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Xu ZM, Gnouamozi GE, Rüeger S, Shea PR, Buti M, Chan HL, Marcellin P, Lawless D, Naret O, Zeller M, Schneuing A, Scheck A, Junier T, Moradpour D, Podlaha O, Suri V, Gaggar A, Subramanian M, Correia B, Gfeller D, Urban S, Fellay J. Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation. Am J Hum Genet 2024; 111:1018-1034. [PMID: 38749427 PMCID: PMC11179264 DOI: 10.1016/j.ajhg.2024.04.013] [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: 01/08/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 06/09/2024] Open
Abstract
Evolutionary changes in the hepatitis B virus (HBV) genome could reflect its adaptation to host-induced selective pressure. Leveraging paired human exome and ultra-deep HBV genome-sequencing data from 567 affected individuals with chronic hepatitis B, we comprehensively searched for the signatures of this evolutionary process by conducting "genome-to-genome" association tests between all human genetic variants and viral mutations. We identified significant associations between an East Asian-specific missense variant in the gene encoding the HBV entry receptor NTCP (rs2296651, NTCP S267F) and mutations within the receptor-binding region of HBV preS1. Through in silico modeling and in vitro preS1-NTCP binding assays, we observed that the associated HBV mutations are in proximity to the NTCP variant when bound and together partially increase binding affinity to NTCP S267F. Furthermore, we identified significant associations between HLA-A variation and viral mutations in HLA-A-restricted T cell epitopes. We used in silico binding prediction tools to evaluate the impact of the associated HBV mutations on HLA presentation and observed that mutations that result in weaker binding affinities to their cognate HLA alleles were enriched. Overall, our results suggest the emergence of HBV escape mutations that might alter the interaction between HBV PreS1 and its cellular receptor NTCP during viral entry into hepatocytes and confirm the role of HLA class I restriction in inducing HBV epitope variations.
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Affiliation(s)
- Zhi Ming Xu
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Gnimah Eva Gnouamozi
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Sina Rüeger
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Patrick R Shea
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Maria Buti
- Liver Unit, Hospital Universitario Vall d'Hebron and CIBEREHD del Instituto Carlos III, Barcelona, Spain
| | - Henry Ly Chan
- The Chinese University of Hong Kong, Hong Kong, China
| | | | - Dylan Lawless
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Olivier Naret
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Matthias Zeller
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Arne Schneuing
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Andreas Scheck
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Thomas Junier
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Darius Moradpour
- Division of Gastroenterology and Hepatology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | | | | | | | - Bruno Correia
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - David Gfeller
- Department of Oncology UNIL-CHUV, Lausanne University Hospital, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany; German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; Precision Medicine Unit, Biomedical Data Science Center, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
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2
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Lang-Meli J, Neumann-Haefelin C, Thimme R. Targeting virus-specific CD8+ T cells for treatment of chronic viral hepatitis: from bench to bedside. Expert Opin Biol Ther 2024; 24:77-89. [PMID: 38290716 DOI: 10.1080/14712598.2024.2313112] [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: 11/14/2023] [Accepted: 01/29/2024] [Indexed: 02/01/2024]
Abstract
INTRODUCTION More than 350 million people worldwide live with chronic viral hepatitis and are thus at risk for severe complications like liver cirrhosis and hepatocellular carcinoma (HCC). To meet the goals of the World Health Organization (WHO) global hepatitis strategy, there is an urgent need for new immunotherapeutic approaches. These are particularly required for chronic hepatitis B virus infection and - B/D coinfection. AREAS COVERED This review summarizes data on mechanisms of CD8+ T cells failure in chronic hepatitis B, D, C and E virus infection. The relative contribution of the different concepts (viral escape, CD8+ T cell exhaustion, defective priming) will be discussed. On this basis, examples for future therapeutic approaches targeting virus-specific CD8+ T cells for the individual hepatitis viruses will be discussed. EXPERT OPINION Immunotherapeutic approaches targeting virus-specific CD8+ T cells have the potential to change clinical practice, especially in chronic hepatitis B virus infection. Further clinical development, however, requires a more detailed understanding of T cell immunology in chronic viral hepatitis. Some important conceptual questions remain to be addressed, e.g. regarding heterogeneity of exhausted virus-specific CD8+ T cells.
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Affiliation(s)
- Julia Lang-Meli
- Department of Medicine II, Medical Center - University of Freiburg and Faculty of Medicine, University Hospital Freiburg, Freiburg, Germany
- IMM-PACT Programm, Faculty of Medicine, University Hospital Freiburg, Freiburg, Germany
| | - Christoph Neumann-Haefelin
- Department of Medicine II, Medical Center - University of Freiburg and Faculty of Medicine, University Hospital Freiburg, Freiburg, Germany
| | - Robert Thimme
- Department of Medicine II, Medical Center - University of Freiburg and Faculty of Medicine, University Hospital Freiburg, Freiburg, Germany
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3
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Walker A, Schwarz T, Brinkmann-Paulukat J, Wisskirchen K, Menne C, Alizei ES, Kefalakes H, Theissen M, Hoffmann D, Schulze zur Wiesch J, Maini MK, Cornberg M, Kraft ARM, Keitel V, Bock HH, Horn PA, Thimme R, Wedemeyer H, Heinemann FM, Luedde T, Neumann-Haefelin C, Protzer U, Timm J. Immune escape pathways from the HBV core 18-27 CD8 T cell response are driven by individual HLA class I alleles. Front Immunol 2022; 13:1045498. [PMID: 36439181 PMCID: PMC9686862 DOI: 10.3389/fimmu.2022.1045498] [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: 09/15/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
Background and aims There is growing interest in T cell-based immune therapies for a functional cure of chronic HBV infection including check-point inhibition, T cell-targeted vaccines or TCR-grafted effector cells. All these approaches depend on recognition of HLA class I-presented viral peptides. The HBV core region 18-27 is an immunodominant target of CD8+ T cells and represents the prime target for T cell-based therapies. Here, a high-resolution analysis of the core18-27 specific CD8+ T cell and the selected escape pathways was performed. Methods HLA class I typing and viral sequence analyses were performed for 464 patients with chronic HBV infection. HBV-specific CD8+ T-cell responses against the prototype and epitope variants were characterized by flow cytometry. Results Consistent with promiscuous presentation of the core18-27 epitope, antigen-specific T cells were detected in patients carrying HLA-A*02:01, HLA-B*35:01, HLA-B*35:03 or HLA-B*51:01. Sequence analysis confirmed reproducible selection pressure on the core18-27 epitope in the context of these alleles. Interestingly, the selected immune escape pathways depend on the presenting HLA-class I-molecule. Although cross-reactive T cells were observed, some epitope variants achieved functional escape by impaired TCR-interaction or disturbed antigen processing. Of note, selection of epitope variants was exclusively observed in HBeAg negative HBV infection and here, detection of variants associated with significantly greater magnitude of the CD8 T cell response compared to absence of variants. Conclusion The core18-27 epitope is highly variable and under heavy selection pressure in the context of different HLA class I-molecules. Some epitope variants showed evidence for impaired antigen processing and reduced presentation. Viruses carrying such escape substitutions will be less susceptible to CD8+ T cell responses and should be considered for T cell-based therapy strategies.
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Affiliation(s)
- Andreas Walker
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tatjana Schwarz
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Janine Brinkmann-Paulukat
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Karin Wisskirchen
- Institute of Virology, School of Medicine, Technical University of Munich, Helmholtz Zentrum München, Munich, Germany
- German Center for Infection Research (DZIF), Site Munich, Munich, Germany
| | - Christopher Menne
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Elahe Salimi Alizei
- Department of Medicine II, University Hospital Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Helenie Kefalakes
- Institute of Virology, University of Duisburg-Essen, University Hospital Essen, Essen, Germany
| | - Martin Theissen
- Research Group Bioinformatics, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Daniel Hoffmann
- Research Group Bioinformatics, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Julian Schulze zur Wiesch
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research (DZIF), Site Hamburg, Hamburg, Germany
| | - Mala K. Maini
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, United Kingdom
| | - Markus Cornberg
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Site Hannover, Hannover, Germany
| | - Anke RM Kraft
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Site Hannover, Hannover, Germany
| | - Verena Keitel
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Hans H. Bock
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Peter A. Horn
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Robert Thimme
- Department of Medicine II, University Hospital Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Heiner Wedemeyer
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), Site Hannover, Hannover, Germany
| | - Falko M. Heinemann
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Tom Luedde
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christoph Neumann-Haefelin
- Department of Medicine II, University Hospital Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ulrike Protzer
- Institute of Virology, School of Medicine, Technical University of Munich, Helmholtz Zentrum München, Munich, Germany
- German Center for Infection Research (DZIF), Site Munich, Munich, Germany
| | - Jörg Timm
- Institute of Virology, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Khatamzas E, Antwerpen MH, Rehn A, Graf A, Hellmuth JC, Hollaus A, Mohr AW, Gaitzsch E, Weiglein T, Georgi E, Scherer C, Stecher SS, Gruetzner S, Blum H, Krebs S, Reischer A, Leutbecher A, Subklewe M, Dick A, Zange S, Girl P, Müller K, Weigert O, Hopfner KP, Stemmler HJ, von Bergwelt-Baildon M, Keppler OT, Wölfel R, Muenchhoff M, Moosmann A. Accumulation of mutations in antibody and CD8 T cell epitopes in a B cell depleted lymphoma patient with chronic SARS-CoV-2 infection. Nat Commun 2022; 13:5586. [PMID: 36151076 PMCID: PMC9508331 DOI: 10.1038/s41467-022-32772-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 08/15/2022] [Indexed: 11/29/2022] Open
Abstract
Antibodies against the spike protein of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) can drive adaptive evolution in immunocompromised patients with chronic infection. Here we longitudinally analyze SARS-CoV-2 sequences in a B cell-depleted, lymphoma patient with chronic, ultimately fatal infection, and identify three mutations in the spike protein that dampen convalescent plasma-mediated neutralization of SARS-CoV-2. Additionally, four mutations emerge in non-spike regions encoding three CD8 T cell epitopes, including one nucleoprotein epitope affected by two mutations. Recognition of each mutant peptide by CD8 T cells from convalescent donors is reduced compared to its ancestral peptide, with additive effects resulting from double mutations. Querying public SARS-CoV-2 sequences shows that these mutations have independently emerged as homoplasies in circulating lineages. Our data thus suggest that potential impacts of CD8 T cells on SARS-CoV-2 mutations, at least in those with humoral immunodeficiency, warrant further investigation to inform on vaccine design. SARS-CoV-2 mutations associated with the escape from antibody-mediated neutralization have been widely reported. Here, in a patient with defective antibody responses, the authors find a potential association between SARS-CoV-2 mutations and CD8 T alterations to implicate possible contributions of CD8 T cells in evasion of SARS-CoV-2 from host immunity.
