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Corcoran MM, Karlsson Hedestam GB. Adaptive immune receptor germline gene variation. Curr Opin Immunol 2024; 87:102429. [PMID: 38805851 DOI: 10.1016/j.coi.2024.102429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/30/2024] [Accepted: 05/09/2024] [Indexed: 05/30/2024]
Abstract
Recognition of antigens by T cell receptors (TCRs) and B cell receptors (BCRs) is a key step in lymphocyte activation. T and B cells mediate adaptive immune responses, which protect us against infections and provide immunological memory, and also, in some instances, drive pathogenic responses in autoimmune diseases. TCRs and BCRs are encoded within loci that are known to be genetically diverse. However, the extent and functional impact of this variation, both in humans and model animals used in immunological research, remain largely unknown. Experimental and genetic evidence has demonstrated that the complementarity determining regions 1 and 2 (HCDR1 and HCDR2), encoded by the variable (V) region of TCRs and BCRs, also often make critical contacts with the targeted antigen. Thus, knowledge about allelic variation in the genes encoding TCRs and BCRs is critically important for understanding adaptive immune responses in outbred populations and to define responder and non-responder phenotypes.
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Affiliation(s)
- Martin M Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
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2
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Bednarska K, Chowdhury R, Tobin JWD, Swain F, Keane C, Boyle S, Khanna R, Gandhi MK. Epstein-Barr virus-associated lymphomas decoded. Br J Haematol 2024; 204:415-433. [PMID: 38155519 DOI: 10.1111/bjh.19255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/15/2023] [Accepted: 11/29/2023] [Indexed: 12/30/2023]
Abstract
Epstein-Barr virus (EBV)-associated lymphomas cover a range of histological B- and T-cell non-Hodgkin and Hodgkin lymphoma subtypes. The role of EBV on B-cell malignant pathogenesis and its impact on the tumour microenvironment are intriguing but incompletely understood. Both the International Consensus Classification (ICC) and 5th Edition of the World Health Organization (WHO-HAEM5) proposals give prominence to the distinct clinical, prognostic, genetic and tumour microenvironmental features of EBV in lymphoproliferative disorders. There have been major advances in our biological understanding, in how to harness features of EBV and its host immune response for targeted therapy, and in using EBV as a method to monitor disease response. In this article, we showcase the latest developments and how they may be integrated to stimulate new and innovative approaches for further lines of investigation and therapy.
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Affiliation(s)
- Karolina Bednarska
- Mater Research Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Rakin Chowdhury
- Frazer Institute, University of Queensland, Brisbane, Queensland, Australia
- Department of Haematology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Joshua W D Tobin
- Mater Research Institute, University of Queensland, Brisbane, Queensland, Australia
- Department of Haematology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Fiona Swain
- Frazer Institute, University of Queensland, Brisbane, Queensland, Australia
- Department of Haematology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Colm Keane
- Frazer Institute, University of Queensland, Brisbane, Queensland, Australia
- Department of Haematology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Stephen Boyle
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Rajiv Khanna
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Maher K Gandhi
- Mater Research Institute, University of Queensland, Brisbane, Queensland, Australia
- Department of Haematology, Princess Alexandra Hospital, Brisbane, Queensland, Australia
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3
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Stephen B, Hajjar J, Sarda S, Duose DY, Conroy JM, Morrison C, Alshawa A, Xu M, Zarifa A, Patel SP, Yuan Y, Kwiatkowski E, Wang L, Rodon Ahnert J, Fu S, Meric-Bernstam F, Lowman GM, Looney T, Naing A. T-cell receptor beta variable gene polymorphism predicts immune-related adverse events during checkpoint blockade immunotherapy. J Immunother Cancer 2023; 11:e007236. [PMID: 37604642 PMCID: PMC10445351 DOI: 10.1136/jitc-2023-007236] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND Immune checkpoint inhibitors have revolutionized cancer treatment. However, they are associated with a unique spectrum of side effects, called immune-related adverse events (irAEs), which can cause significant morbidity and quickly progress to severe or life-threatening events if not treated promptly. Identifying predictive biomarkers for irAEs before immunotherapy initiation is therefore a critical area of research. Polymorphisms within the T-cell receptor beta (TCRB) variable (TRBV) gene have been implicated in autoimmune disease and may be mechanistically linked to irAEs. However, the repetitive nature of the TCRB locus and incomplete genome assembly has hampered the evaluation of TRBV polymorphisms in the past. PATIENTS AND METHODS We used a novel method for long-amplicon next generation sequencing of rearranged TCRB chains from peripheral blood total RNA to evaluate the link between TRBV polymorphisms and irAEs in patients treated with immunotherapy for cancer. We employed multiplex PCR to create amplicons spanning the three beta chain complementarity-determining regions (CDR) regions to enable detection of polymorphism within the germline-encoded framework and CDR1 and CDR2 regions in addition to CDR3 profiling. Resultant amplicons were sequenced via the Ion Torrent and TRBV allele profiles constructed for each individual was correlated with irAE annotations to identify haplotypes associated with severe irAEs (≥ grade 3). RESULTS Our study included 81 patients who had irAEs when treated with immunotherapy for cancer. By using principal component analysis of the 81 TRBV allele profiles followed by k-means clustering, we identified six major TRBV haplotypes. Strikingly, we found that one-third of this cohort possessed a TRBV allele haplotype that appeared to be protective against severe irAEs. CONCLUSION The data suggest that long-amplicon TCRB repertoire sequencing can potentially identify TRBV haplotype groups that correlate with the risk of severe irAEs. Germline-encoded TRBV polymorphisms may serve as a predictive biomarker of severe irAEs.
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Affiliation(s)
- Bettzy Stephen
- Investigational Cancer Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Joud Hajjar
- Adult Allergy and Immunology, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas, USA
| | | | - Dzifa Yawa Duose
- Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Carl Morrison
- Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Anas Alshawa
- Investigational Cancer Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mingxuan Xu
- Investigational Cancer Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Abdulrazzak Zarifa
- Investigational Cancer Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sapna P Patel
- Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ying Yuan
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Evan Kwiatkowski
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Linghua Wang
- Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jordi Rodon Ahnert
- Investigational Cancer Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Siqing Fu
- Investigational Cancer Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Funda Meric-Bernstam
- Investigational Cancer Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Timothy Looney
- Thermo Fisher Scientific, Clinical Next-Generation Sequencing, Austin, Texas, USA
| | - Aung Naing
- Investigational Cancer Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Pettmann J, Awada L, Różycki B, Huhn A, Faour S, Kutuzov M, Limozin L, Weikl TR, van der Merwe PA, Robert P, Dushek O. Mechanical forces impair antigen discrimination by reducing differences in T-cell receptor/peptide-MHC off-rates. EMBO J 2023; 42:e111841. [PMID: 36484367 PMCID: PMC10068313 DOI: 10.15252/embj.2022111841] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 11/08/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022] Open
Abstract
T cells use their T-cell receptors (TCRs) to discriminate between lower-affinity self and higher-affinity foreign peptide major-histocompatibility-complexes (pMHCs) based on the TCR/pMHC off-rate. It is now appreciated that T cells generate mechanical forces during this process but how force impacts the TCR/pMHC off-rate remains debated. Here, we measured the effect of mechanical force on the off-rate of multiple TCR/pMHC interactions. Unexpectedly, we found that lower-affinity TCR/pMHCs with faster solution off-rates were more resistant to mechanical force (weak slip or catch bonds) than higher-affinity interactions (strong slip bonds). This was confirmed by molecular dynamics simulations. Consistent with these findings, we show that the best-characterized catch bond, involving the OT-I TCR, has a low affinity and an exceptionally fast solution off-rate. Our findings imply that reducing forces on the TCR/pMHC interaction improves antigen discrimination, and we suggest a role for the adhesion receptors CD2 and LFA-1 in force-shielding the TCR/pMHC interaction.
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Affiliation(s)
| | - Lama Awada
- Laboratoire Adhesion et InflammationAix Marseille University UM 61, INSERM UMRS 1067, CNRS UMR 7333MarseilleFrance
| | | | - Anna Huhn
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
| | - Sara Faour
- Laboratoire Adhesion et InflammationAix Marseille University UM 61, INSERM UMRS 1067, CNRS UMR 7333MarseilleFrance
| | - Mikhail Kutuzov
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
| | - Laurent Limozin
- Laboratoire Adhesion et InflammationAix Marseille University UM 61, INSERM UMRS 1067, CNRS UMR 7333MarseilleFrance
| | - Thomas R Weikl
- Max Planck Institute of Colloids and InterfacesPotsdamGermany
| | | | - Philippe Robert
- Laboratoire Adhesion et InflammationAix Marseille University UM 61, INSERM UMRS 1067, CNRS UMR 7333MarseilleFrance
- Assistance Publique‐Hôpitaux de MarseilleMarseilleFrance
| | - Omer Dushek
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
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Corcoran M, Chernyshev M, Mandolesi M, Narang S, Kaduk M, Ye K, Sundling C, Färnert A, Kreslavsky T, Bernhardsson C, Larena M, Jakobsson M, Karlsson Hedestam GB. Archaic humans have contributed to large-scale variation in modern human T cell receptor genes. Immunity 2023; 56:635-652.e6. [PMID: 36796364 DOI: 10.1016/j.immuni.2023.01.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/21/2022] [Accepted: 01/23/2023] [Indexed: 02/18/2023]
Abstract
Human T cell receptors (TCRs) are critical for mediating immune responses to pathogens and tumors and regulating self-antigen recognition. Yet, variations in the genes encoding TCRs remain insufficiently defined. Detailed analysis of expressed TCR alpha, beta, gamma, and delta genes in 45 donors from four human populations-African, East Asian, South Asian, and European-revealed 175 additional TCR variable and junctional alleles. Most of these contained coding changes and were present at widely differing frequencies in the populations, a finding confirmed using DNA samples from the 1000 Genomes Project. Importantly, we identified three Neanderthal-derived, introgressed TCR regions including a highly divergent TRGV4 variant, which mediated altered butyrophilin-like molecule 3 (BTNL3) ligand reactivity and was frequent in all modern Eurasian population groups. Our results demonstrate remarkable variation in TCR genes in both individuals and populations, providing a strong incentive for including allelic variation in studies of TCR function in human biology.
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Affiliation(s)
- Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden.
| | - Mark Chernyshev
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Marco Mandolesi
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Sanjana Narang
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Mateusz Kaduk
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Kewei Ye
- Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Christopher Sundling
- Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Infectious Diseases, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Anna Färnert
- Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Infectious Diseases, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Taras Kreslavsky
- Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Carolina Bernhardsson
- Department of Organismal Biology, Human Evolution, Norbyvägen 18C, 752 63 Uppsala, Sweden
| | - Maximilian Larena
- Department of Organismal Biology, Human Evolution, Norbyvägen 18C, 752 63 Uppsala, Sweden
| | - Mattias Jakobsson
- Department of Organismal Biology, Human Evolution, Norbyvägen 18C, 752 63 Uppsala, Sweden
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Narang S, Kaduk M, Chernyshev M, Karlsson Hedestam GB, Corcoran MM. Adaptive immune receptor genotyping using the corecount program. Front Immunol 2023; 14:1125884. [PMID: 37114042 PMCID: PMC10126697 DOI: 10.3389/fimmu.2023.1125884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/27/2023] [Indexed: 04/29/2023] Open
Abstract
We present a new Rep-Seq analysis tool called corecount, for analyzing genotypic variation in immunoglobulin (IG) and T cell receptor (TCR) genes. corecount is highly efficient at identifying V alleles, including those that are infrequently used in expressed repertoires and those that contain 3' end variation that are otherwise refractory to reliable identification during germline inference from expressed libraries. Furthermore, corecount facilitates accurate D and J gene genotyping. The output is highly reproducible and facilitates the comparison of genotypes from multiple individuals, such as those from clinical cohorts. Here, we applied corecount to the genotypic analysis of IgM libraries from 16 individuals. To demonstrate the accuracy of corecount, we Sanger sequenced all the heavy chain IG alleles (65 IGHV, 27 IGHD and 7 IGHJ) from one individual from whom we also produced two independent IgM Rep-seq datasets. Genomic analysis revealed that 5 known IGHV and 2 IGHJ sequences are truncated in current reference databases. This dataset of genomically validated alleles and IgM libraries from the same individual provides a useful resource for benchmarking other bioinformatic programs that involve V, D and J assignments and germline inference, and may facilitate the development of AIRR-Seq analysis tools that can take benefit from the availability of more comprehensive reference databases.
