Abstract 2022: Multilayer-omics (whole-exome, methylome and transcriptome) analysis identifies the Wnt/β-catenin pathway as a key player in the development of renal cell carcinoma.
Authors: Arai Eri , Sakamoto Hiromi , Ichikawa Hitoshi , Totsuka Hirohiko , Gotoh Masahiro , Mori Taisuke , Ohnami Sumiko , Nakagawa Tohru , Fujimoto Hiroyuki , Wang Linghua , Aburatani Hiroyuki , Yoshida Teruhiko , Kanai Yae 
Published: August 2014

Introduction: Even though recent developments in high-throughput sequence capture methods and next-generation sequencing technologies have made exome sequencing technically feasible, the use of an integrated multilayer-omics approach including exome analysis to examine human renal cell carcinomas has never been reported. The aim of this study was to identify pathways that have a significant impact during renal carcinogenesis by multilayer-omics analysis. Methods: Thirty paired specimens of non-cancerous renal cortex tissue and tumorous tissue from patients with clear cell renal cell carcinoma, the major histological subtype of renal cell carcinoma, 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. The other 37 renal cell carcinomas were subjected to the validation study. Results: The exome analysis has revealed for the first time frequent genetic aberrations of GCN1L1, MACF1, ERC2, ABCA13, and MUC16 in clear cell renal cell carcinomas. Somatic non-synonymous mutations of GCN1L1, MED12 and CCNC, which are members of CDK8 mediator complex directly regulating β-catenin-driven transcription, were identified in 17% of the clear cell renal cell carcinomas. In addition, MACF1 functions in the Wnt/β-catenin signaling pathway. Reduced expression associated due to DNA hypermethylation of SFRP1, which downregulates Wnt/β-catenin signaling by competing with Frizzled for Wnt binding via their cysteine-rich domain, was frequent in clear cell renal cell carcinomas. 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 renal cell carcinomas. MetaCore pathway analysis revealed that MTOR mutations were one of the major disrupters of cell signaling during renal carcinogenesis. MTOR mutation may be a marker for predicting the sensitivity of clear cell renal cell carcinomas to mTOR inhibitors, such as rapamycin and its derivatives. Conclusion: Our results confirm that multilayer-omics analysis can be a powerful tool for revealing pathways that play a significant role in carcinogenesis.

Citation Format: Eri Arai, Hiromi Sakamoto, Hitoshi Ichikawa, Hirohiko Totsuka, Masahiro Gotoh, Taisuke Mori, Sumiko Ohnami, Tohru Nakagawa, Hiroyuki Fujimoto, Linghua Wang, Hiroyuki Aburatani, Teruhiko Yoshida, Yae Kanai. Multilayer-omics (whole-exome, methylome and transcriptome) analysis identifies the Wnt/β-catenin pathway as a key player in the development of renal cell carcinoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2022. doi:10.1158/1538-7445.AM2013-2022