1
|
Lopes-Ribeiro Á, Araujo FP, Oliveira PDM, Teixeira LDA, Ferreira GM, Lourenço AA, Dias LCC, Teixeira CW, Retes HM, Lopes ÉN, Versiani AF, Barbosa-Stancioli EF, da Fonseca FG, Martins-Filho OA, Tsuji M, Peruhype-Magalhães V, Coelho-dos-Reis JGA. In silico and in vitro arboviral MHC class I-restricted-epitope signatures reveal immunodominance and poor overlapping patterns. Front Immunol 2022; 13:1035515. [PMID: 36466864 PMCID: PMC9713826 DOI: 10.3389/fimmu.2022.1035515] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/31/2022] [Indexed: 08/27/2023] Open
Abstract
INTRODUCTION The present work sought to identify MHC-I-restricted peptide signatures for arbovirus using in silico and in vitro peptide microarray tools. METHODS First, an in-silico analysis of immunogenic epitopes restricted to four of the most prevalent human MHC class-I was performed by identification of MHC affinity score. For that, more than 10,000 peptide sequences from 5 Arbovirus and 8 different viral serotypes, namely Zika (ZIKV), Dengue (DENV serotypes 1-4), Chikungunya (CHIKV), Mayaro (MAYV) and Oropouche (OROV) viruses, in addition to YFV were analyzed. Haplotype HLA-A*02.01 was the dominant human MHC for all arboviruses. Over one thousand HLA-A2 immunogenic peptides were employed to build a comprehensive identity matrix. Intending to assess HLAA*02:01 reactivity of peptides in vitro, a peptide microarray was designed and generated using a dimeric protein containing HLA-A*02:01. RESULTS The comprehensive identity matrix allowed the identification of only three overlapping peptides between two or more flavivirus sequences, suggesting poor overlapping of virus-specific immunogenic peptides amongst arborviruses. Global analysis of the fluorescence intensity for peptide-HLA-A*02:01 binding indicated a dose-dependent effect in the array. Considering all assessed arboviruses, the number of DENV-derived peptides with HLA-A*02:01 reactivity was the highest. Furthermore, a lower number of YFV-17DD overlapping peptides presented reactivity when compared to non-overlapping peptides. In addition, the assessment of HLA-A*02:01-reactive peptides across virus polyproteins highlighted non-structural proteins as "hot-spots". Data analysis supported these findings showing the presence of major hydrophobic sites in the final segment of non-structural protein 1 throughout 2a (Ns2a) and in nonstructural proteins 2b (Ns2b), 4a (Ns4a) and 4b (Ns4b). DISCUSSION To our knowledge, these results provide the most comprehensive and detailed snapshot of the immunodominant peptide signature for arbovirus with MHC-class I restriction, which may bring insight into the design of future virus-specific vaccines to arboviruses and for vaccination protocols in highly endemic areas.
Collapse
Affiliation(s)
- Ágata Lopes-Ribeiro
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Grupo Integrado de Pesquisas em Biomarcadores, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Franklin Pereira Araujo
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Grupo Integrado de Pesquisas em Biomarcadores, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Patrícia de Melo Oliveira
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Lorena de Almeida Teixeira
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Geovane Marques Ferreira
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Alice Aparecida Lourenço
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Laura Cardoso Corrêa Dias
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Caio Wilker Teixeira
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Henrique Morais Retes
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Élisson Nogueira Lopes
- Laboratorio de Genética Celular e Molecular, Instituto de Ciências Biológicas, Departamento de Genética, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Alice Freitas Versiani
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Department of Pathology da University of Texas Medical Branch, Galveston, TX, United States
| | - Edel Figueiredo Barbosa-Stancioli
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Flávio Guimarães da Fonseca
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Olindo Assis Martins-Filho
- Grupo Integrado de Pesquisas em Biomarcadores, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Moriya Tsuji
- Aaron Diamond AIDS Research Center, Irving Medical School, Columbia University, New York City, NY, United States
| | - Vanessa Peruhype-Magalhães
- Grupo Integrado de Pesquisas em Biomarcadores, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Jordana Grazziela Alves Coelho-dos-Reis
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Grupo Integrado de Pesquisas em Biomarcadores, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| |
Collapse
|
2
|
Alharbi SN, Alrefaei AF. Comparison of the SARS-CoV-2 (2019-nCoV) M protein with its counterparts of SARS-CoV and MERS-CoV species. JOURNAL OF KING SAUD UNIVERSITY. SCIENCE 2021; 33:101335. [PMID: 33432259 PMCID: PMC7787911 DOI: 10.1016/j.jksus.2020.101335] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/13/2020] [Accepted: 12/27/2020] [Indexed: 05/09/2023]
Abstract
Coronaviruses M proteins are well-represented in the major protein component of the viral envelope. During the viral assembly, they play an important role by association with all other viral structural proteins. Despite their crucial functions, very little information regarding the structures and functions of M proteins is available. Here we utilize bioinformatic tools from available sequences and 3D structures of SARS-CoV, SARS-CoV2, and MERS-CoV M proteins in order to predict potential B-cell epitopes and assessing antibody binding affinity. Such study aims to aid finding more effective vaccines and recognize neutralizing antibodies. we found some rather exciting differences between SARS-COV-2, SARS-Cov and MERS-CoV M proteins. Two SARS-CoV-2 peptides with significant antigen presentation scores for human cell surface proteins have been identified. The results reveal that N-terminal domains of M proteins of SARS-CoV and SARS-CoV2 are translocated (outside) whereas it is inside (cytoplasmic side) in MERS-CoV.
Collapse
Affiliation(s)
- Sultan Nafea Alharbi
- National Centre for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia
| | - Abdulwahed Fahad Alrefaei
- Department of Zoology, King Saud University, College of Science, P. O. Box 2455, Riyadh 11451, Saudi Arabia
| |
Collapse
|
3
|
Lima NS, Moon D, Darko S, De La Barrera RA, Lin L, Koren MA, Jarman RG, Eckels KH, Thomas SJ, Michael NL, Modjarrad K, Douek DC, Trautmann L. Pre-existing Immunity to Japanese Encephalitis Virus Alters CD4 T Cell Responses to Zika Virus Inactivated Vaccine. Front Immunol 2021; 12:640190. [PMID: 33717194 PMCID: PMC7943459 DOI: 10.3389/fimmu.2021.640190] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 01/28/2021] [Indexed: 12/16/2022] Open
Abstract
The epidemic spread of Zika virus (ZIKV), associated with devastating neurologic syndromes, has driven the development of multiple ZIKV vaccines candidates. An effective vaccine should induce ZIKV-specific T cell responses, which are shown to improve the establishment of humoral immunity and contribute to viral clearance. Here we investigated how previous immunization against Japanese encephalitis virus (JEV) and yellow fever virus (YFV) influences T cell responses elicited by a Zika purified-inactivated virus (ZPIV) vaccine. We demonstrate that three doses of ZPIV vaccine elicited robust CD4 T cell responses to ZIKV structural proteins, while ZIKV-specific CD4 T cells in pre-immunized individuals with JEV vaccine, but not YFV vaccine, were more durable and directed predominantly toward conserved epitopes, which elicited Th1 and Th2 cytokine production. In addition, T cell receptor repertoire analysis revealed preferential expansion of cross-reactive clonotypes between JEV and ZIKV, suggesting that pre-existing immunity against JEV may prime the establishment of stronger CD4 T cell responses to ZPIV vaccination. These CD4 T cell responses correlated with titers of ZIKV-neutralizing antibodies in the JEV pre-vaccinated group, but not in flavivirus-naïve or YFV pre-vaccinated individuals, suggesting a stronger contribution of CD4 T cells in the generation of neutralizing antibodies in the context of JEV-ZIKV cross-reactivity.
