1
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Zhang T, Zhang X, Chen J, Zhang X, Zhang Y. Harnessing microbial antigens as cancer antigens: a promising avenue for cancer immunotherapy. Front Immunol 2024; 15:1411490. [PMID: 39139570 PMCID: PMC11319170 DOI: 10.3389/fimmu.2024.1411490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 07/16/2024] [Indexed: 08/15/2024] Open
Abstract
Immunotherapy has revolutionized cancer treatment by leveraging the immune system's innate capabilities to combat malignancies. Despite the promise of tumor antigens in stimulating anti-tumor immune responses, their clinical utility is hampered by limitations in eliciting robust and durable immune reactions, exacerbated by tumor heterogeneity and immune evasion mechanisms. Recent insights into the immunogenic properties of host homologous microbial antigens have sparked interest in their potential for augmenting anti-tumor immunity while minimizing off-target effects. This review explores the therapeutic potential of microbial antigen peptides in tumor immunotherapy, beginning with an overview of tumor antigens and their challenges in clinical translation. We further explore the intricate relationship between microorganisms and tumor development, elucidating the concept of molecular mimicry and its implications for immune recognition of tumor-associated antigens. Finally, we discuss methodologies for identifying and characterizing microbial antigen peptides, highlighting their immunogenicity and prospects for therapeutic application.
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Affiliation(s)
- Tao Zhang
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
- Department of Biomedical Engineering, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China
| | - Xilong Zhang
- Department of Burns and Plastic Surgery, First People’s Hospital of Xuzhou City, Xuzhou, China
| | - Jianquan Chen
- Central Laboratory, Translational Medicine Research Center, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
| | - Xiuwei Zhang
- Department of Burns and Plastic Surgery, First People’s Hospital of Xuzhou City, Xuzhou, China
| | - Yunlei Zhang
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
- Department of Biomedical Engineering, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China
- Central Laboratory, Translational Medicine Research Center, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
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2
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Acuto O. T-cell virtuosity in ''knowing thyself". Front Immunol 2024; 15:1343575. [PMID: 38415261 PMCID: PMC10896960 DOI: 10.3389/fimmu.2024.1343575] [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: 11/23/2023] [Accepted: 01/17/2024] [Indexed: 02/29/2024] Open
Abstract
Major Histocompatibility Complex (MHC) I and II and the αβ T-cell antigen receptor (TCRαβ) govern fundamental traits of adaptive immunity. They form a membrane-borne ligand-receptor system weighing host proteome integrity to detect contamination by nonself proteins. MHC-I and -II exhibit the "MHC-fold", which is able to bind a large assortment of short peptides as proxies for self and nonself proteins. The ensuing varying surfaces are mandatory ligands for Ig-like TCRαβ highly mutable binding sites. Conserved molecular signatures guide TCRαβ ligand binding sites to focus on the MHC-fold (MHC-restriction) while leaving many opportunities for its most hypervariable determinants to contact the peptide. This riveting molecular strategy affords many options for binding energy compatible with specific recognition and signalling aimed to eradicated microbial pathogens and cancer cells. While the molecular foundations of αβ T-cell adaptive immunity are largely understood, uncertainty persists on how peptide-MHC binding induces the TCRαβ signals that instruct cell-fate decisions. Solving this mystery is another milestone for understanding αβ T-cells' self/nonself discrimination. Recent developments revealing the innermost links between TCRαβ structural dynamics and signalling modality should help dissipate this long-sought-after enigma.
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Affiliation(s)
- Oreste Acuto
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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3
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Zhang J, Ma W, Yao H. Accurate TCR-pMHC interaction prediction using a BERT-based transfer learning method. Brief Bioinform 2023; 25:bbad436. [PMID: 38040492 PMCID: PMC10783865 DOI: 10.1093/bib/bbad436] [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: 08/04/2023] [Revised: 10/05/2023] [Accepted: 11/06/2023] [Indexed: 12/03/2023] Open
Abstract
Accurate prediction of TCR-pMHC binding is important for the development of cancer immunotherapies, especially TCR-based agents. Existing algorithms often experience diminished performance when dealing with unseen epitopes, primarily due to the complexity in TCR-pMHC recognition patterns and the scarcity of available data for training. We have developed a novel deep learning model, 'TCR Antigen Binding Recognition' based on BERT, named as TABR-BERT. Leveraging BERT's potent representation learning capabilities, TABR-BERT effectively captures essential information regarding TCR-pMHC interactions from TCR sequences, antigen epitope sequences and epitope-MHC binding. By transferring this knowledge to predict TCR-pMHC recognition, TABR-BERT demonstrated better results in benchmark tests than existing methods, particularly for unseen epitopes.
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Affiliation(s)
- Jiawei Zhang
- Fresh Wind Biotechnologies Inc. (Tianjin), Tianjin, China
| | - Wang Ma
- Fresh Wind Biotechnologies Inc. (Tianjin), Tianjin, China
| | - Hui Yao
- Fresh Wind Biotechnologies USA Inc., Houston, TX, USA
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4
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Boughter CT, Meier-Schellersheim M. Conserved biophysical compatibility among the highly variable germline-encoded regions shapes TCR-MHC interactions. eLife 2023; 12:e90681. [PMID: 37861280 PMCID: PMC10631762 DOI: 10.7554/elife.90681] [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: 07/03/2023] [Accepted: 10/19/2023] [Indexed: 10/21/2023] Open
Abstract
T cells are critically important components of the adaptive immune system primarily responsible for identifying and responding to pathogenic challenges. This recognition of pathogens is driven by the interaction between membrane-bound T cell receptors (TCRs) and antigenic peptides presented on major histocompatibility complex (MHC) molecules. The formation of the TCR-peptide-MHC complex (TCR-pMHC) involves interactions among germline-encoded and hypervariable amino acids. Germline-encoded and hypervariable regions can form contacts critical for complex formation, but only interactions between germline-encoded contacts are likely to be shared across many of all the possible productive TCR-pMHC complexes. Despite this, experimental investigation of these interactions have focused on only a small fraction of the possible interaction space. To address this, we analyzed every possible germline-encoded TCR-MHC contact in humans, thereby generating the first comprehensive characterization of these largely antigen-independent interactions. Our computational analysis suggests that germline-encoded TCR-MHC interactions that are conserved at the sequence level are rare due to the high amino acid diversity of the TCR CDR1 and CDR2 loops, and that such conservation is unlikely to dominate the dynamic protein-protein binding interface. Instead, we propose that binding properties such as the docking orientation are defined by regions of biophysical compatibility between these loops and the MHC surface.