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Rodriguez OL, Silver CA, Shields K, Smith ML, Watson CT. Targeted long-read sequencing facilitates phased diploid assembly and genotyping of the human T cell receptor alpha, delta, and beta loci. CELL GENOMICS 2022; 2:100228. [PMID: 36778049 PMCID: PMC9903726 DOI: 10.1016/j.xgen.2022.100228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/25/2022] [Accepted: 11/05/2022] [Indexed: 12/02/2022]
Abstract
T cell receptors (TCRs) recognize peptide fragments presented by the major histocompatibility complex (MHC) and are critical to T cell-mediated immunity. Recent data have indicated that genetic diversity within TCR-encoding gene regions is underexplored, limiting understanding of the impact of TCR loci polymorphisms on TCR function in disease, even though TCR repertoire signatures (1) are heritable and (2) associate with disease phenotypes. To address this, we developed a targeted long-read sequencing approach to generate highly accurate haplotype resolved assemblies of the TCR beta (TRB) and alpha/delta (TRA/D) loci, facilitating the genotyping of all variant types, including structural variants. We validate our approach using two mother-father-child trios and 5 unrelated donors representing multiple populations. This resulted in improved genotyping accuracy and the discovery of 84 undocumented V, D, J, and C alleles, demonstrating the utility of this framework for improving our understanding of TCR diversity and function in disease.
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Affiliation(s)
- Oscar L. Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Catherine A. Silver
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Kaitlyn Shields
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Melissa L. Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Corey T. Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA,Corresponding author
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Fang Y, Liu X, Liu H. Attention-aware contrastive learning for predicting T cell receptor-antigen binding specificity. Brief Bioinform 2022; 23:6696141. [PMID: 36094087 DOI: 10.1093/bib/bbac378] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/06/2022] [Accepted: 08/09/2022] [Indexed: 12/14/2022] Open
Abstract
MOTIVATION It has been proven that only a small fraction of the neoantigens presented by major histocompatibility complex (MHC) class I molecules on the cell surface can elicit T cells. This restriction can be attributed to the binding specificity of T cell receptor (TCR) and peptide-MHC complex (pMHC). Computational prediction of T cells binding to neoantigens is a challenging and unresolved task. RESULTS In this paper, we proposed an attention-aware contrastive learning model, ATMTCR, to infer the TCR-pMHC binding specificity. For each TCR sequence, we used a transformer encoder to transform it to latent representation, and then masked a percentage of amino acids guided by attention weights to generate its contrastive view. Compared to fully-supervised baseline model, we verified that contrastive learning-based pretraining on large-scale TCR sequences significantly improved the prediction performance of downstream tasks. Interestingly, masking a percentage of amino acids with low attention weights yielded best performance compared to other masking strategies. Comparison experiments on two independent datasets demonstrated our method achieved better performance than other existing algorithms. Moreover, we identified important amino acids and their positional preference through attention weights, which indicated the potential interpretability of our proposed model.
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Affiliation(s)
- Yiming Fang
- School of Computer Science and Technology, Nanjing Tech University, 211816, Nanjing, China
| | - Xuejun Liu
- School of Computer Science and Technology, Nanjing Tech University, 211816, Nanjing, China
| | - Hui Liu
- School of Computer Science and Technology, Nanjing Tech University, 211816, Nanjing, China
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9
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Ma K, Chai Y, Guan J, Tan S, Qi J, Kawana-Tachikawa A, Dong T, Iwamoto A, Shi Y, Gao GF. Molecular Basis for the Recognition of HIV Nef138-8 Epitope by a Pair of Human Public T Cell Receptors. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:1652-1661. [PMID: 36130828 DOI: 10.4049/jimmunol.2200191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 08/30/2022] [Indexed: 11/07/2022]
Abstract
Cross-recognized public TCRs against HIV epitopes have been proposed to be important for the control of AIDS disease progression and HIV variants. The overlapping Nef138-8 and Nef138-10 peptides from the HIV Nef protein are HLA-A24-restricted immunodominant T cell epitopes, and an HIV mutant strain with a Y139F substitution in Nef protein can result in immune escape and is widespread in Japan. Here, we identified a pair of public TCRs specific to the HLA-A24-restricted Nef-138-8 epitope using PBMCs from White and Japanese patients, respectively, namely TD08 and H25-11. The gene use of the variable domain for TD08 and H25-11 is TRAV8-3, TRAJ10 for the α-chain and TRBV7-9, TRBD1*01, TRBJ2-5 for the β-chain. Both TCRs can recognize wild-type and Y2F-mutated Nef138-8 epitopes. We further determined three complex structures, including TD08/HLA-A24-Nef138-8, H25-11/HLA-A24-Nef138-8, and TD08/HLA-A24-Nef138-8 (2F). Then, we revealed the molecular basis of the public TCR binding to the peptide HLA, which mostly relies on the interaction between the TCR and HLA and can tolerate the mutation in the Nef138-8 peptide. These findings promote the molecular understanding of T cell immunity against HIV epitopes and provide an important basis for the engineering of TCRs to develop T cell-based immunotherapy against HIV infection.
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Affiliation(s)
- Keke Ma
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.,Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yan Chai
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jiawei Guan
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuguang Tan
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jianxun Qi
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ai Kawana-Tachikawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tao Dong
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, UK; and
| | - Aikichi Iwamoto
- Department of Research Promotion, Japan Agency for Medical Research and Development, Tokyo, Japan
| | - Yi Shi
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China; .,Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - George F Gao
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China; .,Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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An opinion on the debatable function of brain resident immune protein, T-cell receptor beta subunit in the central nervous system. IBRO Neurosci Rep 2022; 13:235-242. [PMID: 36590097 PMCID: PMC9795316 DOI: 10.1016/j.ibneur.2022.09.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/02/2022] [Indexed: 01/04/2023] Open
Abstract
In recent years scientific research has established that the nervous and immune systems have shared molecular signaling components. Proteins native to immune cells, which are also found in the brain, have neuronal functions in the nervous system where they affect synaptic plasticity, axonal regeneration, neurogenesis, and neurotransmission. Certain native immune molecules like major histocompatibility complex I (MHC-I), paired immunoglobulin receptor B (PirB), toll-like receptor (TLR), cluster of differentiation-3 zeta (CD3ζ), CD4 co-receptor, and T-cell receptor beta (TCR-β) expression in neurons have been extensively documented. In this review, we provide our opinion and discussed the possible roles of T-cell receptor beta subunits in modulating the function of neurons in the central nervous system. Based on the previous findings of Syken and Shatz., 2003; Nishiyori et al., 2004; Rodriguez et., 1993 and Komal et., 2014; we discuss whether restrictive expression of TCR-β subunits in selected brain regions could be involved in the pathology of neurological disorders and whether their aberrant enhancement in expression may be considered as a suitable biomarker for aging or neurodegenerative diseases like Huntington's disease (HD).
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11
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Katayama Y, Yokota R, Akiyama T, Kobayashi TJ. Machine Learning Approaches to TCR Repertoire Analysis. Front Immunol 2022; 13:858057. [PMID: 35911778 PMCID: PMC9334875 DOI: 10.3389/fimmu.2022.858057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Sparked by the development of genome sequencing technology, the quantity and quality of data handled in immunological research have been changing dramatically. Various data and database platforms are now driving the rapid progress of machine learning for immunological data analysis. Of various topics in immunology, T cell receptor repertoire analysis is one of the most important targets of machine learning for assessing the state and abnormalities of immune systems. In this paper, we review recent repertoire analysis methods based on machine learning and deep learning and discuss their prospects.
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Affiliation(s)
- Yotaro Katayama
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
- *Correspondence: Yotaro Katayama,
| | - Ryo Yokota
- National Research Institute of Police Science, Kashiwa, Chiba, Japan
| | - Taishin Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Tetsuya J. Kobayashi
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
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12
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pmTR database: population matched (pm) germline allelic variants of T-cell receptor (TR) loci. Genes Immun 2022; 23:99-110. [PMID: 35436998 PMCID: PMC9042698 DOI: 10.1038/s41435-022-00171-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 03/29/2022] [Accepted: 04/04/2022] [Indexed: 11/08/2022]
Abstract
The IMGT database profiles the TR germline alleles for all four TR loci (TRA, TRB, TRG and TRD), however, it does not comprise of the information regarding population specificity and allelic frequencies of these germline alleles. The specificity of allelic variants to different human populations can, however, be a rich source of information when studying the genetic basis of population-specific immune responses in disease and in vaccination. Therefore, we meticulously identified true germline alleles enriched with complete TR allele sequences and their frequencies across 26 different human populations, profiled by “1000 Genomes data”. We identified 205 TRAV, 249 TRBV, 16 TRGV and 5 TRDV germline alleles supported by at least four haplotypes. The diversity of germline allelic variants in the TR loci is the highest in Africans, while the majority of the Non-African alleles are specific to the Asian populations, suggesting a diverse profile of TR germline alleles in different human populations. Interestingly, the alleles in the IMGT database are frequent and common across all five super-populations. We believe that this new set of germline TR sequences represents a valuable new resource which we have made available through the new population-matched TR (pmTR) database, accessible via https://pmtrig.lumc.nl/.
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13
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Pontarotti P, Paganini J. COVID-19 Pandemic: Escape of Pathogenic Variants and MHC Evolution. Int J Mol Sci 2022; 23:ijms23052665. [PMID: 35269808 PMCID: PMC8910380 DOI: 10.3390/ijms23052665] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/23/2022] [Accepted: 02/26/2022] [Indexed: 02/04/2023] Open
Abstract
We propose a new hypothesis that explains the maintenance and evolution of MHC polymorphism. It is based on two phenomena: the constitution of the repertoire of naive T lymphocytes and the evolution of the pathogen and its impact on the immune memory of T lymphocytes. Concerning the latter, pathogen evolution will have a different impact on reinfection depending on the MHC allomorph. If a mutation occurs in a given region, in the case of MHC allotypes, which do not recognize the peptide in this region, the mutation will have no impact on the memory repertoire. In the case where the MHC allomorph binds to the ancestral peptides and not to the mutated peptide, that individual will have a higher chance of being reinfected. This difference in fitness will lead to a variation of the allele frequency in the next generation. Data from the SARS-CoV-2 pandemic already support a significant part of this hypothesis and following up on these data may enable it to be confirmed. This hypothesis could explain why some individuals after vaccination respond less well than others to variants and leads to predict the probability of reinfection after a first infection depending upon the variant and the HLA allomorph.
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Affiliation(s)
- Pierre Pontarotti
- Evolutionary Biology Team, MEPHI, Aix Marseille Université, IRD, APHM, IHU MI, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
- SNC 5039 CNRS, 13005 Marseille, France
- Xegen, 15 Rue Dominique Piazza, 13420 Gemenos, France
- Correspondence: (P.P.); (J.P.)
| | - Julien Paganini
- Xegen, 15 Rue Dominique Piazza, 13420 Gemenos, France
- Correspondence: (P.P.); (J.P.)
