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Dopico E, Vila M, Tabernero D, Gregori J, Rando-Segura A, Pacín-Ruíz B, Guerrero L, Ubillos I, Martínez MJ, Costa J, Quer J, Pérez-Garreta J, González-Sánchez A, Antón A, Pumarola T, Riveiro-Barciela M, Ferrer-Costa R, Buti M, Rodríguez-Frías F, Cortese MF. Genotyping Hepatitis B virus by Next-Generation Sequencing: Detection of Mixed Infections and Analysis of Sequence Conservation. Int J Mol Sci 2024; 25:5481. [PMID: 38791519 PMCID: PMC11122360 DOI: 10.3390/ijms25105481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/01/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Our aim was to develop an accurate, highly sensitive method for HBV genotype determination and detection of genotype mixtures. We examined the preS and 5' end of the HBV X gene (5X) regions of the HBV genome using next-generation sequencing (NGS). The 1852 haplotypes obtained were subjected to genotyping via the Distance-Based discrimination method (DB Rule) using two sets of 95 reference sequences of genotypes A-H. In clinical samples from 125 patients, the main genotypes were A, D, F and H in Caucasian, B and C in Asian and A and E in Sub-Saharan patients. Genotype mixtures were identified in 28 (22.40%) cases, and potential intergenotypic recombination was observed in 29 (23.20%) cases. Furthermore, we evaluated sequence conservation among haplotypes classified into genotypes A, C, D, and E by computing the information content. The preS haplotypes exhibited limited shared conserved regions, whereas the 5X haplotypes revealed two groups of conserved regions across the genotypes assessed. In conclusion, we developed an NGS-based HBV genotyping method utilizing the DB Rule for genotype classification. We identified two regions conserved across different genotypes at 5X, offering promising targets for RNA interference-based antiviral therapies.
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Affiliation(s)
- Eva Dopico
- Department of Microbiology, Metropolitana Sud Territorial Clinical Laboratory, Bellvitge University Hospital, Institut Català de la Salut (ICS), 08907 Hospitalet de Llobregat, Spain; (E.D.); (L.G.); (I.U.)
- Bellvitge Biomedical Research Institute (IDIBELL), 08908 Hospitalet de Llobregat, Spain
| | - Marta Vila
- Liver Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (M.V.); (A.R.-S.); (B.P.-R.); (J.P.-G.); (M.F.C.)
| | - David Tabernero
- Liver Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (M.V.); (A.R.-S.); (B.P.-R.); (J.P.-G.); (M.F.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.Q.); (M.R.-B.); (M.B.); (F.R.-F.)
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain;
| | - Josep Gregori
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain;
| | - Ariadna Rando-Segura
- Liver Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (M.V.); (A.R.-S.); (B.P.-R.); (J.P.-G.); (M.F.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.Q.); (M.R.-B.); (M.B.); (F.R.-F.)
- Virology Section, Microbiology Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (A.G.-S.); (A.A.); (T.P.)
| | - Beatriz Pacín-Ruíz
- Liver Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (M.V.); (A.R.-S.); (B.P.-R.); (J.P.-G.); (M.F.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.Q.); (M.R.-B.); (M.B.); (F.R.-F.)
| | - Laura Guerrero
- Department of Microbiology, Metropolitana Sud Territorial Clinical Laboratory, Bellvitge University Hospital, Institut Català de la Salut (ICS), 08907 Hospitalet de Llobregat, Spain; (E.D.); (L.G.); (I.U.)
| | - Itziar Ubillos
- Department of Microbiology, Metropolitana Sud Territorial Clinical Laboratory, Bellvitge University Hospital, Institut Català de la Salut (ICS), 08907 Hospitalet de Llobregat, Spain; (E.D.); (L.G.); (I.U.)
| | - Miguel J. Martínez
- Department of Microbiology, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain; (M.J.M.); (J.C.)
- ISGlobal, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Josep Costa
- Department of Microbiology, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain; (M.J.M.); (J.C.)
| | - Josep Quer
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.Q.); (M.R.-B.); (M.B.); (F.R.-F.)
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain;
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
| | - Javier Pérez-Garreta
- Liver Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (M.V.); (A.R.-S.); (B.P.-R.); (J.P.-G.); (M.F.C.)
| | - Alejandra González-Sánchez
- Virology Section, Microbiology Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (A.G.-S.); (A.A.); (T.P.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Respiratory Virus Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Andrés Antón
- Virology Section, Microbiology Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (A.G.-S.); (A.A.); (T.P.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Respiratory Virus Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Tomás Pumarola
- Virology Section, Microbiology Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (A.G.-S.); (A.A.); (T.P.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Mar Riveiro-Barciela
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.Q.); (M.R.-B.); (M.B.); (F.R.-F.)
- Liver Unit, Internal Medicine Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Roser Ferrer-Costa
- Clinical Biochemistry, Drug Delivery and Therapy (CB-DDT) Research Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain;
- Biochemistry Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Maria Buti
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.Q.); (M.R.-B.); (M.B.); (F.R.-F.)
- Liver Unit, Internal Medicine Department, Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Francisco Rodríguez-Frías
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.Q.); (M.R.-B.); (M.B.); (F.R.-F.)
- Clinical Biochemistry, Drug Delivery and Therapy (CB-DDT) Research Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain;
- Department of Basic Sciences, Universitat Internacional de Catalunya, 08017 Barcelona, Spain
| | - Maria Francesca Cortese
- Liver Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain; (M.V.); (A.R.-S.); (B.P.-R.); (J.P.-G.); (M.F.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.Q.); (M.R.-B.); (M.B.); (F.R.-F.)
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Jia Y, Zhao J, Wang C, Meng J, Zhao L, Yang H, Zhao X. HBV DNA polymerase upregulates the transcription of PD-L1 and suppresses T cell activity in hepatocellular carcinoma. J Transl Med 2024; 22:272. [PMID: 38475878 DOI: 10.1186/s12967-024-05069-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/06/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND In HBV-associated HCC, T cells often exhibit a state of functional exhaustion, which prevents the immune response from rejecting the tumor and allows HCC to progress. Moreover, polymerase-specific T cells exhibit more severe T-cell exhaustion compared to core-specific T cells. However, whether HBV DNA polymerase drives HBV-specific CD8+ T cell exhaustion in HBV-related HCC remains unclear. METHODS We constructed a Huh7 cell line stably expressing HA-HBV-DNA-Pol and applied co-culture systems to clarify its effect on immune cell function. We also examined how HBV-DNA-Pol modulated PD-L1 expression in HCC cells. In addition, HBV-DNA-Pol transgenic mice were used to elucidate the underlying mechanism of HBV-DNA-Pol/PD-L1 axis-induced T cell exhaustion. RESULTS Biochemical analysis showed that Huh7 cells overexpressing HBV-DNA-Pol inhibited the proliferation, activation, and cytokine secretion of Jurkat cells and that this effect was dependent on their direct contact. A similar inhibitory effect was observed in an HCC mouse model. PD-L1 was brought to our attention during screening. Our results showed that the overexpression of HBV-DNA-Pol upregulated PD-L1 mRNA and protein expression. PD-L1 antibody blockade reversed the inhibitory effect of Huh7 cells overexpressing HBV-DNA-Pol on Jurkat cells. Mechanistically, HBV-DNA-Pol interacts with PARP1, thereby inhibiting the nuclear translocation of PARP1 and further upregulating PD-L1 expression. CONCLUSIONS Our findings suggest that HBV-DNA-Pol can act as a regulator of PD-L1 in HCC, thereby directing anti-cancer immune evasion, which further provides a new idea for the clinical treatment of liver cancer.
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Affiliation(s)
- Yan Jia
- Department of Laboratory Medicine, Tianjin Hospital, Tianjin, 300211, China
| | - Jianing Zhao
- Department of Pathology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050011, China
| | - Chunqing Wang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan, 250014, China
| | - Jing Meng
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, China
| | - Liqing Zhao
- Department of Pediatrics, Zaozhuang Municipal Hospital, Zaozhuang, 277100, China
| | - Hongwei Yang
- Department of Laboratory Medicine, Tianjin Hospital, Tianjin, 300211, China
| | - Xiaoqing Zhao
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, China.
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Patil VS, Harish DR, Charla R, Vetrivel U, Jalalpure SS, Bhandare VV, Deshpande SH, Hegde HV, Roy S. Structural insights into modeling of hepatitis B virus reverse transcriptase and identification of its inhibitors from potential medicinal plants of Western Ghats: an in silico and in vitro study. J Biomol Struct Dyn 2023:1-19. [PMID: 37811543 DOI: 10.1080/07391102.2023.2264400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/21/2023] [Indexed: 10/10/2023]
Abstract
The present study was proposed to model full-length HBV-RT and investigate the intermolecular interactions of known inhibitor and libraries of phytocompounds to probe the potential natural leads by in silico and in vitro studies. Homology modeling of RT was performed by Phyre2 and Modeller and virtual screening of ligands implemented through POAP pipeline. Molecular dynamics (MD) simulation (100 ns) and MM-GBSA calculations were performed using Schrodinger Desmond and Prime, respectively. Phytocompounds probable host protein targets gene set pathway enrichment and network analysis were executed by KEGG database and Cytoscape software. Prioritized plant extracts/enriched fraction LC-MS analysis was performed and along with pure compound, RT inhibitory activity, time-dependent HBsAg and HBeAg secretion, and intracellular HBV DNA, and pgRNA by qRT-PCR was performed in HepG2.2.15 cell line. Among the screened chemical library of 268 phytocompounds from 18 medicinal plants, 15 molecules from Terminalia chebula (6), Bidens pilosa (5), and Centella asiatica (4)) were identified as potential inhibitors of YMDD and RT1 motif of HBV-RT. MD simulation demonstrated stable interactions of 15 phytocompounds with HBV-RT, of which 1,2,3,4,6-Pentagalloyl Glucose (PGG) was identified as lead molecule. Out of 15 compounds, 11 were predicted to modulate 39 proteins and 15 molecular pathways associated with HBV infection. TCN and TCW (500 µg/mL) showed potent RT inhibition, decreased intracellular HBV DNA, and pgRNA, and time-dependent inhibition of HBsAg and HBeAg levels compared to PGG and Tenofovir Disoproxil Fumarate. We propose that the identified lead molecules from T. chebula as promising and cost-effective moieties for the management of HBV infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vishal S Patil
- ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, India
- KLE College of Pharmacy, Belagavi, KLE Academy of Higher Education and Research, Belagavi, Karnataka, India
| | | | - Rajitha Charla
- ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, India
| | - Umashankar Vetrivel
- ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, India
- ICMR-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu, India
| | - Sunil S Jalalpure
- KLE College of Pharmacy, Belagavi, KLE Academy of Higher Education and Research, Belagavi, Karnataka, India
| | - Vishwambhar Vishnu Bhandare
- ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, India
- Department of Microbiology, Shivaji University, Kolhapur, Maharashtra, India
| | - Sanjay H Deshpande
- ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, India
- Regional Centre for Biotechnology, NCR-Biotech Science Cluster, Faridabad, India
| | - Harsha V Hegde
- ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, India
| | - Subarna Roy
- ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, India
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Zhang T, Zheng H, Lu D, Guan G, Li D, Zhang J, Liu S, Zhao J, Guo JT, Lu F, Chen X. RNA binding protein TIAR modulates HBV replication by tipping the balance of pgRNA translation. Signal Transduct Target Ther 2023; 8:346. [PMID: 37699883 PMCID: PMC10497612 DOI: 10.1038/s41392-023-01573-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 06/20/2023] [Accepted: 07/23/2023] [Indexed: 09/14/2023] Open
Abstract
The pregenomic RNA (pgRNA) of hepatitis B virus (HBV) serves not only as a bicistronic message RNA to translate core protein (Cp) and DNA polymerase (Pol), but also as the template for reverse transcriptional replication of viral DNA upon packaging into nucleocapsid. Although it is well known that pgRNA translates much more Cp than Pol, the molecular mechanism underlying the regulation of Cp and Pol translation efficiency from pgRNA remains elusive. In this study, we systematically profiled HBV nucleocapsid- and pgRNA-associated cellular proteins by proteomic analysis and identified TIA-1-related protein (TIAR) as a novel cellular protein that binds pgRNA and promotes HBV DNA replication. Interestingly, loss- and gain-of-function genetic analyses showed that manipulation of TIAR expression did not alter the levels of HBV transcripts nor the secretion of HBsAg and HBeAg in human hepatoma cells supporting HBV replication. However, Ribo-seq and PRM-based mass spectrometry analyses demonstrated that TIAR increased the translation of Pol but decreased the translation of Cp from pgRNA. RNA immunoprecipitation (RIP) and pulldown assays further revealed that TIAR directly binds pgRNA at the 5' stem-loop (ε). Moreover, HBV replication or Cp expression induced the increased expression and redistribution of TIAR from the nucleus to the cytoplasm of hepatocytes. Our results thus imply that TIAR is a novel cellular factor that regulates HBV replication by binding to the 5' ε structure of pgRNA to tip the balance of Cp and Pol translation. Through induction of TIAR translocation from the nucleus to the cytoplasm, Cp indirectly regulates the Pol translation and balances Cp and Pol expression levels in infected hepatocytes to ensure efficient viral replication.
