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Hall-Swan S, Slone J, Rigo MM, Antunes DA, Lizée G, Kavraki LE. PepSim: T-cell cross-reactivity prediction via comparison of peptide sequence and peptide-HLA structure. Front Immunol 2023; 14:1108303. [PMID: 37187737 PMCID: PMC10175663 DOI: 10.3389/fimmu.2023.1108303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
Introduction Peptide-HLA class I (pHLA) complexes on the surface of tumor cells can be targeted by cytotoxic T-cells to eliminate tumors, and this is one of the bases for T-cell-based immunotherapies. However, there exist cases where therapeutic T-cells directed towards tumor pHLA complexes may also recognize pHLAs from healthy normal cells. The process where the same T-cell clone recognizes more than one pHLA is referred to as T-cell cross-reactivity and this process is driven mainly by features that make pHLAs similar to each other. T-cell cross-reactivity prediction is critical for designing T-cell-based cancer immunotherapies that are both effective and safe. Methods Here we present PepSim, a novel score to predict T-cell cross-reactivity based on the structural and biochemical similarity of pHLAs. Results and discussion We show our method can accurately separate cross-reactive from non-crossreactive pHLAs in a diverse set of datasets including cancer, viral, and self-peptides. PepSim can be generalized to work on any dataset of class I peptide-HLAs and is freely available as a web server at pepsim.kavrakilab.org.
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Affiliation(s)
- Sarah Hall-Swan
- Department of Computer Science, Rice University, Houston, TX, United States
| | - Jared Slone
- Department of Computer Science, Rice University, Houston, TX, United States
| | - Mauricio M. Rigo
- Department of Computer Science, Rice University, Houston, TX, United States
| | - Dinler A. Antunes
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
| | - Gregory Lizée
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Lydia E. Kavraki
- Department of Computer Science, Rice University, Houston, TX, United States
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2
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Mendes MFDA, de Souza Bragatte M, Vianna P, de Freitas MV, Pöhner I, Richter S, Wade RC, Salzano FM, Vieira GF. MatchTope: A tool to predict the cross reactivity of peptides complexed with Major Histocompatibility Complex I. Front Immunol 2022; 13:930590. [PMID: 36389840 PMCID: PMC9650389 DOI: 10.3389/fimmu.2022.930590] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/30/2022] [Indexed: 10/12/2023] Open
Abstract
The therapeutic targeting of the immune system, for example in vaccinology and cancer treatment, is a challenging task and the subject of active research. Several in silico tools used for predicting immunogenicity are based on the analysis of peptide sequences binding to the Major Histocompatibility Complex (pMHC). However, few of these bioinformatics tools take into account the pMHC three-dimensional structure. Here, we describe a new bioinformatics tool, MatchTope, developed for predicting peptide similarity, which can trigger cross-reactivity events, by computing and analyzing the electrostatic potentials of pMHC complexes. We validated MatchTope by using previously published data from in vitro assays. We thereby demonstrate the strength of MatchTope for similarity prediction between targets derived from several pathogens as well as for indicating possible cross responses between self and tumor peptides. Our results suggest that MatchTope can enhance and speed up future studies in the fields of vaccinology and cancer immunotherapy.
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Affiliation(s)
- Marcus Fabiano de Almeida Mendes
- Bioinformatic Core, Immunogenetics Laboratory, Genetics Department, Biosciences Institute, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Marcelo de Souza Bragatte
- Bioinformatic Core, Immunogenetics Laboratory, Genetics Department, Biosciences Institute, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Priscila Vianna
- Bioinformatic Core, Immunogenetics Laboratory, Genetics Department, Biosciences Institute, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Martiela Vaz de Freitas
- Bioinformatic Core, Immunogenetics Laboratory, Genetics Department, Biosciences Institute, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Ina Pöhner
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Stefan Richter
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Rebecca C. Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance and Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany
| | - Francisco Mauro Salzano
- Bioinformatic Core, Immunogenetics Laboratory, Genetics Department, Biosciences Institute, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Gustavo Fioravanti Vieira
- Bioinformatic Core, Immunogenetics Laboratory, Genetics Department, Biosciences Institute, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
- Post-Graduation Program in Health and Human Development, Universidade La Salle Canoas, Canoas, Brazil
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3
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Jackson KR, Antunes DA, Talukder AH, Maleki AR, Amagai K, Salmon A, Katailiha AS, Chiu Y, Fasoulis R, Rigo MM, Abella JR, Melendez BD, Li F, Sun Y, Sonnemann HM, Belousov V, Frenkel F, Justesen S, Makaju A, Liu Y, Horn D, Lopez-Ferrer D, Huhmer AF, Hwu P, Roszik J, Hawke D, Kavraki LE, Lizée G. Charge-based interactions through peptide position 4 drive diversity of antigen presentation by human leukocyte antigen class I molecules. PNAS NEXUS 2022; 1:pgac124. [PMID: 36003074 PMCID: PMC9391200 DOI: 10.1093/pnasnexus/pgac124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Human leukocyte antigen class I (HLA-I) molecules bind and present peptides at the cell surface to facilitate the induction of appropriate CD8+ T cell-mediated immune responses to pathogen- and self-derived proteins. The HLA-I peptide-binding cleft contains dominant anchor sites in the B and F pockets that interact primarily with amino acids at peptide position 2 and the C-terminus, respectively. Nonpocket peptide-HLA interactions also contribute to peptide binding and stability, but these secondary interactions are thought to be unique to individual HLA allotypes or to specific peptide antigens. Here, we show that two positively charged residues located near the top of peptide-binding cleft facilitate interactions with negatively charged residues at position 4 of presented peptides, which occur at elevated frequencies across most HLA-I allotypes. Loss of these interactions was shown to impair HLA-I/peptide binding and complex stability, as demonstrated by both in vitro and in silico experiments. Furthermore, mutation of these Arginine-65 (R65) and/or Lysine-66 (K66) residues in HLA-A*02:01 and A*24:02 significantly reduced HLA-I cell surface expression while also reducing the diversity of the presented peptide repertoire by up to 5-fold. The impact of the R65 mutation demonstrates that nonpocket HLA-I/peptide interactions can constitute anchor motifs that exert an unexpectedly broad influence on HLA-I-mediated antigen presentation. These findings provide fundamental insights into peptide antigen binding that could broadly inform epitope discovery in the context of viral vaccine development and cancer immunotherapy.
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Affiliation(s)
- Kyle R Jackson
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Dinler A Antunes
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Amjad H Talukder
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Ariana R Maleki
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Kano Amagai
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Avery Salmon
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Immunology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Arjun S Katailiha
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Yulun Chiu
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Romanos Fasoulis
- Department of Computer Science, Rice University, Houston, TX, USA
| | | | - Jayvee R Abella
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Brenda D Melendez
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Fenge Li
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Yimo Sun
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Heather M Sonnemann
- University of Texas MD Anderson Cancer Center, UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | | | | | | | | | - Yang Liu
- ThermoFisher Scientific, San Jose, CA, USA
| | - David Horn
- ThermoFisher Scientific, San Jose, CA, USA
| | | | | | - Patrick Hwu
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Jason Roszik
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
| | - David Hawke
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Lydia E Kavraki
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Gregory Lizée
- Department of Melanoma, UT MD Anderson Cancer Center, Houston, TX, USA
- Department of Immunology, UT MD Anderson Cancer Center, Houston, TX, USA
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4
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Meshram RJ, Kathwate GH, Gacche RN. Progress, evolving therapeutic/diagnostic approaches, and challenges in the management of hepatitis C virus infections. Arch Virol 2022; 167:717-736. [PMID: 35089390 PMCID: PMC8795940 DOI: 10.1007/s00705-022-05375-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 12/02/2021] [Indexed: 12/11/2022]
Abstract
Hepatitis C virus (HCV) infections are emerging as one of the foremost challenges in healthcare owing to its chronicity and the virus’s quasispecies nature. Worldwide, over 170 million people are chronically infected with HCV, with an annual mortality of over 500,000 people across the world. The emerging pathophysiological evidence links HCV infections to a risk of developing liver diseases such as cirrhosis and hepatocellular carcinoma. Despite the great strides that have been made towards understanding the pathophysiology of disease progression, the tailored treatments of HCV infection remain to be established. The present review provides an update of the literature pertaining to evolving therapeutic approaches and prophylactic measures for the effective management of HCV infections. An extensive discussion of established and experimental immune prophylactic measures also sheds light on current developments in the design of vaccination strategies against HCV infection. We have also attempted to address the application of nanotechnology in formulating effective therapeutic interventions against HCV. Pointing out the limitations of the existing diagnostic methods and therapeutic approaches against HCV might inspire the design and development of novel, efficient, reliable, and cost-effective diagnostic technologies as well as novel therapeutic and immune prophylactic interventions for the effective management of HCV.
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Affiliation(s)
| | | | - Rajesh Nivarti Gacche
- Department of Biotechnology, Savitribai Phule Pune University, Pune, MS, 411007, India.
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5
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Hartlage AS, Kapoor A. Hepatitis C Virus Vaccine Research: Time to Put Up or Shut Up. Viruses 2021; 13:1596. [PMID: 34452460 PMCID: PMC8402855 DOI: 10.3390/v13081596] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/27/2021] [Accepted: 07/31/2021] [Indexed: 12/16/2022] Open
Abstract
Unless urgently needed to prevent a pandemic, the development of a viral vaccine should follow a rigorous scientific approach. Each vaccine candidate should be designed considering the in-depth knowledge of protective immunity, followed by preclinical studies to assess immunogenicity and safety, and lastly, the evaluation of selected vaccines in human clinical trials. The recently concluded first phase II clinical trial of a human hepatitis C virus (HCV) vaccine followed this approach. Still, despite promising preclinical results, it failed to protect against chronic infection, raising grave concerns about our understanding of protective immunity. This setback, combined with the lack of HCV animal models and availability of new highly effective antivirals, has fueled ongoing discussions of using a controlled human infection model (CHIM) to test new HCV vaccine candidates. Before taking on such an approach, however, we must carefully weigh all the ethical and health consequences of human infection in the absence of a complete understanding of HCV immunity and pathogenesis. We know that there are significant gaps in our knowledge of adaptive immunity necessary to prevent chronic HCV infection. This review discusses our current understanding of HCV immunity and the critical gaps that should be filled before embarking upon new HCV vaccine trials. We discuss the importance of T cells, neutralizing antibodies, and HCV genetic diversity. We address if and how the animal HCV-like viruses can be used for conceptualizing effective HCV vaccines and what we have learned so far from these HCV surrogates. Finally, we propose a logical but narrow path forward for HCV vaccine development.
