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Grifoni A, Angelo MA, Lopez B, O'Rourke PH, Sidney J, Cerpas C, Balmaseda A, Silveira CGT, Maestri A, Costa PR, Durbin AP, Diehl SA, Phillips E, Mallal S, De Silva AD, Nchinda G, Nkenfou C, Collins MH, de Silva AM, Lim MQ, Macary PA, Tatullo F, Solomon T, Satchidanandam V, Desai A, Ravi V, Coloma J, Turtle L, Rivino L, Kallas EG, Peters B, Harris E, Sette A, Weiskopf D. Global Assessment of Dengue Virus-Specific CD4 + T Cell Responses in Dengue-Endemic Areas. Front Immunol 2017; 8:1309. [PMID: 29081779 PMCID: PMC5646259 DOI: 10.3389/fimmu.2017.01309] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 09/28/2017] [Indexed: 11/18/2022] Open
Abstract
Background Dengue is a major public health problem worldwide. Assessment of adaptive immunity is important to understanding immunopathology and to define correlates of protection against dengue virus (DENV). To enable global assessment of CD4+ T cell responses, we mapped HLA-DRB1-restricted DENV-specific CD4+ T cell epitopes in individuals previously exposed to DENV in the general population of the dengue-endemic region of Managua, Nicaragua. Methods HLA class II epitopes in the population of Managua were identified by an in vitro IFNγ ELISPOT assay. CD4+ T cells purified by magnetic bead negative selection were stimulated with HLA-matched epitope pools in the presence of autologous antigen-presenting cells, followed by pool deconvolution to identify specific epitopes. The epitopes identified in this study were combined with those previously identified in the DENV endemic region of Sri Lanka, to generate a “megapool” (MP) consisting of 180 peptides specifically designed to achieve balanced HLA and DENV serotype coverage. The DENV CD4MP180 was validated by intracellular cytokine staining assays. Results We detected responses directed against a total of 431 epitopes, representing all 4 DENV serotypes, restricted by 15 different HLA-DRB1 alleles. The responses were associated with a similar pattern of protein immunodominance, overall higher magnitude of responses, as compared to what was observed previously in the Sri Lanka region. Based on these epitope mapping studies, we designed a DENV CD4 MP180 with higher and more consistent coverage, which allowed the detection of CD4+ T cell DENV responses ex vivo in various cohorts of DENV exposed donors worldwide, including donors from Nicaragua, Brazil, Singapore, Sri Lanka, and U.S. domestic flavivirus-naïve subjects immunized with Tetravalent Dengue Live-Attenuated Vaccine (TV005). This broad reactivity reflects that the 21 HLA-DRB1 alleles analyzed in this and previous studies account for more than 80% of alleles present with a phenotypic frequency ≥5% worldwide, corresponding to 92% phenotypic coverage of the general population (i.e., 92% of individuals express at least one of these alleles). Conclusion The DENV CD4 MP180 can be utilized to measure ex vivo responses to DENV irrespective of geographical location.
