Detection of HBV DNA integration in plasma cell-free DNA of different HBV diseases utilizing DNA capture strategy

Zerui Yang; Jingyan Zeng; Yueyue Chen; Mengchun Wang; Hongchun Luo; Ai-Long Huang; Haijun Deng; Yuan Hu

doi:10.1016/j.virs.2024.06.003

August 2024

Citation: Zerui Yang, Jingyan Zeng, Yueyue Chen, Mengchun Wang, Hongchun Luo, Ai-Long Huang, Haijun Deng, Yuan Hu. Detection of HBV DNA integration in plasma cell-free DNA of different HBV diseases utilizing DNA capture strategy .VIROLOGICA SINICA, 2024, 39(4) : 655-666. http://dx.doi.org/10.1016/j.virs.2024.06.003

Detection of HBV DNA integration in plasma cell-free DNA of different HBV diseases utilizing DNA capture strategy

Zerui Yang ^a ,
Jingyan Zeng ^b ,
Yueyue Chen ^a ,
Mengchun Wang ^a ,
Hongchun Luo ^b ,
Ai-Long Huang ^{a
,,} ,
Haijun Deng ^{a
,,} ,
Yuan Hu ^{a
,,}

a. Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, 400016, China;
b. Department of Infectious Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China

Corresponding author: Ai-Long Huang, ahuang@cqmu.edu.cn
Haijun Deng, pepper027@163.com
Yuan Hu, huyuan@cqmu.edu.cn
Received Date: 24 January 2024
Accepted Date: 04 June 2024
Available online: 07 June 2024

Abstract

The landscape of hepatitis B virus (HBV) integration in the plasma cell-free DNA (cfDNA) of HBV-infected patients with different stages of liver diseases [chronic hepatitis B (CHB), liver cirrhosis (LC), and hepatocellular carcinoma (HCC)] remains unclear. In this study, we developed an improved strategy for detecting HBV DNA integration in plasma cfDNA, based on DNA probe capture and next-generation sequencing. Using this optimized strategy, we successfully detected HBV integration events in chimeric artificial DNA samples and HBV-infected HepG2-NTCP cells at day one post infection, with high sensitivity and accuracy. The characteristics of HBV integration events in the HBV-infected HepG2-NTCP cells and plasma cfDNA from HBV-infected individuals (CHB, LC, and HCC) were further investigated. A total of 112 and 333 integration breakpoints were detected in the HepG2-NTCP cells and 22 out of 25 (88%) clinical HBV-infected samples, respectively. In vivo analysis showed that the normalized number of support unique sequences (nnsus) in HCC was significantly higher than in CHB or LC patients (P values < 0.05). All integration breakpoints are randomly distributed on human chromosomes and are enriched in the HBV genome around nt 1800. The majority of integration breakpoints (61.86%) are located in the gene-coding region. Both non-homologous end-joining (NHEJ) and microhomology-mediated end-joining (MMEJ) interactions occurred during HBV integration across the three different stages of liver diseases. Our study provides evidence that HBV DNA integration can be detected in the plasma cfDNA of HBV-infected patients, including those with CHB, LC, or HCC, using this optimized strategy.
- Hepatitis B virus (HBV)
- , DNA integration
- , Cell-free DNA (cfDNA)
- , DNA capture

Electronic Supplementary Material

10.1016j.virs.2024.06.003-ESM.docx
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