Studying the Hepatitis C Virus-Induced Epigenetic Signature After Cure with Direct-Acting Antivirals

  • Shira Perez
  • Meital Gal-TanamyEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1911)


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.

Key words

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



The authors acknowledge grant support from the Leona M. and Harry B. Helmsley Charitable Trust Grant #2012PG-ISL013 and Israel Cancer Association #20160120. The authors thank Prof. Izhak Haviv (Bar-Ilan University), Prof. Assam El-Osta (Monash University), and Dr. Antony Kaspi (Monash University) for their insight and helpful discussions.


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© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.The Azrieli Faculty of MedicineBar-Ilan UniversitySafedIsrael

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