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14
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Heather JM, Spindler MJ, Alonso M, Shui Y, Millar DG, Johnson D, Cobbold M, Hata A. OUP accepted manuscript. Nucleic Acids Res 2022; 50:e68. [PMID: 35325179 PMCID: PMC9262623 DOI: 10.1093/nar/gkac190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/18/2022] [Accepted: 03/09/2022] [Indexed: 11/17/2022] Open
Abstract
The study and manipulation of T cell receptors (TCRs) is central to multiple fields across basic and translational immunology research. Produced by V(D)J recombination, TCRs are often only recorded in the literature and data repositories as a combination of their V and J gene symbols, plus their hypervariable CDR3 amino acid sequence. However, numerous applications require full-length coding nucleotide sequences. Here we present Stitchr, a software tool developed to specifically address this limitation. Given minimal V/J/CDR3 information, Stitchr produces complete coding sequences representing a fully spliced TCR cDNA. Due to its modular design, Stitchr can be used for TCR engineering using either published germline or novel/modified variable and constant region sequences. Sequences produced by Stitchr were validated by synthesizing and transducing TCR sequences into Jurkat cells, recapitulating the expected antigen specificity of the parental TCR. Using a companion script, Thimble, we demonstrate that Stitchr can process a million TCRs in under ten minutes using a standard desktop personal computer. By systematizing the production and modification of TCR sequences, we propose that Stitchr will increase the speed, repeatability, and reproducibility of TCR research. Stitchr is available on GitHub.
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Affiliation(s)
- James M Heather
- To whom correspondence should be addressed. Tel: +1 617 724 0104;
| | | | | | | | - David G Millar
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | | | - Mark Cobbold
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Aaron N Hata
- Correspondence may also be addressed to Aaron N. Hata. Tel: +1 617 724 3442;
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15
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Pasharawipas T. Perspectives Concerning Various Symptoms of SARS-CoV-2 Detected Individuals. Open Microbiol J 2021. [DOI: 10.2174/1874285802115010152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
After exposure to SARS-CoV-2, varying symptoms of COVID-19 ranging from asymptomatic symptoms to morbidity and mortality have been exhibited in each individual. SARS-CoV-2 requires various cellular molecules for penetration into a target host cell. Angiotensin-converting enzyme2 (ACE2) acts as the viral receptor molecule. After attachment, SARS-CoV-2 also requires the transmembrane protease serine-2 (TMPRSS-2) and furin molecules, which serve as co-receptors for penetration into the target cell and for subsequent replication. In the meantime, a major histocompatibility complex (MHC) is required for the induction of adaptive immune cells, especially cytotoxic T cells and helper T cells, to clear the virally infected cells. This perspective review article proposes different aspects to explain the varying symptoms of the individuals who have been exposed to SARS-CoV-2, which relates to the polymorphisms of these involved molecules.
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16
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Seneviratna R, Redmond SJ, McWilliam HE, Reantragoon R, Villadangos JA, McCluskey J, Godfrey DI, Gherardin NA. Differential antigenic requirements by diverse MR1-restricted T cells. Immunol Cell Biol 2021; 100:112-126. [PMID: 34940995 PMCID: PMC9033883 DOI: 10.1111/imcb.12519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/04/2021] [Accepted: 12/20/2021] [Indexed: 11/29/2022]
Abstract
MHC-related protein 1 (MR1) presents microbial riboflavin metabolites to mucosal-associated invariant T (MAIT) cells for surveillance of microbial presence. MAIT cells express a semi-invariant T cell receptor (TCR) which recognises MR1-antigen complexes in a pattern-recognition-like manner. Recently, diverse populations of MR1-restricted T cells have been described that exhibit broad recognition of tumour cells and appear to recognise MR1 in association with tumour-derived self-antigens, though the identity of these antigens remains unclear. Here, we have used TCR gene transfer and engineered MR1-expressing antigen-presenting cells (APCs) to probe the MR1-restriction and antigen reactivity of a range of MR1-restricted TCRs, including model tumour-reactive TCRs. We confirm MR1 reactivity by these TCRs, show differential dependence on lysine at position 43 of MR1 (K43), and demonstrate competitive inhibition by MR1 ligand 6-formylpterin (6-FP). TCR-expressing reporter lines, however, failed to recapitulate the robust tumour specificity previously reported, suggesting an importance of accessory molecules for MR1-dependent tumour-reactivity. Finally, MR1-mutant cell lines showed that distinct residues on the α1/α2 helices were required for TCR-binding by different MR1-restricted T cells and suggested central but distinct docking modes by the broad family of MR1-restrictd αβ TCRs. Collectively, these data are consistent with recognition of distinct antigens by diverse MR1-restricted T cells.
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Affiliation(s)
- Rebecca Seneviratna
- Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, VIC 3000, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Samuel J Redmond
- Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, VIC 3000, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Hamish E McWilliam
- Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, VIC 3000, Australia.,Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Rangsima Reantragoon
- Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, VIC 3000, Australia.,Present address: Immunology Division, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Centre of Excellence in Immunology and Immune-mediated Diseases, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jose A Villadangos
- Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, VIC 3000, Australia.,Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - James McCluskey
- Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, VIC 3000, Australia
| | - Dale I Godfrey
- Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, VIC 3000, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Nicholas A Gherardin
- Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, VIC 3000, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, VIC, 3010, Australia
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17
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Cirac A, Poirey R, Dieckmeyer M, Witter K, Delecluse HJ, Behrends U, Mautner J. Immunoinformatic Analysis Reveals Antigenic Heterogeneity of Epstein-Barr Virus Is Immune-Driven. Front Immunol 2021; 12:796379. [PMID: 34975903 PMCID: PMC8716887 DOI: 10.3389/fimmu.2021.796379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/30/2021] [Indexed: 12/05/2022] Open
Abstract
Whole genome sequencing of Epstein-Barr virus (EBV) isolates from around the world has uncovered pervasive strain heterogeneity, but the forces driving strain diversification and the impact on immune recognition remained largely unknown. Using a data mining approach, we analyzed more than 300 T-cell epitopes in 168 published EBV strains. Polymorphisms were detected in approximately 65% of all CD8+ and 80% of all CD4+ T-cell epitopes and these numbers further increased when epitope flanking regions were included. Polymorphisms in CD8+ T-cell epitopes often involved MHC anchor residues and resulted in changes of the amino acid subgroup, suggesting that only a limited number of conserved T-cell epitopes may represent generic target antigens against different viral strains. Although considered the prototypic EBV strain, the rather low degree of overlap with most other viral strains implied that B95.8 may not represent the ideal reference strain for T-cell epitopes. Instead, a combinatorial library of consensus epitopes may provide better targets for diagnostic and therapeutic purposes when the infecting strain is unknown. Polymorphisms were significantly enriched in epitope versus non-epitope protein sequences, implicating immune selection in driving strain diversification. Remarkably, CD4+ T-cell epitopes in EBNA2, EBNA-LP, and the EBNA3 family appeared to be under negative selection pressure, hinting towards a beneficial role of immune responses against these latency type III antigens in virus biology. These findings validate this immunoinformatics approach for providing novel insight into immune targets and the intricate relationship of host defense and virus evolution that may also pertain to other pathogens.
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Affiliation(s)
- Ana Cirac
- Children’s Hospital, School of Medicine, Technische Universität München, Munich, Germany
- German Centre for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Remy Poirey
- German Cancer Research Center (DKFZ) Unit F100 and Institut National de la Santé et de la Recherche Médicale Unit U1074, Heidelberg, Germany
| | - Michael Dieckmeyer
- Department of Diagnostic and Interventional Neuroradiology, Technische Universität München, Munich, Germany
| | - Klaus Witter
- Laboratory of Immunogenetics, Ludwig-Maximilians-Universität, München, Germany
| | - Henri-Jacques Delecluse
- German Cancer Research Center (DKFZ) Unit F100 and Institut National de la Santé et de la Recherche Médicale Unit U1074, Heidelberg, Germany
| | - Uta Behrends
- Children’s Hospital, School of Medicine, Technische Universität München, Munich, Germany
- German Centre for Infection Research (DZIF), partner site Munich, Munich, Germany
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
| | - Josef Mautner
- Children’s Hospital, School of Medicine, Technische Universität München, Munich, Germany
- German Centre for Infection Research (DZIF), partner site Munich, Munich, Germany
- Institute of Virology, Helmholtz Zentrum München, Munich, Germany
- *Correspondence: Josef Mautner,
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18
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Kedzierska K, Koutsakos M. The ABC of Major Histocompatibility Complexes and T Cell Receptors in Health and Disease. Viral Immunol 2021; 33:160-178. [PMID: 32286182 PMCID: PMC7185345 DOI: 10.1089/vim.2019.0184] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
A seminal discovery of major histocompatibility complex (MHC) restriction in T cell recognition by Peter Doherty and Rolf Zinkernagel has led to 45 years of exciting research on the mechanisms governing peptide MHC (pMHC) recognition by T cell receptors (TCRs) and their importance in health and disease. T cells provide a significant level of protection against viral, bacterial, and parasitic infections, as well as tumors, hence, the generation of protective T cell responses is a primary goal for cell-mediated vaccines and immunotherapies. Understanding the mechanisms underlying generation of optimal high-avidity effector T cell responses, memory development, maintenance, and recall is of major importance for the rational design of preventative and therapeutic vaccines/immunotherapies. In this review, we summarize the lessons learned over the last four decades and outline our current understanding of the basis and consequences of pMHC/TCR interactions on T cell development and function, and TCR diversity and composition, driving better clinical outcomes and prevention of viral escape. We also discuss the current models of T cell memory formation and determinants of immunodominant T cell responses in animal models and humans. As TCR composition and diversity can affect both the protective capacity of T cells and protection against viral escape, defining the spectrum of TCR selection has implications for improving the functional efficacy of effector T cell responsiveness and memory formation.
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Affiliation(s)
- Katherine Kedzierska
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
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19
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TCR Recognition of Peptide-MHC-I: Rule Makers and Breakers. Int J Mol Sci 2020; 22:ijms22010068. [PMID: 33374673 PMCID: PMC7793522 DOI: 10.3390/ijms22010068] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 12/15/2022] Open
Abstract
T cells are a critical part of the adaptive immune system that are able to distinguish between healthy and unhealthy cells. Upon recognition of protein fragments (peptides), activated T cells will contribute to the immune response and help clear infection. The major histocompatibility complex (MHC) molecules, or human leukocyte antigens (HLA) in humans, bind these peptides to present them to T cells that recognise them with their surface T cell receptors (TCR). This recognition event is the first step that leads to T cell activation, and in turn can dictate disease outcomes. The visualisation of TCR interaction with pMHC using structural biology has been crucial in understanding this key event, unravelling the parameters that drive this interaction and their impact on the immune response. The last five years has been the most productive within the field, wherein half of current unique TCR-pMHC-I structures to date were determined within this time. Here, we review the new insights learned from these recent TCR-pMHC-I structures and their impact on T cell activation.