Collapse
Affiliation(s)
- Noemia S Lima
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States.,Cellular Immunology Section, US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Damee Moon
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Samuel Darko
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Rafael A De La Barrera
- Pilot Bioproduction Facility, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Leyi Lin
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Michael A Koren
- Viral Disease Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Richard G Jarman
- Viral Disease Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Kenneth H Eckels
- Pilot Bioproduction Facility, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Stephen J Thomas
- Division of Infectious Diseases, Department of Medicine, State University of New York Upstate, Syracuse, NY, United States
| | - Nelson L Michael
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Kayvon Modjarrad
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Lydie Trautmann
- Cellular Immunology Section, US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States.,Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, United States
| |
Collapse
|
4
|
Pollett S, Gathii K, Figueroa K, Rutvisuttinunt W, Srikanth A, Nyataya J, Mutai BK, Awinda G, Jarman RG, Berry IM, Waitumbi JN. The evolution of dengue-2 viruses in Malindi, Kenya and greater East Africa: Epidemiological and immunological implications. INFECTION GENETICS AND EVOLUTION 2020; 90:104617. [PMID: 33161179 DOI: 10.1016/j.meegid.2020.104617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 10/15/2020] [Accepted: 11/01/2020] [Indexed: 01/17/2023]
Abstract
Kenya experiences a substantial burden of dengue, yet there are very few DENV-2 sequence data available from this country and indeed the entire continent of Africa. We therefore undertook whole genome sequencing and evolutionary analysis of fourteen dengue virus (DENV)-2 strains sampled from Malindi sub-County Hospital during the 2017 DENV-2 outbreak in the Kenyan coast. We further performed an extended East African phylogenetic analysis, which leveraged 26 complete African env genes. Maximum likelihood analysis showed that the 2017 outbreak was due to the Cosmopolitan genotype, indicating that this has been the only confirmed human DENV-2 genotype circulating in Africa to date. Phylogeographic analyses indicated transmission of DENV-2 viruses between East Africa and South/South-West Asia. Time-scaled genealogies show that DENV-2 viruses shows spatial structure at the country level in Kenya, with a time-to-most-common-recent ancestor analysis indicating that these DENV-2 strains were circulating for up to 5.38 years in Kenya before detection in the 2017 Malindi outbreak. Selection pressure analyses indicated sampled Kenyan DENV strains uniquely being under positive selection at 6 sites, predominantly across the non-structural genes, and epitope prediction analyses showed that one of these sites corresponds to a putative predicted MHC-I CD8+ DENV-2 Cosmopolitan virus epitope only evident in a sampled Kenyan virus. Taken together, our findings indicate that the 2017 Malindi DENV-2 outbreak arose from a strain which had circulated for several years in Kenya before recent detection, has experienced diversifying selection pressure, and may contain new putative immunogens relevant to vaccine design. These findings prompt further genomic epidemiology studies in this and other Kenyan locations to further elucidate the transmission dynamics of DENV in this region.
Collapse
Affiliation(s)
- Simon Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Kimita Gathii
- Basic Science Laboratory, US Army Medical Research Directorate - Africa (USAMRD-A), Kisumu, Kenya
| | - Katherine Figueroa
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Wiriya Rutvisuttinunt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Abhi Srikanth
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Josphat Nyataya
- Basic Science Laboratory, US Army Medical Research Directorate - Africa (USAMRD-A), Kisumu, Kenya
| | - Beth K Mutai
- Basic Science Laboratory, US Army Medical Research Directorate - Africa (USAMRD-A), Kisumu, Kenya
| | - George Awinda
- Basic Science Laboratory, US Army Medical Research Directorate - Africa (USAMRD-A), Kisumu, Kenya
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America.
| | - J N Waitumbi
- Basic Science Laboratory, US Army Medical Research Directorate - Africa (USAMRD-A), Kisumu, Kenya
| |
Collapse
|
5
|
Stryhn A, Kongsgaard M, Rasmussen M, Harndahl MN, Østerbye T, Bassi MR, Thybo S, Gabriel M, Hansen MB, Nielsen M, Christensen JP, Randrup Thomsen A, Buus S. A Systematic, Unbiased Mapping of CD8 + and CD4 + T Cell Epitopes in Yellow Fever Vaccinees. Front Immunol 2020; 11:1836. [PMID: 32983097 PMCID: PMC7489334 DOI: 10.3389/fimmu.2020.01836] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 07/08/2020] [Indexed: 12/30/2022] Open
Abstract
Examining CD8+ and CD4+ T cell responses after primary Yellow Fever vaccination in a cohort of 210 volunteers, we have identified and tetramer-validated 92 CD8+ and 50 CD4+ T cell epitopes, many inducing strong and prevalent (i.e., immunodominant) T cell responses. Restricted by 40 and 14 HLA-class I and II allotypes, respectively, these responses have wide population coverage and might be of considerable academic, diagnostic and therapeutic interest. The broad coverage of epitopes and HLA overcame the otherwise confounding effects of HLA diversity and non-HLA background providing the first evidence of T cell immunodomination in humans. Also, double-staining of CD4+ T cells with tetramers representing the same HLA-binding core, albeit with different flanking regions, demonstrated an extensive diversification of the specificities of many CD4+ T cell responses. We suggest that this could reduce the risk of pathogen escape, and that multi-tetramer staining is required to reveal the true magnitude and diversity of CD4+ T cell responses. Our T cell epitope discovery approach uses a combination of (1) overlapping peptides representing the entire Yellow Fever virus proteome to search for peptides containing CD4+ and/or CD8+ T cell epitopes, (2) predictors of peptide-HLA binding to suggest epitopes and their restricting HLA allotypes, (3) generation of peptide-HLA tetramers to identify T cell epitopes, and (4) analysis of ex vivo T cell responses to validate the same. This approach is systematic, exhaustive, and can be done in any individual of any HLA haplotype. It is all-inclusive in the sense that it includes all protein antigens and peptide epitopes, and encompasses both CD4+ and CD8+ T cell epitopes. It is efficient and, importantly, reduces the false discovery rate. The unbiased nature of the T cell epitope discovery approach presented here should support the refinement of future peptide-HLA class I and II predictors and tetramer technologies, which eventually should cover all HLA class I and II isotypes. We believe that future investigations of emerging pathogens (e.g., SARS-CoV-2) should include population-wide T cell epitope discovery using blood samples from patients, convalescents and/or long-term survivors, who might all hold important information on T cell epitopes and responses.
Collapse
Affiliation(s)
- Anette Stryhn
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Kongsgaard
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Rasmussen
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Nors Harndahl
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Østerbye
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Maria Rosaria Bassi
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren Thybo
- Department of Infectious Diseases, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Morten Bagge Hansen
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Morten Nielsen
- Department of Health Technology, The Technical University of Denmark, Lyngby, Denmark
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Jan Pravsgaard Christensen
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Allan Randrup Thomsen
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Soren Buus
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
6
|
Sajeed R, Sarma K, Sarmah K, Biswas D, Borkakoty B. Computational screening of potential MHC class I restricted cytotoxic T lymphocytes-based common multi-epitopes of major arboviral diseases. Future Virol 2020. [DOI: 10.2217/fvl-2019-0160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: Arboviral diseases are a health hazard and Flavivirus and Alphavirus infections are the most common in humans. This study focuses on immunoinformatic approaches to identify potential MHC class I restricted epitopes common for some selected arboviral diseases. Materials & methods: T-cell epitope prediction tool of Immune Epitope Database was employed to identify putative epitopes from the polyproteins of the selected viruses. Further, population coverage, conservancy, antigenic properties and docking analyses were performed to identify potential common epitopes for the selected viruses. Results: Eight common epitopes were screened for the selected viruses based on their population coverage, conservancy, antigenic properties and binding affinity. Conclusion: Considering the in silico potency, identified epitopes may further be subjected for candidate vaccine development against these arboviruses.