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Affiliation(s)
- Alex S. Hartlage
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA;
- Medical Scientist Training Program, College of Medicine and Public Health, The Ohio State University, Columbus, OH 43205, USA
| | - Amit Kapoor
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA;
- Department of Pediatrics, College of Medicine and Public Health, The Ohio State University, Columbus, OH 43205, USA
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6
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Mazouz S, Boisvert M, Abdel-Hakeem MS, Khedr O, Bruneau J, Shoukry NH. Expansion of Unique Hepatitis C Virus-Specific Public CD8 + T Cell Clonotypes during Acute Infection and Reinfection. THE JOURNAL OF IMMUNOLOGY 2021; 207:1180-1193. [PMID: 34341170 DOI: 10.4049/jimmunol.2001386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 06/09/2021] [Indexed: 11/19/2022]
Abstract
Hepatitis C virus (HCV) infection resolves spontaneously in ∼25% of acutely infected humans where viral clearance is mediated primarily by virus-specific CD8+ T cells. Previous cross-sectional analysis of the CD8+ TCR repertoire targeting two immunodominant HCV epitopes reported widespread use of public TCRs shared by different subjects, irrespective of infection outcome. However, little is known about the evolution of the public TCR repertoire during acute HCV and whether cross-reactivity to other Ags can influence infectious outcome. In this article, we analyzed the CD8+ TCR repertoire specific to the immunodominant and cross-reactive HLA-A2-restricted nonstructural 3-1073 epitope during acute HCV in humans progressing to either spontaneous resolution or chronic infection and at ∼1 y after viral clearance. TCR repertoire diversity was comparable among all groups with preferential usage of the TCR-β V04 and V06 gene families. We identified a set of 13 public clonotypes in HCV-infected humans independent of infection outcome. Six public clonotypes used the V04 gene family. Several public clonotypes were long-lived in resolvers and expanded on reinfection. By mining publicly available data, we identified several low-frequency CDR3 sequences in the HCV-specific repertoire matching human TCRs specific for other HLA-A2-restricted epitopes from melanoma, CMV, influenza A, EBV, and yellow fever viruses, but they were of low frequency and limited cross-reactivity. In conclusion, we identified 13 new public human CD8+ TCR clonotypes unique to HCV that expanded during acute infection and reinfection. The low frequency of cross-reactive TCRs suggests that they are not major determinants of infectious outcome.
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Affiliation(s)
- Sabrina Mazouz
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montreal, Montreal, Quebec, Canada
| | - Maude Boisvert
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
| | - Mohamed S Abdel-Hakeem
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montreal, Montreal, Quebec, Canada
| | - Omar Khedr
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
| | - Julie Bruneau
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada.,Département de Médecine Familiale et de Médecine d'Urgence, Université de Montréal, Montreal, Quebec, Canada; and
| | - Naglaa H Shoukry
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada; .,Département de Médecine, Université de Montréal, Montreal, Quebec, Canada
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7
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Factors Influencing the Prevalence of Resistance-Associated Substitutions in NS5A Protein in Treatment-Naive Patients with Chronic Hepatitis C. Biomedicines 2020; 8:biomedicines8040080. [PMID: 32272736 PMCID: PMC7235841 DOI: 10.3390/biomedicines8040080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/24/2020] [Accepted: 04/05/2020] [Indexed: 12/12/2022] Open
Abstract
Direct-acting antivirals (DAAs) revolutionized treatment of hepatitis C virus (HCV) infection. Resistance-associated substitutions (RASs) present at the baseline impair response to DAA due to rapid selection of resistant HCV strains. NS5A is indispensable target of the current DAA treatment regimens. We evaluated prevalence of RASs in NS5A in DAA-naïve patients infected with HCV 1a (n = 19), 1b (n = 93), and 3a (n = 90) before systematic DAA application in the territory of the Russian Federation. Total proportion of strains carrying at least one RAS constituted 35.1% (71/202). In HCV 1a we detected only M28V (57.9%) attributed to a founder effect. Common RASs in HCV 1b were R30Q (7.5%), L31M (5.4%), P58S (4.4%), and Y93H (5.4%); in HCV 3a, A30S (31.0%), A30K (5.7%), S62L (8.9%), and Y93H (2.2%). Prevalence of RASs in NS5A of HCV 1b and 3a was similar to that worldwide, including countries practicing massive DAA application, i.e., it was not related to treatment. NS5A with and without RASs exhibited different co-variance networks, which could be attributed to the necessity to preserve viral fitness. Majority of RASs were localized in polymorphic regions subjected to immune pressure, with selected substitutions allowing immune escape. Altogether, this explains high prevalence of RAS in NS5A and low barrier for their appearance in DAA-inexperienced population.
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8
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Balz K, Trassl L, Härtel V, Nelson PP, Skevaki C. Virus-Induced T Cell-Mediated Heterologous Immunity and Vaccine Development. Front Immunol 2020; 11:513. [PMID: 32296430 PMCID: PMC7137989 DOI: 10.3389/fimmu.2020.00513] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 03/06/2020] [Indexed: 12/15/2022] Open
Abstract
Heterologous immunity (H.I.) is a consequence of an encounter with a specific antigen, which can alter the subsequent immune response to a different antigen. This can happen at the innate immune system level—often called trained immunity or innate immune memory—and/or at the adaptive immune system level involving T memory cells and antibodies. Viruses may also induce T cell-mediated H.I., which can confer protection or drive immunopathology against other virus subtypes, related or unrelated viruses, other pathogens, auto- or allo-antigens. It is important to understand the underlying mechanisms for the development of antiviral “universal” vaccines and broader T cell responses rather than just subtype-specific antibody responses as in the case of influenza. Furthermore, knowledge about determinants of vaccine-mediated H.I. may inform public health policies and provide suggestions for repurposing existing vaccines. Here, we introduce H.I. and provide an overview of evidence on virus- and antiviral vaccine-induced T cell-mediated cross-reactive responses. We also discuss the factors influencing final clinical outcome of virus-mediated H.I. as well as non-specific beneficial effects of live attenuated antiviral vaccines such as measles and vaccinia. Available epidemiological and mechanistic data have implications both for the development of new vaccines and for personalized vaccinology, which are presented. Finally, we formulate future research priorities and opportunities.
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Affiliation(s)
- Kathrin Balz
- German Center for Lung Research (DZL), Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, Marburg, Germany
| | - Lilith Trassl
- German Center for Lung Research (DZL), Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, Marburg, Germany
| | - Valerie Härtel
- German Center for Lung Research (DZL), Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, Marburg, Germany
| | - Philipp P Nelson
- German Center for Lung Research (DZL), Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, Marburg, Germany
| | - Chrysanthi Skevaki
- German Center for Lung Research (DZL), Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, Marburg, Germany
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9
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Vianna P, Mendes MF, Bragatte MA, Ferreira PS, Salzano FM, Bonamino MH, Vieira GF. pMHC Structural Comparisons as a Pivotal Element to Detect and Validate T-Cell Targets for Vaccine Development and Immunotherapy-A New Methodological Proposal. Cells 2019; 8:cells8121488. [PMID: 31766602 PMCID: PMC6952977 DOI: 10.3390/cells8121488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/15/2019] [Accepted: 11/16/2019] [Indexed: 12/02/2022] Open
Abstract
The search for epitopes that will effectively trigger an immune response remains the “El Dorado” for immunologists. The development of promising immunotherapeutic approaches requires the appropriate targets to elicit a proper immune response. Considering the high degree of HLA/TCR diversity, as well as the heterogeneity of viral and tumor proteins, this number will invariably be higher than ideal to test. It is known that the recognition of a peptide-MHC (pMHC) by the T-cell receptor is performed entirely in a structural fashion, where the atomic interactions of both structures, pMHC and TCR, dictate the fate of the process. However, epitopes with a similar composition of amino acids can produce dissimilar surfaces. Conversely, sequences with no conspicuous similarities can exhibit similar TCR interaction surfaces. In the last decade, our group developed a database and in silico structural methods to extract molecular fingerprints that trigger T-cell immune responses, mainly referring to physicochemical similarities, which could explain the immunogenic differences presented by different pMHC-I complexes. Here, we propose an immunoinformatic approach that considers a structural level of information, combined with an experimental technology that simulates the presentation of epitopes for a T cell, to improve vaccine production and immunotherapy efficacy.
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Affiliation(s)
- Priscila Vianna
- Laboratory of Human Teratogenesis and Population Medical Genetics, Department of Genetics, Institute of Biosciences, Federal University of Rio Grande do Sul, Porto Alegre 91.501-970, Brazil;
| | - Marcus F.A. Mendes
- Laboratory of Bioinformatics (NBLI), Department of Genetics, Institute of Biosciences, Federal University of Rio Grande do Sul, Porto Alegre 91.501-970, Brazil (M.A.B.)
| | - Marcelo A. Bragatte
- Laboratory of Bioinformatics (NBLI), Department of Genetics, Institute of Biosciences, Federal University of Rio Grande do Sul, Porto Alegre 91.501-970, Brazil (M.A.B.)
| | - Priscila S. Ferreira
- Program of Immunology and Tumor Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute, Rio de Janeiro 20231-050, Brazil; (P.S.F.); (M.H.B.)
| | - Francisco M. Salzano
- Laboratory of Molecular Evolution, Department of Genetics, Institute of Biosciences, Federal University of Rio Grande do Sul, Porto Alegre 91.501-970, Brazil;
| | - Martin H. Bonamino
- Program of Immunology and Tumor Biology, Division of Experimental and Translational Research, Brazilian National Cancer Institute, Rio de Janeiro 20231-050, Brazil; (P.S.F.); (M.H.B.)
- Vice Presidency of Research and Biological Collections, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil
| | - Gustavo F. Vieira
- Laboratory of Bioinformatics (NBLI), Department of Genetics, Institute of Biosciences, Federal University of Rio Grande do Sul, Porto Alegre 91.501-970, Brazil (M.A.B.)