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20
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Souter MNT, Loh L, Li S, Meehan BS, Gherardin NA, Godfrey DI, Rossjohn J, Fairlie DP, Kedzierska K, Pellicci DG, Chen Z, Kjer-Nielsen L, Corbett AJ, McCluskey J, Eckle SBG. Characterization of Human Mucosal-associated Invariant T (MAIT) Cells. ACTA ACUST UNITED AC 2020; 127:e90. [PMID: 31763790 DOI: 10.1002/cpim.90] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Mucosal-associated invariant T (MAIT) cells are a subset of unconventional T cells restricted by the major histocompatibility complex (MHC) class I-like molecule MHC-related protein 1 (MR1). MAIT cells are found throughout the body, especially in human blood and liver. Unlike conventional T cells, which are stimulated by peptide antigens presented by MHC molecules, MAIT cells recognize metabolite antigens derived from an intermediate in the microbial biosynthesis of riboflavin. MAIT cells mediate protective immunity to infections by riboflavin-producing microbes via the production of cytokines and cytotoxicity. The discovery of stimulating MAIT cell antigens allowed for the development of an analytical tool, the MR1 tetramer, that binds specifically to the MAIT T cell receptor (TCR) and is becoming the gold standard for identification of MAIT cells by flow cytometry. This article describes protocols to characterize the phenotype of human MAIT cells in blood and tissues by flow cytometry using fluorescently labeled human MR1 tetramers alongside antibodies specific for MAIT cell markers. © 2019 by John Wiley & Sons, Inc. The main protocols include: Basic Protocol 1: Determining the frequency and steady-state surface phenotype of human MAIT cells Basic Protocol 2: Determining the activation phenotype of human MAIT cells in blood Basic Protocol 3: Characterizing MAIT cell TCRs using TCR-positive reporter cell lines Alternate protocols are provided for determining the absolute number, transcription factor phenotype, and TCR usage of human MAIT cells; and determining activation phenotype by staining for intracellular markers, measuring secreted cytokines, and measuring fluorescent dye dilution due to proliferation. Additional methods are provided for determining the capacity of MAIT cells to produce cytokine independently of antigen using plate-bound or bead-immobilized CD3/CD28 stimulation; and determining the MR1-Ag dependence of MAIT cell activation using MR1-blocking antibody or competitive inhibition. For TCR-positive reporter cell lines, methods are also provided for evaluating the MAIT TCR-mediated MR1-Ag response, determining the capacity of the reporter lines to produce cytokine independently of antigen, determining the MR1-Ag dependence of the reporter lines, and evaluating the MR1-Ag response of the reporter lines using IL-2 secretion. Support Protocols describe the preparation of PBMCs from human blood, the preparation of single-cell suspensions from tissue, the isolation of MAIT cells by FACS and MACS, cloning MAIT TCRα and β chain genes and MR1 genes for transduction, generating stably and transiently transfected cells lines, generating a stable MR1 knockout antigen-presenting cell line, and generating monocyte-derived dendritic cells.
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Affiliation(s)
- Michael N T Souter
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Australia
| | - Liyen Loh
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Shihan Li
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Australia
| | - Bronwyn S Meehan
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Nicholas A Gherardin
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Australia
| | - Dale I Godfrey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Wales, United Kingdom
| | - David P Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Queensland, Brisbane, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Daniel G Pellicci
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,Murdoch Children's Research Institute, Parkville, Australia
| | - Zhenjun Chen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Lars Kjer-Nielsen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Alexandra J Corbett
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Sidonia B G Eckle
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
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21
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Singh NK, Abualrous ET, Ayres CM, Noé F, Gowthaman R, Pierce BG, Baker BM. Geometrical characterization of T cell receptor binding modes reveals class-specific binding to maximize access to antigen. Proteins 2020; 88:503-513. [PMID: 31589793 PMCID: PMC6982585 DOI: 10.1002/prot.25829] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 08/08/2019] [Accepted: 09/17/2019] [Indexed: 11/11/2022]
Abstract
Recognition of antigenic peptides bound to major histocompatibility complex (MHC) proteins by αβ T cell receptors (TCRs) is a hallmark of T cell mediated immunity. Recent data suggest that variations in TCR binding geometry may influence T cell signaling, which could help explain outliers in relationships between physical parameters such as TCR-pMHC binding affinity and T cell function. Traditionally, TCR binding geometry has been described with simple descriptors such as the crossing angle, which quantifies what has become known as the TCR's diagonal binding mode. However, these descriptors often fail to reveal distinctions in binding geometry that are apparent through visual inspection. To provide a better framework for relating TCR structure to T cell function, we developed a comprehensive system for quantifying the geometries of how TCRs bind peptide/MHC complexes. We show that our system can discern differences not clearly revealed by more common methods. As an example of its potential to impact biology, we used it to reveal differences in how TCRs bind class I and class II peptide/MHC complexes, which we show allow the TCR to maximize access to and "read out" the peptide antigen. We anticipate our system will be of use in not only exploring these and other details of TCR-peptide/MHC binding interactions, but also addressing questions about how TCR binding geometry relates to T cell function, as well as modeling structural properties of class I and class II TCR-peptide/MHC complexes from sequence information. The system is available at https://tcr3d.ibbr.umd.edu/tcr_com or for download as a script.
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MESH Headings
- Binding Sites
- Crystallography, X-Ray
- Histocompatibility Antigens Class I/chemistry
- Histocompatibility Antigens Class I/immunology
- Histocompatibility Antigens Class I/metabolism
- Histocompatibility Antigens Class II/chemistry
- Histocompatibility Antigens Class II/immunology
- Histocompatibility Antigens Class II/metabolism
- Humans
- Models, Molecular
- Principal Component Analysis
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- T-Lymphocytes/chemistry
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Thermodynamics
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Affiliation(s)
- Nishant K. Singh
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States
- Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| | - Esam T. Abualrous
- Molecular Biology Group, Institute for Mathematics, Freie Universität Berlin, Berlin, Germany
| | - Cory M. Ayres
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States
- Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| | - Frank Noé
- Molecular Biology Group, Institute for Mathematics, Freie Universität Berlin, Berlin, Germany
| | - Ragul Gowthaman
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, United States
| | - Brian G. Pierce
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, United States
| | - Brian M. Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States
- Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
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22
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T cell receptor cross-reactivity between gliadin and bacterial peptides in celiac disease. Nat Struct Mol Biol 2019; 27:49-61. [PMID: 31873306 DOI: 10.1038/s41594-019-0353-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 11/18/2019] [Indexed: 12/16/2022]
Abstract
The human leukocyte antigen (HLA) locus is strongly associated with T cell-mediated autoimmune disorders. HLA-DQ2.5-mediated celiac disease (CeD) is triggered by the ingestion of gluten, although the relative roles of genetic and environmental risk factors in CeD is unclear. Here we identify microbially derived mimics of gliadin epitopes and a parental bacterial protein that is naturally processed by antigen-presenting cells and activated gliadin reactive HLA-DQ2.5-restricted T cells derived from CeD patients. Crystal structures of T cell receptors in complex with HLA-DQ2.5 bound to two distinct bacterial peptides demonstrate that molecular mimicry underpins cross-reactivity toward the gliadin epitopes. Accordingly, gliadin reactive T cells involved in CeD pathogenesis cross-react with ubiquitous bacterial peptides, thereby suggesting microbial exposure as a potential environmental factor in CeD.
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23
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Joshi K, Elso C, Motazedian A, Labonne T, Schiesser JV, Cameron F, Mannering SI, Elefanty AG, Stanley EG. Induced pluripotent stem cell macrophages present antigen to proinsulin-specific T cell receptors from donor-matched islet-infiltrating T cells in type 1 diabetes. Diabetologia 2019; 62:2245-2251. [PMID: 31511930 PMCID: PMC6861360 DOI: 10.1007/s00125-019-04988-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/19/2019] [Indexed: 01/04/2023]
Abstract
AIMS/HYPOTHESIS Type 1 diabetes is an autoimmune disorder characterised by loss of insulin-producing beta cells of the pancreas. Progress in understanding the cellular and molecular mechanisms underlying the human disease has been hampered by a dearth of appropriate human experimental models. We previously reported the characterisation of islet-infiltrating CD4+ T cells from a deceased organ donor who had type 1 diabetes. METHODS Induced pluripotent stem cell (iPSC) lines derived from the above donor were differentiated into CD14+ macrophages and tested for their capacity to present antigen to T cell receptors (TCRs) derived from islet-infiltrating CD4+ T cells from the same donor. RESULTS The iPSC macrophages displayed typical macrophage morphology, surface markers (CD14, CD86, CD16 and CD11b) and were phagocytic. In response to IFNγ treatment, iPSC macrophages upregulated expression of HLA class II, a characteristic that correlated with their capacity to present epitopes derived from proinsulin C-peptide to a T cell line expressing TCRs derived from islet-infiltrating CD4+ T cells of the original donor. T cell activation was specifically blocked by anti-HLA-DQ antibodies but not by antibodies directed against HLA-DR. CONCLUSIONS/INTERPRETATION This study provides a proof of principle for the use of iPSC-derived immune cells for modelling key cellular interactions in human type 1 diabetes.
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Affiliation(s)
- Kriti Joshi
- Murdoch Children's Research Institute, Flemington Road, Parkville, VIC, 3052, Australia
- The Royal Children's Hospital, Parkville, VIC, Australia
- Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Colleen Elso
- Immunology and Diabetes Unit, St Vincent's Institute for Medical Research, Fitzroy, VIC, Australia
| | - Ali Motazedian
- Murdoch Children's Research Institute, Flemington Road, Parkville, VIC, 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Tanya Labonne
- Murdoch Children's Research Institute, Flemington Road, Parkville, VIC, 3052, Australia
| | - Jacqueline V Schiesser
- Murdoch Children's Research Institute, Flemington Road, Parkville, VIC, 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Fergus Cameron
- Murdoch Children's Research Institute, Flemington Road, Parkville, VIC, 3052, Australia
- The Royal Children's Hospital, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Stuart I Mannering
- Immunology and Diabetes Unit, St Vincent's Institute for Medical Research, Fitzroy, VIC, Australia
| | - Andrew G Elefanty
- Murdoch Children's Research Institute, Flemington Road, Parkville, VIC, 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - Edouard G Stanley
- Murdoch Children's Research Institute, Flemington Road, Parkville, VIC, 3052, Australia.
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia.
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia.
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Chronic Inflammation Permanently Reshapes Tissue-Resident Immunity in Celiac Disease. Cell 2019; 176:967-981.e19. [PMID: 30739797 DOI: 10.1016/j.cell.2018.12.039] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 11/05/2018] [Accepted: 12/21/2018] [Indexed: 12/20/2022]
Abstract
Tissue-resident lymphocytes play a key role in immune surveillance, but it remains unclear how these inherently stable cell populations respond to chronic inflammation. In the setting of celiac disease (CeD), where exposure to dietary antigen can be controlled, gluten-induced inflammation triggered a profound depletion of naturally occurring Vγ4+/Vδ1+ intraepithelial lymphocytes (IELs) with innate cytolytic properties and specificity for the butyrophilin-like (BTNL) molecules BTNL3/BTNL8. Creation of a new niche with reduced expression of BTNL8 and loss of Vγ4+/Vδ1+ IELs was accompanied by the expansion of gluten-sensitive, interferon-γ-producing Vδ1+ IELs bearing T cell receptors (TCRs) with a shared non-germline-encoded motif that failed to recognize BTNL3/BTNL8. Exclusion of dietary gluten restored BTNL8 expression but was insufficient to reconstitute the physiological Vγ4+/Vδ1+ subset among TCRγδ+ IELs. Collectively, these data show that chronic inflammation permanently reconfigures the tissue-resident TCRγδ+ IEL compartment in CeD. VIDEO ABSTRACT.
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MAIT cells protect against pulmonary Legionella longbeachae infection. Nat Commun 2018; 9:3350. [PMID: 30135490 PMCID: PMC6105587 DOI: 10.1038/s41467-018-05202-8] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 04/27/2018] [Indexed: 02/07/2023] Open
Abstract
Mucosal associated invariant T (MAIT) cells recognise conserved microbial metabolites from riboflavin synthesis. Striking evolutionary conservation and pulmonary abundance implicate them in antibacterial host defence, yet their functions in protection against clinically important pathogens are unknown. Here we show that mouse Legionella longbeachae infection induces MR1-dependent MAIT cell activation and rapid pulmonary accumulation of MAIT cells associated with immune protection detectable in immunocompetent host animals. MAIT cell protection is more evident in mice lacking CD4+ cells, and adoptive transfer of MAIT cells rescues immunodeficient Rag2-/-γC-/- mice from lethal Legionella infection. Protection is dependent on MR1, IFN-γ and GM-CSF, but not IL-17A, TNF or perforin, and enhanced protection is detected earlier after infection of mice antigen-primed to boost MAIT cell numbers before infection. Our findings define a function for MAIT cells in protection against a major human pathogen and indicate a potential role for vaccination to enhance MAIT cell immunity.