Collapse
Affiliation(s)
- Rakshanda Sajeed
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, Telangana, India
| | - Kishore Sarma
- Department of Virology, Indian Council of Medical Research (ICMR), Regional Medical Research Centre for NE Region, Dibrugarh, Assam, India
| | - Kimmi Sarmah
- Department of Virology, Indian Council of Medical Research (ICMR), Regional Medical Research Centre for NE Region, Dibrugarh, Assam, India
| | - Dipankar Biswas
- Department of Virology, Indian Council of Medical Research (ICMR), Regional Medical Research Centre for NE Region, Dibrugarh, Assam, India
| | - Biswajyoti Borkakoty
- Department of Virology, Indian Council of Medical Research (ICMR), Regional Medical Research Centre for NE Region, Dibrugarh, Assam, India
| |
Collapse
|
7
|
A Chimeric Japanese Encephalitis Vaccine Protects against Lethal Yellow Fever Virus Infection without Inducing Neutralizing Antibodies. mBio 2020; 11:mBio.02494-19. [PMID: 32265332 PMCID: PMC7157777 DOI: 10.1128/mbio.02494-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Efficient and safe vaccines against yellow fever (e.g., YFV-17D) that provide long-lasting protection by rapidly inducing neutralizing antibody responses exist. However, the vaccine supply cannot cope with an increasing demand posed by urban outbreaks in recent years. Here we report that JE-CVax/Imojev, a YFV-17D-based chimeric Japanese encephalitis vaccine, also efficiently protects against YFV infection in mice. In case of shortage of the YFV vaccine during yellow fever outbreaks, (off-label) use of JE-CVax/Imojev may be considered. Moreover, wider use of JE-CVax/Imojev in Asia may lower the risk of the much-feared YFV spillover to the continent. More generally, chimeric vaccines that combine surface antigens and replication machineries of two distinct flaviviruses may be considered dual vaccines for the latter pathogen without induction of surface-specific antibodies. Following this rationale, novel flavivirus vaccines that do not hold a risk for antibody-dependent enhancement (ADE) of infection (inherent to current dengue vaccines and dengue vaccine candidates) could be designed. Recent outbreaks of yellow fever virus (YFV) in West Africa and Brazil resulted in rapid depletion of global vaccine emergency stockpiles and raised concerns about being unprepared against future YFV epidemics. Here we report that a live attenuated virus similar to the Japanese encephalitis virus (JEV) vaccine JE-CVax/Imojev that consists of YFV-17D vaccine from which the structural (prM/E) genes have been replaced with those of the JEV SA14-14-2 vaccine strain confers full protection in mice against lethal YFV challenge. In contrast to the YFV-17D-mediated protection against YFV, this protection is not mediated by neutralizing antibodies but correlates with YFV-specific nonneutralizing antibodies and T cell responses against cell-associated YFV NS1 and other YFV nonstructural (NS) proteins. Our findings reveal the potential of YFV NS proteins to mediate protection and demonstrate that chimeric flavivirus vaccines, such as Imojev, could confer protection against two flaviviruses. This dual protection may have implications for the possible off-label use of JE-CVax in case of emergency and vaccine shortage during YFV outbreaks. In addition, populations in Asia that have been vaccinated with Imojev may already be protected against YFV should outbreaks ever occur on that continent, as several countries/regions in the Asia-Pacific are vulnerable to international spread of the YFV.
Collapse
|
8
|
Chesnut M, Muñoz LS, Harris G, Freeman D, Gama L, Pardo CA, Pamies D. In vitro and in silico Models to Study Mosquito-Borne Flavivirus Neuropathogenesis, Prevention, and Treatment. Front Cell Infect Microbiol 2019; 9:223. [PMID: 31338335 PMCID: PMC6629778 DOI: 10.3389/fcimb.2019.00223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/11/2019] [Indexed: 01/07/2023] Open
Abstract
Mosquito-borne flaviviruses can cause disease in the nervous system, resulting in a significant burden of morbidity and mortality. Disease models are necessary to understand neuropathogenesis and identify potential therapeutics and vaccines. Non-human primates have been used extensively but present major challenges. Advances have also been made toward the development of humanized mouse models, but these models still do not fully represent human pathophysiology. Recent developments in stem cell technology and cell culture techniques have allowed the development of more physiologically relevant human cell-based models. In silico modeling has also allowed researchers to identify and predict transmission patterns and discover potential vaccine and therapeutic candidates. This review summarizes the research on in vitro and in silico models used to study three mosquito-borne flaviviruses that cause neurological disease in humans: West Nile, Dengue, and Zika. We also propose a roadmap for 21st century research on mosquito-borne flavivirus neuropathogenesis, prevention, and treatment.
Collapse
Affiliation(s)
- Megan Chesnut
- Center for Alternatives to Animal Testing, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Laura S. Muñoz
- Division of Neuroimmunology, Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States,Neuroviruses Emerging in the Americas Study, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Georgina Harris
- Center for Alternatives to Animal Testing, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Dana Freeman
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Lucio Gama
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, United States,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - Carlos A. Pardo
- Division of Neuroimmunology, Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States,Neuroviruses Emerging in the Americas Study, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - David Pamies
- Center for Alternatives to Animal Testing, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States,Department of Physiology, University of Lausanne, Lausanne, Switzerland,*Correspondence: David Pamies
| |
Collapse
|
9
|
Roth C, Cantaert T, Colas C, Prot M, Casadémont I, Levillayer L, Thalmensi J, Langlade-Demoyen P, Gerke C, Bahl K, Ciaramella G, Simon-Loriere E, Sakuntabhai A. A Modified mRNA Vaccine Targeting Immunodominant NS Epitopes Protects Against Dengue Virus Infection in HLA Class I Transgenic Mice. Front Immunol 2019; 10:1424. [PMID: 31293584 PMCID: PMC6598640 DOI: 10.3389/fimmu.2019.01424] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 06/05/2019] [Indexed: 11/13/2022] Open
Abstract
Dengue virus (DENV) induces strong T and B cell responses upon infection. Hence, it is difficult to determine the contribution of cell-mediated immunity alone in the long lasting protection against DENV infection and disease. Numerous CD4+ and CD8+ T cell epitopes have been identified, mainly in the non-structural proteins of DENV. Taking into account the immunogenicity and peptide sequence conservation among the different DENV serotypes, a minimal DENV antigen, called DENV1-NS, has been designed. This antigen is enriched in conserved and highly antigenic epitopes located in the NS3, NS4B, and NS5 regions of DENV1. To evaluate the ability of the DENV1-NS poly-epitope to express the antigenic peptides in the context of different HLA class I molecules, we established its in vivo immunogenicity by measuring, after DNA immunization and electroporation, the activation of DENV-specific CD8 T cells in transgenic mice expressing the human HLA-A*0201, -A*2402, -B*0702, and -B*3502 class I alleles. We then engineered a lipid nanoparticle (LNP) encapsulated modified mRNA vaccine encoding DENV1-NS and tested immunogenicity and protection in these human HLA class I transgenic mice, after transient blockade of the interferon (IFN) type I receptor. Significant protection was observed, after two injections of the mRNA vaccine. Collectively, these data strongly support the development of T cell-based vaccines targeting immunodominant T cell epitopes that generate potent virus-specific T cell responses conferring immunity against DENV infection.
