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Hu J, Cheng J, Tang L, Hu Z, Luo Y, Li Y, Zhou T, Chang J, Guo JT. Virological Basis for the Cure of Chronic Hepatitis B. ACS Infect Dis 2019; 5:659-674. [PMID: 29893548 DOI: 10.1021/acsinfecdis.8b00081] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hepatitis B virus (HBV) has infected one-third of world population, and 240 million people are chronic carriers, to whom a curative therapy is still not available. Similar to other viruses, persistent HBV infection relies on the virus to exploit host cell functions to support its replication and efficiently evade host innate and adaptive antiviral immunity. Understanding HBV replication and concomitant host cell interactions is thus instrumental for development of therapeutics to disrupt the virus-host interactions critical for its persistence and cure chronic hepatitis B. Although the currently available cell culture systems of HBV infection are refractory to genome-wide high throughput screening of key host cellular factors essential for and/or regulating HBV replication, classic one-gene (or pathway)-at-a-time studies in the last several decades have already revealed many aspects of HBV-host interactions. An overview of the landscape of HBV-hepatocyte interaction indicates that, in addition to more tightly suppressing viral replication by directly targeting viral proteins, disruption of key viral-host cell interactions to eliminate or inactivate the covalently closed circular (ccc) DNA, the most stable HBV replication intermediate that exists as an episomal minichromosome in the nucleus of infected hepatocyte, is essential to achieve a functional cure of chronic hepatitis B. Moreover, therapeutic targeting of integrated HBV DNA and their transcripts may also be required to induce hepatitis B virus surface antigen (HBsAg) seroclearance and prevent liver carcinogenesis.
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Affiliation(s)
- Jin Hu
- Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, 1 Tian-tan Xi-li, Beijing, 100050, China
| | - Junjun Cheng
- Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Liudi Tang
- Microbiology and Immunology Graduate Program, Drexel University College of Medicine, 2900 West Queen Lane, Philadelphia, Pennsylvania 19129, United States
| | - Zhanying Hu
- Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Yue Luo
- Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
- Institute of Hepatology, Second Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, China
| | - Yuhuan Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, 1 Tian-tan Xi-li, Beijing, 100050, China
| | - Tianlun Zhou
- Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Jinhong Chang
- Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Ju-Tao Guo
- Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
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52
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Liu S, Zhou B, Valdes JD, Sun J, Guo H. Serum Hepatitis B Virus RNA: A New Potential Biomarker for Chronic Hepatitis B Virus Infection. Hepatology 2019; 69:1816-1827. [PMID: 30362148 PMCID: PMC6438723 DOI: 10.1002/hep.30325] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/16/2018] [Indexed: 12/24/2022]
Abstract
Chronic hepatitis B infection is one of the major etiological causes of liver failure, cirrhosis, and hepatocellular carcinoma (HCC) worldwide. This condition cannot be completely cured by currently available drugs due to the persistent existence of hepatitis B virus (HBV) covalently closed circular DNA (cccDNA), the bona fide transcription template for HBV RNAs, in infected hepatocytes. Because quantifying cccDNA per se requires an invasive procedure, serum biomarkers reflecting intrahepatic cccDNA activity are warranted. Recently, a growing body of research suggests that the circulating HBV RNA may serve as a serum biomarker for HBV infection, treatment, and prognosis. In order to delineate the molecular and clinical characteristics of serum HBV RNA, we systematically reviewed the available literature on serum HBV RNA dating back to the early 1990s. In this review, we summarize the reported serum HBV RNA quantification methods and discuss the potential HBV RNA species in patient serum. We also compare the reported correlations of serum HBV RNA with other serological markers, including HBV DNA, hepatitis B surface antigen, e antigen, and core-related antigen, as well as their correlations with intrahepatic cccDNA, to assess their potential in clinical applications. Future directions for serum HBV RNA research are also discussed.
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Affiliation(s)
- Shi Liu
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Bin Zhou
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China,Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Juan D. Valdes
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jian Sun
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China,Corresponding Authors: Haitao Guo, Ph.D: Department of Microbiology & Immunology, Indiana University School of Medicine, 635 Barnhill Dr., Indianapolis, IN 46202, USA. Phone: 317-274-0530, Fax: 317-278-3331, ; Jian Sun, M.D/Ph.D: Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China. Phone: 086-20-62787432, Fax: 086-20-62786530,
| | - Haitao Guo
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA,Corresponding Authors: Haitao Guo, Ph.D: Department of Microbiology & Immunology, Indiana University School of Medicine, 635 Barnhill Dr., Indianapolis, IN 46202, USA. Phone: 317-274-0530, Fax: 317-278-3331, ; Jian Sun, M.D/Ph.D: Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China. Phone: 086-20-62787432, Fax: 086-20-62786530,
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53
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Ono R, Yasuhiko Y, Aisaki KI, Kitajima S, Kanno J, Hirabayashi Y. Exosome-mediated horizontal gene transfer occurs in double-strand break repair during genome editing. Commun Biol 2019; 2:57. [PMID: 30775458 PMCID: PMC6368560 DOI: 10.1038/s42003-019-0300-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 01/11/2019] [Indexed: 01/05/2023] Open
Abstract
The CRISPR-Cas9 system has been successfully applied in many organisms as a powerful genome-editing tool. Undoubtedly, it will soon be applied to human genome editing, including gene therapy. We have previously reported that unintentional DNA sequences derived from retrotransposons, genomic DNA, mRNA and vectors are captured at double-strand breaks (DSBs) sites when DSBs are introduced by the CRISPR-Cas9 system. Therefore, it is possible that unintentional insertions associated with DSB repair represent a potential risk for human genome editing gene therapies. To address this possibility, comprehensive sequencing of DSB sites was performed. Here, we report that exosome-mediated horizontal gene transfer occurs in DSB repair during genome editing. Exosomes are present in all fluids from living animals, including seawater and breathing mammals, suggesting that exosome-mediated horizontal gene transfer is the driving force behind mammalian genome evolution. The findings of this study highlight an emerging new risk for this leading-edge technology.
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Affiliation(s)
- Ryuichi Ono
- Division of Cellular and Molecular Toxicology, Center for Biological Safety and Research (CBSR), National Institute of Health Sciences (NIHS), 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa-ken 210-9501 Japan
| | - Yukuto Yasuhiko
- Division of Cellular and Molecular Toxicology, Center for Biological Safety and Research (CBSR), National Institute of Health Sciences (NIHS), 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa-ken 210-9501 Japan
| | - Ken-ichi Aisaki
- Division of Cellular and Molecular Toxicology, Center for Biological Safety and Research (CBSR), National Institute of Health Sciences (NIHS), 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa-ken 210-9501 Japan
| | - Satoshi Kitajima
- Division of Cellular and Molecular Toxicology, Center for Biological Safety and Research (CBSR), National Institute of Health Sciences (NIHS), 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa-ken 210-9501 Japan
| | - Jun Kanno
- Division of Cellular and Molecular Toxicology, Center for Biological Safety and Research (CBSR), National Institute of Health Sciences (NIHS), 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa-ken 210-9501 Japan
- Japan Bioassay Research Center, Japan Organization of Occupational Health and Safety, 2445, Hirasawa, Hadano-shi, Kanagawa-ken 257-0015 Japan
| | - Yoko Hirabayashi
- Division of Cellular and Molecular Toxicology, Center for Biological Safety and Research (CBSR), National Institute of Health Sciences (NIHS), 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa-ken 210-9501 Japan
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54
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Ruan P, Dai X, Sun J, He C, Huang C, Zhou R, Cao Z, Ye L. Different types of viral‑host junction found in HBV integration breakpoints in HBV‑infected patients. Mol Med Rep 2018; 19:1410-1416. [PMID: 30535432 PMCID: PMC6323230 DOI: 10.3892/mmr.2018.9709] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 10/29/2018] [Indexed: 12/13/2022] Open
Abstract
The present study surveyed the characteristics of hepatitis B virus (HBV) integration in the liver genomes of patients with acute hepatitis B (AHB), carriers of inactive hepatitis B surface antigen (HBsAg), and patients with chronic hepatitis B (CHB) receiving antiviral treatment. 'Short‑read' whole genome sequencing (WGS) with an average of 4,879x coverage for HBV integration was performed in three patients with AHB, two carriers of inactive HBsAg, and 13 patients with CHB receiving antiviral treatment. Conventional polymerase chain reaction and Sanger sequencing were used to verify integration breakpoints supported by at least two paired‑end reads, and viral‑host chimeric transcripts were surveyed simultaneously. HBV integration breakpoints were 100% identified with an average of 138.2±379.9 breakpoints per sample. The numbers of HBV integration breakpoints were positively associated with the sequencing depth coverage numbers and levels of intrahepatic covalently closed circular DNA, respectively (P<0.0001 and P<0.0001). Four types of viral‑host junction in 14 HBV integration breakpoints were detected (two viral junctions mapped in the HBs gene, one in the Precore gene, and others within the HBx gene): Forward simple junction, reverse simple junction, forward and reverse complicated junction, and microhomology were found in many of the junctions. Expression of viral‑human chimeric transcripts was observed in several breakpoints, including the HBs gene. As a result, HBV can integrate into the host gene in the same manner as non‑homologous end joining and microhomology‑mediated end joining with numerous sites, and a close association may exist between HBV integration and patient prognosis. HBx integration may be indispensable for viral‑host chimeric transcription and HBsAg may be produced from integrated DNA.
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Affiliation(s)
- Peng Ruan
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Xiufang Dai
- Department of Breast Surgery, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, P.R. China
| | - Jun Sun
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Chunping He
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Chao Huang
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Rui Zhou
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Zhuo Cao
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
| | - Lan Ye
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430060, P.R. China
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55
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Mitra B, Thapa RJ, Guo H, Block TM. Host functions used by hepatitis B virus to complete its life cycle: Implications for developing host-targeting agents to treat chronic hepatitis B. Antiviral Res 2018; 158:185-198. [PMID: 30145242 PMCID: PMC6193490 DOI: 10.1016/j.antiviral.2018.08.014] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/21/2018] [Accepted: 08/22/2018] [Indexed: 02/06/2023]
Abstract
Similar to other mammalian viruses, the life cycle of hepatitis B virus (HBV) is heavily dependent upon and regulated by cellular (host) functions. These cellular functions can be generally placed in to two categories: (a) intrinsic host restriction factors and innate defenses, which must be evaded or repressed by the virus; and (b) gene products that provide functions necessary for the virus to complete its life cycle. Some of these functions may apply to all viruses, but some may be specific to HBV. In certain cases, the virus may depend upon the host function much more than does the host itself. Knowing which host functions regulate the different steps of a virus' life cycle, can lead to new antiviral targets and help in developing novel treatment strategies, in addition to improving a fundamental understanding of viral pathogenesis. Therefore, in this review we will discuss known host factors which influence key steps of HBV life cycle, and further elucidate therapeutic interventions targeting host-HBV interactions.
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Affiliation(s)
- Bidisha Mitra
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Haitao Guo
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA.
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56
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Yang L, Ye S, Zhao X, Ji L, Zhang Y, Zhou P, Sun J, Guan Y, Han Y, Ni C, Hu X, Liu W, Wang H, Zhou B, Huang J. Molecular Characterization of HBV DNA Integration in Patients with Hepatitis and Hepatocellular Carcinoma. J Cancer 2018; 9:3225-3235. [PMID: 30271481 PMCID: PMC6160693 DOI: 10.7150/jca.26052] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 07/06/2018] [Indexed: 01/02/2023] Open
Abstract
Infection by chronic hepatitis B virus (HBV) is one of the major causes of liver cirrhosis and primary hepatocellular carcinoma (HCC). Viral DNA integration into the host cell genome is a key mechanism of hepatocarcinogenesis. However, the molecular characterization and the potential clinical implications of HBV DNA integration into patients suffering from different hepatitis and HCC remain unclear. In this study, we analyzed HBV integrations in patients with hepatitis B and HCC using HBV probe-based capturing and next-generation sequencing. The results revealed that the sizes of the HBV integrations ranged from 28 bp to 3215 bp, including the full-length HBV DNA sequence. The integration breakpoints were preferentially distributed in the viral enhancer, X protein, and core protein regions of the HBV genome. The number of HBV integrations followed an increasing trend from hepatitis to HCC, which was positively correlated with the HBV virus load in patients with hepatitis. The number of HBV integrations in the HBeAg positive chronic hepatitis B group was significantly greater than that in the other hepatitis B groups (P < 0.05). However, the relative abundance of HBV integrations was significantly higher in HCC tissues than in the adjacent liver tissues. Interestingly, 61.6% (8/13) of HBV-human DNA integration fragments could be detected at the RNA level. Our results also showed that HBV integration-targeted genes (ITGs) were significantly enriched in many cancer-related pathways, such as MAPK, extracellular matrix (ECM)-receptor interaction, and the hedgehog signaling pathway. Individuals with HBV integrations exhibited shorter disease-free survival (DFS) and overall survival (OS) than those without HBV integrations in some ITGs including LINC00293 (long intergenic non-protein coding RNA 293; DFS P = 0.008, OS P = 0.009), FSHB (follicle stimulating hormone beta subunit; DFS P = 0.05, OS P = 0.186), and LPHN3 (latrophilin-3; DFS P = 0.493, OS P = 0.033). This study determined the underlying mechanism of HBV DNA integration in liver diseases and laid the foundation for future studies on the pathogenesis of liver cancer.
