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

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  • Additional Information
    • Source:
      Publisher: Elsevier B.V. on behalf of KeAi Communications Co. Ltd Country of Publication: Netherlands NLM ID: 101514185 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1995-820X (Electronic) Linking ISSN: 1995820X NLM ISO Abbreviation: Virol Sin Subsets: MEDLINE
    • Publication Information:
      Publication: 2022- : [Amsterdam, Netherlands] : Elsevier B.V. on behalf of KeAi Communications Co. Ltd.
      Original Publication: Beijing : Science Press
    • Subject Terms:
      Hepatitis B virus*/genetics ; Hepatitis B virus*/isolation & purification ; DNA, Viral*/genetics ; DNA, Viral*/blood ; Virus Integration* ; Cell-Free Nucleic Acids*/blood ; Cell-Free Nucleic Acids*/genetics ; Cell-Free Nucleic Acids*/isolation & purification ; Carcinoma, Hepatocellular*/virology ; Carcinoma, Hepatocellular*/blood ; Hepatitis B, Chronic*/virology ; Hepatitis B, Chronic*/blood ; Liver Neoplasms*/virology ; Liver Neoplasms*/blood ; High-Throughput Nucleotide Sequencing*; Humans ; Hep G2 Cells ; Liver Cirrhosis/virology ; Liver Cirrhosis/blood ; Liver Cirrhosis/diagnosis ; Male ; Middle Aged ; Adult ; Female
    • 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.
      Competing Interests: Conflict of interest The authors declare no potential conflicts of interest.
      (Copyright © 2024 The Authors. Publishing services by Elsevier B.V. All rights reserved.)
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    • Contributed Indexing:
      Keywords: Cell-free DNA (cfDNA); DNA capture; DNA integration; Hepatitis B virus (HBV)
    • Accession Number:
      0 (DNA, Viral)
      0 (Cell-Free Nucleic Acids)
    • Publication Date:
      Date Created: 20240609 Date Completed: 20240823 Latest Revision: 20240916
    • Publication Date:
      20240916
    • Accession Number:
      PMC11401475
    • Accession Number:
      10.1016/j.virs.2024.06.003
    • Accession Number:
      38852920