Collapse
Affiliation(s)
- Claude Roth
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, Paris, France
- CNRS UMR 2000: Génomique Évolutive, Modélisation et Santé, Institut Pasteur, Paris, France
| | | | - Chloé Colas
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, Paris, France
- CNRS UMR 2000: Génomique Évolutive, Modélisation et Santé, Institut Pasteur, Paris, France
| | - Matthieu Prot
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, Paris, France
- CNRS UMR 2000: Génomique Évolutive, Modélisation et Santé, Institut Pasteur, Paris, France
| | - Isabelle Casadémont
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, Paris, France
- CNRS UMR 2000: Génomique Évolutive, Modélisation et Santé, Institut Pasteur, Paris, France
| | - Laurine Levillayer
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, Paris, France
- CNRS UMR 2000: Génomique Évolutive, Modélisation et Santé, Institut Pasteur, Paris, France
| | | | | | | | - Kapil Bahl
- Moderna, Inc., Cambridge, MA, United States
| | | | - Etienne Simon-Loriere
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, Paris, France
- CNRS UMR 2000: Génomique Évolutive, Modélisation et Santé, Institut Pasteur, Paris, France
| | - Anavaj Sakuntabhai
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, Paris, France
- CNRS UMR 2000: Génomique Évolutive, Modélisation et Santé, Institut Pasteur, Paris, France
| |
Collapse
|
10
|
Matey-Hernandez ML, Brunak S, Izarzugaza JMG. Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios. BMC Bioinformatics 2018; 19:239. [PMID: 29940840 PMCID: PMC6019707 DOI: 10.1186/s12859-018-2239-6] [Citation(s) in RCA: 22] [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: 03/01/2018] [Accepted: 06/12/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The adaptive immune response intrinsically depends on hypervariable human leukocyte antigen (HLA) genes. Concomitantly, correct HLA phenotyping is crucial for successful donor-patient matching in organ transplantation. The cost and technical limitations of current laboratory techniques, together with advances in next-generation sequencing (NGS) methodologies, have increased the need for precise computational typing methods. RESULTS We tested two widespread HLA typing methods using high quality full genome sequencing data from 150 individuals in 50 family trios from the Genome Denmark project. First, we computed descendant accuracies assessing the agreement in the inheritance of alleles from parents to offspring. Second, we compared the locus-specific homozygosity rates as well as the allele frequencies; and we compared those to the observed values in related populations. We provide guidelines for testing the accuracy of HLA typing methods by comparing family information, which is independent of the availability of curated alleles. CONCLUSIONS Although current computational methods for HLA typing generally provide satisfactory results, our benchmark - using data with ultra-high sequencing depth - demonstrates the incompleteness of current reference databases, and highlights the importance of providing genomic databases addressing current sequencing standards, a problem yet to be resolved before benefiting fully from personalised medicine approaches HLA phenotyping is essential.
Collapse
Affiliation(s)
- Maria Luisa Matey-Hernandez
- Center for Biological Sequence Analysis, Department of Bio and Health Informatics, Technical University of Denmark, DK-2800 Lyngby, Denmark
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | - Søren Brunak
- Center for Biological Sequence Analysis, Department of Bio and Health Informatics, Technical University of Denmark, DK-2800 Lyngby, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Jose M. G. Izarzugaza
- Center for Biological Sequence Analysis, Department of Bio and Health Informatics, Technical University of Denmark, DK-2800 Lyngby, Denmark
| |
Collapse
|
11
|
Reginald K, Chan Y, Plebanski M, Poh CL. Development of Peptide Vaccines in Dengue. Curr Pharm Des 2018; 24:1157-1173. [PMID: 28914200 PMCID: PMC6040172 DOI: 10.2174/1381612823666170913163904] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/30/2017] [Accepted: 09/06/2017] [Indexed: 12/11/2022]
Abstract
Dengue is one of the most important arboviral infections worldwide, infecting up to 390 million people and causing 25,000 deaths annually. Although a licensed dengue vaccine is available, it is not efficacious against dengue serotypes that infect people living in South East Asia, where dengue is an endemic disease. Hence, there is an urgent need to develop an efficient dengue vaccine for this region. Data from different clinical trials indicate that a successful dengue vaccine must elicit both neutralizing antibodies and cell mediated immunity. This can be achieved by designing a multi-epitope peptide vaccine comprising B, CD8+ and CD4+ T cell epitopes. As recognition of T cell epitopes are restricted by human leukocyte antigens (HLA), T cell epitopes which are able to recognize several major HLAs will be preferentially included in the vaccine design. While peptide vaccines are safe, biocompatible and cost-effective, it is poorly immunogenic. Strategies to improve its immunogenicity by the use of long peptides, adjuvants and nanoparticle delivery mechanisms are discussed.
Collapse
Affiliation(s)
| | | | | | - Chit Laa Poh
- Address correspondence to this author at the Research Centre for Biomedical Sciences, School of Science and Technology, Sunway University, 5 Jalan University, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia; Tel: +60-3-7491 8622 ext. 7338; E-mail:
| |
Collapse
|
12
|
Pradhan D, Yadav M, Verma R, Khan NS, Jena L, Jain AK. Discovery of T-cell Driven Subunit Vaccines from Zika Virus Genome: An Immunoinformatics Approach. Interdiscip Sci 2017; 9:468-477. [PMID: 29094318 PMCID: PMC7091030 DOI: 10.1007/s12539-017-0238-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 02/26/2017] [Accepted: 05/09/2017] [Indexed: 11/16/2022]
Abstract
The recent outbreaks of Zika virus and the absence of a specific therapy have necessitated to identify T-cell-stimulating antigenic peptides as potential subunit vaccine candidates. The translated ssRNA (+) genome of Zika virus was explored in EMBOSS antigenic and VaxiJen to predict 63 peptides as potential antigens. Three MHC-II binding peptide prediction tools, viz. NetMHCIIpan, PREDIVAC and immune epitope database (IEDB) were employed in consensus on 63 antigenic peptides to propose 14 T-helper cell epitopes. Similarly, analysis on 63 antigenic peptides through NetMHC, NetCTL and IEDB MHC-I binding peptide prediction tool led to identification of 14 CTL epitopes. Seven T-cell epitopes, C:44-66, M:135-149, NS2A:124-144, NS3:421-453, NS3:540-554, NS4B:90-134 and NS4B:171-188, are observed to share overlapping MHC-I and MHC-II binding motifs and hence, are being proposed to constitute minimum T-cell antigens to elicit protective T-cell immune response against Zika. Three of them, C:44-66, NS3:421-453 and NS3:540-554 are identified to be conserved across all the selected strains of Zika virus. Moreover, the 21 T-cell epitopes are non-self to humans and exhibited good coverage in variable populations of 14 geographical locations. Therefore, 21 T-cell epitopes are proposed as potential subunit vaccines against Zika virus.