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Affiliation(s)
- Liu Yang
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province and Key Laboratory of Gastroenterology of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical Colleg, Shang Tang Road 158, Hangzhou 310014, Zhejiang, P. R China
| | - Song Ye
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Qing Chun Road 79, Hangzhou 310003, Zhejiang, P. R. China
| | - Xinyi Zhao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University School of Medicine, Hangzhou, 310003, Zhejiang, P. R. China
| | - Liyan Ji
- Binhai Genomics Institute, BGI-Tianjin, Tianjin, 300308, China
| | - Yinxin Zhang
- Binhai Genomics Institute, BGI-Tianjin, Tianjin, 300308, China
| | - Pingyu Zhou
- STD Institute, Shanghai Skin Disease Hospital, Tong Ji University, Shanghai, China
| | - Jun Sun
- STD Institute, Shanghai Skin Disease Hospital, Tong Ji University, Shanghai, China
| | - Yanfang Guan
- Binhai Genomics Institute, BGI-Tianjin, Tianjin, 300308, China
| | - Yingxin Han
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Chinese National Human Genome Center at Shanghai. Shanghai Jiao Tong University, Shanghai, 200240, China.,Binhai Genomics Institute, BGI-Tianjin, Tianjin, 300308, China
| | - Chao Ni
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province and Key Laboratory of Gastroenterology of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical Colleg, Shang Tang Road 158, Hangzhou 310014, Zhejiang, P. R China
| | - Xiaoge Hu
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province and Key Laboratory of Gastroenterology of Zhejiang Province, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical Colleg, Shang Tang Road 158, Hangzhou 310014, Zhejiang, P. R China
| | - Weilong Liu
- Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People's Hospital, Guangdong Medical College, Shenzhen, 518112, China
| | - Haiyan Wang
- Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People's Hospital, Guangdong Medical College, Shenzhen, 518112, China
| | - Boping Zhou
- Shenzhen People's Hospital, Second Clinical Medical College of Jinan University. Shenzhen, 518109, China
| | - Jian Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Chinese National Human Genome Center at Shanghai. Shanghai Jiao Tong University, Shanghai, 200240, China.,Shenzhen People's Hospital, Second Clinical Medical College of Jinan University. Shenzhen, 518109, China.,Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People's Hospital, Guangdong Medical College, Shenzhen, 518112, China
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57
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Zhang P, Du HB, Tong GD, Li XK, Sun XH, Chi XL, Xing YF, Zhou ZH, Li Q, Chen B, Wang H, Wang L, Jin H, Mao DW, Wang XB, Wu QK, Li FP, Hu XY, Lu BJ, Yang ZY, Zhang MX, Shi WB, He Q, Li Y, Jiang KP, Xue JD, Li XD, Jiang JM, Lu W, Tian GJ, Hu ZB, Guo JC, Li CZ, Deng X, Luo XL, Li FY, Zhang XW, Zheng YJ, Zhao G, Wang LC, Wu JH, Guo H, Mi YQ, Gong ZJ, Wang CB, Jiang F, Guo P, Yang XZ, Shi WQ, Yang HZ, Zhou Y, Sun NN, Jiao YT, Gao YQ, Zhou DQ, Ye YA. Serum hepatitis B surface antigen correlates with fibrosis and necroinflammation: A multicentre perspective in China. J Viral Hepat 2018; 25:1017-1025. [PMID: 29624802 DOI: 10.1111/jvh.12903] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 02/22/2018] [Indexed: 12/20/2022]
Abstract
The kinetics of serum hepatitis B surface antigen (HBsAg) during the natural history of hepatitis B virus (HBV) infection has been studied, but the factors affecting them remain unclear. We aimed to investigate the factors affecting HBsAg titres, using data from multicentre, large-sized clinical trials in China. The baseline data of 1795 patients in 3 multicentre trials were studied, and the patients were classified into 3 groups: hepatitis B early antigen (HBeAg)-positive chronic HBV infection (n = 588), HBeAg-positive chronic hepatitis B (n = 596), and HBeAg-negative chronic hepatitis B (n = 611). HBsAg titres in the different phases were compared, and multiple linear progression analyses were performed to investigate the implicated factors. HBsAg titres varied significantly in different phases (P = .000), with the highest (4.60 log10 IU/mL [10%-90% confidence interval: 3.52 log10 IU/mL-4.99 log10 IU/mL]) in patients with HBeAg-positive chronic HBV infection. In all phases, age and HBV DNA were correlated with serum HBsAg level. In HBeAg-positive chronic hepatitis B patients, a negative correlation between HBsAg titres and fibrosis stage was observed. Alanine amonitransferase or necroinflammatory activity was also correlated with HBsAg titres in HBeAg-negative chronic hepatitis B patients. In conclusion, decreased HBsAg titres may be associated with advancing fibrosis in HBeAg-positive chronic hepatitis B patients or increased necroinflammation in those with HBeAg-negative chronic hepatitis B. Our findings may help clinicians better understand the kinetics of HBsAg and provide useful insights into the management of this disease.
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Affiliation(s)
- P Zhang
- Department of Gastroenterology and Hepatology, Beijing University of Chinese Medicine Affiliated Dongzhimen Hospital, Beijing, China.,Institute of liver disease, Beijing University of Chinese Medicine Affiliated Dongzhimen Hospital, Beijing, China
| | - H B Du
- Department of Gastroenterology and Hepatology, Beijing University of Chinese Medicine Affiliated Dongzhimen Hospital, Beijing, China.,Institute of liver disease, Beijing University of Chinese Medicine Affiliated Dongzhimen Hospital, Beijing, China
| | - G D Tong
- Department of Hepatology, Shenzhen Hospital of Traditional Chinese Medicine, Shenzhen, Guangdong Province, China
| | - X K Li
- Department of Gastroenterology and Hepatology, Beijing University of Chinese Medicine Affiliated Dongzhimen Hospital, Beijing, China.,Institute of liver disease, Beijing University of Chinese Medicine Affiliated Dongzhimen Hospital, Beijing, China
| | - X H Sun
- Department of Hepatology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - X L Chi
- Department of Hepatology, Guangdong Hospital of Traditional Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Y F Xing
- Department of Hepatology, Shenzhen Hospital of Traditional Chinese Medicine, Shenzhen, Guangdong Province, China
| | - Z H Zhou
- Department of Hepatology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Q Li
- The Fourth Ward, Fuzhou Infectious Disease Hospital, Fuzhou, Fujian Province, China
| | - B Chen
- Department of Hepatology, The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan Province, China
| | - H Wang
- Department of Infectious Disease, Ruijin Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - L Wang
- Department of Hepatology, Chengdu Infectious Disease Hospital, Chengdu, Sichuan Province, China
| | - H Jin
- Department of Integrated Traditional and Western Medicine on Liver Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - D W Mao
- Department of Hepatology, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning, Guangxi Province, China
| | - X B Wang
- Department of Integrated Traditional and Western Medicine on Liver Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Q K Wu
- The First Department of Hepatology, Shenzhen No. 3 People's Hospital, Shenzhen, Guangdong Province, China
| | - F P Li
- Department of Hepatology, Shanxi Hospital of Traditional Chinese Medicine, Xi'an, Shanxi Province, China
| | - X Y Hu
- Department of Infectious Disease, The Affiliated Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan Province, China
| | - B J Lu
- Department of Hepatology, The Affiliated Hospital of Liaoning University of Traditional Chinese Medicine, Shenyang, Liaoning Province, China
| | - Z Y Yang
- Department of Integrated Traditional and Western Medicine on Liver Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - M X Zhang
- Department of Integrated Traditional and Western Medicine on Liver Diseases, Shenyang Infectious Disease Hospital, Shenyang, Liaoning Province, China
| | - W B Shi
- Department of Infectious Disease, The First Affiliated Hospital of Anhui Academy of Chinese Medicine, Hefei, Anhui Province, China
| | - Q He
- The First Department of Hepatology, Shenzhen No. 3 People's Hospital, Shenzhen, Guangdong Province, China
| | - Y Li
- Department of Hepatology, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong Province, China
| | - K P Jiang
- Department of Hepatology, Foshan Hospital of Traditional Chinese Medicine, Foshan, Guangdong Province, China
| | - J D Xue
- Department of Hepatology, Shanxi Hospital of Traditional Chinese Medicine, Xi'an, Shanxi Province, China
| | - X D Li
- Department of Hepatology, Hubei Province Hospital of Traditional Chinese Medicine, Wuhan, Hubei Province, China
| | - J M Jiang
- Department of Hepatology, Guangdong Hospital of Traditional Chinese Medicine, Guangzhou, Guangdong Province, China
| | - W Lu
- Department of Infectious Disease, Tianjin Infectious Disease Hospital, Tianjin, China
| | - G J Tian
- Department of Hepatology, Guangdong Hospital of Traditional Chinese Medicine, Guangzhou, Guangdong Province, China
| | - Z B Hu
- Department of Hepatology, The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning, Guangxi Province, China
| | - J C Guo
- Department of Hepatology, Hangzhou No. 6 People's Hospital, Hangzhou, Zhejiang Province, China
| | - C Z Li
- Department of Infectious Disease, Changhai Hospital, The Second Military Medical University, Shanghai, China
| | - X Deng
- Department of Hepatology, Ruikang Hospital, Guangxi University of Chinese Medicine, Nanning, Guangxi Province, China
| | - X L Luo
- Department of Hepatology, Hubei Province Hospital of Traditional Chinese Medicine, Wuhan, Hubei Province, China
| | - F Y Li
- Treatment and Research Center of Infectious Disease, 302 Military Hospital of China, Beijing, China
| | - X W Zhang
- Treatment and Research Center of Infectious Disease, 302 Military Hospital of China, Beijing, China
| | - Y J Zheng
- Department of Hepatology, Shenzhen Hospital of Traditional Chinese Medicine, Shenzhen, Guangdong Province, China
| | - G Zhao
- Department of Hepatology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - L C Wang
- Center of Infectious Disease, Huaxi Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - J H Wu
- Center of Hepatology, Xiamen Hospital of Traditional Chinese Medicine, Xiamen, Fujian Province, China
| | - H Guo
- Department of Hepatology, The First Affiliated Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Y Q Mi
- Department of Infectious Disease, Tianjin Infectious Disease Hospital, Tianjin, China
| | - Z J Gong
- Department of Infectious Disease, Hubei People's Hospital, Wuhan, Hubei Province, China
| | - C B Wang
- The Fourth Department of Infectious Disease, Linyi People's Hospital, Linyi, Shandong Province, China
| | - F Jiang
- Department of Gastroenterology and Hepatology, Beijing University of Chinese Medicine Affiliated Dongzhimen Hospital, Beijing, China.,Institute of liver disease, Beijing University of Chinese Medicine Affiliated Dongzhimen Hospital, Beijing, China
| | - P Guo
- Department of Hepatology, Xiyuan Hospital, China Academy of Chinese medical Science, Beijing, China
| | - X Z Yang
- Institute of liver disease, Beijing University of Chinese Medicine Affiliated Dongzhimen Hospital, Beijing, China.,Department of Infectious Disease, Beijing University of Chinese Medicine Affiliated Dongzhimen Hospital, Beijing, China
| | - W Q Shi
- Department of Hepatology, Xinhua Hospital, Zhejiang University of Traditional Chinese medicine, Hangzhou, Zhejiang Province, China
| | - H Z Yang
- Department of Traditional Chinese medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Y Zhou
- Department of Hepatology, Qingdao No. 6 People's Hospital, Qingdao, Shandong Province, China
| | - N N Sun
- Department of Hepatology, Beijing Hospital of Traditional Chinese Medicine, Beijing, China
| | - Y T Jiao
- Shunyi Hospital of Traditional Chinese Medicine, Beijing, China
| | - Y Q Gao
- Department of Hepatology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - D Q Zhou
- Department of Hepatology, Shenzhen Hospital of Traditional Chinese Medicine, Shenzhen, Guangdong Province, China
| | - Y A Ye
- Department of Gastroenterology and Hepatology, Beijing University of Chinese Medicine Affiliated Dongzhimen Hospital, Beijing, China.,Institute of liver disease, Beijing University of Chinese Medicine Affiliated Dongzhimen Hospital, Beijing, China
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58
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Yang Z, Chen S, Xue S, Li X, Hu J, Sun Z, Cui H. Injection of an SV40 transcriptional terminator causes embryonic lethality: a possible zebrafish model for screening nonhomologous end-joining inhibitors. Onco Targets Ther 2018; 11:4945-4953. [PMID: 30154663 PMCID: PMC6103608 DOI: 10.2147/ott.s153576] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Introduction DNA repair by the nonhomologous end joining (NHEJ) pathway promotes tumor recurrence after chemotherapy and radiotherapy. Discovery of rapid and high-throughput techniques to screen for an effective NHEJ inhibitor drug is imperative for the suppression of NHEJ during tumor treatment. However, traditional screening methods are too cumbersome to meet the current need. Zebrafish is an ideal model for drug screening due to the specificity of its early embryonic development and similarity of tumor cell generation. By exploiting the high frequency of NHEJ in early embryonic development, we established a model that uses a transcriptional terminator signal fragment from the Simian virus 40 (SV40) to cause embryonic lethality. SV40 fragment-induced embryonic lethality was alleviated by 5,6-bis ((E)-benzylideneamino)-2-mercaptopyrimidin-4-ol or C18H14N4OS (SCR7), an NHEJ inhibitor. Materials and methods A 122 bp SV40 terminator fragment (10 ng/µL) was microinjected into zebrafish zygotes. SV40 fragment integration into the zebrafish embryonic genome was detected by Southern blot using a DNA probe for the SV40 terminator. Embryonic lethality rates were observed 24 and 48 h after microinjection. A nonhomologous recombinant inhibitor, SCR7 (5 µM), was used to alleviate embryonic lethality. Results Microinjection of zebrafish embryos with the SV40 terminator fragment (10 ng/µL) caused a progressive increase in mortality over time. Using Southern blots, we confirmed that SV40 terminator sequences were integrated into the zebrafish embryonic genome. This phenomenon was effectively alleviated by addition of SCR7. Conclusion Injection of an SV40 terminator into zebrafish embryos may cause embryonic lethality due to NHEJ during early zebrafish development. The high mortality of zebrafish embryos could be alleviated by using the NHEJ inhibitor, SCR7. The zebrafish model presented here is simpler and more convenient than traditional methods of screening for NHEJ inhibitors and can be utilized in large-scale drug screens for NHEJ inhibitors and for the development of novel anticancer drugs.