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Affiliation(s)
- Christopher T Boughter
- Computational Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
| | - Martin Meier-Schellersheim
- Computational Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of HealthBethesdaUnited States
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5
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Boughter CT, Meier-Schellersheim M. An integrated approach to the characterization of immune repertoires using AIMS: An Automated Immune Molecule Separator. PLoS Comput Biol 2023; 19:e1011577. [PMID: 37862356 PMCID: PMC10619816 DOI: 10.1371/journal.pcbi.1011577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 11/01/2023] [Accepted: 10/06/2023] [Indexed: 10/22/2023] Open
Abstract
The adaptive immune system employs an array of receptors designed to respond with high specificity to pathogens or molecular aberrations faced by the host organism. Binding of these receptors to molecular fragments-collectively referred to as antigens-initiates immune responses. These antigenic targets are recognized in their native state on the surfaces of pathogens by antibodies, whereas T cell receptors (TCR) recognize processed antigens as short peptides, presented on major histocompatibility complex (MHC) molecules. Recent research has led to a wealth of immune repertoire data that are key to interrogating the nature of these molecular interactions. However, existing tools for the analysis of these large datasets typically focus on molecular sets of a single type, forcing researchers to separately analyze strongly coupled sequences of interacting molecules. Here, we introduce a software package for the integrated analysis of immune repertoire data, capable of identifying distinct biophysical differences in isolated TCR, MHC, peptide, antibody, and antigen sequence data. This integrated analytical approach allows for direct comparisons across immune repertoire subsets and provides a starting point for the identification of key interaction hotspots in complementary receptor-antigen pairs. The software (AIMS-Automated Immune Molecule Separator) is freely available as an open access package in GUI or command-line form.
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Affiliation(s)
- Christopher T. Boughter
- Computational Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Martin Meier-Schellersheim
- Computational Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
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6
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Morita D, Asa M, Sugita M. Engagement with the TCR induces plasticity in antigenic ligands bound to MHC class I and CD1 molecules. Int Immunol 2023; 35:7-17. [PMID: 36053252 DOI: 10.1093/intimm/dxac046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 08/31/2022] [Indexed: 01/25/2023] Open
Abstract
Complementarity-determining regions (CDRs) of αβ T-cell receptors (TCRs) sense peptide-bound MHC (pMHC) complexes via chemical interactions, thereby mediating antigen specificity and MHC restriction. Flexible finger-like movement of CDR loops contributes to the establishment of optimal interactions with pMHCs. In contrast, peptide ligands captured in MHC molecules are considered more static because of the rigid hydrogen-bond network that stabilizes peptide ligands in the antigen-binding groove of MHC molecules. An array of crystal structures delineating pMHC complexes in TCR-docked and TCR-undocked forms is now available, which enables us to assess TCR engagement-induced conformational changes in peptide ligands. In this short review, we overview conformational changes in MHC class I-bound peptide ligands upon TCR docking, followed by those for CD1-bound glycolipid ligands. Finally, we analyze the co-crystal structure of the TCR:lipopeptide-bound MHC class I complex that we recently reported. We argue that TCR engagement-induced conformational changes markedly occur in lipopeptide ligands, which are essential for exposure of a primary T-cell epitope to TCRs. These conformational changes are affected by amino acid residues, such as glycine, that do not interact directly with TCRs. Thus, ligand recognition by specific TCRs involves not only T-cell epitopes but also non-epitopic amino acid residues. In light of their critical function, we propose to refer to these residues as non-epitopic residues affecting ligand plasticity and antigenicity (NR-PA).
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Affiliation(s)
- Daisuke Morita
- Laboratory of Cell Regulation, Institute for Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.,Laboratory of Cell Regulation and Molecular Network, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Minori Asa
- Laboratory of Cell Regulation, Institute for Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.,Laboratory of Cell Regulation and Molecular Network, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masahiko Sugita
- Laboratory of Cell Regulation, Institute for Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.,Laboratory of Cell Regulation and Molecular Network, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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7
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Nandigrami P, Szczepaniak F, Boughter CT, Dehez F, Chipot C, Roux B. Computational Assessment of Protein-Protein Binding Specificity within a Family of Synaptic Surface Receptors. J Phys Chem B 2022; 126:7510-7527. [PMID: 35787023 DOI: 10.1021/acs.jpcb.2c02173] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Atomic-level information is essential to explain the formation of specific protein complexes in terms of structure and dynamics. The set of Dpr and DIP proteins, which play a key role in the neuromorphogenesis in the nervous system of Drosophila melanogaster, offer a rich paradigm to learn about protein-protein recognition. Many members of the DIP subfamily cross-react with several members of the Dpr family and vice versa. While there exists a total of 231 possible Dpr-DIP heterodimer complexes from the 21 Dpr and 11 DIP proteins, only 57 "cognate" pairs have been detected by surface plasmon resonance (SPR) experiments, suggesting that the remaining 174 pairs have low or unreliable binding affinity. Our goal is to assess the performance of computational approaches to characterize the global set of interactions between Dpr and DIP proteins and identify the specificity of binding between each DIP with their corresponding Dpr binding partners. In addition, we aim to characterize how mutations influence the specificity of the binding interaction. In this work, a wide range of knowledge-based and physics-based approaches are utilized, including mutual information, linear discriminant analysis, homology modeling, molecular dynamics simulations, Poisson-Boltzmann continuum electrostatics calculations, and alchemical free energy perturbation to decipher the origin of binding specificity of the Dpr-DIP complexes examined. Ultimately, the results show that those two broad strategies are complementary, with different strengths and limitations. Biological inter-relations are more clearly revealed through knowledge-based approaches combining evolutionary and structural features, the molecular determinants controlling binding specificity can be predicted accurately with physics-based approaches based on atomic models.
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Affiliation(s)
- Prithviraj Nandigrami
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Florence Szczepaniak
- Unité Mixte de Recherche No. 7019, Université de Lorraine, B.P. 70239, 54506 Vandœuvre-lès-Nancy cedex, France
| | - Christopher T Boughter
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - François Dehez
- Unité Mixte de Recherche No. 7019, Université de Lorraine, B.P. 70239, 54506 Vandœuvre-lès-Nancy cedex, France
| | - Christophe Chipot
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, United States.,Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Unité Mixte de Recherche No. 7019, Université de Lorraine, B.P. 70239, 54506 Vandœuvre-lès-Nancy cedex, France.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
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8
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Abdulhaqq S, Ventura AB, Reed JS, Bashirova AA, Bateman KB, McDonald E, Wu HL, Greene JM, Schell JB, Morrow D, Wisskirchen K, Martin JN, Deeks SG, Carrington M, Protzer U, Früh K, Hansen SG, Picker LJ, Sacha JB, Bimber BN. Identification and Characterization of Antigen-Specific CD8 + T Cells Using Surface-Trapped TNF-α and Single-Cell Sequencing. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:2913-2921. [PMID: 34810222 PMCID: PMC9124229 DOI: 10.4049/jimmunol.2100535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/15/2021] [Indexed: 12/31/2022]
Abstract
CD8+ T cells are key mediators of antiviral and antitumor immunity. The isolation and study of Ag-specific CD8+ T cells, as well as mapping of their MHC restriction, has practical importance to the study of disease and the development of therapeutics. Unfortunately, most experimental approaches are cumbersome, owing to the highly variable and donor-specific nature of MHC-bound peptide/TCR interactions. Here we present a novel system for rapid identification and characterization of Ag-specific CD8+ T cells, particularly well suited for samples with limited primary cells. Cells are stimulated ex vivo with Ag of interest, followed by live cell sorting based on surface-trapped TNF-α. We take advantage of major advances in single-cell sequencing to generate full-length sequence data from the paired TCR α- and β-chains from these Ag-specific cells. The paired TCR chains are cloned into retroviral vectors and used to transduce donor CD8+ T cells. These TCR transductants provide a virtually unlimited experimental reagent, which can be used for further characterization, such as minimal epitope mapping or identification of MHC restriction, without depleting primary cells. We validated this system using CMV-specific CD8+ T cells from rhesus macaques, characterizing an immunodominant Mamu-A1*002:01-restricted epitope. We further demonstrated the utility of this system by mapping a novel HLA-A*68:02-restricted HIV Gag epitope from an HIV-infected donor. Collectively, these data validate a new strategy to rapidly identify novel Ags and characterize Ag-specific CD8+ T cells, with applications ranging from the study of infectious disease to immunotherapeutics and precision medicine.
