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Lobos CA, Chatzileontiadou DSM, Sok B, Almedia C, Halim H, D'Orsogna L, Gras S. Molecular insights into the HLA-B35 molecules' classification associated with HIV control. Immunol Cell Biol 2024; 102:34-45. [PMID: 37811811 PMCID: PMC10952751 DOI: 10.1111/imcb.12698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 10/14/2022] [Revised: 07/04/2023] [Accepted: 09/19/2023] [Indexed: 10/10/2023]
Abstract
Human leukocyte antigen (HLA) class I molecules have been shown to influence the immune response to HIV infection and acquired immunodeficiency syndrome progression. Polymorphisms within the HLA-B35 molecules divide the family into two groups, namely, Px and PY. The Px group is associated with deleterious effects and accelerated disease progression in HIV+ patients, whereas the PY group is not. The classification is based on the preferential binding of a tyrosine at the C-terminal part of the peptide in the PY group, and a nontyrosine residue in the Px group. However, there is a lack of knowledge on the molecular differences between the two groups. Here, we have investigated three HLA-B35 molecules, namely, HLA-B*35:01 (PY), HLA-B*35:03 (Px) and HLA-B*35:05 (unclassified). We selected an HIV-derived peptide, NY9, and demonstrated that it can trigger a polyfunctional CD8+ T-cell response in HLA-B*35:01+ /HIV+ patients. We determined that in the complex with the NY9 peptide, the PY molecule was more stable than the Px molecule. We solved the crystal structures of the three HLA molecules in complex with the NY9 peptide, and structural similarities with HLA-B*35:01 would classify the HLA-B*35:05 within the PY group. Interestingly, we found that HLA-B*35:05 can also bind a small molecule in its cleft, suggesting that small drugs could bind as well.
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Affiliation(s)
- Christian A Lobos
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Molecular BiologyMonash UniversityClaytonVICAustralia
| | - Demetra SM Chatzileontiadou
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Molecular BiologyMonash UniversityClaytonVICAustralia
| | - Bonin Sok
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVICAustralia
| | - Coral‐Ann Almedia
- Department of Clinical Immunology and PathWestFiona Stanley HospitalPerthWAAustralia
- School of MedicineUniversity of Western AustraliaPerthWAAustralia
| | - Hanim Halim
- Department of Biochemistry and Molecular BiologyMonash UniversityClaytonVICAustralia
| | - Lloyd D'Orsogna
- Department of Clinical Immunology and PathWestFiona Stanley HospitalPerthWAAustralia
- School of MedicineUniversity of Western AustraliaPerthWAAustralia
| | - Stephanie Gras
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular ScienceLa Trobe UniversityBundooraVICAustralia
- Department of Biochemistry and Molecular BiologyMonash UniversityClaytonVICAustralia
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2
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Han L, Wu S, Zhang T, Peng W, Zhao M, Yue C, Wen W, Cai W, Li M, Wallny HJ, Avila DW, Mwangi W, Nair V, Ternette N, Guo Y, Zhao Y, Chai Y, Qi J, Liang H, Gao GF, Kaufman J, Liu WJ. A Wider and Deeper Peptide-Binding Groove for the Class I Molecules from B15 Compared with B19 Chickens Correlates with Relative Resistance to Marek's Disease. J Immunol 2023; 210:668-680. [PMID: 36695776 PMCID: PMC7614295 DOI: 10.4049/jimmunol.2200211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 12/19/2022] [Indexed: 01/26/2023]
Abstract
The chicken MHC is known to confer decisive resistance or susceptibility to various economically important pathogens, including the iconic oncogenic herpesvirus that causes Marek's disease (MD). Only one classical class I gene, BF2, is expressed at a high level in chickens, so it was relatively easy to discern a hierarchy from well-expressed thermostable fastidious specialist alleles to promiscuous generalist alleles that are less stable and expressed less on the cell surface. The class I molecule BF2*1901 is better expressed and more thermostable than the closely related BF2*1501, but the peptide motif was not simpler as expected. In this study, we confirm for newly developed chicken lines that the chicken MHC haplotype B15 confers resistance to MD compared with B19. Using gas phase sequencing and immunopeptidomics, we find that BF2*1901 binds a greater variety of amino acids in some anchor positions than does BF2*1501. However, by x-ray crystallography, we find that the peptide-binding groove of BF2*1901 is narrower and shallower. Although the self-peptides that bound to BF2*1901 may appear more various than those of BF2*1501, the structures show that the wider and deeper peptide-binding groove of BF2*1501 allows stronger binding and thus more peptides overall, correlating with the expected hierarchies for expression level, thermostability, and MD resistance. Our study provides a reasonable explanation for greater promiscuity for BF2*1501 compared with BF2*1901, corresponding to the difference in resistance to MD.