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Affiliation(s)
- Zhe Yang
- Institute of Epigenetics and Epigenomics, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China, .,College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China,
| | - Shihao Chen
- Institute of Epigenetics and Epigenomics, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China, .,College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China,
| | - Songlei Xue
- Institute of Epigenetics and Epigenomics, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China, .,College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China,
| | - Xinxiu Li
- Institute of Epigenetics and Epigenomics, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China, .,College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China,
| | - Jiang Hu
- Institute of Epigenetics and Epigenomics, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China, .,College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China,
| | - Zhen Sun
- Institute of Epigenetics and Epigenomics, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China, .,College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China,
| | - Hengmi Cui
- Institute of Epigenetics and Epigenomics, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China, .,College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China, .,Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China, .,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China, .,Joint International Research Laboratory of Agricultural & Agri-Product Safety of Educational Ministry of China, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China,
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59
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Sequence analysis of integrated hepatitis B virus DNA during HBeAg-seroconversion. Emerg Microbes Infect 2018; 7:142. [PMID: 30087321 PMCID: PMC6081408 DOI: 10.1038/s41426-018-0145-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/07/2018] [Accepted: 07/10/2018] [Indexed: 02/07/2023]
Abstract
Hepatitis B virus (HBV) integration into the host cell genome occurs early on in infection and reportedly induces pro-oncogenic changes in hepatocytes that drive HCC initiation. However, it remains unclear when these changes occur during hepatocarcinogenesis. Extensive expansion of hepatocyte clones with a selective advantage was shown to occur prior to cancer formation during the HBeAg-seroconversion phase of chronic HBV infection. We hypothesized that since integrations occur during the early stages of infection, cell phenotype could be altered and induce a selection advantage (e.g., through insertional mutagenesis or cis-mediated activation of downstream genes). Here, we analyzed the enrichment of genomic and functional patterns in the cellular host sequence adjacent to HBV DNA integration events. We examined 717 unique integration events detected in patients who have and have not undergone HBeAg-seroconversion (n = 41) or in an in vitro model system. We also used an in silico model to control for detection biases. We showed that the sites of HBV DNA integration were distributed throughout the entire host genome without obvious enrichment of specific structural or functional genomic features in the adjacent cellular genome during HBeAg-seroconversion. Currently, this is the most comprehensive characterization of HBV DNA integration events prior to hepatocarcinogenesis. Our results suggest no significant selection for (or against) specific cellular sites of HBV DNA integration occur during the clonal expansion phase of chronic HBV infection. Thus, HBV DNA integration events likely represent passenger events rather than active drivers of liver cancer, which was previously suggested.
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60
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Budzinska MA, Shackel NA, Urban S, Tu T. Cellular Genomic Sites of Hepatitis B Virus DNA Integration. Genes (Basel) 2018; 9:E365. [PMID: 30037029 PMCID: PMC6071206 DOI: 10.3390/genes9070365] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 07/12/2018] [Accepted: 07/12/2018] [Indexed: 12/14/2022] Open
Abstract
Infection with the Hepatitis B Virus (HBV) is one of the strongest risk-factors for liver cancer (hepatocellular carcinoma, HCC). One of the reported drivers of HCC is the integration of HBV DNA into the host cell genome, which may induce pro-carcinogenic pathways. These reported pathways include: induction of chromosomal instability; generation of insertional mutagenesis in key cancer-associated genes; transcription of downstream cancer-associated cellular genes; and/or formation of a persistent source of viral protein expression (particularly HBV surface and X proteins). The contribution of each of these specific mechanisms towards carcinogenesis is currently unclear. Here, we review the current knowledge of specific sites of HBV DNA integration into the host genome, which sheds light on these mechanisms. We give an overview of previously-used methods to detect HBV DNA integration and the enrichment of integration events in specific functional and structural cellular genomic sites. Finally, we posit a theoretical model of HBV DNA integration during disease progression and highlight open questions in the field.
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Affiliation(s)
| | - Nicholas A Shackel
- Centenary Institute, University of Sydney, Sydney NSW 2050, Australia.
- South Western Sydney Clinical School, University of New South Wales, Liverpool NSW 2170, Australia.
- Gastroenterology, Liverpool Hospital, Liverpool NSW 2170, Australia.
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, Heidelberg Hospital University, D-69120 Heidelberg, Germany.
- German Center for Infection Research (DZIF), Partner Site Heidelberg, D-69120 Heidelberg, Germany.
| | - Thomas Tu
- Department of Infectious Diseases, Molecular Virology, Heidelberg Hospital University, D-69120 Heidelberg, Germany.
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61
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Hepatitis B Virus DNA Integration Occurs Early in the Viral Life Cycle in an In Vitro Infection Model via Sodium Taurocholate Cotransporting Polypeptide-Dependent Uptake of Enveloped Virus Particles. J Virol 2018; 92:JVI.02007-17. [PMID: 29437961 DOI: 10.1128/jvi.02007-17] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 01/30/2018] [Indexed: 02/08/2023] Open
Abstract
Chronic infection by hepatitis B virus (HBV) is the major contributor to liver disease worldwide. Though HBV replicates via a nuclear episomal DNA (covalently closed circular DNA [cccDNA]), integration of HBV DNA into the host cell genome is regularly observed in the liver in infected patients. While reported as a prooncogenic alteration, the mechanism(s) and timing of HBV DNA integration are not well understood, chiefly due to the lack of in vitro infection models that have detectable integration events. In this study, we have established an in vitro system in which integration can be reliably detected following HBV infection. We measured HBV DNA integration using inverse nested PCR in primary human hepatocytes, HepaRG-NTCP, HepG2-NTCP, and Huh7-NTCP cells after HBV infection. Integration was detected in all cell types at a rate of >1 per 10,000 cells, with the most consistent detection in Huh7-NTCP cells. The integration rate remained stable between 3 and 9 days postinfection. HBV DNA integration was efficiently blocked by treatment with a 200 nM concentration of the HBV entry inhibitor Myrcludex B, but not with 10 μM tenofovir, 100 U of interferon alpha, or a 1 μM concentration of the capsid assembly inhibitor GLS4. This suggests that integration of HBV DNA occurs immediately after infection of hepatocytes and is likely independent of de novo HBV genome replication in this model. Site analysis revealed that HBV DNA integrations were distributed over the entire human genome. Further, integrated HBV DNA sequences were consistent with double-stranded linear HBV DNA being the major precursor. Thus, we have established an in vitro system to interrogate the mechanisms of HBV DNA integration.IMPORTANCE Hepatitis B virus (HBV) is a common blood-borne pathogen and, following a chronic infection, can cause liver cancer and liver cirrhosis. Integration of HBV DNA into the host genome occurs in all known members of the Hepadnaviridae family, despite this form not being necessary for viral replication. HBV DNA integration has been reported to drive liver cancer formation and persistence of virus infection. However, when and the mechanism(s) by which HBV DNA integration occurs are not clear. In this study, we have developed and characterized an in vitro system to reliably detect HBV DNA integrations that result from a true HBV infection event and that closely resemble those found in patient tissues. Using this model, we showed that integration occurs when the infection is first established. Importantly, we provide here a system to analyze molecular factors involved in HBV integration, which can be used to develop strategies to halt its formation.
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62
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Gill US, Pallett LJ, Kennedy PTF, Maini MK. Liver sampling: a vital window into HBV pathogenesis on the path to functional cure. Gut 2018; 67:767-775. [PMID: 29331944 PMCID: PMC6058064 DOI: 10.1136/gutjnl-2017-314873] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 11/29/2017] [Accepted: 12/07/2017] [Indexed: 12/12/2022]
Abstract
In order to optimally refine the multiple emerging drug targets for hepatitis B virus (HBV), it is vital to evaluate virological and immunological changes at the site of infection. Traditionally liver biopsy has been the mainstay of HBV disease assessment, but with the emergence of non-invasive markers of liver fibrosis, there has been a move away from tissue sampling. Here we argue that liver biopsy remains an important tool, not only for the clinical assessment of HBV but also for research progress and evaluation of novel agents. The importance of liver sampling has been underscored by recent findings of specialised subsets of tissue-resident immune subsets capable of efficient pathogen surveillance, compartmentalised in the liver and not sampled in the blood. Importantly, the assessment of virological parameters, such as cccDNA quantitation, also requires access to liver tissue. We discuss strategies to maximise information obtained from the site of infection and disease pathology. Fine needle aspirates of the liver may allow longitudinal sampling of the local virus/host landscape. The careful utilisation of liver tissue and aspirates in conjunction with blood will provide critical information in the assessment of new therapeutics for the functional cure of HBV.
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Affiliation(s)
- Upkar S Gill
- Department of Hepatology, Centre for Immunobiology, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | | | - Patrick T F Kennedy
- Department of Hepatology, Centre for Immunobiology, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Mala K Maini
- Division of Infection and Immunity, UCL, London, UK
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63
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Aravalli RN, Steer CJ. CRISPR/Cas9 therapeutics for liver diseases. J Cell Biochem 2018; 119:4265-4278. [PMID: 29266637 DOI: 10.1002/jcb.26627] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 12/18/2017] [Indexed: 12/20/2022]
Abstract
The development of innovative genome editing techniques in recent years has revolutionized the field of biomedicine. Among the novel approaches, the clustered regularly interspaced short palindromic repeat/CRISPR-associated protein (CRISPR/Cas9) technology has become the most popular, in part due to its matchless ability to carry out gene editing at the target site with great precision. With considerable successes in animal and preclinical studies, CRISPR/Cas9-mediated gene editing has paved the way for its use in human trials, including patients with a variety of liver diseases. Gene editing is a logical therapeutic approach for liver diseases because many metabolic and acquired disorders are caused by mutations within a single gene. In this review, we provide an overview on current and emerging therapeutic strategies for the treatment of liver diseases using the CRISPR/Cas9 technology.
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Affiliation(s)
- Rajagopal N Aravalli
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, Minnesota
| | - Clifford J Steer
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota.,Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota
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64
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Block TM, Locarnini S, McMahon BJ, Rehermann B, Peters MG. Use of Current and New Endpoints in the Evaluation of Experimental Hepatitis B Therapeutics. Clin Infect Dis 2018; 64:1283-1288. [PMID: 28200098 DOI: 10.1093/cid/cix129] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/10/2017] [Indexed: 12/15/2022] Open
Abstract
New hepatitis B virus (HBV) therapies are expected to have breakthrough benefit for patients. HBV functional cure is sustained hepatitis B surface antigen loss and anti-HBs gain, with normalization of serum aminotransferases off therapy. Virologic or complete cure additionally includes loss of HBV covalently closed circular DNA. Currently available endpoints of therapy are inadequate to evaluate the efficacy of many of the new therapeutics. Therefore, either new ways of using the existing virologic endpoints and laboratory values or entirely new biomarkers are needed. In this review, we discuss the currently used endpoints, potential new endpoints, as well as what new markers are needed to assess the ability of HBV therapeutics to achieve functional and virologic cure in various phases of HBV infection. In addition, we discuss how patient selection from differing phases of HBV impacts the choice of HBV drug(s) needed to achieve cure.
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Affiliation(s)
- Timothy M Block
- Hepatitis B Foundation and Baruch S. Blumberg Institute, Doylestown, Pennsylvania, USA
| | - Stephen Locarnini
- Victorian Infectious Diseases Reference Laboratory, Doherty Institute, Melbourne, Australia
| | | | - Barbara Rehermann
- Immunology Section, Liver Diseases Branch, National Institutes of Health, Bethesda, Maryland, USA
| | - Marion G Peters
- Department of Medicine, University of California, San Francisco, USA
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65
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Chakrabarty G, Bruce M, Horner M, Wang B, Agarwal K, Carey I. Can quantitative hepatitis B surface antigen levels predict the severity of liver disease in genotype E Patients? J Viral Hepat 2018; 25:80-87. [PMID: 28710798 DOI: 10.1111/jvh.12756] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 06/01/2017] [Indexed: 12/31/2022]
Abstract
The utility of quantitative Hepatitis B surface antigen (qHBsAg) level as a marker of chronic hepatitis B (CHB)-related liver damage is not fully delineated, but is becoming increasingly relevant. Quantitative HBsAg levels are linked with progression of liver disease in HBeAg-negative genotype B and C patients, but it is not clear whether this is consistent across all HBV genotypes. In this single-centre, cross-sectional observational study, we evaluated whether qHBsAg levels can predict the severity of liver disease in genotype E patients. Demographic characteristics, viral, biochemical markers and qHBsAg levels were assessed at time of liver biopsy [all HBV DNA>2000 IU/mL and/or abnormal alanine transaminase (ALT)]. Patients were divided into three groups according to the severity of fibrosis on biopsy: mild (F0-1), moderate (F2-4), severe (F5-6) liver disease and into two groups according to the NI grading, low (NI 0-3) and high inflammation (NI ≥4). A total of 259 HBeAg-negative CHB treatment-naive genotype E patients were studied. The median age of this cohort was 38 years, and 61% were males. Advanced (severe) fibrosis patients had higher ALT, HBV DNA, and lower HBsAg level and qHBsAg/DNA ratio. Patients with NI ≥4 had higher ALT, HBV DNA, but lower qHBsAg/DNA ratio. There was no correlation between HBsAg and HBV DNA levels. Quantitative HBsAg levels were lower in more advanced liver fibrosis. There was no correlation between qHBsAg and HBV DNA levels. This may reflect discordance between viral replication and transcriptional activity or differential HBsAg expression in HBeAg-negative genotype E patients with advanced liver disease.
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Affiliation(s)
| | - Matthew Bruce
- Institute of Liver Studies, King's College Hospital, London, UK
| | - Mary Horner
- Institute of Liver Studies, King's College Hospital, London, UK
| | - Bo Wang
- Institute of Liver Studies, King's College Hospital, London, UK
| | - Kosh Agarwal
- Institute of Liver Studies, King's College Hospital, London, UK
| | - Ivana Carey
- Institute of Liver Studies, King's College Hospital, London, UK
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66
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Long Q, Yan R, Hu J, Cai D, Mitra B, Kim ES, Marchetti A, Zhang H, Wang S, Liu Y, Huang A, Guo H. The role of host DNA ligases in hepadnavirus covalently closed circular DNA formation. PLoS Pathog 2017; 13:e1006784. [PMID: 29287110 PMCID: PMC5747486 DOI: 10.1371/journal.ppat.1006784] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/01/2017] [Indexed: 12/11/2022] Open
Abstract
Hepadnavirus covalently closed circular (ccc) DNA is the bona fide viral transcription template, which plays a pivotal role in viral infection and persistence. Upon infection, the non-replicative cccDNA is converted from the incoming and de novo synthesized viral genomic relaxed circular (rc) DNA, presumably through employment of the host cell’s DNA repair mechanisms in the nucleus. The conversion of rcDNA into cccDNA requires preparation of the extremities at the nick/gap regions of rcDNA for strand ligation. After screening 107 cellular DNA repair genes, we herein report that the cellular DNA ligase (LIG) 1 and 3 play a critical role in cccDNA formation. Ligase inhibitors or functional knock down/out of LIG1/3 significantly reduced cccDNA production in an in vitro cccDNA formation assay, and in cccDNA-producing cells without direct effect on viral core DNA replication. In addition, transcomplementation of LIG1/3 in the corresponding knock-out or knock-down cells was able to restore cccDNA formation. Furthermore, LIG4, a component in non-homologous end joining DNA repair apparatus, was found to be responsible for cccDNA formation from the viral double stranded linear (dsl) DNA, but not rcDNA. In conclusion, we demonstrate that hepadnaviruses utilize the whole spectrum of host DNA ligases for cccDNA formation, which sheds light on a coherent molecular pathway of cccDNA biosynthesis, as well as the development of novel antiviral strategies for treatment of hepatitis B. Hepadnavirus cccDNA is the persistent form of viral genome, and in terms of human hepatitis B virus (HBV), cccDNA is the basis for viral rebound after the cessation of therapy, as well as the elusiveness of a cure with current medications. Therefore, the elucidation of molecular mechanism of cccDNA formation will aid HBV research at both basic and medical levels. In this study, we screened a total of 107 cellular DNA repair genes and identified DNA ligase 1 and 3 as key factors for cccDNA formation from viral relaxed (open) circular DNA. In addition, we found that the cellular DNA ligase 4 is responsible for converting viral double-stranded linear DNA into cccDNA. Our study further confirmed the involvement of host DNA repair machinery in cccDNA formation, and may reveal new antiviral targets for treatment of hepatitis B in future.