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Affiliation(s)
- Shaheed Abdulhaqq
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Abigail B Ventura
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Jason S Reed
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Arman A Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Katherine B Bateman
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Eric McDonald
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Helen L Wu
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Justin M Greene
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - John B Schell
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - David Morrow
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Karin Wisskirchen
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum Munich, Munich, Germany
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA
| | - Steven G Deeks
- HIV/AIDS Program, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA; and
| | - Ulrike Protzer
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum Munich, Munich, Germany
| | - Klaus Früh
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Scott G Hansen
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Louis J Picker
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR
| | - Jonah B Sacha
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR;
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR
| | - Benjamin N Bimber
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR
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9
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Baxter-Lowe LA. The changing landscape of HLA typing: Understanding how and when HLA typing data can be used with confidence from bench to bedside. Hum Immunol 2021; 82:466-477. [PMID: 34030895 DOI: 10.1016/j.humimm.2021.04.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022]
Abstract
Human leukocyte antigen (HLA) genes are extraordinary for their extreme diversity and widespread impact on human health and disease. More than 30,000 HLA alleles have been officially named and more alleles continue to be discovered at a rapid pace. HLA typing systems which have been developed to detect HLA diversity have advanced rapidly and are revolutionizing our understanding of HLA's clinical importance. However, continuous improvements in knowledge and technology have created challenges for clinicians and scientists. This review explains how differences in HLA typing systems can impact the HLA types that are assigned. The consequences of differences in laboratory testing methods and reference databases are described. The challenges of using HLA types that are not equivalent are illustrated. A fundamental understanding of the continual expansion of our understanding of HLA diversity and limitations in some of the typing data is essential for using typing data appropriately in clinical and research settings.
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Affiliation(s)
- Lee Ann Baxter-Lowe
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, USA; Department of Pathology, University of Southern California, USA.
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10
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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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11
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SARS-CoV-2 transcriptome analysis and molecular cataloguing of immunodominant epitopes for multi-epitope based vaccine design. Genomics 2020; 112:5044-5054. [PMID: 32920121 PMCID: PMC7500163 DOI: 10.1016/j.ygeno.2020.09.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/18/2020] [Accepted: 09/08/2020] [Indexed: 01/12/2023]
Abstract
Genomics-led researches are engaged in tracing virus expression pattern, and induced immune responses in human to develop effective vaccine against COVID-19. In this study, targeted expression profiling and differential gene expression analysis of major histocompatibility complexes and innate immune system genes were performed through SARS-CoV-2 infected RNA-seq data of human cell line, and virus transcriptome was generated for T-and B-cell epitope prediction. Docking studies of epitopes with MHC and B-cell receptors were performed to identify potential T-and B-cell epitopes. Transcriptome analysis revealed the specific multiple allele expressions in cell line, genes for elicited induce immune response, and virus gene expression. Proposed T- and B-cell epitopes have high potential to elicit equivalent immune responses caused by SARS-CoV-2 infection which can be useful to provide links between elicited immune response and virus gene expression. This study will facilitate in vitro and in vivo vaccine related research studies in disease control. SARS-CoV-2 transcriptome construction from RNA-seq data of infected human cell-lines. T- and B-cell epitopes from SARS-CoV-2 transcriptome Gene expression profiling of MHC alleles and innate immune system genes
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12
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Croft NP. Peptide Presentation to T Cells: Solving the Immunogenic Puzzle: Systems Immunology Profiling of Antigen Presentation for Prediction of CD8 + T Cell Immunogenicity. Bioessays 2020; 42:e1900200. [PMID: 31958157 DOI: 10.1002/bies.201900200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/18/2019] [Indexed: 02/02/2023]
Abstract
The vertebrate immune system uses an impressive arsenal of mechanisms to combat harmful cellular states such as infection. One way is via cells delivering real-time snapshots of their protein content to the cell surface in the form of short peptides. Specialized immune cells (T cells) sample these peptides and assess whether they are foreign, warranting an action such as destruction of the infected cell. The delivery of peptides to the cell surface is termed antigen processing and presentation, and decades of research have provided unprecedented understanding of this process. However, predicting the capacity for a given peptide to be immunogenic-to elicit a T cell response-has remained both enigmatic and a long sought-after goal. In the era of big data, a point is being approached where the steps of antigen processing and presentation can be quantified and assessed against peptide immunogenicity in order to build predictive models. This review presents new findings in this area and contemplates challenges ahead.
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Affiliation(s)
- Nathan P Croft
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
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13
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Ji W, Niu L, Peng W, Zhang Y, Cheng H, Gao F, Shi Y, Qi J, Gao GF, Liu WJ. Salt bridge-forming residues positioned over viral peptides presented by MHC class I impacts T-cell recognition in a binding-dependent manner. Mol Immunol 2019; 112:274-282. [PMID: 31226552 PMCID: PMC7112684 DOI: 10.1016/j.molimm.2019.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/05/2019] [Accepted: 06/09/2019] [Indexed: 11/28/2022]
Abstract
Crystal structure of HLA-B*4001 was determined. The salt bridges in HLA-B*4001 and H-2Kd have different structural characteristics. MHC I mutations that disrupt the salt bridge alleviate peptide binding. Mutations of the salt bridge-forming residues may impact TCR recognition, directly or indirectly.
The viral peptides presentation by major histocompatibility complex class I (MHC I) molecules play a pivotal role in T-cell recognition and the subsequent virus clearance. This process is delicately adjusted by the variant residues of MHC I, especially the residues in the peptide binding groove (PBG). In a series of MHC I molecules, a salt bridge is formed above the N-terminus of the peptides. However, the potential impact of the salt bridge on peptide binding and T-cell receptor (TCR) recognition of MHC I, as well as the corresponding molecular basis, are still largely unknown. Herein, we determined the structures of HLA-B*4001 and H-2Kd in which two different types of salt bridges (Arg62-Glu163 or Arg66-Glu163) across the PBG were observed. Although the two salt bridges led to different conformation shifts of both the MHC I α helix and the peptides, binding of the peptides with the salt bridge residues was relatively conserved. Furthermore, through a series of in vitro and in vivo investigations, we found that MHC I mutations that disrupt the salt bridge alleviate peptide binding and can weaken the TCR recognition of MHC I-peptide complexes. Our study may provide key references for understanding MHC I-restricted peptide recognition by T-cells.