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Affiliation(s)
- Ting Zhang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Huiling Zheng
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Danjuan Lu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Guiwen Guan
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Deyao Li
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Jing Zhang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Shuhong Liu
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
| | - Jingmin Zhao
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
| | - Ju-Tao Guo
- Department of Experimental Therapeutics, Baruch S. Blumberg Institute, Doylestown, PA, 18902, USA.
| | - Fengmin Lu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Peking University Hepatology Institute, Peking University People's Hospital, Beijing, 100044, China.
| | - Xiangmei Chen
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
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Olenginski LT, Attionu SK, Henninger EN, LeBlanc RM, Longhini AP, Dayie TK. Hepatitis B Virus Epsilon (ε) RNA Element: Dynamic Regulator of Viral Replication and Attractive Therapeutic Target. Viruses 2023; 15:1913. [PMID: 37766319 PMCID: PMC10534774 DOI: 10.3390/v15091913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Hepatitis B virus (HBV) chronically infects millions of people worldwide, which underscores the importance of discovering and designing novel anti-HBV therapeutics to complement current treatment strategies. An underexploited but attractive therapeutic target is ε, a cis-acting regulatory stem-loop RNA situated within the HBV pregenomic RNA (pgRNA). The binding of ε to the viral polymerase protein (P) is pivotal, as it triggers the packaging of pgRNA and P, as well as the reverse transcription of the viral genome. Consequently, small molecules capable of disrupting this interaction hold the potential to inhibit the early stages of HBV replication. The rational design of such ligands necessitates high-resolution structural information for the ε-P complex or its individual components. While these data are currently unavailable for P, our recent structural elucidation of ε through solution nuclear magnetic resonance spectroscopy marks a significant advancement in this area. In this review, we provide a brief overview of HBV replication and some of the therapeutic strategies to combat chronic HBV infection. These descriptions are intended to contextualize our recent experimental efforts to characterize ε and identify ε-targeting ligands, with the ultimate goal of developing novel anti-HBV therapeutics.
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Affiliation(s)
- Lukasz T. Olenginski
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA (R.M.L.)
- Department of Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Solomon K. Attionu
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA (R.M.L.)
| | - Erica N. Henninger
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA (R.M.L.)
| | - Regan M. LeBlanc
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA (R.M.L.)
| | - Andrew P. Longhini
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA (R.M.L.)
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Theodore K. Dayie
- Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA (R.M.L.)
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Villanueva RA, Loyola A. Pre- and Post-Transcriptional Control of HBV Gene Expression: The Road Traveled towards the New Paradigm of HBx, Its Isoforms, and Their Diverse Functions. Biomedicines 2023; 11:1674. [PMID: 37371770 DOI: 10.3390/biomedicines11061674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/04/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Hepatitis B virus (HBV) is an enveloped DNA human virus belonging to the Hepadnaviridae family. Perhaps its main distinguishable characteristic is the replication of its genome through a reverse transcription process. The HBV circular genome encodes only four overlapping reading frames, encoding for the main canonical proteins named core, P, surface, and X (or HBx protein). However, pre- and post-transcriptional gene regulation diversifies the full HBV proteome into diverse isoform proteins. In line with this, hepatitis B virus X protein (HBx) is a viral multifunctional and regulatory protein of 16.5 kDa, whose canonical reading frame presents two phylogenetically conserved internal in-frame translational initiation codons, and which results as well in the expression of two divergent N-terminal smaller isoforms of 8.6 and 5.8 kDa, during translation. The canonical HBx, as well as the smaller isoform proteins, displays different roles during viral replication and subcellular localizations. In this article, we reviewed the different mechanisms of pre- and post-transcriptional regulation of protein expression that take place during viral replication. We also investigated all the past and recent evidence about HBV HBx gene regulation and its divergent N-terminal isoform proteins. Evidence has been collected for over 30 years. The accumulated evidence simply strengthens the concept of a new paradigm of the canonical HBx, and its smaller divergent N-terminal isoform proteins, not only during viral replication, but also throughout cell pathogenesis.
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Affiliation(s)
| | - Alejandra Loyola
- Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago 8580702, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago 7510602, Chile
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7
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Boora S, Sharma V, Kaushik S, Bhupatiraju AV, Singh S, Kaushik S. Hepatitis B virus-induced hepatocellular carcinoma: a persistent global problem. Braz J Microbiol 2023; 54:679-689. [PMID: 37059940 PMCID: PMC10235410 DOI: 10.1007/s42770-023-00970-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/05/2023] [Indexed: 04/16/2023] Open
Abstract
Hepatitis B virus (HBV) infections are highly prevalent globally, representing a serious public health problem. The diverse modes of transmission and the burden of the chronic carrier population pose challenges to the effective management of HBV. Vaccination is the most effective preventive measure available in the current scenario. Still, HBV is one of the significant health issues in various parts of the globe due to non-response to vaccines, the high number of concealed carriers, and the lack of access and awareness. Universal vaccination programs must be scaled up in neonates, especially in the developing parts of the world, to prevent new HBV infections. Novel treatments like combinational therapy, gene silencing, and new antivirals must be available for effective management. The prolonged infection of HBV, direct and indirect, can promote the growth of hepatocellular carcinoma (HCC). The present review emphasizes the problems and probable solutions for better managing HBV infections, causal risk factors of HCC, and mechanisms of HCC.
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Affiliation(s)
- Sanjit Boora
- Centre for Biotechnology, Maharshi Dayanand University, 124001, Haryana, Rohtak, India
| | - Vikrant Sharma
- Centre for Biotechnology, Maharshi Dayanand University, 124001, Haryana, Rohtak, India
| | | | | | - Sandeep Singh
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Samander Kaushik
- Centre for Biotechnology, Maharshi Dayanand University, 124001, Haryana, Rohtak, India.
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8
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Lin N, Yin W, Miller H, Byazrova MG, Herrada AA, Benlagha K, Lee P, Guan F, Lei J, Gong Q, Yan Y, Filatov A, Liu C. The role of regulatory T cells and follicular T helper cells in HBV infection. Front Immunol 2023; 14:1169601. [PMID: 37275865 PMCID: PMC10235474 DOI: 10.3389/fimmu.2023.1169601] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/20/2023] [Indexed: 06/07/2023] Open
Abstract
Hepatitis B has become one of the major global health threats, especially in developing countries and regions. Hepatitis B virus infection greatly increases the risk for liver diseases such as cirrhosis and cancer. However, treatment for hepatitis B is limited when considering the huge base of infected people. The immune response against hepatitis B is mediated mainly by CD8+ T cells, which are key to fighting invading viruses, while regulatory T cells prevent overreaction of the immune response process. Additionally, follicular T helper cells play a key role in B-cell activation, proliferation, differentiation, and formation of germinal centers. The pathogenic process of hepatitis B virus is generally the result of a disorder or dysfunction of the immune system. Therefore, we present in this review the critical functions and related biological processes of regulatory T cells and follicular T helper cells during HBV infection.
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Affiliation(s)
- Nengqi Lin
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Disease, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Yin
- Wuhan Children’s Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Heather Miller
- Department of Research and Development, BD Biosciences, San Jose, CA, United States
| | - Maria G. Byazrova
- Laboratory of Immunochemistry, National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, Moscow, Russia
| | - Andrés A. Herrada
- Lymphatic Vasculature and Inflammation Research Laboratory, Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Talca, Chile
| | - Kamel Benlagha
- Université de Paris, Institut de Recherche Saint-Louis, EMiLy, Paris, France
| | - Pamela Lee
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Fei Guan
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Disease, Huazhong University of Science and Technology, Wuhan, China
| | - Jiahui Lei
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Disease, Huazhong University of Science and Technology, Wuhan, China
| | - Quan Gong
- Department of Immunology, School of Medicine, Yangtze University, Jingzhou, China
- Clinical Molecular Immunology Center, School of Medicine, Yangtze University, Jingzhou, China
| | - Youqing Yan
- Department of Infectious Disease, Wuhan No.7 Hospital, Wuhan, China
| | - Alexander Filatov
- Laboratory of Immunochemistry, National Research Center Institute of Immunology, Federal Medical Biological Agency of Russia, Moscow, Russia
| | - Chaohong Liu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Disease, Huazhong University of Science and Technology, Wuhan, China
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9
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Ranga A, Gupta A, Yadav L, Kumar S, Jain P. Advancing beyond reverse transcriptase inhibitors: The new era of hepatitis B polymerase inhibitors. Eur J Med Chem 2023; 257:115455. [PMID: 37216809 DOI: 10.1016/j.ejmech.2023.115455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023]
Abstract
Hepatitis B virus (HBV) is a genetically diverse blood-borne virus responsible for chronic hepatitis B. The HBV polymerase plays a key role in viral genome replication within the human body and has been identified as a potential drug target for chronic hepatitis B therapeutics. However, available nucleotide reverse transcriptase inhibitors only target the reverse transcriptase domain of the HBV polymerase; they also pose resistance issues and require lifelong treatment that can burden patients financially. In this study, various chemical classes are reviewed that have been developed to target different domains of the HBV polymerase: Terminal protein, which plays a vital role in the formation of the viral DNA; Reverse transcriptase, which is responsible for the synthesis of the viral DNA from RNA, and; Ribonuclease H, which is responsible for degrading the RNA strand in the RNA-DNA duplex formed during the reverse transcription process. Host factors that interact with the HBV polymerase to achieve HBV replication are also reviewed; these host factors can be targeted by inhibitors to indirectly inhibit polymerase functionality. A detailed analysis of the scope and limitations of these inhibitors from a medicinal chemistry perspective is provided. The structure-activity relationship of these inhibitors and the factors that may affect their potency and selectivity are also examined. This analysis will be useful in supporting the further development of these inhibitors and in designing new inhibitors that can inhibit HBV replication more efficiently.
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Affiliation(s)
- Abhishek Ranga
- Department of Pharmacology, Delhi Institute of Pharmaceutical Sciences and Research, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, MB Road, New Delhi, 110017, India
| | - Aarti Gupta
- Department of Pharmaceutical Biotechnology, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, MB Road, New Delhi, 110017, India
| | - Laxmi Yadav
- Department of Pharmacology, Delhi Institute of Pharmaceutical Sciences and Research, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, MB Road, New Delhi, 110017, India
| | - Sachin Kumar
- Department of Pharmacology, Delhi Institute of Pharmaceutical Sciences and Research, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, MB Road, New Delhi, 110017, India.
| | - Priti Jain
- Department of Pharmaceutical Chemistry, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, MB Road, New Delhi, 110017, India.
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10
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Olenginski LT, Kasprzak WK, Attionu SK, Shapiro BA, Dayie TK. Virtual Screening of Hepatitis B Virus Pre-Genomic RNA as a Novel Therapeutic Target. Molecules 2023; 28:molecules28041803. [PMID: 36838792 PMCID: PMC9963113 DOI: 10.3390/molecules28041803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/07/2023] [Accepted: 02/11/2023] [Indexed: 02/17/2023] Open
Abstract
The global burden imposed by hepatitis B virus (HBV) infection necessitates the discovery and design of novel antiviral drugs to complement existing treatments. One attractive and underexploited therapeutic target is ε, an ~85-nucleotide (nt) cis-acting regulatory stem-loop RNA located at the 3'- and 5'-ends of the pre-genomic RNA (pgRNA). Binding of the 5'-end ε to the viral polymerase protein (P) triggers two early events in HBV replication: pgRNA and P packaging and reverse transcription. Our recent solution nuclear magnetic resonance spectroscopy structure of ε permits structure-informed drug discovery efforts that are currently lacking for P. Here, we employ a virtual screen against ε using a Food and Drug Administration (FDA)-approved compound library, followed by in vitro binding assays. This approach revealed that the anti-hepatitis C virus drug Daclatasvir is a selective ε-targeting ligand. Additional molecular dynamics simulations demonstrated that Daclatasvir targets ε at its flexible 6-nt priming loop (PL) bulge and modulates its dynamics. Given the functional importance of the PL, our work supports the notion that targeting ε dynamics may be an effective anti-HBV therapeutic strategy.
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Affiliation(s)
- Lukasz T. Olenginski
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
- Correspondence: author emails: (L.T.O.); (T.K.D.)
| | - Wojciech K. Kasprzak
- Bioinformatics and Computational Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Solomon K. Attionu
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Bruce A. Shapiro
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Theodore K. Dayie
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
- Correspondence: author emails: (L.T.O.); (T.K.D.)
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11
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Peng S, Wang H, Wang Z, Wang Q. Progression of Antiviral Agents Targeting Viral Polymerases. Molecules 2022; 27:7370. [PMID: 36364196 PMCID: PMC9654062 DOI: 10.3390/molecules27217370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/19/2022] [Accepted: 10/20/2022] [Indexed: 08/08/2023] Open
Abstract
Viral DNA and RNA polymerases are two kinds of very important enzymes that synthesize the genetic materials of the virus itself, and they have become extremely favorable targets for the development of antiviral drugs because of their relatively conserved characteristics. There are many similarities in the structure and function of different viral polymerases, so inhibitors designed for a certain viral polymerase have acted as effective universal inhibitors on other types of viruses. The present review describes the development of classical antiviral drugs targeting polymerases, summarizes a variety of viral polymerase inhibitors from the perspective of chemically synthesized drugs and natural product drugs, describes novel approaches, and proposes promising development strategies for antiviral drugs.
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12
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Pley C, Lourenço J, McNaughton AL, Matthews PC. Spacer Domain in Hepatitis B Virus Polymerase: Plugging a Hole or Performing a Role? J Virol 2022; 96:e0005122. [PMID: 35412348 PMCID: PMC9093120 DOI: 10.1128/jvi.00051-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/14/2022] [Indexed: 11/25/2022] Open
Abstract
Hepatitis B virus (HBV) polymerase is divided into terminal protein, spacer, reverse transcriptase, and RNase domains. Spacer has previously been considered dispensable, merely acting as a tether between other domains or providing plasticity to accommodate deletions and mutations. We explore evidence for the role of spacer sequence, structure, and function in HBV evolution and lineage, consider its associations with escape from drugs, vaccines, and immune responses, and review its potential impacts on disease outcomes.
