Studying the hepatitis C virus-induced epigenetic signature after cure with direct-acting antivirals

Shira Perez, Meital Gal-Tanamy

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

2 Scopus citations


Hepatitis C virus (HCV) is the leading cause of hepatocellular carcinoma (HCC). While direct-acting antiviral (DAA) therapy efficiently eradicates HCV infection, epidemiological studies show that sustained virological response (SVR) following anti-HCV treatment reduces, but does not eliminate, the risk for HCC. We have recently demonstrated that HCV infection induces genome-wide epigenetic changes that reprogram host gene expression and persist as “epigenetic signature” following virus eradication by DAAs. We suggest that this epigenetic signature underlie the residual risk for HCC post-SVR. Here, we provide a methodology to study the HCV-induced epigenetic signature. We describe a ChIP-seq protocol to evaluate changes in epigenome profile following HCV infection, its cure with DAA, and after treatment with epigenetic modifier inhibitor. We also describe evaluation of changes in the gene expression profile using RNA-seq. The integration between detected alterations in epigenetic marks and gene expression allows for identification of biological processes that are involved in HCV-driven oncogenesis before and after cure.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages17
StatePublished - 2019

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745

Bibliographical note

Publisher Copyright:
© Springer Science+Business Media, LLC, part of Springer Nature 2019.


  • Direct-acting antivirals (DAAs)
  • Epigenetic drugs
  • Epigenetics signature
  • Hepatocellular carcinoma (HCC)


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