- Laboratory of Health Bioinformatics, Post Graduate Program in Health and Human Development, La Salle University, Canoas 91.501-970, Brazil
- Correspondence: ; Tel.: +55-51-3308-99-38; Fax: +55-51-3308-73-11
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10
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Luxenburger H, Graß F, Baermann J, Boettler T, Marget M, Emmerich F, Panning M, Thimme R, Nitschke K, Neumann-Haefelin C. Differential virus-specific CD8 + T-cell epitope repertoire in hepatitis C virus genotype 1 versus 4. J Viral Hepat 2018; 25:779-790. [PMID: 29397015 DOI: 10.1111/jvh.12874] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/05/2018] [Indexed: 01/06/2023]
Abstract
Virus-specific CD8+ T-cell responses play an important role in the outcome of hepatitis C virus (HCV) infection. To date, most HCV-specific CD8+ T-cell epitopes have been defined in HCV genotype 1 infection. In contrast, the HCV genotype 4-specific CD8+ T-cell response is poorly defined. Here, we analysed whether known HCV-specific CD8+ T-cell epitopes are also recognized in HCV genotype 4-infected patients and set out to identify the first HCV genotype 4-specific CD8+ T-cell epitopes. We studied patients chronically infected with HCV genotype 1 (n = 20) or 4 (n = 21) using 91 well-described HCV-specific epitope peptides. In addition, we analysed 24 genotype 4-infected patients using 40 epitope candidates predicted using an in silico approach. HCV-specific CD8+ T-cell responses targeting previously described epitopes were detectable in the majority of genotype 1-infected patients (11 of 20). In contrast, patients infected with HCV genotype 4 rarely targeted these epitopes (4 of 21; P = .0247). Importantly, we were able to identify eight novel HCV genotype 4-specific CD8+ T-cell epitopes. Only one of these epitopes was shared between genotype 1 and genotype 4. These results indicate that there is little overlap between CD8+ T-cell repertoires targeting HCV genotype 1 and 4. Prophylactic vaccination studies based on HCV genotype 1 are currently underway. However, in countries with the highest prevalence of HCV infection, such as Egypt, most patients are infected with HCV genotype 4. Thus, prophylactic vaccination strategies need to be adapted to HCV genotype 4 before their application to regions where HCV genotype 4 is endemic.
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Affiliation(s)
- Hendrik Luxenburger
- Faculty of Medicine, Department of Medicine II, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
| | - Franziska Graß
- Faculty of Medicine, Department of Medicine II, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
| | - Janina Baermann
- Faculty of Medicine, Department of Medicine II, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
| | - Tobias Boettler
- Faculty of Medicine, Department of Medicine II, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
| | - Matthias Marget
- Institute of Transfusion Medicine, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Florian Emmerich
- Faculty of Medicine, Institute for Cell and Gene Therapy, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
| | - Marcus Panning
- Faculty of Medicine, Institute of Virology, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
| | - Robert Thimme
- Faculty of Medicine, Department of Medicine II, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
| | - Katja Nitschke
- Faculty of Medicine, Department of Medicine II, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
| | - Christoph Neumann-Haefelin
- Faculty of Medicine, Department of Medicine II, University Hospital Freiburg, University of Freiburg, Freiburg, Germany
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11
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Young KG, Haq K, MacLean S, Dudani R, Elahi SM, Gilbert R, Weeratna RD, Krishnan L. Development of a recombinant murine tumour model using hepatoma cells expressing hepatitis C virus nonstructural antigens. J Viral Hepat 2018; 25:649-660. [PMID: 29316037 DOI: 10.1111/jvh.12856] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 12/14/2017] [Indexed: 12/14/2022]
Abstract
Hepatitis C virus (HCV) chronically infects 2%-3% of the world's population, causing liver disease and cancer with prolonged infection. The narrow host range of the virus, being restricted largely to human hepatocytes, has made the development of relevant models to evaluate the efficacy of vaccines a challenge. We have developed a novel approach to accomplish this by generating a murine hepatoma cell line stably expressing nonstructural HCV antigens which can be used in vitro or in vivo to test HCV vaccine efficacies. These HCV-recombinant hepatoma cells formed large solid-mass tumours when implanted into syngeneic mice, allowing us to test candidate HCV vaccines to demonstrate the development of an HCV-specific immune response that limited tumour growth. Using this model, we tested the therapeutic potential of recombinant anti-HCV-specific vaccines based on two fundamentally different attenuated pathogen vaccine systems-attenuated Salmonella and recombinant adenoviral vector based vaccine. While attenuated Salmonella that secreted HCV antigens limited growth of the HCV-recombinant tumours when used in a therapeutic vaccination trial, replication-competent but noninfectious adenovirus expressing nonstructural HCV antigens showed overall greater survival and reduced weight loss compared to non-replicating nondisseminating adenovirus. Our results demonstrate a model with anti-tumour responses to HCV nonstructural (NS) protein antigens and suggest that recombinant vaccine vectors should be explored as a therapeutic strategy for controlling HCV and HCV-associated cancers.
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Affiliation(s)
- K G Young
- Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - K Haq
- National Research Council Canada, Ottawa, ON, Canada
| | - S MacLean
- National Research Council Canada, Ottawa, ON, Canada
| | - R Dudani
- National Research Council Canada, Ottawa, ON, Canada
| | - S M Elahi
- National Research Council Canada, Montréal, QC, Canada
| | - R Gilbert
- National Research Council Canada, Montréal, QC, Canada
| | - R D Weeratna
- National Research Council Canada, Ottawa, ON, Canada
| | - L Krishnan
- National Research Council Canada, Ottawa, ON, Canada
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12
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Induction of Genotype Cross-Reactive, Hepatitis C Virus-Specific, Cell-Mediated Immunity in DNA-Vaccinated Mice. J Virol 2018; 92:JVI.02133-17. [PMID: 29437963 DOI: 10.1128/jvi.02133-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/11/2018] [Indexed: 12/24/2022] Open
Abstract
A universal hepatitis C virus (HCV) vaccine should elicit multiantigenic, multigenotypic responses, which are more likely to protect against challenge with the range of genotypes and subtypes circulating in the community. A vaccine cocktail and vaccines encoding consensus HCV sequences are attractive approaches to achieve this goal. Consequently, in a series of mouse vaccination studies, we compared the immunogenicity of a DNA vaccine encoding a consensus HCV nonstructural 5B (NS5B) protein to that of a cocktail of DNA plasmids encoding the genotype 1b (Gt1b) and Gt3a NS5B proteins. To complement this study, we assessed responses to a multiantigenic cocktail regimen by comparing a DNA vaccine cocktail encoding Gt1b and Gt3a NS3, NS4, and NS5B proteins to a single-genotype NS3/4/5B DNA vaccine. To thoroughly evaluate in vivo cytotoxic T lymphocyte (CTL) and T helper (Th) cell responses against Gt1b and Gt3a HCV peptide-pulsed target cells, we exploited a novel fluorescent-target array (FTA). FTA and enzyme-linked immunosorbent spot (ELISpot) analyses collectively indicated that the cocktail regimens elicited higher responses to Gt1b and Gt3a NS5B proteins than those with the consensus vaccine, while the multiantigenic DNA cocktail significantly increased the responses to NS3 and NS5B compared to those elicited by the single-genotype vaccines. Thus, a DNA cocktail vaccination regimen is more effective than a consensus vaccine or a monovalent vaccine at increasing the breadth of multigenotypic T cell responses, which has implications for the development of vaccines for communities where multiple HCV genotypes circulate.IMPORTANCE Despite the development of highly effective direct-acting antivirals (DAA), infections with hepatitis C virus (HCV) continue, particularly in countries where the supply of DAA is limited. Furthermore, patients who eliminate the virus as a result of DAA therapy can still be reinfected. Thus, a vaccine for HCV is urgently required, but the heterogeneity of HCV strains makes the development of a universal vaccine difficult. To address this, we developed a novel cytolytic DNA vaccine which elicits robust cell-mediated immunity (CMI) to the nonstructural (NS) proteins in vaccinated animals. We compared the immune responses against genotypes 1 and 3 that were elicited by a consensus DNA vaccine or a DNA vaccine cocktail and showed that the cocktail induced higher levels of CMI to the NS proteins of both genotypes. This study suggests that a universal HCV vaccine can most readily be achieved by use of a DNA vaccine cocktail.
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13
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Antunes DA, Rigo MM, Freitas MV, Mendes MFA, Sinigaglia M, Lizée G, Kavraki LE, Selin LK, Cornberg M, Vieira GF. Interpreting T-Cell Cross-reactivity through Structure: Implications for TCR-Based Cancer Immunotherapy. Front Immunol 2017; 8:1210. [PMID: 29046675 PMCID: PMC5632759 DOI: 10.3389/fimmu.2017.01210] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 09/12/2017] [Indexed: 12/16/2022] Open
Abstract
Immunotherapy has become one of the most promising avenues for cancer treatment, making use of the patient’s own immune system to eliminate cancer cells. Clinical trials with T-cell-based immunotherapies have shown dramatic tumor regressions, being effective in multiple cancer types and for many different patients. Unfortunately, this progress was tempered by reports of serious (even fatal) side effects. Such therapies rely on the use of cytotoxic T-cell lymphocytes, an essential part of the adaptive immune system. Cytotoxic T-cells are regularly involved in surveillance and are capable of both eliminating diseased cells and generating protective immunological memory. The specificity of a given T-cell is determined through the structural interaction between the T-cell receptor (TCR) and a peptide-loaded major histocompatibility complex (MHC); i.e., an intracellular peptide–ligand displayed at the cell surface by an MHC molecule. However, a given TCR can recognize different peptide–MHC (pMHC) complexes, which can sometimes trigger an unwanted response that is referred to as T-cell cross-reactivity. This has become a major safety issue in TCR-based immunotherapies, following reports of melanoma-specific T-cells causing cytotoxic damage to healthy tissues (e.g., heart and nervous system). T-cell cross-reactivity has been extensively studied in the context of viral immunology and tissue transplantation. Growing evidence suggests that it is largely driven by structural similarities of seemingly unrelated pMHC complexes. Here, we review recent reports about the existence of pMHC “hot-spots” for cross-reactivity and propose the existence of a TCR interaction profile (i.e., a refinement of a more general TCR footprint in which some amino acid residues are more important than others in triggering T-cell cross-reactivity). We also make use of available structural data and pMHC models to interpret previously reported cross-reactivity patterns among virus-derived peptides. Our study provides further evidence that structural analyses of pMHC complexes can be used to assess the intrinsic likelihood of cross-reactivity among peptide-targets. Furthermore, we hypothesize that some apparent inconsistencies in reported cross-reactivities, such as a preferential directionality, might also be driven by particular structural features of the targeted pMHC complex. Finally, we explain why TCR-based immunotherapy provides a special context in which meaningful T-cell cross-reactivity predictions can be made.
