends on many factors such as probe labeling efficiency, the type of probe, and the type of dye. Fluorescently-tagged antibodies or streptavidin are bound to the dye molecule. These secondary components are selected so that they have a strong signal. In a further aspect, FISH experiments designed to detect or localize gene expression within cells and tissues can rely on the use of a reporter gene, such as one expressing green fluorescent protein, to provide the fluorescence signal.
In a further aspect, the present invention provides a kit for making a prognosis regarding the likelihood of survival of a carcinoma patient in need thereof comprising: (a) a monoclonal antibody having one or more of the heavy chain CDR antigen binding site amino acid sequences set forth in FIG. 10, and one or more of the light chain CDR antigen binding site amino acid sequences set forth in FIG. 11; and (b) a secondary antibody conjugated to a detectable label. In a further aspect, a kit of the present invention further comprises an antibody or antibody fragment capable of recognizing the estrogen receptor (ER).
In a further aspect, the present invention provides a kit for making a prognosis regarding the status of disease in a breast carcinoma patient comprising: (a) a monoclonal antibody having one or more of the heavy chain CDR antigen binding site amino acid sequences set forth in FIG. 10, and one or more of the light chain CDR antigen binding site amino acid sequences set forth in FIG. 11; and (b) a secondary antibody conjugated to a detectable label.
Kits can include reagents for assaying a sample for a PCBP-1 antigen, where such kits may include: PCBP-1 antigen specific affinity reagents, such as an antibody, or fragment or mimetic thereof, and/or immunoassay devices comprising the same members of a signal producing system, such as antibodies, enzyme substrates, and the like; various buffers for use in carrying out the subject detection assays; a reference for determining the amount of a PCBP-1 antigen in a sample; and the like. Other examples of kits or kit formats are found in Alper, US Publication No. 2008/0293162, and in the Scoring Guide for the Interpretation of Ventana Pathway HER2—Staining of Breast Carcinomas (Ventana Medical Systems, Inc., Tuscon, Ariz., USA), both of which are herein incorporated by reference in their entireties. In a further aspect, a kit including reagents for assaying a sample for a PCBP-1 antigen may further include an antibody or antibody fragment capable of recognizing the estrogen receptor (ER).
In further aspect, the present invention provides a method for diagnosing cancer in humans comprising: (a) contacting a specimen from a patient suspected of having cancer with an antibody or antibody fragment of the present invention; (b) labeling said specimen; and (c) detecting the presence of the antigen-antibody complex by said label. Such a method of diagnosing cancer can be performed in vivo or in vitro. In one aspect, the cancer can be breast cancer. In another aspect, the breast cancer can be lobular or ductal breast cancer.
In further aspect, the present invention provides a method for making a prognosis of the likelihood of survival of a cancer patient in need thereof, or determining appropriate treatment options for a patient in need thereof, comprising: (a) contacting a specimen from a patient suspected of having a cancer with an antibody or antibody fragment of the present invention; (b) labeling said specimen; and (c) detecting the presence of the antigen-antibody complex by said label. Such a method of diagnosing cancer can be performed in vivo or in vitro. In one aspect, the method further comprises detecting the cellular localization of the antibody-antigen complex. In one aspect, the cancer can be breast cancer. In another aspect, the breast cancer can be lobular or ductal breast cancer. In one aspect, the cellular localization of the antibody-antigen complex is cytoplasmic.
In one aspect, the method further comprises detecting the level of the antigen-antibody complex in the cytoplasm. As shown in FIG. 15, a level of 0 (negative) or 1+ (low) can be indicative of lobular breast cancer, while a level of 2+ or 3+ (high) can be indicative of ductal breast cancer. In one aspect of the present invention, greater than 50%, greater than 60% or greater than 70% of patients having levels of 2+ or 3+ have ductal breast cancer. In another aspect of the present invention, less than 60%, less than 50%, or less than 40% of patients having levels of 2+ or 3+ have lobular breast cancer. In one aspect, diagnosis with lobular breast cancer can indicate a higher likelihood of survival than diagnosis of ductal breast cancer.
In a still further aspect, the present invention provides a method for diagnosing cancer in humans comprising: (a) contacting a specimen from a patient suspected of having a cancer with a monoclonal antibody having one or more of the heavy chain CDR antigen binding site amino acid sequences set forth in FIG. 10, and one or more of the light chain CDR antigen binding site amino acid sequences set forth in FIG. 11; (b) labeling said specimen; and (c) detecting the presence of the antigen-antibody complex by said label. The method of diagnosing cancer can be performed in vivo or in vitro. In one aspect, the cancer can be breast cancer. In another aspect, the breast cancer can be lobular or ductal breast cancer.
In a still further aspect, the present invention provides a method for making a prognosis of the likelihood of survival of a cancer patient in need thereof comprising: (a) contacting a specimen from a patient suspected of having a cancer with a monoclonal antibody having one or more of the heavy chain CDR antigen binding site amino acid sequences set forth in FIG. 10, and one or more of the light chain CDR antigen binding site amino acid sequences set forth in FIG. 11; (b) labeling said specimen; and (c) detecting the presence of the antigen-antibody complex by the label. The method of determining an appropriate treatment of a patient having cancer can be performed in vivo or in vitro. In one aspect, the method further comprises detecting the cellular localization of the antibody-antigen complex. In one aspect, the cellular localization of the antigen-antibody complex is cytoplasmic.
The cancer being diagnosed include those that are selected from the group consisting of solid tumors of the breast, ovary, cervix, prostate, colon, stomach, kidney, liver, head, neck, lung, pancreas, skin, testicle, thyroid and brain. In one aspect, the breast cancer is ductal or lobular breast cancer. In an additional aspect, the present invention provides a method for developing drugs useful in treating, diagnosing, or both treating and diagnosing diseases characterized by the expression of gene products of Pcbp-1 and homologues thereof, including identifying gene products expressed by Pcbp-1 and homologues thereof, and utilizing said gene products as biomarkers in the development and identification of drugs selected from the group consisting of PCBP-1 antibodies and antibody fragments, inhibiting peptides, siRNA, antisense oligonucleotides, vaccines, and chemical compounds, which specifically target said gene products.
In another aspect of the invention, a method is provided for determining appropriate treatment options of a patient in need thereof where the patient has symptoms of a disease characterized by the expression of gene products of Pcbp-1 and homologues thereof comprising a) contacting a tissue specimen of said patient in need thereof; with an antibody capable of preferentially detecting a soluble form of PCBP-1 antigen; b) staining said tissue specimen with a immunohistochemical stain; and c) determining the intensity and/or localization of the staining of said tissue specimen; wherein the intensity and/or localization of said staining correlates with the survival of said patient. For example, high cytoplasmic staining (assigned a value of 2+ or 3+) of PCBP-1 using the antibodies or antibody fragments of the present invention may indicate a low likelihood or patient survival. In another aspect, PCBP-1 staining that is negative or low (0 or 1+) relative to suitable controls may indicate a high likelihood of patient survival. In one aspect of the present invention, the intensity of said staining is measured relative to intensity of staining of suitable controls. In one aspect of the invention, said disease is cancer. In another aspect of the present invention, the cancer is breast cancer. In another aspect, the breast cancer is ductal or lobular breast cancer. In one aspect, high cytoplasmic staining (assigned a value of 2+ or 3+) of PCBP-1 using the antibodies or antibody fragments of the present invention may indicate ductal breast cancer. In another aspect, negative or low cytoplasmic staining (assigned a value of 0 or 1+) of PCBP-1 using the antibodies or antibody fragments of the present invention may indicate lobular breast cancer. As shown in FIG. 15, a level of 0 (negative) or 1+ (low) can be indicative of lobular breast cancer, while a level of 2+ or 3+ (high) can be indicative of ductal breast cancer. In one aspect of the present invention, greater than 50%, greater than 60% or greater than 70% of patients having levels of 2+ or 3+ have ductal breast cancer. In another aspect of the present invention, less than 60%, less than 50%, or less than 40% of patients having levels of 2+ or 3+ have lobular breast cancer. In one aspect, diagnosis with lobular breast cancer can indicate a higher likelihood of survival than diagnosis of ductal breast cancer. In a further aspect of the invention, immunohistochemical staining is any of the known methods in skilled art.
In another aspect of the invention, a method is provided for determining a metastatic status of a breast cell or tissue in a sample comprising contacting the sample from a patient in need thereof with an antibody capable of detecting nuclear and cytoplasmic PCBP-1 and determining the subcellular location of said PCBP-1, where localization of said PCBP-1 in a cell cytoplasm of the sample is indicative of cellular metastasis.
In another aspect of the invention, a method is provided for determining a likelihood of survival for a patient of breast cancer comprising contacting the sample from the patient in need thereof with an antibody capable of detecting nuclear and cytoplasmic PCBP-1; and determining the expression level of PCBP-1, where greater expression of said PCBP-1 in the sample is inversely correlated with overall survival.
In another aspect of the invention, a method is provided for determining likelihood of survival for a patient of breast cancer comprising contacting the sample from the patient in need thereof with an DNA probe capable of detecting pcbp-1; and determining the chromosome localization of pcbp-1, wherein detection of more than two copies of said pcbp-1 in the sample is correlated with overall survival.
In another aspect of the invention, a method is provided for determining likelihood of survival for a patient of breast cancer comprising contacting the sample from the patient in need thereof with an DNA probe capable of detecting pcbp-1; and determining the chromosome localization of pcbp-1, wherein detection of more than two copies of said pcbp-1 in the sample is correlated with overall survival. In an aspect, more than two copies of said pcbp-1, can be three, four, five, six or more copies in a cell. In another aspect, the number of copies can be greater than the two copies found in a normal non-cancerous cell. In an aspect, the number of copies may be any additional copies not found on human chromosome 2.