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Affiliation(s)
- Quanxin Long
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ran Yan
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Jieli Hu
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Dawei Cai
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Bidisha Mitra
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Elena S. Kim
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Alexander Marchetti
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Hu Zhang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Soujuan Wang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Yuanjie Liu
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Ailong Huang
- Institute for Viral Hepatitis, Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Haitao Guo
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- * E-mail:
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67
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Induction of DNA Damages upon Marek's Disease Virus Infection: Implication in Viral Replication and Pathogenesis. J Virol 2017; 91:JVI.01658-17. [PMID: 28978699 DOI: 10.1128/jvi.01658-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 09/26/2017] [Indexed: 12/23/2022] Open
Abstract
Marek's disease virus (MDV) is a highly contagious alphaherpesvirus that infects chickens and causes a deadly neoplastic disease. We previously demonstrated that MDV infection arrests cells in S phase and that the tegument protein VP22 plays a major role in this process. In addition, expression of VP22 induces double-strand breaks (DSBs) in the cellular DNA, suggesting that DNA damage and the associated cellular response might be favorable for the MDV life cycle. Here, we addressed the role of DNA damage in MDV replication and pathogenesis. We demonstrated that MDV induces DSBs during lytic infection in vitro and in the peripheral blood mononuclear cells of infected animals. Intriguingly, we did not observe DNA damage in latently infected MDV-induced lymphoblastoid cells, while MDV reactivation resulted in the onset of DNA lesions, suggesting that DNA damage and/or the resulting DNA damage response might be required for efficient MDV replication and reactivation. In addition, reactivation was significantly enhanced by the induction of DNA damage using a number of chemicals. Finally, we used recombinant viruses to show that VP22 is required for the induction of DNA damage in vivo and that this likely contributes to viral oncogenesis.IMPORTANCE Marek's disease virus is an oncogenic alphaherpesvirus that causes fatal T-cell lymphomas in chickens. MDV causes substantial losses in the poultry industry and is also used in small-animal models for virus-induced tumor formation. DNA damage not only is implicated in tumor development but also aids in the life cycle of several viruses; however, its role in MDV replication, latency, and reactivation remains elusive. Here, we demonstrate that MDV induces DNA lesions during lytic replication in vitro and in vivo DNA damage was not observed in latently infected cells; however, it was reinitiated during reactivation. Reactivation was significantly enhanced by the induction of DNA damage. Recombinant viruses that lacked the ability to induce DNA damage were defective in their ability to induce tumors, suggesting that DNA damage might also contribute to cellular transformation processes leading to MDV lymphomagenesis.
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68
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Potential use of serum HBV RNA in antiviral therapy for chronic hepatitis B in the era of nucleos(t)ide analogs. Front Med 2017; 11:502-508. [PMID: 29170915 DOI: 10.1007/s11684-017-0590-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 09/22/2017] [Indexed: 01/05/2023]
Abstract
Although the efficacy of nucleos(t)ide analogue (NA) has been confirmed for treatment of chronic hepatitis B, long-term therapy has been recommended due to the high frequency of off-therapy viral DNA rebound and disease relapse. In this review, the RNA virion-like particles of hepatitis B virus (HBV) are integrated into the life cycle of HBV replication, and the potential significance of serum HBV RNA is systematically described. The production of HBV RNA virion-like particles should not be blocked by NA; in this regard, serum HBV RNA is found to be a suitable surrogate marker for the activity of intrahepatic covalently closed circular DNA (cccDNA), particularly among patients receiving NA therapy. Therefore, the concept of virological response is redefined as persistent loss of serum HBV DNA and HBV RNA. In contrast to hepatitis B surface antigen (HBsAg) that can originate from either the cccDNA or the integrated HBV DNA fragment, serum HBV RNA, with pregenomic RNA origination, can only be transcribed from cccDNA. Therefore, the loss of serum HBV RNA would likely be a promising predicator for safe drug discontinuation. The clinical status of consistent loss of serum HBV RNA accompanied with low serum HBsAg levels might be implicated as a "para-functional cure," a status nearly close to the functional cure of chronic hepatitis B, to distinguish the "functional cure" characterized as serum HBsAg loss with or without anti-HBs seroconversion.
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69
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Gómez-Moreno A, Garaigorta U. Hepatitis B Virus and DNA Damage Response: Interactions and Consequences for the Infection. Viruses 2017; 9:v9100304. [PMID: 29048354 PMCID: PMC5691655 DOI: 10.3390/v9100304] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 10/13/2017] [Accepted: 10/18/2017] [Indexed: 12/12/2022] Open
Abstract
Hepatitis B virus (HBV) is a major etiologic agent of acute and chronic hepatitis, and end-stage liver disease. Establishment of HBV infection, progression to persistency and pathogenesis are determined by viral and cellular factors, some of which remain still undefined. Key steps of HBV life cycle e.g., transformation of genomic viral DNA into transcriptionally active episomal DNA (cccDNA) or transcription of viral mRNAs from cccDNA, take place in the nucleus of infected cells and strongly depend on enzymatic activities provided by cellular proteins. In this regard, DNA damage response (DDR) pathways and some DDR proteins are being recognized as important factors regulating the infection. On one hand, HBV highjacks specific DDR proteins to successfully complete some of the steps of its life cycle. On the other hand, HBV subverts DDR pathways to presumably create a cellular environment that favours its replication. Direct consequences of these interactions are: HBV DNA integration into host chromosomal DNA, and accumulation of mutations in host chromosomal DNA that could eventually trigger carcinogenic processes, which would explain in part the incidence of hepatocellular carcinoma in chronically infected patients. Unravelling the interactions that HBV establishes with DDR pathways might help identify new molecular targets for therapeutic intervention.
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Affiliation(s)
- Andoni Gómez-Moreno
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, 28049 Madrid, Spain.
| | - Urtzi Garaigorta
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Darwin 3, 28049 Madrid, Spain.
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain.
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70
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Tu T, Bühler S, Bartenschlager R. Chronic viral hepatitis and its association with liver cancer. Biol Chem 2017; 398:817-837. [PMID: 28455951 DOI: 10.1515/hsz-2017-0118] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/13/2017] [Indexed: 02/06/2023]
Abstract
Chronic infection with hepatitis viruses represents the major causative factor for end-stage liver diseases, including liver cirrhosis and primary liver cancer (hepatocellular carcinoma, HCC). In this review, we highlight the current understanding of the molecular mechanisms that drive the hepatocarcinogenesis associated with chronic hepatitis virus infections. While chronic inflammation (associated with a persistent, but impaired anti-viral immune response) plays a major role in HCC initiation and progression, hepatitis viruses can also directly drive liver cancer. The mechanisms by which hepatitis viruses induce HCC include: hepatitis B virus DNA integration into the host cell genome; metabolic reprogramming by virus infection; induction of the cellular stress response pathway by viral gene products; and interference with tumour suppressors. Finally, we summarise the limitations of hepatitis virus-associated HCC model systems and the development of new techniques to circumvent these shortcomings.
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71
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Chen S, Zheng H, Kishima Y. Genomic fossils reveal adaptation of non-autonomous pararetroviruses driven by concerted evolution of noncoding regulatory sequences. PLoS Pathog 2017; 13:e1006413. [PMID: 28662199 PMCID: PMC5491270 DOI: 10.1371/journal.ppat.1006413] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/16/2017] [Indexed: 11/19/2022] Open
Abstract
The interplay of different virus species in a host cell after infection can affect the adaptation of each virus. Endogenous viral elements, such as endogenous pararetroviruses (PRVs), have arisen from vertical inheritance of viral sequences integrated into host germline genomes. As viral genomic fossils, these sequences can thus serve as valuable paleogenomic data to study the long-term evolutionary dynamics of virus-virus interactions, but they have rarely been applied for this purpose. All extant PRVs have been considered autonomous species in their parasitic life cycle in host cells. Here, we provide evidence for multiple non-autonomous PRV species with structural defects in viral activity that have frequently infected ancient grass hosts and adapted through interplay between viruses. Our paleogenomic analyses using endogenous PRVs in grass genomes revealed that these non-autonomous PRV species have participated in interplay with autonomous PRVs in a possible commensal partnership, or, alternatively, with one another in a possible mutualistic partnership. These partnerships, which have been established by the sharing of noncoding regulatory sequences (NRSs) in intergenic regions between two partner viruses, have been further maintained and altered by the sequence homogenization of NRSs between partners. Strikingly, we found that frequent region-specific recombination, rather than mutation selection, is the main causative mechanism of NRS homogenization. Our results, obtained from ancient DNA records of viruses, suggest that adaptation of PRVs has occurred by concerted evolution of NRSs between different virus species in the same host. Our findings further imply that evaluation of within-host NRS interactions within and between populations of viral pathogens may be important.
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Affiliation(s)
- Sunlu Chen
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Huizhen Zheng
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yuji Kishima
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
- * E-mail:
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72
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Peters MG, Locarnini S. New Direct-Acting Antiviral Agents and Immunomodulators for Hepatitis B Virus Infection. Gastroenterol Hepatol (N Y) 2017; 13:348-356. [PMID: 28690451 PMCID: PMC5495044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Chronic hepatitis B (CHB) affects over 350 million individuals worldwide and is the most common cause of liver cancer. In the United States, CHB affects at least 2 to 3 million individuals, and current therapies can control the disease but not cure it. There are over 30 new molecules being studied in CHB in preclinical to phase 2 studies, targeting specific parts of the hepatitis B virus (HBV) life cycle and the host immune response. When discussing new therapies for CHB, it is critical to understand both the various phases of CHB and the life cycle of HBV. This article will discuss both of these issues, as well as mechanisms of action of potential therapies and possible ways to combine such therapies in the various phases of CHB.
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Affiliation(s)
- Marion G Peters
- Dr Peters is a professor of medicine and chief of hepatology research in the Department of Medicine at the University of California in San Francisco, California. Dr Locarnini is a professor of microbiology and immunology at the University of Melbourne and is director of the WHO Regional Reference Laboratory for Hepatitis B within the Victorian Infectious Diseases Reference Laboratory at the Doherty Institute in Melbourne, Australia
| | - Stephen Locarnini
- Dr Peters is a professor of medicine and chief of hepatology research in the Department of Medicine at the University of California in San Francisco, California. Dr Locarnini is a professor of microbiology and immunology at the University of Melbourne and is director of the WHO Regional Reference Laboratory for Hepatitis B within the Victorian Infectious Diseases Reference Laboratory at the Doherty Institute in Melbourne, Australia
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73
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Schreiner S, Nassal M. A Role for the Host DNA Damage Response in Hepatitis B Virus cccDNA Formation-and Beyond? Viruses 2017; 9:v9050125. [PMID: 28531167 PMCID: PMC5454437 DOI: 10.3390/v9050125] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/16/2017] [Accepted: 05/18/2017] [Indexed: 12/12/2022] Open
Abstract
Chronic hepatitis B virus (HBV) infection puts more than 250 million people at a greatly increased risk to develop end-stage liver disease. Like all hepadnaviruses, HBV replicates via protein-primed reverse transcription of a pregenomic (pg) RNA, yielding an unusually structured, viral polymerase-linked relaxed-circular (RC) DNA as genome in infectious particles. Upon infection, RC-DNA is converted into nuclear covalently closed circular (ccc) DNA. Associating with cellular proteins into an episomal minichromosome, cccDNA acts as template for new viral RNAs, ensuring formation of progeny virions. Hence, cccDNA represents the viral persistence reservoir that is not directly targeted by current anti-HBV therapeutics. Eliminating cccDNA will thus be at the heart of a cure for chronic hepatitis B. The low production of HBV cccDNA in most experimental models and the associated problems in reliable cccDNA quantitation have long hampered a deeper understanding of cccDNA molecular biology. Recent advancements including cccDNA-dependent cell culture systems have begun to identify select host DNA repair enzymes that HBV usurps for RC-DNA to cccDNA conversion. While this list is bound to grow, it may represent just one facet of a broader interaction with the cellular DNA damage response (DDR), a network of pathways that sense and repair aberrant DNA structures and in the process profoundly affect the cell cycle, up to inducing cell death if repair fails. Given the divergent interactions between other viruses and the DDR it will be intriguing to see how HBV copes with this multipronged host system.
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Affiliation(s)
- Sabrina Schreiner
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg, D-85764 Munich, Germany.
| | - Michael Nassal
- Dept. of Internal Medicine II/Molecular Biology, University Hospital Freiburg, Hugstetter Str. 55, D-79106 Freiburg, Germany.
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74
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Hensel KO, Rendon JC, Navas MC, Rots MG, Postberg J. Virus-host interplay in hepatitis B virus infection and epigenetic treatment strategies. FEBS J 2017; 284:3550-3572. [PMID: 28457020 DOI: 10.1111/febs.14094] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 03/25/2017] [Accepted: 04/26/2017] [Indexed: 12/11/2022]
Abstract
Worldwide, chronic hepatitis B virus (HBV) infection is a major health problem and no cure exists. Importantly, hepatocyte intrusion by HBV particles results in a complex deregulation of both viral and host cellular genetic and epigenetic processes. Among the attempts to develop novel therapeutic approaches against HBV infection, several options targeting the epigenomic regulation of HBV replication are gaining attention. These include the experimental treatment with 'epidrugs'. Moreover, as a targeted approach, the principle of 'epigenetic editing' recently is being exploited to control viral replication. Silencing of HBV by specific rewriting of epigenetic marks might diminish viral replication, viremia, and infectivity, eventually controlling the disease and its complications. Additionally, epigenetic editing can be used as an experimental tool to increase our limited understanding regarding the role of epigenetic modifications in viral infections. Aiming for permanent epigenetic reprogramming of the viral genome without unspecific side effects, this breakthrough may pave the roads for an ambitious technological pursuit: to start designing a curative approach utilizing manipulative molecular therapies for viral infections in vivo.