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Affiliation(s)
- Dinler A Antunes
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Kavraki Lab, Department of Computer Science, Rice University, Houston, TX, United States
| | - Maurício M Rigo
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Laboratório de Imunologia Celular e Molecular, Instituto de Pesquisas Biomédicas (IPB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Martiela V Freitas
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Marcus F A Mendes
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Marialva Sinigaglia
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Gregory Lizée
- Lizée Lab, Department of Melanoma Medical Oncology - Research, The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States
| | - Lydia E Kavraki
- Kavraki Lab, Department of Computer Science, Rice University, Houston, TX, United States
| | - Liisa K Selin
- Selin Lab, Department of Pathology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Markus Cornberg
- Cornberg Lab, Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany.,German Center for Infection Research (DZIF), Partner-Site Hannover-Braunschweig, Hannover, Germany
| | - Gustavo F Vieira
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Programa de Pós-Graduação em Saúde e Desenvolvimento Humano, Universidade La Salle, Porto Alegre, Brazil
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14
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Merani S, Lucas M, Deshpande P, Pfafferott K, Chopra A, Cooper D, Leary S, Luciani F, Gaudieri S. Influence of Transmitted Virus on the Host's Immune Response: A Case Study. Viral Immunol 2017; 30:533-541. [PMID: 28530508 DOI: 10.1089/vim.2017.0001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Host hepatitis C virus (HCV)-specific T cell responses and the ability of the virus to escape this response are important correlates of infection outcome. Understanding this host-viral interplay has been difficult given the often asymptomatic nature of acute HCV infection. We studied a recent transmission case to determine whether adapted viral strains can be transmitted and influence the recipient's anti-HCV T cell response. The diversity of viral populations was examined using next-generation sequencing, and HCV-specific T cell interferon (IFN)-γ responses were assessed using a peptide panel representing the autologous viruses. HCV-specific T cell responses in the source were directed against peptides that did not match the dominant autologous virus but rather low-frequency variants, implying existing viral adaptation in the source strain. Most HCV T cell epitopes that elicited an IFN-γ response in the source did not in the recipient, despite the pair sharing human leukocyte antigen alleles that govern antigen presentation and similar autologous viruses. Intrahost HCV variation in the recipient fell within predicted T cell epitopes, suggesting alternative targets of the immune response. These data suggest that transmission of adapted viral species can direct the host's HCV-specific immune response profile during acute infection.
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Affiliation(s)
- Shahzma Merani
- 1 School of Human Sciences, University of Western Australia , Crawley, Australia
| | - Michaela Lucas
- 2 Institute of Immunology and Infectious Diseases, Murdoch University , Murdoch, Australia .,3 School of Medicine and Pharmacology, Harry Perkins Institute, University of Western Australia , Crawley, Australia .,4 School of Pathology and Laboratory Medicine, University of Western Australia , Crawley, Australia
| | - Pooja Deshpande
- 1 School of Human Sciences, University of Western Australia , Crawley, Australia
| | - Katja Pfafferott
- 2 Institute of Immunology and Infectious Diseases, Murdoch University , Murdoch, Australia
| | - Abha Chopra
- 2 Institute of Immunology and Infectious Diseases, Murdoch University , Murdoch, Australia
| | - Don Cooper
- 2 Institute of Immunology and Infectious Diseases, Murdoch University , Murdoch, Australia
| | - Shay Leary
- 2 Institute of Immunology and Infectious Diseases, Murdoch University , Murdoch, Australia
| | - Fabio Luciani
- 5 Systems Immunology, School of Medical Sciences, University of New South Wales , Sydney, Australia
| | - Silvana Gaudieri
- 1 School of Human Sciences, University of Western Australia , Crawley, Australia .,2 Institute of Immunology and Infectious Diseases, Murdoch University , Murdoch, Australia .,6 Division of Infectious Disease, Department of Medicine, Vanderbilt University Medical Centre , Nashville, Tennessee
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15
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Harada N, Fukaya S, Wada H, Goto R, Osada T, Gomori A, Ikizawa K, Sakuragi M, Oda N. Generation of a Novel HLA Class I Transgenic Mouse Model Carrying a Knock-in Mutation at the β2-Microglobulin Locus. THE JOURNAL OF IMMUNOLOGY 2016; 198:516-527. [DOI: 10.4049/jimmunol.1502367] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 10/07/2016] [Indexed: 11/19/2022]
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16
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Ikram A, Obaid A, Awan FM, Hanif R, Naz A, Paracha RZ, Ali A, Janjua HA. Identification of drug resistance and immune-driven variations in hepatitis C virus (HCV) NS3/4A, NS5A and NS5B regions reveals a new approach toward personalized medicine. Antiviral Res 2016; 137:112-124. [PMID: 27984060 DOI: 10.1016/j.antiviral.2016.10.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 10/06/2016] [Accepted: 10/21/2016] [Indexed: 02/07/2023]
Abstract
Cellular immune responses (T cell responses) during hepatitis C virus (HCV) infection are significant factors for determining the outcome of infection. HCV adapts to host immune responses by inducing mutations in its genome at specific sites that are important for HLA processing/presentation. Moreover, HCV also adapts to resist potential drugs that are used to restrict its replication, such as direct-acting antivirals (DAAs). Although DAAs have significantly reduced disease burden, resistance to these drugs is still a challenge for the treatment of HCV infection. Recently, drug resistance mutations (DRMs) observed in HCV proteins (NS3/4A, NS5A and NS5B) have heightened concern that the emergence of drug resistance may compromise the effectiveness of DAAs. Therefore, the NS3/4A, NS5A and NS5B drug resistance variations were investigated in this study, and their prevalence was examined in a large number of protein sequences from all HCV genotypes. Furthermore, potential CD4+ and CD8+ T cell epitopes were predicted and their overlap with genetic variations was explored. The findings revealed that many reported DRMs within NS3/4A, NS5A and NS5B are not drug-induced; rather, they are already present in HCV strains, as they were also detected in HCV-naïve patients. This study highlights several hot spots in which HLA and drug selective pressure overlap. Interestingly, these overlapping mutations were frequently observed among many HCV genotypes. This study implicates that knowledge of the host HLA type and HCV subtype/genotype can provide important information in defining personalized therapy.
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Affiliation(s)
- Aqsa Ikram
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Pakistan
| | - Ayesha Obaid
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Pakistan
| | - Faryal Mehwish Awan
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Pakistan
| | - Rumeza Hanif
- Department of Healtcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Pakistan
| | - Anam Naz
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Pakistan
| | - Rehan Zafar Paracha
- Department of Computer Sciences, RCMS, National University of Sciences and Technology (NUST), Pakistan
| | - Amjad Ali
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Pakistan
| | - Hussnain Ahmed Janjua
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Pakistan.
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17
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Hepatitis C virus infection from the perspective of heterologous immunity. Curr Opin Virol 2016; 16:41-48. [DOI: 10.1016/j.coviro.2016.01.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 01/08/2016] [Indexed: 01/14/2023]
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18
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von Delft A, Humphreys IS, Brown A, Pfafferott K, Lucas M, Klenerman P, Lauer GM, Cox AL, Gaudieri S, Barnes E. The broad assessment of HCV genotypes 1 and 3 antigenic targets reveals limited cross-reactivity with implications for vaccine design. Gut 2016; 65:112-23. [PMID: 26092843 PMCID: PMC4717358 DOI: 10.1136/gutjnl-2014-308724] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 04/20/2015] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Developing a vaccine that is cross-reactive between HCV genotypes requires data on T cell antigenic targets that extends beyond genotype-1. We characterised T cell immune responses against HCV genotype-3, the most common infecting genotype in the UK and Asia, and assessed within genotype and between genotype cross-reactivity. DESIGN T cell targets were identified in 140 subjects with either acute, chronic or spontaneously resolved HCV genotype-3 infection using (1) overlapping peptides and (2) putative human leucocyte antigens (HLA)-class-I wild type and variant epitopes through the prior assessment of polymorphic HCV genomic sites associated with host HLA, in IFNγ-ELISpot assays. CD4+/CD8+ T cell subsets were defined and viral variability at T cell targets was determined through population analysis and viral sequencing. T cell cross-reactivity between genotype-1 and genotype-3 variants was assessed. RESULTS In resolved genotype-3 infection, T cells preferentially targeted non-structural proteins at a high magnitude, whereas in chronic disease T cells were absent or skewed to target structural proteins. Additional responses to wild type but not variant HLA predicted peptides were defined. Major sequence viral variability was observed within genotype-3 and between genotypes 1 and 3 HCV at T cell targets in resolved infection and at dominant epitopes, with limited T cell cross-reactivity between viral variants. Overall 41 CD4/CD8+ genotype-3 T cell targets were identified with minimal overlap with those described for HCV genotype-1. CONCLUSIONS HCV T cell specificity is distinct between genotypes with limited T cell cross-reactivity in resolved and chronic disease. Therefore, viral regions targeted in natural HCV infection may not serve as attractive targets for a vaccine that aims to protect against multiple HCV genotypes.
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Affiliation(s)
| | | | | | | | - Michaela Lucas
- Institute of Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia,School of Medicine and Pharmacology, Harry Perkins Institute, University of Western Australia, Western Australia, Australia,School of Pathology and Laboratory Medicine, University of Western Australia, Western Australia, Australia
| | | | | | - Andrea L Cox
- John Hopkins University, Baltimore, Maryland, USA
| | - Silvana Gaudieri
- Institute of Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia,School of Anatomy, Physiology and Human Biology, University of Western Australia, Perth, Western Australia, Australia
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19
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DockTope: a Web-based tool for automated pMHC-I modelling. Sci Rep 2015; 5:18413. [PMID: 26674250 PMCID: PMC4682062 DOI: 10.1038/srep18413] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 11/18/2015] [Indexed: 11/08/2022] Open
Abstract
The immune system is constantly challenged, being required to protect the organism against a wide variety of infectious pathogens and, at the same time, to avoid autoimmune disorders. One of the most important molecules involved in these events is the Major Histocompatibility Complex class I (MHC-I), responsible for binding and presenting small peptides from the intracellular environment to CD8+ T cells. The study of peptide:MHC-I (pMHC-I) molecules at a structural level is crucial to understand the molecular mechanisms underlying immunologic responses. Unfortunately, there are few pMHC-I structures in the Protein Data Bank (PDB) (especially considering the total number of complexes that could be formed combining different peptides), and pMHC-I modelling tools are scarce. Here, we present DockTope, a free and reliable web-based tool for pMHC-I modelling, based on crystal structures from the PDB. DockTope is fully automated and allows any researcher to construct a pMHC-I complex in an efficient way. We have reproduced a dataset of 135 non-redundant pMHC-I structures from the PDB (Cα RMSD below 1 Å). Modelling of pMHC-I complexes is remarkably important, contributing to the knowledge of important events such as cross-reactivity, autoimmunity, cancer therapy, transplantation and rational vaccine design.
