Mapping the heterogeneity of histone modifications on hepatitis B virus-DNA using liver needle biopsies obtained from chronically infected patients

Tobias Flecken, Marie-Anne Meier, Peter Skewes-Cox, David T. Barkan, Markus H. Heim, Stefan F. Wieland, Meghan M. Holdorf
<span title="2019-02-20">2019</span> <i title="American Society for Microbiology"> <a target="_blank" rel="noopener" href="" style="color: black;">Journal of Virology</a> </i> &nbsp;
Covalently closed circular DNA (cccDNA) forms the basis for replication and persistence of hepatitis B virus (HBV) in the chronically infected liver. We have previously shown that viral transcription is subject to regulation by posttranslational modifications (PTMs) of histone proteins bound to cccDNA through analysis of de novo HBV infected cell lines. We now report the successful adaptation of this chromatin immunoprecipitation-sequencing (ChIPseq) approach for analysis of fine-needle patient
more &raquo; ... liver biopsy specimens to investigate the role of histone PTMs in chronically HBV-infected patients. Using 18 specimens from patients in different stages of chronic HBV infection, our work shows that the profile of histone PTMs in chronic infection is more nuanced than previously observed in in vitro models of acute infection. In line with our previous findings, we find that the majority of HBV-derived sequences are associated with the activating histone PTM H3K4me3. However, we show a striking interpatient variability of its deposition in this patient cohort correlated to viral transcription and patient HBV early antigen (HBeAg) status. Unexpectedly, we detect deposition of the classical inhibitory histone PTM H3K9me3 on HBV-DNA in around half of the patient biopsies which could not be linked to reduced levels of viral transcripts. Our results show that current in vitro models are unable to fully recapitulate the complex epigenetic landscape of chronic HBV infection observed in vivo and demonstrate that fine needle liver biopsy specimens can provide sufficient material to further investigate the interaction of viral and host proteins on HBV-DNA. Importance Hepatitis B virus (HBV) is a major global health concern, chronically infecting millions of patients and contributing to a rising burden of liver disease. The viral genome forms the basis for chronic infection and has been shown subject to regulation by epigenetic mechanisms, such as posttranslational modification of histone proteins. Here, we confirm and expand on previous results by adapting a high-resolution technique for analysis of histone modifications to the use with patient-derived fine-needle liver biopsies. Our work highlights that the situation in vivo is more complex than predicted by current in vitro models, for example by suggesting a novel, non-canonical role of the histone modification H3K9me3 in the HBV life cycle. Importantly, enabling the use of fine-needle liver biopsies for such high-resolution analyses may facilitate further research into the epigenetic regulation of the HBV genome.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="">doi:10.1128/jvi.02036-18</a> <a target="_blank" rel="external noopener" href="">pmid:30787147</a> <a target="_blank" rel="external noopener" href="">pmcid:PMC6475771</a> <a target="_blank" rel="external noopener" href="">fatcat:va5h6nt4rvdshdeh6upp3dgiwy</a> </span>
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