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Affiliation(s)
- Kai O Hensel
- HELIOS Medical Centre Wuppertal, Paediatrics Centre, Centre for Clinical & Translational Research (CCTR), Faculty of Health, Centre for Biomedical Education & Research (ZBAF), Witten/Herdecke University, Germany
| | - Julio C Rendon
- Epigenetic Editing, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), The Netherlands.,Grupo de Gastrohepatologia, Facultad de Medicina, Universidad de Antioquia (UdeA), Medellin, Colombia
| | - Maria-Cristina Navas
- Grupo de Gastrohepatologia, Facultad de Medicina, Universidad de Antioquia (UdeA), Medellin, Colombia
| | - Marianne G Rots
- Epigenetic Editing, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), The Netherlands
| | - Jan Postberg
- HELIOS Medical Centre Wuppertal, Paediatrics Centre, Centre for Clinical & Translational Research (CCTR), Faculty of Health, Centre for Biomedical Education & Research (ZBAF), Witten/Herdecke University, Germany
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75
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Kennedy PTF, Litwin S, Dolman GE, Bertoletti A, Mason WS. Immune Tolerant Chronic Hepatitis B: The Unrecognized Risks. Viruses 2017; 9:v9050096. [PMID: 28468285 PMCID: PMC5454409 DOI: 10.3390/v9050096] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/14/2017] [Accepted: 04/20/2017] [Indexed: 12/13/2022] Open
Abstract
Chronic infection with hepatitis B virus (HBV) progresses through multiple phases, including immune tolerant, immune active, immune control, and, in a subset of patients who achieve immune control, reactivation. The first, the immune tolerant phase, is considered to be prolonged in duration but essentially benign in nature, lacking long-term consequences, and thus not recommended for antiviral therapy. This review challenges the notion that the immune tolerant phase is truly benign and considers the possibility that events during this phase may contribute significantly to cirrhosis, hepatocellular carcinoma (HCC), and the premature death of 25% of HBV carriers worldwide. Thus, earlier treatment than recommended by current guidelines should be considered. Low therapeutic coverage exacerbated by restrictive treatment guidelines may facilitate disease progression in many patients but also increase the risk of neonatal and horizontal transmission from untreated mothers to their children. While a prophylactic vaccine exists, there are many areas worldwide where the treatment of adults and the delivery of an effective vaccination course to newborns present difficult challenges.
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Affiliation(s)
- Patrick T F Kennedy
- Centre for Immunobiology, Blizard Institute, Barts and the London School of Medicine & Dentistry, QMUL, London E1 2AT, UK.
| | - Samuel Litwin
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
| | - Grace E Dolman
- Centre for Immunobiology, Blizard Institute, Barts and the London School of Medicine & Dentistry, QMUL, London E1 2AT, UK.
| | - Antonio Bertoletti
- Emerging Infectious Diseases Program, Duke-NUS Graduate Medical School, Singapore.
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76
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Initial sites of hepadnavirus integration into host genome in human hepatocytes and in the woodchuck model of hepatitis B-associated hepatocellular carcinoma. Oncogenesis 2017; 6:e317. [PMID: 28414318 PMCID: PMC5520499 DOI: 10.1038/oncsis.2017.22] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 01/11/2017] [Accepted: 03/07/2017] [Indexed: 12/14/2022] Open
Abstract
Hepatitis B virus (HBV) and the closely related woodchuck hepatitis virus (WHV) are potent carcinogens that trigger development of primary hepatocellular carcinoma (HCC). The initial sites of hepadnavirus–host genome integration, their diversity and kinetics of formation can be central to virus persistence and the initiation and progression of HCC. To recognize the nature of the very early virus–host interactions, we explored de novo infection of human hepatocyte-like HepaRG cells with authentic HBV and naive woodchucks with WHV. HepaRG were analyzed from several minutes post exposure to HBV onwards, whereas woodchuck liver biopsies at 1 or 3 h and 6 weeks post infection with WHV. Inverse PCR and clonal sequencing of the amplicons were applied to identify virus–host genomic junctions. HBV and WHV DNA and their replication intermediates became detectable in one hour after virus exposure. Concomitantly, HBV DNA integration into various host genes was detected. Notably, junctions of HBV X gene with retrotransposon sequences, such as LINE1 and LINE2, became prominent shortly after infection. In woodchucks, insertion of WHV X and preS sequences into host genome was evident at 1 and 3 h post infection (h.p.i.), confirming that hepadnavirus under natural conditions integrates into hepatocyte DNA soon after invasion. The HBV and WHV X gene enhancer II/core promotor sequence most often formed initial junctions with host DNA. Moreover, multiple virus–virus DNA fusions appeared from 1 h.p.i. onwards in both infected hepatocytes and woodchuck livers. In summary, HBV DNA integrates almost immediately after infection with a variety of host’s sequences, among which tandemly repeating non-coding DNAs are common. This study revealed that HBV can engage mobile genetic elements from the beginning of infection to induce pro-oncogenic perturbations throughout the host genome. Such swift virus insertion was also evident in natural hepadnaviral infection in woodchucks.
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77
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Tu T, Budzinska MA, Shackel NA, Urban S. HBV DNA Integration: Molecular Mechanisms and Clinical Implications. Viruses 2017; 9:v9040075. [PMID: 28394272 PMCID: PMC5408681 DOI: 10.3390/v9040075] [Citation(s) in RCA: 257] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/03/2017] [Accepted: 04/04/2017] [Indexed: 02/06/2023] Open
Abstract
Chronic infection with the Hepatitis B Virus (HBV) is a major cause of liver-related morbidity and mortality. One peculiar observation in cells infected with HBV (or with closely‑related animal hepadnaviruses) is the presence of viral DNA integration in the host cell genome, despite this form being a replicative dead-end for the virus. The frequent finding of somatic integration of viral DNA suggests an evolutionary benefit for the virus; however, the mechanism of integration, its functions, and the clinical implications remain unknown. Here we review the current body of knowledge of HBV DNA integration, with particular focus on the molecular mechanisms and its clinical implications (including the possible consequences of replication-independent antigen expression and its possible role in hepatocellular carcinoma). HBV DNA integration is likely to influence HBV replication, persistence, and pathogenesis, and so deserves greater attention in future studies.
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Affiliation(s)
- Thomas Tu
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany.
| | - Magdalena A Budzinska
- Centenary Institute, The University of Sydney, Sydney, NSW 2050, Australia.
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.
| | - Nicholas A Shackel
- Centenary Institute, The University of Sydney, Sydney, NSW 2050, Australia.
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.
- Liverpool Hospital, Gastroenterology, Sydney, NSW 2170, Australia.
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany.
- German Center for Infection Research (DZIF), Heidelberg Partner Site, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany.
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78
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Kennedy PTF, Bertoletti A, Mason WS. Reply. Gastroenterology 2017; 152:1246-1247. [PMID: 28273438 DOI: 10.1053/j.gastro.2017.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Affiliation(s)
- Patrick T F Kennedy
- Centre for Immunobiology, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary, University of London, London, United Kingdom
| | - Antonio Bertoletti
- Emerging Infectious Diseases Program, Duke-National University of Singapore Graduate Medical School, Singapore
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79
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Zhang XX, Li MR, Xi HL, Cao Y, Zhang RW, Zhang Y, Xu XY. Dynamic Characteristics of Serum Hepatitis B Surface Antigen in Chinese Chronic Hepatitis B Patients Receiving 7 Years of Entecavir Therapy. Chin Med J (Engl) 2017; 129:929-35. [PMID: 27064037 PMCID: PMC4831527 DOI: 10.4103/0366-6999.179802] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background: The ultimate goal of hepatitis B treatment is hepatitis B surface antigen (HBsAg) seroclearance. Several factors have been suggested to be associated with the rate of HBsAg reduction in antiviral-naive or lamivudine therapy cohorts. However, there are few studies evaluating the factors during long-term entecavir (ETV) therapy. In the present study, we aimed to evaluate the factors to predict the outcome of ETV therapy for 7 years. Methods: A total of 47 chronic hepatitis B (CHB) patients treated with ETV monotherapy were included in this study. Liver biochemistry, hepatitis B virus (HBV) serological markers, serum HBV DNA, and HBsAg titers were tested at baseline, 3 months, 6 months, and yearly from 1 to 7. The associations between factors and HBsAg reduction were assessed using multivariate tests with repeated measure analysis of variance. Results: At baseline, serum HBsAg levels showed a positive correlation with baseline HBV DNA levels (r = 0.625, P < 0.001). The mean HBsAg titers after ETV treatment were significantly lower than the baseline titers (P ranges from 0.025 to 0.000,000,6). The HBsAg reduction rate during the 1st year was greater compared to after 1 year of treatment (P < 0.05). Multivariate test showed that hepatitis B e antigen (HBeAg) seroclearance and/or HBsAg reduction ≥0.5 log10 IU/ml at 6 months had a high negative predictive value (96.77%) for HBsAg seroclearance (P = 0.002, P = 0.012, respectively). Conclusions: The HBsAg reduction rate during the 1st year was greater than that after 1 year of treatment. Further, HBeAg status and HBsAg levels at month 6 are the optimal factors for the early prediction of HBsAg seroclearance after long-term ETV therapy in CHB patients.
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Affiliation(s)
| | | | | | | | | | | | - Xiao-Yuan Xu
- Department of Infectious Disease, Peking University First Hospital, Beijing 100034, China
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80
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Cornberg M, Wong VWS, Locarnini S, Brunetto M, Janssen HLA, Chan HLY. The role of quantitative hepatitis B surface antigen revisited. J Hepatol 2017; 66:398-411. [PMID: 27575311 DOI: 10.1016/j.jhep.2016.08.009] [Citation(s) in RCA: 242] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 08/09/2016] [Accepted: 08/16/2016] [Indexed: 02/06/2023]
Abstract
In the past 10years, there has been a lot of enthusiasm surrounding the use of serum hepatitis B surface antigen (HBsAg) quantification to predict disease activity and monitor treatment response in chronic hepatitis B. The measurement of HBsAg levels have been standardized in IU/ml, and nowadays it is almost a mandatory measurement due to the development of new antiviral treatments aiming at HBsAg seroclearance, i.e., functional cure of hepatitis B. Recently, there has been an improved understanding of the molecular virology of HBsAg, and particularly the relative roles of covalently closed circular DNA and integrated hepatitis B virus (HBV) DNA. This has shed new light on the interpretation of HBsAg levels in different phases of chronic hepatitis B. HBsAg level can assist the differentiation of immune tolerance and immune clearance in hepatitis B e antigen (HBeAg)-positive patients, and it can predict inactive disease and spontaneous HBsAg seroclearance in HBeAg-negative patients. The determination of HBsAg level is pivotal to individualize pegylated interferon (PegIFN) treatment; it is the key investigation to decide early termination of PegIFN among non-responders. Among patients treated by nucleos(t)ide analogues, responders tend to have dramatic reduction of HBsAg to low levels, which may be followed by HBsAg seroclearance. With newer data on combination treatment of PegIFN and nucleos(t)ide analogues as well as emerging new antiviral agents, HBsAg quantification is expected to become increasingly important to monitor and guide antiviral therapy for chronic hepatitis B.
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Affiliation(s)
- Markus Cornberg
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Germany
| | - Vincent Wai-Sun Wong
- Department of Medicine and Therapeutics, Institute of Digestive Disease and State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong
| | - Stephen Locarnini
- Victorian Infectious Diseases Reference Laboratory (VIDRL), Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Maurizia Brunetto
- Hepatology Unit and Laboratory of Molecular Genetics and Pathology of Hepatitis Viruses, Reference Center of the Tuscany Region for Chronic Liver Disease and Cancer, University Hospital of Pisa, Italy
| | - Harry L A Janssen
- Toronto Center for Liver Disease, Toronto General Hospital, University Health Network, Toronto, Canada
| | - Henry Lik-Yuen Chan
- Department of Medicine and Therapeutics, Institute of Digestive Disease and State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong.
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81
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Tu T, Jilbert AR. Detection of Hepatocyte Clones Containing Integrated Hepatitis B Virus DNA Using Inverse Nested PCR. Methods Mol Biol 2017; 1540:97-118. [PMID: 27975311 DOI: 10.1007/978-1-4939-6700-1_9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Chronic hepatitis B virus (HBV) infection is a major cause of liver cirrhosis and hepatocellular carcinoma (HCC), leading to ~600,000 deaths per year worldwide. Many of the steps that occur during progression from the normal liver to cirrhosis and/or HCC are unknown. Integration of HBV DNA into random sites in the host cell genome occurs as a by-product of the HBV replication cycle and forms a unique junction between virus and cellular DNA. Analyses of integrated HBV DNA have revealed that HCCs are clonal and imply that they develop from the transformation of hepatocytes, the only liver cell known to be infected by HBV. Integrated HBV DNA has also been shown, at least in some tumors, to cause insertional mutagenesis in cancer driver genes, which may facilitate the development of HCC. Studies of HBV DNA integration in the histologically normal liver have provided additional insight into HBV-associated liver disease, suggesting that hepatocytes with a survival or growth advantage undergo high levels of clonal expansion even in the absence of oncogenic transformation. Here we describe inverse nested PCR (invPCR), a highly sensitive method that allows detection, sequencing, and enumeration of virus-cell DNA junctions formed by the integration of HBV DNA. The invPCR protocol is composed of two major steps: inversion of the virus-cell DNA junction and single-molecule nested PCR. The invPCR method is highly specific and inexpensive and can be tailored to DNA extracted from large or small amounts of liver. This procedure also allows detection of genome-wide random integration of any known DNA sequence and is therefore a useful technique for molecular biology, virology, and genetic research.
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Affiliation(s)
- Thomas Tu
- Liver Cell Biology Laboratory, Centenary Institute, Sydney, NSW, 2050, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, 2050, Australia
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Allison R Jilbert
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia.