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Wun KS, Reijneveld JF, Cheng TY, Ladell K, Uldrich AP, Le Nours J, Miners KL, McLaren JE, Grant EJ, Haigh OL, Watkins TS, Suliman S, Iwany S, Jimenez J, Calderon R, Tamara KL, Leon SR, Murray MB, Mayfield JA, Altman JD, Purcell AW, Miles JJ, Godfrey DI, Gras S, Price DA, Van Rhijn I, Moody DB, Rossjohn J. T cell autoreactivity directed toward CD1c itself rather than toward carried self lipids. Nat Immunol 2018; 19:397-406. [PMID: 29531339 PMCID: PMC6475884 DOI: 10.1038/s41590-018-0065-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 02/05/2018] [Indexed: 12/13/2022]
Abstract
The hallmark function of αβ T cell antigen receptors (TCRs) involves the highly specific co-recognition of a major histocompatibility complex molecule and its carried peptide. However, the molecular basis of the interactions of TCRs with the lipid antigen-presenting molecule CD1c is unknown. We identified frequent staining of human T cells with CD1c tetramers across numerous subjects. Whereas TCRs typically show high specificity for antigen, both tetramer binding and autoreactivity occurred with CD1c in complex with numerous, chemically diverse self lipids. Such extreme polyspecificity was attributable to binding of the TCR over the closed surface of CD1c, with the TCR covering the portal where lipids normally protrude. The TCR essentially failed to contact lipids because they were fully seated within CD1c. These data demonstrate the sequestration of lipids within CD1c as a mechanism of autoreactivity and point to small lipid size as a determinant of autoreactive T cell responses.
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Affiliation(s)
- Kwok S Wun
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Josephine F Reijneveld
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- Brigham and Women's Hospital Division of Rheumatology, Immunology and Allergy and Harvard Medical School, Boston, MA, USA
| | - Tan-Yun Cheng
- Brigham and Women's Hospital Division of Rheumatology, Immunology and Allergy and Harvard Medical School, Boston, MA, USA
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff, UK
| | - Adam P Uldrich
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
| | - Jérôme Le Nours
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Kelly L Miners
- Division of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff, UK
| | - James E McLaren
- Division of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff, UK
| | - Emma J Grant
- Division of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff, UK
| | - Oscar L Haigh
- QIMR Berghofer Medical Research Institute, Herston, Australia
| | - Thomas S Watkins
- Centre for Biodiscovery and Molecular Development of Therapeutics and Centre for Biosecurity and Tropical Infectious Diseases Australian Institute of Tropical Health and Medicine, James Cook University, Cairn, Australia
| | - Sara Suliman
- Brigham and Women's Hospital Division of Rheumatology, Immunology and Allergy and Harvard Medical School, Boston, MA, USA
| | - Sarah Iwany
- Brigham and Women's Hospital Division of Rheumatology, Immunology and Allergy and Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - Megan B Murray
- Department of Global Health and Social Medicine, and Division of Global Health Equity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jacob A Mayfield
- Brigham and Women's Hospital Division of Rheumatology, Immunology and Allergy and Harvard Medical School, Boston, MA, USA
| | - John D Altman
- Emory University School of Medicine, Atlanta, GA, USA
| | - Anthony W Purcell
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - John J Miles
- Centre for Biodiscovery and Molecular Development of Therapeutics and Centre for Biosecurity and Tropical Infectious Diseases Australian Institute of Tropical Health and Medicine, James Cook University, Cairn, Australia
| | - Dale I Godfrey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria, Australia
| | - Stephanie Gras
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - David A Price
- Division of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff, UK
| | - Ildiko Van Rhijn
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- Brigham and Women's Hospital Division of Rheumatology, Immunology and Allergy and Harvard Medical School, Boston, MA, USA
| | - D Branch Moody
- Brigham and Women's Hospital Division of Rheumatology, Immunology and Allergy and Harvard Medical School, Boston, MA, USA.
| | - Jamie Rossjohn
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia.
- Division of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff, UK.
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Abstract
Human leukocyte antigen (HLA)-I molecules generally bind short peptides (8–10 amino acids), although extended HLA-I restricted peptides (>10 amino acids) can be presented to T cells. However, the function of such extended HLA-I epitopes in tumour immunity, and how they would be recognised by T-cell receptors (TCR) remains unclear. Here we show that the structures of two distinct TCRs (TRAV4+TRAJ21+-TRBV28+TRBJ2-3+ and TRAV4+TRAJ8+-TRBV9+TRBJ2-1+), originating from a polyclonal T-cell repertoire, bind to HLA-B*07:02, presenting a 13-amino-acid-long tumour-associated peptide, NY-ESO-160–72. Comparison of the structures reveals that the two TCRs differentially binds NY-ESO-160–72–HLA-B*07:02 complex, and induces differing extent of conformational change of the NY-ESO-160–72 epitope. Accordingly, polyclonal TCR usage towards an extended HLA-I restricted tumour epitope translates to differing TCR recognition modes, whereby extensive flexibility at the TCR–pHLA-I interface engenders recognition. Human leukocyte antigen (HLA) presents peptides to activate T cells, but many aspects in the T cell receptor (TCR)/HLA interaction remain unclear. Here the authors show, via structural data, that two TCRs differentially recognize the same tumour peptide/HLA complex and induce contrasting conformation changes of the peptide.
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29
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Scally SW, Law SC, Ting YT, van Heemst J, Sokolove J, Deutsch AJ, Clemens EB, Moustakas AK, Papadopoulos GK, van der Woude D, Smolik I, Hitchon CA, Robinson DB, Ferucci ED, Bernstein CN, Meng X, Anaparti V, Huizinga T, Kedzierska K, Reid HH, Raychaudhuri S, Toes RE, Rossjohn J, El-Gabalawy H, Thomas R. Molecular basis for increased susceptibility of Indigenous North Americans to seropositive rheumatoid arthritis. Ann Rheum Dis 2017; 76:1915-1923. [PMID: 28801345 PMCID: PMC6724216 DOI: 10.1136/annrheumdis-2017-211300] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 05/26/2017] [Accepted: 07/01/2017] [Indexed: 12/17/2022]
Abstract
OBJECTIVE The pathogenetic mechanisms by which HLA-DRB1 alleles are associated with anticitrullinated peptide antibody (ACPA)-positive rheumatoid arthritis (RA) are incompletely understood. RA high-risk HLA-DRB1 alleles are known to share a common motif, the 'shared susceptibility epitope (SE)'. Here, the electropositive P4 pocket of HLA-DRB1 accommodates self-peptide residues containing citrulline but not arginine. HLA-DRB1 His/Phe13β stratifies with ACPA-positive RA, while His13βSer polymorphisms stratify with ACPA-negative RA and RA protection. Indigenous North American (INA) populations have high risk of early-onset ACPA-positive RA, whereby HLA-DRB1*04:04 and HLA-DRB1*14:02 are implicated as risk factors for RA in INA. However, HLA-DRB1*14:02 has a His13βSer polymorphism. Therefore, we aimed to verify this association and determine its molecular mechanism. METHODS HLA genotype was compared in 344 INA patients with RA and 352 controls. Structures of HLA-DRB1*1402-class II loaded with vimentin-64Arg59-71, vimentin-64Cit59-71 and fibrinogen β-74Cit69-81 were solved using X-ray crystallography. Vimentin-64Cit59-71-specific and vimentin59-71-specific CD4+ T cells were characterised by flow cytometry using peptide-histocompatibility leukocyte antigen (pHLA) tetramers. After sorting of antigen-specific T cells, TCRα and β-chains were analysed using multiplex, nested PCR and sequencing. RESULTS ACPA+ RA in INA was independently associated with HLA-DRB1*14:02. Consequent to the His13βSer polymorphism and altered P4 pocket of HLA-DRB1*14:02, both citrulline and arginine were accommodated in opposite orientations. Oligoclonal autoreactive CD4+ effector T cells reactive with both citrulline and arginine forms of vimentin59-71 were observed in patients with HLA-DRB1*14:02+ RA and at-risk ACPA- first-degree relatives. HLA-DRB1*14:02-vimentin59-71-specific and HLA-DRB1*14:02-vimentin-64Cit59-71-specific CD4+ memory T cells were phenotypically distinct populations. CONCLUSION HLA-DRB1*14:02 broadens the capacity for citrullinated and native self-peptide presentation and T cell expansion, increasing risk of ACPA+ RA.
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Affiliation(s)
- Stephen W Scally
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute Monash University, Clayton, Australia
| | - Soi-Cheng Law
- The University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Brisbane, Australia
| | - Yi Tian Ting
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute Monash University, Clayton, Australia
| | - Jurgen van Heemst
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeremy Sokolove
- Department of Medicine/Immunology and Rheumatology, Stanford University, VA Palo Alto Health Care System, Palo Alto, California
| | - Aaron J Deutsch
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - E Bridie Clemens
- Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Antonis K Moustakas
- Faculty of Agricultural Technology, Technological Educational Institute of Ionian Islands, Argostoli Kefalonia, Greece
| | - George K Papadopoulos
- Laboratory of Biochemistry and Biophysics, Faculty of Agricultural Technology, Epirus Institute of Technology, Arta, Greece
| | - Diane van der Woude
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Irene Smolik
- Arthritis Centre, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Carol A Hitchon
- Arthritis Centre, University of Manitoba, Winnipeg, Manitoba, Canada
| | - David B Robinson
- Arthritis Centre, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Elizabeth D Ferucci
- Division of Community Health Services, Alaska Native Tribal Health Consortium, Anchorage, Alaska, USA
| | | | - Xiaobo Meng
- Arthritis Centre, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Tom Huizinga
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, The University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Hugh H Reid
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute Monash University, Clayton, Australia
| | - Soumya Raychaudhuri
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, USA
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, Massachusetts, USA
- Arthritis Research UK Centre for Genetics and Genomics, University of Manchester, Manchester, UK
| | - René E Toes
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jamie Rossjohn
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Biomedicine Discovery Institute Monash University, Clayton, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Australia
| | - Hani El-Gabalawy
- Arthritis Centre, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ranjeny Thomas
- The University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, Brisbane, Australia
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Germline bias dictates cross-serotype reactivity in a common dengue-virus-specific CD8 + T cell response. Nat Immunol 2017; 18:1228-1237. [PMID: 28945243 DOI: 10.1038/ni.3850] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/05/2017] [Indexed: 12/12/2022]
Abstract
Adaptive immune responses protect against infection with dengue virus (DENV), yet cross-reactivity with distinct serotypes can precipitate life-threatening clinical disease. We found that clonotypes expressing the T cell antigen receptor (TCR) β-chain variable region 11 (TRBV11-2) were 'preferentially' activated and mobilized within immunodominant human-leukocyte-antigen-(HLA)-A*11:01-restricted CD8+ T cell populations specific for variants of the nonstructural protein epitope NS3133 that characterize the serotypes DENV1, DENV3 and DENV4. In contrast, the NS3133-DENV2-specific repertoire was largely devoid of such TCRs. Structural analysis of a representative TRBV11-2+ TCR demonstrated that cross-serotype reactivity was governed by unique interplay between the variable antigenic determinant and germline-encoded residues in the second β-chain complementarity-determining region (CDR2β). Extensive mutagenesis studies of three distinct TRBV11-2+ TCRs further confirmed that antigen recognition was dependent on key contacts between the serotype-defined peptide and discrete residues in the CDR2β loop. Collectively, these data reveal an innate-like mode of epitope recognition with potential implications for the outcome of sequential exposure to heterologous DENVs.