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Affiliation(s)
- Elham Khatamzas
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany. .,Division of Infectious Diseases and Tropical Medicine, Center for Infectious Diseases, Heidelberg Hospital, Heidelberg, Germany. .,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.
| | - Markus H Antwerpen
- Bundeswehr, Institute of Microbiology Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Alexandra Rehn
- Bundeswehr, Institute of Microbiology Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians University Munich, Munich, Germany
| | - Johannes Christian Hellmuth
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Alexandra Hollaus
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Anne-Wiebe Mohr
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Erik Gaitzsch
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Tobias Weiglein
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Enrico Georgi
- Bundeswehr, Institute of Microbiology Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Clemens Scherer
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,Department of Medicine I, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Stephanie-Susanne Stecher
- Department of Medicine II, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Stefanie Gruetzner
- Institute for Transfusion Medicine and Haemostasis, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians University Munich, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians University Munich, Munich, Germany
| | - Anna Reischer
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Alexandra Leutbecher
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Marion Subklewe
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Andrea Dick
- Laboratory for Immunogenetics, University of Munich, LMU, Munich, Germany
| | - Sabine Zange
- Bundeswehr, Institute of Microbiology Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Philipp Girl
- Bundeswehr, Institute of Microbiology Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Katharina Müller
- Bundeswehr, Institute of Microbiology Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Oliver Weigert
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany
| | - Karl-Peter Hopfner
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hans-Joachim Stemmler
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Michael von Bergwelt-Baildon
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,German Cancer Consortium (DKTK), Munich, Germany
| | - Oliver T Keppler
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany.,Max von Pettenkofer Institute & Gene Center, Virology, Faculty of Medicine, Ludwig-Maximilians University, Munich, Germany
| | - Roman Wölfel
- Bundeswehr, Institute of Microbiology Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Maximilian Muenchhoff
- COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany.,Max von Pettenkofer Institute & Gene Center, Virology, Faculty of Medicine, Ludwig-Maximilians University, Munich, Germany
| | - Andreas Moosmann
- Department of Medicine III, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany.,German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
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Mutational escape from cellular immunity in viral hepatitis: variations on a theme. Curr Opin Virol 2021; 50:110-118. [PMID: 34454351 DOI: 10.1016/j.coviro.2021.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/05/2021] [Indexed: 12/19/2022]
Abstract
Approx. 320 million individuals worldwide are chronically infected with hepatitis viruses, contributing to viral hepatitis being one of the 10 leading causes of death. Cellular adaptive immunity, namely CD4+ and CD8+ T cells, plays an important role in viral clearance and control. Two main mechanisms, however, may lead to failure of the virus-specific T-cell response: T-cell exhaustion and mutational viral escape. Viral escape has been studied in detail in hepatitis C virus (HCV) infection, where it is thought to affect approx. 50% of virus-specific CD8+ T-cell responses in persistent infection, to influence natural infection outcome and to contribute to failure of preventive vaccination strategies. In hepatitis B virus (HBV) as well as HBV/hepatitis D virus (HDV) co-infection, the impact of viral escape has been studied in detail only recently.
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Xiong S, Zhu D, Liang B, Li M, Pan W, He J, Wang H, Sutter K, Dittmer U, Lu M, Liu D, Yang D, Liu J, Zheng X. Longitudinal characterization of phenotypic profile of T cells in chronic hepatitis B identifies immune markers associated with HBsAg loss. EBioMedicine 2021; 69:103464. [PMID: 34233260 PMCID: PMC8261015 DOI: 10.1016/j.ebiom.2021.103464] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 02/08/2023] Open
Abstract
Background The current desirable endpoint of treatment against chronic hepatitis B virus infection (cHBV) is to achieve a functional cure, which is defined as HBsAg loss (sAg-L) with or without anti-HBs seroconversion. However, the immunological features that are associated with functional cure have not been studied in detail. Methods 172 cHBV patients (67 HBeAg+ and 105 HBeAg-), including 141 HBsAg retained (sAg-R) patients (115 chronic hepatitis and 26 asymptomatic carriers), 31 sAg-L patients, and 24 healthy individuals (vaccinated but not infected with HBV) were examined for their T cell phenotypic profile and HBV-specific T cell responses by flow cytometry. 18 cHBV patients with low serum HBsAg levels were also longitudinally followed for their T cell phenotypic profile and HBV-specific T cell responses up to 60 weeks. Findings sAg-L patients showed distinct CD4+ and CD8+ T cell phenotype fingerprints compared to those of sAg-R patients, as mainly indicated by the upregulation of HLA-DR on both CD4+ and CD8+ T cells, and a potent HBcAg-specific CD8+ T cell response. The changes in the T cell phenotype in cHBV patients were even more profound during rapid HBsAg decrease and was associated with interferon α treatment. The expression of HLA-DR (r = 0·3269, p = 0·0037), CD95 (r = 0·2796, p = 0·0151), CD40L (r = 0·2747, p = 0·0156), CTLA-4 (r = 0·2786, p = 0·0148), TIM-3 (r = 0·3082, p = 0·0068), CD107a (r = 0·3597, p = 0·0013) on CD4+ T cells, and HLA-DR (r = 0·3542, p = 0·0016), CD69 (r = 0·2507, p = 0·0279), CD107a (r = 0·2875, p = 0·0112) on CD8+ T cells were positively correlated with the rate of HBsAg decrease. The expression of HLA-DR (r = 0·2846, p = 0·0009) and CD95 (r = 0·2442, p = 0·0049) on CD8+ T cells were positively correlated with the magnitude of the HBcAg-specific T cell responses in cHBV patients. Importantly, CTLA-4, CD95 and CD107a expression on CD4+ T cells, as well as HLA-DR and TIM-3 expression on CD8+ T cells in combination with HBsAg quantification were identified as potential predictive factors for sAg-L within 48 weeks in cHBV patients. Interpretation The onset of HBsAg decrease and subsequent loss in cHBV patients on treatment is associated with significant alterations of both CD4+ and CD8+ T cell phenotypes. Characterization of the T cell phenotype in cHBV patients may present predicative value for sAg-L. Funding National Natural Science Foundation of China, National Scientific and Technological Major Project of China, Integrated Innovative Team for Major Human Diseases Program of Tongji Medical College, “Double-First Class” Project for the International Cooperation Center on Infection and Immunity, HUST.
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Affiliation(s)
- Shue Xiong
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Dan Zhu
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Boyun Liang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Mingyue Li
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Wen Pan
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Junyi He
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Hua Wang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Kathrin Sutter
- Institute for Virology, University Hospital of Essen, University of Duisburg-Essen, Essen 45147, Germany; Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Ulf Dittmer
- Institute for Virology, University Hospital of Essen, University of Duisburg-Essen, Essen 45147, Germany; Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Mengji Lu
- Institute for Virology, University Hospital of Essen, University of Duisburg-Essen, Essen 45147, Germany; Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Di Liu
- Pritzker School of Medicine, University of Chicago, Chicago, USA
| | - Dongliang Yang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Jia Liu
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan 430022, China.
| | - Xin Zheng
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Joint International Laboratory of Infection and Immunity, Huazhong University of Science and Technology, Wuhan 430022, China.
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7
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Discovery and Selection of Hepatitis B Virus-Derived T Cell Epitopes for Global Immunotherapy Based on Viral Indispensability, Conservation, and HLA-Binding Strength. J Virol 2020; 94:JVI.01663-19. [PMID: 31852786 PMCID: PMC7081907 DOI: 10.1128/jvi.01663-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 12/10/2019] [Indexed: 12/15/2022] Open
Abstract
Multiple HBV-derived T cell epitopes have been reported, which can be useful in a therapeutic vaccination strategy. However, these epitopes are largely restricted to HLA-A*02, which is not dominantly expressed in populations with high HBV prevalence. Thus, current epitopes are falling short in the development of a global immunotherapeutic approach. Therefore, we aimed to identify novel epitopes for 6 HLA supertypes most prevalent in the infected population. Moreover, established epitopes might not all be equally effective as they can be subject to different levels of immune escape. It is therefore important to identify targets that are crucial in viral replication and conserved in the majority of the infected population. Here, we applied a stringent selection procedure to compose a combined overview of existing and novel HBV-derived T cell epitopes most promising for viral eradication. This set of T cell epitopes now lays the basis for the development of globally effective HBV antigen-specific immunotherapies. Immunotherapy represents an attractive option for the treatment of chronic hepatitis B virus (HBV) infection. The HBV proteins polymerase (Pol) and HBx are of special interest for antigen-specific immunotherapy because they are essential for viral replication and have been associated with viral control (Pol) or are still expressed upon viral DNA integration (HBx). Here, we scored all currently described HBx- and Pol-derived epitope sequences for viral indispensability and conservation across all HBV genotypes. This yielded 7 HBx-derived and 26 Pol-derived reported epitopes with functional association and high conservation. We subsequently predicted novel HLA-binding peptides for 6 HLA supertypes prevalent in HBV-infected patients. Potential epitopes expected to be the least prone to immune escape were subjected to a state-of-the-art in vitro assay to validate their HLA-binding capacity. Using this method, a total of 13 HLA binders derived from HBx and 33 binders from Pol were identified across HLA types. Subsequently, we demonstrated interferon gamma (IFN-γ) production in response to 5 of the novel HBx-derived binders and 17 of the novel Pol-derived binders. In addition, we validated several infrequently described epitopes. Collectively, these results specify a set of highly potent T cell epitopes that represent a valuable resource for future HBV immunotherapy design. IMPORTANCE Multiple HBV-derived T cell epitopes have been reported, which can be useful in a therapeutic vaccination strategy. However, these epitopes are largely restricted to HLA-A*02, which is not dominantly expressed in populations with high HBV prevalence. Thus, current epitopes are falling short in the development of a global immunotherapeutic approach. Therefore, we aimed to identify novel epitopes for 6 HLA supertypes most prevalent in the infected population. Moreover, established epitopes might not all be equally effective as they can be subject to different levels of immune escape. It is therefore important to identify targets that are crucial in viral replication and conserved in the majority of the infected population. Here, we applied a stringent selection procedure to compose a combined overview of existing and novel HBV-derived T cell epitopes most promising for viral eradication. This set of T cell epitopes now lays the basis for the development of globally effective HBV antigen-specific immunotherapies.
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8
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Hoogeveen RC, Boonstra A. Checkpoint Inhibitors and Therapeutic Vaccines for the Treatment of Chronic HBV Infection. Front Immunol 2020; 11:401. [PMID: 32194573 PMCID: PMC7064714 DOI: 10.3389/fimmu.2020.00401] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/20/2020] [Indexed: 12/11/2022] Open
Abstract
Treatment of chronic hepatitis B virus (HBV) infection is highly effective in suppressing viral replication, but complete cure is rarely achieved. In recent years, substantial progress has been made in the development of immunotherapy to treat cancer. Applying these therapies to improve the management of chronic HBV infection is now being attempted, and has become an area of active research. Immunotherapy with vaccines and checkpoint inhibitors can boost T cell functions in vitro, and therefore may be used to reinvigorate the impaired HBV-specific T cell response. However, whether these approaches will suffice and restore antiviral T cell immunity to induce long-term HBV control remains an open question. Recent efforts have begun to describe the phenotype and function of HBV-specific T cells on the single epitope level. An improved understanding of differing T cell specificities and their contribution to HBV control will be instrumental for advancement of the field. In this review, we outline correlates of successful versus inadequate T cell responses to HBV, and discuss the rationale behind therapeutic vaccines and checkpoint inhibitors for the treatment of chronic HBV infection.