An antibody or antibody fragment of the present invention can also be used in diagnosis of diseases characterized by the expression of PBCP-1, such as cancer. In another aspect, an antibody or antibody fragment of the present invention can also be used in determining appropriate treatment options of a patient having symptoms of a disease characterized by the expression of PBCP-1, such as cancer. In another aspect of the present invention, the cancer is breast cancer. In another aspect, the breast cancer is ductal or lobular breast cancer. For example, in vivo diagnosis and imaging of a solid tumor of the breast, ovary, cervix, prostate, colon, stomach, kidney, liver, head, neck, lung, blood, pancreas, skin, testicle, thyroid and brain that expresses PBCP-1 can be performed in accordance with the methods of the invention. An antibody or antibody fragment of the present invention can also be used for diagnosis of diseases characterized by the expression of PBCP-1, for determining appropriate treatment options, or for prognosis regarding the likelihood of survival of a patient in vitro, for example, by using an antibody or antibody fragment to detect the presence of the cancer marker PBCP-1 in a fluid or tissue sample.
Antibodies and antibody fragments can be used in immunoassays to screen body fluids, such as serum, sputum, effusions, urine, cerebrospinal fluid, and the like, for the presence of PCBP-1. Antibodies and antibody fragments can be used for scanning or radioimaging, when labeled with an appropriate radiolabel, to detect primary or metastatic foci of tumor cells. Furthermore, the antibodies are useful in lymphoscintigraphy to detect lymph node involvement in the disease.
In one aspect, an antibody or antibody fragment of the present invention can be used to detect an increase in PCBP-1 expression. In another aspect, an antibody or antibody fragment of the present invention can be used to detect a decrease in PCBP-1 expression. In another aspect, an antibody or antibody fragment of the present invention can be used to detect a change in the cellular localization of PCBP-1. A PCBP-1 antibody or antibody fragment, which can include any or all of the antibodies or antibody fragments specific for PCBP-1-related gene products, and/or chimeric, humanized, or other variants thereof, can be used therapeutically, or in developing and performing assays, in vivo or in vitro diagnostic procedures, and imaging. The antibodies can be used alone or in combination with a pharmaceutically-acceptable or diagnostic or prognostic carrier formulation. PCBP-1 antibodies or antibody fragments can be incorporated into a pharmaceutically or diagnostically acceptable, non-toxic, sterile carrier as a suspension or solution. They can be used as separately administered compositions or given in conjunction with chemotherapeutic or immunosuppressive agents.
The present invention provides therapeutic, diagnostic and prognostic compositions comprising an antibody or antibody fragment of the present invention in combination with a pharmaceutically acceptable excipient, diluent or carrier. The present invention also includes a process for preparation of a therapeutic, diagnostic or prognostic composition comprising admixing an antibody molecule of the present invention together with a pharmaceutically acceptable excipient, diluent or carrier. An antibody molecule can be the sole active ingredient in the therapeutic, diagnostic or prognostic composition, or can be accompanied by other active ingredients including other antibody ingredients, for example anti-T cell, anti-IFNγ or anti-LPS antibodies, or non-antibody ingredients such as xanthines. Compositions can be incorporated into kits for diagnosing or treating diseases or predicting the outcomes of diseases characterized by the expression of PCBP-1, including, without limitation, solid tumors, and particularly solid tumors of the breast, ovary, cervix, prostate, colon, stomach, kidney, liver, head, neck, lung, pancreas, skin, testicle, thyroid and brain. In a particularly preferred aspect, the cancer is breast cancer. In one aspect, the present invention provides therapeutic, diagnostic and prognostic compositions for determining whether a breast cancer is ductal or lobular.
Antibodies or antibody fragments of the present invention are useful for immunoassays which detect or quantitate PCBP-1 or cells bearing PCBP-1 in a sample. Such an immunoassay typically comprises incubating a biological sample in the presence of a detectably labeled antibody of the present invention capable of identifying the tumor antigen, and detecting the labeled antibody which is bound in a sample.
In an aspect of the present invention the level, localization or both of one or more forms of PCBP-1 can determine, confirm or indicate the status of a cell, collection of cells, or sample from a subject. As used herein, “confirm” means that based on the level, localization, or both of one or more forms of PCBP in a cell, collection of cells or sample, subject etc provides a sufficient basis to characterize the status of a cell, collection of cells, sample or subject etc. As used herein, “confirm” means that based on the level, localization or both of one or more forms of PCBP in a cell, collection of cells or sample, subject etc provides in combination with other analysis a basis to characterize the status of a cell, collection of cells, sample or subject etc. As used herein, “indicate” means that based on the level, localization or both of one or more forms of PCBP in a cell, collection of cells or sample, subject etc provides that more likely than not or greater probability of determining the status of a cell, collection of cells, sample or subject etc. is of a particular status. In one aspect, high (2+ or 3+) cytoplasmic staining of breast cancer samples can indicate that a patient has ductal breast cancer, while negative (0) or low (1+) cytoplasmic staining of breast cancer samples can indicate that a patient has lobular breast cancer.
A status of a cell or collection of cells can include any aspect and in one aspect is whether that a cell, collection of cells, sample, etc. are metastatic, non-metastatic tumor cells or normal cells. A status of a subject can include whether the analysis provides information on whether a metastatic cancer or non-metastatic tumor is present in the subject. In one aspect, a status of a subject can include whether a breast cancer is ductal or lobular.
Examples of confirmatory analysis, assays, tests etc. that can be used to confirm or in combination with those disclosed include, without limitation, those set forth in Alper, US Publication No. 2008/0293162, as well as histological examination of samples.
In an aspect of the present invention the level, localization, or both, of one or more forms of PCBP-1 is diagnostic or prognostic of a disease or outcome probability. In one aspect, high cytoplasmic staining (2+ or 3+) of PCBP-1 relative to suitable controls using the antibodies or antibody fragments of the present invention may indicate a low likelihood of patient survival. In another aspect, nuclear PCBP-1 staining that is negative (0) or low (1+) relative to suitable controls using the antibodies or antibody fragments of the present invention may indicate a higher likelihood of patient survival. In another aspect, high cytoplasmic staining (2+ or 3+) of breast cancer samples can indicate that a patient has ductal breast cancer, while negative (0) or low (1+) cytoplasmic staining of breast cancer samples can indicate that a patient has lobular breast cancer. In one aspect, a suitable positive control can be SKBR3 cells or MDA-MB-231 cells, and a suitbale negative control can be healthy bladder cells.
In an aspect of the present invention a reduced level of a soluble form of PCPB-1 in a cell, collection of cells or sample can diagnose, prognose, monitor, determine, confirm or indicate that such derived is from a metastatic tissue. In one aspect, “reduced” can mean reduced relative to a control, with the control being a normal cell of the same type that is non-metastatic. In this aspect, the reduction can be greater than 10, 20, 30, 40, 50, 60, 70, 80, 90, 95, or 99%. In another aspect, the reduction can be two-, four-, ten-, or twenty-fold or more.
In an aspect of the present invention an increased level of a soluble form of PCPB-1 in a cell, collection of cells or sample can diagnose, prognose, monitor, determine, confirm or indicate that such derived is from a metastatic tissue. In one aspect, “increased” can mean increased relative to a control, with the control being a normal cell of the same type that is non-metastatic. In this aspect, the increase can be greater than 10, 20, 30, 40, 50, 60, 70, 80, 90, 95, or 99%. In another aspect, the increase can be two-, four-, ten-, or twenty-fold or more.
In one aspect of the present invention, PCBP-1 expression is measured using immunohistochemistry followed by a quantitative method. In one aspect, a quantitative method can be software such as AQUANALYSISTM software (HistoRx, Inc., New Haven, Conn., USA). In another aspect, a quantitative method such as AQUANALYSISTM software can be used in addition to the methods described in Example 13. In one aspect of the present invention, PCBP-1 expression is relative to PCBP-1 expression in normal controls. In another aspect, PCBP-1 expression in cancer cells can be expressed as a percentage of PCBP-1 expression in normal controls. Statistical significance of differences in PCBP-1 expression can be measured using the Student's t-test. In one aspect, t=0.99. In another aspect, t=0.95. In another aspect, t=0.90.
In one aspect of the present invention, “strong expression” of PCBP-1 can be at least a 3-fold, 4-fold, 5-fold or greater increase in PCBP-1 expression as compared to normal tissues. In another aspect, “moderate expression” of PCBP-1 can be at least a 2- to 3-fold increase in PCBP-1 expression as compared to normal tissues. In another aspect, “moderate expression” of PCBP-1 can be between a 2- to 3-fold increase in PCBP-1 expression as compared to normal tissues. In another aspect, “weak expression” of PCBP-1 can be a 1-fold or less increase in PCBP-1 expression as compared to normal tissues. In another aspect, “weak expression” of PCBP-1 can be a decrease in PCBP-1 expression as compared to normal tissues.
