Three-dimensional and single-cell sequencing of liver cancer reveals comprehensive host-virus interactions in HBV infection

Mengbiao Guo; Zhicheng Yao; Chen Jiang; Zhou Songyang; Lian Gan; Yuanyan Xiong

doi:10.3389/fimmu.2023.1161522

Three-dimensional and single-cell sequencing of liver cancer reveals comprehensive host-virus interactions in HBV infection

Front Immunol. 2023 Mar 31:14:1161522. doi: 10.3389/fimmu.2023.1161522. eCollection 2023.

Authors

Mengbiao Guo¹, Zhicheng Yao², Chen Jiang¹, Zhou Songyang¹, Lian Gan^{3

4}, Yuanyan Xiong¹

Affiliations

¹ Key Laboratory of Gene Engineering of the Ministry of Education, Institute of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
² Department of General Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
³ Nansha-South China Agricultural University Fishery Research Institute, Guangzhou, China.
⁴ College of Marine Sciences, South China Agricultural University, Guangzhou, China.

Abstract

Backgrounds: Hepatitis B virus (HBV) infection is a major risk factor for chronic liver diseases and liver cancer (mainly hepatocellular carcinoma, HCC), while the underlying mechanisms and host-virus interactions are still largely elusive.

Methods: We applied HiC sequencing to HepG2 (HBV-) and HepG2-2.2.15 (HBV+) cell lines and combined them with public HCC single-cell RNA-seq data, HCC bulk RNA-seq data, and both genomic and epigenomic ChIP-seq data to reveal potential disease mechanisms of HBV infection and host-virus interactions reflected by 3D genome organization.

Results: We found that HBV enhanced overall proximal chromatin interactions (CIs) of liver cells and primarily affected regional CIs on chromosomes 13, 14, 17, and 22. Interestingly, HBV altered the boundaries of many topologically associating domains (TADs), and genes nearby these boundaries showed functional enrichment in cell adhesion which may promote cancer metastasis. Moreover, A/B compartment analysis revealed dramatic changes on chromosomes 9, 13 and 21, with more B compartments (inactive or closed) shifting to A compartments (active or open). The A-to-B regions (closing) harbored enhancers enriched in the regulation of inflammatory responses, whereas B-to-A regions (opening) were enriched for transposable elements (TE). Furthermore, we identified large HBV-induced structural variations (SVs) that disrupted tumor suppressors, NLGN4Y and PROS1. Finally, we examined differentially expressed genes and TEs in single hepatocytes with or without HBV infection, by using single-cell RNA-seq data. Consistent with our HiC sequencing findings, two upregulated genes that promote HBV replication, HNF4A and NR5A2, were located in regions with HBV-enhanced CIs, and five TEs were located in HBV-activated regions. Therefore, HBV may promote liver diseases by affecting the human 3D genome structure.

Conclusion: Our work promotes mechanistic understanding of HBV infection and host-virus interactions related to liver diseases that affect billions of people worldwide. Our findings may also have implications for novel immunotherapeutic strategies targeting HBV infection.

Keywords: HBV; Hi-C; TAD and A/B compartments; host-virus interaction; liver cancer; single cell sequencing; structural variation (SV); transposable element (TE).

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Carcinoma, Hepatocellular* / pathology
Hepatitis B virus / physiology
Hepatitis B* / complications
Host Microbial Interactions
Humans
Liver Neoplasms* / pathology

Grants and funding

The research has been supported by Integrated Project of Major Research Plan of National Natural Science Foundation of China (NSFC) (Grant 92249303), Guangdong Basic and Applied Basic Research Foundation (2021A1515110972), and the Plan Project of Science and Technology of Heyuan (No. Heke2021039).