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82
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Mason WS, Gill US, Litwin S, Zhou Y, Peri S, Pop O, Hong ML, Naik S, Quaglia A, Bertoletti A, Kennedy PT. HBV DNA Integration and Clonal Hepatocyte Expansion in Chronic Hepatitis B Patients Considered Immune Tolerant. Gastroenterology 2016; 151:986-998.e4. [PMID: 27453547 PMCID: PMC8406433 DOI: 10.1053/j.gastro.2016.07.012] [Citation(s) in RCA: 294] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 06/30/2016] [Accepted: 07/07/2016] [Indexed: 12/20/2022]
Abstract
BACKGROUND & AIMS Chronic infection with hepatitis B virus (HBV) progresses through different phases. The first, called the immune-tolerant phase, has been associated with a lack of disease activity. We examined HBV-DNA integration, clonal hepatocyte expansion, HBV antigen expression, and HBV-specific immune responses in patients in the immune-tolerant phase to assess whether this designation is appropriate or if there is evidence of disease activity. METHODS We studied HBV-DNA integration, clonal hepatocyte expansion, and expression of hepatitis B surface antigen and core antigen in liver tissues from 26 patients with chronic HBV infection (ages, 14-39 y); 9 patients were positive for hepatitis B e antigen (HBeAg) in the immune-tolerant phase and were matched for age with 10 HBeAg-positive patients with active disease and 7 HBeAg-negative patients with active disease. Peripheral blood samples were collected and HBV-specific T cells were quantified for each group. RESULTS Detection of HBV antigens differed among groups. However, unexpectedly high numbers of HBV-DNA integrations, randomly distributed among chromosomes, were detected in all groups. Clonal hepatocyte expansion in patients considered immune tolerant also was greater than expected, potentially in response to hepatocyte turnover mediated by HBV-specific T cells, which were detected in peripheral blood cells from patients in all phases of infection. CONCLUSIONS We measured HBV-specific T cells, HBV-DNA integration, and clonal hepatocyte expansion in different disease phases of young patients with chronic hepatitis B, with emphasis on the so-called immune-tolerant phase. A high level of HBV-DNA integration and clonal hepatocyte expansion in patients considered immune tolerant indicated that hepatocarcinogenesis could be underway-even in patients with early stage chronic HBV infection. Our findings do not support the concepts that this phase is devoid of markers of disease progression or that an immune response has not been initiated. We propose that this early phase be called a high-replication, low-inflammation stage. The timing of therapeutic interventions to minimize further genetic damage to the hepatocyte population should be reconsidered.
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Affiliation(s)
| | - Upkar S. Gill
- Centre for Immunobiology, Blizard Institute, Barts and The London School of Medicine & Dentistry, QMUL, London, UK
| | - Samuel Litwin
- Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Yan Zhou
- Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Suraj Peri
- Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Oltin Pop
- Histopathology, Institute of Liver Studies, Kings College Hospital, London, UK
| | - Michelle L.W. Hong
- Emerging Infectious Diseases Program, Duke-NUS Graduate Medical School, Singapore
| | - Sandhia Naik
- Department of Paediatric Gastroenterology & Hepatology, The Royal London Hospital, Barts Health NHS Trust, London, UK
| | - Alberto Quaglia
- Histopathology, Institute of Liver Studies, Kings College Hospital, London, UK
| | - Antonio Bertoletti
- Emerging Infectious Diseases Program, Duke-NUS Graduate Medical School, Singapore
| | - Patrick T.F. Kennedy
- Centre for Immunobiology, Blizard Institute, Barts and The London School of Medicine & Dentistry, QMUL, London, UK
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83
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Lamontagne RJ, Bagga S, Bouchard MJ. Hepatitis B virus molecular biology and pathogenesis. HEPATOMA RESEARCH 2016; 2:163-186. [PMID: 28042609 PMCID: PMC5198785 DOI: 10.20517/2394-5079.2016.05] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
As obligate intracellular parasites, viruses need a host cell to provide a milieu favorable to viral replication. Consequently, viruses often adopt mechanisms to subvert host cellular signaling processes. While beneficial for the viral replication cycle, virus-induced deregulation of host cellular signaling processes can be detrimental to host cell physiology and can lead to virus-associated pathogenesis, including, for oncogenic viruses, cell transformation and cancer progression. Included among these oncogenic viruses is the hepatitis B virus (HBV). Despite the availability of an HBV vaccine, 350-500 million people worldwide are chronically infected with HBV, and a significant number of these chronically infected individuals will develop hepatocellular carcinoma (HCC). Epidemiological studies indicate that chronic infection with HBV is the leading risk factor for the development of HCC. Globally, HCC is the second highest cause of cancer-associated deaths, underscoring the need for understanding mechanisms that regulate HBV replication and the development of HBV-associated HCC. HBV is the prototype member of the Hepadnaviridae family; members of this family of viruses have a narrow host range and predominately infect hepatocytes in their respective hosts. The extremely small and compact hepadnaviral genome, the unique arrangement of open reading frames, and a replication strategy utilizing reverse transcription of an RNA intermediate to generate the DNA genome are distinguishing features of the Hepadnaviridae. In this review, we provide a comprehensive description of HBV biology, summarize the model systems used for studying HBV infections, and highlight potential mechanisms that link a chronic HBV-infection to the development of HCC. For example, the HBV X protein (HBx), a key regulatory HBV protein that is important for HBV replication, is thought to play a cofactor role in the development of HBV-induced HCC, and we highlight the functions of HBx that may contribute to the development of HBV-associated HCC.
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Affiliation(s)
- R. Jason Lamontagne
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
- The Wistar Institute, Philadelphia, PA 19104, USA
| | - Sumedha Bagga
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Michael J. Bouchard
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
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84
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Shapiro JA. Nothing in Evolution Makes Sense Except in the Light of Genomics: Read-Write Genome Evolution as an Active Biological Process. BIOLOGY 2016; 5:E27. [PMID: 27338490 PMCID: PMC4929541 DOI: 10.3390/biology5020027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/20/2016] [Accepted: 06/02/2016] [Indexed: 01/15/2023]
Abstract
The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess "Read-Write Genomes" they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
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85
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Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer. Nat Genet 2016; 48:500-9. [PMID: 27064257 DOI: 10.1038/ng.3547] [Citation(s) in RCA: 507] [Impact Index Per Article: 63.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 03/16/2016] [Indexed: 12/11/2022]
Abstract
Liver cancer, which is most often associated with virus infection, is prevalent worldwide, and its underlying etiology and genomic structure are heterogeneous. Here we provide a whole-genome landscape of somatic alterations in 300 liver cancers from Japanese individuals. Our comprehensive analysis identified point mutations, structural variations (STVs), and virus integrations, in noncoding and coding regions. We discovered mutational signatures related to liver carcinogenesis and recurrently mutated coding and noncoding regions, such as long intergenic noncoding RNA genes (NEAT1 and MALAT1), promoters, CTCF-binding sites, and regulatory regions. STV analysis found a significant association with replication timing and identified known (CDKN2A, CCND1, APC, and TERT) and new (ASH1L, NCOR1, and MACROD2) cancer-related genes that were recurrently affected by STVs, leading to altered expression. These results emphasize the value of whole-genome sequencing analysis in discovering cancer driver mutations and understanding comprehensive molecular profiles of liver cancer, especially with regard to STVs and noncoding mutations.
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86
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Zhao XL, Yang JR, Lin SZ, Ma H, Guo F, Yang RF, Zhang HH, Han JC, Wei L, Pan XB. Serum viral duplex-linear DNA proportion increases with the progression of liver disease in patients infected with HBV. Gut 2016; 65:502-11. [PMID: 26045139 DOI: 10.1136/gutjnl-2014-308989] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 05/19/2015] [Indexed: 02/07/2023]
Abstract
OBJECTIVE HBV has two forms of genomic DNA, relaxed-circular DNA (rcDNA) and duplex-linear DNA (dlDNA). Compared to rcDNA, dlDNA has been demonstrated to integrate more frequently into host cellular chromosomes, which may have oncogenic consequences. However, the dlDNA proportion relative to total HBV DNA and its clinical significance in patients remain to be investigated. DESIGN Based on the structural difference between rcDNA and dlDNA, we developed a peptide nucleic acid (PNA)-mediated quantitative real-time PCR (qPCR) clamping assay to measure the proportions of dlDNA in total HBV DNA in sera obtained from patients with chronic hepatitis B (CHB), liver cirrhosis (LC) or LC-developed hepatocellular carcinoma (HCC). The factors that influence the proportion of dlDNA were also investigated. RESULTS The average dlDNA proportion was approximately 7% in the sera of chronic HBV-infected patients and was elevated in CHB patients with abnormal levels of alanine aminotransferase. The sera dlDNA proportions increased to approximately 14% and 20% in the patients with LC and HCC, respectively. Interferon-α treatment slightly increased the dlDNA proportion in the responders; and nucleotide analogue therapy spuriously elevated the proportion. Moreover, treatment of human hepatoma cells supporting HBV replication with inflammatory cytokines significantly altered the dlDNA proportion in vitro. CONCLUSIONS Using a novel PNA-mediated qPCR clamping assay, we first showed that serum dlDNA proportions progressively increased during the development of HBV-related liver diseases. The dlDNA proportion can be regulated by inflammatory cytokines, suggesting an association among inflammation, increased production of HBV dlDNA and development of HCC.
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Affiliation(s)
- Xing-Liang Zhao
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing, P.R. China
| | - Jian-Rong Yang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Sheng-Zhang Lin
- Department of Hepato-Biliary-Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, P.R. China
| | - Hui Ma
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing, P.R. China
| | - Fang Guo
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing, P.R. China Department of Microbiology and Immunology, Drexel Institute for Biotechnology and Virology Research, Drexel University College of Medicine, Doylestown, Pennsylvania, USA
| | - Rui-Feng Yang
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing, P.R. China
| | - Heng-Hui Zhang
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing, P.R. China
| | - Jin-Chao Han
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing, P.R. China
| | - Lai Wei
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing, P.R. China
| | - Xiao-Ben Pan
- Peking University People's Hospital, Peking University Hepatology Institute, Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Beijing, P.R. China
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87
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Huang W, Zhang H, Hao Y, Xu X, Zhai Y, Wang S, Li Y, Ma F, Li Y, Wang Z, Zhang Y, Zhang X, Liang R, Wei Z, Cui Y, Li Y, Yu X, Ji H, He F, Xie W, Zhou G. A Non-Synonymous Single Nucleotide Polymorphism in the HJURP Gene Associated with Susceptibility to Hepatocellular Carcinoma among Chinese. PLoS One 2016; 11:e0148618. [PMID: 26863619 PMCID: PMC4749235 DOI: 10.1371/journal.pone.0148618] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 12/24/2015] [Indexed: 01/08/2023] Open
Abstract
Objective HJURP (Holliday Junction-Recognizing Protein) plays dual roles in DNA repair and in accurate chromosome segregation during mitosis. We examined whether the single nucleotide polymorphisms (SNPs) of HJURP were associated with the risk of occurrence of hepatocellular carcinoma (HCC) among chronic hepatitis B virus (HBV) carriers from well-known high-risk regions for HCC in China. Methods Twenty-four haplotype-tagging SNPs across HJURP were selected from HapMap data using the Haploview software. We genotyped these 24 SNPs using the using Sequenom's iPLEX assay in the Fusui population, consisting of 348 patients with HCC and 359 cancer-free controls, and further investigated the significantly associated SNP using the TaqMan assay in the Haimen population, consisting of 100 cases and 103 controls. The genetic associations with the risk of HCC were analyzed by logistic regression. Results We observed an increased occurrence of HCC consistently associated with A/C or C/C genotypes of the non-synonymous SNP rs3771333 compared with the A/A genotype in both the Fusui and Haimen populations, with a pooled odds ratio 1.82 (95% confidence interval, 1.33–2.49; P = 1.9 × 10−4). Case-only analysis further indicated that carriers of the at-risk C allele were younger than those carrying the A/A genotype (P = 0.0016). In addition, the expression levels of HJURP in C allele carriers were lower than that in A/A genotype carriers (P = 0.0078 and 0.0010, for mRNA and protein levels, respectively). Conclusion Our findings suggest that rs3771333 in HJURP may play a role in mediating the susceptibility to HCC among Chinese.