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Chen X, Poncette L, Blankenstein T. Human TCR-MHC coevolution after divergence from mice includes increased nontemplate-encoded CDR3 diversity. J Exp Med 2017; 214:3417-3433. [PMID: 28835417 PMCID: PMC5679170 DOI: 10.1084/jem.20161784] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 06/19/2017] [Accepted: 07/19/2017] [Indexed: 12/14/2022] Open
Abstract
Chen et al. demonstrate that human MHC selects a larger human TCR repertoire than mouse MHC. They show how humans optimized TCR diversity and suggest that CDR3 length adjusts for different V segment–MHC affinity. For thymic selection and responses to pathogens, T cells interact through their αβ T cell receptor (TCR) with peptide–major histocompatibility complex (MHC) molecules on antigen-presenting cells. How the diverse TCRs interact with a multitude of MHC molecules is unresolved. It is also unclear how humans generate larger TCR repertoires than mice do. We compared the TCR repertoire of CD4 T cells selected from a single mouse or human MHC class II (MHC II) in mice containing the human TCR gene loci. Human MHC II yielded greater thymic output and a more diverse TCR repertoire. The complementarity determining region 3 (CDR3) length adjusted for different inherent V-segment affinities to MHC II. Humans evolved with greater nontemplate-encoded CDR3 diversity than did mice. Our data, which demonstrate human TCR–MHC coevolution after divergence from rodents, explain the greater T cell diversity in humans and suggest a mechanism for ensuring that any V–J gene combination can be selected by a single MHC II.
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Affiliation(s)
- Xiaojing Chen
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.,Charité Campus Buch, Institute of Immunology, Berlin, Germany
| | - Lucia Poncette
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Thomas Blankenstein
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany .,Charité Campus Buch, Institute of Immunology, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
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Josephs TM, Grant EJ, Gras S. Molecular challenges imposed by MHC-I restricted long epitopes on T cell immunity. Biol Chem 2017; 398:1027-1036. [PMID: 28141543 DOI: 10.1515/hsz-2016-0305] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/25/2017] [Indexed: 11/15/2022]
Abstract
It has widely been accepted that major histocompatibility complex class I molecules (MHC-I) are limited to binding small peptides of 8-10 residues in length. However, this consensus has recently been challenged with the identification of longer peptides (≥11 residues) that can also elicit cytotoxic CD8+ T cell responses. Indeed, a growing number of studies demonstrate that these non-canonical epitopes are important targets for the immune system. As long epitopes represent up to 10% of the peptide repertoire bound to MHC-I molecules, here we review their impact on antigen presentation by MHC-I, TCR recognition, and T cell immunity.
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Drugs and drug-like molecules can modulate the function of mucosal-associated invariant T cells. Nat Immunol 2017; 18:402-411. [PMID: 28166217 DOI: 10.1038/ni.3679] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 01/03/2017] [Indexed: 02/08/2023]
Abstract
The major-histocompatibility-complex-(MHC)-class-I-related molecule MR1 can present activating and non-activating vitamin-B-based ligands to mucosal-associated invariant T cells (MAIT cells). Whether MR1 binds other ligands is unknown. Here we identified a range of small organic molecules, drugs, drug metabolites and drug-like molecules, including salicylates and diclofenac, as MR1-binding ligands. Some of these ligands inhibited MAIT cells ex vivo and in vivo, while others, including diclofenac metabolites, were agonists. Crystal structures of a T cell antigen receptor (TCR) from a MAIT cell in complex with MR1 bound to the non-stimulatory and stimulatory compounds showed distinct ligand orientations and contacts within MR1, which highlighted the versatility of the MR1 binding pocket. The findings demonstrated that MR1 was able to capture chemically diverse structures, spanning mono- and bicyclic compounds, that either inhibited or activated MAIT cells. This indicated that drugs and drug-like molecules can modulate MAIT cell function in mammals.
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Hoffmann T, Marion A, Antes I. DynaDom: structure-based prediction of T cell receptor inter-domain and T cell receptor-peptide-MHC (class I) association angles. BMC STRUCTURAL BIOLOGY 2017; 17:2. [PMID: 28148269 PMCID: PMC5289058 DOI: 10.1186/s12900-016-0071-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 12/29/2016] [Indexed: 11/22/2022]
Abstract
Background T cell receptor (TCR) molecules are involved in the adaptive immune response as they distinguish between self- and foreign-peptides, presented in major histocompatibility complex molecules (pMHC). Former studies showed that the association angles of the TCR variable domains (Vα/Vβ) can differ significantly and change upon binding to the pMHC complex. These changes can be described as a rotation of the domains around a general Center of Rotation, characterized by the interaction of two highly conserved glutamine residues. Methods We developed a computational method, DynaDom, for the prediction of TCR Vα/Vβ inter-domain and TCR/pMHC orientations in TCRpMHC complexes, which allows predicting the orientation of multiple protein-domains. In addition, we implemented a new approach to predict the correct orientation of the carboxamide endgroups in glutamine and asparagine residues, which can also be used as an external, independent tool. Results The approach was evaluated for the remodeling of 75 and 53 experimental structures of TCR and TCRpMHC (class I) complexes, respectively. We show that the DynaDom method predicts the correct orientation of the TCR Vα/Vβ angles in 96 and 89% of the cases, for the poses with the best RMSD and best interaction energy, respectively. For the concurrent prediction of the TCR Vα/Vβ and pMHC orientations, the respective rates reached 74 and 72%. Through an exhaustive analysis, we could show that the pMHC placement can be further improved by a straightforward, yet very time intensive extension of the current approach. Conclusions The results obtained in the present remodeling study prove the suitability of our approach for interdomain-angle optimization. In addition, the high prediction rate obtained specifically for the energetically highest ranked poses further demonstrates that our method is a powerful candidate for blind prediction. Therefore it should be well suited as part of any accurate atomistic modeling pipeline for TCRpMHC complexes and potentially other large molecular assemblies. Electronic supplementary material The online version of this article (doi:10.1186/s12900-016-0071-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas Hoffmann
- Department of Biosciences and Center for Integrated Protein Science Munich, Technische Universität München, Emil-Erlenmeyer-Forum 8, 85354, Freising, Germany
| | - Antoine Marion
- Department of Biosciences and Center for Integrated Protein Science Munich, Technische Universität München, Emil-Erlenmeyer-Forum 8, 85354, Freising, Germany
| | - Iris Antes
- Department of Biosciences and Center for Integrated Protein Science Munich, Technische Universität München, Emil-Erlenmeyer-Forum 8, 85354, Freising, Germany.
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35
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Cole DK, van den Berg HA, Lloyd A, Crowther MD, Beck K, Ekeruche-Makinde J, Miles JJ, Bulek AM, Dolton G, Schauenburg AJ, Wall A, Fuller A, Clement M, Laugel B, Rizkallah PJ, Wooldridge L, Sewell AK. Structural Mechanism Underpinning Cross-reactivity of a CD8+ T-cell Clone That Recognizes a Peptide Derived from Human Telomerase Reverse Transcriptase. J Biol Chem 2016; 292:802-813. [PMID: 27903649 PMCID: PMC5247654 DOI: 10.1074/jbc.m116.741603] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 11/18/2016] [Indexed: 01/20/2023] Open
Abstract
T-cell cross-reactivity is essential for effective immune surveillance but has also been implicated as a pathway to autoimmunity. Previous studies have demonstrated that T-cell receptors (TCRs) that focus on a minimal motif within the peptide are able to facilitate a high level of T-cell cross-reactivity. However, the structural database shows that most TCRs exhibit less focused antigen binding involving contact with more peptide residues. To further explore the structural features that allow the clonally expressed TCR to functionally engage with multiple peptide-major histocompatibility complexes (pMHCs), we examined the ILA1 CD8+ T-cell clone that responds to a peptide sequence derived from human telomerase reverse transcriptase. The ILA1 TCR contacted its pMHC with a broad peptide binding footprint encompassing spatially distant peptide residues. Despite the lack of focused TCR-peptide binding, the ILA1 T-cell clone was still cross-reactive. Overall, the TCR-peptide contacts apparent in the structure correlated well with the level of degeneracy at different peptide positions. Thus, the ILA1 TCR was less tolerant of changes at peptide residues that were at, or adjacent to, key contact sites. This study provides new insights into the molecular mechanisms that control T-cell cross-reactivity with important implications for pathogen surveillance, autoimmunity, and transplant rejection.
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Affiliation(s)
- David K Cole
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom,
| | - Hugo A van den Berg
- the Mathematics Institute, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Angharad Lloyd
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Michael D Crowther
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Konrad Beck
- the Cardiff University School of Dentistry, Heath Park, Cardiff CF14 4XY, United Kingdom
| | - Julia Ekeruche-Makinde
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - John J Miles
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom.,the Queensland Institute of Medical Research Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia.,James Cook University, Cairns, Queensland 4870, Australia, and
| | - Anna M Bulek
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Garry Dolton
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Andrea J Schauenburg
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Aaron Wall
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Anna Fuller
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Mathew Clement
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Bruno Laugel
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Pierre J Rizkallah
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Linda Wooldridge
- the Faculty of Health Sciences, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Andrew K Sewell
- From the Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom,
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36
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T cell receptor reversed polarity recognition of a self-antigen major histocompatibility complex. Nat Immunol 2015; 16:1153-61. [DOI: 10.1038/ni.3271] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 08/10/2015] [Indexed: 12/12/2022]
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Motozono C, Bridgeman JS, Price DA, Sewell AK, Ueno T. Clonotypically similar hybrid αβ T cell receptors can exhibit markedly different surface expression, antigen specificity and cross-reactivity. Clin Exp Immunol 2015; 180:560-70. [PMID: 25721491 PMCID: PMC4449784 DOI: 10.1111/cei.12610] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 02/17/2015] [Accepted: 02/19/2015] [Indexed: 11/29/2022] Open
Abstract
Emerging data indicate that particular major histocompatibility complex (MHC)‐bound antigenic peptides can be recognized by identical or near‐identical αβ T cell receptors (TCRs) in different individuals. To establish the functional relevance of this phenomenon, we artificially paired α and β chains from closely related TCRs specific for the human leucocyte antigen (HLA)‐B*35:01‐restricted HIV‐1 negative regulatory factor (Nef)‐derived epitope VY8 (VPLRPMTY, residues 74–81). Several hybrid TCRs generated in this manner failed to express at the cell surface, despite near homology with naturally isolated αβ chain combinations. Moreover, a substantial proportion of those αβ TCRs that did express lost specificity for the index VY8 peptide sequence. One such hybrid αβ pair gained neo‐variant specificity in the context of the VY8 backbone. Collectively, these data show that clonotypically similar TCRs can display profound differences in surface expression, antigen specificity and cross‐reactivity with potential relevance for the control of mutable viruses.
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Affiliation(s)
- C Motozono
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan.,Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - J S Bridgeman
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - D A Price
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - A K Sewell
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - T Ueno
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan.,International Research Center for Medical Research, Kumamoto University, Kumamoto, Japan
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38
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Rödström KEJ, Regenthal P, Lindkvist-Petersson K. Structure of Staphylococcal Enterotoxin E in Complex with TCR Defines the Role of TCR Loop Positioning in Superantigen Recognition. PLoS One 2015; 10:e0131988. [PMID: 26147596 PMCID: PMC4492778 DOI: 10.1371/journal.pone.0131988] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 06/09/2015] [Indexed: 11/18/2022] Open
Abstract
T cells are crucial players in cell-mediated immunity. The specificity of their receptor, the T cell receptor (TCR), is central for the immune system to distinguish foreign from host antigens. Superantigens are bacterial toxins capable of inducing a toxic immune response by cross-linking the TCR and the major histocompatibility complex (MHC) class II and circumventing the antigen specificity. Here, we present the structure of staphylococcal enterotoxin E (SEE) in complex with a human T cell receptor, as well as the unligated T cell receptor structure. There are clear structural changes in the TCR loops upon superantigen binding. In particular, the HV4 loop moves to circumvent steric clashes upon complex formation. In addition, a predicted ternary model of SEE in complex with both TCR and MHC class II displays intermolecular contacts between the TCR α-chain and the MHC, suggesting that the TCR α-chain is of importance for complex formation.