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Affiliation(s)
- Wei Ji
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Ling Niu
- CAS Key Laboratory for Pathogenic Microbiology and Immunology, Chinese Academy of Sciences, Beijing 100101, China
| | - Weiyu Peng
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Yongli Zhang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Hao Cheng
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Feng Gao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yi Shi
- CAS Key Laboratory for Pathogenic Microbiology and Immunology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Qi
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - George F Gao
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China; CAS Key Laboratory for Pathogenic Microbiology and Immunology, Chinese Academy of Sciences, Beijing 100101, China; Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.
| | - William J Liu
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China; School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
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14
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Tedeschi V, Alba J, Paladini F, Paroli M, Cauli A, Mathieu A, Sorrentino R, D'Abramo M, Fiorillo MT. Unusual Placement of an EBV Epitope into the Groove of the Ankylosing Spondylitis-Associated HLA-B27 Allele Allows CD8+ T Cell Activation. Cells 2019; 8:cells8060572. [PMID: 31212633 PMCID: PMC6627668 DOI: 10.3390/cells8060572] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/06/2019] [Accepted: 06/08/2019] [Indexed: 02/02/2023] Open
Abstract
The human leukocyte antigen HLA-B27 is a strong risk factor for Ankylosing Spondylitis (AS), an immune-mediated disorder affecting axial skeleton and sacroiliac joints. Additionally, evidence exists sustaining a strong protective role for HLA-B27 in viral infections. These two aspects could stem from common molecular mechanisms. Recently, we have found that the HLA-B*2705 presents an EBV epitope (pEBNA3A-RPPIFIRRL), lacking the canonical B27 binding motif but known as immunodominant in the HLA-B7 context of presentation. Notably, 69% of B*2705 carriers, mostly patients with AS, possess B*2705-restricted, pEBNA3A-specific CD8+ T cells. Contrarily, the non-AS-associated B*2709 allele, distinguished from the B*2705 by the single His116Asp polymorphism, is unable to display this peptide and, accordingly, B*2709 healthy subjects do not unleash specific T cell responses. Herein, we investigated whether the reactivity towards pEBNA3A could be a side effect of the recognition of the natural longer peptide (pKEBNA3A) having the classical B27 consensus (KRPPIFIRRL). The stimulation of PBMC from B*2705 positive patients with AS in parallel with both pEBNA3A and pKEBNA3A did not allow to reach an unambiguous conclusion since the differences in the magnitude of the response measured as percentage of IFNγ-producing CD8+ T cells were not statistically significant. Interestingly, computational analysis suggested a structural shift of pEBNA3A as well as of pKEBNA3A into the B27 grooves, leaving the A pocket partially unfilled. To our knowledge this is the first report of a viral peptide: HLA-B27 complex recognized by TCRs in spite of a partially empty groove. This implies a rethinking of the actual B27 immunopeptidome crucial for viral immune-surveillance and autoimmunity.
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Affiliation(s)
- Valentina Tedeschi
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, 00185 Rome, Italy.
| | - Josephine Alba
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy.
| | - Fabiana Paladini
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, 00185 Rome, Italy.
| | - Marino Paroli
- Division of Clinical Immunology and Rheumatology, Department of Biotechnology and Medical Surgical Sciences, Sapienza University of Rome, 00185 Rome, Italy.
| | - Alberto Cauli
- Rheumatology Unit, Department of Medical Sciences and Public Health, University and AOU of Cagliari, Monserrato, 09042 Cagliari, Italy.
| | - Alessandro Mathieu
- Rheumatology Unit, Department of Medical Sciences and Public Health, University and AOU of Cagliari, Monserrato, 09042 Cagliari, Italy.
| | - Rosa Sorrentino
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, 00185 Rome, Italy.
| | - Marco D'Abramo
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy.
| | - Maria Teresa Fiorillo
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, 00185 Rome, Italy.
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15
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Genomic evidence for shared common ancestry of East African hunting-gathering populations and insights into local adaptation. Proc Natl Acad Sci U S A 2019; 116:4166-4175. [PMID: 30782801 DOI: 10.1073/pnas.1817678116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Anatomically modern humans arose in Africa ∼300,000 years ago, but the demographic and adaptive histories of African populations are not well-characterized. Here, we have generated a genome-wide dataset from 840 Africans, residing in western, eastern, southern, and northern Africa, belonging to 50 ethnicities, and speaking languages belonging to four language families. In addition to agriculturalists and pastoralists, our study includes 16 populations that practice, or until recently have practiced, a hunting-gathering (HG) lifestyle. We observe that genetic structure in Africa is broadly correlated not only with geography, but to a lesser extent, with linguistic affiliation and subsistence strategy. Four East African HG (EHG) populations that are geographically distant from each other show evidence of common ancestry: the Hadza and Sandawe in Tanzania, who speak languages with clicks classified as Khoisan; the Dahalo in Kenya, whose language has remnant clicks; and the Sabue in Ethiopia, who speak an unclassified language. Additionally, we observed common ancestry between central African rainforest HGs and southern African San, the latter of whom speak languages with clicks classified as Khoisan. With the exception of the EHG, central African rainforest HGs, and San, other HG groups in Africa appear genetically similar to neighboring agriculturalist or pastoralist populations. We additionally demonstrate that infectious disease, immune response, and diet have played important roles in the adaptive landscape of African history. However, while the broad biological processes involved in recent human adaptation in Africa are often consistent across populations, the specific loci affected by selective pressures more often vary across populations.
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16
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Riley TP, Baker BM. The intersection of affinity and specificity in the development and optimization of T cell receptor based therapeutics. Semin Cell Dev Biol 2018; 84:30-41. [DOI: 10.1016/j.semcdb.2017.10.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 10/07/2017] [Accepted: 10/17/2017] [Indexed: 12/29/2022]
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17
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CD8 + T-Cell Response-Associated Evolution of Hepatitis B Virus Core Protein and Disease Progress. J Virol 2018; 92:JVI.02120-17. [PMID: 29950410 DOI: 10.1128/jvi.02120-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 06/05/2018] [Indexed: 12/13/2022] Open
Abstract
Under the immune pressure of cytotoxic T cells (CTLs), hepatitis B virus (HBV) evolves to accumulate mutations more likely within epitopes to evade immune detection. However, little is known about the specific patterns of the immune pressure-associated HBV mutation of T-cell epitopes and their link to disease progression. Here, we observed a correlation of the accumulated variants on HBV core protein (HBc) with the disease severity of HBV infection. Further analysis indicated that these substitutions were mostly located within CD8+ T-cell epitopes of HBc protein, which were systematically screened and identified in an unbiased manner in our study. From individual peptide level to the human leukocyte antigen I (HLA-I)-restricted population level, we elucidated that the mutations in these well-defined HLA-I-restricted T-cell epitopes significantly decreased antiviral activity-specific CTLs and were positively associated with clinical parameters and disease progression in HBV-infected patients. The molecular pattern for viral epitope variations based on the sequencing of 105 HBV virus genomes indicated that the C-terminal portion (Pc), especially the Pc-1 and Pc-2 positions, have the highest mutation rates. Further structural analysis of HLA-A*02 complexed to diverse CD8+ T-cell epitopes revealed that the highly variable C-terminal bulged peak of M-shaped HBc-derived epitopes are solvent exposed, and most of the CDR3βs of the T-cell receptor hover over them. These data shed light on the molecular and immunological mechanisms of T-cell immunity-associated viral evolution in hepatitis B progression, which is beneficial for designing immunotherapies and vaccines.IMPORTANCE The specific patterns of sequence polymorphisms of T-cell epitopes and the immune mechanisms of the HBV epitope mutation-linked disease progression are largely unclear. In this study, we systematically evaluated the contribution of CD8+ T cells to the disease progress-associated evolution of HBV. By evaluation of patient T-cell responses based on the peptide repertoire, we comprehensively characterized the association of clinical parameters in chronic hepatitis B with the antiviral T-cell response-associated mutations of the viruses from the single-epitope level to the overall HLA-I-restricted peptide levels. Furthermore, we investigated the molecular basis of the HLA-A2-restricted peptide immune escape and found that the solvent-exposed C-terminal portion of the epitopes is highly variable under CDR3β recognition. Our work may provide a comprehensive evaluation of viral mutations impacted by the host CTL response in HBV disease progression in the context of the full repertoire of HBc-derived epitopes.