Quantitative or semi-quantitative detection of PCBP-1 may be evaluated within the context of a patient's clinical history and other diagnostic tests evaluated by a qualified pathologist. In one aspect, diagnosing a breast cancer as a carcinoma based on PCBP-1 expression is done based on intensity of staining and percent of stained cells from the total population of well-preserved cells. Suitable positive controls for PCBP-1 staining include SKBR3 and MDA-MB-231 cell lines. Suitable negative controls for PCBP-1 staining include bladder cells. In one aspect, the intensity of cell staining can range from no staining to faint staining to weak staining to intense staining. In another aspect, the percentage of well-preserved, stained cells is 0%, less than 50%, greater than 10%, greater than 30%, greater than 40%, greater than 50%, greater than 60%, greater than 70% or greater than 90%. In an aspect of the present invention, staining is localized to the cytoplasm. In another aspect, nuclear staining may still be present, but this staining is not included in the determination of positivity. In one aspect, tissue specimens can be analyzed for PCBP-1 expression via microscopy at low (10-20×) resolution to locate well-preserved and well-stained areas. Identified well-preserved and well-stained areas can be used to make a determination of the intensity of cytoplasmic staining. The percentage of well-preserved, stained cells can be estimated as 0%, less than 50%, or greater than 10%, greater than 30%, greater than 40%, greater than 50%, greater than 60%, greater than 70% or greater than 90%. In one aspect of the present invention, the cells of a single representative field is used and the area of a single representative field is used to make a determination according the methods of the present invention. In another aspect of the present invention, the number of cells examined can be at least 50, at least 100, at least 200, at least 300, at least 400, and 500 or more. In another aspect, the number of cells used to make a determination according the methods of the present invention are at least 100 cells. In one aspect of the present invention, quantitation of PCBP-1 expression can be determined by assigning a value of 0 to 3+ for cells stained with an antibody of the present invention, preferably Alper PCBP-1 antibody or any antibody having a staining pattern like Alper PCBP-1 antibody. In one aspect, the criteria for quantitation of cell staining are as follows: 0: no staining is observed; 1+: faint, partial cytoplasmic staining is observed; 2+: weak, complete cytoplasmic staining of greater than 50% of the cells in the sample is observed; 3+: intense, complete cytoplasmic staining of greater than 50% of the cells in the sample is observed. Examples of a negative sample and of 1+, 2+ and 3+ staining in ductal and lobular breast cancer cells are shown in FIGS. 16-18.
In one aspect, a score of 2+ includes a sample with a percentage of well-preserved cells in a tissue sample having stained cytoplasm is greater than 50%, while the percentage of well-preserved cells in a tissue sample having non-stained cytoplasm is less than 50%. In another aspect, a score of 2+ or more is associated with ductal breast cancer.
In another aspect, a score of 3+ includes a sample with a percentage of greater than 90% of well-preserved cells in a tissue sample having a stained cytoplasm, while the percentage of well-preserved cells in a tissue sample having non-stained cytoplasm is less than 10%. In another aspect, a score of 3+ is associated with ductal breast cancer. In another aspect, tissue samples assigned a score of 3+ will have a higher number of stained cells, and the cells will be stained at a higher intensity than that seen in a tissue sample assigned a score of 2+.
In another aspect of the present invention, increases in PCBP-1 expression can be expressed as increases in cells or tissues as a whole. In another aspect, increases in PCBP-1 expression can be expressed as increases in the cytoplasm of cells. In another aspect, increases in PCBP-1 expression can be expressed as increases in the nucleus of cells.
In another aspect of the present invention, decreases in PCBP-1 expression can be expressed as decreases in cells or tissues as a whole. In another aspect, decreases in PCBP-1 expression can be expressed as decreases in the cytoplasm of cells. In another aspect, decreases in PCBP-1 depression can be expressed as increases in the nucleus of cells.
In one aspect of the present invention, PCBP-1 expression in colon cancer cells is increased as compared to PCBP-1 expression in normal colon cells. In another aspect, colon cancer cells can exhibit strong cytoplasmic PCBP-1 expression as compared to normal colon cells.
In one aspect of the present invention, PCBP-1 expression in squamous carcinoma cells is increased as compared to PCBP-1 expression in normal skin cells. In another aspect, squamous carcinoma cells can exhibit a greater than 3-fold increase cytoplasmic PCBP-1 expression as compared to normal skin cells.
In another aspect of the present invention, PCBP-1 expression in melanoma cells is increased as compared to PCBP-1 expression in normal skin cells. In another aspect, melanoma cells can exhibit strong cytoplasmic PCBP-1 expression, while normal skin cells can exhibit weak nuclear expression of PCBP-1.
In one aspect of the present invention, PCBP-1 expression in glioblastoma multiforme cells is increased as compared to PCBP-1 expression in normal brain cells. In another aspect, glioblastoma multiforme cells can exhibit moderate cytoplasmic expression of PCBP-1, while neurons and astrocytes do not exhibit any PCBP-1 expression.
In one aspect of the present invention, PCBP-1 expression in astrocytoma cells is increased as compared to PCBP-1 expression in normal brain cells. In another aspect, astrocytoma cells can exhibit moderate cytoplasmic expression of PCBP-1, while neurons and astrocytes do not exhibit any PCBP-1 expression.
In one aspect of the present invention, PCBP-1 expression in ovarian cancer cells is decreased as compared to PCBP-1 expression in normal skin cells. In another aspect, ovarian cancer cells can exhibit little or no nuclear and/or cytoplasmic expression of PCBP-1, while normal ovarian cells can exhibit strong nuclear and cytoplasmic expression of PCBP-1.
In one aspect of the present invention, PCBP-1 expression in endometrial cancer cells is increased as compared to PCBP-1 expression in normal endometrial cells. In another aspect, endometrial cancer cells can exhibit strong nuclear and cytoplasmic PCBP-1 expression, while normal endometrial cells can exhibit little or no cytoplasmic expression of PCBP-1.
In one aspect of the present invention, PCBP-1 expression in sarcoma cells is increased as compared to PCBP-1 expression in normal muscle cells. In another aspect, sarcoma cells can exhibit moderate to high levels of cytoplasmic PCBP-1 expression as compared to normal muscle cells.
In one aspect of the present invention, PCBP-1 expression in bladder cancer cells is increased as compared to PCBP-1 expression in normal bladder cells. In another aspect, bladder cancer cells can exhibit moderate to high levels of cytoplasmic PCBP-1 expression as compared to normal bladder cells.
In one aspect of the present invention, PCBP-1 expression in breast cancer cells can be increased as compared to PCBP-1 expression in normal breast cells. In another aspect, breast cancer cells can exhibit strong cytoplasmic PCBP-1 expression and moderately strong nuclear PCBP-1 expression, while normal breast cells can exhibit weak nuclear PCBP-1 expression. In another aspect, breast cancer cells can exhibit strong cytoplasmic PCBP-1 expression and moderately strong nuclear PCBP-1 expression, while normal breast cells can exhibit strong nuclear PCBP-1 expression.
In one aspect of the present invention, cytoplasmic PCBP-1 expression in ductal carcinoma cells can be higher than cytoplasmic PCBP-1 expression in lobular breast carcinoma cells. In an aspect of the present invention a similar level of a soluble form of PCBP-1 in a cell, collection of cells or sample to a normal control can diagnose, prognose, monitor, determine, confirm or indicate that such cell was derived from a non-metastatic tissue.
In an aspect of the present invention, a lack of localization of a soluble form of PCPB-1 in a cell nucleus can diagnose, prognose, monitor, determine, confirm or indicate that such derived is from a metastatic tissue.
In an aspect of the present invention, localization of a soluble form of PCPB-1 in a cell, collection of cells or sample to a normal control can diagnose, prognose, monitor, determine, confirm or indicate that such derived from a non-metastatic tissue.
In an aspect, a diagnostic or prognostic method or other method of the present invention is indicative of metastatic status, where the level of nuclear PCBP-1 is indicative of the metastatic status of a cell or tissue. In an aspect, a level of nuclear PCBP-1 that is lower than a non-metastatic control tissue or cell is indicative of metastatic ability. In this aspect, an indicative level can be less than 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 95% of the control, or between less than 1% and less than 20% of the control.
In an aspect, a diagnostic or prognostic method or other method of the present invention is indicative of metastatic status, wherein the level of cytoplasmic PCBP-1 is indicative of the metastatic status of a cell or tissue. In an aspect, a level of cytoplasmic PCBP1 that is higher than a non-metastatic control tissue or cell is indicative of metastatic ability. In this aspect, an indicative level can be greater than 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 95% of the control, or between greater than 1% and greater than 20% of the control.
In an aspect, a diagnostic or prognostic method or other method of the present invention is indicative of non-metastatic status, wherein the level of nuclear PCBP-1 is indicative of the non-metastatic status of a cell or tissue. In an aspect, a level of nuclear PCBP1 that is similar to a non-metastatic control tissue or cell is indicative of non-metastatic ability. In this aspect, an indicative level can be equal to or within 1%, 5%, or 10% of the control, or equal to or within 1% and greater than 10% of the control. In another aspect, a diagnostic or prognostic method or other method of the present invention is indicative of non-metastatic status, where subcellular localization of PCBP-1 and estrogen receptor (ER), progesterone receptor (PR), or ER and PR is similar. In this aspect, the absence of similar localization can include a lack of ER or PR staining where PCBP-1 staining is present in a ductal breast cancer cell cytoplasm. For example, ER in the nucleus and PCBP-1 in the nucleus is indicative of normal or non-metastatic ductal breast cancer cells.
In an aspect, a diagnostic or prognostic method or other method of the present invention is indicative of non-metastatic status, wherein the level of cytoplasmic PCBP-1 is indicative of the non-metastatic status of a cell or tissue. In an aspect, a level of cytoplasmic PCBP1 that is similar to a non-metastatic control tissue or cell is indicative of non-metastatic ability. In this aspect, an indicative level can be equal to or within 1%, 5%, or 10% of the control, or between 0% and less than 10% of the control.