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20
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Improved structural method for T-cell cross-reactivity prediction. Mol Immunol 2015; 67:303-10. [PMID: 26141239 DOI: 10.1016/j.molimm.2015.06.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/03/2015] [Accepted: 06/16/2015] [Indexed: 10/23/2022]
Abstract
Cytotoxic T-lymphocytes (CTLs) are the key players of adaptive cellular immunity, being able to identify and eliminate infected cells through the interaction with peptide-loaded major histocompatibility complexes class I (pMHC-I). Despite the high specificity of this interaction, a given lymphocyte is actually able to recognize more than just one pMHC-I complex, a phenomenon referred as cross-reactivity. In the present work we describe the use of pMHC-I structural features as input for multivariate statistical methods, to perform standardized structure-based predictions of cross-reactivity among viral epitopes. Our improved approach was able to successfully identify cross-reactive targets among 28 naturally occurring hepatitis C virus (HCV) variants and among eight epitopes from the four dengue virus serotypes. In both cases, our results were supported by multiscale bootstrap resampling and by data from previously published in vitro experiments. The combined use of data from charges and accessible surface area (ASA) of selected residues over the pMHC-I surface provided a powerful way of assessing the structural features involved in triggering cross-reactive responses. Moreover, the use of an R package (pvclust) for assessing the uncertainty in the hierarchical cluster analysis provided a statistical support for the interpretation of results. Taken together, these methods can be applied to vaccine design, both for the selection of candidates capable of inducing immunity against different targets, or to identify epitopes that could trigger undesired immunological responses.
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21
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Frequency, Private Specificity, and Cross-Reactivity of Preexisting Hepatitis C Virus (HCV)-Specific CD8+ T Cells in HCV-Seronegative Individuals: Implications for Vaccine Responses. J Virol 2015; 89:8304-17. [PMID: 26041301 DOI: 10.1128/jvi.00539-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/22/2015] [Indexed: 12/28/2022] Open
Abstract
UNLABELLED T cell responses play a critical role in controlling or clearing viruses. Therefore, strategies to prevent or treat infections include boosting T cell responses. T cells specific for various pathogens have been reported in unexposed individuals and an influence of such cells on the response toward vaccines is conceivable. However, little is known about their frequency, repertoire, and impact on vaccination. We performed a detailed characterization of CD8(+) T cells specific to a hepatitis C virus (HCV) epitope (NS3-1073) in 121 HCV-seronegative individuals. We show that in vitro HCV NS3-1073-specific CD8(+) T cell responses were rather abundantly detectable in one-third of HCV-seronegative individuals irrespective of risk factors for HCV exposure. Ex vivo, these NS3-1073-specific CD8(+) T cells were found to be both naive and memory cells. Importantly, recognition of various peptides derived from unrelated viruses by NS3-1073-specific CD8(+) T cells showed a considerable degree of T cell cross-reactivity, suggesting that they might in part originate from previous heterologous infections. Finally, we further provide evidence that preexisting NS3-1073-specific CD8(+) T cells can impact the T cell response toward peptide vaccination. Healthy, vaccinated individuals who showed an in vitro response toward NS3-1073 already before vaccination displayed a more vigorous and earlier response toward the vaccine. IMPORTANCE Preventive and therapeutic vaccines are being developed for many viral infections and often aim on inducing T cell responses. Despite effective antiviral drugs against HCV, there is still a need for a preventive vaccine. However, the responses to vaccines can be highly variable among different individuals. Preexisting T cells in unexposed individuals could be one reason that helps to explain the variable T cell responses to vaccines. Based on our findings, we suggest that HCV CD8(+) T cells are abundant in HCV-seronegative individuals but that their repertoire is highly diverse due to the involvement of both naive precursors and cross-reactive memory cells of different specificities, which can influence the response to vaccines. The data may emphasize the need to personalize immune-based therapies based on the individual's T cell repertoire that is present before the immune intervention.
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22
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Reguzova AY, Karpenko LI, Mechetina LV, Belyakov IM. Peptide-MHC multimer-based monitoring of CD8 T-cells in HIV-1 infection and AIDS vaccine development. Expert Rev Vaccines 2014; 14:69-84. [PMID: 25373312 DOI: 10.1586/14760584.2015.962520] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The use of MHC multimers allows precise and direct detecting and analyzing of antigen-specific T-cell populations and provides new opportunities to characterize T-cell responses in humans and animals. MHC-multimers enable us to enumerate specific T-cells targeting to viral, tumor and vaccine antigens with exceptional sensitivity and specificity. In the field of HIV/SIV immunology, this technique provides valuable information about the frequencies of HIV- and SIV-specific CD8(+) cytotoxic T lymphocytes (CTLs) in different tissues and sites of infection, AIDS progression, and pathogenesis. Peptide-MHC multimer technology remains a very sensitive tool in detecting virus-specific T -cells for evaluation of the immunogenicity of vaccines against HIV-1 in preclinical trials. Moreover, it helps to understand how immune responses are formed following vaccination in the dynamics from priming point until T-cell memory is matured. Here we review a diversity of peptide-MHC class I multimer applications for fundamental immunological studies in different aspects of HIV/SIV infection and vaccine development.
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Affiliation(s)
- Alena Y Reguzova
- State Research Center of Virology and Biotechnology "Vector", Koltsovo, Novosibirsk region, 630559, Russia
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23
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Kelly C, Swadling L, Brown A, Capone S, Folgori A, Salio M, Klenerman P, Barnes E. Cross-reactivity of hepatitis C virus specific vaccine-induced T cells at immunodominant epitopes. Eur J Immunol 2014; 45:309-16. [PMID: 25263407 PMCID: PMC4784727 DOI: 10.1002/eji.201444686] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 08/02/2014] [Accepted: 09/24/2014] [Indexed: 12/24/2022]
Abstract
Viral diversity is a challenge to the development of a hepatitis C virus (HCV) vaccine. Following vaccination of humans with adenoviral vectors, we determined the capacity of T cells to target common viral variants at immundominant epitopes ex vivo. We identified two major variants for epitopes NS31073 and NS31446, and multiple variants for epitope NS31406 that occurred in >5% of genotype 1 and 3 sequences at a population level. Cross‐reactivity of vaccine‐induced T cells was determined using variant peptides in IFN‐γ ELISPOT assays. Vaccine‐induced T cells targeted approximately 90% of NS31073 genotype 1 sequences and 50% of NS31446 genotype 1 and 3 sequences. For NS31406, 62% of subtype‐1b sequences were targeted. Next, we assessed whether an in vitro priming system, using dendritic cells and T cells from healthy donors, could identify a variant of NS31406 that was maximally cross‐reactive. In vitro priming assays showed that of those tested the NS31406 vaccine variant was the most immunogenic. T cells primed with genotype 1 variants from subtype 1a or 1b were broadly cross‐reactive with other variants from the same subtype. We conclude that immunization with candidate HCV adenoviral vaccines generates cross‐reactive T cells at immunodominant epitopes. The degree of cross‐reactivity varies between epitopes and may be HCV‐subtype specific.
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Affiliation(s)
- Christabel Kelly
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Martin B, Hennecke N, Lohmann V, Kayser A, Neumann-Haefelin C, Kukolj G, Böcher WO, Thimme R. Restoration of HCV-specific CD8+ T cell function by interferon-free therapy. J Hepatol 2014; 61:538-43. [PMID: 24905492 DOI: 10.1016/j.jhep.2014.05.043] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 05/26/2014] [Accepted: 05/26/2014] [Indexed: 12/22/2022]
Abstract
BACKGROUND & AIMS Chronic hepatitis C virus (HCV) infection is characterised by a failure of virus-specific CD8+ T cells that is mainly caused by viral escape and T cell exhaustion. Constant antigen stimulation has been suggested to contribute to HCV-specific CD8+ T cell exhaustion. However, IFN-based therapies failed to recover HCV-specific CD8+ T cell function suggesting that the damage to CD8+ T cells may be permanent even after antigen removal. It was therefore the objective of this study to analyse the impact of inhibition of ongoing viral replication by IFN-free therapy with direct acting antivirals (DAA) on the phenotype and function of HCV-specific CD8+ T cells. METHODS Virus-specific CD8+ T cells obtained from a patient cohort of 51 previously untreated chronically infected patients undergoing IFN-free therapy with a combination of faldaprevir (a protease inhibitor) and deleobuvir (a non-nucleoside polymerase inhibitor) with or without ribavirin were analysed ex vivo and after in vitro expansion at baseline, wk4, wk 12, and after treatment. RESULTS Our results show the rapid restoration of proliferative HCV-specific CD8+ T cells in the majority of patients with SVR12 within 4 weeks of therapy suggesting that IFN-free therapy mediated antigen removal may restore CD8+ T cell function. CONCLUSIONS This study indicates a specific restoration of proliferative HCV-specific CD8+ T cells under IFN-free therapy. This is in contrast to PegIFN-based therapies that have been shown not to restore T cell function during and after chronic infection.
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Affiliation(s)
- Bianca Martin
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany
| | - Nadine Hennecke
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany
| | - Volker Lohmann
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Antonin Kayser
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany
| | | | | | | | - Robert Thimme
- Department of Medicine II, University Hospital Freiburg, Freiburg, Germany.