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Affiliation(s)
- Karin E. J. Rödström
- Department of Experimental Medical Science, Lund University, BMC C13, 22 184, Lund, Sweden
| | - Paulina Regenthal
- Department of Experimental Medical Science, Lund University, BMC C13, 22 184, Lund, Sweden
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39
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Attaf M, Legut M, Cole DK, Sewell AK. The T cell antigen receptor: the Swiss army knife of the immune system. Clin Exp Immunol 2015; 181:1-18. [PMID: 25753381 PMCID: PMC4469151 DOI: 10.1111/cei.12622] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2015] [Indexed: 01/01/2023] Open
Abstract
The mammalian T cell receptor (TCR) orchestrates immunity by responding to many billions of different ligands that it has never encountered before and cannot adapt to at the protein sequence level. This remarkable receptor exists in two main heterodimeric isoforms: αβ TCR and γδ TCR. The αβ TCR is expressed on the majority of peripheral T cells. Most αβ T cells recognize peptides, derived from degraded proteins, presented at the cell surface in molecular cradles called major histocompatibility complex (MHC) molecules. Recent reports have described other αβ T cell subsets. These 'unconventional' T cells bear TCRs that are capable of recognizing lipid ligands presented in the context of the MHC-like CD1 protein family or bacterial metabolites bound to the MHC-related protein 1 (MR1). γδ T cells constitute a minority of the T cell pool in human blood, but can represent up to half of total T cells in tissues such as the gut and skin. The identity of the preferred ligands for γδ T cells remains obscure, but it is now known that this receptor can also functionally engage CD1-lipid, or immunoglobulin (Ig) superfamily proteins called butyrophilins in the presence of pyrophosphate intermediates of bacterial lipid biosynthesis. Interactions between TCRs and these ligands allow the host to discriminate between self and non-self and co-ordinate an attack on the latter. Here, we describe how cells of the T lymphocyte lineage and their antigen receptors are generated and discuss the various modes of antigen recognition by these extraordinarily versatile receptors.
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Affiliation(s)
- M Attaf
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - M Legut
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - D K Cole
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - A K Sewell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
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40
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Miles JJ, McCluskey J, Rossjohn J, Gras S. Understanding the complexity and malleability of T-cell recognition. Immunol Cell Biol 2015; 93:433-41. [PMID: 25582337 DOI: 10.1038/icb.2014.112] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 11/21/2014] [Accepted: 11/23/2014] [Indexed: 12/15/2022]
Abstract
T cells are the master regulators of immune system function, continually walking the biological tightrope between adequate host defence and accidental host pathology. Tolerance is maintained or broken through an intricate structural interplay between the T-cell receptor (TCR) and major histocompatibility complex (MHC) molecule cradling peptide antigens (p). Recent advances in structural biology have shown that the TCR/pMHC interface is surprising precise and extraordinarily malleable. We have seen that seemingly minor changes in the TCR/pMHC interface can abrogate function, as well as substantial conformational changes before and after TCR docking. Our understanding of T-cell biology has also been altered with the knowledge that MHC molecules can bind not only peptides, but also an array of natural and synthetic compounds. Here, we review some examples of the precision and flexibility intrinsic to the TCR/p/MHCI axis.
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Affiliation(s)
- John J Miles
- 1] QIMR Berghofer Medical Research Institute and QIMR Berghofer Centre for Immunotherapy and Vaccine Development, Brisbane, Queensland, Australia [2] School of Medicine, The University of Queensland, Brisbane, Queensland, Australia [3] Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales, UK
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Jamie Rossjohn
- 1] Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales, UK [2] Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia [3] ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Stephanie Gras
- 1] Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia [2] ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
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41
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Rossjohn J, Gras S, Miles JJ, Turner SJ, Godfrey DI, McCluskey J. T cell antigen receptor recognition of antigen-presenting molecules. Annu Rev Immunol 2014; 33:169-200. [PMID: 25493333 DOI: 10.1146/annurev-immunol-032414-112334] [Citation(s) in RCA: 508] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Major Histocompatibility Complex (MHC) locus encodes classical MHC class I and MHC class II molecules and nonclassical MHC-I molecules. The architecture of these molecules is ideally suited to capture and present an array of peptide antigens (Ags). In addition, the CD1 family members and MR1 are MHC class I-like molecules that bind lipid-based Ags and vitamin B precursors, respectively. These Ag-bound molecules are subsequently recognized by T cell antigen receptors (TCRs) expressed on the surface of T lymphocytes. Structural and associated functional studies have been highly informative in providing insight into these interactions, which are crucial to immunity, and how they can lead to aberrant T cell reactivity. Investigators have determined over thirty unique TCR-peptide-MHC-I complex structures and twenty unique TCR-peptide-MHC-II complex structures. These investigations have shown a broad consensus in docking geometry and provided insight into MHC restriction. Structural studies on TCR-mediated recognition of lipid and metabolite Ags have been mostly confined to TCRs from innate-like natural killer T cells and mucosal-associated invariant T cells, respectively. These studies revealed clear differences between TCR-lipid-CD1, TCR-metabolite-MR1, and TCR-peptide-MHC recognition. Accordingly, TCRs show remarkable structural and biological versatility in engaging different classes of Ag that are presented by polymorphic and monomorphic Ag-presenting molecules of the immune system.
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Affiliation(s)
- Jamie Rossjohn
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia; ,
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42
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Pellicci DG, Uldrich AP, Le Nours J, Ross F, Chabrol E, Eckle SBG, de Boer R, Lim RT, McPherson K, Besra G, Howell AR, Moretta L, McCluskey J, Heemskerk MHM, Gras S, Rossjohn J, Godfrey DI. The molecular bases of δ/αβ T cell-mediated antigen recognition. ACTA ACUST UNITED AC 2014; 211:2599-615. [PMID: 25452463 PMCID: PMC4267242 DOI: 10.1084/jem.20141764] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Godfrey, Rossjohn, and colleagues define a population of T cells in healthy humans that express T cell receptors (TCRs) comprised of δ variable gene segments fused to α joining and constant domains and paired with a variety of TCR-β chains. Functional and structural analyses reveal how components of αβ and γδ TCR gene loci combine to create T cells with unique patterns of antigen recognition. αβ and γδ T cells are disparate T cell lineages that can respond to distinct antigens (Ags) via the use of the αβ and γδ T cell Ag receptors (TCRs), respectively. Here we characterize a population of human T cells, which we term δ/αβ T cells, expressing TCRs comprised of a TCR-δ variable gene (Vδ1) fused to joining α and constant α domains, paired with an array of TCR-β chains. We demonstrate that these cells, which represent ∼50% of all Vδ1+ human T cells, can recognize peptide- and lipid-based Ags presented by human leukocyte antigen (HLA) and CD1d, respectively. Similar to type I natural killer T (NKT) cells, CD1d-lipid Ag-reactive δ/αβ T cells recognized α-galactosylceramide (α-GalCer); however, their fine specificity for other lipid Ags presented by CD1d, such as α-glucosylceramide, was distinct from type I NKT cells. Thus, δ/αβTCRs contribute new patterns of Ag specificity to the human immune system. Furthermore, we provide the molecular bases of how δ/αβTCRs bind to their targets, with the Vδ1-encoded region providing a major contribution to δ/αβTCR binding. Our findings highlight how components from αβ and γδTCR gene loci can recombine to confer Ag specificity, thus expanding our understanding of T cell biology and TCR diversity.
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Affiliation(s)
- Daniel G Pellicci
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria 3010, Australia Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Adam P Uldrich
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria 3010, Australia Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jérôme Le Nours
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia Department of Biochemistry and Molecular Biology, School of Biomedical Sciences and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Fiona Ross
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria 3010, Australia Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Eric Chabrol
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Sidonia B G Eckle
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Renate de Boer
- Department of Hematology, Leiden University Medical Center, 2300 RC Leiden, Netherlands
| | - Ricky T Lim
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Kirsty McPherson
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Gurdyal Besra
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, England, UK
| | - Amy R Howell
- Department of Chemistry, University of Connecticut, Storrs, CT 06269
| | | | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Mirjam H M Heemskerk
- Department of Hematology, Leiden University Medical Center, 2300 RC Leiden, Netherlands
| | - Stephanie Gras
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia Department of Biochemistry and Molecular Biology, School of Biomedical Sciences and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Jamie Rossjohn
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia Department of Biochemistry and Molecular Biology, School of Biomedical Sciences and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia Institute of Infection and Immunity, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, Wales, UK
| | - Dale I Godfrey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria 3010, Australia Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria 3010, Australia
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43
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Yanaka S, Ueno T, Shi Y, Qi J, Gao GF, Tsumoto K, Sugase K. Peptide-dependent conformational fluctuation determines the stability of the human leukocyte antigen class I complex. J Biol Chem 2014; 289:24680-90. [PMID: 25028510 DOI: 10.1074/jbc.m114.566174] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In immune-mediated control of pathogens, human leukocyte antigen (HLA) class I presents various antigenic peptides to CD8(+) T-cells. Long-lived peptide presentation is important for efficient antigen-specific T-cell activation. Presentation time depends on the peptide sequence and the stability of the peptide-HLA complex (pHLA). However, the determinant of peptide-dependent pHLA stability remains elusive. Here, to reveal the pHLA stabilization mechanism, we examined the crystal structures of an HLA class I allomorph in complex with HIV-derived peptides and evaluated site-specific conformational fluctuations using NMR. Although the crystal structures of various pHLAs were almost identical independent of the peptides, fluctuation analyses identified a peptide-dependent minor state that would be more tightly packed toward the peptide. The minor population correlated well with the thermostability and cell surface presentation of pHLA, indicating that this newly identified minor state is important for stabilizing the pHLA and facilitating T-cell recognition.
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Affiliation(s)
- Saeko Yanaka
- From the Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 277-8562, Japan
| | - Takamasa Ueno
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan, International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto 860-0811, Japan
| | - Yi Shi
- Research Network of Immunity and Health, Beijing Institute of Life Science, Chinese Academy of Sciences, Beijing 100101, China, CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Qi
- Research Network of Immunity and Health, Beijing Institute of Life Science, Chinese Academy of Sciences, Beijing 100101, China, CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - George F Gao
- Research Network of Immunity and Health, Beijing Institute of Life Science, Chinese Academy of Sciences, Beijing 100101, China, CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Kouhei Tsumoto
- From the Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 277-8562, Japan, Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 108-8693, Japan, Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, Tokyo 108-8693, Japan, and
| | - Kenji Sugase
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Osaka 618-8503, Japan
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44
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Cárdenas Sierra D, Vélez Colmenares G, Orfao de Matos A, Fiorentino Gómez S, Quijano Gómez SM. Age-associated Epstein-Barr virus-specific T cell responses in seropositive healthy adults. Clin Exp Immunol 2014; 177:320-32. [PMID: 24666437 PMCID: PMC4089182 DOI: 10.1111/cei.12337] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2014] [Indexed: 12/13/2022] Open
Abstract
Epstein-Barr virus (EBV) is present in 95% of the world's adult population. The immune response participates in immune vigilance and persistent infection control, and this condition is maintained by both a good quality (functionality) and quantity of specific T cells throughout life. In the present study, we evaluated EBV-specific CD4(+) and CD8(+) T lymphocyte responses in seropositive healthy individuals younger and older than 50 years of age. The assessment comprised the frequency, phenotype, functionality and clonotypic distribution of T lymphocytes. We found that in both age groups a similar EBV-specific T cell response was found, with overlapping numbers of tumour necrosis factor (TNF)-α(+) T lymphocytes (CD4(+) and CD8(+)) within the memory and effector cell compartments, in addition to monofunctional and multi-functional T cells producing interleukin (IL)-2 and/or interferon (IFN)-γ. However, individuals aged more than 50 years showed significantly higher frequencies of IL-2-producing CD4(+) T lymphocytes in association with greater production of soluble IFN-γ, TNF-α and IL-6 than subjects younger than 50 years. A polyclonal T cell receptor (TCR)-variable beta region (Vβ) repertoire exists in both age groups under basal conditions and in response to EBV; the major TCR families found in TNF-α(+) /CD4(+) T lymphocytes were Vβ1, Vβ2, Vβ17 and Vβ22 in both age groups, and the major TCR family in TNF-α(+) /CD8(+) T cells was Vβ13·1 for individuals younger than 50 years and Vβ9 for individuals aged more than 50 years. Our findings suggest that the EBV-specific T cell response (using a polyclonal stimulation model) is distributed throughout several T cell differentiation compartments in an age-independent manner and includes both monofunctional and multi-functional T lymphocytes.
