Cancer biomarkers and methods of use thereof

Abstract

Detection methods, assay kits and reagents are provided for detecting pre-cancerous mammary epithelial cell signatures. The disclosed cell signatures comprise a collection of measurements of at least two characteristics of the mammary epithelial cells. Related imaging and diagnostic methods are also disclosed.

1 - 39 . (canceled) 
   
   
       40 . An assay kit for detecting a risk that a mammary epithelial cell will become malignant, comprising reagents for determining a mammary epithelial cell signature, wherein the signature comprises a collection of measurements of at least two characteristics of the mammary epithelial cell, said at least two characteristics selected from one or more of the following: presence and/or level of a protein; presence and/or level of a mRNA; presence and/or level of a posttranslationally modified polypeptide; presence of a chromatin modification; presence and/or level of a sequence of DNA; presence and/or level of a microRNA; integrity of a nucleic acid; methylation status of a nucleic acid; secretion and/or release of a factor; and alteration in a metabolism. 
   
   
       41 . The assay kit of  claim 40 , wherein said protein is differentially expressed in the mammary epithelial cells at risk of becoming malignant. 
   
   
       42 . The assay kit of  claim 40 , wherein said mRNA is differentially transcribed in the mammary epithelial cells at risk of becoming malignant. 
   
   
       43 . The assay kit of  claim 40 , wherein said protein is selected from the group consisting of COX-2, Ki67, p16, CD73, CD138, notch receptor-3, CD90, BMI-1, IGF2, YKL-40, EGF-R, c-jun, PCNA, jnk, cyclin B1, c-kit, STAT3, cyclin D1, PI3K, MAPK, MAPKK, DDR2, TRF2, activin, and MEK1/2. 
   
   
       44 . The assay kit of  claim 40 , wherein said mRNA is selected from the group consisting of mRNAs encoding COX-2, Ki67, p16, CD73, CD138, notch receptor-3, CD90, BMI-1, IGF2, YKL-40, EGF-R, c-jun, PCNA, jnk, cyclin B1, c-kit, STAT3, cyclin D1, PI3K, MAPK, MAPKK, DDR2, TRF2, activin, and MEK1/2. 
   
   
       45 . The assay kit of  claim 40 , wherein said posttranslationally modified polypeptide is selected from the group consisting of one or more components of Histone Deacetylases, one or more intracellular polypeptides, and one or more components of extracellular matrix. 
   
   
       46 . The assay kit of  claim 40 , wherein said DNA may have a different sequence and/or a copy number in a mammary epithelial cell at risk of becoming malignant compared to a normal mammary epithelial cell. 
   
   
       47 . The assay kit of  claim 40 , wherein said microRNA is selected from the group consisting of mir 196b (HoxA9), p14, 328, 30A-3P, 125b5, 30E-3P, 680, 134, 604, 128b, 128a, 331, 520F, 299-3P, 520H, 510, 365, 520G, 9, 324-3P, 351, 125A, 764-5P, 302D, 520D, 652, 520C, 350, 585, 621, 542-5P, 560, 126, and 341. 
   
   
       48 . The assay kit of  claim 40 , wherein said integrity of the nucleic acid comprises deletion, translocation, inversion, aberrant pattern formation of the nucleic acid, telomere integrity and any combinations thereof. 
   
   
       49 . The assay kit of  claim 40 , wherein said nucleic acid subject to methylation comprises a DNA sequence of p16 promoter. 
   
   
       50 . The assay kit of  claim 40 , wherein said secreted and/or released factor comprises a protein, a nucleic acid, a carbohydrate, a lipid, an ion, and any combinations thereof. 
   
   
       51 . The assay kit of  claim 40  comprises one or more antibodies and/or one or more nucleic acid probes, wherein the antibodies and nucleic acid probes are specific to one or more of said characteristics. 
   
   
       52 . The assay kit of  claim 51 , wherein said antibodies and nucleic acid probes are coupled with a detectable label selected from gold, a fluorescent protein, a chromogenic protein, a fluorescent dye, an enzyme, a biotin, a radioisotope and any combinations thereof. 
   
