Composite biomarkers for non-invasive screening, diagnosis and prognosis of colorectal cancer

Abstract

The present invention concerns particular biomarkers for diagnosing and/or prognosticating colorectal cancer, in particular in a non-invasive manner. The methods and compositions concern analysis of methylation patterns of one or more genes from a set of 29 genes identified as described herein. In certain embodiments, the gene set includes at least P15.INK4b, SST, GAS7, CNRIP1, and PIK3CG.

What is claimed is: 
     
         1 . A method for screening, diagnosing, and/or prognosticating colorectal cancer in an individual, comprising the steps of:
 obtaining a sample from the individual; and   assaying the sample for methylation status of at least two, at least three, at least four, or all of the following genes: P15.INK4b, somatostatin, GAS7, CNRIP1, and PIK3CG.   
     
     
         2 . The method of  claim 1 , further comprising the step of assaying the sample for methylation status of a gene selected from the group consisting of NPY, JAM2, MAL, LAMA1, SLIT2, RERG, and a combination thereof. 
     
     
         3 . The method of  claim 1 , wherein the methylation status of one or more of P15.INK4b, somatostatin, GAS7, CNRIP1, and PIK3CG is compared to a standard. 
     
     
         4 . The method of  claim 1 , wherein the standard is a methylation threshold value from a normal sample. 
     
     
         5 . The method of  claim 1 , further comprising the step of assaying the sample for methylation status of a gene selected from the group consisting of ADHFE1, COL1A2, EPHA7, RUNX3, MDR1, CHFR, N33.TUMOR_SUPPRESSOR_CANDIDATE_3, RASSF2, DAB2IP, HPP1, SFRP1, CXX1, ESTROGEN_RECEPTOR_1, FAS, DSC3, MUC2, RETINOIC_RECEPTOR_ACID_BETA_2, and a combination thereof. 
     
     
         6 . The method of  claim 2 , further comprising the step of assaying the sample for methylation status of a gene selected from the group consisting of ADHFE1, COL1A2, EPHA7, RUNX3, MDR1, CHFR, N33.TUMOR_SUPPRESSOR_CANDIDATE_3, RASSF2, DAB2IP, HPP1, SFRP1, CXX1, ESTROGEN_RECEPTOR_1, FAS, DSC3, MUC2, RETINOIC_RECEPTOR_ACID_BETA_2, and a combination thereof. 
     
     
         7 . The method of  claim 1 , further comprising the step of assaying the sample for methylation status of a gene selected from the group consisting of NPY, JAM2, MAL, LAMA1, SLIT2, and a combination thereof. 
     
     
         8 . The method of  claim 1 , further comprising the step of assaying the sample for methylation status of JAM2. 
     
     
         9 . The method of  claim 1 , further comprising the step of assaying the sample for methylation status of NPY. 
     
     
         10 . The method of  claim 1 , further comprising the step of assaying the sample for methylation status of MAL. 
     
     
         11 . The method of  claim 1 , further comprising the step of assaying the sample for methylation status of LAMA1. 
     
     
         12 . The method of  claim 1 , further comprising the step of assaying the sample for methylation status of RERG. 
     
     
         13 . The method of  claim 1 , further comprising the step of assaying the sample for methylation status of SLIT2. 
     
     
         14 . The method of  claim 1 , wherein the sample is selected from the group consisting of tissue, blood, spittle, serum, plasma, urine, sputum, biopsy and stool. 
     
     
         15 . The method of  claim 1 , wherein the individual is 50 years or older in age. 
     
     
         16 . The method of  claim 1 , wherein the individual has one or more symptoms of colorectal cancer. 
     
     
         17 . The method of  claim 1 , wherein the individual is asymptomatic for colorectal cancer. 
     
     
         18 . The method of  claim 1 , wherein the individual has a prior history of having cancer. 
     
     
         19 . The method of  claim 16 , wherein the one or more symptoms is selected from the group consisting of a change in bowel habits, constipation that lasts more than a couple of weeks, diarrhea that lasts more than a couple of weeks, a feeling that the bowel does not empty completely, blood in the stool, narrow or thinner than normal stool, abdominal discomfort, gas pains, bloating, fullness, cramps, weight loss, fatigue, anemia, and a combination thereof. 
     
     
         20 . The method of  claim 1 , wherein the individual is at risk for developing colorectal cancer. 
     
     
         21 . The method of  claim 20 , wherein the individual has a personal or family history of colorectal cancer, has or has had colon polyps, bowel inflammatory disease, or is or was positive for hemoccult test. 
     
     
         22 . The method of  claim 20 , wherein the individual has a personal or family history of familial adenomatous polyposis, Lynch syndrome, Peutz-Jeghers syndrome or juvenile polyposis syndrome. 
     
     
         23 . The method of  claim 1 , wherein the individual is subjected to one or more other assays for determination of colorectal cancer. 
     
     
         24 . The method of  claim 23 , wherein the one or more other assays is selected from the group consisting of stool testing, barium enema, virtual colonoscopy, sigmoidoscopy, and colonoscopy. 
     
     
         25 . The method of  claim 1 , wherein when an individual is diagnosed as having colorectal cancer, the colorectal cancer originates in the colon of the individual. 
     
