Methods and biomarkers for detection of bladder cancer

Abstract

The invention relates to methods and biomarkers (e.g., epigenetic biomarkers) for detection of bladder cancer in biological samples (e.g., tissue samples, urine samples, urine sediments). In some embodiments, methods and biomarkers of the present invention find use in discriminating between bladder cancer, prostate cancer and renal epithelial tumors.

1 . A method for predicting a predisposition to bladder cancer in a subject, diagnosing a bladder cancer in a subject, predicting the likelihood of recurrence of bladder cancer in a subject, providing a prognosis for a subject with bladder cancer, or selecting a subject with bladder cancer for treatment with a particular therapy, comprising:
 a) contacting a biological sample from a subject with a reagent for detecting the methylation status of a nucleic acid segment corresponding to the VIM locus; and   b) detecting the methylation status of said nucleic acid segment corresponding to the VIM locus using an in vitro assay,   wherein an increased degree of methylation of said nucleic acid segment corresponding to the VIM locus in said sample relative to a reference methylation status provides an indication selected from the group consisting of an indication of a predisposition of the subject to bladder cancer, an indication that the subject has bladder cancer, an indication of the likelihood of recurrence of bladder cancer in the subject, an indication of survival of the subject, and an indication that the subject is a candidate for treatment with a particular therapy.   
     
     
         2 . The method of  claim 1 , further comprising detecting the methylation status of one more nucleic acid segments corresponding to a locus selected from the group consisting of the GDF15 locus, HSPA2 locus, and TMEFF2 locus, wherein an increased degree of methylation of at least one of said nucleic acid segments corresponding to a locus selected from the group consisting of the GDF15 locus, HSPA2 locus, and TMEFF2 locus in said sample relative to a reference methylation status in addition to said the methylation status of said nucleic acid segment corresponding to the VIM locus provides an indication selected from the group consisting of an indication of a predisposition of the subject to bladder cancer, an indication that the subject has bladder cancer, an indication of the likelihood of recurrence of bladder cancer in the subject, an indication of survival of the subject, and an indication that the subject is a candidate for treatment with a particular therapy. 
     
     
         3 . The method of  claim 1 , further comprising detecting the methylation status nucleic acid segments corresponding to the GDF15, HSPA2, and TMEFF2 loci, wherein an increased degree of methylation of each of said nucleic acid segments corresponding to a locus selected from the group consisting of the GDF15 locus, HSPA2 locus, and TMEFF2 locus in said sample relative to a reference methylation status in addition to said the methylation status of said nucleic acid segment corresponding to the VIM locus provides an indication selected from the group consisting of an indication of a predisposition of the subject to bladder cancer, an indication that the subject has bladder cancer, an indication of the likelihood of recurrence of bladder cancer in the subject, an indication of survival of the subject, and an indication that the subject is a candidate for treatment with a particular therapy. 
     
     
         4 . The method of  claim 1 , further comprising: c) generating a risk profile using the results of steps a) and b). 
     
     
         5 . The method of  claim 1 , wherein said bladder cancer is premalignant. 
     
     
         6 . The method of  claim 1 , wherein said bladder cancer is malignant. 
     
     
         7 . The method of  claim 1 , wherein said biological sample is selected from the group consisting of a tissue sample, a urine sample, and a sample of urine sediment. 
     
     
         8 . The method of  claim 1 , wherein said methylation status of said nucleic acid segments is used to discriminate between bladder cancer and another cancer. 
     
     
         9 . The method of  claim 8 , wherein said another cancer is selected from the group consisting of prostate cancer and renal epithelial tumors. 
     
     
         10 . The method of  claim 1 , wherein said nucleic acid segment comprises a region selected from the group consisting of a CpG island and a CpG island shore. 
     
     
         11 . The method of  claim 1 , wherein said CpG island or shore is present in a coding region or a regulatory region. 
     
     
         12 . The method of  claim 1 , wherein said regulatory region is a promoter. 
     
     
         13 . The method of  claim 1 , wherein said determining of the level of altered methylation of said nucleic acid segment comprises determining the methylation frequency of said CpG island or island shore. 
     
     
         14 . The method of  claim 1 , wherein said determining of the level of a nucleic acid polymer with altered methylation is achieved by a technique selected from the group consisting of methylation-specific PCR, quantitative methylation-specific PCR, methylation-sensitive DNA restriction enzyme analysis, quantitative bisulfite pyrosequencing, and bisulfite genomic sequencing PCR. 
     
     
         15 . The method of  claim 1 , wherein said method permits detection of bladder cancer in said subject with a sensitivity of at least 85% at a specificity of at least 85%. 
     
     
         16 . The method of  claim 1 , wherein said method permits detection of bladder cancer in said subject with a sensitivity of at least 80% at a specificity of at least 90%. 
     
     
         17 . The method of  claim 1 , further comprising determining a prognosis for said subject, determining a diagnosis for said subject, or selecting said subject for treatment with a particular therapy. 
     
     
         18 . A methylation specific nucleic acid detection reagent corresponding to a VIM locus nucleic acid sequence. 
     
     
         19 . A set of methylation specific nucleic acid detection reagents specific for potentially methylated regions of one or more specific loci being suitable to diagnose or predict bladder cancer, wherein said loci comprise one or more of the VIM locus, GDF15 locus, HSPA2 locus, and TMEFF2 locus. 
     
     
         20 . A kit for detecting the presence of a bladder neoplasm in a mammal, said kit comprising reagents useful, sufficient, or necessary for detecting and/or characterizing level, presence, or frequency of methylation of a VIM locus. 
     
     
         21 . The kit of  claim 20 , further comprising reagents for detecting and/or characterizing level, presence, or frequency of methylation of one or more additional nucleic acid polymers corresponding to a locus selected from the group consisting of GDF15, HSPA2, and TMEFF2.