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Impact of sequence variation in a dominant HLA-A*02-restricted epitope in hepatitis C virus on priming and cross-reactivity of CD8+ T cells. J Virol 2014; 88:11080-90. [PMID: 25008925 DOI: 10.1128/jvi.01590-14] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
UNLABELLED CD8+ T cells are an essential component of successful adaptive immune responses against hepatitis C virus (HCV). A major obstacle to vaccine design against HCV is its inherent viral sequence diversity. Here, we test the hypothesis that different sequence variants of an immunodominant CD8+ T cell epitope, all binding with high affinity to HLA class I, target different T cell receptor repertoires and thereby influence the quality of the CD8+ T cell response. The impacts of sequence differences in the HLA-A*02-restricted HCV NS31406-1415 epitope on in vitro priming of naive CD8+ T cells from seronegative donors and cross-reactivity of primed T cells with other epitope variants were characterized. Although the six epitope variants tested were all high-affinity binders to HLA-A*02:01, substantial differences in priming and cross-reactivity of CD8+ T cells were observed. The variant associated with the most reproducible priming and induction of T cells with broad cross-reactivity was a genotype 1b variant (KLSALGLNAV) that is more common in HCV isolates collected in Asia but is rare in sequences from Europe and North America. The superior immunogenicity and cross-reactivity of this relatively rare epitope variant were confirmed by using HCV-specific memory CD8+ T cells from people who inject drugs, who are frequently exposed to HCV. Collectively, the data suggest that sequence differences at the epitope level between HCV isolates substantially impact CD8+ T cell priming and the degree of cross-reactivity with other epitope variants. IMPORTANCE The results have important implications for vaccine design against highly variable pathogens and suggest that evidence-based selection of the vaccine antigen sequence may improve immunogenicity and T cell cross-reactivity. Cross-reactive CD8+ T cells are likely beneficial for immune control of transmitted viruses carrying epitope variants and for prevention of immune escape during acute infection. To this end, rare epitope variants and potentially even altered epitope sequences associated with priming of broadly cross-reactive T cell receptors should be considered for vaccine design and need further testing.
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Kang W, Sung PS, Park SH, Yoon S, Chang DY, Kim S, Han KH, Kim JK, Rehermann B, Chwae YJ, Shin EC. Hepatitis C virus attenuates interferon-induced major histocompatibility complex class I expression and decreases CD8+ T cell effector functions. Gastroenterology 2014; 146:1351-60.e1-4. [PMID: 24486950 PMCID: PMC4478444 DOI: 10.1053/j.gastro.2014.01.054] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 01/13/2014] [Accepted: 01/25/2014] [Indexed: 01/09/2023]
Abstract
BACKGROUND & AIMS Major histocompatibility complex (MHC) class I-restricted CD8(+) T cells are required for clearance of hepatitis C virus (HCV) infection. MHC class I expression is up-regulated by type I and II interferons (IFNs). However, little is known about the effects of HCV infection on IFN-induced expression of MHC class I. METHODS We used the HCV cell culture system (HCVcc) with the genotype 2a Japanese fulminant hepatitis-1 strain to investigate IFN-induced expression of MHC class I and its regulatory mechanisms. HCVcc-infected Huh-7.5 cells were analyzed by flow cytometry, metabolic labeling, immunoprecipitation, and immunoblotting analyses. Protein kinase R (PKR) was knocked down with lentiviruses that express small hairpin RNAs. The functional effects of MHC class I regulation by HCV were demonstrated in co-culture studies, using HCV-specific CD8(+) T cells. RESULTS Although the baseline level of MHC class I was not affected by HCV infection, IFN-induced expression of MHC class I was notably attenuated in HCV-infected cells. This was associated with replicating HCV RNA, not with viral protein. HCV infection reduced IFN-induced synthesis of MHC class I protein and induced phosphorylation of PKR and eIF2α. IFN-induced MHC class I expression was restored by small hairpin RNA-mediated knockdown of PKR in HCV-infected cells. Co-culture of HCV-specific CD8(+) T cells and HCV-infected cells that expressed HLA-A2 demonstrated that HCV infection reduced the effector functions of HCV-specific CD8(+) T cells; these functions were restored by small hairpin RNA-mediated knockdown of PKR. CONCLUSIONS IFN-induced expression of MHC class I is attenuated in HCV-infected cells by activation of PKR, which reduces the effector functions of HCV-specific CD8(+) T cells. This appears to be an important mechanism by which HCV circumvents antiviral adaptive immune responses.
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Affiliation(s)
- Wonseok Kang
- Laboratory of Immunology and Infectious Diseases, Graduate School of Medical Science and Engineering, KAIST, Daejeon, Korea,Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Pil Soo Sung
- Laboratory of Immunology and Infectious Diseases, Graduate School of Medical Science and Engineering, KAIST, Daejeon, Korea
| | - Su-Hyung Park
- 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, USA
| | - Sarah Yoon
- Department of Microbiology, Ajou University School of Medicine, Suwon, Korea
| | - Dong-Yeop Chang
- Laboratory of Immunology and Infectious Diseases, Graduate School of Medical Science and Engineering, KAIST, Daejeon, Korea
| | - Seungtaek Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Kwang Hyub Han
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Ja Kyung Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - 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, USA
| | - Yong-Joon Chwae
- Department of Microbiology, Ajou University School of Medicine, Suwon, Korea
| | - Eui-Cheol Shin
- Laboratory of Immunology and Infectious Diseases, Graduate School of Medical Science and Engineering, KAIST, Daejeon, Korea.
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Galal IF, Zakaria Z, Allam WR, Mahmoud MA, Ezzat AR, Osman A, Waked I, Strickland GT, Abdelwahab SF. Cross reactive cellular immune response to HCV genotype 1 and 4 antigens among genotype 4 exposed subjects. PLoS One 2014; 9:e101264. [PMID: 24979366 PMCID: PMC4076338 DOI: 10.1371/journal.pone.0101264] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 06/04/2014] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Hepatitis C Virus (HCV) infection is a global health burden particularly in Egypt, where HCV genotype 4a (GT-4a) predominates. The prevention and control of HCV infection will remain a challenge until the development of an effective vaccine that protects against different genotypes. Several HCV GT-1-based vaccines are in different stages of clinical trials, but antigenic differences could make protection against other genotypes problematic. In this regard, data comparing the cell-mediated immune (CMI) response to different HCV genotypes are limited. We aimed to ex vivo investigate whether GT-1-based vaccine may protect against HCV GT-4 infections. This was carried out on samples collected from genotype 4 infected/exposed subjects. METHODS/PRINCIPAL FINDINGS The CMI responses of 35 subjects; infected with HCV GT-4/or who had spontaneously-resolved the infection and 10 healthy control subjects; to two sets of seven HCV overlapping 15-mer peptide pools derived from both genotypes; and covering most of the viral proteins; were evaluated. This was carried out using an interferon gamma (IFNγ) enzyme-linked immunospot (ELISpot) assay. Peripheral blood mononuclear cells (PBMC) from 17 subjects (48%) responded to at least one peptide pool derived from GT-1b/GT-4a with 13 subjects responding to peptide pools from both genotypes. A strong correlation was found in the responses to both genotypes (r = 0.82, p<0.001; 95% confidence interval = 0.562-0.933). The average IFNγ total spot forming cells (SFC)/10(6) PBMC (±SE) from the responding subjects for GT-1b and GT-4a was 216±56 and 199±55, respectively (p = 0.833). Also, there were no significant differences between those who cleared their HCV infection or who remained HCV-RNA positive (p = 0.8). CONCLUSION/SIGNIFICANCE Our data suggest that an effective GT-1b vaccine could protect from GT-4a infection. These data could help in HCV rationale vaccine design and efficacy studies and further our understanding of HCV cross protection against different genotypes.
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Affiliation(s)
- Iman F. Galal
- Egyptian Company for Blood Transfusion Services (Egyblood)/VACSERA; Agouza, Giza, Egypt
| | - Zainab Zakaria
- Egyptian Company for Blood Transfusion Services (Egyblood)/VACSERA; Agouza, Giza, Egypt
| | - Walaa R. Allam
- Egyptian Company for Blood Transfusion Services (Egyblood)/VACSERA; Agouza, Giza, Egypt
| | - Mohamed A. Mahmoud
- Department of Hepatology, National Liver Institute, Menoufiya University, Menoufiya, Egypt
| | - Ahmed R. Ezzat
- Department of Zoology, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Ahmed Osman
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo
| | - Imam Waked
- Department of Hepatology, National Liver Institute, Menoufiya University, Menoufiya, Egypt
| | - G. Thomas Strickland
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Sayed F. Abdelwahab
- Egyptian Company for Blood Transfusion Services (Egyblood)/VACSERA; Agouza, Giza, Egypt
- Department of Microbiology and Immunology, Faculty of Medicine, Minia University, Minia, Egypt
- * E-mail:
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28
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Larrubia JR, Lokhande MU, Moreno-Cubero E, García-Garzón S, Miquel J, Parra-Cid T, González-Praetorious A, Perna C, Lázaro A, Sanz-de-Villalobos E. HCV-specific CD8+ cell detection at week 12 of chronic hepatitis C treatment with PEG-interferon-α2b/ribavirin correlates with infection resolution. Cell Immunol 2013; 286:31-8. [PMID: 24287274 DOI: 10.1016/j.cellimm.2013.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 10/08/2013] [Accepted: 11/04/2013] [Indexed: 12/14/2022]
Abstract
Lower than 2-log viral-load (VL) decrease at week 12 (w12) of chronic hepatitis C (CHC) treatment with Peg-interferon/ribavirin has 100% negative predictive value (PV) of sustained virologic response (SVR), and this could be related with absence of HCV-specific cytotoxic T lymphocyte (CTL) response. In this study, percentage of cases with SVR, according to peripheral HCV-specific cytotoxic response at w12, was analysed (Group-1: detection(+), Group-2: detection(-)). SVR was higher in group-1 (93%) than in group-2 (47%) (p=0.003). An increase on HCV-specific CTL frequency between baseline and w12 and higher specific reactivity were observed in group-1 (p=0.011 and p=0.025). HCV-specific CTL detection at w12 correlated with level of VL decrease (p=0.016, r=0.389), and among HCV genotype-1 patients with either early or delayed virologic response (EDVR), 100% positive PV of SVR was observed. In summary, HCV-specific CTL detection at w12 of Peg-interferon/ribavirin treatment correlates with SVR and in EDVR genotype-1 cases predicts SVR.
