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

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Hepatitis C Virus Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1911))

Abstract

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.

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Acknowledgment

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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Authors and Affiliations

  1. The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel

    Shira Perez & Meital Gal-Tanamy

Authors
  1. Shira Perez
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  2. Meital Gal-Tanamy
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Corresponding author

Correspondence to Meital Gal-Tanamy .

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Editors and Affiliations

  1. Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA

    Mansun Law

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Perez, S., Gal-Tanamy, M. (2019). Studying the Hepatitis C Virus-Induced Epigenetic Signature After Cure with Direct-Acting Antivirals. In: Law, M. (eds) Hepatitis C Virus Protocols . Methods in Molecular Biology, vol 1911. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8976-8_13

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  • DOI: https://doi.org/10.1007/978-1-4939-8976-8_13

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8975-1

  • Online ISBN: 978-1-4939-8976-8

  • eBook Packages: Springer Protocols

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