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Affiliation(s)
- Caitlin Pley
- School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
- Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - José Lourenço
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Biosystems and Integrative Sciences Institute, University of Lisbon, Lisbon, Portugal
| | - Anna L. McNaughton
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Nuffield Department of Medicine, University of Oxford Medawar Building, Oxford, United Kingdom
| | - Philippa C. Matthews
- Nuffield Department of Medicine, University of Oxford Medawar Building, Oxford, United Kingdom
- The Francis Crick Institute, London, United Kingdom
- Division of Infection and Immunity, University College London, London, United Kingdom
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13
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Multiomics Analysis of Endocytosis upon HBV Infection and Identification of SCAMP1 as a Novel Host Restriction Factor against HBV Replication. Int J Mol Sci 2022; 23:ijms23042211. [PMID: 35216324 PMCID: PMC8874515 DOI: 10.3390/ijms23042211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 02/04/2023] Open
Abstract
Hepatitis B virus (HBV) infection remains a major global health problem and the primary cause of cirrhosis and hepatocellular carcinoma (HCC). HBV intrusion into host cells is prompted by virus–receptor interactions in clathrin-mediated endocytosis. Here, we report a comprehensive view of the cellular endocytosis-associated transcriptome, proteome and ubiquitylome upon HBV infection. In this study, we quantified 273 genes in the transcriptome and 190 endocytosis-associated proteins in the proteome by performing multi-omics analysis. We further identified 221 Lys sites in 77 endocytosis-associated ubiquitinated proteins. A weak negative correlation was observed among endocytosis-associated transcriptome, proteome and ubiquitylome. We found 33 common differentially expressed genes (DEGs), differentially expressed proteins (DEPs), and Kub-sites. Notably, we reported the HBV-induced ubiquitination change of secretory carrier membrane protein (SCAMP1) for the first time, differentially expressed across all three omics data sets. Overexpression of SCAMP1 efficiently inhibited HBV RNAs/pgRNA and secreted viral proteins, whereas knockdown of SCAMP1 significantly increased viral production. Mechanistically, the EnhI/XP, SP1, and SP2 promoters were inhibited by SCAMP1, which accounts for HBV X and S mRNA inhibition. Overall, our study unveils the previously unknown role of SCAMP1 in viral replication and HBV pathogenesis and provides cumulative and novel information for a better understanding of endocytosis in response to HBV infection.
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14
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Qin YP, Yu HB, Yuan SY, Yang Z, Ren F, Wang Q, Li F, Ren JH, Cheng ST, Zhou YJ, He X, Zhou HZ, Zhang Y, Tan M, Yang ML, Zhang DP, Wen X, Dong ML, Zhang H, Liu J, Li ZH, Chen Y, Huang AL, Chen WX, Chen J. KAT2A Promotes Hepatitis B Virus Transcription and Replication Through Epigenetic Regulation of cccDNA Minichromosome. Front Microbiol 2022; 12:795388. [PMID: 35140694 PMCID: PMC8818952 DOI: 10.3389/fmicb.2021.795388] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/13/2021] [Indexed: 01/05/2023] Open
Abstract
Hepatitis B virus (HBV) infection remains a major health problem worldwide. Sufficient maintenance of the HBV covalently closed circular DNA (cccDNA), which serves as a template for HBV transcription, is responsible for the failure of antiviral therapies. While accumulating evidence suggests that cccDNA transcription is regulated by epigenetic machinery, particularly the acetylation and methylation of cccDNA-bound histone 3 (H3) and histone 4 (H4), the potential contributions of histone succinylation and related host factors remain obscured. Here, by screening a series of succinyltransferases and desuccinylases, we identified KAT2A as an important host factor of HBV transcription and replication. By using HBV-infected cells and mouse models with HBV infection, KAT2A was found to affect the transcriptional activity of cccDNA but did not affect cccDNA production. Mechanism studies showed that KAT2A is mainly located in the nucleus and could bind to cccDNA through interaction with HBV core protein (HBc). Moreover, we confirmed histone H3K79 succinylation (H3K79succ) as a histone modification on cccDNA minichromosome by using the cccDNA ChIP-Seq approach. Importantly, KAT2A silencing specifically reduced the level of cccDNA-bound succinylated H3K79. In conclusion, KAT2A promotes HBV transcription and replication through epigenetic machinery, and our findings may provide new insight into the treatment of HBV infection.
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Affiliation(s)
- Yi-Ping Qin
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Hai-Bo Yu
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Si-Yu Yuan
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Zhen Yang
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Fang Ren
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Qing Wang
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Fan Li
- Department of Endocrine and Breast Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ji-Hua Ren
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Sheng-Tao Cheng
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Yu-Jiao Zhou
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Xin He
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Hong-Zhong Zhou
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Yuan Zhang
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Ming Tan
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Min-Li Yang
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Da-Peng Zhang
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Xu Wen
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Mei-Ling Dong
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Hui Zhang
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Jing Liu
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Zhi-Hong Li
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Yao Chen
- Department of Medical Examination Centre, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ai-Long Huang
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
| | - Wei-Xian Chen
- Department of Clinical Laboratory, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Juan Chen
- The Key Laboratory of Molecular Biology of Infectious Diseases Designated by the Chinese Ministry of Education, Chongqing Medical University, Chongqing, China
- *Correspondence: Juan Chen,
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15
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Abstract
The hepatitis B virus (HBV) is a member of the Hepadnaviridae family, which includes small DNA enveloped viruses that infect primates, rodents, and birds and is the causative factor of chronic hepatitis B. A common feature of all these viruses is their great specificity by species and cell type, as well as a peculiar genomic and replication organization similar to that of retroviruses. The HBV virion consists of an external lipid envelope and an internal icosahedral protein capsid containing the viral genome and a DNA polymerase, which also functions as a reverse transcriptase.
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Affiliation(s)
- Alessandro Loglio
- Division of Gastroenterology and Hepatology, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122 Milan, Italy
| | - Mauro Viganò
- Hepatology Division, San Giuseppe Hospital Multimedica Spa, Via San Vittore 12, 20123 Milan, Italy
| | - Pietro Lampertico
- Division of Gastroenterology and Hepatology, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, 20122 Milan, Italy; Department of Pathophysiology and Transplantation, CRC "A. M. and A. Migliavacca" Center for Liver Disease, University of Milan, Via F. Sforza 35, Milan 20122, Italy.
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16
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Nakajima S, Watashi K, Kato T, Muramatsu M, Wakita T, Tamura N, Hattori SI, Maeda K, Mitsuya H, Yasutake Y, Toyoda T. Biochemical and Structural Properties of Entecavir-Resistant Hepatitis B Virus Polymerase with L180M/M204V Mutations. J Virol 2021; 95:e0240120. [PMID: 34076480 PMCID: PMC8312879 DOI: 10.1128/jvi.02401-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/19/2021] [Indexed: 02/07/2023] Open
Abstract
Entecavir (ETV) is a widely used anti-hepatitis B virus (HBV) drug. However, the emergence of resistant mutations in HBV reverse transcriptase (RT) results in treatment failure. To understand the mechanism underlying the development of ETV resistance by HBV RT, we analyzed the L180M, M204V, and L180M/M204V mutants using a combination of biochemical and structural techniques. ETV-triphosphate (ETV-TP) exhibited competitive inhibition with dGTP in both wild-type (wt) RT and M204V RT, as observed using Lineweaver-Burk plots. In contrast, RT L180M or L180M/M204V did not fit either competitive, uncompetitive, noncompetitive, or typical mixed inhibition, although ETV-TP was a competitive inhibitor of dGTP. Crystallography of HIV RTY115F/F116Y/Q151M/F160M/M184V, mimicking HBV RT L180M/M204V, showed that the F115 bulge (F88 in HBV RT) caused by the F160M mutation induced deviated binding of dCTP from its normal tight binding position. Modeling of ETV-TP on the deviated dCTP indicated that a steric clash could occur between ETV-TP methylene and the 3'-end nucleoside ribose. ETV-TP is likely to interact primarily with HBV RT M171 prior to final accommodation at the deoxynucleoside triphosphate (dNTP) binding site (Y. Yasutake, S. Hattori, H. Hayashi, K. Matsuda, et al., Sci Rep 8:1624, 2018, https://doi.org/10.1038/s41598-018-19602-9). Therefore, in HBV RT L180M/M204V, ETV-TP may be stuck at M171, a residue that is conserved in almost all HBV isolates, leading to the strange inhibition pattern observed in the kinetic analysis. Collectively, our results provide novel insights into the mechanism of ETV resistance of HBV RT caused by L180M and M204V mutations. IMPORTANCE HBV infects 257 million people in the world, who suffer from elevated risks of liver cirrhosis and cancer. ETV is one of the most potent anti-HBV drugs, and ETV resistance mutations in HBV RT have been extensively studied. Nevertheless, the mechanisms underlying ETV resistance have remained elusive. We propose an attractive hypothesis to explain ETV resistance and effectiveness using a combination of kinetic and structural analyses. ETV is likely to have an additional interaction site, M171, beside the dNTP pocket of HBV RT; this finding indicates that nucleos(t)ide analogues (NAs) recognizing multiple interaction sites within RT may effectively inhibit the enzyme. Modification of ETV may render it more effective and enable the rational design of efficient NA inhibitors.
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Affiliation(s)
- Shogo Nakajima
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
- Choju Medical Institute, Toyohashi, Japan
| | - Koichi Watashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, Tokyo, Japan
- MIRAI, Japan Science and Technology Agency, Saitama, Japan
| | - Takanobu Kato
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masamichi Muramatsu
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Takaji Wakita
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Noriko Tamura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, Japan
| | - Shin-Ichiro Hattori
- National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Kenji Maeda
- National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Hiroaki Mitsuya
- National Center for Global Health and Medicine Research Institute, Tokyo, Japan
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Yoshiaki Yasutake
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, Japan
- Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
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17
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LeBlanc RM, Kasprzak WK, Longhini AP, Olenginski LT, Abulwerdi F, Ginocchio S, Shields B, Nyman J, Svirydava M, Del Vecchio C, Ivanic J, Schneekloth JS, Shapiro BA, Dayie TK, Le Grice SFJ. Structural insights of the conserved "priming loop" of hepatitis B virus pre-genomic RNA. J Biomol Struct Dyn 2021; 40:9761-9773. [PMID: 34155954 PMCID: PMC10167916 DOI: 10.1080/07391102.2021.1934544] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/20/2021] [Indexed: 12/16/2022]
Abstract
Initiation of protein-primed (-) strand DNA synthesis in hepatitis B virus (HBV) requires interaction of the viral polymerase with a cis-acting regulatory signal, designated epsilon (ε), located at the 5'-end of its pre-genomic RNA (pgRNA). Binding of polymerase to ε is also necessary for pgRNA encapsidation. While the mechanistic basis of this interaction remains elusive, mutagenesis studies suggest its internal 6-nt "priming loop" provides an important structural contribution. ε might therefore be considered a promising target for small molecule interventions to complement current nucleoside-analog based anti-HBV therapies. An ideal prerequisite to any RNA-directed small molecule strategy would be a detailed structural description of this important element. Herein, we present a solution NMR structure for HBV ε which, in combination with molecular dynamics and docking simulations, reports on a flexible ligand "pocket", reminiscent of those observed in proteins. We also demonstrate the binding of the selective estrogen receptor modulators (SERMs) Raloxifene, Bazedoxifene, and a de novo derivative to the priming loop.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Regan M. LeBlanc
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, USA
- Vertex Pharmaceuticals, Boston, MA, USA
| | - Wojciech K. Kasprzak
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Andrew P. Longhini
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Lukasz T. Olenginski
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | - Fardokht Abulwerdi
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Stefano Ginocchio
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Brigit Shields
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Julie Nyman
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Maryia Svirydava
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | | | - Joseph Ivanic
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Bruce A. Shapiro
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Theodore Kwaku Dayie
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
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18
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Liu Y, Veeraraghavan V, Pinkerton M, Fu J, Douglas MW, George J, Tu T. Viral Biomarkers for Hepatitis B Virus-Related Hepatocellular Carcinoma Occurrence and Recurrence. Front Microbiol 2021; 12:665201. [PMID: 34194408 PMCID: PMC8236856 DOI: 10.3389/fmicb.2021.665201] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 05/06/2021] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the sixth most common cancer worldwide and the fourth leading cause of cancer-related death. The most common risk factor for developing HCC is chronic infection with hepatitis B virus (HBV). Early stages of HBV-related HCC (HBV-HCC) are generally asymptomatic. Moreover, while serum alpha-fetoprotein (AFP) and abdominal ultrasound are widely used to screen for HCC, they have poor sensitivity. Thus, HBV-HCC is frequently diagnosed at an advanced stage, in which there are limited treatment options and high mortality rates. Serum biomarkers with high sensitivity and specificity are crucial for earlier diagnosis of HCC and improving survival rates. As viral-host interactions are key determinants of pathogenesis, viral biomarkers may add greater diagnostic power for HCC than host biomarkers alone. In this review, we summarize recent research on using virus-derived biomarkers for predicting HCC occurrence and recurrence; including circulating viral DNA, RNA transcripts, and viral proteins. Combining these viral biomarkers with AFP and abdominal ultrasound could improve sensitivity and specificity of early diagnosis, increasing the survival of patients with HBV-HCC. In the future, as the mechanisms that drive HBV-HCC to become clearer, new biomarkers may be identified which can further improve early diagnosis of HBV-HCC.
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Affiliation(s)
- Yuanyuan Liu
- Department of Infectious Diseases, The Affiliated Xi'an Central Hospital of Xi'an Jiaotong University, Xi'an, China.,Storr Liver Centre, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Sydney, NSW, Australia
| | - Vaishnavi Veeraraghavan
- Storr Liver Centre, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Sydney, NSW, Australia.,School of Medical Science, The University of Sydney, Camperdown, NSW, Australia
| | - Monica Pinkerton
- Storr Liver Centre, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Sydney, NSW, Australia.,School of Medical Science, The University of Sydney, Camperdown, NSW, Australia
| | - Jianjun Fu
- Department of Infectious Diseases, The Affiliated Xi'an Central Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Mark W Douglas
- Storr Liver Centre, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology, Westmead Hospital, Sydney, NSW, Australia
| | - Jacob George
- Storr Liver Centre, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Sydney, NSW, Australia
| | - Thomas Tu
- Storr Liver Centre, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Sydney, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW, Australia
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19
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Prifti GM, Moianos D, Giannakopoulou E, Pardali V, Tavis JE, Zoidis G. Recent Advances in Hepatitis B Treatment. Pharmaceuticals (Basel) 2021; 14:417. [PMID: 34062711 PMCID: PMC8147224 DOI: 10.3390/ph14050417] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 01/10/2023] Open
Abstract
Hepatitis B virus infection affects over 250 million chronic carriers, causing more than 800,000 deaths annually, although a safe and effective vaccine is available. Currently used antiviral agents, pegylated interferon and nucleos(t)ide analogues, have major drawbacks and fail to completely eradicate the virus from infected cells. Thus, achieving a "functional cure" of the infection remains a real challenge. Recent findings concerning the viral replication cycle have led to development of novel therapeutic approaches including viral entry inhibitors, epigenetic control of cccDNA, immune modulators, RNA interference techniques, ribonuclease H inhibitors, and capsid assembly modulators. Promising preclinical results have been obtained, and the leading molecules under development have entered clinical evaluation. This review summarizes the key steps of the HBV life cycle, examines the currently approved anti-HBV drugs, and analyzes novel HBV treatment regimens.
