Identification of novel epigenetic markers for clear cell renal cell carcinoma.
OBJECTIVE
We identified significantly hypermethylated genes in clear cell renal cell carcinoma.


METHODS
We previously identified a set of under expressed genes in renal cell carcinoma tissue through transcriptional profiling and a robust computational screen. We selected 19 of these genes for hypermethylation analysis using a rigorous search for the best candidate regions, considering CpG islands and transcription factor binding sites. The genes were analyzed for hypermethylation in the DNA of 38 matched clear cell renal cell carcinoma and normal samples using matrix assisted laser desorption ionization time-of-flight mass spectrometry. The significance of hypermethylation was assessed using 3 statistical tests. We validated the down-regulation of significantly hypermethylated genes at the RNA and protein levels in a separate set of patients using reverse transcriptase-polymerase chain reaction, immunohistochemistry and Western blots.


RESULTS
We found 7 significantly hypermethylated regions from 6 down-regulated genes, including SFRP1, which was previously shown to be hypermethylated in renal cell carcinoma and other cancer types.


CONCLUSIONS
To our knowledge we report for the first time that another 5 genes (SCNN1B, SYT6, DACH1, and the tumor suppressors TFAP2A and MT1G) are hypermethylated in renal cell carcinoma. Robust computational screens and the high throughput methylation assay resulted in an enriched set of novel genes that are epigenetically altered in clear cell renal cell carcinoma. Overall the detection of hypermethylation in these highly down-regulated genes suggests that assaying for their methylation using cells from urine or blood could provide the basis for a viable diagnostic test.
Dalgin
Gul S
GS
Molecular and Cell Biology and Biochemistry Program, Boston University, Boston, Massachusetts, USA.
Drever
Michele
M
Williams
Tara
T
King
Thomas
T
DeLisi
Charles
C
Liou
Louis S
LS
D014408:Biomarkers, Tumor / Q000235:genetics*; D015153:Blotting, Western; D002292:Carcinoma, Renal Cell / Q000235:genetics*; D018899:CpG Islands / Q000235:genetics*; D019175:DNA Methylation; D015536:Down-Regulation; D044127:Epigenesis, Genetic; D053503:Epithelial Sodium Channels / Q000235:genetics; D005136:Eye Proteins / Q000235:genetics; D006801:Humans; D036341:Intercellular Signaling Peptides and Proteins / Q000235:genetics; D007680:Kidney Neoplasms / Q000235:genetics*; D008565:Membrane Proteins / Q000235:genetics; D008668:Metallothionein / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D050857:Synaptotagmins / Q000235:genetics; D050656:Transcription Factor AP-2 / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics; D000094742:Secreted Frizzled-Related Proteins
D014408:Biomarkers, Tumor; D053503:Epithelial Sodium Channels; D005136:Eye Proteins; D036341:Intercellular Signaling Peptides and Proteins; D008565:Membrane Proteins; D008668:Metallothionein; D050857:Synaptotagmins; D050656:Transcription Factor AP-2; D014157:Transcription Factors; C486747:DACH1 protein, human; C499629:MT1G protein, human; C507048:SCNN1B protein, human; C117636:SFRP1 protein, human; D000094742:Secreted Frizzled-Related Proteins; C494298:SYT6 protein, human; C493673:TFAP2A protein, human