     
         26 . The method of  claim 1 , wherein when an individual is diagnosed as having colorectal cancer, the colorectal cancer originates in the rectum of the individual. 
     
     
         27 . The method of  claim 1 , wherein when an individual is diagnosed as having colorectal cancer, the individual has stage 0, 1, 2, 3, or 4 colorectal cancer. 
     
     
         28 . The method of  claim 1 , wherein following a positive diagnosis for colorectal cancer, the individual is treated for colorectal cancer. 
     
     
         29 . The method of  claim 28 , wherein the treatment for colorectal cancer comprises surgery, chemotherapy, radiation, gene therapy, or a combination thereof. 
     
     
         30 . The method of  claim 29 , wherein the chemotherapy is selected from the group consisting of fluorouracil, bevacizumab, irinotecan, capecitabine, cetuximab, oxaliplatin, cetuximab, leucovorin, panitumumab, and a combination thereof. 
     
     
         31 . The method of  claim 29 , wherein the gene therapy modifies methylation status of a gene selected from the group consisting of P15.INK4b, somatostatin, GAS7, CNRIP1, and PIK3CG. 
     
     
         32 . A substrate, comprising nucleic acids each comprising part or all of P15.INK4b, somatostatin, GAS7, CNRIP1, and PIK3CG genes or nucleic acids that are complementary thereto. 
     
     
         33 . The substrate of  claim 32 , further each comprising nucleic acids comprising part or all of NPY, JAM2, MAL, LAMA1, SLIT2, RERG, or a combination thereof, or nucleic acids that are complementary thereto. 
     
     
         34 . The substrate of  claim 32 , further comprising nucleic acids each comprising part or all of ADHFE1, COL1A2, EPHA7, RUNX3, MDR1, CHFR, N33.TUMOR_SUPPRESSOR_CANDIDATE_3, RASSF2, DAB2IP, HPP1, SFRP1, CXX1, ESTROGEN_RECEPTOR_1, FAS, DSC3, MUC2, RETINOIC_RECEPTOR_ACID_BETA_2, or a combination thereof, or nucleic acids that are complementary thereto. 
     
     
         35 . The substrate of  claim 32 , further defined as a microchip. 
     
     
         36 . A method for screening, diagnosing, and/or prognosticating colorectal cancer in an individual, comprising the steps of:
 obtaining a sample from the individual; and   assaying the sample for methylation status of at least two, at least three, at least four, or all of the following genes: P15.INK4b, SST, NPY, JAM2, CNRIP1, GAS7, PIK3CG, MAL, LAMA1, SLIT2 and REREG.   
     
     
         37 . A method for screening, diagnosing, and/or prognosticating colorectal cancer in an individual, comprising the steps of:
 obtaining a sample from the individual; and   assaying the sample for methylation status of at least two, at least three, at least four, or all of the following genes: P15.INK4b, SST.SOMATOSTATIN, JAM2, GAS7, CNRIP1 and PIK3CG.   
     
     
         38 . A method for screening, diagnosing, and/or prognosticating colorectal cancer in an individual, comprising the steps of:
 obtaining a sample from the individual; and   assaying the sample for methylation status of at least two, at least three, at least four, or all of the following genes: P15.INK4b, SST.SOMATOSTATIN, GAS7, NPY, CNRIP1 and PIK3CG.   
     
     
         39 . A method for screening, diagnosing, and/or prognosticating colorectal cancer in an individual, comprising the steps of:
 obtaining a sample from the individual; and   assaying the sample for methylation status of at least two, at least three, at least four, or all of the following genes: P15.INK4b, SST.SOMATOSTATIN, GAS7, CNRIP1, MAL and PIK3CG.   
     
     
         40 . A method for screening, diagnosing, and/or prognosticating colorectal cancer in an individual, comprising the steps of:
 obtaining a sample from the individual; and   assaying the sample for methylation status of at least two, at least three, at least four, or all of the following genes: P15.INK4b, SST.SOMATOSTATIN, GAS7, CNRIP1, PIK3CG and LAMA1.   
     
     
         41 . A method for screening, diagnosing, and/or prognosticating colorectal cancer in an individual, comprising the steps of:
 obtaining a sample from the individual; and   assaying the sample for methylation status of at least two, at least three, at least four, or all of the following genes: P15.INK4b, SST.SOMATOSTATIN, GAS7, CNRIP1, PIK3CG and RERG.   
     
     
         42 . A method for screening, diagnosing, and/or prognosticating colorectal cancer in an individual, comprising the steps of:
 obtaining a sample from the individual; and   assaying the sample for methylation status of at least two, at least three, at least four, or all of the following genes: P15.INK4b, SST.SOMATOSTATIN, GAS7, CNRIP1, PIK3CG and SLIT2.   
     
     
         43 . A method of treating an individual for colorectal cancer, comprising the step of providing to the individual one or more suitable therapies for colorectal cancer when the individual has a particular methylation status of at least two, at least three, at least four, or all of P15.INK4b, somatostatin, GAS7, CNRIP1, and PIK3CG that is indicative of the presence of colorectal cancer.