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Affiliation(s)
- Georgia-Myrto Prifti
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (G.-M.P.); (D.M.); (E.G.); (V.P.)
| | - Dimitrios Moianos
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (G.-M.P.); (D.M.); (E.G.); (V.P.)
| | - Erofili Giannakopoulou
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (G.-M.P.); (D.M.); (E.G.); (V.P.)
| | - Vasiliki Pardali
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (G.-M.P.); (D.M.); (E.G.); (V.P.)
| | - John E. Tavis
- Molecular Microbiology and Immunology, Saint Louis University, Saint Louis, MO 63104, USA;
| | - Grigoris Zoidis
- Department of Pharmacy, Division of Pharmaceutical Chemistry, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (G.-M.P.); (D.M.); (E.G.); (V.P.)
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20
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Zhao X, Fan H, Chen X, Zhao X, Wang X, Feng Y, Liu M, Li S, Tang H. Hepatitis B Virus DNA Polymerase Restrains Viral Replication Through the CREB1/HOXA Distal Transcript Antisense RNA Homeobox A13 Axis. Hepatology 2021; 73:503-519. [PMID: 32314410 DOI: 10.1002/hep.31284] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 02/20/2020] [Accepted: 04/04/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS Long noncoding RNAs (lncRNAs) have been associated with infection and hepatitis B virus (HBV)-related diseases, though the underlying mechanisms remain unclear. APPROACH AND RESULTS We obtained HBV-HCC lncRNA profiles by deep sequencing and found HOXA distal transcript antisense RNA (HOTTIP) to be significantly up-regulated. RT-qPCR indicated that HOTTIP is highly expressed in HBV-positive hepatoma tissue and induced by HBV in vitro. Virological experiments showed that HOTTIP significantly suppresses the generation of hepatitis B viral surface antigen, hepatitis B viral e antigen and HBV replication. Homeobox A13 (HOXA13), a downstream factor of HOTTIP, was found to bind to HBV enhancer I and X promotor to repress the production of HBV pregenome RNA (pgRNA) and total RNA as well as HBV replication, suggesting that HOXA13 mediates HOTTIP-induced suppression of HBV replication. More interestingly, HBV DNA polymerase (DNA pol) binds to and stabilizes cAMP-responsive element-binding protein 1 (CREB1) mRNA to facilitate translation of the protein, which, in turn, binds to the regulatory element of HOTTIP to promote its expression. CONCLUSIONS Our findings demonstrate that HBV DNA pol attenuates HBV replication through activation of the CREB1-HOTTIP-HOXA13 axis. These findings shed light on the mechanism by which HBV restrains replication to contribute to persistent infection.
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Affiliation(s)
- Xiaopei Zhao
- Tianjin Life Science Research CenterTianjin Key Laboratory of Inflammation BiologyCollaborative Innovation Center of Tianjin for Medical EpigeneticsDepartment of Pathogen BiologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Hongxia Fan
- Tianjin Life Science Research CenterTianjin Key Laboratory of Inflammation BiologyCollaborative Innovation Center of Tianjin for Medical EpigeneticsDepartment of Pathogen BiologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Xi Chen
- Tianjin Life Science Research CenterTianjin Key Laboratory of Inflammation BiologyCollaborative Innovation Center of Tianjin for Medical EpigeneticsDepartment of Pathogen BiologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Xiaoqing Zhao
- Tianjin Life Science Research CenterTianjin Key Laboratory of Inflammation BiologyCollaborative Innovation Center of Tianjin for Medical EpigeneticsDepartment of Pathogen BiologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Xu Wang
- Tianjin Life Science Research CenterTianjin Key Laboratory of Inflammation BiologyCollaborative Innovation Center of Tianjin for Medical EpigeneticsDepartment of Pathogen BiologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Yujie Feng
- Tianjin Life Science Research CenterTianjin Key Laboratory of Inflammation BiologyCollaborative Innovation Center of Tianjin for Medical EpigeneticsDepartment of Pathogen BiologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Min Liu
- Tianjin Life Science Research CenterTianjin Key Laboratory of Inflammation BiologyCollaborative Innovation Center of Tianjin for Medical EpigeneticsDepartment of Pathogen BiologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Shengping Li
- State Key Laboratory of Oncology in Southern ChinaDepartment of Hepatobiliary OncologySun Yat-sen UniversityCancer CenterGuangzhouChina
| | - Hua Tang
- Tianjin Life Science Research CenterTianjin Key Laboratory of Inflammation BiologyCollaborative Innovation Center of Tianjin for Medical EpigeneticsDepartment of Pathogen BiologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
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21
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Hu S, Xiong H, Kang X, Wang S, Zhang T, Yuan Q, Tian D. Preparation and functional evaluation of monoclonal antibodies targeting Hepatitis B Virus Polymerase. Virulence 2021; 12:188-194. [PMID: 33356842 PMCID: PMC7834045 DOI: 10.1080/21505594.2020.1869391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
HBV pol plays a critical role in the replication of hepatitis B virus (HBV). Previous studies conducted on HBV pol have produced limited evidence on HBV pol expression due to the lack of effective detection methods. The present study used the HBV pol (159–406 aa) protein as a target to screen for specific monoclonal antibodies that recognize HBV pol and subsequently evaluate their diagnostic and therapeutic value. Four antibodies (P3, P5, P12, P20) against HBV pol were obtained. Among them, the P20 antibody indicated optimal binding with HBV pol as demonstrated by Western blotting (WB) in a cell model transfected with the HBV genome. We also expressed P5 and P12 antibodies in mouse liver cells by transfection and the results indicated significant antiviral effects caused by these two antibodies especially P12. In summary, the present study established an antibody which was denoted P20. This antibody can be used to detect HBV pol expression by four HBV genomes via WB analysis. In addition, the antibody denoted P12 could exert antiviral effects via intracellular expression, which may provide a promising approach for the treatment of chronic hepatitis B.
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Affiliation(s)
- Song Hu
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan, Hubei Province, China
| | - Hualong Xiong
- School of Life Science & School of Public Health; State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University , Xiamen, China
| | - Xiaozhen Kang
- School of Life Science & School of Public Health; State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University , Xiamen, China
| | - Shaojuan Wang
- School of Life Science & School of Public Health; State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University , Xiamen, China
| | - Tianying Zhang
- School of Life Science & School of Public Health; State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University , Xiamen, China
| | - Quan Yuan
- School of Life Science & School of Public Health; State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University , Xiamen, China
| | - Deying Tian
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan, Hubei Province, China
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22
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Abstract
Hepatitis B virus (HBV) is a major cause of hepatocellular carcinoma (HCC). There are approximately 250 million people in the world that are chronically infected by this virus, resulting in nearly 1 million deaths every year. Many of these patients die from severe liver diseases, including HCC. HBV may induce HCC through the induction of chronic liver inflammation, which can cause oxidative stress and DNA damage. However, many studies also indicated that HBV could induce HCC via the alteration of hepatocellular physiology that may involve genetic and epigenetic changes of the host DNA, the alteration of cellular signaling pathways, and the inhibition of DNA repair mechanisms. This alteration of cellular physiology can lead to the accumulation of DNA damages and the promotion of cell cycles and predispose hepatocytes to oncogenic transformation.
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Affiliation(s)
- Jiyoung Lee
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, 2011 Zonal Avenue, HMR-401, Los Angeles, CA, 90033, USA
| | - Kuen-Nan Tsai
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, 2011 Zonal Avenue, HMR-401, Los Angeles, CA, 90033, USA
| | - Jing-Hsiung James Ou
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, 2011 Zonal Avenue, HMR-401, Los Angeles, CA, 90033, USA.
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23
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Bak E, Miller JT, Noronha A, Tavis J, Gallicchio E, Murelli RP, Le Grice SFJ. 3,7-Dihydroxytropolones Inhibit Initiation of Hepatitis B Virus Minus-Strand DNA Synthesis. Molecules 2020; 25:molecules25194434. [PMID: 32992516 PMCID: PMC7583054 DOI: 10.3390/molecules25194434] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/15/2020] [Accepted: 09/19/2020] [Indexed: 02/07/2023] Open
Abstract
Initiation of protein-primed (-) strand DNA synthesis in hepatitis B virus (HBV) requires interaction of the viral reverse transcriptase with epsilon (ε), a cis-acting regulatory signal located at the 5' terminus of pre-genomic RNA (pgRNA), and several host-encoded chaperone proteins. Binding of the viral polymerase (P protein) to ε is necessary for pgRNA encapsidation and synthesis of a short primer covalently attached to its terminal domain. Although we identified small molecules that recognize HBV ε RNA, these failed to inhibit protein-primed DNA synthesis. However, since initiation of HBV (-) strand DNA synthesis occurs within a complex of viral and host components (e.g., Hsp90, DDX3 and APOBEC3G), we considered an alternative therapeutic strategy of allosteric inhibition by disrupting the initiation complex or modifying its topology. To this end, we show here that 3,7-dihydroxytropolones (3,7-dHTs) can inhibit HBV protein-primed DNA synthesis. Since DNA polymerase activity of a ribonuclease (RNase H)-deficient HBV reverse transcriptase that otherwise retains DNA polymerase function is also abrogated, this eliminates direct involvement of RNase (ribonuclease) H activity of HBV reverse transcriptase and supports the notion that the HBV initiation complex might be therapeutically targeted. Modeling studies also provide a rationale for preferential activity of 3,7-dHTs over structurally related α-hydroxytropolones (α-HTs).
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Affiliation(s)
- Ellen Bak
- Basic Research Laboratory National Cancer Institute, Frederick, MD 21702, USA; (E.B.); (J.T.M.); (A.N.)
| | - Jennifer T. Miller
- Basic Research Laboratory National Cancer Institute, Frederick, MD 21702, USA; (E.B.); (J.T.M.); (A.N.)
| | - Andrea Noronha
- Basic Research Laboratory National Cancer Institute, Frederick, MD 21702, USA; (E.B.); (J.T.M.); (A.N.)
| | - John Tavis
- Department of Molecular Microbiology and Immunology, St. Louis University, St. Louis, MO 63104, USA;
| | - Emilio Gallicchio
- Department of Chemistry, Brooklyn College, The City University of New York, Brooklyn, NY 11210, USA; (E.G.); (R.P.M.)
- PhD Program in Chemistry, The Graduate Center of The City University of New York, New York, NY 10016, USA
- PhD Program in Biochemistry, The Graduate Center of The City University of New York, New York, NY 10016, USA
| | - Ryan P. Murelli
- Department of Chemistry, Brooklyn College, The City University of New York, Brooklyn, NY 11210, USA; (E.G.); (R.P.M.)
- PhD Program in Chemistry, The Graduate Center of The City University of New York, New York, NY 10016, USA
- PhD Program in Biochemistry, The Graduate Center of The City University of New York, New York, NY 10016, USA
| | - Stuart F. J. Le Grice
- Basic Research Laboratory National Cancer Institute, Frederick, MD 21702, USA; (E.B.); (J.T.M.); (A.N.)
- Correspondence:
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24
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Gu Y, Lian Y, Zheng Q, Huang Z, Gu L, Bi Y, Li J, Huang Y, Wu Y, Chen L, Huang Y. Association among cytokine profiles of innate and adaptive immune responses and clinical-virological features in untreated patients with chronic hepatitis B. BMC Infect Dis 2020; 20:509. [PMID: 32664850 PMCID: PMC7362653 DOI: 10.1186/s12879-020-05233-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 07/07/2020] [Indexed: 02/07/2023] Open
Abstract
Background Complete clearance of intracellular viruses depends on effector cells of innate and adaptive immune systems. This study aimed to identify the relationships among antiviral cytokines produced by natural killer (NK) and T cells and clinical-virological characteristics in untreated chronic hepatitis B (CHB) patients. Methods We measured antiviral cytokines interferon-gamma (IFN-γ), tumor necrosis factor-alpha (TNF-α), and interleukin-2 (IL-2) produced by T, NK and natural killer T (NKT) cells, respectively, in a cohort with chronic hepatitis B virus (HBV) infection (CHB). We also correlated these cytokines with clinical-virological characteristics using a linear regression model. Results levels of IFN-γ+ and TNF-α+ CD4+ and CD8+ T cells were significantly higher in immune active (IA) phase than in other phases. Immune tolerant (IT) patients showed the lowest expression of IFN-γ by NK and NKT cells, and TNF-α by NK cells. IFN-γ+, TNF-α+ and IL-2+ CD4+ and CD8+ T cells frequencies were similar between IA and gray zone (GZ) phases. Principal component analysis based on cytokines confirmed that most IT patients significantly differed from inactive carriers (IC) and IA patients, while GZ patients were widely scattered. Multivariate analysis showed both T and NK cells producing IFN-γ and TNF-α, but not IL-2, had significant association with serum alanine aminotransferase (ALT). Moreover, IFN-γ+ NKT cells were associated with HBV DNA, while IFN-γ+ CD4+ and CD8+ T cells were correlated with age. Conclusion HBV clinical phases are characterized by distinct cytokine signatures, which showed relationship to viral features in these untreated CHB patients.
