A versatile method to profile hepatitis B virus DNA integration
Copyright © 2023 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Association for the Study of Liver Diseases..
BACKGROUND: HBV DNA integration into the host genome is frequently found in HBV-associated HCC tissues and is associated with hepatocarcinogenesis. Multiple detection methods, including hybrid capture-sequencing, have identified integration sites and provided clinical implications; however, each has advantages and disadvantages concerning sensitivity, cost, and throughput. Therefore, methods that can comprehensively and cost-effectively detect integration sites with high sensitivity are required. Here, we investigated the efficiency of RAISING (Rapid Amplification of Integration Site without Interference by Genomic DNA contamination) as a simple and inexpensive method to detect viral integration by amplifying HBV-integrated fragments using virus-specific primers covering the entire HBV genome.
METHODS AND RESULTS: Illumina sequencing of RAISING products from HCC-derived cell lines (PLC/PRF/5 and Hep3B cells) identified HBV-human junction sequences as well as their frequencies. The HBV-human junction profiles identified using RAISING were consistent with those determined using hybrid capture-sequencing, and the representative junctions could be validated by junction-specific nested PCR. The comparison of these detection methods revealed that RAISING-sequencing outperforms hybrid capture-sequencing in concentrating junction sequences. RAISING-sequencing was also demonstrated to determine the sites of de novo integration in HBV-infected HepG2-NTCP cells, primary human hepatocytes, liver-humanized mice, and clinical specimens. Furthermore, we made use of xenograft mice subcutaneously engrafted with PLC/PRF/5 or Hep3B cells, and HBV-human junctions determined by RAISING-sequencing were detectable in the plasma cell-free DNA using droplet digital PCR.
CONCLUSIONS: RAISING successfully profiles HBV-human junction sequences with smaller amounts of sequencing data and at a lower cost than hybrid capture-sequencing. This method is expected to aid basic HBV integration and clinical diagnosis research.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2023 |
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| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:7 |
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| Enthalten in: |
Hepatology communications - 7(2023), 12 vom: 01. Dez. |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Fukano, Kento [VerfasserIn] |
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| Anmerkungen: |
Date Completed 07.12.2023 Date Revised 07.12.2023 published: Electronic-eCollection Citation Status MEDLINE |
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| doi: |
10.1097/HC9.0000000000000328 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| 245 | 1 | 2 | |a A versatile method to profile hepatitis B virus DNA integration |
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| 520 | |a Copyright © 2023 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Association for the Study of Liver Diseases. | ||
| 520 | |a BACKGROUND: HBV DNA integration into the host genome is frequently found in HBV-associated HCC tissues and is associated with hepatocarcinogenesis. Multiple detection methods, including hybrid capture-sequencing, have identified integration sites and provided clinical implications; however, each has advantages and disadvantages concerning sensitivity, cost, and throughput. Therefore, methods that can comprehensively and cost-effectively detect integration sites with high sensitivity are required. Here, we investigated the efficiency of RAISING (Rapid Amplification of Integration Site without Interference by Genomic DNA contamination) as a simple and inexpensive method to detect viral integration by amplifying HBV-integrated fragments using virus-specific primers covering the entire HBV genome | ||
| 520 | |a METHODS AND RESULTS: Illumina sequencing of RAISING products from HCC-derived cell lines (PLC/PRF/5 and Hep3B cells) identified HBV-human junction sequences as well as their frequencies. The HBV-human junction profiles identified using RAISING were consistent with those determined using hybrid capture-sequencing, and the representative junctions could be validated by junction-specific nested PCR. The comparison of these detection methods revealed that RAISING-sequencing outperforms hybrid capture-sequencing in concentrating junction sequences. RAISING-sequencing was also demonstrated to determine the sites of de novo integration in HBV-infected HepG2-NTCP cells, primary human hepatocytes, liver-humanized mice, and clinical specimens. Furthermore, we made use of xenograft mice subcutaneously engrafted with PLC/PRF/5 or Hep3B cells, and HBV-human junctions determined by RAISING-sequencing were detectable in the plasma cell-free DNA using droplet digital PCR | ||
| 520 | |a CONCLUSIONS: RAISING successfully profiles HBV-human junction sequences with smaller amounts of sequencing data and at a lower cost than hybrid capture-sequencing. This method is expected to aid basic HBV integration and clinical diagnosis research | ||
| 650 | 4 | |a Journal Article | |
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| 700 | 1 | |a Nao, Naganori |e verfasserin |4 aut | |
| 700 | 1 | |a Saito, Masumichi |e verfasserin |4 aut | |
| 700 | 1 | |a Tsubota, Akihito |e verfasserin |4 aut | |
| 700 | 1 | |a Toyoshima, Takae |e verfasserin |4 aut | |
| 700 | 1 | |a Aizaki, Hideki |e verfasserin |4 aut | |
| 700 | 1 | |a Iijima, Hiroko |e verfasserin |4 aut | |
| 700 | 1 | |a Matsudaira, Takahiro |e verfasserin |4 aut | |
| 700 | 1 | |a Kimura, Moto |e verfasserin |4 aut | |
| 700 | 1 | |a Watashi, Koichi |e verfasserin |4 aut | |
| 700 | 1 | |a Sugiura, Wataru |e verfasserin |4 aut | |
| 700 | 1 | |a Muramatsu, Masamichi |e verfasserin |4 aut | |
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