Collapse
Affiliation(s)
- Dibyabhaba Pradhan
- Biomedical Informatics Centre, National Institute of Pathology-ICMR, New Delhi, 110029, India
| | - Monika Yadav
- Biomedical Informatics Centre, National Institute of Pathology-ICMR, New Delhi, 110029, India
| | - Rashi Verma
- Biomedical Informatics Centre, National Institute of Pathology-ICMR, New Delhi, 110029, India
| | - Noor Saba Khan
- Biomedical Informatics Centre, National Institute of Pathology-ICMR, New Delhi, 110029, India
| | - Lingaraja Jena
- Bioinformatics Centre, Mahatma Gandhi Institute of Medical Sciences, Sevagram, Wardha, 442102, India
| | - Arun Kumar Jain
- Biomedical Informatics Centre, National Institute of Pathology-ICMR, New Delhi, 110029, India.
| |
Collapse
|
13
|
Schmidt J, Guillaume P, Dojcinovic D, Karbach J, Coukos G, Luescher I. In silico and cell-based analyses reveal strong divergence between prediction and observation of T-cell-recognized tumor antigen T-cell epitopes. J Biol Chem 2017; 292:11840-11849. [PMID: 28536262 DOI: 10.1074/jbc.m117.789511] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/11/2017] [Indexed: 11/06/2022] Open
Abstract
Tumor exomes provide comprehensive information on mutated, overexpressed genes and aberrant splicing, which can be exploited for personalized cancer immunotherapy. Of particular interest are mutated tumor antigen T-cell epitopes, because neoepitope-specific T cells often are tumoricidal. However, identifying tumor-specific T-cell epitopes is a major challenge. A widely used strategy relies on initial prediction of human leukocyte antigen-binding peptides by in silico algorithms, but the predictive power of this approach is unclear. Here, we used the human tumor antigen NY-ESO-1 (ESO) and the human leukocyte antigen variant HLA-A*0201 (A2) as a model and predicted in silico the 41 highest-affinity, A2-binding 8-11-mer peptides and assessed their binding, kinetic complex stability, and immunogenicity in A2-transgenic mice and on peripheral blood mononuclear cells from ESO-vaccinated melanoma patients. We found that 19 of the peptides strongly bound to A2, 10 of which formed stable A2-peptide complexes and induced CD8+ T cells in A2-transgenic mice. However, only 5 of the peptides induced cognate T cells in humans; these peptides exhibited strong binding and complex stability and contained multiple large hydrophobic and aromatic amino acids. These results were not predicted by in silico algorithms and provide new clues to improving T-cell epitope identification. In conclusion, our findings indicate that only a small fraction of in silico-predicted A2-binding ESO peptides are immunogenic in humans, namely those that have high peptide-binding strength and complex stability. This observation highlights the need for improving in silico predictions of peptide immunogenicity.
Collapse
Affiliation(s)
- Julien Schmidt
- Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
| | - Philippe Guillaume
- Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
| | - Danijel Dojcinovic
- Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
| | | | - George Coukos
- Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland; Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Immanuel Luescher
- Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland.
| |
Collapse
|
14
|
Muthusamy K, Gopinath K, Nandhini D. Computational prediction of immunodominant antigenic regions & potential protective epitopes for dengue vaccination. Indian J Med Res 2017; 144:587-591. [PMID: 28256468 PMCID: PMC5345306 DOI: 10.4103/0971-5916.200894] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Background & objectives: Epitope-based vaccines (EVs) are specific, safe and easy to produce. However, vaccine failure has been frequently reported due to variation within epitopic regions. Therefore, development of vaccines based on conserved epitopes may prevent such vaccine failure. This study was undertaken to identify highly conserved antigenic regions in the four dengue serotypes to produce an epitope-based dengue vaccine. Methods: Polyprotein sequences of all four dengue serotypes were collected and aligned using MAFFT multiple sequence alignment plugin with Geneious Pro v6.1. Consensus sequences of the polyproteins for all four dengue serotypes were designed and screened against experimentally proven epitopes to predict potential antigenic regions that are conserved among all four dengue serotypes. Results: The antigenic region VDRGWGNGCGLFGKG was 100 per cent conserved in the consensus polyprotein sequences of all four dengue serotypes. Fifteen experimentally proven epitopes were identical to the immunodominant antigenic region. Interpretation & conclusions: Computationally predicted antigenic regions may be considered for use in the development of EVs for protection against dengue virus. Such vaccines would be expected to provide protection against dengue infections caused by all dengue serotypes because these would contain antigenic regions highly conserved across those serotypes. Therefore, the immunodominant antigenic region (VDRGWGNGCGLFGKG) and 15 potential epitopes may be considered for use in dengue vaccines.
Collapse
Affiliation(s)
| | - Krishnasamy Gopinath
- Department of Bioinformatics, Science Campus, Alagappa University, Karaikudi, India
| | | |
Collapse
|
15
|
Paul S, Sidney J, Sette A, Peters B. TepiTool: A Pipeline for Computational Prediction of T Cell Epitope Candidates. ACTA ACUST UNITED AC 2016; 114:18.19.1-18.19.24. [PMID: 27479659 DOI: 10.1002/cpim.12] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Computational prediction of T cell epitope candidates is currently being used in several applications including vaccine discovery studies, development of diagnostics, and removal of unwanted immune responses against protein therapeutics. There have been continuous improvements in the performance of MHC binding prediction tools, but their general adoption by immunologists has been slow due to the lack of user-friendly interfaces and guidelines. Current tools only provide minimal advice on what alleles to include, what lengths to consider, how to deal with homologous peptides, and what cutoffs should be considered relevant. This protocol provides step-by-step instructions with necessary recommendations for prediction of the best T cell epitope candidates with the newly developed online tool called TepiTool. TepiTool, which is part of the Immune Epitope Database (IEDB), provides some of the top MHC binding prediction algorithms for number of species including humans, chimpanzees, bovines, gorillas, macaques, mice, and pigs. The TepiTool is freely accessible at http://tools.iedb.org/tepitool/. © 2016 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- Sinu Paul
- La Jolla Institute for Allergy and Immunology, Division of Vaccine Discovery, La Jolla, California
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, Division of Vaccine Discovery, La Jolla, California
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, Division of Vaccine Discovery, La Jolla, California
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, Division of Vaccine Discovery, La Jolla, California
| |
Collapse
|
16
|
Comber JD, Karabudak A, Huang X, Piazza PA, Marques ETA, Philip R. Dengue virus specific dual HLA binding T cell epitopes induce CD8+ T cell responses in seropositive individuals. Hum Vaccin Immunother 2015; 10:3531-43. [PMID: 25668665 DOI: 10.4161/21645515.2014.980210] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Dengue virus infects an estimated 300 million people each year and even more are at risk of becoming infected as the virus continues to spread into new areas. Despite the increase in viral prevalence, no anti-viral medications or vaccines are approved for treating or preventing infection. CD8+ T cell responses play a major role in viral clearance. Therefore, effective vaccines that induce a broad, multi-functional T cell response with substantial cross-reactivity between all virus serotypes can have major impacts on reducing infection rates and infection related complications. Here, we took an immunoproteomic approach to identify novel MHC class I restricted T cell epitopes presented by dengue virus infected cells, representing the natural and authentic targets of the T cell response. Using this approach we identified 4 novel MHC-I restricted epitopes: 2 with the binding motif for HLA-A24 molecules and 2 with both HLA-A2 and HLA-A24 binding motifs. These peptides were able to activate CD8+ T cell responses in both healthy, seronegative individuals and in seropositive individuals who have previously been infected with dengue virus. Importantly, the dual binding epitopes activated pre-existing T cell precursors in PBMCs obtained from both HLA-A2+ and HLA-A24+ seropositive individuals. Together, the data indicate that these epitopes are immunologically relevant T cell activating peptides presented on infected cells during a natural infection and therefore may serve as candidate antigens for the development of effective multi-serotype specific dengue virus vaccines.
