GSE113879
Mapping the heterogeneity of histone modifications on hepatitis B virus-DNA using liver needle biopsies obtained from chronically infected patients
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 through the analysis of de novo HBV infected cell lines that viral transcription is subject to regulation by posttranslational modifications (PTMs) of histone proteins bound to cccDNA. We now report the successful adaptation of this ChIPseq approach for the analysis of fine-needle patient 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 observed in our previous work largely focused on acute infection in in vitro models. Specifically, we find that the majority of recovered HBV sequences are associated with the activating histone PTM H3K4me3, in line with our previous findings. We further find that the striking interpatient variability of its deposition in this patient cohort is linked to viral transcription and patient HBeAg status. Unexpectedly, we detect a significant localized deposition of the inhibitory histone PTM H3K9me3 on HBV-DNA in select patient biopsies which was not observed previously. Altogether, our results show that current in vitro models of HBV infection 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. Overall design: 18 liver biopsy specimens were analyzed with input, H3K4me3, and H3K27me3-ChIP for all of them as well as H3 and H3K9me3 ChIPs for select biopsies, as indicated in sample descriptions. Additionally, in vitro infected primary human hepatocytes and cell lines with or without known integrated HBV-DNA (HepG2-hNTCP, HepG2-HBV, Hep3B, PLC/PRF/5) were included as controls. All ChIPseq results for H3, H3K4me3, H3K9me3 were obtained in duplicate with independently constructed libraries. Input and H3K27me3 sequencing results were replicated for 5 and 2 biopsies, respectively. All sequencing results from in vitro models were obtained in duplicate. An overview as well as the average HBV-derived readcounts normalized to 106 total reads are found in avgRPM.xlsx