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Affiliation(s)
- Ruben C Hoogeveen
- Division of Gastroenterology and Hepatology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - André Boonstra
- Division of Gastroenterology and Hepatology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
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9
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Trinks J, Marciano S, Esposito I, Franco A, Mascardi MF, Mendizabal M, Livellara B, Arrigo D, Calzetta P, Vujacich C, Giunta D, Gadano A, Flichman D. The genetic variability of hepatitis B virus subgenotype F1b precore/core gene is related to the outcome of the acute infection. Virus Res 2019; 277:197840. [PMID: 31846615 DOI: 10.1016/j.virusres.2019.197840] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/03/2019] [Accepted: 12/13/2019] [Indexed: 02/07/2023]
Abstract
AIM To assess the association of viral and host genetic variability with the outcome of acute infection with hepatitis B virus subgenotype F1b (HBV/F1b). METHODS The cohort consisted of 26 patients with acute HBV/F1b infection who exhibit different outcomes: spontaneous resolution (n = 10), progression to chronic hepatitis (n = 10) and acute liver failure (n = 6). HLA SNPs (rs3077, rs9277542, rs2856718 and rs7453920) were determined. The S gene and core promoter/precore/core region were direct sequenced, and this latter region was also ultra-deep sequenced. Mean number of mutations, mutation rate, Shannon entropy, positive selection sites and mutational patterns of quasispecies were compared between groups. RESULTS HLA SNPs were associated with spontaneous resolution or progression to chronic hepatitis, but not with the development of acute liver failure. The mean number of mutations in the S gene was similar among the three groups. Patients with spontaneous resolution had the lowest number of mutations, mutation rates and Shannon entropy values in the precore/core compared to the other two groups. Ten positive selection sites mapped on HLA-restricted epitopes were related to progression to chronic hepatitis and acute liver failure. Mutations T1753C, A1762T, G1764A, C1766T, T1768A G1896A, G2092T and T2107C were associated with acute liver failure and progression to chronic hepatitis. CONCLUSION Highly heterogeneous and complex HBV precore/core carrying specific point mutations, combined with the host HLA background, were associated with a worse clinical outcome of acute HBV/F1b infection.
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Affiliation(s)
- Julieta Trinks
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI) - Hospital Italiano (HIBA), Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Sebastián Marciano
- Sección de Hepatología, Servicio de Clínica Médica, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina; Departamento de Investigación, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Isabella Esposito
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI) - Hospital Italiano (HIBA), Buenos Aires, Argentina
| | - Alejandra Franco
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI) - Hospital Italiano (HIBA), Buenos Aires, Argentina
| | - Maria Florencia Mascardi
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI) - Hospital Italiano (HIBA), Buenos Aires, Argentina
| | - Manuel Mendizabal
- Unidad de Hígado y Trasplante Hepático, Hospital Universitario Austral, Buenos Aires, Argentina
| | - Beatriz Livellara
- Laboratorio Central, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Diego Arrigo
- Laboratorio Central, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Pablo Calzetta
- División de Gastroenterología, Hospital Juan A. Fernández, Buenos Aires, Argentina
| | - Claudia Vujacich
- Fundación Centro de Estudios Infectológicos (FUNCEI), Buenos Aires, Argentina
| | - Diego Giunta
- Departamento de Investigación, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina; Área de Investigación de Medicina Interna, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Adrián Gadano
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI) - Hospital Italiano (HIBA), Buenos Aires, Argentina; Sección de Hepatología, Servicio de Clínica Médica, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina; Departamento de Investigación, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Diego Flichman
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina; Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Universidad de Buenos Aires-CONICET, Buenos Aires, Argentina
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10
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Maini MK, Burton AR. Restoring, releasing or replacing adaptive immunity in chronic hepatitis B. Nat Rev Gastroenterol Hepatol 2019; 16:662-675. [PMID: 31548710 DOI: 10.1038/s41575-019-0196-9] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/01/2019] [Indexed: 02/06/2023]
Abstract
Multiple new therapeutic approaches are currently being developed to achieve sustained, off-treatment suppression of HBV, a persistent hepatotropic infection that kills ~2,000 people a day. A fundamental therapeutic goal is the restoration of robust HBV-specific adaptive immune responses that are able to maintain prolonged immunosurveillance of residual infection. Here, we provide insight into key components of successful T cell and B cell responses to HBV, discussing the importance of different specificities and effector functions, local intrahepatic immunity and pathogenic potential. We focus on the parallels and interactions between T cell and B cell responses, highlighting emerging areas for future investigation. We review the potential for different immunotherapies in development to restore or release endogenous adaptive immunity by direct or indirect approaches, including limitations and risks. Finally, we consider an alternative HBV treatment strategy of replacing failed endogenous immunity with infusions of highly targeted T cells or antibodies.
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Affiliation(s)
- Mala K Maini
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, UK.
| | - Alice R Burton
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, UK
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11
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Sung PS, Park DJ, Kim JH, Han JW, Lee EB, Lee GW, Nam HC, Jang JW, Bae SH, Choi JY, Shin EC, Park SH, Yoon SK. Ex vivo Detection and Characterization of Hepatitis B Virus-Specific CD8 + T Cells in Patients Considered Immune Tolerant. Front Immunol 2019; 10:1319. [PMID: 31244857 PMCID: PMC6563765 DOI: 10.3389/fimmu.2019.01319] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 05/23/2019] [Indexed: 12/21/2022] Open
Abstract
In this study, we aimed to detect and characterize ex vivo virus-specific CD8+ T cells in patients with immune-tolerant hepatitis B virus (HBV) infection. We investigated a Korean chronic hepatitis B cohort composed of 15 patients in the immune-tolerant phase, 17 in the immune-active phase, and 13 under antiviral treatment. We performed enzyme-linked immunospot (ELISpot) assays ex vivo and intracellular cytokine staining after in vitro culture. We also performed ex vivo multimer staining assays and examined the expression of programmed death-1 (PD-1) and CD127 in pentamer-positive cells. Ex vivo ELISpot revealed that HBV-specific T cell function was weaker in immune-tolerant patients than in those under antiviral treatment. In vitro culture of peripheral blood mononuclear cells for 10 days revealed that HBV-specific CD8+ T cells produced interferon-γ in some immune-tolerant patients. We detected HBV-specific CD8+ T cells ex vivo (using the HBV core18-27 pentamer) in patients from all three groups. The PD-1+ subset of pentamer+ CD8+ T cells was smaller ex vivo in the immune-tolerant phase than in the immune-active phase or under antiviral treatment. Interestingly, the proportion of PD-1+ CD8+ T cells in HBV-specific CD8+ T cells correlated with patient age when all enrolled patients were analyzed. Overall, HBV-specific CD8+ T cells are present in patients considered as immune-tolerant, although their ex vivo functionality is significantly weaker than that in patients under antiviral treatment (P < 0.05). Despite the high viral load, the proportion of PD-1 expression in HBV-specific CD8+ T cells is lower in the immune-tolerant phase than in other phases. Our results indicate appropriate stimulation may enhance the effector function of HBV-specific CD8+ T cells in patients considered as being in the immune-tolerant phase.
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Affiliation(s)
- Pil Soo Sung
- Department of Internal Medicine, College of Medicine, Eunpyeong St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea.,Department of Biomedicine & Health Sciences, The Catholic University Liver Research Center, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Dong Jun Park
- Department of Biomedicine & Health Sciences, The Catholic University Liver Research Center, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Jung-Hee Kim
- Department of Biomedicine & Health Sciences, The Catholic University Liver Research Center, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Ji Won Han
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, South Korea
| | - Eun Byul Lee
- Department of Biomedicine & Health Sciences, The Catholic University Liver Research Center, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Gil Won Lee
- Department of Biomedicine & Health Sciences, The Catholic University Liver Research Center, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Hee Chul Nam
- Department of Biomedicine & Health Sciences, The Catholic University Liver Research Center, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Internal Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea
| | - Jeong Won Jang
- Department of Biomedicine & Health Sciences, The Catholic University Liver Research Center, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Internal Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea
| | - Si Hyun Bae
- Department of Internal Medicine, College of Medicine, Eunpyeong St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea.,Department of Biomedicine & Health Sciences, The Catholic University Liver Research Center, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Jong Young Choi
- Department of Biomedicine & Health Sciences, The Catholic University Liver Research Center, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Internal Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea
| | - Eui-Cheol Shin
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, South Korea
| | - Su-Hyung Park
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, South Korea
| | - Seung Kew Yoon
- Department of Biomedicine & Health Sciences, The Catholic University Liver Research Center, College of Medicine, The Catholic University of Korea, Seoul, South Korea.,Department of Internal Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, South Korea
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12
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Zhu W, Liu H, Zhang X. Toward Curative Immunomodulation Strategies for Chronic Hepatitis B Virus Infection. ACS Infect Dis 2019; 5:703-712. [PMID: 30907080 DOI: 10.1021/acsinfecdis.8b00297] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Chronic hepatitis B virus (HBV) infection remains a major cause of morbidity and mortality worldwide. HBV surface antigen loss is considered a functional cure and is an ideal goal for antiviral therapy. However, current treatment regimens, including nucleos(t)ide analogues or interferons monotherapy and combination therapy, rarely achieve this goal in chronic hepatitis B patients. Nucleos(t)ide analogues (NAs), as well as many direct antiviral drugs in ongoing development, are able to inhibit HBV replication and gene expression, but it is hard to achieve immune control and prevent recurrence after therapy cessation. Host immunity, especially HBV-specific T cell response, is proven to play a critical role in control or clearance of HBV infection. Considering HBV chronically infected patients display varying degrees of dysfunction regarding their immune system, novel approaches to enhancing antiviral immune responses are necessary in order to combine with current antiviral agents. In this Review, we focus on the role of innate and adaptive immune responses in HBV immunopathogenesis and discuss attractive strategies or drugs that aim to activate or rebuild antiviral immunity to achieve the goal of an HBV functional cure.