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18
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Sant S, Grzelak L, Wang Z, Pizzolla A, Koutsakos M, Crowe J, Loudovaris T, Mannering SI, Westall GP, Wakim LM, Rossjohn J, Gras S, Richards M, Xu J, Thomas PG, Loh L, Nguyen THO, Kedzierska K. Single-Cell Approach to Influenza-Specific CD8 + T Cell Receptor Repertoires Across Different Age Groups, Tissues, and Following Influenza Virus Infection. Front Immunol 2018; 9:1453. [PMID: 29997621 PMCID: PMC6030351 DOI: 10.3389/fimmu.2018.01453] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/12/2018] [Indexed: 11/13/2022] Open
Abstract
CD8+ T cells recognizing antigenic peptides derived from conserved internal viral proteins confer broad protection against distinct influenza viruses. As memory CD8+ T cells change throughout the human lifetime and across tissue compartments, we investigated how T cell receptor (TCR) composition and diversity relate to memory CD8+ T cells across anatomical sites and immunological phases of human life. We used ex vivo peptide-HLA tetramer magnetic enrichment, single-cell multiplex RT-PCR for both the TCR-alpha (TCRα) and TCR-beta (TCRβ) chains, and new TCRdist and grouping of lymphocyte interactions by paratope hotspots (GLIPH) algorithms to compare TCRs directed against the most prominent human influenza epitope, HLA-A*02:01-M158–66 (A2+M158). We dissected memory TCR repertoires directed toward A2+M158 CD8+ T cells within human tissues and compared them to human peripheral blood of young and elderly adults. Furthermore, we compared these memory CD8+ T cell repertoires to A2+M158 CD8+ TCRs during acute influenza disease in patients hospitalized with avian A/H7N9 virus. Our study provides the first ex vivo comparative analysis of paired antigen-specific TCR-α/β clonotypes across different tissues and peripheral blood across different age groups. We show that human A2+M158 CD8+ T cells can be readily detected in human lungs, spleens, and lymph nodes, and that tissue A2+M158 TCRαβ repertoires reflect A2+M158 TCRαβ clonotypes derived from peripheral blood in healthy adults and influenza-infected patients. A2+M158 TCRαβ repertoires displayed distinct features only in elderly adults, with large private TCRαβ clonotypes replacing the prominent and public TRBV19/TRAV27 TCRs. Our study provides novel findings on influenza-specific TCRαβ repertoires within human tissues, raises the question of how we can prevent the loss of optimal TCRαβ signatures with aging, and provides important insights into the rational design of T cell-mediated vaccines and immunotherapies.
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Affiliation(s)
- Sneha Sant
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Ludivine Grzelak
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia.,École Normale Supérieure Paris-Saclay, Université Paris-Saclay, Cachan, France
| | - Zhongfang Wang
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Angela Pizzolla
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Jane Crowe
- Deepdene Surgery, Deepdene, VIC, Australia
| | - Thomas Loudovaris
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC, Australia
| | - Stuart I Mannering
- Immunology and Diabetes Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC, Australia
| | - Glen P Westall
- Lung Transplant Unit, Alfred Hospital, Melbourne, VIC, Australia
| | - Linda M Wakim
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia.,School of Medicine, Institute of Infection and Immunity, Cardiff University, Cardiff, United Kingdom
| | - Stephanie Gras
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Michael Richards
- Victorian Infectious Diseases Service, The Royal Melbourne Hospital, Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Jianqing Xu
- Shanghai Public Health Clinical Center, Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Medical College, Fudan University, Shanghai, China
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, United States
| | - Liyen Loh
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
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19
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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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20
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Vermijlen D, Gatti D, Kouzeli A, Rus T, Eberl M. γδ T cell responses: How many ligands will it take till we know? Semin Cell Dev Biol 2018; 84:75-86. [PMID: 29402644 DOI: 10.1016/j.semcdb.2017.10.009] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 09/06/2017] [Accepted: 10/09/2017] [Indexed: 12/20/2022]
Abstract
γδ T cells constitute a sizeable and non-redundant fraction of the total T cell pool in all jawed vertebrates, but in contrast to conventional αβ T cells they are not restricted by classical MHC molecules. Progress in our understanding of the role of γδ T cells in the immune system has been hampered, and is being hampered, by the considerable lack of knowledge regarding the antigens γδ T cells respond to. The past few years have seen a wealth of data regarding the TCR repertoires of distinct γδ T cell populations and a growing list of confirmed and proposed molecules that are recognised by γδ T cells in different species. Yet, the physiological contexts underlying the often restricted TCR usage and the chemical diversity of γδ T cell ligands remain largely unclear, and only few structural studies have confirmed direct ligand recognition by the TCR. We here review the latest progress in the identification and validation of putative γδ T cell ligands and discuss the implications of such findings for γδ T cell responses in health and disease.
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Affiliation(s)
- David Vermijlen
- Department of Pharmacotherapy and Pharmaceutics and Institute for Medical Immunology, Université Libre de Bruxelles (ULB), Belgium.
| | - Deborah Gatti
- Department of Pharmacotherapy and Pharmaceutics and Institute for Medical Immunology, Université Libre de Bruxelles (ULB), Belgium
| | - Ariadni Kouzeli
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Teja Rus
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Matthias Eberl
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom; Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom.