In another aspect, the present invention includes a method of determining a metastatic status of a breast cell or tissue in a sample comprising contacting the sample from a patient in need thereof with an antibody capable of detecting nuclear and cytoplasmic PCBP-1 and determining the subcellular location of said PCBP-1, where similar subcellular co-localization of PCBP-1 and estrogen receptor (ER), progesterone receptor (PR), or ER and PR, is positively correlated with overall survival, non-metastasis, or overall survival and non-metastasis. In this aspect, the absence of co-localization can include a lack of ER or PR staining where PCBP-1 staining is present in a ductal breast cancer cell cytoplasm.
In another aspect, the present invention includes a method of determining a metastatic status of a breast cell or tissue in a sample comprising contacting the sample from a patient in need thereof with an antibody capable of detecting nuclear and cytoplasmic PCBP-1 and determining the subcellular location pattern of said PCBP-1, where the absence of similar subcellular localization of PCBP-1 and estrogen receptor (ER), progesterone receptor (PR), or ER and PR, is inversely correlated with overall survival. In this aspect, the absence of similar localization pattern can include a lack of ER or PR staining where PCBP-1 staining is present in a ductal breast cancer cell cytoplasm.
In an aspect of the present invention, the cell, collection of cells or sample is a cervical or breast cell collection of cells or sample.
In an aspect of the present invention, the cell, collection of cells or sample is a lobular breast cell collection of cells or sample. In another aspect of the present invention, the cell, collection of cells or sample is a ductal breast cell collection of cells or sample.
Antibodies and antibody fragments of the present invention are also useful for immunopathological analysis, such as the differential diagnosis of tumor type, and the subclassification of the tumor based on its expression of PCBP-1, including, without limitation, assessment of metastatic potential, predicted responses to therapy, and overall prognosis. In one aspect, the immunopathological analysis using the antibodies and antibody fragments of the present invention can indicate whether a breast cancer sample is ductal or lobular breast cancer.
PCBP-1 antibodies and antibody fragments permit the definition of subpopulations of tumor cells among the heterogeneous cells present in a growing tumor and can be used, for example, in the typing and cross-matching of the tumor cell “lines,” including, without limitation, by means of flow cytometry, both at the time of surgery and prior to therapy. An analysis of the tumor cell populations or subpopulations with antibodies or antibody fragments of this invention, and a battery of additional antibodies or antibody fragments, can be used to define (a) which antigen preparation would be the most appropriate for specific active immunotherapy, (b) which antibody or antibody fragment or chimeric antibody would be efficacious for the particular cancer; and (c) which antibody or combination of antibodies or antibody fragments should be used for imaging the patient at a later date in search for recurrent or metastatic tumors.
A biological sample can be treated with nitrocellulose, or other solid support or carrier which is capable of immobilizing cells, cell particles or soluble proteins or glycoproteins. The support can then be washed with suitable buffers followed by treatment with the detectably labeled antibody of the present invention. The solid phase support can then be washed with the buffer a second time to remove unbound antibody. The amount of bound label on said solid support can then be detected by conventional means.
One of the ways in which the antibody of the present invention can be detectably labeled is by linking the same to an enzyme and use in an enzyme immunoassay (EIA) or enzyme-linked immunosorbent assay (ELISA). This enzyme, when subsequently exposed to its substrate, will react with the substrate generating a chemical moiety which can be detected, for example, by spectrophotometric, fluorometric or by visual means. In an alternate embodiment, the enzyme is used to label a binding partner for the antibody of the invention. Such a binding partner can be an antibody against the constant or variable region of the antibody of the invention, such as a heterologous anti-mouse immunoglobulin antibody. Alternatively, the binding partner can be a non-antibody protein capable of binding to the antibody of the present invention.
By radioactively labeling the antibodies of the present invention, it is possible to detect PCBP-1 through the use of a radioimmunoassay (RIA). The radioactive isotope can be detected by such means as the use of a gamma counter or a scintillation counter or by autoradiography. Isotopes which are particularly useful for the purpose of the present invention are known in the art.
It is also possible to label the antibodies of the present invention with a fluorescent compound. When the fluorescently labeled antibody is exposed to light of the proper wave length, its presence can then be detected due to fluorescence. The antibodies of the present invention also can be detectably labeled by coupling to a chemiluminescent compound. The presence of the chemiluminescently labeled antibody is then determined by detecting the presence of luminescence that arises during the course of a chemical reaction. A bioluminescent compound can also be used to label the antibodies of the present invention. Bioluminescence is a type of chemiluminescence found in biological systems, in which a catalytic protein increases the efficiency of the chemiluminescent reaction. The presence of a bioluminescent protein is determined by detecting the presence of luminescence. Important bioluminescent compounds for purposes of labeling are luciferin, luciferase and aequorin.
Detection of the antibody, fragment or derivative can be accomplished by a scintillation counter, for example, if the detectable label is a radioactive gamma emitter, or by a fluorometer, for example, if the label is a fluorescent material. In the case of an enzyme label, the detection can be accomplished by colorimetric methods which employ a substrate for the enzyme. Detection can also be accomplished by visual comparison of the extent of enzymatic reaction of a substrate in comparison with similarly prepared standards. Alternatively, detection may be accomplished by counting the intensity and number of pixels of a fluorescent image.
In situ detection can be accomplished by removing a specimen from a patient, and providing the labeled antibody, or the unlabelled antibody plus a labeled binding partner to such a specimen. Through the use of such a procedure, it is possible to determine not only the presence of the antigen but also its distribution in the examined tissue. Using the present invention, those of ordinary skill will readily perceive that any of a wide variety of histological methods (such as staining procedures) can be modified in order to achieve such in situ detection. Such methods include, for example, immunohistochemical staining procedures. In an aspect, an avidin-biotin immunoperoxidase staining system can be used, and a kit utilizing this system is also contemplated, although the methods of the present invention can utilize any suitable staining procedures known in the art.
Kits according to the present invention can include frozen or lyophilized antibodies to be reconstituted by thawing or by suspension in a liquid vehicle. The kits can also include a carrier or buffer. Preferably, the kit also comprises instructions for reconstituting and using the antibody. The kit employing antibodies, including chimeric and humanized antibodies of the present invention, can be used for immunohistochemical evaluation of cancers, including cancer of the breast, ovary, cervix, prostate, colon, stomach, kidney, liver, head, neck, lung, blood, pancreas, skin, testicle, thyroid and brain.
The kits including the reagents necessary for immunohistochemical analysis can be provided as follows: a) PCBP-1 antibody or antibody fragment of the present invention, or chimeric or humanized variants thereof; b) blocking reagent (in the form of, for example, goat serum) and secondary antibody (such as, for example, goat anti-mouse antibody); c) detectable marker (such as, for example, immunoperoxidase or alkaline phosphatase); and d) developing reagents. The primary antibody (PCBP-1 antibody or antibody fragment or variants thereof) serves as an antigen which can bind more than one secondary antibody. The secondary antibodies form a “bridge” between the primary antibody and the complex formed by the detectable marker and developing reagent (for example, a horseradish peroxidase-antiperoxidase complex).
Any suitable detection system can be used in accordance with the methods and kits of the present invention. Such detection systems are widely used in immunofluorescence applications, and can be imaged using techniques including, but not limited to, flow cytometry, microscopy, Western blotting, and ELISAs. Suitable detection systems can employ conjugates of secondary antibodies, conjugates of colloidal gold, or conjugates of secondary proteins, in order to amplify the signal from a primary protein (in the context of the present invention, the primary protein signal being amplified is bound a PCBP-1 antibody, which can or cannot be labeled, for example with a protein such as biotin), which is in turn being used to detect a specific target (in the context of the present invention, the target is a PCBP-1 expression product).
Suitable secondary conjugates for use in the methods and kits of the present invention can include, but are not limited to, enzyme conjugates of a secondary antibody and an enzyme such as horseradish peroxidase or alkaline phosphatase; enzyme conjugates of avidin or streptavidin and an enzyme such as horseradish peroxidase or alkaline phosphatase; enzyme conjugates of protein A or protein G and an enzyme such as horseradish peroxidase or alkaline phosphatase; conjugates of colloidal gold and a secondary antibody; conjugates of colloidal gold and avidin or streptavidin; conjugates of magnetic particles and a secondary antibody; and conjugates of secondary antibodies and labels such as fluorescent dyes and biotin. The present invention is not limited to any particular detection systems, and it is considered within the ability of the person of ordinary skill in the art to utilize these or other detection systems in accordance with the present invention. These secondary conjugates (also referred to as labels in the context of the present invention) are useful for visualizing antigen-antibody complexes.
The antibody or antibody fragment of the present invention can also be adapted for utilization in an immunometric assay, also known as a “two-site” or “sandwich” assay. In a typical immunometric assay, a quantity of unlabelled antibody (or fragment of antibody), is bound to a solid support that is insoluble in the fluid being tested and a quantity of detectably labeled soluble antibody is added to permit detection and/or quantitation of the ternary complex formed between solid-phase antibody, antigen, and labeled antibody.
For purposes of in vivo imaging of colon, breast, ovarian and other cancers using the antibodies or antibody fragments of the present invention, there are many different labels and methods of labeling known to those of ordinary skill in the art. Examples of the types of labels which can be used in the present invention include radioactive isotopes, paramagnetic isotopes, and compounds which can be imaged by positron emission tomography (PET).