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Affiliation(s)
- Lingxia Han
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
- National Poultry Laboratory Animal Resource Center, Harbin 150001, China
- Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, Harbin 150069, China
| | - Shaolian Wu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ting Zhang
- Biosafety Level-3 Laboratory, Life Sciences Institute & Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application, Guangxi Medical University, Nanning, Guangxi 530021, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Weiyu Peng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Min Zhao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Can Yue
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing 100052, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wanxin Wen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Wenbo Cai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Min Li
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | | | - David W. Avila
- The Basel Institute for Immunology, Basel CH4001, Switzerland
| | - William Mwangi
- The Pirbright Institute, Pirbright GU24 0NF, United Kingdom
| | - Venugopal Nair
- The Pirbright Institute, Pirbright GU24 0NF, United Kingdom
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, United Kingdom
| | - Nicola Ternette
- Nuffield Department of Medicine, University of Oxford, Headington OX37BN, United Kingdom
| | - Yaxin Guo
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing 100052, China
| | - Yingze Zhao
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing 100052, China
| | - Yan Chai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hao Liang
- Biosafety Level-3 Laboratory, Life Sciences Institute & Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application, Guangxi Medical University, Nanning, Guangxi 530021, China
| | - George F. Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing 100052, China
| | - Jim Kaufman
- The Basel Institute for Immunology, Basel CH4001, Switzerland
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
- Department of Veterinary Science, University of Cambridge, Cambridge CB3 0ES, United Kingdom
- Institute for Immunology and Infection Research, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - William J. Liu
- Biosafety Level-3 Laboratory, Life Sciences Institute & Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application, Guangxi Medical University, Nanning, Guangxi 530021, China
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
- Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing 100052, China
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Finton KAK, Rupert PB, Friend DJ, Dinca A, Lovelace ES, Buerger M, Rusnac DV, Foote-McNabb U, Chour W, Heath JR, Campbell JS, Pierce RH, Strong RK. Effects of HLA single chain trimer design on peptide presentation and stability. Front Immunol 2023; 14:1170462. [PMID: 37207206 PMCID: PMC10189100 DOI: 10.3389/fimmu.2023.1170462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/21/2023] [Indexed: 05/21/2023] Open
Abstract
MHC class I "single-chain trimer" molecules, coupling MHC heavy chain, β2-microglobulin, and a specific peptide into a single polypeptide chain, are widely used in research. To more fully understand caveats associated with this design that may affect its use for basic and translational studies, we evaluated a set of engineered single-chain trimers with combinations of stabilizing mutations across eight different classical and non-classical human class I alleles with 44 different peptides, including a novel human/murine chimeric design. While, overall, single-chain trimers accurately recapitulate native molecules, care was needed in selecting designs for studying peptides longer or shorter than 9-mers, as single-chain trimer design could affect peptide conformation. In the process, we observed that predictions of peptide binding were often discordant with experiment and that yields and stabilities varied widely with construct design. We also developed novel reagents to improve the crystallizability of these proteins and confirmed novel modes of peptide presentation.