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Affiliation(s)
- Yurong Gu
- Department of Infectious Diseases, the Third Affiliated Hospital of Sun Yat-sen University, 600 Tian He Rd, Guangzhou, 510630, China
| | - Yifan Lian
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, 600 Tian He Rd, Guangzhou, 510630, China
| | - Qiaolan Zheng
- Journal Center, The Third Affiliated Hospital of Sun Yat-sen University, 600 Tian He Rd, Guangzhou, 510630, China
| | - Zexuan Huang
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, 600 Tian He Rd, Guangzhou, 510630, China
| | - Lin Gu
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, 600 Tian He Rd, Guangzhou, 510630, China
| | - Yanhua Bi
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, 600 Tian He Rd, Guangzhou, 510630, China
| | - Jing Li
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, 600 Tian He Rd, Guangzhou, 510630, China
| | - Yanlin Huang
- Department of Infectious Diseases, the Third Affiliated Hospital of Sun Yat-sen University, 600 Tian He Rd, Guangzhou, 510630, China
| | - Yuankai Wu
- Department of Infectious Diseases, the Third Affiliated Hospital of Sun Yat-sen University, 600 Tian He Rd, Guangzhou, 510630, China
| | - Lubiao Chen
- Department of Infectious Diseases, the Third Affiliated Hospital of Sun Yat-sen University, 600 Tian He Rd, Guangzhou, 510630, China.
| | - Yuehua Huang
- Department of Infectious Diseases, the Third Affiliated Hospital of Sun Yat-sen University, 600 Tian He Rd, Guangzhou, 510630, China. .,Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, 600 Tian He Rd, Guangzhou, 510630, China.
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25
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Mohammadzadeh I, Qujeq D, Yousefi T, Ferns GA, Maniati M, Vaghari-Tabari M. CRISPR/Cas9 gene editing: A new therapeutic approach in the treatment of infection and autoimmunity. IUBMB Life 2020; 72:1603-1621. [PMID: 32344465 DOI: 10.1002/iub.2296] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 12/19/2022]
Abstract
CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein9) may be viewed as an adaptive bacterial immune system. When a virus infects a bacterium, a fragment of the virus genome is inserted into the CRISPR sequence of the bacterial genome as a memory. When the bacterium becomes infected again with the same virus, an RNA molecule that is a transcript of the memory sequence, directs Cas9, an endonuclease, to the complementary region of the virus genome, and Cas9 disables the virus by a double-strand break. In recent years, studies have shown that by designing synthetic RNA molecules and delivering them along with Cas9 into eukaryotic cells, different regions of the cell's genome can be targeted and manipulated. These findings have drawn much attention to this new technology and it has been shown that CRISPR/Cas9 gene editing can be used to treat some human diseases. These include infectious diseases and autoimmune diseases. In this review article, in addition to a brief overview of the biology of the CRISPR/Cas9 system, we collected the most recent findings on the applications of CRISPR/Cas9 technology for better investigation of the pathogenesis and treatment of viral infections (human immunodeficiency virus infection, hepatitis virus infections, and onco-virus infections), non-viral infections (parasitic, fungal, and bacterial infections), and autoimmune diseases.
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Affiliation(s)
- Iraj Mohammadzadeh
- Non-Communicable Pediatric Diseases Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Durdi Qujeq
- Cellular and Molecular Biology Research Center (CMBRC), Health Research Institute, Babol University of Medical Sciences, Babol, Iran.,Department of Clinical Biochemistry, Babol University of Medical Sciences, Babol, Iran
| | - Tooba Yousefi
- Department of Clinical Biochemistry, Babol University of Medical Sciences, Babol, Iran
| | - Gordon A Ferns
- Department of Medical Education, Brighton & Sussex Medical School, Brighton, UK
| | - Mahmood Maniati
- English Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mostafa Vaghari-Tabari
- Department of Clinical Biochemistry and Laboratory Medicine, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.,Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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26
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Chinnakannan SK, Cargill TN, Donnison TA, Ansari MA, Sebastian S, Lee LN, Hutchings C, Klenerman P, Maini MK, Evans T, Barnes E. The Design and Development of a Multi-HBV Antigen Encoded in Chimpanzee Adenoviral and Modified Vaccinia Ankara Viral Vectors; A Novel Therapeutic Vaccine Strategy against HBV. Vaccines (Basel) 2020; 8:E184. [PMID: 32295168 PMCID: PMC7348829 DOI: 10.3390/vaccines8020184] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/09/2020] [Accepted: 04/12/2020] [Indexed: 12/23/2022] Open
Abstract
Chronic hepatitis B virus (HBV) infection affects 257 million people globally. Current therapies suppress HBV but viral rebound occurs on cessation of therapy; novel therapeutic strategies are urgently required. To develop a therapeutic HBV vaccine that can induce high magnitude T cells to all major HBV antigens, we have developed a novel HBV vaccine using chimpanzee adenovirus (ChAd) and modified vaccinia Ankara (MVA) viral vectors encoding multiple HBV antigens. ChAd vaccine alone generated very high magnitude HBV specific T cell responses to all HBV major antigens. The inclusion of a shark Invariant (SIi) chain genetic adjuvant significantly enhanced the magnitude of T-cells against HBV antigens. Compared to ChAd alone vaccination, ChAd-prime followed by MVA-boost vaccination further enhanced the magnitude and breadth of the vaccine induced T cell response. Intra-cellular cytokine staining study showed that HBV specific CD8+ and CD4+ T cells were polyfunctional, producing combinations of IFNγ, TNF-α, and IL-2. In summary, we have generated genetically adjuvanted ChAd and MVA vectored HBV vaccines with the potential to induce high-magnitude T cell responses through a prime-boost therapeutic vaccination approach. These pre-clinical studies pave the way for new studies of HBV therapeutic vaccination in humans with chronic hepatitis B infection.
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Affiliation(s)
- Senthil K. Chinnakannan
- Peter Medawar Building, Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, UK; (S.K.C.); (T.N.C.); (T.A.D.); (L.N.L.); (C.H.); (P.K.)
| | - Tamsin N. Cargill
- Peter Medawar Building, Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, UK; (S.K.C.); (T.N.C.); (T.A.D.); (L.N.L.); (C.H.); (P.K.)
| | - Timothy A. Donnison
- Peter Medawar Building, Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, UK; (S.K.C.); (T.N.C.); (T.A.D.); (L.N.L.); (C.H.); (P.K.)
| | - M. Azim Ansari
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK;
| | - Sarah Sebastian
- Vaccitech, The Oxford Science Park, The Schrodinger Building, Heatley Road, Oxford OX4 4GE, UK; (S.S.); (T.E.)
| | - Lian Ni Lee
- Peter Medawar Building, Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, UK; (S.K.C.); (T.N.C.); (T.A.D.); (L.N.L.); (C.H.); (P.K.)
| | - Claire Hutchings
- Peter Medawar Building, Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, UK; (S.K.C.); (T.N.C.); (T.A.D.); (L.N.L.); (C.H.); (P.K.)
| | - Paul Klenerman
- Peter Medawar Building, Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, UK; (S.K.C.); (T.N.C.); (T.A.D.); (L.N.L.); (C.H.); (P.K.)
| | - Mala K. Maini
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London WC1E 6JF, UK;
| | - Tom Evans
- Vaccitech, The Oxford Science Park, The Schrodinger Building, Heatley Road, Oxford OX4 4GE, UK; (S.S.); (T.E.)
| | - Eleanor Barnes
- Peter Medawar Building, Nuffield Department of Medicine, University of Oxford, Oxford OX1 3SY, UK; (S.K.C.); (T.N.C.); (T.A.D.); (L.N.L.); (C.H.); (P.K.)
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27
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Masood I, Waheed U, Arshad M, Saeed M, Farooq A, Moneeba S, Basharat N, Zaheer HA. Molecular epidemiology of hepatitis B virus genotypes in blood donors in Islamabad, Pakistan. J Lab Physicians 2020; 11:240-243. [PMID: 31579261 PMCID: PMC6771316 DOI: 10.4103/jlp.jlp_150_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND: Hepatitis B virus (HBV) is a major causative agent of early, severe and prolonged liver infection that subsequently leads to cirrhosis of liver and hepatocellular carcinoma. The aim of this study was to evaluate the molecular epidemiology of hepatitis B virus (HBV) genotypes and comparison of serological assay performance versus polymerase chain reaction (PCR) in HBV screening. METHODS: Blood samples of 8517 healthy blood donors were collected during the period of January to June 2017 from Blood Bank of Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad. Samples were screened for HBsAg assay using technique of chemiluminescence immunoassay. PCR of positive samples was carried out using already reported genotype-specific primers by Naito et al. (2001). The results were confirmed by visualizing genotype bands. RESULTS: The study confirmed the presence of HBV in 2.5% of blood donors, and PCR confirmed the presence of HBV-DNA in 92 samples. The genotyping was done by PCR using type-specific primer sequences. PCR was dogged to check six genotypes, i.e., A, B, C, D, E, and F. The results of this study show high levels of Genotype D is this region, i.e., 52.17% with less dominating Genotype C, which is 16.30% with decreasing ratio of Genotype E (14.13%), Genotype A and B (9.78%), and mixed D + E (2.17%). The presence of coinfection is found at lowest rate. Due to the high percentage of HBV/D, it is concluded that D genotype is common in our population. CONCLUSION: The most prevalent HBV genotype in ICT region was genotype D, which is responsible for liver cirrhosis and hepatocellular carcinoma. Efficacy of drugs varies with variation in genotypes of hepatitis B virus and also with geographical distribution.
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Affiliation(s)
- Iram Masood
- Department of Bioinformatics and Biotechnology, International Islamic University, Islamabad, Pakistan
| | - Usman Waheed
- Safe Blood Transfusion Programme, Ministry of National Health Services, Government of Pakistan, Islamabad, Pakistan.,Department of Pathology and Blood Bank, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Muhammad Arshad
- Department of Bioinformatics and Biotechnology, International Islamic University, Islamabad, Pakistan
| | - Muhammad Saeed
- Department of Pathology and Transfusion Medicine, District Headquarter Hospital, Mandi Bahauddin, Pakistan
| | - Ahmad Farooq
- Department of Bioinformatics and Biotechnology, International Islamic University, Islamabad, Pakistan
| | - Sadaf Moneeba
- Department of Bioinformatics and Biotechnology, International Islamic University, Islamabad, Pakistan
| | - Nosheen Basharat
- Department of Bioinformatics and Biotechnology, International Islamic University, Islamabad, Pakistan
| | - Hasan Abbas Zaheer
- Safe Blood Transfusion Programme, Ministry of National Health Services, Government of Pakistan, Islamabad, Pakistan.,Department of Pathology and Blood Bank, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
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Non-nucleoside hepatitis B virus polymerase inhibitors identified by an in vitro polymerase elongation assay. J Gastroenterol 2020; 55:441-452. [PMID: 31768802 DOI: 10.1007/s00535-019-01643-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/12/2019] [Indexed: 02/04/2023]
Abstract
BACKGROUND Hepatitis B virus (HBV) polymerase is the only virus-encoded enzyme essential for producing the HBV genome and is regarded as an attractive drug target. However, the difficulty of synthesizing and purifying recombinant HBV polymerase protein has hampered the development of new drugs targeting this enzyme, especially compounds unrelated to the nucleoside structure. We recently have developed a technique for the synthesis and purification of recombinant HBV polymerase containing the reverse transcriptase (RT) domain that carried DNA elongation activity in vitro. METHODS We used the overproduced protein to establish an in vitro high-throughput screening system to identify compounds that inhibit the elongation activity of HBV polymerase. RESULTS We screened 1120 compounds and identified a stilbene derivative, piceatannol, as a potential anti-HBV agent. Derivative analysis identified another stilbene derivative, PDM2, that was able to inhibit HBV replication with an IC50 of 14.4 ± 7.7 μM. An infection experiment suggested that the compounds inhibit the replication of HBV rather than the entry process, as expected. Surface plasmon resonance analysis demonstrated a specific interaction between PDM2 and the RT domain. Importantly, PDM2 showed similar inhibitory activity against the replication of both wild-type HBV and a lamivudine/entecavir-resistant HBV variant. Furthermore, PDM2 showed an additive effect in combination with clinically used nucleos(t)ide analogs. CONCLUSIONS We report the development of a screening system that is useful for identifying non-nucleos(t)ide RT inhibitors.
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Mu T, Zhao X, Zhu Y, Fan H, Tang H. The E3 Ubiquitin Ligase TRIM21 Promotes HBV DNA Polymerase Degradation. Viruses 2020; 12:v12030346. [PMID: 32245233 PMCID: PMC7150939 DOI: 10.3390/v12030346] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 12/26/2022] Open
Abstract
The tripartite motif (TRIM) protein family is an E3 ubiquitin ligase family. Recent reports have indicated that some TRIM proteins have antiviral functions, especially against retroviruses. However, most studies mainly focus on the relationship between TRIM21 and interferon or other antiviral effectors. The effect of TRIM21 on virus-encoded proteins remains unclear. In this study, we screened candidate interacting proteins of HBV DNA polymerase (Pol) by FLAG affinity purification and mass spectrometry assay and identified TRIM21 as its regulator. We used a coimmunoprecipitation (co-IP) assay to demonstrate that TRIM21 interacted with the TP domain of HBV DNA Pol. In addition, TRIM21 promoted the ubiquitination and degradation of HBV DNA Pol using its RING domain, which has E3 ubiquitin ligase activity. Lys260 and Lys283 of HBV DNA Pol were identified as targets for ubiquitination mediated by TRIM21. Finally, we uncovered that TRIM21 degrades HBV DNA Pol to restrict HBV DNA replication, and its SPRY domain is critical for this activity. Taken together, our results indicate that TRIM21 suppresses HBV DNA replication mainly by promoting the ubiquitination of HBV DNA Pol, which may provide a new potential target for the treatment of HBV.