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Affiliation(s)
- Wei Zhu
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, No. 1838, North Guangzhou Avenue, Guangzhou, Guangdong 510515, China
| | - Hongyan 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, No. 1838, North Guangzhou Avenue, Guangzhou, Guangdong 510515, China
| | - Xiaoyong Zhang
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, No. 1838, North Guangzhou Avenue, Guangzhou, Guangdong 510515, China
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13
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Schuch A, Salimi Alizei E, Heim K, Wieland D, Kiraithe MM, Kemming J, Llewellyn-Lacey S, Sogukpinar Ö, Ni Y, Urban S, Zimmermann P, Nassal M, Emmerich F, Price DA, Bengsch B, Luxenburger H, Neumann-Haefelin C, Hofmann M, Thimme R. Phenotypic and functional differences of HBV core-specific versus HBV polymerase-specific CD8+ T cells in chronically HBV-infected patients with low viral load. Gut 2019; 68:905-915. [PMID: 30622109 DOI: 10.1136/gutjnl-2018-316641] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 10/31/2018] [Accepted: 10/31/2018] [Indexed: 12/12/2022]
Abstract
OBJECTIVE A hallmark of chronic HBV (cHBV) infection is the presence of impaired HBV-specific CD8+ T cell responses. Functional T cell exhaustion induced by persistent antigen stimulation is considered a major mechanism underlying this impairment. However, due to their low frequencies in chronic infection, it is currently unknown whether HBV-specific CD8+ T cells targeting different epitopes are similarly impaired and share molecular profiles indicative of T cell exhaustion. DESIGN By applying peptide-loaded MHC I tetramer-based enrichment, we could detect HBV-specific CD8+ T cells targeting epitopes in the HBV core and the polymerase proteins in the majority of 85 tested cHBV patients with low viral loads. Lower detection rates were obtained for envelope-specific CD8+ T cells. Subsequently, we performed phenotypic and functional in-depth analyses. RESULTS HBV-specific CD8+ T cells are not terminally exhausted but rather exhibit a memory-like phenotype in patients with low viral load possibly reflecting weak ongoing cognate antigen recognition. Moreover, HBV-specific CD8+ T cells targeting core versus polymerase epitopes significantly differed in frequency, phenotype and function. In particular, in comparison with core-specific CD8+ T cells, a higher frequency of polymerase-specific CD8+ T cells expressed CD38, KLRG1 and Eomes accompanied by low T-bet expression and downregulated CD127 indicative of a more severe T cell exhaustion. In addition, polymerase-specific CD8+ T cells exhibited a reduced expansion capacity that was linked to a dysbalanced TCF1/BCL2 expression. CONCLUSIONS Overall, the molecular mechanisms underlying impaired T cell responses differ with respect to the targeted HBV antigens. These results have potential implications for immunotherapeutic approaches in HBV cure.
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Affiliation(s)
- Anita Schuch
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Elahe Salimi Alizei
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Chemistry and Pharmacy, University of Freiburg, Freiburg, Germany
| | - Kathrin Heim
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Dominik Wieland
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michael Muthamia Kiraithe
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Janine Kemming
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Sian Llewellyn-Lacey
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Özlem Sogukpinar
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Yi Ni
- Department of Infectious Diseases, Molecular Virology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stephan Urban
- Department of Infectious Diseases, Molecular Virology, Heidelberg University Hospital, Heidelberg, Germany.,German Center for Infection Research (DZIF), Partner Site Heidelberg, Heidelberg, Germany
| | - Peter Zimmermann
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Michael Nassal
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Florian Emmerich
- Institute for Cell and Gene Therapy, University Hospital Freiburg, Freiburg, Germany
| | - David A Price
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Bertram Bengsch
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hendrik Luxenburger
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Christoph Neumann-Haefelin
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Maike Hofmann
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Robert Thimme
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
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14
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Hoogeveen RC, Robidoux MP, Schwarz T, Heydmann L, Cheney JA, Kvistad D, Aneja J, Melgaço JG, Fernandes CA, Chung RT, Boonstra A, Kim AY, Baumert TF, Timm J, Lewis-Ximenez LL, Tonnerre P, Lauer GM. Phenotype and function of HBV-specific T cells is determined by the targeted epitope in addition to the stage of infection. Gut 2019; 68:893-904. [PMID: 30580250 DOI: 10.1136/gutjnl-2018-316644] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 11/16/2018] [Accepted: 11/17/2018] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Chronic HBV infection affects more than 250 million people worldwide and remains a global healthcare problem in part because we lack curative treatment. Sustained viral control requires HBV-specific T cells, but these become functionally impaired in chronic infection. Clinical evidence indicates that functional cure of HBV infection by the host immune response is feasible. Developing T cell-based therapies able to achieve functional cure will require identification of the requirements for a successful T cell response against HBV and the relative contribution of individual T cell specificities to HBV control. DESIGN The phenotype and function of HBV-specific T cells were studied directly ex vivo using fluorochrome-labelled multimers. We studied multiple HBV-specific T cell specificities targeting different HBV proteins in individuals with either an acute self-limiting or chronic HBV infection. RESULTS We detected strong T cell responses targeting multiple HBV viral proteins in acute self-limiting and low-frequency core and polymerase-specific T cells in chronic infection. Expression of the T cell inhibitory receptor PD-1, as well as T cell differentiation, T cell function and T cell regulation differed by stages and outcomes of infection. In addition, these features differed significantly between T cells targeting different HBV specificities. CONCLUSION HBV-specific T cells with different target specificities are characterised by distinct phenotypical and functional profiles. These results have direct implications for the design of immunological studies in HBV infection, and are potentially relevant for informing immunotherapeutic approaches to induce functional cure.
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Affiliation(s)
- Ruben C Hoogeveen
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Gastroenterology and Hepatology, Erasmus MC, Rotterdam, The Netherlands
| | - Maxwell P Robidoux
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Tatjana Schwarz
- Institute of Virology, Heinrich Heine University, University Hospital, Düsseldorf, Germany
| | - Laura Heydmann
- Institut de Recherche sur les Maladies Virales et Hépatiques, Inserm U1110, Strasbourg, France
| | - James A Cheney
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel Kvistad
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jasneet Aneja
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Juliana G Melgaço
- Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Carlos A Fernandes
- Laboratório Central de Saúde Pública Noel Nutels, Rio de Janeiro, Brazil
| | - Raymond T Chung
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Andre Boonstra
- Department of Gastroenterology and Hepatology, Erasmus MC, Rotterdam, The Netherlands
| | - Arthur Y Kim
- Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas F Baumert
- Institut de Recherche sur les Maladies Virales et Hépatiques, Inserm U1110, Strasbourg, France
| | - Jörg Timm
- Institute of Virology, Heinrich Heine University, University Hospital, Düsseldorf, Germany
| | | | - Pierre Tonnerre
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Georg M Lauer
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
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15
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Karimzadeh H, Kiraithe MM, Oberhardt V, Salimi Alizei E, Bockmann J, Schulze Zur Wiesch J, Budeus B, Hoffmann D, Wedemeyer H, Cornberg M, Krawczyk A, Rashidi-Alavijeh J, Rodríguez-Frías F, Casillas R, Buti M, Smedile A, Alavian SM, Heinold A, Emmerich F, Panning M, Gostick E, Price DA, Timm J, Hofmann M, Raziorrouh B, Thimme R, Protzer U, Roggendorf M, Neumann-Haefelin C. Mutations in Hepatitis D Virus Allow It to Escape Detection by CD8 + T Cells and Evolve at the Population Level. Gastroenterology 2019; 156:1820-1833. [PMID: 30768983 PMCID: PMC6486497 DOI: 10.1053/j.gastro.2019.02.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 01/16/2019] [Accepted: 02/03/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Hepatitis D virus (HDV) superinfection in patients with hepatitis B virus (HBV) is associated with rapid progression to liver cirrhosis and hepatocellular carcinoma. Treatment options are limited, and no vaccine is available. Although HDV-specific CD8+ T cells are thought to control the virus, little is known about which HDV epitopes are targeted by virus-specific CD8+ T cells or why these cells ultimately fail to control the infection. We aimed to define how HDV escapes the CD8+ T-cell-mediated response. METHODS We collected plasma and DNA samples from 104 patients with chronic HDV and HBV infection at medical centers in Europe and the Middle East, sequenced HDV, typed human leukocyte antigen (HLA) class I alleles from patients, and searched for polymorphisms in HDV RNA associated with specific HLA class I alleles. We predicted epitopes in HDV that would be recognized by CD8+ T cells and corresponded with the identified virus polymorphisms in patients with resolved (n = 12) or chronic (n = 13) HDV infection. RESULTS We identified 21 polymorphisms in HDV that were significantly associated with specific HLA class I alleles (P < .005). Five of these polymorphisms were found to correspond to epitopes in HDV that are recognized by CD8+ T cells; we confirmed that CD8+ T cells in culture targeted these HDV epitopes. HDV variant peptides were only partially cross-recognized by CD8+ T cells isolated from patients, indicating that the virus had escaped detection by these cells. These newly identified HDV epitopes were restricted by relatively infrequent HLA class I alleles, and they bound most frequently to HLA-B. In contrast, frequent HLA class I alleles were not associated with HDV sequence polymorphisms. CONCLUSIONS We analyzed sequences of HDV RNA and HLA class I alleles that present epitope peptides to CD8+ T cells in patients with persistent HDV infection. We identified polymorphisms in the HDV proteome that associate with HLA class I alleles. Some variant peptides in epitopes from HDV were only partially recognized by CD8+ T cells isolated from patients; these could be mutations that allow HDV to escape the immune response, resulting in persistent infection. HDV escape from the immune response was associated with uncommon HLA class I alleles, indicating that HDV evolves, at the population level, to evade recognition by common HLA class I alleles.
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Affiliation(s)
- Hadi Karimzadeh
- Institute of Virology, School of Medicine, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany; Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany; Department of Internal Medicine II, University Hospital Munich-Grosshadern, Munich, Germany
| | - Muthamia M Kiraithe
- Department of Medicine II, University Hospital Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Valerie Oberhardt
- Department of Medicine II, University Hospital Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Elahe Salimi Alizei
- Department of Medicine II, University Hospital Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Faculty of Chemistry and Pharmacy, University of Freiburg, Freiburg, Germany
| | - Jan Bockmann
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; German Center for Infection Research (DZIF), Sites Hamburg-Lübeck-Borstel-Riems, Hannover-Braunschweig and Munich, Germany
| | - Julian Schulze Zur Wiesch
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; German Center for Infection Research (DZIF), Sites Hamburg-Lübeck-Borstel-Riems, Hannover-Braunschweig and Munich, Germany
| | - Bettina Budeus
- Department of Bioinformatics, University of Duisburg-Essen, Essen, Germany
| | - Daniel Hoffmann
- Department of Bioinformatics, University of Duisburg-Essen, Essen, Germany
| | - Heiner Wedemeyer
- German Center for Infection Research (DZIF), Sites Hamburg-Lübeck-Borstel-Riems, Hannover-Braunschweig and Munich, Germany; Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany; Department of Gastroenterology and Hepatology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Markus Cornberg
- German Center for Infection Research (DZIF), Sites Hamburg-Lübeck-Borstel-Riems, Hannover-Braunschweig and Munich, Germany; Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Adalbert Krawczyk
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany; Department of Infectious Diseases, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Jassin Rashidi-Alavijeh
- Department of Gastroenterology and Hepatology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Francisco Rodríguez-Frías
- CIBERehd and Departments of Biochemistry/Microbiology and Hepatology, Vall d'Hebron Hospital, University Autónoma de Barcelona (UAB), Barcelona, Spain
| | - Rosario Casillas
- CIBERehd and Departments of Biochemistry/Microbiology and Hepatology, Vall d'Hebron Hospital, University Autónoma de Barcelona (UAB), Barcelona, Spain
| | - Maria Buti
- CIBERehd and Departments of Biochemistry/Microbiology and Hepatology, Vall d'Hebron Hospital, University Autónoma de Barcelona (UAB), Barcelona, Spain
| | - Antonina Smedile
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Seyed Moayed Alavian
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Andreas Heinold
- Institute of Transfusion Medicine, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Florian Emmerich
- Institute for Transfusion Medicine and Gene Therapy, University Hospital Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marcus Panning
- Institute of Virology, University Hospital Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Emma Gostick
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Jörg Timm
- Institute of Virology, Heinrich-Heine-University, University Hospital, Duesseldorf, Germany
| | - Maike Hofmann
- Department of Medicine II, University Hospital Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Bijan Raziorrouh
- Department of Internal Medicine II, University Hospital Munich-Grosshadern, Munich, Germany
| | - Robert Thimme
- Department of Medicine II, University Hospital Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ulrike Protzer
- Institute of Virology, School of Medicine, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany; German Center for Infection Research (DZIF), Sites Hamburg-Lübeck-Borstel-Riems, Hannover-Braunschweig and Munich, Germany
| | - Michael Roggendorf
- Institute of Virology, School of Medicine, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany; Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany; German Center for Infection Research (DZIF), Sites Hamburg-Lübeck-Borstel-Riems, Hannover-Braunschweig and Munich, Germany.