6. Pharmaceutical Compositions and Methods of Treatment
Another aspect of the invention provides a composition comprising any of these antibodies, optionally in combination with a pharmaceutically acceptable carrier. In another aspect, an antibody of the present invention is optionally in combination with one or more active agents, drugs or hormones.
The present invention also provides a method of treating human or animal subjects suffering from or at risk of a cancer that expresses PBCP-1, such as solid tumors of the breast, ovary, cervix, prostate, colon, stomach, kidney, liver, head, neck, lung, pancreas, skin, testicle, thyroid and brain, the method comprising administering to the subject a therapeutically effective amount of an antibody of the present invention, or a pharmaceutical composition comprising a therapeutically effective amount of an antibody of the present invention.
The term “subject” as used herein refers to any subject in need of treatment.
The term “therapeutically effective amount” as used herein refers to an amount of a therapeutic agent needed to treat, ameliorate or prevent a targeted disease or condition, or to exhibit a detectable therapeutic or preventative effect. For any antibody, the therapeutically effective dose can be estimated initially either in cell culture assays or in animal models, usually in rodents, rabbits, dogs, pigs, or primates. The animal model can also be used to determine the appropriate concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans.
An effective amount for a human subject can depend upon the severity of the disease state, the general health of the subject, the age, weight and gender of the subject, diet, time and frequency of administration, drug combination(s), reaction sensitivities and tolerance/response to therapy and can be determined by routine experimentation and is within the judgment of the clinician. Generally, an effective dose will be from 0.01 mg/kg to 50 mg/kg, preferably 0.1 mg/kg to 20 mg/kg, more preferably from about 1 mg/kg to about 15 mg/kg.
Compositions can be administered individually to a patient or can be administered in combination with other agents, drugs or hormones. According to some aspects, antibodies can be conjugated with these agents. A summary of the ways in which the antibodies of the present invention can be used therapeutically includes direct cytotoxicity by the antibody, either mediated by complement or by effector cells, or conjugated to anti-tumor drugs, toxins, and radionuclides. Antibodies can also be used for ex vivo removal of tumor cells from the circulation or from bone marrow.
Cytotoxic proteins can include, but are not limited to, Ricin-A, Pseudomonas toxin, Diphtheria toxin, and tumor necrosis factor. Diagnostic radionuclides and cytotoxic agents such as cytotoxic radionuclides, drug and proteins can also be conjugated to the antibodies of the present invention. Examples of radionuclides which can be coupled to antibodies and selectively delivered in vivo to sites of antigen include 212Bi, 131I, 186Re, and 90Y, among others. Radionuclides can exert their cytotoxic effect by locally irradiating the cells, leading to various intracellular lesions, as is known in the art of radiotherapy. Examples of cytotoxic drugs which can be conjugated to antibodies and subsequently used for in vivo therapy include, but are not limited to, daunorubicin, doxorubicin, methotrexate, and Mitomycin C. Cytotoxic drugs can interface with critical cellular processes including DNA, RNA, and protein synthesis.
A dose at which the antibody molecule of the present invention is administered depends on the nature of the condition to be treated, and on whether the antibody molecule is being used prophylactically or to treat an existing condition. If administered prophylactically, i.e., as a vaccine, the antibody is administered in an amount effective to elicit an immune response in the subject.
If the antibody molecule has a short half-life (e.g. 2 to 10 hours) it can be necessary to give one or more doses per day. Alternatively, if the antibody molecule has a long half life (e.g. 2 to 15 days) it can only be necessary to give a dosage once per day, per week or even once every 1 or 2 months.
A pharmaceutical composition can also contain a pharmaceutically acceptable carrier for administration of the antibody. The carrier should not itself induce the production of antibodies harmful to the individual receiving the composition and should not be toxic. Suitable carriers include those known in the art, and can be selected from large, slowly metabolized macromolecules such as proteins, polypeptides, liposomes, polysaccharides, polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers and inactive virus particles, although suitable carriers are not limited to these examples.
Preferred forms for administration include forms suitable for parenteral administration, e.g. by injection or infusion, for example by bolus injection or continuous infusion. Where the product is for injection or infusion, it can take the form of a suspension, solution or emulsion in an oily or aqueous vehicle and it can contain formulatory agents, such as suspending, preservative, stabilizing and/or dispersing agents. Alternatively, the antibody molecule can be in dry form, for reconstitution before use with an appropriate sterile liquid.
Once formulated, the compositions of the invention can be administered directly to the subject. The subjects to be treated can be animals. However, it is preferred that the compositions are adapted for administration to human subjects.
A pharmaceutical compositions of this invention can be administered by any number of routes including, but not limited to, oral, intravenous, intramuscular, intra-arterial, intramedullary, intrathecal, intraventricular, transdermal, transcutaneous, subcutaneous, intraperitoneal, intranasal, enteral, topical, sublingual, intravaginal or rectal routes. Hyposprays can also be used to administer the pharmaceutical compositions of the invention. Therapeutic compositions can be prepared as injectables, either as liquid solutions or suspensions. Solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection can also be prepared.
Direct delivery of the compositions will generally be accomplished by injection, subcutaneously, intraperitoneally, intravenously or intramuscularly, or delivered to the interstitial space of a tissue. Dosage treatment can be a single dose schedule or a multiple dose schedule.
When an antibody or antibody fragment composition is to be administered by a route using the gastrointestinal tract, the composition can to contain additional agents which protect the antibody from degradation but which release the antibody once it has been absorbed from the gastrointestinal tract. Such additional agents are well-known to those skilled in the art.
Antibodies of the present invention can also be administered in methods of conducting gene therapy. In order to achieve this, DNA sequences encoding the heavy and light chains of the antibody molecule under the control of appropriate DNA components are introduced into a patient such that the antibody chains are expressed from the DNA sequences and assembled in situ.
The antibodies and antibody fragments of the present invention may also be used in the treatment of cancer in a patient in need thereof. In one aspect, the cancer is breast, ovary, cervix, prostate, colon, stomach, kidney, liver, head, neck, lung, blood, pancreas, skin, testicle, thyroid or brain cancer. In one aspect, the cancer is breast cancer. In another aspect, the breast cancer is ductal or lobular breast cancer.
In another aspect, the method for the treatment of breast cancer in a patient in need thereof comprises the steps of: (a) diagnosing said patient with breast cancer; (b) determining the level, localization, or both of PCBP-1 in a sample obtained from said patient; (c) determining whether said breast cancer is ductal carcinoma or lobular carcinoma; (d) determining whether said breast cancer is HER2-positive or HER2-negative; (e) determining whether said breast cancer is estrogen receptor-positive or estrogen receptor-negative; (f) determining whether said breast cancer is progesterone receptor-positive or progesterone receptor-negative; and (g) administering one or more chemotherapeutic agents to said patient.
In one aspect, the one or more chemotherapeutic agents are selected from the group consisting of an aromatase inhibitor, a hormone therapy agent, a taxane, an alkylating agent, an anthracycline, an antifolate, a pyrimidine analog, and a monoclonal antibody.
In another aspect, the aromatase inhibitor is selected from the group consisting of exemestane, anastrozole and letrozole. In another aspect, the hormonal therapy is selected from the group consisting of tamoxifen, FarestonTM, ArimidexTM, AromasinTM, FemaraTM, ZoladexTM, MegaceTM and HalotestinTM. In another aspect, the taxane is selected from the group consisting of docetaxel and paclitaxel. In another aspect, the alkylating agent is selected from the group consisting of cyclophosaphamide, meclorethamine, uramustine, melphalan, chlorambucil, ifosfamide, carmustine, lomustine, streptozocin, thiotepa and busulfan. In another aspect, the anthracycline is selected from the group consisting of daunorubicin, doxorubicin, epirubicin, idarubicin, valrubicin and mitoxanthrone. In another aspect, the antifolate is selected from the group consisting of methotrexate, trimethoprim, pyrimethane and pemetrexed. In another aspect, the pyrimidine analog is selected from the group consisting of 5-fluorouracil, floxuridine, cytosine arabinoside, and gemcitabine. In another aspect, the monoclonal antibody is selected from the group consisting of herceptin, Alper PCBP-1 antibody and Alper HER2 antibody.
7. PCBP-1 Expression Products as Drug Development Targets
In addition, the present invention relates to the discovery that Pcbp-1 and homologues thereof can cause the expression of PCBP-1 antigens by cells in patients suffering from various diseases, such as cancers, and more specifically solid tumors of the breast, ovary, cervix, prostate, colon, stomach, kidney, liver, head, neck, lung, pancreas, skin, testicle, thyroid and brain. This expression of PCBP-1 antigens presents a drug development target, and accordingly the present invention also relates to the use of such PCBP-1 antigens as biomarkers that can be targeted not only by the PCBP-1 antibodies or antibody fragments of the present invention, but also by various other molecules, such as siRNA, antisense oligonucleotides, vaccines, and chemical compounds.
Methods for developing drugs useful in treating and/or diagnosing diseases characterized by the expression of gene products of Pcbp-1 and homologues thereof can include the steps of identifying the gene products expressed by Pcbp-1 and homologues thereof in a subject having a disease, and utilizing those gene products as to development and identify drugs that specifically target the gene products.
Once candidate drugs have been developed based on the PCBP-1 antigens, the PCBP-1 antigens and PCBP-1 antibodies and antibody fragments of the present invention can be used to aid in screening the various drug candidates, in order to identify those drug candidates that exhibit a desired level of specificity for diseased cells presenting PCBP-1 expression products.