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Affiliation(s)
- Kathryn A. K. Finton
- Division of Basic Science, Fred Hutchinson Cancer Research Center (FHCC), Seattle, WA, United States
| | - Peter B. Rupert
- Division of Basic Science, Fred Hutchinson Cancer Research Center (FHCC), Seattle, WA, United States
| | - Della J. Friend
- Division of Basic Science, Fred Hutchinson Cancer Research Center (FHCC), Seattle, WA, United States
| | - Ana Dinca
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Erica S. Lovelace
- Division of Basic Science, Fred Hutchinson Cancer Research Center (FHCC), Seattle, WA, United States
| | - Matthew Buerger
- Division of Basic Science, Fred Hutchinson Cancer Research Center (FHCC), Seattle, WA, United States
| | - Domnita V. Rusnac
- Division of Basic Science, Fred Hutchinson Cancer Research Center (FHCC), Seattle, WA, United States
| | - Ulysses Foote-McNabb
- Division of Basic Science, Fred Hutchinson Cancer Research Center (FHCC), Seattle, WA, United States
| | - William Chour
- Institute for Systems Biology, Seattle, WA, United States
| | - James R. Heath
- Institute for Systems Biology, Seattle, WA, United States
| | - Jean S. Campbell
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Robert H. Pierce
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Roland K. Strong
- Division of Basic Science, Fred Hutchinson Cancer Research Center (FHCC), Seattle, WA, United States
- *Correspondence: Roland K. Strong,
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4
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Hopkins JR, MacLachlan BJ, Harper S, Sewell AK, Cole DK. Unconventional modes of peptide-HLA-I presentation change the rules of TCR engagement. Discov Immunol 2022; 1:kyac001. [PMID: 38566908 PMCID: PMC10917088 DOI: 10.1093/discim/kyac001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/18/2022] [Accepted: 04/06/2022] [Indexed: 04/04/2024]
Abstract
The intracellular proteome of virtually every nucleated cell in the body is continuously presented at the cell surface via the human leukocyte antigen class I (HLA-I) antigen processing pathway. This pathway classically involves proteasomal degradation of intracellular proteins into short peptides that can be presented by HLA-I molecules for interrogation by T-cell receptors (TCRs) expressed on the surface of CD8+ T cells. During the initiation of a T-cell immune response, the TCR acts as the T cell's primary sensor, using flexible loops to mould around the surface of the pHLA-I molecule to identify foreign or dysregulated antigens. Recent findings demonstrate that pHLA-I molecules can also be highly flexible and dynamic, altering their shape according to minor polymorphisms between different HLA-I alleles, or interactions with different peptides. These flexible presentation modes have important biological consequences that can, for example, explain why some HLA-I alleles offer greater protection against HIV, or why some cancer vaccine approaches have been ineffective. This review explores how these recent findings redefine the rules for peptide presentation by HLA-I molecules and extend our understanding of the molecular mechanisms that govern TCR-mediated antigen discrimination.
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Affiliation(s)
- Jade R Hopkins
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Bruce J MacLachlan
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | | | - Andrew K Sewell
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - David K Cole
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, UK
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5
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Buckley PR, Lee CH, Pereira Pinho M, Ottakandathil Babu R, Woo J, Antanaviciute A, Simmons A, Ogg G, Koohy H. HLA-dependent variation in SARS-CoV-2 CD8 + T cell cross-reactivity with human coronaviruses. Immunology 2022; 166:78-103. [PMID: 35143694 PMCID: PMC9111820 DOI: 10.1111/imm.13451] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/26/2021] [Accepted: 01/17/2022] [Indexed: 11/29/2022] Open
Abstract
The conditions and extent of cross-protective immunity between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and common-cold human coronaviruses (HCoVs) remain open despite several reports of pre-existing T cell immunity to SARS-CoV-2 in individuals without prior exposure. Using a pool of functionally evaluated SARS-CoV-2 peptides, we report a map of 126 immunogenic peptides with high similarity to 285 MHC-presented peptides from at least one HCoV. Employing this map of SARS-CoV-2-non-homologous and homologous immunogenic peptides, we observe several immunogenic peptides with high similarity to human proteins, some of which have been reported to have elevated expression in severe COVID-19 patients. After combining our map with SARS-CoV-2-specific TCR repertoire data from COVID-19 patients and healthy controls, we show that public repertoires for the majority of convalescent patients are dominated by TCRs cognate to non-homologous SARS-CoV-2 peptides. We find that for a subset of patients, >50% of their public SARS-CoV-2-specific repertoires consist of TCRs cognate to homologous SARS-CoV-2-HCoV peptides. Further analysis suggests that this skewed distribution of TCRs cognate to homologous or non-homologous peptides in COVID-19 patients is likely to be HLA-dependent. Finally, we provide 10 SARS-CoV-2 peptides with known cognate TCRs that are conserved across multiple coronaviruses and are predicted to be recognized by a high proportion of the global population. These findings may have important implications for COVID-19 heterogeneity, vaccine-induced immune responses, and robustness of immunity to SARS-CoV-2 and its variants.
