Hepatocellular carcinoma (HCC) is the most common primary liver malignancy. Here, we performed high-resolution copy-number analysis on 125 HCC tumors and whole-exome sequencing on 24 of these tumors. We identified 135 homozygous deletions and 994 somatic mutations of genes with predicted functional consequences. We found new recurrent alterations in four genes (ARID1A, RPS6KA3, NFE2L2 and IRF2) not previously described in HCC. Functional analyses showed tumor suppressor properties for IRF2, whose inactivation, exclusively found in hepatitis B virus (HBV)-related tumors, led to impaired TP53 function. In contrast, inactivation of chromatin remodelers was frequent and predominant in alcohol-related tumors. Moreover, association of mutations in specific genes (RPS6KA3-AXIN1 and NFE2L2-CTNNB1) suggested that Wnt/β-catenin signaling might cooperate in liver carcinogenesis with both oxidative stress metabolism and Ras/mitogen-activated protein kinase (MAPK) pathways. This study provides insight into the somatic mutational landscape in HCC and identifies interactions between mutations in oncogene and tumor suppressor gene mutations related to specific risk factors.
This is a preview of subscription content, access via your institution
Open Access articles citing this article.
CTNNB1 mutations, TERT polymorphism and CD8+ cell densities in resected hepatocellular carcinoma are associated with longer time to recurrence
BMC Cancer Open Access 13 August 2022
CTNNB1 polymorphism (rs121913407) in circulating tumor DNA (ctDNA) in Egyptian hepatocellular carcinoma patients
Egyptian Liver Journal Open Access 20 July 2022
Roles of ARID1A variations in colorectal cancer: a collaborative review
Molecular Medicine Open Access 14 April 2022
Subscribe to this journal
Receive 12 print issues and online access
$189.00 per year
only $15.75 per issue
Rent or buy this article
Get just this article for as long as you need it
Prices may be subject to local taxes which are calculated during checkout
Gene Expression Omnibus
El-Serag, H.B. & Rudolph, K.L. Hepatocellular carcinoma: epidemiology and molecular carcinogenesis. Gastroenterology 132, 2557–2576 (2007).
Ferlay, J. et al. Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008. Int. J. Cancer 127, 2893–2917 (2010).
Greenman, C. et al. Patterns of somatic mutation in human cancer genomes. Nature 446, 153–158 (2007).
Tao, Y. et al. Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data. Proc. Natl. Acad. Sci. USA 108, 12042–12047 (2011).
Totoki, Y. et al. High-resolution characterization of a hepatocellular carcinoma genome. Nat. Genet. 43, 464–469 (2011).
Denissenko, M.F., Pao, A., Pfeifer, G.P. & Tang, M. Slow repair of bulky DNA adducts along the nontranscribed strand of the human p53 gene may explain the strand bias of transversion mutations in cancers. Oncogene 16, 1241–1247 (1998).
Hainaut, P. & Pfeifer, G.P. Patterns of p53 G→T transversions in lung cancers reflect the primary mutagenic signature of DNA-damage by tobacco smoke. Carcinogenesis 22, 367–374 (2001).
Bressac, B., Kew, M., Wands, J. & Ozturk, M. Selective G to T mutations of p53 gene in hepatocellular carcinoma from southern Africa. Nature 350, 429–431 (1991).
Hsu, I.C. et al. Mutational hotspot in the p53 gene in human hepatocellular carcinomas. Nature 350, 427–428 (1991).
Nault, J.C. & Zucman-Rossi, J. Genetics of hepatobiliary carcinogenesis. Semin. Liver Dis. 31, 173–187 (2011).
Sawey, E.T. et al. Identification of a therapeutic strategy targeting amplified FGF19 in liver cancer by Oncogenomic screening. Cancer Cell 19, 347–358 (2011).
Rebouissou, S. et al. Frequent in-frame somatic deletions activate gp130 in inflammatory hepatocellular tumours. Nature 457, 200–204 (2009).
Bluteau, O. et al. Bi-allelic inactivation of TCF1 in hepatic adenomas. Nat. Genet. 32, 312–315 (2002).
Li, M. et al. Inactivating mutations of the chromatin remodeling gene ARID2 in hepatocellular carcinoma. Nat. Genet. 43, 828–829 (2011).
Boyault, S. et al. Transcriptome classification of HCC is related to gene alterations and to new therapeutic targets. Hepatology 45, 42–52 (2007).
Tamura, T., Yanai, H., Savitsky, D. & Taniguchi, T. The IRF family transcription factors in immunity and oncogenesis. Annu. Rev. Immunol. 26, 535–584 (2008).
Han, K.J., Jiang, L. & Shu, H.B. Regulation of IRF2 transcriptional activity by its sumoylation. Biochem. Biophys. Res. Commun. 372, 772–778 (2008).
Pettersson, S., Kelleher, M., Pion, E., Wallace, M. & Ball, K.L. Role of Mdm2 acid domain interactions in recognition and ubiquitination of the transcription factor IRF-2. Biochem. J. 418, 575–585 (2009).