The following examples are non-limiting illustrative examples.
Example 1
Before tumor resection, 10 ml samples of blood are collected from ovarian or breast cancer patients into EDTA-containing tubes and placed on ice immediately. Within two hours of collection, blood samples are centrifuged at 1000×g for 20 minutes. The buffy coat and red blood cell layers are removed and the plasma is stored as 250-500 μl aliquots at −70° C. until analysis. Patients with stage II, III, and IV ovarian or breast cancers are selected for this study. Controls are obtained from healthy, cancer-free women who donated blood to the Brigham and Women's Hospital Blood Bank. Blood from breast cancer patients is collected in sodium citrate tubes (Becton-Dickinson) and processed according to the manufacturer's instructions. Plasma samples are aliquotted and stored at −80° C. until analyzed.
Plasma samples isolated from 20 patients with stage II-IV ovarian cancer are obtained from Brigham and Women's Hospital. Plasma samples (C: control breast blood sample, NM: non-metastatic breast blood sample, M: metastatic breast blood sample) obtained from control and patient groups are diluted with PBS at a ratio of 1:100. An increase in soluble plasma filamin-A levels have been reported to be associated with cancer. Plasma filamin-A levels are measured with an enzyme-linked immunosorbent enzyme assay. The ELISA plates (Nalge NUNCTM International, Rochester, N.Y.) are coated with 100 μl/well of diluted plasma and incubated at 4° C. overnight. The blood plasma samples are analyzed in a blinded fashion. The wells are washed with PBS and incubated at room temperature for one hour with blocking buffer (5% BSA in PBS). After washing with PBS, the primary antibody, A-FLNA is added in dilution buffer (45 μg/ml) (PBS buffer, 1% BSA, 0.01% Tween-20 TM). The wells are washed with PBS/0.03% Tween-20TM and incubated at room temperature for one hour with 100 μl/well secondary antibody (HRP-Donkey anti-mouse IgG, Jackson ImmunoResearch, West Grove, Pa.) diluted 1:3000. After washing the wells, 100 μl Immunopure TMBTM substrate solution (Pierce, Rockford, Ill.) is added. Color reaction is stopped by the addition of 100 μl/well 1N H2SO4 and the analysis is performed with an ELISA Reader. The figures represent optical density (OD) values of plasma readings for filamin-A levels. P-values are derived using the Mann Whitney Test and show a significant difference among control, non-metastatic and metastatic groups (p<0.001). P values are determined by comparison with controls by ANOVA. Data are representative of four independent experiments performed in triplicate. All analyses are performed under blinded conditions. See FIG. 1.
Plasma samples from breast cancer patients are subjected to ELISA analysis using the anti-PCBP-1 monoclonal antibody. Plasma samples (C: control breast blood sample, NM: non-metastatic breast blood sample, M: metastatic breast blood sample) obtained from control and patient groups are diluted with PBS at a ratio of 1:100. Plasma PCBP-1 levels are measured with an enzyme-linked immunosorbent enzyme assay. The ELISA plates (Nalge NUNC International, Rochester, N.Y.) are coated with 100 μl/well of diluted plasma and incubated at 4° C. overnight. The blood plasma samples are analyzed in a blinded fashion. The wells are washed with PBS and incubated at room temperature for one hour with blocking buffer (5% BSA in PBS). After washing with PBS, the primary antibody, anti-PCBP-1 is added in dilution buffer (45 μg/ml) (PBS buffer, 1% BSA, 0.01% Tween-20TM). The wells are washed with PBS/0.03% Tween-20 and incubated at room temperature for one hour with 100 μl/well secondary antibody (HRP-Donkey anti-mouse IgG, Jackson ImmunoResearch, West Grove, Pa.) diluted 1:3000. After washing the wells, 100 μl Immunopure TMBTM substrate solution (Pierce, Rockford, Ill.) is added. Color reaction is stopped by the addition of 100 μl/well 1N H2SO4 and the analysis is performed with an ELISA Reader. The figures represent optical density (OD) values of plasma readings for PCBP-1 levels. P-values are derived using the Mann Whitney Test. Control and metastatic group showed a significant difference (p<0.001). Control and non-metastatic groups did not show a significant difference. There is a significant difference between non-metastatic and metastatic groups (p<0.001). P values are determined by comparison with controls by ANOVA. Data are representative of four independent experiments performed in triplicate. All analyses are performed under blinded conditions. See FIGS. 2A and 2B.
Example 2
Cellular Localization of PCBP-1 in Human Breast Cancer Cells
Human normal mammary epithelial cells (HMECs), SKBR3 cells (human non-metastatic breast cancer cells) and MDA-MB-231 cells (human metastatic breast cancer cells) are seeded and grown on glass slides. The cells are fixed with formalin (10% with 0.1% TritonTM-X), washed with PBS and stained with anti-PCBP-1 mouse monoclonal antibody. Cells are then labeled with a FITC-labeled secondary goat-anti-mouse antibody and subjected to laser confocal microscopy. Indirect immunofluorescent staining is observed in the cytoplasm of HMECs. SKBR3 cells exhibit cytoplasmic and nuclear staining. MDA-MB-231 cells exhibit cytoplasmic staining. See FIG. 3.
Example 3
Cellular Localization of PCBP-1 in Human Cervical Cells
Cervical cells obtained from pap smears of healthy and cervical cancer patients are seeded and grown on glass slides. The cells are fixed with formalin (10% with 0.1% Triton-X), washed with PBS and stained with anti-PCBP-1 mouse monoclonal antibody. Cells are then labeled with a FITC-labeled secondary goat-anti-mouse antibody and subjected to laser confocal microscopy. Indirect immunofluorescent staining is observed in the cytoplasm and nucleus of normal cervical cells. Cervical cancer cells (CIN III) display cytoplasmic staining only. See FIG. 4.
Example 4
Approximately 2 μg of a purified 7SK mAb is suspended in PBS, and is applied under reducing (boiled 3 minutes in sample buffer with beta-mercaptoethanol and 10% SDS) and non-reducing (not boiled, and without beta-mercaptoethanol) conditions to 6 and 8% Tris-glycine gels and run at 120 volts. The gels are then stained with Coomassie Blue (0.1% (w/v) Coomassie blue R350, 20% (v/v) methanol, and 10% (v/v) acetic acid), destained in 50% (v/v) methanol in water with 10% (v/v) acetic acid, and images of the gels are taken. Molecular weight markers are shown on the right. The 6% Tris-glycine gel shows the IgG1 antibody (7SK) at  ̃150 kDa under non-reduced conditions. The 8% Tris-glycine gel shows the heavy chain of the IgG1 antibody (7SK) at  ̃50 kDa. See FIG. 5.
Example 5
Approximately 1 μg of a purified 7SK mAb is suspended in PBS, and is applied under reducing (boiled 3 minutes in sample buffer with beta-mercaptoethanol and 10% SDS) and non-reducing (not boiled, and without beta-mercaptoethanol) conditions to 8% Tris-glycine gels and run at 120 volts. The gels are then stained with Coomassie Blue (0.1% (w/v) Coomassie blue R350, 20% (v/v) methanol, and 10% (v/v) acetic acid), destained in 50% (v/v) methanol in water with 10% (v/v) acetic acid, and images of the gels are taken. Molecular weight markers are shown on the left. Under denatured conditions, the heavy chain of IgG1 Ab (7SK) is detected at  ̃50 kDa and light chain of IgG1 (7SK) is detected at  ̃25 kDa. In a non-reducing gel, intact IgG1 (7SK) is detected at 150 kDa. See FIG. 6.
Example 6
SKBR3 cells are fixed with 10% gluteraldehyde, permeabilized with 0.1% Triton-X100. PCBP-1 expression is then visualized with the 7SK mAb and secondary FITC-labeled anti-mouse antibodies (Jackson ImmunoResearch, West Grove, Pa.). Nuclei are visualized by DAPI staining (Molecular Probes, Eugene, Oreg.). The images are analyzed using a Olympus microscope equipped with 63× objective lens. See FIG. 7.
Example 7
Spot 1 is digested with trypsin and analyzed by MALDI-MS. The major protein identified is poly(rC)-binding protein 1, SwissProt Q15365. Also present, probably as contaminants, are albumin (fragment) and hemoglobin alpha and beta.
Example 8
Plasma samples (C: control breast blood sample, NM: non-metastatic breast blood sample, M: metastatic breast blood sample) obtained from control and patient groups are diluted with PBS at a ratio of 1:100. Plasma PCBP-1 levels are measured with an enzyme-linked immunosorbent enzyme assay. The ELISA plates (Nalge NUNC International, Rochester, N.Y.) are coated with 100 μl/well of diluted plasma and incubated at 4° C. overnight. The blood plasma samples are analyzed in a blinded fashion. The wells are washed with PBS and incubated at room temperature for one hour with blocking buffer (5% BSA in PBS). After washing with PBS, the primary antibody, 7SK (clone name: Alper-pCBP-1) is added in dilution buffer (45 μg/ml) (PBS buffer, 1% BSA, 0.01% Tween-20). The wells are washed with PBS/0.03% Tween-20 and incubated at room temperature for one hour with 100 μl/well secondary antibody (HRP-Donkey anti-mouse IgG, Jackson ImmunoResearch, West Grove, Pa.) diluted 1:3000. After washing the wells, 100 μl Immunopure TMB substrate solution (Pierce, Rockford, Ill.) is added. Color reaction is stopped by the addition of 100 μl/well 1N H2SO4 and the analysis is performed with an ELISA Reader. The figures represent optical density (OD) values of plasma readings for PCBP-1 levels. See FIG. 8.