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21
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Tsuchiya Y, Namiuchi Y, Wako H, Tsurui H. A study of CDR3 loop dynamics reveals distinct mechanisms of peptide recognition by T-cell receptors exhibiting different levels of cross-reactivity. Immunology 2017; 153:466-478. [PMID: 28992359 DOI: 10.1111/imm.12849] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 10/04/2017] [Accepted: 10/05/2017] [Indexed: 01/09/2023] Open
Abstract
T-cell receptors (TCRs) can productively interact with many different peptides bound within the MHC binding groove. This property varies with the level of cross-reactivity of TCRs; some TCRs are particularly hyper cross-reactive while others exhibit greater specificity. To elucidate the mechanism behind these differences, we studied five TCRs in complex with the same class II MHC (1Ab )-peptide (3K), that are known to exhibit different levels of cross-reactivity. Although these complexes have similar binding affinities, the interface areas between the TCR and the peptide-MHC (pMHC) differ significantly. We investigated static and dynamic structural features of the TCR-pMHC complexes and of TCRs in a free state, as well as the relationship between binding affinity and interface area. It was found that the TCRs known to exhibit lower levels of cross-reactivity bound to pMHC using an induced-fitting mechanism, forming large and tight interfaces rich in specific hydrogen bonds. In contrast, TCRs known to exhibit high levels of cross-reactivity used a more rigid binding mechanism where non-specific π-interactions involving the bulky Trp residue in CDR3β dominated. As entropy loss upon binding in these highly degenerate and rigid TCRs is smaller than that in less degenerate TCRs, they can better tolerate changes in residues distal from the major contacts with MHC-bound peptide. Hence, our dynamics study revealed that differences in the peptide recognition mechanisms by TCRs appear to correlate with the levels of T-cell cross-reactivity.
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Affiliation(s)
- Yuko Tsuchiya
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | | | - Hiroshi Wako
- School of Social Sciences, Waseda University, Tokyo, Japan
| | - Hiromichi Tsurui
- Department of Pathology, Juntendo University School of Medicine, Tokyo, Japan
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22
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MtHsp70-CLIC1-pulsed dendritic cells enhance the immune response against ovarian cancer. Biochem Biophys Res Commun 2017; 494:13-19. [PMID: 29061300 DOI: 10.1016/j.bbrc.2017.10.094] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 10/17/2017] [Indexed: 12/11/2022]
Abstract
Approximately 80% of ovarian cancer (OC) is diagnosed at late stages, and most patients die within 5 years of diagnosis due to recurrence or drug resistance. Novel treatments are required to improve patient survival. Immune therapy against cancer is promising; however, therapeutic vaccination has been limited by the inability of tumor antigens to induce effective immune responses. Chloride intracellular channel 1 (CLIC1) was previously identified as a possible tumor marker for OC. In this study, we constructed a recombinant protein by conjugating the extracellular domain of CLIC1 to the carboxyl terminus of Mycobacterium tuberculosis heat shock protein 70 (MtHsp70). Human dendritic cells (DCs) derived from cortical blood were pulsed with the fusion protein, and the antitumor effect of human cytotoxic T lymphocytes (CTLs) stimulated by autologous DCs was assessed in NOG mice. MtHsp70-CLIC1 promoted the phenotypic maturation of human DCs and the secretion of Th1-associated cytokines in vitro. MtHsp70-CLIC1-stimulated CTLs generated a CLIC1-specific immune response both in vitro and in vivo. These results indicate that DCs pulsed with MtHsp70-CLIC1 can enhance antitumor immunity against OC, providing a novel immune therapeutic strategy.
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23
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Antunes DA, Rigo MM, Freitas MV, Mendes MFA, Sinigaglia M, Lizée G, Kavraki LE, Selin LK, Cornberg M, Vieira GF. Interpreting T-Cell Cross-reactivity through Structure: Implications for TCR-Based Cancer Immunotherapy. Front Immunol 2017; 8:1210. [PMID: 29046675 PMCID: PMC5632759 DOI: 10.3389/fimmu.2017.01210] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 09/12/2017] [Indexed: 12/16/2022] Open
Abstract
Immunotherapy has become one of the most promising avenues for cancer treatment, making use of the patient’s own immune system to eliminate cancer cells. Clinical trials with T-cell-based immunotherapies have shown dramatic tumor regressions, being effective in multiple cancer types and for many different patients. Unfortunately, this progress was tempered by reports of serious (even fatal) side effects. Such therapies rely on the use of cytotoxic T-cell lymphocytes, an essential part of the adaptive immune system. Cytotoxic T-cells are regularly involved in surveillance and are capable of both eliminating diseased cells and generating protective immunological memory. The specificity of a given T-cell is determined through the structural interaction between the T-cell receptor (TCR) and a peptide-loaded major histocompatibility complex (MHC); i.e., an intracellular peptide–ligand displayed at the cell surface by an MHC molecule. However, a given TCR can recognize different peptide–MHC (pMHC) complexes, which can sometimes trigger an unwanted response that is referred to as T-cell cross-reactivity. This has become a major safety issue in TCR-based immunotherapies, following reports of melanoma-specific T-cells causing cytotoxic damage to healthy tissues (e.g., heart and nervous system). T-cell cross-reactivity has been extensively studied in the context of viral immunology and tissue transplantation. Growing evidence suggests that it is largely driven by structural similarities of seemingly unrelated pMHC complexes. Here, we review recent reports about the existence of pMHC “hot-spots” for cross-reactivity and propose the existence of a TCR interaction profile (i.e., a refinement of a more general TCR footprint in which some amino acid residues are more important than others in triggering T-cell cross-reactivity). We also make use of available structural data and pMHC models to interpret previously reported cross-reactivity patterns among virus-derived peptides. Our study provides further evidence that structural analyses of pMHC complexes can be used to assess the intrinsic likelihood of cross-reactivity among peptide-targets. Furthermore, we hypothesize that some apparent inconsistencies in reported cross-reactivities, such as a preferential directionality, might also be driven by particular structural features of the targeted pMHC complex. Finally, we explain why TCR-based immunotherapy provides a special context in which meaningful T-cell cross-reactivity predictions can be made.
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Affiliation(s)
- Dinler A Antunes
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Kavraki Lab, Department of Computer Science, Rice University, Houston, TX, United States
| | - Maurício M Rigo
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Laboratório de Imunologia Celular e Molecular, Instituto de Pesquisas Biomédicas (IPB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil
| | - Martiela V Freitas
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Marcus F A Mendes
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Marialva Sinigaglia
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Gregory Lizée
- Lizée Lab, Department of Melanoma Medical Oncology - Research, The University of Texas M. D. Anderson Cancer Center, Houston, TX, United States
| | - Lydia E Kavraki
- Kavraki Lab, Department of Computer Science, Rice University, Houston, TX, United States
| | - Liisa K Selin
- Selin Lab, Department of Pathology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Markus Cornberg
- Cornberg Lab, Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany.,German Center for Infection Research (DZIF), Partner-Site Hannover-Braunschweig, Hannover, Germany
| | - Gustavo F Vieira
- Núcleo de Bioinformática do Laboratório de Imunogenética (NBLI), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Programa de Pós-Graduação em Saúde e Desenvolvimento Humano, Universidade La Salle, Porto Alegre, Brazil
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24
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Immunosequencing identifies signatures of cytomegalovirus exposure history and HLA-mediated effects on the T cell repertoire. Nat Genet 2017; 49:659-665. [DOI: 10.1038/ng.3822] [Citation(s) in RCA: 302] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 02/28/2017] [Indexed: 12/16/2022]
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25
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Serçinoğlu O, Ozbek P. Computational characterization of residue couplings and micropolymorphism-induced changes in the dynamics of two differentially disease-associated human MHC class-I alleles. J Biomol Struct Dyn 2017; 36:724-740. [DOI: 10.1080/07391102.2017.1295884] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Onur Serçinoğlu
- Department of Bioengineering, Institute of Pure and Applied Sciences, Marmara University, Istanbul, Turkey
- Faculty of Engineering, Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Pemra Ozbek
- Faculty of Engineering, Department of Bioengineering, Marmara University, Istanbul, Turkey
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26
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Broad TCR repertoire and diverse structural solutions for recognition of an immunodominant CD8 + T cell epitope. Nat Struct Mol Biol 2017; 24:395-406. [PMID: 28250417 PMCID: PMC5383516 DOI: 10.1038/nsmb.3383] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 01/30/2017] [Indexed: 12/16/2022]
Abstract
A keystone of antiviral immunity is CD8 T-cell recognition of viral peptides bound to MHC-I proteins. The recognition mode of individual T cell receptors (TCRs) has been studied in some detail, but how TCR variation functions in providing a robust response to viral antigen is unclear. The influenza M1 epitope is an immunodominant target of CD8 T cells helping to control influenza in HLA-A2+ individuals. Here, we show that many distinct TCRs are used by CD8 T cells to recognize HLA-A2/M1, encoding different structural solutions to the problem of specifically recognizing a relatively featureless peptide antigen. The vast majority of responding TCRs target small clefts between peptide and MHC. These broad repertoires lead to plasticity in antigen recognition and protection against T cell clonal loss and viral escape.
