Transcription profiling by array of renal cell carcinoma lines after treatment with 5-aza-2'-deoxycytidine

Promoter region hypermethylation and transcriptional silencing is a frequent cause of tumour suppressor gene (TSG) inactivation in many types of human cancers. Functional epigenetic studies, in which gene expression is induced by treatment with demethylating agents, may identify novel genes with tumour-specific methylation. We used high-density gene expression microarrays in a functional epigenetic study of 11 renal cell carcinoma (RCC) cell lines. Twenty eight genes were then selected for analysis of promoter methylation status in cell lines and primary RCC. Eight genes (BNC1, PDLIM4/RIL, REPRIMORPRM, CST6, SFRP1, GREM1, COL14A1 and COL15A1) demonstrated frequent (>30% of RCC tested) tumour-specific promoter region methylation. Hypermethylation was associated with transcriptional silencing. Re-expression of BNC1, CST6, RPRM, and SFRP1 suppressed the growth of RCC cell lines. Whereas, RNAi-knock-down of BNC1, SFRP1 and COL14A1 increased the growth potential of RCC cell lines. Methylation of BNC1 or COL14A1 was associated with a poorer prognosis independent of tumour size, stage or grade. The identification of these epigenetically inactivated candidate RCC tumour suppressor genes can provide insights into renal tumourigenesis and a basis for developing novel therapies and biomarkers for prognosis and detection. We used expression microarrays to identified genes that were frequently methylated and silenced in RCC by determining the globlal expression patterns of RCC-derived cell lines following de-methylation by treatment with 5-Aza-2'-deoxycytidine.