Quantitative promoter methylation analysis of multiple cancer-related genes in renal cell tumors

Background: Aberrant promoter hypermethylation of cancer- associated genes occurs frequently during carcinogenesis and may serve as a cancer biomarker. In this study we aimed at defining a quantitative gene promoter methylation panel that might identify the most prevalent types of renal cell tumors. Methods: A panel of 18 gene promoters was assessed by quantitative methylation- specific PCR ( QMSP) in 85 primarily resected renal tumors representing the four major histologic subtypes ( 52 clear cell ( ccRCC), 13 papillary ( pRCC), 10 chromophobe ( chRCC), and 10 oncocytomas) and 62 paired normal tissue samples. After genomic DNA isolation and sodium bisulfite modification, methylation levels were determined and correlated with standard clinicopathological parameters. Results: Significant differences in methylation levels among the four subtypes of renal tumors were found for CDH1 ( p = 0.0007), PTGS2 ( p = 0.002), and RASSFIA ( p = 0.0001). CDH1 hypermethylation levels were significantly higher in ccRCC compared to chRCC and oncocytoma ( p = 0.00016 and p = 0.0034, respectively), whereas PTGS2 methylation levels were significantly higher in ccRCC compared to pRCC ( p = 0.004). RASSFIA methylation levels were significantly higher in pRCC than in normal tissue ( p = 0.035). In pRCC, CDH1 and RASSFIA methylation levels were inversely correlated with tumor stage ( p = 0.031) and nuclear grade ( p = 0.022), respectively. Conclusion: The major subtypes of renal epithelial neoplasms display differential aberrant CDH1, PTGS2, and RASSFIA promoter methylation levels. This gene panel might contribute to a more accurate discrimination among common renal tumors, improving preoperative assessment and therapeutic decision- making in patients harboring suspicious renal masses.