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Affiliation(s)
- Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Michael A Angelo
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Benjamin Lopez
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Patrick H O'Rourke
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Cristhiam Cerpas
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministerio de Salud, Managua, Nicaragua
| | - Angel Balmaseda
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministerio de Salud, Managua, Nicaragua
| | - Cassia G T Silveira
- Division of Clinical Immunology and Allergy, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Alvino Maestri
- Division of Clinical Immunology and Allergy, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Priscilla R Costa
- Division of Clinical Immunology and Allergy, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Anna P Durbin
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, United States
| | - Sean A Diehl
- Vaccine Testing Center, Department of Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, United States
| | - Elizabeth Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Aruna D De Silva
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States.,Genetech Research Institute, Colombo, Sri Lanka
| | - Godwin Nchinda
- Chantal BIYA International Reference Centre for Research on the Prevention and Management of HIV/AIDS CIRCB, Yaoundé, Cameroon
| | - Celine Nkenfou
- Chantal BIYA International Reference Centre for Research on the Prevention and Management of HIV/AIDS CIRCB, Yaoundé, Cameroon
| | - Matthew H Collins
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Aravinda M de Silva
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Mei Qiu Lim
- Emerging Infectious Disease Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Paul A Macary
- Immunology Programme, Department of Microbiology and Immunology, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Filippo Tatullo
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Tom Solomon
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom.,National Institute for Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, United Kingdom
| | - Vijaya Satchidanandam
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Anita Desai
- Neurovirology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Vasanthapram Ravi
- Neurovirology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Josefina Coloma
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Lance Turtle
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom.,National Institute for Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, United Kingdom
| | - Laura Rivino
- Emerging Infectious Disease Programme, Duke-NUS Medical School, Singapore, Singapore
| | - Esper G Kallas
- Division of Clinical Immunology and Allergy, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
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Weiskopf D, Angelo MA, Grifoni A, O'Rourke PH, Sidney J, Paul S, De Silva AD, Phillips E, Mallal S, Premawansa S, Premawansa G, Wijewickrama A, Peters B, Sette A. HLA-DRB1 Alleles Are Associated With Different Magnitudes of Dengue Virus-Specific CD4+ T-Cell Responses. J Infect Dis 2016; 214:1117-24. [PMID: 27443615 DOI: 10.1093/infdis/jiw309] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/15/2016] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Each year dengue virus (DENV) infects 400 million human but causes symptomatic disease in only a subset of patients, suggesting that host genetic factors may play a role. HLA molecules that restrict T-cell responses are one of the most polymorphic host factors in humans. METHODS Here we map HLA DRB1-restricted DENV-specific epitopes in individuals previously exposed to DENV, to identify the breadth and specificity of CD4(+) T-cell responses. To investigate whether HLA-specific variations in the magnitude of response might predict associations between dengue outcomes and HLA-DRB1 alleles, we assembled samples from hospitalized patients with known severity of disease. RESULTS The capsid protein followed by nonstructural protein 3 (NS3), NS2A, and NS5 were the most targeted proteins. We further noticed a wide variation in magnitude of T-cell responses as a function of the restricting DRB1 allele and found several HLA alleles that showed trends toward a lower risk of hospitalized disease were associated with a higher magnitude of T-cell responses. CONCLUSIONS Comprehensive identification of unique CD4(+) T-cell epitopes across the 4 DENV serotypes allows the testing of T-cell responses by use of a simple, approachable technique and points to important implications for vaccine design.
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Affiliation(s)
- Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California
| | - Michael A Angelo
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California
| | - Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California
| | - Patrick H O'Rourke
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California
| | - Sinu Paul
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California
| | - Aruna D De Silva
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California Genetech Research Institute
| | - Elizabeth Phillips
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Australia
| | - Simon Mallal
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Australia
| | - Sunil Premawansa
- Department of Zoology and Environmental Science, Science Faculty, University of Colombo
| | | | | | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, California
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Weiskopf D, Cerpas C, Angelo MA, Bangs DJ, Sidney J, Paul S, Peters B, Sanches FP, Silvera CGT, Costa PR, Kallas EG, Gresh L, de Silva AD, Balmaseda A, Harris E, Sette A. Human CD8+ T-Cell Responses Against the 4 Dengue Virus Serotypes Are Associated With Distinct Patterns of Protein Targets. J Infect Dis 2015; 212:1743-51. [PMID: 25980035 DOI: 10.1093/infdis/jiv289] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 05/06/2015] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND All 4 dengue virus (DENV) serotypes are now simultaneously circulating worldwide and responsible for up to 400 million human infections each year. Previous studies of CD8(+) T-cell responses in HLA-transgenic mice and human vaccinees demonstrated that the hierarchy of immunodominance among structural versus nonstructural proteins differs as a function of the infecting serotype. This led to the hypothesis that there are intrinsic differences in the serotype-specific reactivity of CD8(+) T-cell responses. METHODS We tested this hypothesis by analyzing serotype-specific CD8(+) T-cell reactivity in naturally infected human donors from Sri Lanka and Nicaragua, using ex vivo interferon γ-specific enzyme-linked immunosorbent spot assays. RESULTS Remarkably similar and clear serotype-specific patterns of immunodominance in both cohorts were identified. Pooling of epitopes that accounted for 90% of the interferon γ response in both cohorts resulted in a global epitope pool. Its reactivity was confirmed in naturally infected donors from Brazil, demonstrating its global applicability. CONCLUSIONS This study provides new insight into differential serotype-specific immunogenicity of DENV proteins. It further provides a potentially valuable tool for future investigations of CD8(+) T-cell responses in the typically small sample volumes available from patients with acute fever and children without requiring prior knowledge of either infecting DENV serotype or HLA type.