Example 9
Plasma samples (C: control breast blood sample, NM: non-metastatic breast blood sample, M: metastatic breast blood sample) obtained from control and patient groups are diluted with PBS at a ratio of 1:100. Plasma PCBP-1 levels are measured with an enzyme-linked immunosorbent enzyme assay. The ELISA plates (Nalge NUNC International, Rochester, N.Y.) are coated with 100 μl/well of diluted plasma and incubated at 4° C. overnight. The plasma samples are analyzed in a blinded fashion. The wells are washed with PBS and incubated at room temperature for one hour with blocking buffer (5% BSA in PBS). After washing with PBS, the primary antibody, 7SK MoAb (clone name: Alper-pCBP-1) is added in dilution buffer (45 μg/ml) (PBS buffer, 1% BSA, 0.01% Tween-20). The wells are washed with PBS/0.03% Tween-20 and incubated at room temperature for one hour with 100 μl/well secondary antibody (HRP-Donkey anti-mouse IgG, Jackson ImmunoResearch, West Grove, Pa.) diluted 1:3000. After washing the wells, 100 μl Immunopure TMB substrate solution (Pierce, Rockford, Ill.) is added. Color reaction is stopped by the addition of 100 μl/well 1N H2SO4 and the analysis is performed with an ELISA Reader. Optical density is represented by OD and shows PCBP-1 levels in plasma. Series 1-2 represent controls, series 3-4 represent nonmetastatic and series 5-6 represent metastatic plasma samples. 1: metastatic, 2: nonmetastatic, 3: control plasma samples. See FIG. 9.
Example 10
FWRs and CDRs of the heavy chain of the PCBP-1 mAb 7SK, in which the polypeptide sequence provided in the top line corresponds to the sequence of the PCBP-1 mAb. Amino acid residues are numbered using the convention of Kabat et al. The bold residues set forth in underlined text indicate the specificity determining residues (SDRs). See FIG. 10.
Example 11
FWRs and CDRs of the light chain of the PCBP-1 mAb 7SK, in which the polypeptide sequence provided in the top line corresponds to the sequence of the PCBP-1 mAb. Amino acid residues are numbered using the convention of Kabat et al. The bold residues set forth in underlined text indicate the specificity determining residues (SDRs). See FIG. 11.
Example 12
Cell lysates from SKBR3 cells are run on a 2D polyacrylamide gel and proteins are transferred to a nitrocellulose membrane. Membranes are probed with PCBP-1 mAb. Spot 1, corresponding to PCBP-1, is cut out of a corresponding Coomassie-Blue stained 2D gel and subjected to tryptic digest. Tryptic peptides are analyzed by MALDI-TOF to determine the sequences of the digested peptides. All peptides obtained from the digest have sequences that correspond to the sequence of PCBP-1. See FIG. 12.
Example 13
Tissue arrays containing tissue samples of various normal and human cancer tissues are subjected to immunohistochemistry using Alper PCBP-1 mouse monoclonal antibody (7SK). Slides of the 117-2 multi-tissue array, the YTMAF96 array and the YTMAF179-3 are depaaafinized and rehydrated with distilled water. Heat-induced epitope retrieval is performed at 95-101° C. in citrate buffer at pH 6.0 for 20 minutes, then the slides are allowed to cool to room temperature and are rinsed with Tris buffer. A peroxidase block is applied to the slides for 5 minutes, and the slides are again rinsed with Tris buffer. BACKGROUND SNIPERTM (Biocare Medical Products, Concord, Calif.) is applied to the slides for 5 minutes, and the slides are rinsed with Tris buffer. A 1:50 dilution of Alper PBCP-1 mouse monoclonal antibody is then applied to the array slides for 30 minutes at room temperature, followed by a Tris buffer rinse. MACH 3TM Probe (Biocare Medical Products, Concord, Calif., USA) is applied to the slides for 15 minutes, the slides are rinsed with Tris buffer, and MACH 3TM Polymer (Biocare Medical Products, Concord, Calif., USA) is then added to the slides for 15 minutes. After a rinse with Tris buffer, diaminobenzenetetrahydrochloride is applied to the slides for 5 minutes. The slides are then contacted with hematoxylin counterstain. Tissue arrays are analyzed via microscopy for staining intensity. Results are summarized in FIG. 13. Intensity of PCBP-1 staining is increased in colon cancer, melanoma, squamous carcinoma, glioblastoma, endometrial cancer, sarcoma and bladder cancers as compared to normal controls, while PCBP-1 intensity is decreased in ovarian cancer as compared to normal controls.
Normal breast epithelial cells showed a 1- to 3-fold increase in nuclear staining intensity while breast cancer cells showed 3-fold cytoplasmic and sometimes 2- to 3-fold nuclear staining intensity for PCBP-1. Breast cancer cells showing increased cytoplasmic staining intensity for PCBP-1 are correlated with lower likelihood of patient survival than breast cells with normal nuclear staining. Globular breast carcinoma cells show a lower PCBP-1 cytoplasmic staining intensity as compared to ductal breast carcinoma cells.
Colon cancer tissue epithelial cells showed a 3-fold increase in cytoplasmic PCBP-1 staining intensity compared to normal colon tissue epithelial cells. A 3-fold increase in cytoplasmic staining intensity was observed in both melanoma and squamous carcinoma cells, while normal skin cells showed weak nuclear staining for PCBP-1. A 2-fold increase in cytoplasmic staining was observed in Glioblastoma multiforme and astrocytomas, while no staining was observed in normal brain neurons and astrocytes. Sarcomas and bladder cancer cells showed 2- to 3-fold increases in cytoplasmic staining compared to normal muscle and normal bladder cells. While normal endometrial cells showed negative or weak cytoplasmic staining for PCBP-1, endometrial cancer cells showed a 3-fold increase in nuclear and cytoplasmic staining for PCBP-1. Normal ovarian epithelial cells showed a 3-fold increase in cytoplasmic and nuclear staining for PCBP-1 as compared to ovarian cancer cells.
Example 14
The soluble, native form of PCBP-1 is purified from SKBR3 human breast cancer cell conditioned media. An affinity approach is taken, in which Alper PCBP-1 mouse monoclonal antibody is cross-linked to sepharose (i.e. CNBr-activated sepharose or similar kit available from GE Healthcare Bio-Sciences Corp., Piscataway, N.J., USA, or from Pierce Chemical Co., Rockford, Ill., USA) to purify the native PCBP-1 antigen. Conditioned media is generated and affinity purification of PCBP-1 is performed.
The purified PCBP-1 is characterized with respect to size (SDS-PAGE), purity (SDS-PAGE, SEC-HPLC, Western blot), and aggregation (Western blot). The stability of the purified PCBP-1 preparation is monitored over time by SDS-PAGE and SEC-HPLC. The purification can be scaled up using non-affinity techniques which can include, but are not limited to, ion exchange chromatography, filtration, aqueous phase partitioning and/or counter-current chromatography.
Example 15
Purified PCBP-1 is injected to six-week-old Balb/c mice and six-lb. NZW rabbits via iv, ip, or intramuscular routes using Kohler and Milstein's original injection and monoclonal antibody production conventional technique over a period of 3-5 months (Kohler et al., Nature 256(5517): 495-497, 1975). During the injections, at certain time intervals several test bleedings are performed to test immunologic response as well as antibody production in mice and rabbits. Production of monoclonal and polyclonal antibodies is tested using ELISA, western blot and immunofluorescence staining techniques.
Example 16
The YTMA 49-10 array, a node-positive and node-negative invasive breast carcinoma tissue microarray containing 700 samples, is subjected to immunohistochemistry using Alper PCBP-1 mouse monoclonal antibody (7SK). Slides of the YTMA 49-10 multi-tissue array are deparrafinized by immersing twice in xylene and incubating for 15 minutes. Slides are then immersed in a 1:1 solution of xylene:ethanol for 5 minutes. Slides are then immersed in 100% ethanol for 5 minutes, followed by immersion in 95%, 75% and 50% ethanol for 3 minutes each. Slides are rinsed with reagent-quality water for 5 minutes and are rehydrated by immersing in distilled water until ready to perform antigen retrieval. Heat-induced epitope retrieval is performed at 95-100° C. in citrate retrieval buffer at pH 6.0 for 40 minutes, then the slides are allowed to cool to room temperature and are rinsed with Tris buffer (Tris buffered saline with Tween 20, pH 7.6). A peroxidase block (3% hydrogen peroxide) is applied to the slides for 5 minutes, and the slides are again rinsed with Tris buffer. BACKGROUND SNIPERTM (Biocare Medical Products, Concord, Calif.; Catalog No. BS966 G) blocking reagent is applied to the slides for 5 minutes, and the slides are rinsed with Tris buffer. A 1:50 dilution of Alper PBCP-1 mouse monoclonal antibody is then applied to the array slides for one hour at room temperature, followed by three washes with Tris buffer. MACH 3TM Probe (Biocare Medical Products, Concord, Calif., USA; Catalog No. M3M530) is applied to the slides for 15 minutes, the slides are rinsed three times with Tris buffer, and MACH 3TM Polymer (Biocare Medical Products, Concord, Calif., USA; Catalog No. M3M530) is then added to the slides for 15 minutes. After three rinses with Tris buffer, diaminobenzenetetrahydrochloride (DAB) is applied to the slides and slides are incubated until desired stain intensity develops. The slides are then contacted with hematoxylin counterstain if desired. Slides are then fixed by immersing in 70% ethanol, 80% ethanol, 95% ethanol and 100% ethanol for two minutes each, followed by immersion in xylene twice for two minutes. Tissue arrays are analyzed via microscopy at low (10-20×) resolution to locate well-preserved and well-stained areas. Identified well-preserved and well-stained areas are used to make a determination of the intensity of PCBP-1 expression. Percentage of stained cells is estimated as 0%, less than 50%, or greater than 50% of the total number of well-preserved cells. Stained cells are then assayed for staining intensity, which can range from negative to faint to weak to intense. Results are summarized in FIGS. 14 and 15. Examples of negative and 1+, 2+ and 3+ staining in ductal and lobular breast cancer cells are shown in FIGS. 16-18.