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Affiliation(s)
| | | | | | | | - Hua Tang
- Correspondence: ; Tel./Fax: +86-22-2354-2503
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30
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Wang Q, Qin Y, Zhang J, Jia L, Fu S, Wang Y, Li J, Tong S. Tracing the evolutionary history of hepadnaviruses in terms of e antigen and middle envelope protein expression or processing. Virus Res 2019; 276:197825. [PMID: 31785305 DOI: 10.1016/j.virusres.2019.197825] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 12/11/2022]
Abstract
Hepatitis B virus (HBV) is the prototype of hepadnaviruses, which can be subgrouped into orthohepadnaviruses infecting mammals, avihehepadnaviruses of birds, metahepadnaviruses of fish, and herpetohepadnaviruses of amphibians and reptiles. The middle (M) envelope protein and e antigen are new additions in the evolution of hepadnaviruses. They are alternative translation products of the transcripts for small (S) envelope and core proteins, respectively. For HBV, e antigen is converted from precore/core protein by removal of N-terminal signal peptide followed by furin-mediated cleavage of the basic C-terminus. This study compared old and newly discovered hepadnaviruses for their envelope protein and e antigen expression or processing. The S protein of bat hepatitis B virus (BHBV) and two metahepadnaviruses is probably myristoylated, in addition to two avihepadnaviruses. While most orthohepadnaviruses express a functional M protein with N-linked glycosylation near the amino-terminus, most metahepadnaviruses and herpetohepadnaviruses probably do not. These viruses and one orthohepadnavirus, the shrew hepatitis B virus, lack an open precore region required for e antigen expression. Potential furin cleavage sites (RXXR sequence) can be found in e antigen precursors of orthohepadnaviruses and avihepadnaviruses. Despite much larger precore/core proteins of avihepadnaviruses and their limited sequence homology with those of orthohepadnaviruses, their proximal RXXR motif can be aligned with a distal RXXR motif for orthohepadnaviruses. Thus, furin or another basic endopeptidase is probably the shared enzyme for hepadnaviral e antigen maturation. A precore-derived cysteine residue is involved in forming intramolecular disulfide bond of HBV e antigen to prevent particle formation, and such a cysteine residue is conserved for both orthohepadnaviruses and avihepadnaviruses. All orthohepadnaviruses have an X gene, while all avihepadnaviruses can express the e antigen. M protein expression appears to be the most recent event in the evolution of hepadnaviruses.
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Affiliation(s)
- Qianru Wang
- Department of Pathobiology, Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yanli Qin
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jing Zhang
- Department of Pathobiology, Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Lucy Jia
- Liver Research Center, Rhode Island Hospital and Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Shuwen Fu
- Department of Pathobiology, Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yongxiang Wang
- Department of Pathobiology, Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jisu Li
- Liver Research Center, Rhode Island Hospital and Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Shuping Tong
- Department of Pathobiology, Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fudan University, Shanghai, China; Liver Research Center, Rhode Island Hospital and Warren Alpert Medical School of Brown University, Providence, RI, USA.
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31
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Gao M, Feng C, Ying R, Nie Y, Deng X, Zhu Y, Tang X, Guan Y, Hu F, Li F. A novel one-step quantitative reverse transcription PCR assay for selective amplification of hepatitis B virus pregenomic RNA from a mixture of HBV DNA and RNA in serum. Arch Virol 2019; 164:2683-2690. [PMID: 31428915 DOI: 10.1007/s00705-019-04372-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 07/11/2019] [Indexed: 12/11/2022]
Abstract
Current antiviral therapies against hepatitis B virus (HBV) infections, such as treatment with nucleos(t)ide analogs (NAs) and interferon alpha, can significantly lower HBV DNA titers, eventually to undetectable levels. However, it is still difficult to completely eliminate the stable template of HBV, the covalently closed circular DNA (cccDNA), and this contributes to viral rebound when treatment is discontinued. HBV pregenomic RNA (pgRNA), which was recently found to be present in the enveloped mature HBV viral particle in blood, is tentatively regarded, with still accumulating clinical evidence, as a novel bona fide virological marker reflecting the amount and status of cccDNA when serum HBV DNA becomes undetectable. HBV pgRNA and DNA share almost identical sequences, and it is therefore difficult to differentiate pgRNA from viral DNA using normal PCR methods. To exclude interference from viral DNA, methods for measuring pgRNA usually require a selective DNA degradation step, which is complicated and time-consuming and also compromises the accuracy of detection. In this study, we developed a simplified quantitative reverse transcription polymerase chain reaction (qRT-PCR) assay with improved accuracy achieved by probing the polyA tail of pgRNA. Using clinical serum samples, we observed that not all patients share the same 3' sequence, suggesting slight differences between HBV strains in the way they end transcription. We then designed and evaluated a universal primer and probe set for distinguishing HBV pgRNA from HBV DNA. Our results demonstrated that a one-step qRT-PCR assay could selectively amplify HBV pgRNA from a mixture of HBV RNA and DNA, which is valuable for clinical applications.
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Affiliation(s)
- Ming Gao
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, 627 Dongfeng Dong Rd, Guangzhou, 510060, Guangdong, China
| | - Chengqian Feng
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, 627 Dongfeng Dong Rd, Guangzhou, 510060, Guangdong, China
| | - Ruosu Ying
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, 627 Dongfeng Dong Rd, Guangzhou, 510060, Guangdong, China
| | - Yuan Nie
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, 627 Dongfeng Dong Rd, Guangzhou, 510060, Guangdong, China
| | - Xizi Deng
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, 627 Dongfeng Dong Rd, Guangzhou, 510060, Guangdong, China
| | - Ying Zhu
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, 627 Dongfeng Dong Rd, Guangzhou, 510060, Guangdong, China
| | - Xiaoping Tang
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, 627 Dongfeng Dong Rd, Guangzhou, 510060, Guangdong, China
| | - Yujuan Guan
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, 627 Dongfeng Dong Rd, Guangzhou, 510060, Guangdong, China
| | - Fengyu Hu
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, 627 Dongfeng Dong Rd, Guangzhou, 510060, Guangdong, China.
| | - Feng Li
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, 627 Dongfeng Dong Rd, Guangzhou, 510060, Guangdong, China.
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32
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Qiao L, Luo GG. Human apolipoprotein E promotes hepatitis B virus infection and production. PLoS Pathog 2019; 15:e1007874. [PMID: 31393946 PMCID: PMC6687101 DOI: 10.1371/journal.ppat.1007874] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/27/2019] [Indexed: 12/16/2022] Open
Abstract
Hepatitis B virus (HBV) is a common cause of liver diseases, including chronic hepatitis, steatosis, fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). HBV chronically infects about 240 million people worldwide, posing a major global health problem. The current standard antiviral therapy effectively inhibits HBV replication but does not eliminate the virus unlike direct-acting antivirals (DAA) for curing hepatitis C. Our previous studies have demonstrated that human apolipoprotein E (apoE) plays important roles in hepatitis C virus infection and morphogenesis. In the present study, we have found that apoE is also associated with HBV and is required for efficient HBV infection. An apoE-specific monoclonal antibody was able to capture HBV similar to anti-HBs. More importantly, apoE monoclonal antibody could effectively block HBV infection, resulting in a greater than 90% reduction of HBV infectivity. Likewise, silencing of apoE expression or knockout of apoE gene by CRISPR/Cas9 resulted in a greater than 90% reduction of HBV infection and more than 80% decrease of HBV production, which could be fully restored by ectopic apoE expression. However, apoE silencing or knockout did not significantly affect HBV DNA replication or the production of nonenveloped (naked) nucleocapsids. These findings demonstrate that human apoE promotes HBV infection and production. We speculate that apoE may also play a role in persistent HBV infection by evading host immune response similar to its role in the HCV life cycle and pathogenesis. Inhibitors interfering with apoE biogenesis, secretion, and/or binding to receptors may serve as antivirals for elimination of chronic HBV infection.
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Affiliation(s)
- Luhua Qiao
- Department of Microbiology, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, United States of America
| | - Guangxiang George Luo
- Department of Microbiology, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, United States of America
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33
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Puray-Chavez MN, Farghali MH, Yapo V, Huber AD, Liu D, Ndongwe TP, Casey MC, Laughlin TG, Hannink M, Tedbury PR, Sarafianos SG. Effects of Moloney Leukemia Virus 10 Protein on Hepatitis B Virus Infection and Viral Replication. Viruses 2019; 11:v11070651. [PMID: 31319455 PMCID: PMC6669478 DOI: 10.3390/v11070651] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 12/16/2022] Open
Abstract
Moloney leukemia virus 10 (MOV10) is an RNA helicase that has been shown to affect the replication of several viruses. The effect of MOV10 on Hepatitis B virus (HBV) infection is not known and its role on the replication of this virus is poorly understood. We investigated the effect of MOV10 down-regulation and MOV10 over-expression on HBV in a variety of cell lines, as well as in an infection system using a replication competent virus. We report that MOV10 down-regulation, using siRNA, shRNA, and CRISPR/Cas9 gene editing technology, resulted in increased levels of HBV DNA, HBV pre-genomic RNA, and HBV core protein. In contrast, MOV10 over-expression reduced HBV DNA, HBV pre-genomic RNA, and HBV core protein. These effects were consistent in all tested cell lines, providing strong evidence for the involvement of MOV10 in the HBV life cycle. We demonstrated that MOV10 does not interact with HBV-core. However, MOV10 binds HBV pgRNA and this interaction does not affect HBV pgRNA decay rate. We conclude that the restriction of HBV by MOV10 is mediated through effects at the level of viral RNA.
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Affiliation(s)
- Maritza N Puray-Chavez
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
| | - Mahmoud H Farghali
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Tanta University, Tanta QXXV+C5, Egypt
| | - Vincent Yapo
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
| | - Andrew D Huber
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Dandan Liu
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
| | - Tanyaradzwa P Ndongwe
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
| | - Mary C Casey
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
| | - Thomas G Laughlin
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Mark Hannink
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Philip R Tedbury
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA.
| | - Stefan G Sarafianos
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA.
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
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34
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Feng J, Yang G, Liu Y, Gao Y, Zhao M, Bu Y, Yuan H, Yuan Y, Yun H, Sun M, Gao H, Zhang S, Liu Z, Yin M, Song X, Miao Z, Lin Z, Zhang X. LncRNA PCNAP1 modulates hepatitis B virus replication and enhances tumor growth of liver cancer. Am J Cancer Res 2019; 9:5227-5245. [PMID: 31410212 PMCID: PMC6691589 DOI: 10.7150/thno.34273] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 06/06/2019] [Indexed: 02/06/2023] Open
Abstract
Rationale: Hepatitis B virus (HBV) is a major risk factor for liver cancer, in which HBV covalently closed circular DNA (cccDNA) plays crucial roles. However, the effect of pseudogene-derived long noncoding RNAs (lncRNAs) acting as functional regulators of their ancestral gene expression on HBV replication and hepatocellular carcinoma (HCC) remains unclear. In this study, we speculated that the pseudogene-derived lncRNA PCNAP1 and its ancestor PCNA might modulate HBV replication and promote hepatocarcinogenesis. Methods: We investigated the roles of lncRNA PCNAP1 in contribution of HBV replication through modulating miR-154/PCNA/HBV cccDNA signaling in hepatocarcinogenesis by using CRISPR/Cas9, Southern blot analysis, confocal assays, et al. in primary human hepatocytes (PHH), HepaRG cells, HepG2-NTCP cells, hepatoma carcinoma cells, human liver-chimeric mice model, transgenetic mice model, in vitro tumorigenicity and clinical patients. Results: Interestingly, the expression levels of PCNAP1 and PCNA were significantly elevated in the liver of HBV-infectious human liver-chimeric mice. Clinically, the mRNA levels of PCNAP1 and PCNA were increased in the liver of HBV-positive/HBV cccDNA-positive HCC patients. Mechanistically, PCNA interacted with HBV cccDNA in a HBc-dependent manner. PCNAP1 enhanced PCNA through sponging miR-154 targeting PCNA mRNA 3′UTR. Functionally, PCNAP1 or PCNA remarkably enhanced HBV replication and accelerated the growth of HCC in vitro and in vivo. Conclusion: We conclude that lncRNA PCNAP1 enhances the HBV replication through modulating miR-154/PCNA/HBV cccDNA signaling and the PCNAP1/PCNA signaling drives the hepatocarcinogenesis. Our finding provides new insights into the mechanism by which lncRNA PCNAP1 enhances HBV replication and hepatocarcinogenesis.
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Lin Y, Wu C, Wang X, Liu S, Zhao K, Kemper T, Yu H, Li M, Zhang J, Chen M, Zhu Y, Chen X, Lu M. Glucosamine promotes hepatitis B virus replication through its dual effects in suppressing autophagic degradation and inhibiting MTORC1 signaling. Autophagy 2019; 16:548-561. [PMID: 31204557 DOI: 10.1080/15548627.2019.1632104] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Glucosamine (GlcN), a dietary supplement widely utilized to promote joint health and effective in the treatment of osteoarthritis, is an effective macroautophagy/autophagy activator in vitro and in vivo. Previous studies have shown that autophagy is required for hepatitis B virus (HBV) replication and envelopment. The objective of this study was to determine whether and how GlcN affects HBV replication, using in vitro and in vivo experiments. Our data demonstrated that HBsAg production and HBV replication were significantly increased by GlcN treatment. Confocal microscopy and western blot analysis showed that the amount of autophagosomes and the levels of autophagic markers MAP1LC3/LC3-II and SQSTM1 were clearly elevated by GlcN treatment. GlcN strongly blocked autophagic degradation of HBV virions and proteins by inhibiting lysosomal acidification through its amino group. Moreover, GlcN further promoted HBV replication by inducing autophagosome formation via feedback inhibition of mechanistic target of rapamycin kinase complex 1 (MTORC1) signaling in an RRAGA (Ras related GTP binding A) GTPase-dependent manner. In vivo, GlcN application promoted HBV replication and blocked autophagic degradation in an HBV hydrodynamic injection mouse model. In addition, GlcN promoted influenza A virus, enterovirus 71, and vesicular stomatitis virus replication in vitro. In conclusion, GlcN efficiently promotes virus replication by inducing autophagic stress through its dual effects in suppressing autophagic degradation and inhibiting MTORC1 signaling. Thus, there is a potential risk of enhanced viral replication by oral GlcN intake in chronically virally infected patients.Abbreviations: ACTB: actin beta; ATG: autophagy-related; CMIA: chemiluminescence immunoassay; ConA: concanavalin A; CQ: chloroquine; CTSD: cathepsin D; DAPI: 4',6-diamidino-2-phenylindole; EV71: enterovirus 71; GalN: galactosamine; GFP: green fluorescence protein; GlcN: glucosamine; GNPNAT1: glucosamine-phosphate N-acetyltransferase 1; HBP: hexosamine biosynthesis pathway; HBV: hepatitis B virus; HBcAg: hepatitis B core antigen; HBsAg: hepatitis B surface antigen; HBeAg: hepatitis B e antigen; HBV RI: hepatitis B replicative intermediate; IAV: influenza A virus; LAMP1: lysosomal associated membrane protein 1; LAMTOR: late endosomal/lysosomal adaptor, MAPK and MTOR activator; ManN: mannosamine; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MTORC1: mechanistic target of rapamycin kinase complex 1; PHH: primary human hepatocyte; RAB7: RAB7A, member RAS oncogene family; RPS6KB1: ribosomal protein S6 kinase B1; RRAGA: Ras related GTP binding A; RT-PCR: reverse transcriptase polymerase chain reaction; SEM: standard error of the mean; siRNA: small interfering RNA; SQSTM1/p62: sequestosome 1; UAP1: UDP-N-acetylglucosamine pyrophosphorylase 1; VSV: vesicular stomatitis virus.