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MESH Headings
- Adult
- Antiviral Agents/therapeutic use
- Biomarkers/analysis
- Drug Therapy, Combination
- Female
- Hepacivirus/drug effects
- Hepacivirus/immunology
- Hepatitis C, Chronic/diagnosis
- Hepatitis C, Chronic/drug therapy
- Hepatitis C, Chronic/immunology
- Hepatitis C, Chronic/virology
- Humans
- Interferon-alpha/therapeutic use
- Lymphocyte Count
- Male
- Middle Aged
- Polyethylene Glycols/therapeutic use
- RNA, Viral/antagonists & inhibitors
- RNA, Viral/immunology
- Recombinant Proteins/therapeutic use
- Ribavirin/therapeutic use
- T-Lymphocytes, Cytotoxic/drug effects
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/virology
- Treatment Outcome
- Viral Load/drug effects
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Affiliation(s)
- Juan-Ramón Larrubia
- Translational Hepatology Unit, Guadalajara University Hospital, University of Alcalá, Donante de Sangre St., 19002 Guadalajara, Spain.
| | - Megha-Uttam Lokhande
- Translational Hepatology Unit, Guadalajara University Hospital, University of Alcalá, Donante de Sangre St., 19002 Guadalajara, Spain.
| | - Elia Moreno-Cubero
- Translational Hepatology Unit, Guadalajara University Hospital, University of Alcalá, Donante de Sangre St., 19002 Guadalajara, Spain.
| | - Silvia García-Garzón
- Translational Hepatology Unit, Guadalajara University Hospital, University of Alcalá, Donante de Sangre St., 19002 Guadalajara, Spain.
| | - Joaquín Miquel
- Translational Hepatology Unit, Guadalajara University Hospital, University of Alcalá, Donante de Sangre St., 19002 Guadalajara, Spain.
| | - Trinidad Parra-Cid
- Translational Hepatology Unit, Guadalajara University Hospital, University of Alcalá, Donante de Sangre St., 19002 Guadalajara, Spain.
| | - Alejandro González-Praetorious
- Translational Hepatology Unit, Guadalajara University Hospital, University of Alcalá, Donante de Sangre St., 19002 Guadalajara, Spain.
| | - Cristian Perna
- Translational Hepatology Unit, Guadalajara University Hospital, University of Alcalá, Donante de Sangre St., 19002 Guadalajara, Spain.
| | - Alicia Lázaro
- Translational Hepatology Unit, Guadalajara University Hospital, University of Alcalá, Donante de Sangre St., 19002 Guadalajara, Spain.
| | - Eduardo Sanz-de-Villalobos
- Translational Hepatology Unit, Guadalajara University Hospital, University of Alcalá, Donante de Sangre St., 19002 Guadalajara, Spain.
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Prabdial-Sing N, Puren AJ, Bowyer SM. Sequence-based in silico analysis of well studied hepatitis C virus epitopes and their variants in other genotypes (particularly genotype 5a) against South African human leukocyte antigen backgrounds. BMC Immunol 2012; 13:67. [PMID: 23227878 PMCID: PMC3552980 DOI: 10.1186/1471-2172-13-67] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 11/30/2012] [Indexed: 02/07/2023] Open
Abstract
Background Host genetics influence the outcome of HCV disease. HCV is also highly mutable and escapes host immunity. HCV genotypes are geographically distributed and HCV subtypes have been shown to have distinct repertoires of HLA-restricted viral epitopes which explains the lack of cross protection across genotypes observed in some studies. Despite this, immune databases and putative epitope vaccines concentrate almost exclusively on HCV genotype 1 class I-epitopes restricted by the HLA-A*02 allele. While both genotype and allele predominate in developed countries, we hypothesise that HCV variation and population genetics will affect the efficacy of proposed epitope vaccines in South Africa. This in silico study investigates HCV viral variability within well-studied epitopes identified in genotype 1 and uses algorithms to predict the immunogenicity of their variants from other less studied genotypes and thus rate the most promising vaccine candidates for the South African population. Six class I- and seven class II- restricted epitope sequences within the core, NS3, NS4B and NS5B regions were compared across the six HCV genotypes using local genotype 5a sequence data together with global data. Common HLA alleles in the South African population are A30:01, A02:01, B58:02, B07:02; DRB1*13:01 and DRB1*03:01. Epitope binding to 13 class I- and 8 class –II alleles were described using web-based prediction servers, Immune Epitope Database, (IEDB) and Propred. Online population coverage tools were used to assess vaccine efficacy. Results Despite the homogeneity of genotype 1 and genotype 5 over the epitopes, there was limited promiscuity to local HLA-alleles.Host differences will make a putative vaccine less effective in South Africa. Of the 6 well-characterized class I- epitopes, only 2 class I- epitopes were promiscuous and 3 of the 7 class-II epitopes were better conserved and promiscuous. By fine tuning the putative vaccine using an optimal cocktail of genotype 1 and 5a epitopes and local HLA data, the coverage was raised from 65.85% to 91.87% in South African Blacks. Conclusion While in vivo and in vitro studies are needed to confirm immunogenic epitopes, in silico HCV epitope vaccine design which takes into account HCV variation and host allele frequency will maximize population coverage in different ethnic groups.
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Affiliation(s)
- Nishi Prabdial-Sing
- Specialized Molecular Diagnostics, Hepatitis Unit, National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa.
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30
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Ahlén G, Chen A, Roe B, Falkeborn T, Frelin L, Hall WW, Sällberg M, Söderholm J. Limited effect on NS3-NS4A protein cleavage after alanine substitutions within the immunodominant HLA-A2-restricted epitope of the hepatitis C virus genotype 3a non-structural 3/4A protease. J Gen Virol 2012; 93:1680-1686. [PMID: 22592266 DOI: 10.1099/vir.0.043745-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It has been well established that immunological escape mutations within the hepatitis C virus genotype (gt) 1a non-structural (NS) 3/4A protease are partly prevented by a reduction in viral protease fitness. Surprisingly little is known about whether similar mutations affect proteases from other genotypes. In the present study, we assessed both the HLA-A2-restricted CTL response and gt3a NS3/4A protease fitness. Similar to gt1, the 1073-1081 epitope was immunodominant within the gt3a-specific HLA-A2-restricted CTL response, despite sequence similarity of only 56 % between the gt1a and gt3a genes. However, unlike the gt1a NS3/4A protease, all residues within the gt3a 1073-1081 epitope could be replaced sequentially by alanine while retaining protease activity, at least in part.
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Affiliation(s)
- Gustaf Ahlén
- Department of Laboratory Medicine, Division of Clinical Microbiology, F68, Karolinska Institutet at Karolinska University Hospital Huddinge, S-141 86 Stockholm, Sweden
| | - Antony Chen
- Department of Laboratory Medicine, Division of Clinical Microbiology, F68, Karolinska Institutet at Karolinska University Hospital Huddinge, S-141 86 Stockholm, Sweden
| | - Barbara Roe
- Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Tina Falkeborn
- Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, S-581 83 Linköping, Sweden
| | - Lars Frelin
- Department of Laboratory Medicine, Division of Clinical Microbiology, F68, Karolinska Institutet at Karolinska University Hospital Huddinge, S-141 86 Stockholm, Sweden
| | - William W Hall
- Centre for Research in Infectious Diseases, School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Matti Sällberg
- Department of Laboratory Medicine, Division of Clinical Microbiology, F68, Karolinska Institutet at Karolinska University Hospital Huddinge, S-141 86 Stockholm, Sweden
| | - Jonas Söderholm
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, S-413 46 Gothenburg, Sweden
- Department of Laboratory Medicine, Division of Clinical Microbiology, F68, Karolinska Institutet at Karolinska University Hospital Huddinge, S-141 86 Stockholm, Sweden
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Roohvand F, Kossari N. Advances in hepatitis C virus vaccines, part two: advances in hepatitis C virus vaccine formulations and modalities. Expert Opin Ther Pat 2012; 22:391-415. [PMID: 22455502 DOI: 10.1517/13543776.2012.673589] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Developing a vaccine against HCV is an important medical and global priority. Unavailability and potential dangers associated with using attenuated HCV viral particles for vaccine preparation have resulted in the use of HCV genes and proteins formulated in novel vaccine modalities. AREAS COVERED In part one of this review, advances in basic knowledge for HCV vaccine design were provided. Herein, a detailed and correlated patents (searched by Espacenet) and literatures (searched by Pubmed) review on HCV vaccine formulations and modalities is provided, including: subunit, DNA, epitopic-peptide/polytopic, live vector- and whole yeast-based vaccines. Less-touched areas in vaccine studies such as mucosal, plant-based, and chimeric HBV/HCV vaccines are also discussed. Furthermore, results of preclinical/clinical studies on selected HCV vaccines as well as pros and cons of different strategies are reviewed. Finally, potential strategies for creation and/or improvement of HCV vaccine formulations are discussed. EXPERT OPINION Promising outcomes of a few HCV vaccine modalities in phase I/II clinical trials predict the accessibility of at least partially effective vaccines to inhibit or treat the chronic state of HCV infection (specially in combination with standard antiviral therapy). ChronVac-C (plasmid DNA), TG4040 (MVA-based), and GI-5005 (whole yeast-based) might be the most obvious HCV vaccine candidates to be approved in the near future.
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Affiliation(s)
- Farzin Roohvand
- Hepatitis & AIDS Department, Pasteur Institute of Iran, Tehran, Iran.
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32
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Gupte GM, Arankalle VA. Evaluation of the immunogenicity of liposome encapsulated HVR1 and NS3 regions of genotype 3 HCV, either singly or in combination. Virol J 2012; 9:74. [PMID: 22452828 PMCID: PMC3349533 DOI: 10.1186/1743-422x-9-74] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 03/27/2012] [Indexed: 01/15/2023] Open
Abstract
Background Hepatitis C virus displays a high rate of mutation and exists as a quasispecies in infected patients. In the absence of an effective universal vaccine, genotype-specific vaccine development represents an alternative. We have attempted to develop a genotype 3 based, liposome encapsulated HCV vaccine with hypervariable region-1 (HVR1) and non-structural region-3 (NS3) components. Results HCV RNA extracted from serum samples of 49 chronically infected patients was PCR amplified to obtain HVR1 region. These amplified products were cloned to obtain 20 clones per sample in order to identify the quasispecies pattern. The HVR1 consensus sequence, along with three variants was reverse transcribed to obtain peptides. The peptides were checked for immunoreactivity individually, as a pool or as a single peptide tetramer interspersed with four glycine residues. Anti-HCV positivity varied from 42.6% (tetramer) to 92.2% (variant-4) when 115 anti-HCV positive sera representing genotypes 1, 3, 4 and 6 were screened. All the 95 anti-HCV negatives were scored negative by all antigens. Mice were immunized with different liposome encapsulated or Al(OH)3 adjuvanted formulations of HVR1 variants and recombinant NS3 protein, and monitored for anti-HVR1 and anti-NS3 antibody titres, IgG isotypes and antigen specific cytokine levels. A balanced Th1/Th2 isotyping response with high antibody titres was observed in most of the liposome encapsulated antigen groups. The effect of liposomes and aluminium hydroxide on the expression of immune response genes was studied using Taqman Low Density Array. Both Th1 (IFN-gamma, Il18) and Th2 (Il4) genes were up regulated in the liposome encapsulated HVR1 variant pool-NS3 combination group. In-vitro binding of the virus to anti-HVR1 antibodies was demonstrated. Conclusion The optimum immunogen was identified to be combination of peptides of HVR1 consensus sequence and its variants along with pNS3 encapsulated in liposomes, which could generate both cellular and humoral immune responses in mice deserving further evaluation in a suitable cell culture system/non-human primate model.