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Affiliation(s)
- Paul R. Buckley
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
- MRC WIMM Centre for Computational BiologyMedical Research Council (MRC) Weatherall Institute of Molecular MedicineJohn Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Chloe H. Lee
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
- MRC WIMM Centre for Computational BiologyMedical Research Council (MRC) Weatherall Institute of Molecular MedicineJohn Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Mariana Pereira Pinho
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Rosana Ottakandathil Babu
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
- MRC WIMM Centre for Computational BiologyMedical Research Council (MRC) Weatherall Institute of Molecular MedicineJohn Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Jeongmin Woo
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
- MRC WIMM Centre for Computational BiologyMedical Research Council (MRC) Weatherall Institute of Molecular MedicineJohn Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Agne Antanaviciute
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
- MRC WIMM Centre for Computational BiologyMedical Research Council (MRC) Weatherall Institute of Molecular MedicineJohn Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Alison Simmons
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Graham Ogg
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Hashem Koohy
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology UnitMRC Weatherall Institute of Molecular Medicine (WIMM)John Radcliffe HospitalUniversity of OxfordOxfordUK
- MRC WIMM Centre for Computational BiologyMedical Research Council (MRC) Weatherall Institute of Molecular MedicineJohn Radcliffe HospitalUniversity of OxfordOxfordUK
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6
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Buckley PR, Lee CH, Ma R, Woodhouse I, Woo J, Tsvetkov VO, Shcherbinin DS, Antanaviciute A, Shughay M, Rei M, Simmons A, Koohy H. Evaluating performance of existing computational models in predicting CD8+ T cell pathogenic epitopes and cancer neoantigens. Brief Bioinform 2022; 23:6573960. [PMID: 35471658 PMCID: PMC9116217 DOI: 10.1093/bib/bbac141] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [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: 01/20/2022] [Revised: 03/09/2022] [Accepted: 03/26/2022] [Indexed: 12/16/2022] Open
Abstract
T cell recognition of a cognate peptide-major histocompatibility complex (pMHC) presented on the surface of infected or malignant cells is of the utmost importance for mediating robust and long-term immune responses. Accurate predictions of cognate pMHC targets for T cell receptors would greatly facilitate identification of vaccine targets for both pathogenic diseases and personalized cancer immunotherapies. Predicting immunogenic peptides therefore has been at the center of intensive research for the past decades but has proven challenging. Although numerous models have been proposed, performance of these models has not been systematically evaluated and their success rate in predicting epitopes in the context of human pathology has not been measured and compared. In this study, we evaluated the performance of several publicly available models, in identifying immunogenic CD8+ T cell targets in the context of pathogens and cancers. We found that for predicting immunogenic peptides from an emerging virus such as severe acute respiratory syndrome coronavirus 2, none of the models perform substantially better than random or offer considerable improvement beyond HLA ligand prediction. We also observed suboptimal performance for predicting cancer neoantigens. Through investigation of potential factors associated with ill performance of models, we highlight several data- and model-associated issues. In particular, we observed that cross-HLA variation in the distribution of immunogenic and non-immunogenic peptides in the training data of the models seems to substantially confound the predictions. We additionally compared key parameters associated with immunogenicity between pathogenic peptides and cancer neoantigens and observed evidence for differences in the thresholds of binding affinity and stability, which suggested the need to modulate different features in identifying immunogenic pathogen versus cancer peptides. Overall, we demonstrate that accurate and reliable predictions of immunogenic CD8+ T cell targets remain unsolved; thus, we hope our work will guide users and model developers regarding potential pitfalls and unsettled questions in existing immunogenicity predictors.