Collapse
|
17
|
Duan Z, Guo J, Huang X, Liu H, Chen X, Jiang M, Wen J. Identification of cytotoxic T lymphocyte epitopes in dengue virus serotype 1. J Med Virol 2015; 87:1077-89. [PMID: 25777343 DOI: 10.1002/jmv.24167] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2015] [Indexed: 11/12/2022]
Abstract
Dengue virus (DENV) has a serious and growing impact on global health and the exact role of DENV-specific CD8(+) T-cells in DENV infection is still uncertain. In the present study, SYFPEITHI algorithm was used to screen the amino acid sequence of Dengue virus serotype 1 (DENV-1) for potential epitopes, and seven putative HLA-A*1101-restricted and five putative HLA-A*2402-restricted epitopes conserved in hundreds of DENV-1 strains were synthesized. The binding affinity of these epitope candidates to corresponding HLA molecules was evaluated using competitive peptide-binding assay. The immunogenicity and specificity of peptides were further tested in HLA-A*1101 transgenic mice, HLA-A*2402 transgenic mice and peripheral blood mononuclear cells (PBMCs) of patients infected with DENV-1. Percentage inhibition (PI) values calculated in competitive peptide-binding assay showed that six peptides (E39-47 PTLDIELLK, NS5(505-513) GVEGEGLHK, NS2b(15-23) SILLSSLLK, NS5(561-569) ALLATSIFK, NS3(99-107) AVEPGKNPK, and NS4b(159-167) VVYDAKFEK) could bind to HLA-A*1101 molecule with high affinity and five peptides (NS3472-480 QYIYMGQPL, NS4a40-48 AYRHAMEEL, NS5(880-888) DYMTSMKRF, NS3(548-556) SYKVASEGF, and NS3(22-30) IYRILQRGL) have a high affinity for HLA-A*2402 molecule. Enzyme-linked immunospot (ELISPOT) results indicated that these high-affinity peptides were recognized by splenocytes of DENV-1-infected transgenic mice and high-affinity peptide-immunized transgenic mice displayed high levels of peptide-specific IFN-γ-secreting cells. In addition, both peptide-pulsed splenocytes and DENV-1-infected splenic monocytes were efficiently killed by these peptide-specific cytotoxic T lymphocytes. Finally, except NS2b(15-23), 10 high-affinity peptides were recognized by PBMCs of patients infected with DENV-1. These identified epitopes would contribute to the understanding of the function of DENV-specific CD8(+) T-cells.
Collapse
Affiliation(s)
- Zhiliang Duan
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China; Department of Clinical Laboratory, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | | | | | | | | | | | | |
Collapse
|
18
|
Duan ZL, Liu HF, Huang X, Wang SN, Yang JL, Chen XY, Li DZ, Zhong XZ, Chen BK, Wen JS. Identification of conserved and HLA-A*2402-restricted epitopes in Dengue virus serotype 2. Virus Res 2014; 196:5-12. [PMID: 25449574 DOI: 10.1016/j.virusres.2014.10.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 10/24/2014] [Accepted: 10/27/2014] [Indexed: 11/28/2022]
Abstract
In this study, we set out to identify dengue virus serotype 2 (DENV-2)-specific HLA-A*2402-restricted epitopes and determine the characteristics of T cells generated to these epitopes. We screened the full-length amino-acid sequence of DENV-2 to find potential epitopes using the SYFPEITHI algorithm. Twelve putative HLA-A*2402-binding peptides conserved in hundreds of DENV-2 strains were synthesized, and the HLA restriction of peptides was tested in HLA-A*2402 transgenic mice. Nine peptides (NS4b(228-237), NS2a(73-81), E(298-306), M(141-149), NS4a(96-105), NS4b(159-168), NS5(475-484), NS1(162-171), and NS5(611-620)) induced high levels of peptide-specific IFN-γ-secreting cells in HLA-A*2402 transgenic mice. Apart from IFN-γ, NS4b(228-237-), NS2a(73-81-) and E(298-306)-specific CD8(+) cells produced TNF-α and IL-6 simultaneously, whereas M(141-149-) and NS5(475-484-) CD8(+) cells produced only IL-6. Moreover, splenic mononuclear cells (SMCs) efficiently recognized and killed peptide-pulsed splenocytes. Furthermore, each of nine peptides could be recognized by splenocytes from DENV-2-infected HLA-A*2402 transgenic mice. The SMCs from HLA-A*2402 transgenic mice immunized with nine immunogenic peptides efficiently killed DENV-2-infected splenic monocytes. The present identified epitopes have the potential to be new diagnostic tools for characterization of T-cell immunity in DENV infection and may serve as part of a universal epitope-based vaccine.
Collapse
Affiliation(s)
- Zhi-Liang Duan
- Department of Microbiology and Immunology, Wenzhou Medical University, Wenzhou, China; Department of Clinical Laboratory, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China; Institute of Arboviruses, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Hui-Fang Liu
- Department of Microbiology and Immunology, Wenzhou Medical University, Wenzhou, China
| | - Xi Huang
- Department of Immunology, Institute of Tuberculosis Control, Institute of Human Virology, Sun Yat-sen University, Zhongshan School of Medicine, Guangzhou, China; Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Si-Na Wang
- Department of Microbiology and Immunology, Wenzhou Medical University, Wenzhou, China
| | - Jin-Lin Yang
- Department of Microbiology and Immunology, Wenzhou Medical University, Wenzhou, China
| | - Xin-Yu Chen
- Department of Clinical Laboratory, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - De-Zhou Li
- Department of Liver, The Secondary Hospital of Ningbo, Ningbo, China
| | - Xiao-Zhi Zhong
- Department of Microbiology and Immunology, Wenzhou Medical University, Wenzhou, China
| | - Bo-Kun Chen
- Department of Microbiology and Immunology, Wenzhou Medical University, Wenzhou, China
| | - Jin-Sheng Wen
- Department of Microbiology and Immunology, Wenzhou Medical University, Wenzhou, China; Institute of Arboviruses, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China.
| |
Collapse
|
19
|
Paul S, Weiskopf D, Angelo MA, Sidney J, Peters B, Sette A. HLA class I alleles are associated with peptide-binding repertoires of different size, affinity, and immunogenicity. THE JOURNAL OF IMMUNOLOGY 2013; 191:5831-9. [PMID: 24190657 DOI: 10.4049/jimmunol.1302101] [Citation(s) in RCA: 200] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Prediction of HLA binding affinity is widely used to identify candidate T cell epitopes, and an affinity of 500 nM is routinely used as a threshold for peptide selection. However, the fraction (percentage) of peptides predicted to bind with affinities of 500 nM varies by allele. For example, of a large collection of ~30,000 dengue virus-derived peptides only 0.3% were predicted to bind HLA A*0101, whereas nearly 5% were predicted for A*0201. This striking difference could not be ascribed to variation in accuracy of the algorithms used, as predicted values closely correlated with affinity measured in vitro with purified HLA molecules. These data raised the question whether different alleles would also vary in terms of epitope repertoire size, defined as the number of associated epitopes or, alternatively, whether alleles vary drastically in terms of the affinity threshold associated with immunogenicity. To address this issue, strains of HLA transgenic mice with wide (A*0201), intermediate (B*0702), or narrow (A*0101) repertoires were immunized with peptides of varying binding affinity and relative percentile ranking. The results show that absolute binding capacity is a better predictor of immunogenicity, and analysis of epitopes from the Immune Epitope Database revealed that predictive efficacy is increased using allele-specific affinity thresholds. Finally, we investigated the genetic and structural basis of the phenomenon. Although no stringent correlate was defined, on average HLA B alleles are associated with significantly narrower repertoires than are HLA A alleles.
