title: A pre-neoplastic epigenetic field defect in HCV-infected liver at transcription factor binding sites and polycomb targets.
abstract: The predisposition of patients with Hepatitis C virus (HCV) infection to hepatocellular carcinoma (HCC) involves components of viral infection, inflammation and time. The development of multifocal, genetically distinct tumours is suggestive of a field defect affecting the entire liver. The molecular susceptibility mediating such a field defect is not understood. One potential mediator of long-term cellular reprogramming is heritable (epigenetic) regulation of transcription, exemplified by DNA methylation. We studied epigenetic and transcriptional changes in HCV-infected livers in comparison with control, uninfected livers and HCC, allowing us to identify pre-neoplastic epigenetic and transcriptional events. We find the HCV-infected liver to have a pattern of acquisition of DNA methylation targeted to candidate enhancers active in liver cells, enriched for the binding sites of the FOXA1, FOXA2 and HNF4A transcription factors. These enhancers can be subdivided into those proximal to genes implicated in liver cancer or to genes involved in stem cell development, the latter distinguished by increased CG dinucleotide density and polycomb-mediated repression, manifested by the additional acquisition of histone H3 lysine 27 trimethylation (H3K27me3). Transcriptional studies on our samples showed that the increased DNA methylation at enhancers was associated with decreased local gene expression, results validated in independent samples from The Cancer Genome Atlas. Pharmacological depletion of H3K27me3 using the EZH2 inhibitor GSK343 in HepG2 cells suppressed cell growth and also revealed that local acquired DNA methylation was not dependent upon the presence of polycomb-mediated repression. The results support a model of HCV infection influencing the binding of transcription factors to cognate sites in the genome, with consequent local acquisition of DNA methylation, and the added repressive influence of polycomb at a subset of CG-dense cis-regulatory sequences. These epigenetic events occur before neoplastic transformation, resulting in what may be a pharmacologically reversible epigenetic field defect in HCV-infected liver.
authors.affiliation: Department of Genetics and Center for Epigenomics, Bronx, NY, USA.
authors.forename: N A
authors.initials: NA
authors.lastname: Wijetunga
authors.affiliation: Department of Genetics and Center for Epigenomics, Bronx, NY, USA.|Centro de Investigación Médica Aplicada (CIMA), IDISNA, Oncohematology Department, Pamplona, Spain.
authors.forename: M
authors.initials: M
authors.lastname: Pascual
authors.affiliation: Department of Genetics and Center for Epigenomics, Bronx, NY, USA.
authors.forename: J
authors.initials: J
authors.lastname: Tozour
authors.affiliation: Department of Obstetrics, Gynecology and Women's Health, Bronx, NY, USA.
authors.forename: F
authors.initials: F
authors.lastname: Delahaye
authors.affiliation: Department of Medicine (Division of Gastroenterology and Liver Diseases), Bronx, NY, USA.|Marion Bessin Liver Research Center, Bronx, NY, USA.
authors.forename: M
authors.initials: M
authors.lastname: Alani
authors.affiliation: Department of Genetics and Center for Epigenomics, Bronx, NY, USA.
authors.forename: M
authors.initials: M
authors.lastname: Adeyeye
authors.affiliation: Department of Medicine (Division of Gastroenterology and Liver Diseases), Bronx, NY, USA.|Marion Bessin Liver Research Center, Bronx, NY, USA.
authors.forename: A W
authors.initials: AW
authors.lastname: Wolkoff
authors.affiliation: Department of Medicine (Oncology), Albert Einstein College of Medicine, Bronx, NY, USA.
authors.forename: A
authors.initials: A
authors.lastname: Verma
authors.affiliation: Department of Genetics and Center for Epigenomics, Bronx, NY, USA.
authors.forename: J M
authors.initials: JM
authors.lastname: Greally
mesh_terms: D001665:Binding Sites / Q000235:genetics; D006528:Carcinoma, Hepatocellular / Q000235:genetics / Q000473:pathology / Q000821:virology; D019175:DNA Methylation / Q000235:genetics; D044127:Epigenesis, Genetic; D015972:Gene Expression Regulation, Neoplastic; D056945:Hep G2 Cells; D016174:Hepacivirus / Q000502:physiology*; D006526:Hepatitis C / Q000150:complications* / Q000235:genetics / Q000378:metabolism; D006801:Humans; D008099:Liver / Q000378:metabolism / Q000473:pathology / Q000821:virology*; D008113:Liver Neoplasms / Q000235:genetics / Q000473:pathology / Q000821:virology; D009154:Mutation / Q000502:physiology; D063146:Polycomb-Group Proteins / Q000378:metabolism*; D011230:Precancerous Conditions / Q000235:genetics / Q000378:metabolism / Q000473:pathology / Q000821:virology; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding; D014158:Transcription, Genetic
chemical_list: D063146:Polycomb-Group Proteins