| | - Christoph Neumann-Haefelin
- Department of Medicine II, University Hospital Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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16
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Bertoletti A, Kennedy PTF. HBV antiviral immunity: not all CD8 T cells are born equal. Gut 2019; 68:770-773. [PMID: 30700541 DOI: 10.1136/gutjnl-2018-317959] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 01/10/2019] [Accepted: 01/10/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Antonio Bertoletti
- Emerging Infectious Diseases Program, Duke-NUS Medical School, Singapore.,Singapore Immunology Network, A*STAR, Singapore
| | - Patrick T F Kennedy
- Liver Centre, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
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17
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Anastasiou OE, Widera M, Westhaus S, Timmer L, Korth J, Gerken G, Canbay A, Todt D, Steinmann E, Schwarz T, Timm J, Verheyen J, Ciesek S. Clinical Outcome and Viral Genome Variability of Hepatitis B Virus-Induced Acute Liver Failure. Hepatology 2019; 69:993-1003. [PMID: 30229977 DOI: 10.1002/hep.30279] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 09/01/2018] [Indexed: 12/29/2022]
Abstract
Acute hepatitis B virus (HBV) infection remains a frequent cause of acute liver failure (ALF) worldwide. ALF occurs in 0.1%-0.5% of infected patients. The aim of this study was to scrutinize the outcome of patients with HBV-induced ALF and mutational patterns of HBV variants, which might contribute to ALF. From 2005 to 2016, 42 patients were treated for HBV-induced ALF in the University Hospital Essen, Germany. Clinical and virological data from these patients were collected. As a control, 38 patients with acute hepatitis B (AHB) without liver failure were included. The HBV genome was sequenced by next-generation sequencing (NGS). Mutations that were found by NGS were analyzed in vitro. Of 42 patients, 8 had ALF without spontaneous recovery (NSR): Seven patients underwent liver transplantation (LT) and one patient died before LT. Of 42 patients, 34 (81%) had spontaneous recovery (SR) and cleared the infection, achieving either anti-HBs seroconversion or hepatitis B surface antigen (HBsAg) loss. HBV genotype (GT)-D was the most frequent GT in patients with ALF. Mutations in HBV core, preS2, and small hepatitis B surface antigen (SHB) were more frequent in patients with ALF-NSR compared with those with ALF-SR or AHB. Amino acid deletions (del; 16-22 and 20-22) in preS2 and SHB mutation L49R were exclusively detected in patients with ALF-NSR. In vitro analyses reveal that these mutations did not influence HBsAg secretion or infectivity. Conclusion: HBV GT-D and increased variability in HBV core, preS2 region, and SHB are associated with a worse clinical outcome of acute HBV infection.
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Affiliation(s)
- Olympia E Anastasiou
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany.,Department of Gastroenterology and Hepatology, University Hospital of Essen, Essen, Germany
| | - Marek Widera
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Sandra Westhaus
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Lejla Timmer
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Johannes Korth
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Guido Gerken
- Department of Gastroenterology and Hepatology, University Hospital of Essen, Essen, Germany
| | - Ali Canbay
- Department of Gastroenterology and Hepatology, University Hospital of Magdeburg, Magdeburg, Germany
| | - Daniel Todt
- Department of Molecular and Medical Virology, Ruhr University, Bochum, Germany
| | - Eike Steinmann
- Department of Molecular and Medical Virology, Ruhr University, Bochum, Germany
| | - Tatjana Schwarz
- Institute of Virology, University Hospital of Düsseldorf, University of Düsseldorf, Düsseldorf, Germany
| | - Jörg Timm
- Institute of Virology, University Hospital of Düsseldorf, University of Düsseldorf, Düsseldorf, Germany
| | - Jens Verheyen
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Sandra Ciesek
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
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18
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Cheng Y, Zhu YO, Becht E, Aw P, Chen J, Poidinger M, de Sessions PF, Hibberd ML, Bertoletti A, Lim SG, Newell EW. Multifactorial heterogeneity of virus-specific T cells and association with the progression of human chronic hepatitis B infection. Sci Immunol 2019; 4:4/32/eaau6905. [DOI: 10.1126/sciimmunol.aau6905] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 01/02/2019] [Indexed: 12/11/2022]
Abstract
Associations between chronic antigen stimulation, T cell dysfunction, and the expression of various inhibitory receptors are well characterized in several mouse and human systems. During chronic hepatitis B virus (HBV) infection (CHB), T cell responses are blunted with low frequencies of virus-specific T cells observed, making these parameters difficult to study. Here, using mass cytometry and a highly multiplexed combinatorial peptide–major histocompatibility complex (pMHC) tetramer strategy that allows for the detection of rare antigen-specific T cells, we simultaneously probed 484 unique HLA-A*1101–restricted epitopes spanning the entire HBV genome on T cells from patients at various stages of CHB. Numerous HBV-specific T cell populations were detected, validated, and profiled. T cells specific for two epitopes (HBVpol387and HBVcore169) displayed differing and complex heterogeneities that were associated with the disease progression, and the expression of inhibitory receptors on these cells was not linearly related with their extent of T cell dysfunction. For HBVcore169-specific CD8+T cells, we found cellular markers associated with long-term memory, polyfunctionality, and the presence of several previously unidentified public TCR clones that correlated with viral control. Using high-dimensional trajectory analysis of these cellular phenotypes, a pseudo-time metric was constructed that fit with the status of viral infection in corresponding patients. This was validated in a longitudinal cohort of patients undergoing antiviral therapy. Our study uncovers complex relationships of inhibitory receptors between the profiles of antigen-specific T cells and the status of CHB with implications for new strategies of therapeutic intervention.
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19
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20
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Chen QY, Hu YL, Wang XY, Harrison TJ, Wang C, Hu LP, Yang QL, Ren CC, Jia HH, Fang AZL. Locus 5p13.1 may be associated with the selection of cancer-related HBV core promoter mutations. Int J Med Sci 2019; 16:990-997. [PMID: 31341412 PMCID: PMC6643130 DOI: 10.7150/ijms.34297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/21/2019] [Indexed: 11/16/2022] Open
Abstract
Background: The basal core promoter (BCP) double mutations (A1762T and G1764A) of hepatitis B virus (HBV) have been reported to be an aetiological factor of hepatocellular carcinoma (HCC). What distinguishes the subset of HBV carriers in whom these mutations are selected? Methods: A genome-wide association study (GWAS) was carried out on 218 asymptomatic HBsAg carriers infected with HBV with BCP double mutations and 191 controls infected with HBV with the wild type BCP. The highest ranking nucleotide polymorphisms (SNPs) were validated with other study subjects, 203 cases and 181 controls. The expression of the gene nearest a SNP found to be significant was examined using RT-PCR. Results: Forty-five candidate SNPs were identified in the GWAS. Three SNPs were found to be associated with the selection of HBV BCP double mutations in the replication stage, including rs7717457 at 5p13.1, rs670011 at 17q21.2, rs2071611 at 6p22.2. Especially, rs7717457 (P= 4.57×10-5 combined P) reached the potential GWAS significance level. The expression of gene complement component 7 (C7), nearest to SNP rs7717457, differed significantly between the case and control groups (t=2.045, P=0.04), suggesting that SNP rs7717457 was associated with the expression of its nearest gene. Conclusions: SNP rs7717457 is associated with the selection of HBV BCP double mutations, providing an important clue to understanding the mechanisms of oncogenesis of HBV BCP double mutations.
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Affiliation(s)
- Qin-Yan Chen
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
| | - Yan-Ling Hu
- Center for Genomic and Personalized Medicine, Guangxi Medical University, 22 ShuangYong Road, Nanning, Guangxi 530021, China
| | - Xue-Yan Wang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
| | | | - Chao Wang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
| | - Li-Ping Hu
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
| | - Qing-Li Yang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
| | - Chuang-Chuang Ren
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China.,School of Preclinical Medicine, Guangxi Medical University, 22 ShuangYong Road, Nanning, Guangxi 530021, China
| | - Hui-Hua Jia
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China.,School of Preclinical Medicine, Guangxi Medical University, 22 ShuangYong Road, Nanning, Guangxi 530021, China
| | - And Zhong-Liao Fang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
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21
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Rehermann B, Thimme R. Insights From Antiviral Therapy Into Immune Responses to Hepatitis B and C Virus Infection. Gastroenterology 2019; 156:369-383. [PMID: 30267712 PMCID: PMC6340757 DOI: 10.1053/j.gastro.2018.08.061] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/05/2018] [Accepted: 08/21/2018] [Indexed: 12/17/2022]
Abstract
There are 257 million persons worldwide with chronic hepatitis B virus (HBV) infection, a leading causes of liver cancer. Almost all adults with acute HBV infection have a rapid immune response to the virus, resulting in life-long immunity, but there is no cure for individuals with chronic HBV infection, which they acquire during early life. The mechanisms that drive the progression of HBV through distinct clinical phases to end-stage liver disease are poorly understood. Likewise, it is not clear whether and how immune responses can be modulated to allow control and/or clearance of intrahepatic HBV DNA. We review the innate and adaptive immune responses to acute and chronic HBV infections and responses to antiviral therapy. Comparisons with hepatitis C virus infection provide insights into the reversibility of innate inflammatory responses and the potential for successful therapy to recover virus-specific memory immune responses.
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Affiliation(s)
- Barbara Rehermann
- Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland.
| | - Robert Thimme
- Klinik für Innere Medizin II, University Hospital Freiburg, Faculty of Medicine, Hugstetter Straße 55, 79106 Freiburg, Germany
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22
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van der Ree MH, Jansen L, Welkers MRA, Reesink HW, Feenstra KA, Kootstra NA. Deep sequencing identifies hepatitis B virus core protein signatures in chronic hepatitis B patients. Antiviral Res 2018; 158:213-225. [PMID: 30121196 DOI: 10.1016/j.antiviral.2018.08.009] [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: 01/07/2018] [Revised: 08/10/2018] [Accepted: 08/13/2018] [Indexed: 11/16/2022]
Abstract
BACKGROUND We aimed to identify HBc amino acid differences between subgroups of chronic hepatitis B (CHB) patients. METHODS Deep sequencing of HBc was performed in samples of 89 CHB patients (42 HBeAg positive, 47 HBeAg negative). Amino acid types were compared using Sequence Harmony to identify subgroup specific sites between HBeAg-positive and -negative patients, and between patients with combined response and non-response to peginterferon/adefovir combination therapy. RESULTS We identified 54 positions in HBc where the frequency of appearing amino acids was significantly different between HBeAg-positive and -negative patients. In HBeAg negative patients, 22 positions in HBc were identified which differed between patients with treatment response and those with non-response. The fraction non-consensus sequence on selected positions was significantly higher in HBeAg-negative patients, and was negatively correlated with HBV DNA and HBsAg levels. CONCLUSIONS Sequence Harmony identified a number of amino acid changes associated with HBeAg-status and response to peginterferon/adefovir combination therapy.