Collapse
Affiliation(s)
- Sinu Paul
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
| | - Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
| | - Michael A Angelo
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, 92037, USA
| |
Collapse
|
20
|
Nascimento EJM, Mailliard RB, Khan AM, Sidney J, Sette A, Guzman N, Paulaitis M, de Melo AB, Cordeiro MT, Gil LVG, Lemonnier F, Rinaldo C, August JT, Marques ETA. Identification of conserved and HLA promiscuous DENV3 T-cell epitopes. PLoS Negl Trop Dis 2013; 7:e2497. [PMID: 24130917 PMCID: PMC3794980 DOI: 10.1371/journal.pntd.0002497] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 09/09/2013] [Indexed: 12/31/2022] Open
Abstract
Anti-dengue T-cell responses have been implicated in both protection and immunopathology. However, most of the T-cell studies for dengue include few epitopes, with limited knowledge of their inter-serotype variation and the breadth of their human leukocyte antigen (HLA) affinity. In order to expand our knowledge of HLA-restricted dengue epitopes, we screened T-cell responses against 477 overlapping peptides derived from structural and non-structural proteins of the dengue virus serotype 3 (DENV3) by use of HLA class I and II transgenic mice (TgM): A2, A24, B7, DR2, DR3 and DR4. TgM were inoculated with peptides pools and the T-cell immunogenic peptides were identified by ELISPOT. Nine HLA class I and 97 HLA class II novel DENV3 epitopes were identified based on immunogenicity in TgM and their HLA affinity was further confirmed by binding assays analysis. A subset of these epitopes activated memory T-cells from DENV3 immune volunteers and was also capable of priming naïve T-cells, ex vivo, from dengue IgG negative individuals. Analysis of inter- and intra-serotype variation of such an epitope (A02-restricted) allowed us to identify altered peptide ligands not only in DENV3 but also in other DENV serotypes. These studies also characterized the HLA promiscuity of 23 HLA class II epitopes bearing highly conserved sequences, six of which could bind to more than 10 different HLA molecules representing a large percentage of the global population. These epitope data are invaluable to investigate the role of T-cells in dengue immunity/pathogenesis and vaccine design. Although there is an increased recognition of the role of T-cells in both dengue pathogenesis and protection, comprehensive analysis of T-cell activation during dengue infection is hampered by the small repertoire of known human dengue T-cell epitopes. Although dengue serotype 3 (DENV3) is responsible for numerous outbreaks worldwide, most of the known epitopes are from studies of dengue 2 serotype (DENV2). In this study, we identified novel DENV3 T-cell epitopes in HLA transgenic mice that were confirmed by HLA binding assays. A subset of these epitopes activated memory T-cells from subjects who were dengue IgG positive and primed naïve T-cells from dengue IgG negative individuals. Notably, some of HLA class II epitopes bearing highly conserved regions common to all four dengue serotypes could bind to multiple HLAs. We postulate that these highly conserved and HLA promiscuous T-helper epitopes can be important components of a dengue tetravalent vaccine.
Collapse
Affiliation(s)
- Eduardo J. M. Nascimento
- Department of Infectious Disease and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail: (EJMN); , (ETAM)
| | - Robbie B. Mailliard
- Department of Infectious Disease and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Asif M. Khan
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University, Baltimore, Maryland, United States of America
- Perdana University Graduate School of Medicine, Serdang, Selangor Darul Ehsan, Malaysia
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Nicole Guzman
- Department of Chemical & Biomolecular Engineering, Ohio State University, Columbus, Ohio, United States of America
| | - Michael Paulaitis
- Department of Chemical & Biomolecular Engineering, Ohio State University, Columbus, Ohio, United States of America
| | - Andréa Barbosa de Melo
- Department of Virology and Experimental Therapy, CPqAM/FIOCRUZ, Recife, Pernambuco, Brazil
| | - Marli T. Cordeiro
- Department of Virology and Experimental Therapy, CPqAM/FIOCRUZ, Recife, Pernambuco, Brazil
| | - Laura V. G. Gil
- Department of Virology and Experimental Therapy, CPqAM/FIOCRUZ, Recife, Pernambuco, Brazil
| | | | - Charles Rinaldo
- Department of Infectious Disease and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - J. Thomas August
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Ernesto T. A. Marques
- Department of Infectious Disease and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Virology and Experimental Therapy, CPqAM/FIOCRUZ, Recife, Pernambuco, Brazil
- * E-mail: (EJMN); , (ETAM)
| |
Collapse
|
21
|
Metadata-driven comparative analysis tool for sequences (meta-CATS): an automated process for identifying significant sequence variations that correlate with virus attributes. Virology 2013; 447:45-51. [PMID: 24210098 DOI: 10.1016/j.virol.2013.08.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 07/18/2013] [Accepted: 08/19/2013] [Indexed: 12/25/2022]
Abstract
The Virus Pathogen Resource (ViPR; www.viprbrc.org) and Influenza Research Database (IRD; www.fludb.org) have developed a metadata-driven Comparative Analysis Tool for Sequences (meta-CATS), which performs statistical comparative analyses of nucleotide and amino acid sequence data to identify correlations between sequence variations and virus attributes (metadata). Meta-CATS guides users through: selecting a set of nucleotide or protein sequences; dividing them into multiple groups based on any associated metadata attribute (e.g. isolation location, host species); performing a statistical test at each aligned position; and identifying all residues that significantly differ between the groups. As proofs of concept, we have used meta-CATS to identify sequence biomarkers associated with dengue viruses isolated from different hemispheres, and to identify variations in the NS1 protein that are unique to each of the 4 dengue serotypes. Meta-CATS is made freely available to virology researchers to identify genotype-phenotype correlations for development of improved vaccines, diagnostics, and therapeutics.
Collapse
|
22
|
Abstract
PURPOSE OF REVIEW Dengue is one of the most rapidly spreading vector-borne diseases in the world, with the incidence increasing 30-fold in the past 50 years. There are currently no licensed treatments or vaccines for dengue. This review covers the recent advances in our understanding of dengue pathogenesis, including host and viral determinants. RECENT FINDINGS The pathogenesis of severe dengue is thought to be immune-mediated due to the timing of the clinical manifestations and higher incidence in secondary infections with a heterologous serotype. Recent evidence has provided further information of neutralizing versus enhancing monoclonal antibodies and their target epitopes on the dengue virion, which has major implications for vaccine design. The role of T-cell immunopathology has also been advanced with recent evidence of cross-reactive high pro-inflammatory cytokine producing T cells predominating in severe dengue. Recent large genome-wide association studies have identified specific susceptibility loci associated with severe disease. Epidemiological studies have served to define certain at-risk groups and specific viral virulence factors have recently been described. SUMMARY The pathogenesis of dengue is likely to be a complex interplay of host immunity and genetic predisposition combined with certain viral virulence factors. Better understanding of the underlying mechanisms leading to severe dengue is crucial if we are to develop prognostic markers, novel diagnostics and therapeutics and ultimately a balanced and safe vaccine.
Collapse
Affiliation(s)
- Sophie Yacoub
- Department of Medicine, Imperial College, Hammersmith Campus, London, UK.
| | | | | |
Collapse
|
23
|
de Melo AB, Nascimento EJM, Braga-Neto U, Dhalia R, Silva AM, Oelke M, Schneck JP, Sidney J, Sette A, Montenegro SML, Marques ETA. T-cell memory responses elicited by yellow fever vaccine are targeted to overlapping epitopes containing multiple HLA-I and -II binding motifs. PLoS Negl Trop Dis 2013; 7:e1938. [PMID: 23383350 PMCID: PMC3561163 DOI: 10.1371/journal.pntd.0001938] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2011] [Accepted: 10/22/2012] [Indexed: 11/19/2022] Open
Abstract
The yellow fever vaccines (YF-17D-204 and 17DD) are considered to be among the safest vaccines and the presence of neutralizing antibodies is correlated with protection, although other immune effector mechanisms are known to be involved. T-cell responses are known to play an important role modulating antibody production and the killing of infected cells. However, little is known about the repertoire of T-cell responses elicited by the YF-17DD vaccine in humans. In this report, a library of 653 partially overlapping 15-mer peptides covering the envelope (Env) and nonstructural (NS) proteins 1 to 5 of the vaccine was utilized to perform a comprehensive analysis of the virus-specific CD4(+) and CD8(+) T-cell responses. The T-cell responses were screened ex-vivo by IFN-γ ELISPOT assays using blood samples from 220 YF-17DD vaccinees collected two months to four years after immunization. Each peptide was tested in 75 to 208 separate individuals of the cohort. The screening identified sixteen immunodominant antigens that elicited activation of circulating memory T-cells in 10% to 33% of the individuals. Biochemical in-vitro binding assays and immunogenetic and immunogenicity studies indicated that each of the sixteen immunogenic 15-mer peptides contained two or more partially overlapping epitopes that could bind with high affinity to molecules of different HLAs. The prevalence of the immunogenicity of a peptide in the cohort was correlated with the diversity of HLA-II alleles that they could bind. These findings suggest that overlapping of HLA binding motifs within a peptide enhances its T-cell immunogenicity and the prevalence of the response in the population. In summary, the results suggests that in addition to factors of the innate immunity, "promiscuous" T-cell antigens might contribute to the high efficacy of the yellow fever vaccines.