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Affiliation(s)
- Paul R Buckley
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom,MRC WIMM Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Chloe H Lee
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom,MRC WIMM Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Ruichong Ma
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom,Department of Neurosurgery, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom,Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Isaac Woodhouse
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jeongmin Woo
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom,MRC WIMM Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | | | - Dmitrii S Shcherbinin
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, 117997, Russia
| | - Agne Antanaviciute
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom,MRC WIMM Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Mikhail Shughay
- Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, 117997, Russia
| | - Margarida Rei
- The Ludwig Institute for Cancer Research, Old Road Campus Research Building, University of Oxford, Oxford, United Kingdom
| | - Alison Simmons
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Hashem Koohy
- MRC Human Immunology Unit, Medical Research Council (MRC) Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom,MRC WIMM Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom,Alan Turning Fellow, University of Oxford, Oxford, United Kingdom,Corresponding author: Hashem Koohy, Associate Professor of Systems immunology, Alan Turing Fellow, Group Head, MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK. Tel: 44(0)1865222430; E-mail:
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7
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Nersisyan SA, Shkurnikov MY, Zhiyanov AP, Novosad VO, Tonevitsky AG. Differences in Presentation of SARS-CoV-2 Omicron Strain Variant BA.1-BA.5 Peptides by HLA Molecules. DOKL BIOCHEM BIOPHYS 2022; 507:298-301. [PMID: 36786990 PMCID: PMC9926403 DOI: 10.1134/s1607672922060084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 02/15/2023]
Abstract
In this work, we analyzed the binding affinities of mutated peptides of Omicron strain variants BA.1-BA.5 and the worldwide prevalent HLA alleles. Bioinformatics analysis was conducted with the use of T-CoV web portal. We showed that, for all five viral variants, mutations cause a significant reduction in the number of tightly binding peptides for HLA-B*07:02 and HLA-C*01:02 molecules. At the same time, there were novel potential mutant epitopes (binding affinity less than 50 nM) in case of HLA-A*32:01 allele. Interestingly, mutations caused multidirectional effect on the binding affinities of the viral peptides and HLA-DRB1*03:01. Specifically, Spike protein mutations in the BA.1 variant caused more than 100-fold decrease in PINLVRDLPQGFSAL binding affinity, 10-fold decrease in affinity in the case of BA.2, BA.4, and BA.5 variants, and 30% increase in affinity for the BA.3 variant.
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Affiliation(s)
- S. A. Nersisyan
- Laboratory of Microfluidic Technologies for Biomedicine, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia ,Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow, Russia
| | - M. Yu. Shkurnikov
- Laboratory of Microfluidic Technologies for Biomedicine, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia ,Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow, Russia
| | - A. P. Zhiyanov
- Laboratory of Microfluidic Technologies for Biomedicine, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia ,Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow, Russia
| | - V. O. Novosad
- Laboratory of Microfluidic Technologies for Biomedicine, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia ,Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow, Russia
| | - A. G. Tonevitsky
- Laboratory of Microfluidic Technologies for Biomedicine, Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia ,Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Moscow, Russia
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8
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Shkurnikov M, Nersisyan S, Jankevic T, Galatenko A, Gordeev I, Vechorko V, Tonevitsky A. Association of HLA Class I Genotypes With Severity of Coronavirus Disease-19. Front Immunol 2021; 12:641900. [PMID: 33732261 PMCID: PMC7959787 DOI: 10.3389/fimmu.2021.641900] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/02/2021] [Indexed: 01/11/2023] Open
Abstract
Human leukocyte antigen (HLA) class I molecules play a crucial role in the development of a specific immune response to viral infections by presenting viral peptides at the cell surface where they will be further recognized by T cells. In the present manuscript, we explored whether HLA class I genotypes can be associated with the critical course of Coronavirus Disease-19 by searching possible connections between genotypes of deceased patients and their age at death. HLA-A, HLA-B, and HLA-C genotypes of n = 111 deceased patients with COVID-19 (Moscow, Russia) and n = 428 volunteers were identified with next-generation sequencing. Deceased patients were split into two groups according to age at the time of death: n = 26 adult patients aged below 60 and n = 85 elderly patients over 60. With the use of HLA class I genotypes, we developed a risk score (RS) which was associated with the ability to present severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) peptides by the HLA class I molecule set of an individual. The resulting RS was significantly higher in the group of deceased adults compared to elderly adults [p = 0.00348, area under the receiver operating characteristic curve (AUC ROC = 0.68)]. In particular, presence of HLA-A*01:01 allele was associated with high risk, while HLA-A*02:01 and HLA-A*03:01 mainly contributed to low risk. The analysis of patients with homozygosity strongly highlighted these results: homozygosity by HLA-A*01:01 accompanied early deaths, while only one HLA-A*02:01 homozygote died before 60 years of age. Application of the constructed RS model to an independent Spanish patients cohort (n = 45) revealed that the score was also associated with the severity of the disease. The obtained results suggest the important role of HLA class I peptide presentation in the development of a specific immune response to COVID-19.