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27
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Liu WJ, Lan J, Liu K, Deng Y, Yao Y, Wu S, Chen H, Bao L, Zhang H, Zhao M, Wang Q, Han L, Chai Y, Qi J, Zhao J, Meng S, Qin C, Gao GF, Tan W. Protective T Cell Responses Featured by Concordant Recognition of Middle East Respiratory Syndrome Coronavirus-Derived CD8+ T Cell Epitopes and Host MHC. THE JOURNAL OF IMMUNOLOGY 2016; 198:873-882. [PMID: 27903740 DOI: 10.4049/jimmunol.1601542] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/06/2016] [Indexed: 12/20/2022]
Abstract
The coordinated recognition of virus-derived T cell epitopes and MHC molecules by T cells plays a pivotal role in cellular immunity-mediated virus clearance. It has been demonstrated that the conformation of MHC class I (MHC I) molecules can be adjusted by the presented peptide, which impacts T cell activation. However, it is still largely unknown whether the conformational shift of MHC I influences the protective effect of virus-specific T cells. In this study, utilizing the Middle East respiratory syndrome coronavirus-infected mouse model, we observed that through the unusual secondary anchor Ile5, a CD8+ T cell epitope drove the conformational fit of Trp73 on the α1 helix of murine MHC I H-2Kd In vitro renaturation and circular dichroism assays indicated that this shift of the structure did not influence the peptide/MHC I binding affinity. Nevertheless, the T cell recognition and the protective effect of the peptide diminished when we made an Ile to Ala mutation at position 5 of the original peptide. The molecular bases of the concordant recognition of T cell epitopes and host MHC-dependent protection were demonstrated through both crystal structure determination and tetramer staining using the peptide-MHC complex. Our results indicate a coordinated MHC I/peptide interaction mechanism and provide a beneficial reference for T cell-oriented vaccine development against emerging viruses such as Middle East respiratory syndrome coronavirus.
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Affiliation(s)
- William J Liu
- College of Laboratory Medicine and Life Sciences, Institute of Medical Virology, Wenzhou Medical University, Wenzhou 325035, China.,Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jiaming Lan
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.,Department of Pathogenic Biology, Hebei Medical University, Shijiazhuang 050017, China
| | - Kefang Liu
- College of Laboratory Medicine and Life Sciences, Institute of Medical Virology, Wenzhou Medical University, Wenzhou 325035, China.,Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yao Deng
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yanfeng Yao
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Key Laboratory of Human Disease Comparative Medicine, Ministry of Health, Beijing 100021, China
| | - Shaolian Wu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Hong Chen
- Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Lingling Bao
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Key Laboratory of Human Disease Comparative Medicine, Ministry of Health, Beijing 100021, China
| | - Haifeng Zhang
- College of Laboratory Medicine and Life Sciences, Institute of Medical Virology, Wenzhou Medical University, Wenzhou 325035, China
| | - Min Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qihui Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lingxia Han
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150001, China
| | - Yan Chai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China; and
| | - Songdong Meng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chuan Qin
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Key Laboratory of Human Disease Comparative Medicine, Ministry of Health, Beijing 100021, China
| | - George F Gao
- College of Laboratory Medicine and Life Sciences, Institute of Medical Virology, Wenzhou Medical University, Wenzhou 325035, China; .,Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,Research Network of Immunity and Health, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenjie Tan
- College of Laboratory Medicine and Life Sciences, Institute of Medical Virology, Wenzhou Medical University, Wenzhou 325035, China; .,Key Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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28
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T cell receptor recognition of CD1b presenting a mycobacterial glycolipid. Nat Commun 2016; 7:13257. [PMID: 27807341 PMCID: PMC5095289 DOI: 10.1038/ncomms13257] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/15/2016] [Indexed: 01/15/2023] Open
Abstract
CD1 proteins present microbial lipids to T cells. Germline-encoded mycolyl lipid-reactive (GEM) T cells with conserved αβ T cell receptors (TCRs) recognize CD1b presenting mycobacterial mycolates. As the molecular basis underpinning TCR recognition of CD1b remains unknown, here we determine the structure of a GEM TCR bound to CD1b presenting glucose-6-O-monomycolate (GMM). The GEM TCR docks centrally above CD1b, whereby the conserved TCR α-chain extensively contacts CD1b and GMM. Through mutagenesis and study of T cells from tuberculosis patients, we identify a consensus CD1b footprint of TCRs present among GEM T cells. Using both the TCR α- and β-chains as tweezers to surround and grip the glucose moiety of GMM, GEM TCRs create a highly specific mechanism for recognizing this mycobacterial glycolipid. Germline-encoded mycolyl lipid-reactive (GEM) T cells recognize CD1b proteins presenting mycobacterial mycolates via their T-cell receptors (TCRs). Here, the authors present the structure of this interaction and provide a molecular basis for the co-recognition of CD1b and a mycobacterial glycolipid.