Collapse
Affiliation(s)
- Andréa Barbosa de Melo
- Virology and Experimental Therapeutics Laboratory, Aggeu Magalhães Research Center, Fiocruz, Recife, Pernambuco, Brazil
| | - Eduardo J. M. Nascimento
- Center for Vaccine Research, Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ulisses Braga-Neto
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Rafael Dhalia
- Virology and Experimental Therapeutics Laboratory, Aggeu Magalhães Research Center, Fiocruz, Recife, Pernambuco, Brazil
| | - Ana Maria Silva
- Virology and Experimental Therapeutics Laboratory, Aggeu Magalhães Research Center, Fiocruz, Recife, Pernambuco, Brazil
| | - Mathias Oelke
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jonathan P. Schneck
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, Vaccine Discovery, La Jolla, California, United States of America
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, Vaccine Discovery, La Jolla, California, United States of America
| | - Silvia M. L. Montenegro
- Department of Immunology, Aggeu Magalhães Research Center, Fiocruz, Recife, Pernambuco, Brazil
| | - Ernesto T. A. Marques
- Virology and Experimental Therapeutics Laboratory, Aggeu Magalhães Research Center, Fiocruz, Recife, Pernambuco, Brazil
- Center for Vaccine Research, Department of Infectious Diseases and Microbiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
24
|
Duan ZL, Li Q, Wang ZB, Xia KD, Guo JL, Liu WQ, Wen JS. HLA-A*0201-restricted CD8+ T-cell epitopes identified in dengue viruses. Virol J 2012; 9:259. [PMID: 23121866 PMCID: PMC3546861 DOI: 10.1186/1743-422x-9-259] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Accepted: 10/24/2012] [Indexed: 02/03/2023] Open
Abstract
Background All four dengue virus (DV) serotypes (D1V, D2V, D3V and D4V) can cause a series of disorders, ranging from mild dengue fever (DF) to severe dengue hemorrhagic fever and dengue shock syndrome (DHF/DSS). Previous studies have revealed that DV serotype-specific CD8+ T cells are involved in controlling DV infection. Serotype cross-reactive CD8+ T-cells may contribute to the immunopathogenesis of DHF/DSS. The aim of the study was to identify HLA-A*0201-binding peptides from four DV serotypes. We then examined their immunogenicity in vivo and cross-reactivity within heterologous peptides. Methods D1V-derived candidate CD8+ T-cell epitopes were synthesized and evaluated for their affinity to the HLA-A*0201 molecule. Variant peptides representing heterologous D2V, D3V, D4V serotypes were synthesized. The immunogenicity of the high-affinity peptides were evaluated in HLA-A*0201 transgenic mice. Results Of the seven D1V-derived candidate epitopes [D1V-NS4a56–64(MLLALIAVL), D1V-C46–54(LVMAFMAFL), D1V-NS4b562–570(LLATSIFKL), D1V-NS2a169–177(AMVLSIVSL), D1V-NS4a140–148(GLLFMILTV), D1V-NS2a144–152(QLWAALLSL) and D1V-NS4b183–191(LLMRTTWAL)], three peptides [D1V-NS4a140–148, D1V-NS2a144–152 and D1V-NS4b183–191] had a high affinity for HLA-A*0201 molecules. Moreover, their variant peptides for D2V, D3V and D4V [D2V-NS4a140–148(AILTVVAAT), D3V-NS4a140-148(GILTLAAIV), D4V-NS4a140-148(TILTIIGLI), D2V-NS2a144–152(QLAVTIMAI), D3V-NS2a144–152(QLWTALVSL), D4V-NS2a143–151(QVGTLALSL), D2V-NS4b182–190(LMMRTTWAL), D3V-NS4b182–190 (LLMRTSWAL) and D4V-NS4b179–187(LLMRTTWAF)] also had a high affinity for HLA-A*0201 molecules. Furthermore, CD8+ T cells directed to these twelve peptides were induced in HLA-A*0201 transgenic mice following immunization with these peptides. Additionally, cross-reactivity within four peptides (D1V-NS4b183–191, D2V-NS4b182–190, D3V-NS4b182–190 and D4V-NS4b179–187) was observed. Conclusions Two novel serotype-specific HLA-A*0201-restricted CD8+ T-cell epitopes (NS4a140-148 and NS2a144–152) and one cross-reactive HLA-A*0201-restricted CD8+ T-cell epitopes which is similar to a previously identified epitope were identified in D1V-D4V. Combining prediction algorithms and HLA transgenic mice is an effective strategy to identify HLA-restricted epitopes. Serotype-specific epitopes would be used to determine the protective role of serotype-specific CD8+ T cells, while cross-reactive epitopes may provide assistance in exploring the role of serotype cross-reactive CD8+ T cells in the immunopathogenesis of DHF/DSS.
Collapse
Affiliation(s)
- Zhi-Liang Duan
- Department of Microbiology and Immunology, Wenzhou Medical College, Wenzhou, China
| | | | | | | | | | | | | |
Collapse
|
25
|
Zvi A, Rotem S, Cohen O, Shafferman A. Clusters versus affinity-based approaches in F. tularensis whole genome search of CTL epitopes. PLoS One 2012; 7:e36440. [PMID: 22563500 PMCID: PMC3341354 DOI: 10.1371/journal.pone.0036440] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 04/02/2012] [Indexed: 12/31/2022] Open
Abstract
Deciphering the cellular immunome of a bacterial pathogen is challenging due to the enormous number of putative peptidic determinants. State-of-the-art prediction methods developed in recent years enable to significantly reduce the number of peptides to be screened, yet the number of remaining candidates for experimental evaluation is still in the range of ten-thousands, even for a limited coverage of MHC alleles. We have recently established a resource-efficient approach for down selection of candidates and enrichment of true positives, based on selection of predicted MHC binders located in high density “hotspots" of putative epitopes. This cluster-based approach was applied to an unbiased, whole genome search of Francisella tularensis CTL epitopes and was shown to yield a 17–25 fold higher level of responders as compared to randomly selected predicted epitopes tested in Kb/Db C57BL/6 mice. In the present study, we further evaluate the cluster-based approach (down to a lower density range) and compare this approach to the classical affinity-based approach by testing putative CTL epitopes with predicted IC50 values of <10 nM. We demonstrate that while the percent of responders achieved by both approaches is similar, the profile of responders is different, and the predicted binding affinity of most responders in the cluster-based approach is relatively low (geometric mean of 170 nM), rendering the two approaches complimentary. The cluster-based approach is further validated in BALB/c F. tularensis immunized mice belonging to another allelic restriction (Kd/Dd) group. To date, the cluster-based approach yielded over 200 novel F. tularensis peptides eliciting a cellular response, all were verified as MHC class I binders, thereby substantially increasing the F. tularensis dataset of known CTL epitopes. The generality and power of the high density cluster-based approach suggest that it can be a valuable tool for identification of novel CTLs in proteomes of other bacterial pathogens.
Collapse
Affiliation(s)
- Anat Zvi
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Shahar Rotem
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ofer Cohen
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Avigdor Shafferman
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
- * E-mail:
| |
Collapse
|