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Affiliation(s)
- D Cárdenas Sierra
- Grupo de Inmunobiología y Biología Celular, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
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45
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Effects of polymorphisms in immunity-related genes on the immune system and successful aging. Curr Opin Immunol 2014; 29:49-55. [PMID: 24780188 DOI: 10.1016/j.coi.2014.04.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 04/03/2014] [Accepted: 04/06/2014] [Indexed: 12/20/2022]
Abstract
Aging is associated with the dysregulation of immune system. Despite a progressive decline in immune function resulting in hyporesponsiveness to infection and vaccination, aging is also characterized by a chronic, low-grade, pro-inflammatory condition. An elderly individual with a systemic inflammation is at an increased risk of age-related diseases. Polymorphisms in the genes coding for inflammatory or anti-inflammatory molecules associated with immune related processes can affect the balance between the pro-inflammatory and anti-inflammatory networks. An improved understanding of the interactions among endogenous and environmental factors and genetic polymorphisms in anti-inflammatory and immune-related genes will increase the possibility of treating major age-related diseases to achieve longevity. The major challenge is to fully understand the complex interactions between genetic variations and multiple factors and their relative contributions to immunosenescence and age-related diseases in various populations. The results of studies that examined polymorphisms in immune-related genes associated with successful aging are reviewed here.
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46
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Liu YC, Chen Z, Neller MA, Miles JJ, Purcell AW, McCluskey J, Burrows SR, Rossjohn J, Gras S. A molecular basis for the interplay between T cells, viral mutants, and human leukocyte antigen micropolymorphism. J Biol Chem 2014; 289:16688-98. [PMID: 24759101 DOI: 10.1074/jbc.m114.563502] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mutations within T cell epitopes represent a common mechanism of viral escape from the host protective immune response. The diverse T cell repertoire and the extensive human leukocyte antigen (HLA) polymorphism across populations is the evolutionary response to viral mutation. However, the molecular basis underpinning the interplay between HLA polymorphism, the T cell repertoire, and viral escape is unclear. Here we investigate the T cell response to a HLA-B*35:01- and HLA-B*35:08-restricted (407)HPVGEADYFEY(417) epitope from Epstein-Barr virus and naturally occurring variants at positions 4 and 5 thereof. Each viral variant differently impacted on the epitope's flexibility and conformation when bound to HLA-B*35:08 or HLA-B*35:01. We provide a molecular basis for understanding how the single residue polymorphism that discriminates between HLA-B*35:01/08 profoundly impacts on T cell receptor recognition. Surprisingly, one viral variant (P5-Glu to P5-Asp) effectively changed restriction preference from HLA-B*35:01 to HLA-B*35:08. Collectively, our study portrays the interplay between the T cell response, viral escape, and HLA polymorphism, whereby HLA polymorphism enables altered presentation of epitopes from different strains of Epstein-Barr virus.
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Affiliation(s)
- Yu Chih Liu
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Melbourne 3800, Australia
| | - Zhenjun Chen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Michelle A Neller
- QIMR Berghofer Medical Research Institute and QIMR Berghofer Centre for Immunotherapy and Vaccine Development, Brisbane, Queensland 4006, Australia
| | - John J Miles
- QIMR Berghofer Medical Research Institute and QIMR Berghofer Centre for Immunotherapy and Vaccine Development, Brisbane, Queensland 4006, Australia
| | - Anthony W Purcell
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Melbourne 3800, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Scott R Burrows
- QIMR Berghofer Medical Research Institute and QIMR Berghofer Centre for Immunotherapy and Vaccine Development, Brisbane, Queensland 4006, Australia
| | - Jamie Rossjohn
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Melbourne 3800, Australia, Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN Wales, United Kingdom, and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Stephanie Gras
- From the Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Melbourne 3800, Australia, Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
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47
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Thorborn G, Young GR, Kassiotis G. Effective T helper cell responses against retroviruses: are all clonotypes equal? J Leukoc Biol 2014; 96:27-37. [PMID: 24737804 DOI: 10.1189/jlb.2ri0613-347r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The critical importance of CD4(+) T cells in coordinating innate and adaptive immune responses is evidenced by the susceptibility to various pathogenic and opportunistic infections that arises from primary or acquired CD4(+) T cell immunodeficiency, such as following HIV-1 infection. However, despite the clearly defined roles of cytotoxic CD8(+) T cells and antibodies in host protection from retroviruses, the ability of CD4(+) T cells to exert a similar function remains unclear. Recent studies in various settings have drawn attention to the complexity of the T cell response within and between individuals. Distinct TCR clonotypes within an individual differ substantially in their response to the same epitope. Functionally similar, "public" TCR clonotypes can also dominate the response of different individuals. TCR affinity for antigen directly influences expansion and differentiation of responding T cells, also likely affecting their ultimate protective capacity. With this increasing understanding of the parameters that determine the magnitude and effector type of the T cell response, we are now better equipped to address the protective capacity against retroviruses of CD4(+) T cell clonotypes induced by natural infection or vaccination.
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Affiliation(s)
| | - George R Young
- Divisions of Immunoregulation and Virology, Medical Research Council National Institute for Medical Research, The Ridgeway, London, United Kingdom; and
| | - George Kassiotis
- Divisions of Immunoregulation and Department of Medicine, Faculty of Medicine, Imperial College London, United Kingdom
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48
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Brennan RM, Burrows JM, Elliott T, Neller MA, Gras S, Rossjohn J, Miles JJ, Burrows SR. Missense single nucleotide polymorphisms in the human T cell receptor loci control variable gene usage in the T cell repertoire. Br J Haematol 2014; 166:148-52. [PMID: 24646048 DOI: 10.1111/bjh.12830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rebekah M Brennan
- QIMR Berghofer Medical Research Institute, Brisbane, Qld, Australia.
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49
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Bhati M, Cole DK, McCluskey J, Sewell AK, Rossjohn J. The versatility of the αβ T-cell antigen receptor. Protein Sci 2014; 23:260-72. [PMID: 24375592 DOI: 10.1002/pro.2412] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Revised: 12/20/2013] [Accepted: 12/20/2013] [Indexed: 02/06/2023]
Abstract
The T-cell antigen receptor is a heterodimeric αβ protein (TCR) expressed on the surface of T-lymphocytes, with each chain of the TCR comprising three complementarity-determining regions (CDRs) that collectively form the antigen-binding site. Unlike antibodies, which are closely related proteins that recognize intact protein antigens, TCRs classically bind, via their CDR loops, to peptides (p) that are presented by molecules of the major histocompatibility complex (MHC). This TCR-pMHC interaction is crucially important in cell-mediated immunity, with the specificity in the cellular immune response being attributable to MHC polymorphism, an extensive TCR repertoire and a variable peptide cargo. The ensuing structural and biophysical studies within the TCR-pMHC axis have been highly informative in understanding the fundamental events that underpin protective immunity and dysfunctional T-cell responses that occur during autoimmunity. In addition, TCRs can recognize the CD1 family, a family of MHC-related molecules that instead of presenting peptides are ideally suited to bind lipid-based antigens. Structural studies within the CD1-lipid antigen system are beginning to inform us how lipid antigens are specifically presented by CD1, and how such CD1-lipid antigen complexes are recognized by the TCR. Moreover, it has recently been shown that certain TCRs can bind to vitamin B based metabolites that are bound to an MHC-like molecule termed MR1. Thus, TCRs can recognize peptides, lipids, and small molecule metabolites, and here we review the basic principles underpinning this versatile and fascinating receptor recognition system that is vital to a host's survival.
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Affiliation(s)
- Mugdha Bhati
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, 3800, Australia
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50
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Cole DK, Miles KM, Madura F, Holland CJ, Schauenburg AJA, Godkin AJ, Bulek AM, Fuller A, Akpovwa HJE, Pymm PG, Liddy N, Sami M, Li Y, Rizkallah PJ, Jakobsen BK, Sewell AK. T-cell receptor (TCR)-peptide specificity overrides affinity-enhancing TCR-major histocompatibility complex interactions. J Biol Chem 2014; 289:628-38. [PMID: 24196962 PMCID: PMC3887192 DOI: 10.1074/jbc.m113.522110] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 10/22/2013] [Indexed: 11/17/2022] Open
Abstract
αβ T-cell receptors (TCRs) engage antigens using complementarity-determining region (CDR) loops that are either germ line-encoded (CDR1 and CDR2) or somatically rearranged (CDR3). TCR ligands compose a presentation platform (major histocompatibility complex (MHC)) and a variable antigenic component consisting of a short "foreign" peptide. The sequence of events when the TCR engages its peptide-MHC (pMHC) ligand remains unclear. Some studies suggest that the germ line elements of the TCR engage the MHC prior to peptide scanning, but this order of binding is difficult to reconcile with some TCR-pMHC structures. Here, we used TCRs that exhibited enhanced pMHC binding as a result of mutations in either CDR2 and/or CDR3 loops, that bound to the MHC or peptide, respectively, to dissect the roles of these loops in stabilizing TCR-pMHC interactions. Our data show that TCR-peptide interactions play a strongly dominant energetic role providing a binding mode that is both temporally and energetically complementary with a system requiring positive selection by self-pMHC in the thymus and rapid recognition of non-self-pMHC in the periphery.
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MESH Headings
- Amino Acid Sequence
- Binding, Competitive
- Complementarity Determining Regions/chemistry
- Complementarity Determining Regions/genetics
- Complementarity Determining Regions/metabolism
- Crystallography, X-Ray
- HLA Antigens/chemistry
- HLA Antigens/genetics
- HLA Antigens/metabolism
- HLA-A2 Antigen/chemistry
- HLA-A2 Antigen/genetics
- HLA-A2 Antigen/metabolism
- Humans
- Kinetics
- Ligands
- Models, Molecular
- Molecular Sequence Data
- Mutation
- Oligopeptides/chemistry
- Oligopeptides/metabolism
- Peptides/chemistry
- Peptides/metabolism
- Protein Binding
- Protein Structure, Tertiary
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- T-Cell Antigen Receptor Specificity
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Affiliation(s)
- David K. Cole
- From Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN
| | - Kim M. Miles
- From Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN
| | - Florian Madura
- From Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN
| | | | | | - Andrew J. Godkin
- From Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN
| | - Anna M. Bulek
- From Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN
| | - Anna Fuller
- From Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN
| | | | - Phillip G. Pymm
- From Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN
- the Medical Research Council Human Immunology Unit, Weatherall Institute for Molecular Medicine, University of Oxford, Oxford 0X3 9DS, and
| | - Nathaniel Liddy
- Immunocore Ltd., 57C Milton Park, Abingdon OX14 4RX, United Kingdom
| | - Malkit Sami
- Immunocore Ltd., 57C Milton Park, Abingdon OX14 4RX, United Kingdom
| | - Yi Li
- Immunocore Ltd., 57C Milton Park, Abingdon OX14 4RX, United Kingdom
| | | | - Bent K. Jakobsen
- Immunocore Ltd., 57C Milton Park, Abingdon OX14 4RX, United Kingdom
| | - Andrew K. Sewell
- From Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN
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