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Affiliation(s)
- Meike H van der Ree
- Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, The Netherlands; Department of Experimental Immunology, Academic Medical Center, Amsterdam, The Netherlands
| | - Louis Jansen
- Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, The Netherlands; Department of Experimental Immunology, Academic Medical Center, Amsterdam, The Netherlands
| | - Matthijs R A Welkers
- Department of Medical Microbiology, Academic Medical Center, Amsterdam, The Netherlands
| | - Hendrik W Reesink
- Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, The Netherlands; Department of Experimental Immunology, Academic Medical Center, Amsterdam, The Netherlands
| | - K Anton Feenstra
- Center for Integrative Bioinformatics VU (IBIVU), Department of Computer Science, Amsterdam Institute for Molecules, Medicine and Systems (AIMMS), VU University Amsterdam, The Netherlands
| | - Neeltje A Kootstra
- Department of Experimental Immunology, Academic Medical Center, Amsterdam, The Netherlands.
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23
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CD8 + T-Cell Response-Associated Evolution of Hepatitis B Virus Core Protein and Disease Progress. J Virol 2018; 92:JVI.02120-17. [PMID: 29950410 DOI: 10.1128/jvi.02120-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 06/05/2018] [Indexed: 12/13/2022] Open
Abstract
Under the immune pressure of cytotoxic T cells (CTLs), hepatitis B virus (HBV) evolves to accumulate mutations more likely within epitopes to evade immune detection. However, little is known about the specific patterns of the immune pressure-associated HBV mutation of T-cell epitopes and their link to disease progression. Here, we observed a correlation of the accumulated variants on HBV core protein (HBc) with the disease severity of HBV infection. Further analysis indicated that these substitutions were mostly located within CD8+ T-cell epitopes of HBc protein, which were systematically screened and identified in an unbiased manner in our study. From individual peptide level to the human leukocyte antigen I (HLA-I)-restricted population level, we elucidated that the mutations in these well-defined HLA-I-restricted T-cell epitopes significantly decreased antiviral activity-specific CTLs and were positively associated with clinical parameters and disease progression in HBV-infected patients. The molecular pattern for viral epitope variations based on the sequencing of 105 HBV virus genomes indicated that the C-terminal portion (Pc), especially the Pc-1 and Pc-2 positions, have the highest mutation rates. Further structural analysis of HLA-A*02 complexed to diverse CD8+ T-cell epitopes revealed that the highly variable C-terminal bulged peak of M-shaped HBc-derived epitopes are solvent exposed, and most of the CDR3βs of the T-cell receptor hover over them. These data shed light on the molecular and immunological mechanisms of T-cell immunity-associated viral evolution in hepatitis B progression, which is beneficial for designing immunotherapies and vaccines.IMPORTANCE The specific patterns of sequence polymorphisms of T-cell epitopes and the immune mechanisms of the HBV epitope mutation-linked disease progression are largely unclear. In this study, we systematically evaluated the contribution of CD8+ T cells to the disease progress-associated evolution of HBV. By evaluation of patient T-cell responses based on the peptide repertoire, we comprehensively characterized the association of clinical parameters in chronic hepatitis B with the antiviral T-cell response-associated mutations of the viruses from the single-epitope level to the overall HLA-I-restricted peptide levels. Furthermore, we investigated the molecular basis of the HLA-A2-restricted peptide immune escape and found that the solvent-exposed C-terminal portion of the epitopes is highly variable under CDR3β recognition. Our work may provide a comprehensive evaluation of viral mutations impacted by the host CTL response in HBV disease progression in the context of the full repertoire of HBc-derived epitopes.
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24
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Lumley SF, McNaughton AL, Klenerman P, Lythgoe KA, Matthews PC. Hepatitis B Virus Adaptation to the CD8+ T Cell Response: Consequences for Host and Pathogen. Front Immunol 2018; 9:1561. [PMID: 30061882 PMCID: PMC6054973 DOI: 10.3389/fimmu.2018.01561] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 06/25/2018] [Indexed: 12/11/2022] Open
Abstract
Chronic viral hepatitis infections are a major public health concern, with an estimated 290 million individuals infected with hepatitis B virus (HBV) globally. This virus has been a passenger in human populations for >30,000 years, and remains highly prevalent in some settings. In order for this endemic pathogen to persist, viral adaptation to host immune responses is pre-requisite. Here, we focus on the interplay between HBV infection and the CD8+ T cell response. We present the evidence that CD8+ T cells play an important role in control of chronic HBV infection and that the selective pressure imposed on HBV through evasion of these immune responses can potentially influence viral diversity, chronicity, and the outcome of infection, and highlight where there are gaps in current knowledge. Understanding the nature and mechanisms of HBV evolution and persistence could shed light on differential disease outcomes, including cirrhosis and hepatocellular carcinoma, and help reach the goal of global HBV elimination by guiding the design of new strategies, including vaccines and therapeutics.
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Affiliation(s)
- Sheila F. Lumley
- Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Anna L. McNaughton
- Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Paul Klenerman
- Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
- Oxford BRC, John Radcliffe Hospital, Oxford, United Kingdom
| | - Katrina A. Lythgoe
- Nuffield Department of Medicine, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Philippa C. Matthews
- Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
- Oxford BRC, John Radcliffe Hospital, Oxford, United Kingdom
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Karimzadeh H, Kiraithe MM, Kosinska AD, Glaser M, Fiedler M, Oberhardt V, Salimi Alizei E, Hofmann M, Mok JY, Nguyen M, van Esch WJE, Budeus B, Grabowski J, Homs M, Olivero A, Keyvani H, Rodríguez-Frías F, Tabernero D, Buti M, Heinold A, Alavian SM, Bauer T, Schulze Zur Wiesch J, Raziorrouh B, Hoffmann D, Smedile A, Rizzetto M, Wedemeyer H, Timm J, Antes I, Neumann-Haefelin C, Protzer U, Roggendorf M. Amino Acid Substitutions within HLA-B*27-Restricted T Cell Epitopes Prevent Recognition by Hepatitis Delta Virus-Specific CD8 + T Cells. J Virol 2018; 92:JVI.01891-17. [PMID: 29669837 PMCID: PMC6002722 DOI: 10.1128/jvi.01891-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 03/22/2018] [Indexed: 02/07/2023] Open
Abstract
Virus-specific CD8 T cell response seems to play a significant role in the outcome of hepatitis delta virus (HDV) infection. However, the HDV-specific T cell epitope repertoire and mechanisms of CD8 T cell failure in HDV infection have been poorly characterized. We therefore aimed to characterize HDV-specific CD8 T cell epitopes and the impacts of viral mutations on immune escape. In this study, we predicted peptide epitopes binding the most frequent human leukocyte antigen (HLA) types and assessed their HLA binding capacities. These epitopes were characterized in HDV-infected patients by intracellular gamma interferon (IFN-γ) staining. Sequence analysis of large hepatitis delta antigen (L-HDAg) and HLA typing were performed in 104 patients. The impacts of substitutions within epitopes on the CD8 T cell response were evaluated experimentally and by in silico studies. We identified two HLA-B*27-restricted CD8 T cell epitopes within L-HDAg. These novel epitopes are located in a relatively conserved region of L-HDAg. However, we detected molecular footprints within the epitopes in HLA-B*27-positive patients with chronic HDV infections. The variant peptides were not cross-recognized in HLA-B*27-positive patients with resolved HDV infections, indicating that the substitutions represent viral escape mutations. Molecular modeling of HLA-B*27 complexes with the L-HDAg epitope and its potential viral escape mutations indicated that the structural and electrostatic properties of the bound peptides differ considerably at the T cell receptor interface, which provides a possible molecular explanation for the escape mechanism. This viral escape from the HLA-B*27-restricted CD8 T cell response correlates with a chronic outcome of hepatitis D infection. T cell failure resulting from immune escape may contribute to the high chronicity rate in HDV infection.IMPORTANCE Hepatitis delta virus (HDV) causes severe chronic hepatitis, which affects 20 million people worldwide. Only a small number of patients are able to clear the virus, possibly mediated by a virus-specific T cell response. Here, we performed a systematic screen to define CD8 epitopes and investigated the role of CD8 T cells in the outcome of hepatitis delta and how they fail to eliminate HDV. Overall the number of epitopes identified was very low compared to other hepatotropic viruses. We identified, two HLA-B*27-restricted epitopes in patients with resolved infections. In HLA-B*27-positive patients with chronic HDV infections, however, we detected escape mutations within these identified epitopes that could lead to viral evasion of immune responses. These findings support evidence showing that HLA-B*27 is important for virus-specific CD8 T cell responses, similar to other viral infections. These results have implications for the clinical prognosis of HDV infection and for vaccine development.
