Method for determining prognosis of renal cell carcinoma

Abstract

It is intended to provide a rapid, convenient, and highly accurate method for determining the prognosis of cancer. The present invention provides a method for determining the prognosis of a renal cell carcinoma patient, comprising: (1) treating genomic DNA prepared from a renal tissue of a subject with bisulfite; (2) amplifying the bisulfite-treated DNA by PCR; (3) subjecting the obtained PCR amplification product to ion exchange chromatography; (4) obtaining the retention time of a detection signal obtained by the chromatography; and (5) determining the renal cell carcinoma of the subject as having poor prognosis when the result of the step (4) is shorter than a retention time serving as a reference.

1 : A method for determining a tissue having renal cell carcinoma, comprising:
 (1) treating genomic DNA prepared from a renal tissue of a subject with bisulfite;   (2) amplifying the bisulfite-treated genomic DNA by PCR;   (3) subjecting the PCR amplification product obtained in (2) to ion exchange chromatography;   (4) obtaining a retention time of a detection signal obtained by the chromatography; and   (5) determining the tissue as a tissue having renal cell carcinoma obtained from a renal cell carcinoma patient with poor prognosis when the retention time of the detection signal obtained by the chromatography is shorter than a retention time serving as a reference.   
     
     
         2 : The method of  claim 1 , wherein the bisulfite-treated genomic DNA to be amplified by PCR comprises a CpG island in at least one gene selected from the group consisting of FAM150A, GRM6, ZNF540, ZFP42, ZNF154, RIMS4, PCDHAC1, KHDRBS2, ASCL2, KCNQ1, PRAC, WNT3A, TRH, FAM78A, ZNF671, SLC13A5, and NKX6-2. 
     
     
         3 : The method of  claim 1 , wherein the bisulfite-treated genomic DNA to be amplified by PCR comprises a FAM150A gene promoter region. 
     
     
         4 : The method of  claim 1 , wherein the amplifying of the bisulfite-treated genomic DNA employs PCR primers having the nucleotide sequences of SEQ ID NOs: 51 and 52. 
     
     
         5 : The method of  claim 1 , further comprising, before the obtaining of the retention time:
 (1′) treating unmethylated DNA corresponding to a region in the genomic DNA to be amplified by the PCR with bisulfite;   (2′) amplifying the bisulfite-treated unmethylated DNA by PCR;   (3′) subjecting the PCR amplification product obtained in (2′) to ion exchange chromatography; and   (3a) obtaining difference data by subtracting a detection signal obtained by the chromatography in (3′) from a detection signal obtained by the chromatography in (3).   
     
     
         6 : A method for determining the prognosis of a renal cell carcinoma patient, comprising:
 (1) treating genomic DNA prepared from a renal tissue of a subject with bisulfite;   (2) amplifying the bisulfite-treated genomic DNA by PCR;   (3) subjecting the PCR amplification product to ion exchange chromatography;   (4) obtaining a retention time of a detection signal obtained by the chromatography; and   (5) determining the renal cell carcinoma of the subject as having poor prognosis when the retention time of the detection signal obtained by the chromatography is shorter than a retention time serving as a reference.   
     
     
         7 : The method of  claim 6 , wherein the bisulfite-treated genomic DNA to be amplified by PCR comprises a CpG island in at least one gene selected from the group consisting of FAM150A, GRM6, ZNF540, ZFP42, ZNF154, RIMS4, PCDHAC1, KHDRBS2, ASCL2, KCNQ1, PRAC, WNT3A, TRH, FAM78A, ZNF671, SLC13A5, and NKX6-2. 
     
     
         8 : The method of  claim 6 , wherein the bisulfite-treated genomic DNA to be amplified by PCR comprises a FAM150A gene promoter region. 
     
     
         9 : The method of  claim 6 , wherein the amplifying of the bisulfite-treated genomic DNA employs PCR primers having the nucleotide sequences of SEQ ID NOs: 51 and 52. 
     
     
         10 : The method of  claim 6 , further comprising, before the obtaining of the retention time:
 (1′) treating unmethylated DNA corresponding to a region in the genomic DNA to be amplified by the PCR with bisulfite;   (2′) amplifying the bisulfite-treated unmethylated DNA by PCR;   (3′) subjecting the PCR amplification product obtained in (2′) to ion exchange chromatography; and   (3a) obtaining difference data by subtracting a detection signal obtained by the chromatography in (3′) from a detection signal obtained by the chromatography in (3).   
     
     
         11 : A method for obtaining data for determining a tissue having renal cell carcinoma, comprising:
 (1) treating genomic DNA prepared from a renal tissue of a subject with bisulfite;   (2) amplifying the bisulfite-treated genomic DNA by PCR;   (3) subjecting the PCR amplification product to ion exchange chromatography;   (4) obtaining a retention time of a detection signal obtained by the chromatography; and   (5) determining whether or not the retention time obtained in (4) is shorter than a retention time serving as a reference and determining whether or not the tissue is a tissue having renal cell carcinoma obtained from a renal cell carcinoma patient with poor prognosis.   
     
     
         12 : The method of  claim 11 , wherein the bisulfite-treated genomic DNA to be amplified by PCR comprises a CpG island in at least one gene selected from the group consisting of FAM150A, GRM6, ZNF540, ZFP42, ZNF154, RIMS4, PCDHAC1, KHDRBS2, ASCL2, KCNQ1, PRAC, WNT3A, TRH, FAM78A, ZNF671, SLC13A5, and NKX6-2. 
     
     
         13 : The method of  claim 11 , wherein the bisulfite-treated genomic DNA to be amplified by PCR comprises a FAM150A gene promoter region. 
     
     
         14 : The method of  claim 11 , wherein the amplifying of the bisulfite-treated genomic DNA employs PCR primers having the nucleotide sequences of SEQ ID NOs: 51 and 52. 
     
     
         15 : The method of  claim 11 , further comprising, before the obtaining of the retention time:
 (1′) treating unmethylated DNA corresponding to a region in the genomic DNA to be amplified by the PCR with bisulfite;   (2′) amplifying the bisulfite-treated unmethylated DNA by PCR;   (3′) subjecting the PCR amplification product obtained in (2′) to ion exchange chromatography; and   (3a) obtaining difference data by subtracting a detection signal obtained by the chromatography in (3′) from a detection signal obtained by the chromatography in (3).