   
       53 . A method of determining a risk of developing breast cancer in a subject, comprising:
 providing a biological sample from said subject;   determining a mammary epithelial cell signature for said biological sample, wherein the signature comprises a collection of measurements of at least two characteristics of the mammary epithelial cell, said at least two characteristics selected from one or more of following: presence and/or level of a protein; presence and/or level of a mRNA; presence and/or level of a posttranslationally modified polypeptide; presence of a chromatin modification; presence and/or level of a sequence of DNA; presence and/or level of a microRNA; integrity of a nucleic acid; methylation status of a nucleic acid; secretion and/or release of a factor; and alteration in a metabolism;   comparing the mammary epithelial cell signature of said biological sample with a mammary epithelial cell signature of a control sample; and   determining the risk of developing breast cancer.   
   
   
       54 . The method of  claim 53 , wherein said biological sample is selected from the group consisting of a living cell, a dead cell, any non-cellular liquid samples comprising nipple aspirate fluid, urine, blood, serum, plasma and a lavage sample, and any combinations thereof. 
   
   
       55 . The assay kit of  claim 53 , wherein said protein is differentially expressed in the mammary epithelial cells at risk of becoming malignant. 
   
   
       56 . The assay kit of  claim 53 , wherein said mRNA is differentially transcribed in the mammary epithelial cells at risk of becoming malignant. 
   
   
       57 . The method of  claim 53 , wherein said protein is selected from the group consisting of COX-2, Ki67, p16, CD73, CD138, notch receptor-3, CD90, BMI-1, IGF2, YKL-40, EGF-R, c-jun, PCNA, jnk, cyclin B1, c-kit, STAT3, cyclin D1, PI3K, MAPK, MAPKK, DDR2, TRF2, activin, and MEK1/2. 
   
   
       58 . The method of  claim 53 , wherein said mRNA is selected from the group consisting of mRNAs encoding COX-2, Ki67, p16, CD73, CD138, notch receptor-3, CD90, BMI-1, IGF2, YKL-40, EGF-R, c-jun, PCNA, jnk, cyclin B1, c-kit, STAT3, cyclin D1, PI3K, MAPK, MAPKK, DDR2, TRF2, activin, and MEK1/2. 
   
   
       59 . The method of  claim 53 , wherein said posttranslationally modified polypeptide is selected from the group consisting of one or more components of Histone Deacetylases, one or more intracellular polypeptides, and one or more components of extracellular matrix. 
   
   
       60 . The method of  claim 53 , wherein said DNA may have a different sequence and/or a copy number in a mammary epithelial cell at risk of becoming malignant compared to a normal mammary epithelial cell. 
   
   
       61 . The method of  claim 53 , wherein said microRNA is selected from the group consisting of mir 196b (HoxA9), p14, 328, 30A-3P, 125b5, 30E-3P, 680, 134, 604, 128b, 128a, 331, 520F, 299-3P, 520H, 510. 365, 520G, 9, 324-3P, 351, 125A, 764-5P, 302D, 520D, 652, 520C, 350, 585, 621, 542-5P, 560, 126, and 341. 
   
   
       62 . The method of  claim 53 , wherein said integrity of the nucleic acid comprises deletion, translocation, inversion, aberrant pattern formation of the nucleic acid, telomere integrity, and any combinations thereof. 
   
   
       63 . The method of  claim 53 , wherein said nucleic acid subject to methylation comprises a DNA sequence of p16 promoter. 
   
   
       64 . The method of  claim 53 , wherein said secreted and/or released factor comprises a protein, a nucleic acid, a carbohydrate, a lipid, an ion, and any combinations thereof. 
   
   
       65 . The method of  claim 53 , wherein the mammary cell signature of the control sample is determined in parallel with the mammary epithelial cell signature of the biological sample, wherein the parallel determination may be done simultaneously with the biological sample or at another time. 
   
   
       66 . The method of  claim 53 , wherein the mammary cell signature of the control sample is obtained from a database. 
   
   
       67 . The method of  claim 53 , wherein at least part of the method is performed by automated means. 
   
   
       68 . The method of  claim 67 , wherein said automated means comprises a computer-based system configured to carry out at least one of the following:
 measuring the mammary epithelial cell signature;   recording data obtained from the measurement;   analyzing the data;   determining the risk of developing breast cancer; and   generating a report.   
   
   
       69 . The method of  claim 68 , wherein said computer-based system comprises any hardware, software, firmware, processor, and any combinations thereof. 
   
   
       70 . The method of  claim 68 , wherein said computer-based system is configured to access and/or use a database comprising a cell signature of a pre-cancerous epithelial cell and/or a control epithelial cell via a network system. 
   
   
       71 . The method of  claim 53 , further comprising administering to said subject one or more agents that selectively label at least one of said characteristics of the mammary epithelial cell; and imaging said subject. 
   
