Multi-Omics Panoramic Analysis of HBV Integration, Transcriptional
Regulation, Translation, and Epigenetic Modifications in the Classical
HBV-Integrated Cell Line PLC/PRF/5
Abstract
Background: The clearance or transcriptional silencing of
integrated HBV DNA is crucial for achieving a functional cure in
patients with chronic hepatitis B (CHB) and reducing the risk of
hepatocellular carcinoma (HCC) development. The PLC/PRF/5 cell line is
commonly used as an in vitro model for studying HBV integration. In this
study, we employed a range of multi-omics techniques to gain a panoramic
understanding of the characteristics of HBV integration in PLC/PRF/5
cells. Methods: Transcriptome long-read sequencing (ONT) was
conducted to analyze characterize the transcriptional activity of
different HBV DNA integrations in PLC/PRF/5 cells. Additionally, data
pertaining to epigenetic regulation such as whole-genome bisulfite
sequencing (WGBS), histone chromatin immunoprecipitation sequencing
(ChIP-seq), and assay for transposase-accessible chromatin using
sequencing (ATAC-seq) were collected to investigate the potential
mechanisms associated with the transcriptional regulation of integrated
HBV DNA. Result: Our findings indicate that transcriptional
activity of integrated HBV DNA in PLC/PRF/5 cells is influenced by
methylation levels of the surrounding host genome near the integration
site. The result indicated that elevated methylation of the adjacent
host genome adversely impacts transcription activity of integrated HBV
DNA. Furthermore, we observed a positive association between histone
modification H3K4me3 and the transcription of integrated HBV DNA. These
results suggest that host may regulate transcriptional activity of
integrated HBV DNA through DNA methylation and histone modifications.
Potentially leading to the silencing of integrated HBV DNA.
Conclusion: Our study brought a better understanding on the
transcriptional regulation of integrated HBV DNA. This knowledge can be
valuable in the development of novel strategy for functional cure of
CHB.