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Affiliation(s)
- Hadi Karimzadeh
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Muthamia M Kiraithe
- University Hospital Freiburg, Department of Medicine II, University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Anna D Kosinska
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
- German Center for Infection Research (DZIF), Munich and Hannover Sites, Braunschweig, Germany
| | - Manuel Glaser
- Center for Integrated Protein Science Munich at the Department of Biosciences, Technische Universität München, Freising, Germany
| | - Melanie Fiedler
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Valerie Oberhardt
- University Hospital Freiburg, Department of Medicine II, University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Elahe Salimi Alizei
- University Hospital Freiburg, Department of Medicine II, University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Maike Hofmann
- University Hospital Freiburg, Department of Medicine II, University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | | | | | | | - Bettina Budeus
- Department of Bioinformatics, University of Duisburg-Essen, Essen, Germany
| | - Jan Grabowski
- German Center for Infection Research (DZIF), Munich and Hannover Sites, Braunschweig, Germany
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Maria Homs
- CIBERehd and Departments of Biochemistry/Microbiology and Hepatology, Vall d'Hebron Hospital, University Autònoma de Barcelona (UAB), Barcelona, Spain
| | | | - Hossein Keyvani
- Department of Virology, Iran University of Medical Sciences, Tehran, Iran
| | - Francisco Rodríguez-Frías
- CIBERehd and Departments of Biochemistry/Microbiology and Hepatology, Vall d'Hebron Hospital, University Autònoma de Barcelona (UAB), Barcelona, Spain
| | - David Tabernero
- CIBERehd and Departments of Biochemistry/Microbiology and Hepatology, Vall d'Hebron Hospital, University Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Maria Buti
- CIBERehd and Departments of Biochemistry/Microbiology and Hepatology, Vall d'Hebron Hospital, University Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Andreas Heinold
- Institute of Transfusion Medicine, University of Duisburg-Essen, University Hospital, Essen, Germany
| | - Seyed Moayed Alavian
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Tanja Bauer
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
- German Center for Infection Research (DZIF), Munich and Hannover Sites, Braunschweig, Germany
| | - Julian Schulze Zur Wiesch
- Department of Medicine, Section of Infectious Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Bijan Raziorrouh
- University Hospital Munich-Grosshadern, Department of Medicine II, Munich, Germany
| | - Daniel Hoffmann
- Department of Bioinformatics, University of Duisburg-Essen, Essen, Germany
| | - Antonina Smedile
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Mario Rizzetto
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Heiner Wedemeyer
- German Center for Infection Research (DZIF), Munich and Hannover Sites, Braunschweig, Germany
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Jörg Timm
- Institute of Virology, Heinrich-Heine-University, University Hospital, Duesseldorf, Germany
| | - Iris Antes
- Center for Integrated Protein Science Munich at the Department of Biosciences, Technische Universität München, Freising, Germany
| | - Christoph Neumann-Haefelin
- University Hospital Freiburg, Department of Medicine II, University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Ulrike Protzer
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
- German Center for Infection Research (DZIF), Munich and Hannover Sites, Braunschweig, Germany
| | - Michael Roggendorf
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Munich, Germany
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
- German Center for Infection Research (DZIF), Munich and Hannover Sites, Braunschweig, Germany
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26
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Zheng J, Ou Z, Lin X, Wang L, Liu Y, Jin S, Wu J. Analysis of epitope-based vaccine candidates against the E antigen of the hepatitis B virus based on the B genotype sequence: An in silico and in vitro approach. Cell Immunol 2018; 329:56-65. [PMID: 29724463 DOI: 10.1016/j.cellimm.2018.04.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 04/08/2018] [Accepted: 04/27/2018] [Indexed: 12/30/2022]
Abstract
Chronic hepatitis B virus infection is a worldwide health problem with no current effective strategy to achieve a cure. The Hepatitis B virus (HBV) E antigen (HBeAg) has a negative effect on the immune system and a therapeutic vaccine is a promising strategy in order to treat chronic virus infection. In this study, we analyzed and identified the MHC-I, MHC-II and B cell epitopes of the HBeAg based on a B genotype sequence of HBV using a bioinformatic approach and in vitro experiments. The computational approach provided us with four epitopes (LLWFHISCL, YLVSFGVWI, MQLFHLCLI, TVLEYLVSF) of the specific MHC-I allele HLA-A0201 that conformed to all criteria. Molecular docking and a peptide binding assay showed that epitope TVLEYLVSF had the lowest binding energy and epitope LLWFHISCL had the highest binding affinity to the HLA-A0201 molecule. An interferonγenzyme-linked immunospot assay and cytotoxicity assay revealed that epitope LLWFHISCL had the highest ability to induce and stimulate T cells. Furthermore, we determined four core peptides of MHC-II epitopes and a region of the B cell epitope. The epitopes and region identified in this research may be helpful in designing epitope-based vaccines and boosting the mechanism research of HBeAg and its effect on the immune system.
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Affiliation(s)
- Juzeng Zheng
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Zhanfan Ou
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Xianfan Lin
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Lingling Wang
- Department of Gastroenterology, The Affiliated Taizhou Hospital of Wenzhou Medical University, Taizhou 318000, China
| | - Yang Liu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Sisi Jin
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Jinming Wu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China.
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27
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Maini MK, Pallett LJ. Defective T-cell immunity in hepatitis B virus infection: why therapeutic vaccination needs a helping hand. Lancet Gastroenterol Hepatol 2018; 3:192-202. [PMID: 29870733 DOI: 10.1016/s2468-1253(18)30007-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/18/2017] [Accepted: 09/22/2017] [Indexed: 12/11/2022]
Abstract
Hepatitis B virus (HBV) remains a major cause of morbidity and mortality worldwide. Treatments that can induce functional cure in patients chronically infected with this hepatotropic, non-cytopathic virus are desperately needed. Attempts to use therapeutic vaccines to expand the weak antiviral T-cell response and induce sustained immunity have been unsuccessful. However, exciting progress has been made in defining the molecular defects that must be overcome to harness T-cell immunity. A large arsenal of immunotherapeutic agents and direct-acting antivirals targeting multiple steps of the viral lifecycle is emerging. In this Review, we discuss how to translate the new insights into T-cell manipulation, combined with better understanding of patient heterogeneity, into optimisation of therapeutic vaccines against HBV. We review the opportunities and risks involved in boosting endogenous T-cell responses using combinations of next generation therapeutic vaccines and immunotherapy agents.
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Affiliation(s)
- Mala K Maini
- Division of Infection and Immunity and Institute of Immunity and Transplantation, University College London, London, UK.
| | - Laura J Pallett
- Division of Infection and Immunity and Institute of Immunity and Transplantation, University College London, London, UK
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28
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Bertoletti A, Tan AT, Koh S. T-cell therapy for chronic viral hepatitis. Cytotherapy 2017; 19:1317-1324. [DOI: 10.1016/j.jcyt.2017.07.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/27/2017] [Indexed: 02/07/2023]
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29
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Anastasiou OE, Widera M, Verheyen J, Korth J, Gerken G, Helfritz FA, Canbay A, Wedemeyer H, Ciesek S. Clinical course and core variability in HBV infected patients without detectable anti-HBc antibodies. J Clin Virol 2017. [DOI: 10.1016/j.jcv.2017.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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Jia J, Li H, Wang H, Chen S, Wang M, Feng H, Gao Y, Wang Y, Fang M, Gao C. Hepatitis B virus core antigen mutations predict post-operative prognosis of patients with primary hepatocellular carcinoma. J Gen Virol 2017; 98:1399-1409. [PMID: 28640739 PMCID: PMC5656792 DOI: 10.1099/jgv.0.000790] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/26/2017] [Indexed: 12/11/2022] Open
Abstract
The aim of this study was to explore the relationship between hepatitis B virus (HBV) core antigen (HBc) mutations and the post-operative prognosis of HBV-related hepatocellular carcinoma (HCC). In total, 98 patients suffering from HBV-related HCC and treated with surgery were enrolled, with a 48 month follow-up. The preCore/Core region of the HBV genome from tumour tissue (TT) and paired adjacent non-tumour tissue (ANTT) of these patients was sequenced, and a phylogenetic tree was reconstructed. The correlations between the viral features and evolutionary divergence of preCore/Core amino acid sequences from 67 paired TTs and ANTTs were analysed. Cox proportional hazard model analysis was applied for post-operative hazard risk evaluation. Phylogenetic analysis revealed that all of the sequences were ascribed to genotype C. The evolutionary divergence of amino acid sequences from matched TTs and ANTTs was significantly negatively correlated with serum and intrahepatic HBV DNA levels. Multivariate analysis showed that the HBc E77 mutation was associated with shorter overall survival, and HBc S87 and P156 mutations were independent risk factors for relapse. Furthermore, in contrast to with patients without the S87 mutation, no correlation was observed between serum HBV DNA and intrahepatic HBV DNA in HCC patients with the S87 mutation. Analysis of the intrahepatic sequence may advance our understanding of viral status; thus, it is useful for prognosis prediction for HBV-related HCC.
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Affiliation(s)
- Jian’an Jia
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, PR China
- Department of Laboratory Medicine, 105th Hospital of PLA, Hefei 230031, PR China
| | - Huiming Li
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, PR China
| | - Hui Wang
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, PR China
- Department of Clinical Laboratory, First Affiliated Hospital of Chinese PLA’s General Hospital, Beijing 100048, PR China
| | - Shipeng Chen
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, PR China
| | - Mengmeng Wang
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, PR China
| | - Huijuan Feng
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, PR China
| | - Yuzhen Gao
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, PR China
| | - Yunjiu Wang
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, PR China
| | - Meng Fang
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, PR China
| | - Chunfang Gao
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, PR China
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31
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Boeijen LL, Hoogeveen RC, Boonstra A, Lauer GM. Hepatitis B virus infection and the immune response: The big questions. Best Pract Res Clin Gastroenterol 2017; 31:265-272. [PMID: 28774408 DOI: 10.1016/j.bpg.2017.05.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 04/26/2017] [Accepted: 05/13/2017] [Indexed: 01/31/2023]
Abstract
Clinical events and the host immune response during hepatitis B virus (HBV) infection are intricately linked. Despite decades of research, important questions concerning the immunopathogenesis of chronic HBV infection remain unanswered. For example, it is unclear which immune parameters facilitate persistence, and if HBV can be completely cleared from the human liver. Recent technological breakthroughs now allow researchers to address these seemingly basic, but essential questions surrounding HBV immunity. It will be important to better define the molecular underpinnings of immune cell function and dysfunction during chronic disease and in controlled infection, with particular focus on the liver, as little information is available on the intrahepatic compartment. In the near future, it may be possible to solve some of the controversy surrounding the immune responses to HBV, and establish the features of both the innate and adaptive arms of the immune system required to achieve sustained control of HBV infection.
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Affiliation(s)
- Lauke L Boeijen
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Ruben C Hoogeveen
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, The Netherlands; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Andre Boonstra
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, The Netherlands.
| | - Georg M Lauer
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
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32
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Multi-omics analyses reveal metabolic alterations regulated by hepatitis B virus core protein in hepatocellular carcinoma cells. Sci Rep 2017; 7:41089. [PMID: 28112229 PMCID: PMC5253728 DOI: 10.1038/srep41089] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 12/15/2016] [Indexed: 02/06/2023] Open
Abstract
Chronic hepatitis B virus (HBV) infection is partly responsible for hepatitis, fatty liver disease and hepatocellular carcinoma (HCC). HBV core protein (HBc), encoded by the HBV genome, may play a significant role in HBV life cycle. However, the function of HBc in the occurrence and development of liver disease is still unclear. To investigate the underlying mechanisms, HBc-transfected HCC cells were characterized by multi-omics analyses. Combining proteomics and metabolomics analyses, our results showed that HBc promoted the expression of metabolic enzymes and the secretion of metabolites in HCC cells. In addition, glycolysis and amino acid metabolism were significantly up-regulated by HBc. Moreover, Max-like protein X (MLX) might be recruited and enriched by HBc in the nucleus to regulate glycolysis pathways. This study provides further insights into the function of HBc in the molecular pathogenesis of HBV-induced diseases and indicates that metabolic reprogramming appears to be a hallmark of HBc transfection.