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Affiliation(s)
- Yong Lin
- Institute of Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of Education, Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Chunchen Wu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, China
| | - Xueyu Wang
- Institute of Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Shi Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Kaitao Zhao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, China
| | - Thekla Kemper
- Institute of Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Haisheng Yu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Mengqi Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Jiming Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Mingzhou Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Ying Zhu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xinwen Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, China
| | - Mengji Lu
- Institute of Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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36
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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: 120] [Impact Index Per Article: 24.0] [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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RNA-Binding Motif Protein 24 (RBM24) Is Involved in Pregenomic RNA Packaging by Mediating Interaction between Hepatitis B Virus Polymerase and the Epsilon Element. J Virol 2019; 93:JVI.02161-18. [PMID: 30626666 DOI: 10.1128/jvi.02161-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 12/18/2018] [Indexed: 12/14/2022] Open
Abstract
Encapsidation of pregenomic RNA (pgRNA) is a crucial step in hepatitis B virus (HBV) replication. Binding by viral polymerase (Pol) to the epsilon stem-loop (ε) on the 5'-terminal region (TR) of pgRNA is required for pgRNA packaging. However, the detailed mechanism is not well understood. RNA-binding motif protein 24 (RBM24) inhibits core translation by binding to the 5'-TR of pgRNA. Here, we demonstrate that RBM24 is also involved in pgRNA packaging. RBM24 directly binds to the lower bulge of ε via RNA recognition submotifs (RNPs). RBM24 also interacts with Pol in an RNA-independent manner. The alanine-rich domain (ARD) of RBM24 and the reverse transcriptase (RT) domain of Pol are essential for binding between RBM24 and Pol. In addition, overexpression of RBM24 increases Pol-ε interaction, whereas RBM24 knockdown decreases the interaction. RBM24 was able to rescue binding between ε and mutant Pol lacking ε-binding activity, further showing that RBM24 mediates the interaction between Pol and ε by forming a Pol-RBM24-ε complex. Finally, RBM24 significantly promotes the packaging efficiency of pgRNA. In conclusion, RBM24 mediates Pol-ε interaction and formation of a Pol-RBM24-ε complex, which inhibits translation of pgRNA and results in pgRNA packing into capsids/virions for reverse transcription and DNA synthesis.IMPORTANCE Hepatitis B virus (HBV) is a ubiquitous human pathogen, and HBV infection is a major global health burden. Chronic HBV infection is associated with the development of liver diseases, including fulminant hepatitis, hepatic fibrosis, cirrhosis, and hepatocellular carcinoma. A currently approved vaccine can prevent HBV infection, and medications are able to reduce viral loads and prevent liver disease progression. However, current treatments rarely achieve a cure for chronic infection. Thus, it is important to gain insight into the mechanisms of HBV replication. In this study, we found that the host factor RBM24 is involved in pregenomic RNA (pgRNA) packaging and regulates HBV replication. These findings highlight a potential target for antiviral therapeutics of HBV infection.
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Common and Distinct Capsid and Surface Protein Requirements for Secretion of Complete and Genome-Free Hepatitis B Virions. J Virol 2018; 92:JVI.00272-18. [PMID: 29743374 DOI: 10.1128/jvi.00272-18] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/04/2018] [Indexed: 02/06/2023] Open
Abstract
During the morphogenesis of hepatitis B virus (HBV), an enveloped virus, two types of virions are secreted: (i) a minor population of complete virions containing a mature nucleocapsid with the characteristic, partially double-stranded, relaxed circular DNA genome and (ii) a major population containing an empty capsid with no DNA or RNA (empty virions). Secretion of both types of virions requires interactions between the HBV capsid or core protein (HBc) and the viral surface or envelope proteins. We have studied the requirements from both HBc and envelope proteins for empty virion secretion in comparison with those for secretion of complete virions. Substitutions within the N-terminal domain of HBc that block secretion of DNA-containing virions reduced but did not prevent secretion of empty virions. The HBc C-terminal domain was not essential for empty virion secretion. Among the three viral envelope proteins, the smallest, S, alone was sufficient for empty virion secretion at a basal level. The largest protein, L, essential for complete virion secretion, was not required but could stimulate empty virion secretion. Also, substitutions in L that eliminated secretion of complete virions reduced but did not eliminate empty virion secretion. S mutations that blocked secretion of the hepatitis D virus (HDV), an HBV satellite, did not block secretion of either empty or complete HBV virions. Together, these results indicate that both common and distinct signals on empty capsids and mature nucleocapsids interact with the S and L proteins during the formation of complete and empty virions.IMPORTANCE Hepatitis B virus (HBV) is a major cause of severe liver diseases, including cirrhosis and cancer. In addition to the complete infectious virion particle, which contains an outer envelope layer and an interior capsid that, in turn, encloses a DNA genome, HBV-infected cells also secrete noninfectious, incomplete viral particles in large excess over the number of complete virions. In particular, the empty (or genome-free) virion shares with the complete virion the outer envelope and interior capsid but contains no genome. We have carried out a comparative study on the capsid and envelope requirements for the secretion of these two types of virion particles and uncovered both shared and distinct determinants on the capsid and envelope for their secretion. These results provide new information on HBV morphogenesis and have implications for efforts to develop empty HBV virions as novel biomarkers and a new generation of HBV vaccine.
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Wang J, Zhang L, Zhao J, Zhang Y, Liu Q, Tian C, Zhang Z, Liu J, Wang X. 2-Arylthio-5-iodo pyrimidine derivatives as non-nucleoside HBV polymerase inhibitors. Bioorg Med Chem 2018; 26:1573-1578. [PMID: 29459146 DOI: 10.1016/j.bmc.2018.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 01/31/2018] [Accepted: 02/02/2018] [Indexed: 11/16/2022]
Abstract
In this study, a series of 2-arylthio-5-iodo pyrimidine derivatives, as non-nucleoside hepatitis B virus inhibitors, were evaluated and firstly reported as potential anti-HBV agents. To probe the mechanism of active agents, DHBV polymerase was isolated and a non-radioisotopic assay was established for measuring HBV polymerase. The biological results demonstrated that 2-arylthio-5-iodo pyrimidine derivatives targeted HBV polymerase. In addition, pharmacophore models were constructed for future optimization of lead compounds. Further study will be performed for the development of non-nucleoside anti-HBV agents.
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Affiliation(s)
- Jie Wang
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, 100191, China
| | - Liang Zhang
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, 100191, China
| | - Jianxiong Zhao
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, 100191, China
| | - Yu Zhang
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, 100191, China
| | - Qingchuan Liu
- Beijing Weijian Jiye Institute of Biotechnology, 100041, China
| | - Chao Tian
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, 100191, China
| | - Zhili Zhang
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, 100191, China
| | - Junyi Liu
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, 100191, China.
| | - Xiaowei Wang
- Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, 100191, China.
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Singh US, Mulamoottil VA, Chu CK. 2′-Fluoro-6′-methylene carbocyclic adenosine and its phosphoramidate prodrug: A novel anti-HBV agent, active against drug-resistant HBV mutants. Med Res Rev 2018; 38:977-1002. [DOI: 10.1002/med.21490] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/04/2018] [Accepted: 01/12/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Uma S. Singh
- Department of Pharmaceutical and Biomedical Sciences; University of Georgia; Athens GA USA
| | | | - Chung K. Chu
- Department of Pharmaceutical and Biomedical Sciences; University of Georgia; Athens GA USA
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Long KR, Lomonosova E, Li Q, Ponzar NL, Villa JA, Touchette E, Rapp S, Liley RM, Murelli RP, Grigoryan A, Buller RM, Wilson L, Bial J, Sagartz JE, Tavis JE. Efficacy of hepatitis B virus ribonuclease H inhibitors, a new class of replication antagonists, in FRG human liver chimeric mice. Antiviral Res 2018; 149:41-47. [PMID: 29129708 PMCID: PMC5743599 DOI: 10.1016/j.antiviral.2017.11.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/11/2017] [Accepted: 11/07/2017] [Indexed: 12/20/2022]
Abstract
Chronic hepatitis B virus infection cannot be cured by current therapies, so new treatments are urgently needed. We recently identified novel inhibitors of the hepatitis B virus ribonuclease H that suppress viral replication in cell culture. Here, we employed immunodeficient FRG KO mice whose livers had been engrafted with primary human hepatocytes to ask whether ribonuclease H inhibitors can suppress hepatitis B virus replication in vivo. Humanized FRG KO mice infected with hepatitis B virus were treated for two weeks with the ribonuclease H inhibitors #110, an α-hydroxytropolone, and #208, an N-hydroxypyridinedione. Hepatitis B virus viral titers and S and e antigen plasma levels were measured. Treatment with #110 and #208 caused significant reductions in plasma viremia without affecting hepatitis B virus S or e antigen levels, and viral titers rebounded following treatment cessation. This is the expected pattern for inhibitors of viral DNA synthesis. Compound #208 suppressed viral titers of both hepatitis B virus genotype A and C isolates. These data indicate that Hepatitis B virus replication can be suppressed during infection in an animal by inhibiting the viral ribonuclease H, validating the ribonuclease H as a novel target for antiviral drug development.
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Affiliation(s)
- Kelly R Long
- Seventh Wave Laboratories LLC, 19 Worthington Access Drive, Maryland Heights, MO 63043, USA.
| | - Elena Lomonosova
- Department of Molecular Microbiology and Immunology & the Saint Louis University Liver Center, Saint Louis University School of Medicine, 1100 S. Grand Blvd., St. Louis, MO 63104, USA.
| | - Qilan Li
- Department of Molecular Microbiology and Immunology & the Saint Louis University Liver Center, Saint Louis University School of Medicine, 1100 S. Grand Blvd., St. Louis, MO 63104, USA.
| | - Nathan L Ponzar
- Department of Molecular Microbiology and Immunology & the Saint Louis University Liver Center, Saint Louis University School of Medicine, 1100 S. Grand Blvd., St. Louis, MO 63104, USA.
| | - Juan A Villa
- Department of Molecular Microbiology and Immunology & the Saint Louis University Liver Center, Saint Louis University School of Medicine, 1100 S. Grand Blvd., St. Louis, MO 63104, USA.
| | - Erin Touchette
- Seventh Wave Laboratories LLC, 19 Worthington Access Drive, Maryland Heights, MO 63043, USA.
| | - Stephen Rapp
- Seventh Wave Laboratories LLC, 19 Worthington Access Drive, Maryland Heights, MO 63043, USA.
| | - R Matt Liley
- Seventh Wave Laboratories LLC, 19 Worthington Access Drive, Maryland Heights, MO 63043, USA.
| | - Ryan P Murelli
- Brookyln College & PhD Program in Chemistry at the Graduate Center of the City University of New York, NY 11210, USA.
| | - Alexandre Grigoryan
- Brookyln College & PhD Program in Chemistry at the Graduate Center of the City University of New York, NY 11210, USA.
| | - R Mark Buller
- Department of Molecular Microbiology and Immunology & the Saint Louis University Liver Center, Saint Louis University School of Medicine, 1100 S. Grand Blvd., St. Louis, MO 63104, USA
| | - Lisa Wilson
- Yecuris Corporation, P.O. Box 4645, Tualatin, OR 97062, USA.
| | - John Bial
- Yecuris Corporation, P.O. Box 4645, Tualatin, OR 97062, USA.
| | - John E Sagartz
- Seventh Wave Laboratories LLC, 19 Worthington Access Drive, Maryland Heights, MO 63043, USA.
| | - John E Tavis
- Department of Molecular Microbiology and Immunology & the Saint Louis University Liver Center, Saint Louis University School of Medicine, 1100 S. Grand Blvd., St. Louis, MO 63104, USA.
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Tsai KN, Kuo CF, Ou JHJ. Mechanisms of Hepatitis B Virus Persistence. Trends Microbiol 2017; 26:33-42. [PMID: 28823759 PMCID: PMC5741523 DOI: 10.1016/j.tim.2017.07.006] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/07/2017] [Accepted: 07/21/2017] [Indexed: 12/15/2022]
Abstract
Hepatitis B virus (HBV) chronically infects 250 million people worldwide, resulting in nearly one million deaths annually. Studies in recent years have significantly improved our knowledge on the mechanisms of HBV persistence. HBV uses multiple pathways to harness host innate immunity to enhance its replication. It can also take advantage of the developing immune system and the not-yet-stabilized gut microbiota of young children to facilitate its persistence, and use maternal viral e antigen to educate immunity of the offspring to support its persistence after vertical transmission. The knowledge gained from these recent studies paves the way for the development of new therapies for the treatment of chronic HBV infection, which has so far been very challenging.
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Affiliation(s)
- Kuen-Nan Tsai
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Cheng-Fu Kuo
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Jing-Hsiung James Ou
- Department of Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA.
