Mapping the Heterogeneity of Histone Modifications on Hepatitis B Virus DNA Using Liver Needle Biopsies Obtained from...

Area of Science:

• Hepatology
• Virology
• Epigenetics

Background:

• Covalently closed circular DNA (cccDNA) is central to hepatitis B virus (HBV) replication and persistence in chronic infection.
• Previous studies indicated that histone posttranslational modifications (PTMs) regulate HBV transcription in vitro.
• Chronic HBV infection affects millions globally, contributing significantly to liver disease burden.

Purpose of the Study:

• To adapt and apply chromatin immunoprecipitation sequencing (ChIPseq) for analyzing histone PTMs on HBV cccDNA in patient liver biopsy specimens.
• To investigate the epigenetic landscape of HBV DNA in patients with chronic HBV infection.
• To compare in vivo findings with existing in vitro models of HBV infection.

Main Methods:

• Chromatin immunoprecipitation sequencing (ChIPseq) was adapted for fine-needle liver biopsy specimens.
• Analysis was performed on 18 specimens from patients with varying stages of chronic HBV infection.
• Histone PTMs, including H3K4me3 and H3K9me3, were profiled on HBV DNA.

Main Results:

• Histone PTM profiles in chronic HBV infection are more complex in vivo than in vitro models suggest.
• The activating histone PTM H3K4me3 was associated with most HBV sequences, but showed significant interpatient variability correlated with viral transcription and HBeAg status.
• The inhibitory histone PTM H3K9me3 was unexpectedly found on HBV DNA in about half of patients, without a clear link to reduced viral transcripts.

Conclusions:

• Current in vitro models do not fully recapitulate the epigenetic complexity of chronic HBV infection in vivo.
• Fine-needle liver biopsies provide sufficient material for high-resolution epigenetic analysis of HBV DNA.
• The study suggests a potential novel, noncanonical role for H3K9me3 in the HBV life cycle, warranting further investigation.