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33
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Lumley S, Noble H, Hadley MJ, Callow L, Malik A, Chua YY, Duffey OJ, Grolmusova N, Kumar A, Ravenscroft S, Spencer JI, Neumann-Haefelin C, Thimme R, Andersson M, Klenerman P, Barnes E, Matthews PC. Hepitopes: A live interactive database of HLA class I epitopes in hepatitis B virus. Wellcome Open Res 2016; 1:9. [PMID: 27976751 PMCID: PMC5142601 DOI: 10.12688/wellcomeopenres.9952.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Increased clinical and scientific scrutiny is being applied to hepatitis B virus (HBV), with focus on the development of new therapeutic approaches, ultimately aiming for cure. Defining the optimum natural CD8+ T cell immune responses that arise in HBV, mediated by HLA class I epitope presentation, may help to inform novel immunotherapeutic strategies. Therefore, we have set out to develop a comprehensive database of these epitopes in HBV, coined ‘Hepitopes’. This undertaking has its foundations in a systematic literature review to identify the sites and sequences of all published class I epitopes in HBV. We also collected information regarding the methods used to define each epitope, and any reported associations between an immune response to this epitope and disease outcome. The results of this search have been collated into a new open-access interactive database that is available at
http://www.expmedndm.ox.ac.uk/hepitopes. Over time, we will continue to refine and update this resource, as well as inviting contributions from others in the field to support its development. This unique new database is an important foundation for ongoing investigations into the nature and impact of the CD8+ T cell response to HBV.
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Affiliation(s)
- Sheila Lumley
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | | | | | - Liz Callow
- Bodleian Health Care Libraries, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Amna Malik
- Department of Paediatrics, University of Oxford, Oxford, UK
| | - Yi Yi Chua
- University of Oxford Medical School, John Radcliffe Hospital, Oxford, UK
| | - Owen J Duffey
- University of Oxford Medical School, John Radcliffe Hospital, Oxford, UK
| | - Natalia Grolmusova
- University of Oxford Medical School, John Radcliffe Hospital, Oxford, UK
| | - Arvind Kumar
- University of Oxford Medical School, John Radcliffe Hospital, Oxford, UK
| | - Samuel Ravenscroft
- University of Oxford Medical School, John Radcliffe Hospital, Oxford, UK
| | - Jonathan I Spencer
- University of Oxford Medical School, John Radcliffe Hospital, Oxford, UK
| | | | - Robert Thimme
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany
| | - Monique Andersson
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Paul Klenerman
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK.,Nuffield Department of Experimental Medicine, University of Oxford, Oxford, UK.,NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Eleanor Barnes
- Nuffield Department of Experimental Medicine, University of Oxford, Oxford, UK.,NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Philippa C Matthews
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK.,Nuffield Department of Experimental Medicine, University of Oxford, Oxford, UK
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34
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Huang M, Zhang W, Guo J, Wei X, Phiwpan K, Zhang J, Zhou X. Improved Transgenic Mouse Model for Studying HLA Class I Antigen Presentation. Sci Rep 2016; 6:33612. [PMID: 27634283 PMCID: PMC5025652 DOI: 10.1038/srep33612] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/30/2016] [Indexed: 11/16/2022] Open
Abstract
HLA class I (HLA-I) transgenic mice have proven to be useful models for studying human MHC-related immune responses over the last two decades. However, differences in the processing and presentation machinery between humans and mice may have profound effects on HLA-I restricted antigen presentation. In this study, we generated a novel human TAP-LMP (hTAP-LMP) gene cluster transgenic mouse model carrying an intact human TAP complex and two human immunoproteasome LMP subunits, PSMB8/PSMB9. By crossing the hTAP-LMP strain with different HLA-I transgenic mice, we found that the expression levels of human HLA-I molecules, especially the A3 supertype members (e.g., A11 and A33), were remarkably enhanced in corresponding HLA-I/hTAP-LMP transgenic mice. Moreover, we found that humanized processing and presentation machinery increased antigen presentation of HLA-A11-restricted epitopes and promoted the rapid reduction of hepatitis B virus (HBV) infection in HLA-A11/hTAP-LMP mice. Together, our study highlights that HLA-I/hTAP-LMP mice are an improved model for studying antigen presentation of HLA-I molecules and their related CTL responses.
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Affiliation(s)
- Man Huang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wei Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - Jie Guo
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - Xundong Wei
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Krung Phiwpan
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.,University of Phayao 19 Moo 2 Maeka, Muang Phayao district, Phayao, 56000, Thailand
| | - Jianhua Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
| | - Xuyu Zhou
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing 101408, China
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35
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Abstract
Hepatitis A virus (HAV), hepatitis B virus (HBV) and hepatitis C virus (HCV) are responsible for most cases of viral hepatitis. Infection by each type of virus results in a different typical natural disease course and clinical outcome that are determined by virological and immunological factors. HCV tends to establish a chronic persistent infection, whereas HAV does not. HBV is effectively controlled in adults, although it persists for a lifetime after neonatal infection. In this Review, we discuss the similarities and differences in immune responses to and immunopathogenesis of HAV, HBV and HCV infections, which may explain the distinct courses and outcomes of each hepatitis virus infection.
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36
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Matthews PC, Carlson JM, Beloukas A, Malik A, Jooste P, Ogwu A, Shapiro R, Riddell L, Chen F, Luzzi G, Jesuthasan G, Jeffery K, Jojic N, Ndung'u T, Carrington M, Goulder PJR, Geretti AM, Klenerman P. HLA-A is a Predictor of Hepatitis B e Antigen Status in HIV-Positive African Adults. J Infect Dis 2016; 213:1248-52. [PMID: 26655301 PMCID: PMC4799671 DOI: 10.1093/infdis/jiv592] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 12/01/2015] [Indexed: 01/06/2023] Open
Abstract
Outcomes of chronic infection with hepatitis B virus (HBV) are varied, with increased morbidity reported in the context of human immunodeficiency virus (HIV) coinfection. The factors driving different outcomes are not well understood, but there is increasing interest in an HLA class I effect. We therefore studied the influence of HLA class I on HBV in an African HIV-positive cohort. We demonstrated that virologic markers of HBV disease activity (hepatitis B e antigen status or HBV DNA level) are associated with HLA-A genotype. This finding supports the role of the CD8(+) T-cell response in HBV control, and potentially informs future therapeutic T-cell vaccine strategies.
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Affiliation(s)
- Philippa C Matthews
- Nuffield Department of Medicine Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Trust
| | | | - Apostolos Beloukas
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool
| | - Amna Malik
- Department of Paediatrics, University of Oxford
| | - Pieter Jooste
- Paediatric Department, Kimberley Hospital, Northern Cape
| | - Anthony Ogwu
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston
| | - Lynn Riddell
- Integrated Sexual Health Services, Northampton General Hospital, Cliftonville
| | - Fabian Chen
- Department of Sexual Health, Royal Berkshire Hospital, Reading
| | - Graz Luzzi
- Department of Sexual Health, High Wycombe Hospital, Buckinghamshire, United Kingdom
| | - Gerald Jesuthasan
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Trust
| | - Katie Jeffery
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Trust
| | - Nebojsa Jojic
- Microsoft Research, eScience Group, Redmond, Washington
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine KwaZulu-Natal Research Institute for Tuberculosis and HIV, University of KwaZulu-Natal, South Africa Max Planck Institute for Infection Biology, Berlin, Germany The Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts
| | - Mary Carrington
- The Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Maryland
| | - Philip J R Goulder
- Department of Paediatrics, University of Oxford HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine
| | - Anna Maria Geretti
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool
| | - Paul Klenerman
- Nuffield Department of Medicine Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Trust NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford
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37
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Bertoletti A, Ferrari C. Adaptive immunity in HBV infection. J Hepatol 2016; 64:S71-S83. [PMID: 27084039 DOI: 10.1016/j.jhep.2016.01.026] [Citation(s) in RCA: 300] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 01/12/2016] [Accepted: 01/25/2016] [Indexed: 02/06/2023]
Abstract
During hepatitis B virus (HBV) infection, the presence of HBV-specific antibody producing B cells and functional HBV-specific T cells (with helper or cytotoxic effects) ultimately determines HBV infection outcome. In this review, in addition to summarizing the present state of knowledge of HBV-adaptive immunity, we will highlight controversies and uncertainties concerning the HBV-specific B and T lymphocyte response, and propose future directions for research aimed at the generation of more efficient immunotherapeutic strategies.
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Affiliation(s)
- Antonio Bertoletti
- Emerging Infectious Diseases (EID) Program, Duke-NUS Medical School, Singapore; Viral Hepatitis Laboratory, Singapore Institute for Clinical Sciences, Agency of Science Technology and Research (A*STAR), Singapore.
| | - Carlo Ferrari
- Divisione Malattie Infettive, Ospdale Maggiore Parma, Parma, Italy
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38
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Zhang ZH, Wu CC, Chen XW, Li X, Li J, Lu MJ. Genetic variation of hepatitis B virus and its significance for pathogenesis. World J Gastroenterol 2016; 22:126-144. [PMID: 26755865 PMCID: PMC4698480 DOI: 10.3748/wjg.v22.i1.126] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 11/13/2015] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) has a worldwide distribution and is endemic in many populations. Due to its unique life cycle which requires an error-prone reverse transcriptase for replication, it constantly evolves, resulting in tremendous genetic variation in the form of genotypes, sub-genotypes, and mutations. In recent years, there has been considerable research on the relationship between HBV genetic variation and HBV-related pathogenesis, which has profound implications in the natural history of HBV infection, viral detection, immune prevention, drug treatment and prognosis. In this review, we attempted to provide a brief account of the influence of HBV genotype on the pathogenesis of HBV infection and summarize our current knowledge on the effects of HBV mutations in different regions on HBV-associated pathogenesis, with an emphasis on mutations in the preS/S proteins in immune evasion, occult HBV infection and hepatocellular carcinoma (HCC), mutations in polymerase in relation to drug resistance, mutations in HBV core and e antigen in immune evasion, chronicalization of infection and hepatitis B-related acute-on-chronic liver failure, and finally mutations in HBV x proteins in HCC.
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39
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Budeus B, Timm J, Hoffmann D. SeqFeatR for the Discovery of Feature-Sequence Associations. PLoS One 2016; 11:e0146409. [PMID: 26731669 PMCID: PMC4701496 DOI: 10.1371/journal.pone.0146409] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/15/2015] [Indexed: 12/20/2022] Open
Abstract
Specific selection pressures often lead to specifically mutated genomes. The open source software SeqFeatR has been developed to identify associations between mutation patterns in biological sequences and specific selection pressures ("features"). For instance, SeqFeatR has been used to discover in viral protein sequences new T cell epitopes for hosts of given HLA types. SeqFeatR supports frequentist and Bayesian methods for the discovery of statistical sequence-feature associations. Moreover, it offers novel ways to visualize results of the statistical analyses and to relate them to further properties. In this article we demonstrate various functions of SeqFeatR with real data. The most frequently used set of functions is also provided by a web server. SeqFeatR is implemented as R package and freely available from the R archive CRAN (http://cran.r-project.org/web/packages/SeqFeatR/index.html). The package includes a tutorial vignette. The software is distributed under the GNU General Public License (version 3 or later). The web server URL is https://seqfeatr.zmb.uni-due.de.
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Affiliation(s)
- Bettina Budeus
- Research Group Bioinformatics, Faculty of Biology, University of Duisburg-Essen, Essen, NRW, Germany
| | - Jörg Timm
- Institute for Virology, University Hospital Düsseldorf, Düsseldorf, NRW, Germany
| | - Daniel Hoffmann
- Research Group Bioinformatics, Faculty of Biology, University of Duisburg-Essen, Essen, NRW, Germany
- * E-mail:
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