Example 17
A. Labeling of RP11-175A7 BAC Clone
DNA of Homo sapiens BAC clone RP11-175A7 (SEQ ID NO: 51; Genbank Accession No. AC016700.8) is fluorescently labeled with by nick translation using standard protocols. DNA from BAC clone RP11-175A7 is prepared by standard methods. A nick translation reaction is prepared including BAC DNA (8 μl), dNTPs (5 μl), 10× Nick translation buffer (5 μl), 10× beta-mercaptoethanol, Orange-dUTP (1 μl), DNA polymerase (2 μl), DNAse (3 μl of 1:1000 dilution), nuclease free H2O (21 μl) and incubated at 15° C. for 90 minutes. The reaction is stopped with 1 μl of 0.5 M EDTA. The reaction is ethanol precipitated by the addition of 10 μl of salmon sperm DNA, 40 μl Cot-1 DNA, 10 μl of 3 M NaOAc, pH 5.2 and 200 μl of 100% EtOH followed by incubation at −80° C. for 30 minutes. The precipitated Orange-dUTP labeled DNA is collected by centrifugation at 14,000 rpm for 15 minutes. The pellet is dried and resuspended in 32 μl of nuclease free water, 8 μl 20×SSC and 40 μl 20% dextran sulfate in formamide to prepare 80 μl of hybridization mix.
B. Hybridization
Slides of chromosomal DNA in metaphase of breast cancer cell lines SK-BR 3, MDA-MB-231 and C2T2 are prepared and pretreated to denature the chromosomal DNA and block non-specific hybridization to repetitive DNA. The hybridization probe prepared in step A above is briefly denatured by boiling followed by quick chilling and applied to the chromosome slide preparations and incubated for approximately 12 hours to allow hybridization. Hybridized slides are washed according to standard methods to remove unhybridized and partially hybridized probes. The results are visualized and quantified by fluorescent microscopy. Images of chromosome spreads of individual cells for each of the three lines are recorded and presented in FIG. 19.
Example 18
The staining protocol listed above in Example 16 is used on approximately 300 untreated breast tissue samples from healthy subjects, nonmetastatic ductal cancer patients and metastatic ductal cancer patients. Stained tissue samples are included on the ‘Breast normal adjacent tissue and cancer tissue array’ (Biomax #BRN801a). The BRN801a array has tissue samples with both normal and breast carcinoma pathology diagnoses. The array includes 70 cases of adjacent normal breast tissue, plus 10 tissue sections of malignant invasive ductal breast carcinoma tissue obtained from different samples. The staining protocol listed above in Example 16 is also used on the ‘Breast invasive ductal carcinoma and matched metastatic carcinoma tissue microarray’ (Biomax BR10010). The BR10010 array contains tissue sections from 50 samples of breast carcinoma (46 invasive ductal carcinoma, 1 micropapillary carcinoma, 2 invasive lobular carcinoma, 1 neuroendocrine carcinoma), and 50 matched metastacised breast carcinomas obtained from a lymph node. The staining protocol is also used on the ‘Breast Tumor Tissue Array’ (Biochain Institute, Inc; Z7020009). The Z7020009 array has duplicate tissue samples obtained by surgical resection from six pathological tissue types including normal breast tissue, hyperplasia breast tissue, fibroadenoma breast tissue, invasive ductual carcinoma, invasive lobular carcinoma and Paget's disease.
Results show that PCBP-1 is localized and expressed in high amounts in the nucleus in healthy breast tissue epithelial cells. As a cell undergoes transformation, PCBP-1 expression becomes more cytoplasmic with some nuclear expression as well, and overall increased expression than in the healthy cells. As the ductal carcinoma cells become metastatic, PCBP-1 expression is entirely in the cytoplasm of the cells with no staining in the nucleus. Of 100 cases of metastatic ductal breast cancers, no nuclear expression of PCBP-1 is observed.
Example 19
The staining protocol listed above in Example 16 is used with the Alper PCBP-1 mouse monoclonal antibody (7SK) and the Yale Breast Cancer Cohort YTMA 49_9 array. The Yale Cancer Center/Pathology Tissue Microarray Facility collects and provides pathological analysis on tissue samples and arrays the samples on a slide. The Facility provides a map of the arrayed samples so researchers can correlate results to cancer pathology, including determination of ductal cancer. These samples are analyzed blindly for PCBP-1 staining. Results show that higher levels of PCBP-1 expression (PCBP-1 score of +2 or +3) are correlated with a decrease in a ductal breast cancer patient's overall prognosis or survival relative to ductal breast cancer patients with a lower level of PCBP-1 expression (PCBP-1 score of 0 or +1). See FIG. 20. This correlation is statistically significant with a p-value of 0.0243. PCBP-1 scores are determined in a blind analysis, where a score of 0 or +1 is a low level of PCBP-1 staining. The difference between 0/+1 and +2/+3 in ductal cancer samples is particularly apparent in the higher amount of cytoplasmic staining of arrayed tissue samples scored +2 or +3.
General guidelines are as follows, and samples can be scored by standard pathology guidelines.
Score 0=No staining is observed in invasive tumor cells
Score 1+=Weak, nuclear staining is observed in any proportion of invasive tumor cells, or weak, cytoplasmic staining is observed in less than 30% of cells
Score 2+=Weak cytoplasmic is observed in 50% or more cells or strong cytoplasmic staining of more than 30% is observed in invasive tumor cells
Score 3+=Strong cytoplasmic staining is observed that is in more than 50% of tumor cells
Example 20
The protocol listed above in Example 16 is used with the Alper PCBP-1 mouse monoclonal antibody (7SK) and the Yale Breast Cancer Cohort YTMA 49_9 array. Mapping of patient pathology, including lymph node status, is provided by the Yale Facility. Results show that higher levels of PCBP-1 expression are correlated with a decrease in the overall prognosis of a ductal breast cancer patient with three or more positive lymph nodes. See FIG. 21. This correlation is statistically significant with a p-value of 0.0277. PCBP-1 scores are determined in a blind anaysis, where a score of 0 or +1 is a low level of PCBP-1 staining. The difference between 0/+1 and +2/+3 was particularly apparent in the higher amount of cytoplasmic staining of arrayed tissue samples scored +2 or +3.
Example 21
The protocol listed above in Example 16 is used with the Alper PCBP-1 mouse monoclonal antibody (7SK) and a array of normal breast tissues and untreated non-metastatic breast cancer tissues from the Cytology Services of Maryland. Detection of the estrogen receptor (ER) and progesterone receptor (PR) subcellular localization for these arrays is provided by Cytology Services of Maryland using commercial antibodies. Results show a strong positive correlation between ER (nuclear) positivity with PCBP-1 (nuclear) positivity in untreated non-metastatic breast cancer patients and controls, the correlation is >75% of staining in the nucleus for ER and PCBP-1. See FIG. 22. There is also a strong positive correlation in expression and staining intensity between high levels of PR staining (2+/3+) and high levels of PCBP-1 staining (2+/3+) with 81% of staining in the nucleus for PR and PCBP-1 (39/41).

## Claims

1. A prognostic method for determining the severity of disease in a patient diagnosed with or suspected of having breast cancer comprising:
a) obtaining a cell or tissue sample from a human subject diagnosed with or suspected of having breast cancer;
b) contacting the sample with an antibody that binds a PCBP-1 antigen, wherein the antibody comprises a heavy chain variable domain comprising three complementarity determining regions (CDRs) comprising the amino acid sequences of SEQ ID NO: 45, SEQ ID NO: 46, and SEQ ID NO: 47, and a light chain variable domain comprising three CDRs comprising the amino acid sequences of SEQ ID NO: 48, SEQ ID NO: 49, and SEQ ID NO: 50;
c) detecting the antibody;
d) scoring the detection pathologically, wherein a pathology score of 0 indicates no staining in the cell, a score of 1+ indicates weak nuclear staining in any number of cells, or cytoplasmic staining in less than 30% of cells; a score of 2+ indicates weak cytoplasmic staining in 50% or more cells or strong cytoplasmic staining in more than 30% of cells; and a score of 3+ indicates strong cytoplasmic staining in more than 50% of cells; and
e) providing a prognosis to the patient, wherein the pathology score correlates with the severity of disease, wherein a score of 0 or 1+ indicates a higher likelihood of patient survival and a score of 2+ or 3+ indicates a lower likelihood of patient survival.

2. The method of claim 1, wherein the antibody is detectably labeled.

3. The method of claim 1, wherein the antibody is detected with a labeled secondary antibody.

4. The method of claim 2, wherein the label is fluorescent.

5. The method of claim 1, wherein the cancerous breast cell or tissue is ductal.