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Zhang W, Chen J, Wu M, Zhang X, Zhang M, Yue L, Li Y, Liu J, Li B, Shen F, Wang Y, Bai L, Protzer U, Levrero M, Yuan Z. PRMT5 restricts hepatitis B virus replication through epigenetic repression of covalently closed circular DNA transcription and interference with pregenomic RNA encapsidation. Hepatology 2017; 66:398-415. [PMID: 28236308 DOI: 10.1002/hep.29133] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 02/16/2017] [Accepted: 02/20/2017] [Indexed: 12/11/2022]
Abstract
UNLABELLED Chronic hepatitis B virus (HBV) infection remains a major health problem worldwide. The covalently closed circular DNA (cccDNA) minichromosome, which serves as the template for the transcription of viral RNAs, plays a key role in viral persistence. While accumulating evidence suggests that cccDNA transcription is regulated by epigenetic machinery, particularly the acetylation of cccDNA-bound histone 3 (H3) and H4, the potential contributions of histone methylation and related host factors remain obscure. Here, by screening a series of methyltransferases and demethylases, we identified protein arginine methyltransferase 5 (PRMT5) as an effective restrictor of HBV transcription and replication. In cell culture-based models for HBV infection and in liver tissues of patients with chronic HBV infection, we found that symmetric dimethylation of arginine 3 on H4 on cccDNA was a repressive marker of cccDNA transcription and was regulated by PRMT5 depending on its methyltransferase domain. Moreover, PRMT5-triggered symmetric dimethylation of arginine 3 on H4 on the cccDNA minichromosome involved an interaction with the HBV core protein and the Brg1-based human SWI/SNF chromatin remodeler, which resulted in down-regulation of the binding of RNA polymerase II to cccDNA. In addition to the inhibitory effect on cccDNA transcription, PRMT5 inhibited HBV core particle DNA production independently of its methyltransferase activity. Further study revealed that PRMT5 interfered with pregenomic RNA encapsidation by preventing its interaction with viral polymerase protein through binding to the reverse transcriptase-ribonuclease H region of polymerase, which is crucial for the polymerase-pregenomic RNA interaction. CONCLUSION PRMT5 restricts HBV replication through a two-part mechanism including epigenetic suppression of cccDNA transcription and interference with pregenomic RNA encapsidation; these findings improve the understanding of epigenetic regulation of HBV transcription and host-HBV interaction, thus providing new insights into targeted therapeutic intervention. (Hepatology 2017;66:398-415).
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Affiliation(s)
- Wen Zhang
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jieliang Chen
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Min Wu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Xiaonan Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Min Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Lei Yue
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yaming Li
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiangxia Liu
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Baocun Li
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fang Shen
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yang Wang
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lu Bai
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ulrike Protzer
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
| | | | - Zhenghong Yuan
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
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Ko C, Michler T, Protzer U. Novel viral and host targets to cure hepatitis B. Curr Opin Virol 2017; 24:38-45. [DOI: 10.1016/j.coviro.2017.03.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/06/2017] [Accepted: 03/30/2017] [Indexed: 02/07/2023]
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Structural Insights into HIV Reverse Transcriptase Mutations Q151M and Q151M Complex That Confer Multinucleoside Drug Resistance. Antimicrob Agents Chemother 2017; 61:AAC.00224-17. [PMID: 28396546 DOI: 10.1128/aac.00224-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/28/2017] [Indexed: 12/26/2022] Open
Abstract
HIV-1 reverse transcriptase (RT) is targeted by multiple drugs. RT mutations that confer resistance to nucleoside RT inhibitors (NRTIs) emerge during clinical use. Q151M and four associated mutations, A62V, V75I, F77L, and F116Y, were detected in patients failing therapies with dideoxynucleosides (didanosine [ddI], zalcitabine [ddC]) and/or zidovudine (AZT). The cluster of the five mutations is referred to as the Q151M complex (Q151Mc), and an RT or virus containing Q151Mc exhibits resistance to multiple NRTIs. To understand the structural basis for Q151M and Q151Mc resistance, we systematically determined the crystal structures of the wild-type RT/double-stranded DNA (dsDNA)/dATP (complex I), wild-type RT/dsDNA/ddATP (complex II), Q151M RT/dsDNA/dATP (complex III), Q151Mc RT/dsDNA/dATP (complex IV), and Q151Mc RT/dsDNA/ddATP (complex V) ternary complexes. The structures revealed that the deoxyribose rings of dATP and ddATP have 3'-endo and 3'-exo conformations, respectively. The single mutation Q151M introduces conformational perturbation at the deoxynucleoside triphosphate (dNTP)-binding pocket, and the mutated pocket may exist in multiple conformations. The compensatory set of mutations in Q151Mc, particularly F116Y, restricts the side chain flexibility of M151 and helps restore the DNA polymerization efficiency of the enzyme. The altered dNTP-binding pocket in Q151Mc RT has the Q151-R72 hydrogen bond removed and has a switched conformation for the key conserved residue R72 compared to that in wild-type RT. On the basis of a modeled structure of hepatitis B virus (HBV) polymerase, the residues R72, Y116, M151, and M184 in Q151Mc HIV-1 RT are conserved in wild-type HBV polymerase as residues R41, Y89, M171, and M204, respectively; functionally, both Q151Mc HIV-1 and wild-type HBV are resistant to dideoxynucleoside analogs.
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Synergistic Interactions between Hepatitis B Virus RNase H Antagonists and Other Inhibitors. Antimicrob Agents Chemother 2017; 61:AAC.02441-16. [PMID: 27956427 DOI: 10.1128/aac.02441-16] [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: 11/15/2016] [Accepted: 12/07/2016] [Indexed: 12/15/2022] Open
Abstract
Combination therapies are standard for management of human immunodeficiency virus (HIV) and hepatitis C virus (HCV) infections; however, no such therapies are established for human hepatitis B virus (HBV). Recently, we identified several promising inhibitors of HBV RNase H (here simply RNase H) activity that have significant activity against viral replication in vitro Here, we investigated the in vitro antiviral efficacy of combinations of two RNase H inhibitors with the current anti-HBV drug nucleoside analog lamivudine, with HAP12, an experimental core protein allosteric modulator, and with each other. Anti-HBV activities of the compounds were tested in a HepG2-derived cell line by monitoring intracellular core particle DNA levels, and cytotoxicity was assessed by 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assay. The antiviral efficiencies of the drug combinations were evaluated using the median-effect equation derived from the mass-action law principle and combination index theorem of Chou and Talalay. We found that combinations of two RNase H inhibitors from different chemical classes were synergistic with lamivudine against HBV DNA synthesis. Significant synergism was also observed for the combination of the two RNase H inhibitors. Combinations of RNase H inhibitors with HAP12 had additive antiviral effects. Enhanced cytotoxicity was not observed in the combination experiments. Because of these synergistic and additive effects, the antiviral activity of combinations of RNase H inhibitors with drugs that act by two different mechanisms and with each other can be achieved by administering the compounds in combination at doses below the respective single drug doses.
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Mapping of Functional Subdomains in the Terminal Protein Domain of Hepatitis B Virus Polymerase. J Virol 2017; 91:JVI.01785-16. [PMID: 27852858 DOI: 10.1128/jvi.01785-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 11/12/2016] [Indexed: 01/08/2023] Open
Abstract
Hepatitis B virus (HBV) encodes a multifunction reverse transcriptase or polymerase (P), which is composed of several domains. The terminal protein (TP) domain is unique to HBV and related hepadnaviruses and is required for specifically binding to the viral pregenomic RNA (pgRNA). Subsequently, the TP domain is necessary for pgRNA packaging into viral nucleocapsids and the initiation of viral reverse transcription for conversion of the pgRNA to viral DNA. Uniquely, the HBV P protein initiates reverse transcription via a protein priming mechanism using the TP domain as a primer. No structural homologs or high-resolution structure exists for the TP domain. Secondary structure prediction identified three disordered loops in TP with highly conserved sequences. A meta-analysis of mutagenesis studies indicated these predicted loops are almost exclusively where functionally important residues are located. Newly constructed TP mutations revealed a priming loop in TP which plays a specific role in protein-primed DNA synthesis beyond simply harboring the site of priming. Substitutions of potential sites of phosphorylation surrounding the priming site demonstrated that these residues are involved in interactions critical for priming but are unlikely to be phosphorylated during viral replication. Furthermore, the first 13 and 66 TP residues were shown to be dispensable for protein priming and pgRNA binding, respectively. Combining current and previous mutagenesis work with sequence analysis has increased our understanding of TP structure and functions by mapping specific functions to distinct predicted secondary structures and will facilitate antiviral targeting of this unique domain. IMPORTANCE HBV is a major cause of viral hepatitis, liver cirrhosis, and hepatocellular carcinoma. One important feature of this virus is its polymerase, the enzyme used to create the DNA genome from a specific viral RNA by reverse transcription. One region of this polymerase, the TP domain, is required for association with the viral RNA and production of the DNA genome. Targeting the TP domain for antiviral development is difficult due to the lack of homology to other proteins and high-resolution structure. This study mapped the TP functions according to predicted secondary structure, where it folds into alpha helices or unstructured loops. Three predicted loops were found to be the most important regions functionally and the most conserved evolutionarily. Identification of these functional subdomains in TP will facilitate its targeting for antiviral development.
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48
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Sung FY, Lan CY, Huang CJ, Lin CL, Liu CJ, Chen PJ, Lin SM, Yu MW. Progressive accumulation of mutations in the hepatitis B virus genome and its impact on time to diagnosis of hepatocellular carcinoma. Hepatology 2016; 64:720-31. [PMID: 27228506 DOI: 10.1002/hep.28654] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/16/2016] [Indexed: 12/20/2022]
Abstract
UNLABELLED To evaluate how hepatitis B virus (HBV) genetic variation affected progression from chronic carrier state to hepatocellular carcinoma (HCC), we analyzed HBV full-length sequences in blood obtained <1-20 years before diagnosis from 117 HCC cases and 118 controls nested in a cohort of 4,841 HBV carriers, for whom HBV genotypes B and C are predominant. The relationship between each viral single-nucleotide polymorphism (SNP) and HCC development was assessed using ordinal logistic models according to five periods of time to diagnosis (TTD). Thirty-one HBV-SNPs showed significant association with TTD after adjustment for HBV genotype, 24 of which could also be analyzed with an extended analysis on the full-length data in conjunction with 512 partial sequences (nucleotides 2,436-1,623) from the cohort. The obtained 10 robust candidate HBV-SNPs (P ≤ 0.0304), which showed odds ratios ranging from 1.89 to 8.68, were further confirmed in 163 GenBank HBV-HCC sequences from nine Asia regions, assayed after HCC diagnosis, representing the end stage of progressive hepatic diseases. The prevalence of these HBV-SNPs and their cumulative number, presented in terms of mutation score, increased with time approaching HCC diagnosis, with an odds ratio of 2.17, 4.21, 8.15, and 19.15, respectively, for the mutation score of 1, 2, 3, and ≥4 versus 0. The mutation score for predicting short-term HCC risk outperformed other factors, including HBV-DNA levels, viral genotype, and various combinations of risk factors, and revealed increasing accuracy with shorter TTD (<4.5 years before diagnosis: area under the curve = 0.83-0.89; sensitivity = 72.7%-94.1%; specificity = 58.3%-70.5%; conditioned on optimized cutoff for genotype B and C, respectively). CONCLUSIONS Identifying and tracking viral mutations is important for monitoring hepatitis B progression and early detection of HCC. (Hepatology 2016;64:720-731).
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Affiliation(s)
- Feng-Yu Sung
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Chia-Ying Lan
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Chi-Jung Huang
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Chih-Lin Lin
- Department of Gastroenterology, Ren-Ai Branch, Taipei City Hospital, Taipei, Taiwan
| | - Chun-Jen Liu
- Division of Gastroenterology, Department of Internal Medicine, National Taiwan University Hospital and Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Pei-Jer Chen
- Division of Gastroenterology, Department of Internal Medicine, National Taiwan University Hospital and Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Shi-Ming Lin
- Liver Research Unit, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Ming-Whei Yu
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
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Xu X, Thai H, Kitrinos KM, Xia G, Gaggar A, Paulson M, Ganova-Raeva L, Khudyakov Y, Lara J. Modeling the functional state of the reverse transcriptase of hepatitis B virus and its application to probing drug-protein interaction. BMC Bioinformatics 2016; 17 Suppl 8:280. [PMID: 27587008 PMCID: PMC5009823 DOI: 10.1186/s12859-016-1116-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Herein, the predicted atomic structures of five representative sequence variants of the reverse transcriptase protein (RT) of hepatitis B virus (HBV), sampled from patients with rapid or slow response to tenofovir disoproxil fumarate (TDF) treatment, have been examined to identify structural variations between them in order to assess structural and functional properties of HBV-RT variants associated with the differential responses to TDF treatment. RESULTS We utilized a hybrid computational approach to model the atomistic structures of HBV-RT/DNA-RNA/dATP and HBV-RT/DNA-RNA/TFV-DP (tenofovir diphosphate) complexes with the native hybrid DNA-RNA substrate in place. Multi-nanosecond molecular dynamics (MD) simulations of HBV-RT/DNA-RNA/dATP complexes revealed strong coupling of the natural nucleotide substrate, dATP, to the active site of the RT, and the differential involvement of the two putative magnesium cations (Mg(2+)) at the active site, whereby one Mg(2+) directly bridges the interaction between dATP and HBV-RT and the other serves as a coordinator to maintain an optimal configuration of the active site. Solvated interaction energy (SIE) calculated in MD simulations of HBV-RT/DNA-RNA/TFV-DP complexes indicate no differential binding affinity between TFV-DP and HBV-RT variants identified in patients with slow or rapid response to TDF treatment. CONCLUSION The predicted atomic structures accurately represent functional states of HBV-RT. The equivalent interaction between TFV-DP and each examined HBV-RT variants suggests that binding affinity of TFV-DP to HBV-RT is not associated with delayed viral clearance.
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Affiliation(s)
- Xiaojun Xu
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Hong Thai
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | | | - Guoliang Xia
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | | | | | - Lilia Ganova-Raeva
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Yury Khudyakov
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - James Lara
- Division of Viral Hepatitis, National Center for HIV, Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA.
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50
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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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