Abstract 3745: Comprehensive integrative characterization of hepatocellular carcinoma: The TCGA HCC project

Background: Hepatocellular carcinomas (HCCs) are heterogenous primary liver cancers with pleomorphic histologic features. We present a comprehensive genetic, genomic, transcriptomic and proteomic analysis of 203 HCCs in The Cancer Genome Atlas Program (TCGA) on behalf of the TCGA Liver analysis working group to provide a deeper understanding of the molecular features of HCCs, to classify them in a clinically-relevant manner, and to provide a public resource that identifies potential targets for emerging therapies.Results: Mutation analyses confirmed the presence of TERT promoter mutations in 40% of HCCs. The analysis also revealed the first reported germline mutation in the TERT promoter in a 30 year old male, possibly reflecting an inherited predisposition to HCC. TERT promoter mutations were enriched in hepatitis C virus infected subjects. Analyses of hepatitis B virus (HBV)-induced HCCs demonstrated recurrent integrations of HBV in the TERT locus. Thus, HBV integration may substitute for TERT promoter mutations as an alternate mechanism of telomerase activation. Other tumor suppressor genes inactivated by mutation included the cell cycle genes TP53 (32% of cases), RB1 (8%), and PTEN (3%), the Wnt/beta catenin pathway gene AXIN1 (4%), and the chromatin remodeling genes ARID1A (9%), BAP1 (6%), ARID1B (4%), ARID2 (4%), and PBRM1 (3%). The oncogene CTNNB1 was mutated in 27% of HCCs. Mutations were also found in the MTOR pathway genes, MTOR (4%), TSC2 (4%) and TSC1 (3%). The patterns of mutational signatures observed included signatures characteristic of the known carcinogens aristolochic acid and aflatoxin B1. Clustering of mRNA, miRNA, or protein expression, DNA hypermethylation and DNA copy number profiles identified five, four, two, five and three clusters, respectively. Analysis of mRNA expression data identified five groups. In particular, Group 1 was associated with Asian race, higher histologic grade, and micro- and macrovascular invasion. Integrated clustering showed a grouping of HCCs into three superclusters: iCluster 1 had a low frequency of CDKN2A silencing, lack of CTNNB1 mutation, a normal-like methylation pattern, and overexpression of proliferation marker genes; iClusters 2 and 3 had a high frequency of CDKN2A silencing, CTNNB1 mutation, and overexpression of oxidative response genes; iCluster 3 tumors had a higher degree of chromosomal instability, high frequency of 17p loss, and a highly altered methylation profile. Copy number aberrations included gains in the MYC, VEGFA, CCND1, TERT, and MET loci and losses in the TP53, RB1, ERFFI1, CDKN2A, ARID1A and PTEN loci. Discussion: Based on integrated analysis of genome, transcriptome, methylome and proteome we showed that HCCs naturally separate into three to five distinct groups with associated molecular and clinical characteristics. Importantly, we identified a novel germline mutation in the TERT promoter that may be associated with an inherited risk for HCC. Note: This abstract was not presented at the meeting. Citation Format: Lewis R. Roberts, David A. Wheeler. Comprehensive integrative characterization of hepatocellular carcinoma: The TCGA HCC project. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3745. doi:10.1158/1538-7445.AM2015-3745