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Affiliation(s)
- Maxim Shkurnikov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Tatjana Jankevic
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alexei Galatenko
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia
| | - Ivan Gordeev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
- O.M. Filatov City Clinical Hospital, Moscow, Russia
| | | | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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Attia JVD, Dessens CE, van de Water R, Houvast RD, Kuppen PJK, Krijgsman D. The Molecular and Functional Characteristics of HLA-G and the Interaction with Its Receptors: Where to Intervene for Cancer Immunotherapy? Int J Mol Sci 2020; 21:ijms21228678. [PMID: 33213057 PMCID: PMC7698525 DOI: 10.3390/ijms21228678] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/06/2020] [Accepted: 11/13/2020] [Indexed: 12/12/2022] Open
Abstract
Human leukocyte antigen G (HLA-G) mediates maternal-fetal immune tolerance. It is also considered an immune checkpoint in cancer since it may mediate immune evasion and thus promote tumor growth. HLA-G is, therefore, a potential target for immunotherapy. However, existing monoclonal antibodies directed against HLA-G lack sufficient specificity and are not suitable for immune checkpoint inhibition in a clinical setting. For this reason, it is essential that alternative approaches are explored to block the interaction between HLA-G and its receptors. In this review, we discuss the structure and peptide presentation of HLA-G, and its interaction with the receptors Ig-like transcript (ILT) 2, ILT4, and Killer cell immunoglobulin-like receptor 2DL4 (KIR2DL4). Based on our findings, we propose three alternative strategies to block the interaction between HLA-G and its receptors in cancer immunotherapy: (1) prevention of HLA-G dimerization, (2) targeting the peptide-binding groove of HLA-G, and (3) targeting the HLA-G receptors. These strategies should be an important focus of future studies that aim to develop immune checkpoint inhibitors to block the interaction between HLA-G and its receptors for the treatment of cancer.
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Yuan H, Ma L, Zhang L, Li X, Xia C. Crystal structure of the giant panda MHC class I complex: First insights into the viral peptide presentation profile in the bear family. Protein Sci 2020; 29:2468-2481. [PMID: 33078460 DOI: 10.1002/pro.3980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 09/15/2020] [Revised: 10/13/2020] [Accepted: 10/16/2020] [Indexed: 01/03/2023]
Abstract
The viral cytotoxic T lymphocyte (CTL) epitope peptides presented by classical MHC-I molecules require the assembly of a peptide-MHC-I-β2m (pMHC-I) trimolecular complex for T cell receptor (TCR) recognition, which is the critical activation link for triggering antiviral T cell immunity. Research on T cell immunology in the Ursidae family, especially structural immunology, is still lacking. In this study, the structure of the key trimolecular complex pMHC-I, which binds a peptide from canine distemper virus, was solved for the first time using giant panda as a representative species of Ursidae. The structural characteristics of the giant panda pMHC-I complex (pAime-128), including the unique pockets in the peptide-binding groove (PBG), were analyzed in detail. Comparing the pAime-128 to others in the bear family and extending the comparison to other mammals revealed distinct features. The interaction between MHC-I and β2m, the features of pAime-128 involved in TCR docking and cluster of differentiation 8 (CD8) binding, the anchor sites in the PBG, and the CTL epitopes of potential viruses that infect pandas were clarified. Unique features of pMHC-I viral antigen presentation in the panda were revealed by solving the three-dimensional (3D) structure of pAime-128. The distinct characteristics of pAime-128 indicate an unusual event that emerged during the evolution of the MHC system in the bear family. These results provide a new platform for research on panda CTL immunity and the design of vaccines for application in the bear family.