   
       72 . The method of  claim 71 , wherein imaging is accomplished by mammography, positron emission tomography, computer-assisted tomography, magnetic resonance imaging or any combination thereof. 
   
   
       73 . A method of making a medical report related to the risk of developing breast cancer in a subject, comprising:
 providing a biological sample from said subject;   determining a mammary epithelial cell signature for said biological sample, wherein the signature comprises a collection of measurements of at least two characteristics of the mammary epithelial cell, said at least two characteristics selected from one or more of following: presence and/or level of a protein; presence and/or level of a mRNA; presence and/or level of a posttranslationally modified polypeptide; presence of a chromatin modification; presence and/or level of a sequence of DNA; presence and/or level of a microRNA; integrity of a nucleic acid; methylation status of a nucleic acid; secretion and/or release of a factor; and alteration in a metabolism;   comparing the mammary epithelial cell signature of said biological sample with a mammary epithelial cell signature of a control sample;   determining the risk of developing breast cancer; and   generating a report related to the risk of developing breast cancer.   
   
   
       74 . A method of determining a risk of developing breast cancer in a subject, comprising:
 providing at least two imaging agents to a subject, wherein said imaging agents label at least two characteristics of a mammary epithelial cell, said at least two characteristics selected from one or more of the following: a protein; an mRNA; a posttranslationally modified polypeptide; a chromatin modification; a sequence of DNA; a microRNA; integrity of a nucleic acid; methylation status of a nucleic acid; secretion and/or release of a factor; and alteration in a metabolism; and   imaging the subject to visualize labeling of the at least two characteristics.   
   
   
       75 . The method of  claim 74 , wherein said imaging agents comprise an antibody, nucleic acid, protein, or carbohydrate. 
   
   
       76 . The method of  claim 75 , wherein said antibody, nucleic acid, protein, or carbohydrate further comprises a detectable label selected from gold, a fluorescent protein, a chromogenic protein, a fluorescent dye, an enzyme, a biotin, a radioisotope and any combinations thereof. 
   
   
       77 . The method of  claim 74 , wherein said imaging is done via mammography, positron emission tomography, computer-assisted tomography, magnetic resonance imaging or any combination thereof. 
   
   
       78 . A combination of at least two different imaging agents, each of which binds to a mammary epithelial cell structure, wherein said structure is selected from the group consisting of:
 a protein selected from the group consisting of COX-2, Ki67, p16, CD73, CD 138, notch receptor-3, CD90, BMI-1, IGF2, YKL-40, EGF-R, c-jun, PCNA, jnk, cyclin B1, c-kit, STAT3, cyclin D1, PI3K, MAPK, MAPKK, DDR2, TRF2, activin, and MEK1/2;   an mRNA encoding said protein;   a posttranslationally modified polypeptide selected from one or more components of histone deacetylases, one or more intracellular polypeptides, or one or more components of extracellular matrix;   a DNA having a different sequence and/or a copy number in a mammary epithelial cell at risk of becoming malignant compared to a normal mammary epithelial cell;   a microRNA selected from the group consisting of mir 196b (HoxA9), p14, 328, 30A-3P, 125b5, 30E-3P, 680, 134, 604, 128b, 128a, 331, 520F, 299-3P, 520H, 510, 365, 520G, 9, 324-3P, 351, 125A, 764-5P, 302D, 520D, 652, 520C, 350, 585, 621, 542-5P, 560, 126, and 341;   a structure associated with the integrity of a nucleic acid, wherein said integrity of the nucleic acid comprises deletion, translocation, inversion, aberrant pattern formation of the nucleic acid, telomere integrity, and any combinations thereof;   a structure associated with the methylation status of a nucleic acid and comprises a DNA sequence of p16 promoter;   a secreted factor comprising a protein, a nucleic acid, a carbohydrate, a lipid, an ion, and any combinations thereof; and   a structure associated with a metabolic alteration,   wherein each of said at least two different imaging agents comprise a selective binding moiety and a detectable label.   
   
   
       79 . The composition of  claim 78 , wherein said selective binding moiety comprises an antibody, nucleic acid, protein, or carbohydrate. 
   
   
       80 . The composition of  claim 78 , wherein said detectable label is selected from the group consisting of gold, a fluorescent protein, a chromogenic protein, a fluorescent dye, an enzyme, a biotin, and a radioisotope, and combinations thereof.