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Affiliation(s)
- Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology
| | - Cristhiam Cerpas
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministerio de Salud
| | - Michael A Angelo
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology
| | - Derek J Bangs
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology
| | - Sinu Paul
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology
| | - Françoise P Sanches
- Division of Clinical Immunology and Allergy (LIM-60), School of Medicine, University of São Paulo, Brazil
| | - Cassia G T Silvera
- Division of Clinical Immunology and Allergy (LIM-60), School of Medicine, University of São Paulo, Brazil
| | - Priscilla R Costa
- Division of Clinical Immunology and Allergy (LIM-60), School of Medicine, University of São Paulo, Brazil
| | - Esper G Kallas
- Division of Clinical Immunology and Allergy (LIM-60), School of Medicine, University of São Paulo, Brazil
| | - Lionel Gresh
- Sustainable Sciences Institute, Managua, Nicaragua
| | - Aruna D de Silva
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology Genetech Research Institute, Colombo, Sri Lanka
| | - Angel Balmaseda
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministerio de Salud
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California-Berkeley
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology
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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. J Immunol 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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Weiskopf D, Yauch LE, Angelo MA, John DV, Greenbaum JA, Sidney J, Kolla RV, De Silva AD, de Silva AM, Grey H, Peters B, Shresta S, Sette A. Insights into HLA-restricted T cell responses in a novel mouse model of dengue virus infection point toward new implications for vaccine design. J Immunol 2011; 187:4268-79. [PMID: 21918184 DOI: 10.4049/jimmunol.1101970] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The frequency of dengue virus (DENV) infection has increased dramatically in the last few decades, and the lack of a vaccine has led to significant morbidity and mortality worldwide. To date, a convenient murine system to study human T cell responses to DENV has not been available. Mice transgenic for HLA are widely used to model human immune responses, and it has been shown that mouse-passaged DENV is able to replicate to significant levels in IFN-α/βR(-/-) mice. To cover a wide range of HLA phenotypes, we backcrossed IFN-α/βR(-/-) mice with HLA A*0201, A*0101, A*1101, B*0702, and DRB1*0101-transgenic mice. A DENV proteome-wide screen identified a total of 42 epitopes across all HLA-transgenic IFN-α/βR(-/-) strains tested. In contrast, only eight of these elicited responses in the corresponding IFN-α/βR(+/+) mice. We were able to identify T cell epitopes from 9 out of the 10 DENV proteins. However, the majority of responses were derived from the highly conserved nonstructural proteins NS3 and NS5. The relevance of this model is further demonstrated by the fact that most of the epitopes identified in our murine system are also recognized by PBMC from DENV-exposed human donors, and a dominance of HLA B*0702-restricted responses has been detected in both systems. Our results provide new insights into HLA-restricted T cell responses against DENV, and we describe in this study a novel murine model that allows the investigation of T cell-mediated immune mechanisms relevant to vaccine design.
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Affiliation(s)
- Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
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