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Kojima R, Nakamoto S, Kogure T, Ma Y, Ogawa K, Iwanaga T, Qiang N, Ao J, Nakagawa R, Muroyama R, Nakamura M, Chiba T, Kato J, Kato N. Re-analysis of hepatitis B virus integration sites reveals potential new loci associated with oncogenesis in hepatocellular carcinoma. World J Virol 2023; 12:209-220. [PMID: 37396703 PMCID: PMC10311580 DOI: 10.5501/wjv.v12.i3.209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/12/2023] [Accepted: 04/12/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND Hepatitis B virus (HBV) is a major cause of hepatocellular carcinoma (HCC). HBV DNA can get integrated into the hepatocyte genome to promote carcinogenesis. However, the precise mechanism by which the integrated HBV genome promotes HCC has not been elucidated.
AIM To analyze the features of HBV integration in HCC using a new reference database and integration detection method.
METHODS Published data, consisting of 426 Liver tumor samples and 426 paired adjacent non-tumor samples, were re-analyzed to identify the integration sites. Genome Reference Consortium Human Build 38 (GRCh38) and Telomere-to-Telomere Consortium CHM13 (T2T-CHM13 (v2.0)) were used as the human reference genomes. In contrast, human genome 19 (hg19) was used in the original study. In addition, GRIDSS VIRUSBreakend was used to detect HBV integration sites, whereas high-throughput viral integration detection (HIVID) was applied in the original study (HIVID-hg19).
RESULTS A total of 5361 integration sites were detected using T2T-CHM13. In the tumor samples, integration hotspots in the cancer driver genes, such as TERT and KMT2B, were consistent with those in the original study. GRIDSS VIRUSBreakend detected integrations in more samples than by HIVID-hg19. Enrichment of integration was observed at chromosome 11q13.3, including the CCND1 pro-moter, in tumor samples. Recurrent integration sites were observed in mitochondrial genes.
CONCLUSION GRIDSS VIRUSBreakend using T2T-CHM13 is accurate and sensitive in detecting HBV integration. Re-analysis provides new insights into the regions of HBV integration and their potential roles in HCC development.
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Affiliation(s)
- Ryuta Kojima
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Shingo Nakamoto
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Tadayoshi Kogure
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Yaojia Ma
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Keita Ogawa
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Terunao Iwanaga
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Na Qiang
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Junjie Ao
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Ryo Nakagawa
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Ryosuke Muroyama
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Masato Nakamura
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Tetsuhiro Chiba
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Jun Kato
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | - Naoya Kato
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
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Yang M, Yang G, Li F, Ou M, Li C, Chen J, Lin H, Zhang Y, Xue W, Wu Y, Xu Y, Sui W, Dai Y. HBV integrated genomic characterization revealed hepatocyte genomic alterations in HBV-related hepatocellular carcinomas. Mol Clin Oncol 2020; 13:79. [PMID: 33062269 PMCID: PMC7549396 DOI: 10.3892/mco.2020.2149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 08/28/2020] [Indexed: 12/04/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most lethal malignancies that is closely associated with the Hepatitis B virus (HBV). HBV integration into host genomes can induce instability and the aberrant expression of human genomic DNA. To directly assess HBV integration breakpoints at whole genome level, four small sequencing libraries were constructed and the HBV integration profiles of four patients with HCC were characterized. In total, the current study identified 11,800,974, 11,216,998, 11,026,546 and 11,607,842 clean reads for patients 1-3 and 4, respectively, of which 92.82, 95.95, 97.21 and 97.29% were properly aligned to the hybrid reference genome. In addition, 220 HBV integration events were detected from the tumor tissues of four patients with HCC and an average of 55 breakpoints per sample was calculated. The results indicated that HBV integration events may be implicated in HCC physiologies and diseases. The results acquired may also provide insight into the pathogenesis of HCC, which may be valuable for future HCC therapy.
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Affiliation(s)
- Ming Yang
- Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory, Nephrology Department of Guilin No. 924 Hospital, Guilin, Guangxi 541002, P.R. China
| | - Guiqi Yang
- Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory, Nephrology Department of Guilin No. 924 Hospital, Guilin, Guangxi 541002, P.R. China
| | - Fengyan Li
- Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory, Nephrology Department of Guilin No. 924 Hospital, Guilin, Guangxi 541002, P.R. China
| | - Minglin Ou
- Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory, Nephrology Department of Guilin No. 924 Hospital, Guilin, Guangxi 541002, P.R. China.,Clinical Medical Research Center of The Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Chunhong Li
- Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory, Nephrology Department of Guilin No. 924 Hospital, Guilin, Guangxi 541002, P.R. China.,College of Life Science, Guangxi Normal University, Guilin, Guangxi 541004, P.R. China
| | - Jiejing Chen
- Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory, Nephrology Department of Guilin No. 924 Hospital, Guilin, Guangxi 541002, P.R. China
| | - Hua Lin
- Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory, Nephrology Department of Guilin No. 924 Hospital, Guilin, Guangxi 541002, P.R. China
| | - Yue Zhang
- Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory, Nephrology Department of Guilin No. 924 Hospital, Guilin, Guangxi 541002, P.R. China
| | - Wen Xue
- Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory, Nephrology Department of Guilin No. 924 Hospital, Guilin, Guangxi 541002, P.R. China
| | - Yan Wu
- Clinical Medical Research Center of The Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Yong Xu
- Clinical Medical Research Center of The Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Weiguo Sui
- Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory, Nephrology Department of Guilin No. 924 Hospital, Guilin, Guangxi 541002, P.R. China
| | - Yong Dai
- Guangxi Key Laboratory of Metabolic Disease Research, Central Laboratory, Nephrology Department of Guilin No. 924 Hospital, Guilin, Guangxi 541002, P.R. China.,Clinical Medical Research Center of The Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
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Ozkal-Baydin P. How did hepatitis B virus effect the host genome in the last decade? World J Hepatol 2014; 6:851-859. [PMID: 25544872 PMCID: PMC4269904 DOI: 10.4254/wjh.v6.i12.851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 06/06/2014] [Accepted: 10/16/2014] [Indexed: 02/06/2023] Open
Abstract
The principal reason of chronic liver disease, cirrhosis and hepatocellular carcinoma is chronic viral hepatitis all over the world. Hepatitis B virus (HBV) has some mutagenic effects on the host genome. HBV may be exhibiting these mutagenic effects through integrating into the host genome, through its viral proteins or through some epigenetic mechanisms related with HBV proteins. This review aims to summarize the molecular mechanisms used by HBV for effecting host genome determined in the last decade. The focus will be on the effects of integration, HBV proteins, especially HBV X protein and epigenetic mechanisms on the host genome. These interactions between HBV and the host genome also forms the underlying mechanisms of the evolution of hepatocellular carcinoma.
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