Epigenetic signatures of alcohol abuse and hepatitis infection during human hepatocarcinogenesis

// Ryan A. Hlady 1 , Rochelle L. Tiedemann 1,2 , William Puszyk 3 , Ivan Zendejas 4 , Lewis R. Roberts 5 , Jeong-Hyeon Choi 2 , Chen Liu 3 and Keith D. Robertson 1 1 Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA 2 Cancer Center, Georgia Regents University, Augusta, GA, USA 3 Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA 4 Department of Surgery, University of Florida, Gainesville, FL, USA 5 Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA Correspondence: Keith D. Robertson, email: // Chen Liu, email: // Keywords : hepatocellular carcinoma, cirrhosis, etiology, epigenetics, DNA methylation Received : August 28, 2014 Accepted : September 07, 2014 Published : September 08, 2014 Abstract Hepatocellular carcinoma (HCC) is the second most common cause of cancer deaths worldwide. Deregulated DNA methylation landscapes are ubiquitous in human cancers. Interpretation of epigenetic aberrations in HCC is confounded by multiple etiologic drivers and underlying cirrhosis. We globally profiled the DNA methylome of 34 normal and 122 liver disease tissues arising in settings of hepatitis B (HBV) or C (HCV) viral infection, alcoholism (EtOH), and other causes to examine how these environmental agents impact DNA methylation in a manner that contributes to liver disease. Our results demonstrate that each ‘exposure’ leaves unique and overlapping signatures on the methylome. CpGs aberrantly methylated in cirrhosis-HCV and conserved in HCC were enriched for cancer driver genes, suggesting a pathogenic role for HCV-induced methylation changes. Additionally, large genomic regions displaying stepwise hypermethylation or hypomethylation during disease progression were identified. HCC-HCV/EtOH methylomes overlap highly with cryptogenic HCC, suggesting shared epigenetically deregulated pathways for hepatocarcinogenesis. Finally, overlapping methylation abnormalities between primary and cultured tumors unveil conserved epigenetic signatures in HCC. Taken together, this study reveals profound epigenome deregulation in HCC beginning during cirrhosis and influenced by common environmental agents. These results lay the foundation for defining epigenetic drivers and clinically useful methylation markers for HCC.