Epigenetic Alterations of Chromosome 3 Revealed by NotI-Microarrays in Clear Cell Renal Cell Carcinoma

Abstract

This study aimed to clarify epigenetic and genetic alterations that occur during renal carcinogenesis. The original method includes chromosome 3 specific NotI-microarrays containing 180 NotI-clones associated with 188 genes for hybridization with 23 paired normal/tumor DNA samples of primary clear cell renal cell carcinomas (ccRCC). Twenty-two genes showed methylation and/or deletion in 17–57% of tumors. These genes include tumor suppressors or candidates (VHL, CTDSPL, LRRC3B, ALDH1L1, andEPHB1) and genes that were not previously considered as cancer-associated (e.g.,LRRN1, GORASP1, FGD5, andPLCL2). Bisulfite sequencing analysis confirmed methylation as a frequent event in ccRCC. A set of six markers (NKIRAS1/RPL15, LRRN1, LRRC3B, CTDSPL, GORASP1/TTC21A, andVHL) was suggested for ccRCC detection in renal biopsies. The mRNA level decrease was shown for 6 NotI-associated genes in ccRCC using quantitative PCR:LRRN1, GORASP1, FOXP1, FGD5, PLCL2,andALDH1L1. The majority of examined genes showed distinct expression profiles in ccRCC and papillary RCC. The strongest extent and frequency of downregulation were shown forALDH1L1gene both in ccRCC and papillary RCC. Moreover, the extent ofALDH1L1mRNA level decrease was more pronounced in both histological types of RCC stage III compared with stages I and II (P=0.03). The same was observed forFGD5gene in ccRCC (P<0.06).