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Affiliation(s)
- Gouri M Gupte
- Hepatitis Division, National Institute of Virology, Microbial Containment Complex, Sus Road, Pashan, Pune, India 411021
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33
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Pasetto A, Frelin L, Brass A, Yasmeen A, Koh S, Lohmann V, Bartenschlager R, Magalhaes I, Maeurer M, Sällberg M, Chen M. Generation of T-cell receptors targeting a genetically stable and immunodominant cytotoxic T-lymphocyte epitope within hepatitis C virus non-structural protein 3. J Gen Virol 2011; 93:247-258. [PMID: 22071510 PMCID: PMC3352347 DOI: 10.1099/vir.0.037903-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Hepatitis C virus (HCV) is a major cause of severe liver disease, and one major contributing factor is thought to involve a dysfunction of virus-specific T-cells. T-cell receptor (TCR) gene therapy with HCV-specific TCRs would increase the number of effector T-cells to promote virus clearance. We therefore took advantage of HLA-A2 transgenic mice to generate multiple TCR candidates against HCV using DNA vaccination followed by generation of stable T-cell–BW (T-BW) tumour hybrid cells. Using this approach, large numbers of non-structural protein 3 (NS3)-specific functional T-BW hybrids can be generated efficiently. These predominantly target the genetically stable HCV genotype 1 NS31073–1081 CTL epitope, frequently associated with clearance of HCV in humans. These T-BW hybrid clones recognized the NS31073 peptide with a high avidity. The hybridoma effectively recognized virus variants and targeted cells with low HLA-A2 expression, which has not been reported previously. Importantly, high-avidity murine TCRs effectively redirected human non-HCV-specific T-lymphocytes to recognize human hepatoma cells with HCV RNA replication driven by a subgenomic HCV replicon. Taken together, TCR candidates with a range of functional avidities, which can be used to study immune recognition of HCV-positive targets, have been generated. This has implications for TCR-related immunotherapy against HCV.
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Affiliation(s)
- Anna Pasetto
- Department of Laboratory Medicine, Stockholm, Sweden.,Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lars Frelin
- Department of Laboratory Medicine, Stockholm, Sweden
| | - Anette Brass
- Department of Laboratory Medicine, Stockholm, Sweden
| | - Anila Yasmeen
- Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sarene Koh
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore.,Department of Laboratory Medicine, Stockholm, Sweden
| | - Volker Lohmann
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Germany
| | - Isabelle Magalhaes
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet and Swedish Institute for Infectious Disease Control, Stockholm, Sweden
| | - Markus Maeurer
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet and Swedish Institute for Infectious Disease Control, Stockholm, Sweden
| | | | - Margaret Chen
- Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
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Antunes DA, Rigo MM, Silva JP, Cibulski SP, Sinigaglia M, Chies JA, Vieira GF. Structural in silico analysis of cross-genotype-reactivity among naturally occurring HCV NS3-1073-variants in the context of HLA-A*02:01 allele. Mol Immunol 2011; 48:1461-7. [DOI: 10.1016/j.molimm.2011.03.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 02/15/2011] [Accepted: 03/28/2011] [Indexed: 12/17/2022]
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Bengsch B, Seigel B, Ruhl M, Timm J, Kuntz M, Blum HE, Pircher H, Thimme R. Coexpression of PD-1, 2B4, CD160 and KLRG1 on exhausted HCV-specific CD8+ T cells is linked to antigen recognition and T cell differentiation. PLoS Pathog 2010; 6:e1000947. [PMID: 20548953 PMCID: PMC2883597 DOI: 10.1371/journal.ppat.1000947] [Citation(s) in RCA: 303] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Accepted: 05/10/2010] [Indexed: 02/07/2023] Open
Abstract
Exhausted CD8+ T cell responses during chronic viral infections are defined by a complex expression pattern of inhibitory receptors. However, very little information is currently available about the coexpression patterns of these receptors on human virus-specific CD8+ T cells and their correlation with antiviral functions, T cell differentiation and antigen recognition. We addressed these important aspects in a cohort of 38 chronically HCV infected patients and found a coexpression of inhibitory receptors such as 2B4, CD160 and KLRG1 in association with PD-1 in about half of the HCV-specific CD8+ T cell responses. Importantly, this exhaustive phenotype was associated with low and intermediate levels of CD127 expression, an impaired proliferative capacity, an intermediate T cell differentiation stage and absence of sequence variations within the corresponding epitopes, indicating ongoing antigen triggering. In contrast, a low expression of inhibitory receptors by the remaining HCV-specific CD8+ T cells occurred in concert with a CD127hi phenotype, an early T cell differentiation stage and presence of viral sequence variations within the corresponding epitopes. In sum, these results suggest that T cell exhaustion contributes to the failure of about half of HCV-specific CD8+ T cell responses and that it is determined by a complex interplay of immunological (e.g. T cell differentiation) and virological (e.g. ongoing antigen triggering) factors. About 170 million people are infected with hepatitis C virus (HCV), which may cause severe liver disease and liver cancer. Upon acute infection, only about 30% of patients are able to eliminate the virus spontaneously while about 70% of patients develop chronic infection. It is known that a successful immune response against HCV depends on virus-specific CD8+ T cells. However, during chronic infection, these cells are impaired in their antiviral function. In this study, we found that the exhaustion is characterized by the expression of multiple inhibitory receptors, such as PD-1, 2B4, CD160 and KLRG1. Of note, the coexpression of these receptors depends on the ongoing recognition of the viral antigen and the maturation stage of the T cell. The remaining virus-specific T cell responses that are not exhausted do not recognize the virus present in the patients any more due to viral mutations, indicating viral escape. Thus, they fail to exert antiviral activity, although they share characteristics of fully functional memory T cells. In sum, we have found that T cell exhaustion contributes to the failure of about half of HCV-specific CD8+ T cell responses and that it is determined by a complex interplay of immunological and virological factors. These findings will be important to consider in the design of new antiviral vaccination strategies.
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Affiliation(s)
- Bertram Bengsch
- Department of Medicine II, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Bianca Seigel
- Department of Medicine II, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Marianne Ruhl
- Department of Virology, University of Essen, Essen, Germany
| | - Jörg Timm
- Department of Virology, University of Essen, Essen, Germany
| | - Martin Kuntz
- Department of Medicine II, University of Freiburg, Freiburg, Germany
| | - Hubert E. Blum
- Department of Medicine II, University of Freiburg, Freiburg, Germany
| | | | - Robert Thimme
- Department of Medicine II, University of Freiburg, Freiburg, Germany
- * E-mail:
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Beauvillain C, Meloni F, Sirard JC, Blanchard S, Jarry U, Scotet M, Magistrelli G, Delneste Y, Barnaba V, Jeannin P. The scavenger receptors SRA-1 and SREC-I cooperate with TLR2 in the recognition of the hepatitis C virus non-structural protein 3 by dendritic cells. J Hepatol 2010; 52:644-51. [PMID: 20338659 DOI: 10.1016/j.jhep.2009.11.031] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Revised: 11/24/2009] [Accepted: 11/25/2009] [Indexed: 12/23/2022]
Abstract
BACKGROUNDS & AIMS The hepatitis C virus NS3 protein is taken up by myeloid cells in a TLR2-independent manner and activates myeloid cells via TLR2. This study aimed to identify the endocytic receptor(s) involved in the uptake of NS3 by myeloid cells and its relation with TLR2. METHODS Inhibitors and transfected cells were used to identify the nature of the NS3-binding receptors expressed by myeloid cells. The cooperation between scavenger receptors (SRs) and TLR2 in the NS3-mediated activation of myeloid cells was evaluated using inhibitors, cells from TLR2(-/-) mice, and confocal microscopy. The involvement of SRs in NS3 cross-presentation was evaluated in vitro using an NS3-specific human T-cell clone. RESULTS We observed that SRs are the main binding structures for NS3 on myeloid cells and identified the SRs SRA-1 and SREC-I as endocytic receptors for NS3. Moreover, both SRs and TLR2 cooperate in NS3-induced myeloid cell activation. CONCLUSION This study highlights a central role for SRs in NS3 uptake and cross-presentation, and demonstrates a tightly orchestrated cooperation between signalling and endocytic innate receptors in NS3 recognition.
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Affiliation(s)
- Céline Beauvillain
- Institut National de la Santé et de la Recherche Médicale, Unité 892, Centre de Recherche en Cancérologie Nantes-Angers, Bâtiment Montéclair, 4 rue Larrey, Angers 49933, France
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Characterization of NS3 protease from an Egyptian HCV genotype 4a isolate. Arch Virol 2009; 154:1649-57. [PMID: 19763775 DOI: 10.1007/s00705-009-0500-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Accepted: 08/17/2009] [Indexed: 10/20/2022]
Abstract
The role of the NS3 protease in HCV replication was demonstrated by the ability of a protease inhibitor cocktail (10 microg/ml) to abolish the induced cytopathic effect in RAW macrophages upon infection with Egyptian sera. The HCV protease gene was amplified from Egyptian sera by nested PCR and cloned downstream of the CMV promotor in a mammalian expression plasmid, which was then used to transform bacteria. Colonies carrying the gene in the correct orientation were subjected to large-scale plasmid purification followed by sequencing. Phylogenetic comparison of the sequence obtained with published sequences from different genotypes confirmed that our sequence belongs to genotype 4a. Of the other genotypes, the most closely related ones were from genotype 1. Multiple alignments of protease peptides showed that the catalytic triads and binding residues for substrate, Zn2+ and the NS4 cofactor are conserved among different isolates, including ours, and confirmed the closer homology between NS3 of genotypes 4 and 1. The HCV-protease-encoding construct was successfully transcribed in both mammalian cells and mice. Mouse antibodies produced against the protease-encoding-construct detected the 18-kDa enzyme in lysates of cells transfected with the construct by Western blotting, and in the media of infected cells by ELISA.
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Klade C, Kubitschke A, Stauber R, Meyer M, Zinke S, Wiegand J, Zauner W, Aslan N, Lehmann M, Cornberg M, Manns M, Reisner P, Wedemeyer H. Hepatitis C virus-specific T cell responses against conserved regions in recovered patients. Vaccine 2009; 27:3099-108. [DOI: 10.1016/j.vaccine.2009.02.088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Revised: 02/16/2009] [Accepted: 02/24/2009] [Indexed: 01/06/2023]
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