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Affiliation(s)
- Wenfeng Huang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- National Engineering Research Center for Protein Drugs, Beijing, China
- National Center for Protein Sciences Beijing, Beijing, China
- Affiliated Cancer Hospital of Guangxi Medical University, Nanning, Guangxi, China
- The Third Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Hongxing Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- National Engineering Research Center for Protein Drugs, Beijing, China
- National Center for Protein Sciences Beijing, Beijing, China
| | - Yumin Hao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- National Engineering Research Center for Protein Drugs, Beijing, China
- National Center for Protein Sciences Beijing, Beijing, China
| | - Xiaobing Xu
- Department of Gastroenterology and Hepatology, Jinling Hospital, Clinical School of Nanjing, Second Military Medical University, Nanjing, Jiangsu, China
| | - Yun Zhai
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- National Engineering Research Center for Protein Drugs, Beijing, China
- National Center for Protein Sciences Beijing, Beijing, China
| | - Shaoxia Wang
- Department of Experimental Pathology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Yang Li
- Department of Experimental Pathology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Fuchao Ma
- The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yuanfeng Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- National Engineering Research Center for Protein Drugs, Beijing, China
- National Center for Protein Sciences Beijing, Beijing, China
| | - Zhifu Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- National Engineering Research Center for Protein Drugs, Beijing, China
- National Center for Protein Sciences Beijing, Beijing, China
| | - Yang Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- National Engineering Research Center for Protein Drugs, Beijing, China
- National Center for Protein Sciences Beijing, Beijing, China
| | - Xiumei Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- National Engineering Research Center for Protein Drugs, Beijing, China
- National Center for Protein Sciences Beijing, Beijing, China
| | | | | | - Ying Cui
- Affiliated Cancer Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yongqiang Li
- Affiliated Cancer Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xinsen Yu
- Disease Prevention and Control Center at Haimen County, Jiangsu, China
| | - Hongzan Ji
- Department of Gastroenterology and Hepatology, Jinling Hospital, Clinical School of Nanjing, Second Military Medical University, Nanjing, Jiangsu, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- National Engineering Research Center for Protein Drugs, Beijing, China
- National Center for Protein Sciences Beijing, Beijing, China
| | - Weimin Xie
- Affiliated Cancer Hospital of Guangxi Medical University, Nanning, Guangxi, China
- * E-mail: (GZ); (WX)
| | - Gangqiao Zhou
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
- National Engineering Research Center for Protein Drugs, Beijing, China
- National Center for Protein Sciences Beijing, Beijing, China
- * E-mail: (GZ); (WX)
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88
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Ie SI, Turyadi, Sidarta E, Sadhewa A, Purnomo GA, Soedarmono YSM, Pattiiha MZ, Thedja MD, Harahap AR, Muljono DH. High Prevalence of Hepatitis B Virus Infection in Young Adults in Ternate, Eastern Indonesia. Am J Trop Med Hyg 2015; 93:1349-55. [PMID: 26392157 DOI: 10.4269/ajtmh.15-0331] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 08/05/2015] [Indexed: 12/29/2022] Open
Abstract
The incidence of hepatitis B virus (HBV) infection has been declining thanks to the universal hepatitis B infant immunization program. Nevertheless, young adults born before the program implementation might have acquired HBV in early childhood or remain susceptible to infection. This study aimed to evaluate hepatitis B epidemiology in asymptomatic young adult population in Ternate, eastern Indonesia. Serum samples of 376 subjects (aged 17-25, mean 19.82 ± 1.69 years; male/female 138/238) were screened for HBV parameters serologically (HBV surface antigen [HBsAg]; its antibody [anti-HBs]; anti-core antigen [anti-HBc]), and molecularly (HBV DNA). HBsAg, anti-HBc, anti-HBs, and HBV DNA prevalence were 15.7%, 36.2%, 24.2%, and 27.9%, respectively, with male predominance. Of all subjects, 13.0% were HBsAg negative with detectable HBV DNA (occult hepatitis B [OHB]), and 56.4% showed negativity for all seromarkers. This population showed high hepatitis B prevalence with substantial occurrence of OHB. However, a high percentage of the population were still susceptible and at risk of HBV infection. This study emphasizes the necessity to improve prevention strategies to screen and manage HBV carriers, including the adoption of catch-up or booster vaccination targeted to young adult populations. Investigations on the roles of host-virus interactions associated with OHB and its implications are warranted.
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Affiliation(s)
- Susan Irawati Ie
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; School of Life Sciences and Technology, Bandung Institute of Technology, Bandung, Indonesia; Central Blood Center, Indonesian Red Cross, Jakarta, Indonesia; Department of Internal Medicine, Ternate General Hospital, Ternate, Maluku, Indonesia; Department of Clinical Pathology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia; Faculty of Medicine, Hasanuddin University, Makassar, Indonesia; Sydney Medical School, University of Sydney, New South Wales, Australia
| | - Turyadi
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; School of Life Sciences and Technology, Bandung Institute of Technology, Bandung, Indonesia; Central Blood Center, Indonesian Red Cross, Jakarta, Indonesia; Department of Internal Medicine, Ternate General Hospital, Ternate, Maluku, Indonesia; Department of Clinical Pathology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia; Faculty of Medicine, Hasanuddin University, Makassar, Indonesia; Sydney Medical School, University of Sydney, New South Wales, Australia
| | - Erick Sidarta
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; School of Life Sciences and Technology, Bandung Institute of Technology, Bandung, Indonesia; Central Blood Center, Indonesian Red Cross, Jakarta, Indonesia; Department of Internal Medicine, Ternate General Hospital, Ternate, Maluku, Indonesia; Department of Clinical Pathology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia; Faculty of Medicine, Hasanuddin University, Makassar, Indonesia; Sydney Medical School, University of Sydney, New South Wales, Australia
| | - Arkasha Sadhewa
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; School of Life Sciences and Technology, Bandung Institute of Technology, Bandung, Indonesia; Central Blood Center, Indonesian Red Cross, Jakarta, Indonesia; Department of Internal Medicine, Ternate General Hospital, Ternate, Maluku, Indonesia; Department of Clinical Pathology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia; Faculty of Medicine, Hasanuddin University, Makassar, Indonesia; Sydney Medical School, University of Sydney, New South Wales, Australia
| | - Gludhug Ariyo Purnomo
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; School of Life Sciences and Technology, Bandung Institute of Technology, Bandung, Indonesia; Central Blood Center, Indonesian Red Cross, Jakarta, Indonesia; Department of Internal Medicine, Ternate General Hospital, Ternate, Maluku, Indonesia; Department of Clinical Pathology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia; Faculty of Medicine, Hasanuddin University, Makassar, Indonesia; Sydney Medical School, University of Sydney, New South Wales, Australia
| | - Yuyun S M Soedarmono
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; School of Life Sciences and Technology, Bandung Institute of Technology, Bandung, Indonesia; Central Blood Center, Indonesian Red Cross, Jakarta, Indonesia; Department of Internal Medicine, Ternate General Hospital, Ternate, Maluku, Indonesia; Department of Clinical Pathology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia; Faculty of Medicine, Hasanuddin University, Makassar, Indonesia; Sydney Medical School, University of Sydney, New South Wales, Australia
| | - Mochtar Zein Pattiiha
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; School of Life Sciences and Technology, Bandung Institute of Technology, Bandung, Indonesia; Central Blood Center, Indonesian Red Cross, Jakarta, Indonesia; Department of Internal Medicine, Ternate General Hospital, Ternate, Maluku, Indonesia; Department of Clinical Pathology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia; Faculty of Medicine, Hasanuddin University, Makassar, Indonesia; Sydney Medical School, University of Sydney, New South Wales, Australia
| | - Meta Dewi Thedja
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; School of Life Sciences and Technology, Bandung Institute of Technology, Bandung, Indonesia; Central Blood Center, Indonesian Red Cross, Jakarta, Indonesia; Department of Internal Medicine, Ternate General Hospital, Ternate, Maluku, Indonesia; Department of Clinical Pathology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia; Faculty of Medicine, Hasanuddin University, Makassar, Indonesia; Sydney Medical School, University of Sydney, New South Wales, Australia
| | - Alida R Harahap
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; School of Life Sciences and Technology, Bandung Institute of Technology, Bandung, Indonesia; Central Blood Center, Indonesian Red Cross, Jakarta, Indonesia; Department of Internal Medicine, Ternate General Hospital, Ternate, Maluku, Indonesia; Department of Clinical Pathology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia; Faculty of Medicine, Hasanuddin University, Makassar, Indonesia; Sydney Medical School, University of Sydney, New South Wales, Australia
| | - David H Muljono
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia; School of Life Sciences and Technology, Bandung Institute of Technology, Bandung, Indonesia; Central Blood Center, Indonesian Red Cross, Jakarta, Indonesia; Department of Internal Medicine, Ternate General Hospital, Ternate, Maluku, Indonesia; Department of Clinical Pathology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia; Faculty of Medicine, Hasanuddin University, Makassar, Indonesia; Sydney Medical School, University of Sydney, New South Wales, Australia
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89
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Goyal SK, Jain AK, Dixit VK, Shukla SK, Kumar M, Ghosh J, Ranjan A, Gupta N, Tripathi M. HBsAg Level as Predictor of Liver Fibrosis in HBeAg Positive Patients With Chronic Hepatitis B Virus Infection. J Clin Exp Hepatol 2015; 5:213-20. [PMID: 26628839 PMCID: PMC4632094 DOI: 10.1016/j.jceh.2015.04.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 04/18/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND AND AIMS Preliminary data suggests lower serum hepatitis B surface antigen level is associated with more severe liver fibrosis in HBeAg positive patients. We evaluated the association of HBsAg level with biochemical, virological, and histological features in asymptomatic patients with chronic HBV infection. METHODS HBsAg levels were measured at baseline in 481 asymptomatic, treatment naive patients with chronic HBV infection. Subjects were followed-up prospectively (median, 12; range, 8-36 months). Phases of HBV infection were defined after regular monitoring of HBV-DNA and transaminases. Liver histology was scored using the METAVIR system. RESULTS HBeAg positive (n, 126) patients were significantly younger than HBeAg negative (n, 355), median age 26 vs 30 years; P < 0.01. HBV genotype could be determined in 350 patients, 240 (68.57%) had genotype D and 100 (28.57%) had genotype A. HBsAg level had modest correlation with serum HBV DNA(r = 0.6 vs 0.4 in eAg positive & negative respectively). HBeAg + ve patients with fibrosis score ≥ F2 showed significantly lower median serum HBsAg levels and serum HBV DNA levels compared with patients with F0-F1 score (median, range; 4.51, 2.99-6.10 vs 5.06, 4.13-5.89, P < 0.01) and (8.39, 3.85-10.60, P < 0.01) respectively. Significant inverse correlation of HBsAg level was found with liver fibrosis in eAg positive group (r = -0.76; P < 0.001). HBsAg level cut off value 4.7 log10 IU/ml predicted moderate to advance fibrosis (F ≥ 2) with 92% sensitivity, 85% specificity & 91% negative predictive value. CONCLUSION Lower HBsAg level might reflect the status of advanced liver fibrosis in HBeAg positive chronic hepatitis B subjects.
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Affiliation(s)
- Sundeep K. Goyal
- Department of Gastroenterology, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India,Address for correspondence: Sundeep K. Goyal, Department of Gastroenterology, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India. Tel.: +91 9451763766.
| | - Ashok K. Jain
- Department of Gastroenterology, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Vinod K. Dixit
- Department of Gastroenterology, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Suneet K. Shukla
- Department of Gastroenterology, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Mohan Kumar
- Department of Pathology, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Jayant Ghosh
- Department of Gastroenterology, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Arttrika Ranjan
- Department of Gastroenterology, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Neha Gupta
- Department of Gastroenterology, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Manish Tripathi
- Department of Gastroenterology, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, India
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90
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Tu T, Mason WS, Clouston AD, Shackel NA, McCaughan GW, Yeh MM, Schiff ER, Ruszkiewicz AR, Chen JW, Harley HAJ, Stroeher UH, Jilbert AR. Clonal expansion of hepatocytes with a selective advantage occurs during all stages of chronic hepatitis B virus infection. J Viral Hepat 2015; 22:737-53. [PMID: 25619231 DOI: 10.1111/jvh.12380] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 11/15/2014] [Indexed: 12/23/2022]
Abstract
Hepatocyte clone size was measured in liver samples of 21 patients in various stages of chronic hepatitis B virus (HBV) infection and from 21 to 76 years of age. Hepatocyte clones containing unique virus-cell DNA junctions formed by the integration of HBV DNA were detected using inverse nested PCR. The maximum hepatocyte clone size tended to increase with age, although there was considerable patient-to-patient variation in each age group. There was an upward trend in maximum clone size with increasing fibrosis, inflammatory activity and with seroconversion from HBV e-antigen (HBeAg)-positive to HBeAg-negative, but these differences did not reach statistical significance. Maximum hepatocyte clone size did not differ between patients with and without a coexisting hepatocellular carcinoma. Thus, large hepatocyte clones containing integrated HBV DNA were detected during all stages of chronic HBV infection. Using laser microdissection, no significant difference in clone size was observed between foci of HBV surface antigen (HBsAg)-positive and HBsAg-negative hepatocytes, suggesting that expression of HBsAg is not a significant factor in clonal expansion. Laser microdissection also revealed that hepatocytes with normal-appearing histology make up a major fraction of the cells undergoing clonal expansion. Thus, preneoplasia does not appear to be a factor in the clonal expansion detected in our assays. Computer simulations suggest that the large hepatocyte clones are not produced by random hepatocyte turnover but have an as-yet-unknown selective advantage that drives increased clonal expansion in the HBV-infected liver.
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Affiliation(s)
- T Tu
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia.,Centenary Institute, Sydney, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - W S Mason
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - A D Clouston
- Centre for Liver Disease Research, School of Medicine, Faculty of Health Sciences, University of Queensland, Brisbane, QLD, Australia
| | - N A Shackel
- Centenary Institute, Sydney, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia.,A. W. Morrow Gastroenterology and Liver Centre, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - G W McCaughan
- Centenary Institute, Sydney, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia.,A. W. Morrow Gastroenterology and Liver Centre, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - M M Yeh
- Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - E R Schiff
- Schiff Liver Institute and Center for Liver Diseases, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - A R Ruszkiewicz
- Department of Anatomical Pathology and Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia
| | - J W Chen
- South Australian Liver Transplant Unit, Flinders Medical Centre, Adelaide, SA, Australia
| | - H A J Harley
- Department of Gastroenterology and Hepatology, Royal Adelaide Hospital, Adelaide, SA, Australia
| | - U H Stroeher
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - A R Jilbert
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
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91
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Guo JT, Guo H. Metabolism and function of hepatitis B virus cccDNA: Implications for the development of cccDNA-targeting antiviral therapeutics. Antiviral Res 2015; 122:91-100. [PMID: 26272257 DOI: 10.1016/j.antiviral.2015.08.005] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 08/07/2015] [Indexed: 02/07/2023]
Abstract
Persistent hepatitis B virus (HBV) infection relies on the stable maintenance and proper functioning of a nuclear episomal form of the viral genome called covalently closed circular (ccc) DNA. One of the major reasons for the failure of currently available antiviral therapeutics to achieve a cure of chronic HBV infection is their inability to eradicate or inactivate cccDNA. In this review article, we summarize our current understanding of cccDNA metabolism in hepatocytes and the modulation of cccDNA by host pathophysiological and immunological cues. Perspectives on the future investigation of cccDNA biology, as well as strategies and progress in therapeutic elimination and/or transcriptional silencing of cccDNA through rational design and phenotypic screenings, are also discussed. This article forms part of a symposium in Antiviral Research on "An unfinished story: from the discovery of the Australia antigen to the development of new curative therapies for hepatitis B."
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Affiliation(s)
- Ju-Tao Guo
- Baruch S. Blumberg Institute, Hepatitis B Foundation, Doylestown, PA 18902, USA.
| | - Haitao Guo
- Department of Microbiology and Immunology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA.
