Multilayer-omics analysis of renal cell carcinoma, including the whole exome, methylome and transcriptome

Abstract

The aim of this study was to identify pathways that have a significant impact during renal carcinogenesis. Sixty-seven paired samples of both noncancerous renal cortex tissue and cancerous tissue from patients with clear cell renal cell carcinomas (RCCs) were subjected to whole-exome, methylome and transcriptome analyses using Agilent SureSelect All Exon capture followed by sequencing on an Illumina HiSeq 2000 platform, Illumina Infinium HumanMethylation27 BeadArray and Agilent SurePrint Human Gene Expression microarray, respectively. Sanger sequencing and quantitative reverse transcription-PCR were performed for technical verification. MetaCore software was used for pathway analysis. Somatic nonsynonymous single-nucleotide mutations, insertions/deletions and intragenic breaks of 2,153, 359 and 8 genes were detected, respectively. Mutations of GCN1L1, MED12 and CCNC, which are members of CDK8 mediator complex directly regulating β-catenin-driven transcription, were identified in 16% of the RCCs. Mutations of MACF1, which functions in the Wnt/β-catenin signaling pathway, were identified in 4% of the RCCs. A combination of methylome and transcriptome analyses further highlighted the significant role of the Wnt/β-catenin signaling pathway in renal carcinogenesis. Genetic aberrations and reduced expression of ERC2 and ABCA13 were frequent in RCCs, and MTOR mutations were identified as one of the major disrupters of cell signaling during renal carcinogenesis. Our results confirm that multilayer-omics analysis can be a powerful tool for revealing pathways that play a significant role in carcinogenesis.

Keywords: CDK8 mediator complex; Wnt/β-catenin signaling pathway; clear cell renal cell carcinoma (RCC); multilayer-omics analysis; whole exome analysis.

Figure 1

Genes for which a correlation with Wnt/β-catenin signaling was indicated by MetaCore pathway analysis. The numbers of genetic aberrations, DNA hyper- or hypo-methylation and/or increased or reduced mRNA expression (shown in Supporting Information Table S6) detected among the 67 examined RCCs are indicated schematically: legends are shown at the left of the panel. The 36 marked genes that showed genetic aberration, DNA methylation alterations and/or mRNA expression alterations in one or more RCCs were correlated with Wnt/β-catenin signaling.