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Affiliation(s)
- Hongyu Yuan
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Beijing Institute of Biotechnology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Lizhen Ma
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lijie Zhang
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiaoying Li
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China.,College of Veterinary Medicine, Henan Agricultural University, No. 15 Longzihu University Area, Zhengzhou New District, Zhengzhou, Henan, China
| | - Chun Xia
- Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China
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11
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Weinstein-Marom H, Hendel L, Laron EA, Sharabi-Nov A, Margalit A, Gross G. MHC-I presentation of peptides derived from intact protein products of the pioneer round of translation. FASEB J 2019; 33:11458-11468. [PMID: 31343935 DOI: 10.1096/fj.201802717rrr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Among the earliest protein products of most cellular genes are those synthesized during the pioneer round of translation (PRT), a key step in nonsense-mediated mRNA decay (NMD) that allows scanning of new transcripts for the presence of a premature termination codon (PTC). It has been demonstrated that at least some PRT degradation products can be targeted to major histocompatibility (MHC)-I presentation. To gain new insight into this putative PRT-to-MHC-I route, we have assembled 2 pairs of reporter genes so that the 2 genes in each pair encode an identical fusion protein between a model antigenic peptide and enhanced green fluorescent protein (EGFP), one of which harbors a PTC. We expressed these genes in different mouse and human cell lines and confirmed enhanced NMD activity for the PTC(+) gene in each pair by monitoring the effect of cycloheximide on the level of the respective mRNA. We then exploited several strategies for establishing the ratio between level of peptide presentation and total amount of protein product. We consistently observed significantly higher ratios for the PTC(+) mRNAs compared with the PTC(-) ones, pointing to correlation between the turnover of otherwise identical proteins and the fate of their template mRNA. Using confocal microscopy, we showed a clear link between NMD, the presence of misfolded EGFP polypeptides, and enhanced MHC-I peptide presentation. Altogether, these findings imply that identical full-length gene products differing only in 3' noncoding sequences can be differentially degraded and targeted to the MHC-I presentation pathway, suggesting a more general role for the PRT in establishing the MHC-I peptidome.-Weinstein-Marom, H., Hendel, L., Laron, E. A., Sharabi-Nov, A., Margalit, A., Gross, G. MHC-I presentation of peptides derived from intact protein products of the pioneer round of translation.
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Affiliation(s)
- Hadas Weinstein-Marom
- Laboratory of Immunology, MIGAL-Galilee Research Institute, Kiryat Shmona, Israel.,Tel-Hai College, Upper Galilee, Israel.,Inter-Faculty Biotechnology Program, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Liron Hendel
- Laboratory of Immunology, MIGAL-Galilee Research Institute, Kiryat Shmona, Israel.,Tel-Hai College, Upper Galilee, Israel
| | - Efrat Avigad Laron
- Laboratory of Immunology, MIGAL-Galilee Research Institute, Kiryat Shmona, Israel.,Tel-Hai College, Upper Galilee, Israel
| | | | - Alon Margalit
- Laboratory of Immunology, MIGAL-Galilee Research Institute, Kiryat Shmona, Israel.,Tel-Hai College, Upper Galilee, Israel
| | - Gideon Gross
- Laboratory of Immunology, MIGAL-Galilee Research Institute, Kiryat Shmona, Israel.,Tel-Hai College, Upper Galilee, Israel
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12
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Zeng H, Gifford DK. Quantification of Uncertainty in Peptide-MHC Binding Prediction Improves High-Affinity Peptide Selection for Therapeutic Design. Cell Syst 2019; 9:159-166.e3. [PMID: 31176619 DOI: 10.1016/j.cels.2019.05.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [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: 12/19/2018] [Revised: 03/25/2019] [Accepted: 05/07/2019] [Indexed: 12/30/2022]
Abstract
The computational identification of peptides that can bind the major histocompatibility complex (MHC) with high affinity is an essential step in developing personal immunotherapies and vaccines. We introduce PUFFIN, a deep residual network-based computational approach that quantifies uncertainty in peptide-MHC affinity prediction that arises from observational noise and the lack of relevant training examples. With PUFFIN's uncertainty metrics, we define binding likelihood, the probability a peptide binds to a given MHC allele at a specified affinity threshold. Compared to affinity point estimates, we find that binding likelihood correlates better with the observed affinity and reduces false positives in high-affinity peptide design. When applied to examine an existing peptide vaccine, PUFFIN identifies an alternative vaccine formulation with higher binding likelihood. PUFFIN is freely available for download at http://github.com/gifford-lab/PUFFIN.
