Clear cell renal cell carcinoma (ccRCC) is the most common form of adult kidney cancer. The most frequent genetic event in the evolution of ccRCC is inactivation of the von Hippel-Lindau (VHL) tumor suppressor gene. Recent studies have revealed frequent mutations of PBRM1 as well as other epigenetic regulators including BAP1, SETD2 and KDM5C, but their impact on therapeutics remains unclear. In this study, to obtain a better understanding of molecular pathogenesis of ccRCC, we performed an integrated genetic study of ccRCC including whole exome sequencing, copy number analysis as well as transcriptome and methylome analysis. A total of 106 paired specimens were analyzed by massively parallel sequencing of whole exomes (Agilent SureSelect, Illumina HiSeq2000) and SNP array-based copy number analysis (Affymetrix 250K array) as well as gene expression (Agilent Human Gene Expression 4x44k v2) and methylation (Illumina Infinium 450K) profiling and RNA sequencing (Illumina HiSeq2000). On average, 48.8 somatic mutations per sample were identified in whole exome analysis, in which VHL mutations were most frequent. PBRM1, BAP1 and SETD2 were also recurrently mutated and were further analyzed in 240 cases together with an additional 80 genes involved in chromatin regulation. PBRM1 mutations were found in 42% of the cases, while BAP1 and SETD2 were mutated in 12% and 10%, respectively. BAP1 mutations correlated with poor prognosis and SETD2 mutation was associated with the risk for metastatic diseases. Pathway analysis revealed frequent mutations of genes involved in mRNA processing. Among them, mutations of genes involved in 3’ splice site recognition, which were frequently mutated in MDS, were rare. Most of them were involved in release of intron, 3’-end processing or export to cytoplasm. In expression analysis, tumors were clustered into two clusters known as ccA and ccB, in which the ccA type was characterized by overexpressed genes involved in angiogenesis, whereas expression of genes in cell cycle regulators were a prominent feature in the ccB type tumors. In methylome analysis, 15 samples were clustered into hypermethylated subtype where all cases were included in the ccB type and were associated with poor prognosis. Homeobox genes were differently methylated in hypermethylated subtype which indicate deregulation of polycomb mediated gene silencing induce high-grade ccRCC. RUNX1 and SRPX2 were differently methylated between ccA type and ccB type, which may affect the differences of expression profile between two subtypes. In RNA sequencing, known fusion gene involving TFE3 and NONO was detected in single case. In total, 34 fusion genes were detected in 23 samples, although no recurrent fusion genes have been identified. Our results indicate that genomic analyses are useful for classification, prognostic prediction and development of treatment strategy in ccRCC.

Citation Format: Yusuke Sato, Shigekatsu Maekawa, Yusuke Okuno, Yuichi Shiraishi, Aiko Sato, Genta Nagae, Teppei Shimamura, Yasunobu Nagata, Kenichi Yoshida, Masashi Sanada, Haruki Kume, Hiroyuki Aburatani, Satoru Miyano, Yukio Homma, Seishi Ogawa. Integrative analysis of clear cell 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 3184. doi:10.1158/1538-7445.AM2013-3184