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92
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Vy-PER: eliminating false positive detection of virus integration events in next generation sequencing data. Sci Rep 2015; 5:11534. [PMID: 26166306 PMCID: PMC4499804 DOI: 10.1038/srep11534] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 05/07/2015] [Indexed: 11/10/2022] Open
Abstract
Several pathogenic viruses such as hepatitis B and human immunodeficiency viruses may integrate into the host genome. These virus/host integrations are detectable using paired-end next generation sequencing. However, the low number of expected true virus integrations may be difficult to distinguish from the noise of many false positive candidates. Here, we propose a novel filtering approach that increases specificity without compromising sensitivity for virus/host chimera detection. Our detection pipeline termed Vy-PER (Virus integration detection bY Paired End Reads) outperforms existing similar tools in speed and accuracy. We analysed whole genome data from childhood acute lymphoblastic leukemia (ALL), which is characterised by genomic rearrangements and usually associated with radiation exposure. This analysis was motivated by the recently reported virus integrations at genomic rearrangement sites and association with chromosomal instability in liver cancer. However, as expected, our analysis of 20 tumour and matched germline genomes from ALL patients finds no significant evidence for integrations by known viruses. Nevertheless, our method eliminates 12,800 false positives per genome (80× coverage) and only our method detects singleton human-phiX174-chimeras caused by optical errors of the Illumina HiSeq platform. This high accuracy is useful for detecting low virus integration levels as well as non-integrated viruses.
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93
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Tu T, Budzinska MA, Shackel NA, Jilbert AR. Conceptual models for the initiation of hepatitis B virus-associated hepatocellular carcinoma. Liver Int 2015; 35:1786-800. [PMID: 25640596 DOI: 10.1111/liv.12773] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 12/18/2014] [Indexed: 12/18/2022]
Abstract
Although chronic hepatitis B virus (HBV) infection is a known risk factor for the development of hepatocellular carcinoma (HCC), the steps involved in the progression from normal liver to HCC are poorly understood. In this review, we apply five conceptual models, previously proposed by Vineis et al. to explain carcinogenesis in general, to explore the possible steps involved in the initiation and evolution of HBV-associated HCC. Available data suggest that the most suitable and inclusive model is based on evolution of hepatocyte subpopulations. In this evolutionary model, HCC-associated changes are driven by selection and subsequent clonal expansion of phenotypically altered hepatocyte subpopulations in the microenvironment of the HBV-infected liver. This model can incorporate the wide range of mechanisms proposed to play a role in the initiation of HCC including oncogenic HBV proteins, integration of HBV DNA and chronic inflammation of the liver. The model may assist in the early prevention, detection and treatment of HCC and may guide future studies of the initiation of HBV-associated HCC.
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Affiliation(s)
- Thomas Tu
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia.,Liver Cell Biology, Centenary Institute, Sydney, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Magdalena A Budzinska
- Liver Cell Biology, Centenary Institute, Sydney, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Nicholas A Shackel
- Liver Cell Biology, Centenary Institute, Sydney, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia.,A.W. Morrow Gastroenterology and Liver Centre, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Allison R Jilbert
- Department of Molecular and Cellular Biology, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
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94
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Jain S, Chang TT, Chen S, Boldbaatar B, Clemens A, Lin SY, Yan R, Hu CT, Guo H, Block TM, Song W, Su YH. Comprehensive DNA methylation analysis of hepatitis B virus genome in infected liver tissues. Sci Rep 2015; 5:10478. [PMID: 26000761 PMCID: PMC4650678 DOI: 10.1038/srep10478] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 04/15/2015] [Indexed: 12/14/2022] Open
Abstract
Hepatitis B virus (HBV) is a hepatotropic virus causing hepatitis, cirrhosis and hepatocellular carcinoma (HCC). The methylation status of the HBV DNA in its different forms can potentially provide insight into the pathogenesis of HBV-related liver diseases, including HCC, however this is unclear. The goal of this study is to obtain comprehensive DNA methylation profiles of the three putative CpG islands in the HBV DNA in infected livers, with respect to liver disease progression. The extent of methylation in these CpG islands was first assessed using bisulfite PCR sequencing with a small set of tissue samples, followed by analysis using both quantitative bisulfite-specific PCR and quantitative methylation-specific PCR assays in a larger sample size (n = 116). The level of HBV CpG island 3 methylation significantly correlated with hepatocarcinogenesis. We also obtained, for the first time, evidence of rare, non-CpG methylation in CpG island 2 of the HBV genome in infected liver. Comparing methylation of the HBV genome to three known HCC-associated host genes, APC, GSTP1, and RASSF1A, we did not identify a significant correlation between these two groups.
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Affiliation(s)
| | - Ting-Tsung Chang
- Department of Internal Medicine, National Cheng Kung University Medical College and Hospital, Tainan, Taiwan, Republic of China
| | | | | | | | - Selena Y Lin
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Ran Yan
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Chi-Tan Hu
- Department of Medicine, Buddhist Tzu Chi General Hospital and Tzu Chi University, Hualien, Taiwan, Republic of China
| | - Haitao Guo
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Timothy M Block
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Wei Song
- JBS Science, Inc., Doylestown, Pennsylvania
| | - Ying-Hsiu Su
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
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95
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Seeger C, Mason WS. Molecular biology of hepatitis B virus infection. Virology 2015; 479-480:672-86. [PMID: 25759099 PMCID: PMC4424072 DOI: 10.1016/j.virol.2015.02.031] [Citation(s) in RCA: 566] [Impact Index Per Article: 62.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 02/09/2015] [Accepted: 02/16/2015] [Indexed: 02/06/2023]
Abstract
Human hepatitis B virus (HBV) is the prototype of a family of small DNA viruses that productively infect hepatocytes, the major cell of the liver, and replicate by reverse transcription of a terminally redundant viral RNA, the pregenome. Upon infection, the circular, partially double-stranded virion DNA is converted in the nucleus to a covalently closed circular DNA (cccDNA) that assembles into a minichromosome, the template for viral mRNA synthesis. Infection of hepatocytes is non-cytopathic. Infection of the liver may be either transient (<6 months) or chronic and lifelong, depending on the ability of the host immune response to clear the infection. Chronic infections can cause immune-mediated liver damage progressing to cirrhosis and hepatocellular carcinoma (HCC). The mechanisms of carcinogenesis are unclear. Antiviral therapies with nucleoside analog inhibitors of viral DNA synthesis delay sequelae, but cannot cure HBV infections due to the persistence of cccDNA in hepatocytes.
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96
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Thézé J, Leclercq S, Moumen B, Cordaux R, Gilbert C. Remarkable diversity of endogenous viruses in a crustacean genome. Genome Biol Evol 2015; 6:2129-40. [PMID: 25084787 PMCID: PMC4231630 DOI: 10.1093/gbe/evu163] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Recent studies in paleovirology have uncovered myriads of endogenous viral elements (EVEs) integrated in the genome of their eukaryotic hosts. These fragments result from endogenization, that is, integration of the viral genome into the host germline genome followed by vertical inheritance. So far, most studies have used a virus-centered approach, whereby endogenous copies of a particular group of viruses were searched in all available sequenced genomes. Here, we follow a host-centered approach whereby the genome of a given species is comprehensively screened for the presence of EVEs using all available complete viral genomes as queries. Our analyses revealed that 54 EVEs corresponding to 10 different viral lineages belonging to 5 viral families (Bunyaviridae, Circoviridae, Parvoviridae, and Totiviridae) and one viral order (Mononegavirales) became endogenized in the genome of the isopod crustacean Armadillidium vulgare. We show that viral endogenization occurred recurrently during the evolution of isopods and that A. vulgare viral lineages were involved in multiple host switches that took place between widely divergent taxa. Furthermore, 30 A. vulgare EVEs have uninterrupted open reading frames, suggesting they result from recent endogenization of viruses likely to be currently infecting isopod populations. Overall, our work shows that isopods have been and are still infected by a large variety of viruses. It also extends the host range of several families of viruses and brings new insights into their evolution. More generally, our results underline the power of paleovirology in characterizing the viral diversity currently infecting eukaryotic taxa.
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Affiliation(s)
- Julien Thézé
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Poitiers, France
| | - Sébastien Leclercq
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Poitiers, France State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Bouziane Moumen
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Poitiers, France
| | - Richard Cordaux
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Poitiers, France
| | - Clément Gilbert
- Université de Poitiers, UMR CNRS 7267 Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Poitiers, France
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97
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Aiewsakun P, Katzourakis A. Endogenous viruses: Connecting recent and ancient viral evolution. Virology 2015; 479-480:26-37. [PMID: 25771486 DOI: 10.1016/j.virol.2015.02.011] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 12/15/2014] [Accepted: 02/04/2015] [Indexed: 12/17/2022]
Abstract
The rapid rates of viral evolution allow us to reconstruct the recent history of viruses in great detail. This feature, however, also results in rapid erosion of evolutionary signal within viral molecular data, impeding studies of their deep history. Thus, the further back in time, the less accurate the inference becomes. Furthermore, reconstructing complex histories of transmission can be challenging, especially where extinct viral lineages are concerned. This problem has been partially solved by the discovery of viruses embedded in host genomes, known as endogenous viral elements (EVEs). Some of these endogenous viruses are derived from ancient relatives of extant viruses, allowing us to better examine ancient viral host range, geographical distribution and transmission routes. Moreover, our knowledge of viral evolutionary timescales and rate dynamics has also been greatly improved by their discovery, thereby bridging the gap between recent and ancient viral evolution.
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Affiliation(s)
| | - Aris Katzourakis
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK.
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98
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Castanera R, Pérez G, López L, Sancho R, Santoyo F, Alfaro M, Gabaldón T, Pisabarro AG, Oguiza JA, Ramírez L. Highly expressed captured genes and cross-kingdom domains present in Helitrons create novel diversity in Pleurotus ostreatus and other fungi. BMC Genomics 2014; 15:1071. [PMID: 25480150 PMCID: PMC4289320 DOI: 10.1186/1471-2164-15-1071] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 11/14/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Helitrons are class-II eukaryotic transposons that transpose via a rolling circle mechanism. Due to their ability to capture and mobilize gene fragments, they play an important role in the evolution of their host genomes. We have used a bioinformatics approach for the identification of helitrons in two Pleurotus ostreatus genomes using de novo detection and homology-based searching. We have analyzed the presence of helitron-captured genes as well as the expansion of helitron-specific helicases in fungi and performed a phylogenetic analysis of their conserved domains with other representative eukaryotic species. RESULTS Our results show the presence of two helitron families in P. ostreatus that disrupt gene colinearity and cause a lack of synteny between their genomes. Both putative autonomous and non-autonomous helitrons were transcriptionally active, and some of them carried highly expressed captured genes of unknown origin and function. In addition, both families contained eukaryotic, bacterial and viral domains within the helitron's boundaries. A phylogenetic reconstruction of RepHel helicases using the Helitron-like and PIF1-like helicase conserved domains revealed a polyphyletic origin for eukaryotic helitrons. CONCLUSION P. ostreatus helitrons display features similar to other eukaryotic helitrons and do not tend to capture host genes or gene fragments. The occurrence of genes probably captured from other hosts inside the helitrons boundaries pose the hypothesis that an ancient horizontal transfer mechanism could have taken place. The viral domains found in some of these genes and the polyphyletic origin of RepHel helicases in the eukaryotic kingdom suggests that virus could have played a role in a putative lateral transfer of helitrons within the eukaryotic kingdom. The high similarity of some helitrons, along with the transcriptional activity of its RepHel helicases indicates that these elements are still active in the genome of P. ostreatus.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Lucía Ramírez
- Department of Agrarian Production, Genetics and Microbiology Research Group, Public University of Navarre, 31006 Pamplona, Navarre, Spain.
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99
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Rice genomes recorded ancient pararetrovirus activities: Virus genealogy and multiple origins of endogenization during rice speciation. Virology 2014; 471-473:141-52. [PMID: 25461539 DOI: 10.1016/j.virol.2014.09.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 09/11/2014] [Indexed: 11/21/2022]
Abstract
Viral fossils in rice genomes are a best entity to understand ancient pararetrovirus activities through host plant history because of our advanced knowledge of the genomes and evolutionary history with rice and its related species. Here, we explored organization, geographic origins and genealogy of rice pararetroviruses, which were turned into endogenous rice tungro bacilliform virus-like (eRTBVL) sequences. About 300 eRTBVL sequences from three representative rice genomes were clearly classified into six families. Most of the endogenization events of the eRTBVLs were initiated before differentiation of the rice progenitor (> 160,000 years ago). We successfully followed the genealogy of old relic viruses during rice speciation, and inferred the geographical origins for these viruses. Possible virus genomic sequences were explained mostly by recombinations between different virus families. Interestingly, we discovered that only a few recombination events among the numerous occasions had determined the virus genealogy.
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100
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Chen Y, Williams V, Filippova M, Filippov V, Duerksen-Hughes P. Viral carcinogenesis: factors inducing DNA damage and virus integration. Cancers (Basel) 2014; 6:2155-86. [PMID: 25340830 PMCID: PMC4276961 DOI: 10.3390/cancers6042155] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 10/03/2014] [Accepted: 10/09/2014] [Indexed: 12/13/2022] Open
Abstract
Viruses are the causative agents of 10%-15% of human cancers worldwide. The most common outcome for virus-induced reprogramming is genomic instability, including accumulation of mutations, aberrations and DNA damage. Although each virus has its own specific mechanism for promoting carcinogenesis, the majority of DNA oncogenic viruses encode oncogenes that transform infected cells, frequently by targeting p53 and pRB. In addition, integration of viral DNA into the human genome can also play an important role in promoting tumor development for several viruses, including HBV and HPV. Because viral integration requires the breakage of both the viral and the host DNA, the integration rate is believed to be linked to the levels of DNA damage. DNA damage can be caused by both endogenous and exogenous factors, including inflammation induced by either the virus itself or by co-infections with other agents, environmental agents and other factors. Typically, cancer develops years to decades following the initial infection. A better understanding of virus-mediated carcinogenesis, the networking of pathways involved in transformation and the relevant risk factors, particularly in those cases where tumorigenesis proceeds by way of virus integration, will help to suggest prophylactic and therapeutic strategies to reduce the risk of virus-mediated cancer.
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Affiliation(s)
- Yan Chen
- Department of Basic Science, Loma Linda University, Loma Linda, CA 92354, USA.
| | - Vonetta Williams
- Department of Basic Science, Loma Linda University, Loma Linda, CA 92354, USA.
| | - Maria Filippova
- Department of Basic Science, Loma Linda University, Loma Linda, CA 92354, USA.
| | - Valery Filippov
- Department of Basic Science, Loma Linda University, Loma Linda, CA 92354, USA.
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