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Affiliation(s)
- Haoyang Zeng
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David K Gifford
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Wang Y, Sosinowski T, Novikov A, Crawford F, Neau DB, Yang J, Kwok WW, Marrack P, Kappler JW, Dai S. C-terminal modification of the insulin B:11-23 peptide creates superagonists in mouse and human type 1 diabetes. Proc Natl Acad Sci U S A 2018; 115:162-7. [PMID: 29255035 DOI: 10.1073/pnas.1716527115] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Insulin is a target of CD4 T cells in type 1 diabetes in mice and humans. Why the major epitope in the insulin B chain is presented poorly to the diabetogenic CD4 T cells by the disease-associated major histocompatibility class II (MHCII) alleles has been highly debated. Here we present high-resolution mouse and human MHCII structures and T-cell functional data to show that C-terminal modifications of this epitope are required for binding and presentation in the appropriate position in the MHCII binding groove. These results suggest that pancreas-specific posttranslational modifications of this peptide may play a role in the induction of diabetes and explain how the pathogenic T cells escape deletion in the thymus. A polymorphism at β57 in some major histocompatibility complex class II (MHCII) alleles of rodents and humans is associated with a high risk for developing type 1 diabetes (T1D). However, a highly diabetogenic insulin B chain epitope within the B:9–23 peptide is presented poorly by these alleles to a variety of mouse and human CD4 T cells isolated from either nonobese diabetic (NOD) mice or humans with T1D. We have shown for both species that mutations at the C-terminal end of this epitope dramatically improve presentation to these T cells. Here we present the crystal structures of these mutated peptides bound to mouse IAg7 and human HLA-DQ8 that show how the mutations function to improve T-cell activation. In both peptide binding grooves, the mutation of B:22R to E in the peptide changes a highly unfavorable side chain for the p9 pocket to an optimal one that is dependent on the β57 polymorphism, accounting for why these peptides bind much better to these MHCIIs. Furthermore, a second mutation of the adjacent B:21 (E to G) removes a side chain from the surface of the complex that is highly unfavorable for a subset of NOD mouse CD4 cells, thereby greatly enhancing their response to the complex. These results point out the similarities between the mouse and human responses to this B chain epitope in T1D and suggest there may be common posttranslational modifications at the C terminus of the peptide in vivo to create the pathogenic epitopes in both species.
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Méchin MC, Der Vartanian M, Martin C. The major subunit ClpG of Escherichia coli CS31A fibrillae as an expression vector for different combinations of two TGEV coronavirus epitopes. Gene 1996; 179:211-8. [PMID: 8972902 PMCID: PMC7131745 DOI: 10.1016/s0378-1119(96)00348-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Previously, two B-cell epitopes from the entero-pathogenic transmissible gastroenteritis virus (TGEV), namely the C epitope (TGEV-C) amino acids (aa) 363-371 and the A epitope (TGEV-A) aa 522-531 of the spike S protein (TGEV-S), have been separately expressed on the CS31A fibrillae at the surface of Escherichia coli following insertion into a same region of ClpG. However, the resulting chimeras induced a marginal TGEV-neutralizing antibody (Ab) response in mice. Here, with the view to improving this response, we introduced TGEV-C alone or in different tandem association with TGEV-A (A::C or C::A) in twelve putatively exposed regions of ClpG. Among the 28 resulting engineered proteins only 15, carrying up to 51 extra aa, had not essentially disturbed the correct CS31A fibrillae formation process. Six partially permissive sites accepting only TGEV-C and three highly permissive sites tolerating A::C or C::A tandem peptide, were identified throughout ClpG. Intact bacteria or extracted CS31A hybrid fibrillae expressing TGEV epitopes at any of the permissive sites, were recognized by Ab directed against the foreign parent protein, providing a direct argument for exposure of the corresponding CIpG region at the cell surface and for antigenicity of the epitopes in the polymeric CS31A fibrillae context. The potential of CS31A fibrillae as carriers of the TGEV peptides indicates that there may be three positions (N terminus, aa 202-204 and 202-218) in ClpG which may turn out to be important fusion sites and therefore be relevant for the eventual design of TGEV vaccines. Unexpectedly, TGEV-A, whatever its position in ClpG, mediated the partial proteolytic degradation of the hybrid proteins, suggesting that it functions as a substrate for a cellular protease, and thereby that its suitability as a vaccine antigen candidate is doubtful.
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Affiliation(s)
- M C Méchin
- Laboratoire de Microbiologie, Institut National de la Recherche Agronomique, Centre de Recherches de Clermont-Ferrand-Theix, Saint-Genès-Champanelle, France
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