Guan, B., Wang, T.L. & Shih Ie, M. ARID1A, a factor that promotes formation of SWI/SNF-mediated chromatin remodeling, is a tumor suppressor in gynecologic cancers. Cancer Res. 71, 6718–6727 (2011).
Wilson, B.G. & Roberts, C.W. SWI/SNF nucleosome remodellers and cancer. Nat. Rev. Cancer 11, 481–492 (2011).
Jones, S. et al. Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma. Science 330, 228–231 (2010).
Wiegand, K.C. et al. ARID1A mutations in endometriosis-associated ovarian carcinomas. N. Engl. J. Med. 363, 1532–1543 (2010).
Jones, S. et al. Somatic mutations in the chromatin remodeling gene ARID1A occur in several tumor types. Hum. Mutat. 33, 100–103 (2012).
Wang, K. et al. Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer. Nat. Genet. 43, 1219–1223 (2011).
Douville, E. & Downward, J. EGF induced SOS phosphorylation in PC12 cells involves P90 RSK-2. Oncogene 15, 373–383 (1997).
Schneider, A., Mehmood, T., Pannetier, S. & Hanauer, A. Altered ERK/MAPK signaling in the hippocampus of the mrsk2_KO mouse model of Coffin-Lowry syndrome. J. Neurochem. 119, 447–459 (2011).
DeNicola, G.M. et al. Oncogene-induced Nrf2 transcription promotes ROS detoxification and tumorigenesis. Nature 475, 106–109 (2011).
Kim, Y.R. et al. Oncogenic NRF2 mutations in squamous cell carcinomas of oesophagus and skin. J. Pathol. 220, 446–451 (2010).
Shibata, T. et al. Cancer related mutations in NRF2 impair its recognition by Keap1-Cul3 E3 ligase and promote malignancy. Proc. Natl. Acad. Sci. USA 105, 13568–13573 (2008).
Gnirke, A. et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol. 27, 182–189 (2009).
Adzhubei, I.A. et al. A method and server for predicting damaging missense mutations. Nat. Methods 7, 248–249 (2010).
Robinson, J.T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011).
Peiffer, D.A. et al. High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. Genome Res. 16, 1136–1148 (2006).
Staaf, J. et al. Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios. BMC Bioinformatics 9, 409 (2008).
Popova, T. et al. Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays. Genome Biol. 10, R128 (2009).
Beroukhim, R. et al. The landscape of somatic copy-number alteration across human cancers. Nature 463, 899–905 (2010).
Draghici, S. et al. A systems biology approach for pathway level analysis. Genome Res. 17, 1537–1545 (2007).
Antonov, A.V., Schmidt, E.E., Dietmann, S., Krestyaninova, M. & Hermjakob, H. R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases. Nucleic Acids Res. 38, W78–W83 (2010).
Rebouissou, S. et al. HNF1α inactivation promotes lipogenesis in human hepatocellular adenoma independently of SREBP-1 and carbohydrate-response element–binding protein (ChREBP) activation. J. Biol. Chem. 282, 14437–14446 (2007).
Livak, K.J. & Schmittgen, T.D. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 25, 402–408 (2001).
We warmly thank T. Burguiere, G. Thomas, R. Fahraeus and C. Mlynarczyk for their helpful participation in this work. We also thank J. Saric, C. Laurent, B. Le Bail, A. Rullier, A. Sa Cunha, J.T. Van Nhieu, D. Cherqui and D. Azoulay for contributing to tissue collection. This work was supported by INCa with the ICGC project, the Ligue Nationale Contre le Cancer (Cartes d'Identité des Tumeurs program), the PAIR-CHC project NoFLIC (funded by INCa and the Association pour la Recherche Contre le Cancer, ARC), the Réseau National Centre de Recherches Biocosmétiques (CRB) Foie, HEPTROMIC (Framework Programme 7, FP7) and BioIntelligence (OSEO). G.A. is supported by a fellowship from the Agence Nationale de Recherches sur le Sida et les Hepatites Virales (ANRS).
The authors declare no competing financial interests.
Rights and permissions
About this article
Cite this article
Guichard, C., Amaddeo, G., Imbeaud, S. et al. Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma. Nat Genet 44, 694–698 (2012). https://doi.org/10.1038/ng.2256
This article is cited by
Hepatocellular carcinoma: molecular mechanism, targeted therapy, and biomarkers
Cancer and Metastasis Reviews (2023)
Expression Patterns of HOX Gene Family Defines Tumor Microenvironment and Immunotherapy in Hepatocellular Carcinoma
Applied Biochemistry and Biotechnology (2023)
Genetic variants of SOS2, MAP2K1 and RASGRF2 in the RAS pathway genes predict survival of HBV-related hepatocellular carcinoma patients
Archives of Toxicology (2023)
Liquid biopsy using cell-free DNA in the early diagnosis of hepatocellular carcinoma
Investigational New Drugs (2023)
Identification and development of a novel risk model based on cuproptosis-associated RNA methylation regulators for predicting prognosis and characterizing immune status in hepatocellular carcinoma
Hepatology International (2023)