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29
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Prevosto C, Usmani MF, McDonald S, Gumienny AM, Key T, Goodman RS, Gaston JSH, Deery MJ, Busch R. Allele-Independent Turnover of Human Leukocyte Antigen (HLA) Class Ia Molecules. PLoS One 2016; 11:e0161011. [PMID: 27529174 PMCID: PMC4987023 DOI: 10.1371/journal.pone.0161011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 07/28/2016] [Indexed: 11/29/2022] Open
Abstract
Major histocompatibility complex class I (MHCI) glycoproteins present cytosolic peptides to CD8+ T cells and regulate NK cell activity. Their heavy chains (HC) are expressed from up to three MHC gene loci (human leukocyte antigen [HLA]-A, -B, and -C in humans), whose extensive polymorphism maps predominantly to the antigen-binding groove, diversifying the bound peptide repertoire. Codominant expression of MHCI alleles is thus functionally critical, but how it is regulated is not fully understood. Here, we have examined the effect of polymorphism on the turnover rates of MHCI molecules in cell lines with functional MHCI peptide loading pathways and in monocyte-derived dendritic cells (MoDCs). Proteins were labeled biosynthetically with heavy water (2H2O), folded MHCI molecules immunoprecipitated, and tryptic digests analysed by mass spectrometry. MHCI-derived peptides were assigned to specific alleles and isotypes, and turnover rates quantified by 2H incorporation, after correcting for cell growth. MHCI turnover half-lives ranged from undetectable to a few hours, depending on cell type, activation state, donor, and MHCI isotype. However, in all settings, the turnover half-lives of alleles of the same isotype were similar. Thus, MHCI protein turnover rates appear to be allele-independent in normal human cells. We propose that this is an important feature enabling the normal function and codominant expression of MHCI alleles.
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Affiliation(s)
- Claudia Prevosto
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - M. Farooq Usmani
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Sarah McDonald
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Tim Key
- Tissue Typing Laboratory, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Reyna S. Goodman
- Tissue Typing Laboratory, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - J. S. Hill Gaston
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Michael J. Deery
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge, United Kingdom
| | - Robert Busch
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Department of Life Sciences, University of Roehampton, London, United Kingdom
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30
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Hickman ES, Lomax ME, Jakobsen BK. Antigen Selection for Enhanced Affinity T-Cell Receptor-Based Cancer Therapies. ACTA ACUST UNITED AC 2016; 21:769-85. [PMID: 26993321 DOI: 10.1177/1087057116637837] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 03/15/2016] [Indexed: 12/11/2022]
Abstract
Evidence of adaptive immune responses in the prevention of cancer has been accumulating for decades. Spontaneous T-cell responses occur in multiple indications, bringing the study of de novo expressed cancer antigens to the fore and highlighting their potential as targets for cancer immunotherapy. Circumventing the immune-suppressive mechanisms that maintain tumor tolerance and driving an antitumor cytotoxic T-cell response in cancer patients may eradicate the tumor or block disease progression. Multiple strategies are being pursued to harness the cytotoxic potential of T cells clinically. Highly promising results are now emerging. The focus of this review is the target discovery process for cancer immune therapeutics based on affinity-matured T-cell receptors (TCRs). Target cancer antigens in the context of adoptive cell transfer technologies and soluble biologic agents are discussed. To appreciate the impact of TCR-based technology and understand the TCR discovery process, it is necessary to understand key differences between TCR-based therapy and other immunotherapy approaches. The review first summarizes key advances in the cancer immunotherapy field and then discusses the opportunities that TCR technology provides. The nature and breadth of molecular targets that are tractable to this approach are discussed, together with the challenges associated with finding them.
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31
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Abstract
CD8 T lymphocytes are a major cell population of the adaptive immune system. A fundamental characteristic of the CD8 T lymphocyte pool is that it is composed of millions of clones; each with a unique T cell receptor capable of recognizing a limited number of peptides displayed at the cell surface bound to the grooves of major histocompatibility complex class I (MHC I) molecules. Naïve CD8 T lymphocytes are normally resting and circulate between the blood and secondary lymphoid organs in search of their cognate peptide–MHC complexes. During viral infections, bone marrow–derived professional antigen-presenting cells (pAPCs) in secondary lymphoid organs display viral peptides on their MHC I molecules. Specific CD8 T lymphocytes that recognize these peptide–MHC adducts become activated (primed), proliferate extensively, and develop into effectors capable of killing infected cells, identified by the presence at their surface of the pertinent viral peptide–MHC complexes. This article describes how the process of priming naïve CD8 T lymphocytes occurs.
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32
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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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33
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Improved structural method for T-cell cross-reactivity prediction. Mol Immunol 2015; 67:303-10. [PMID: 26141239 DOI: 10.1016/j.molimm.2015.06.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/03/2015] [Accepted: 06/16/2015] [Indexed: 10/23/2022]
Abstract
Cytotoxic T-lymphocytes (CTLs) are the key players of adaptive cellular immunity, being able to identify and eliminate infected cells through the interaction with peptide-loaded major histocompatibility complexes class I (pMHC-I). Despite the high specificity of this interaction, a given lymphocyte is actually able to recognize more than just one pMHC-I complex, a phenomenon referred as cross-reactivity. In the present work we describe the use of pMHC-I structural features as input for multivariate statistical methods, to perform standardized structure-based predictions of cross-reactivity among viral epitopes. Our improved approach was able to successfully identify cross-reactive targets among 28 naturally occurring hepatitis C virus (HCV) variants and among eight epitopes from the four dengue virus serotypes. In both cases, our results were supported by multiscale bootstrap resampling and by data from previously published in vitro experiments. The combined use of data from charges and accessible surface area (ASA) of selected residues over the pMHC-I surface provided a powerful way of assessing the structural features involved in triggering cross-reactive responses. Moreover, the use of an R package (pvclust) for assessing the uncertainty in the hierarchical cluster analysis provided a statistical support for the interpretation of results. Taken together, these methods can be applied to vaccine design, both for the selection of candidates capable of inducing immunity against different targets, or to identify epitopes that could trigger undesired immunological responses.
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34
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Croft NP, Purcell AW, Tscharke DC. Quantifying epitope presentation using mass spectrometry. Mol Immunol 2015; 68:77-80. [PMID: 26118903 DOI: 10.1016/j.molimm.2015.06.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 06/01/2015] [Accepted: 06/04/2015] [Indexed: 02/01/2023]
Abstract
Understanding the absolute quantities of MHC-bound epitopes (pMHC) presented on the surface of cells has long been a critical missing element in our knowledge of antigen presentation to T cells. Until recently, attaining such information has been restricted to the use of pMHC complex-specific monoclonal antibodies or T cell assays probing fractionated peptides eluted from cells. Although successful in a variety of cases, such approaches are limited in their scope and feasibility due to the nature of the reagents they are reliant upon. Here we report on the advancement of targeted mass spectrometry techniques to provide simultaneous and direct measurements of the relative and absolute levels of pMHC molecules and its potential for impact upon the field of antigen processing and presentation.
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Affiliation(s)
- Nathan P Croft
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3141, Australia.
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3141, Australia
| | - David C Tscharke
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia; The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia.
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35
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Immunogenicity of infectious pathogens and vaccine antigens. BMC Immunol 2015; 16:31. [PMID: 26021448 PMCID: PMC4446803 DOI: 10.1186/s12865-015-0095-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 02/20/2015] [Indexed: 12/28/2022] Open
Abstract
The concept of the immunogenicity of an antigen is frequently encountered in the context of vaccine development, an area of intense interest currently due to the emergence or re-emergence of infectious pathogens with the potential for worldwide spread. However, the theoretical notion of immunogenicity as discussed in older textbooks of immunology needs reconsideration due to advances in our understanding of immunologic responses. Immunogenicity is a property that can either be a desirable attribute, for example in the generation of an effective protective immunity against infectious pathogens or an undesirable trait, for example when it relates to novel therapeutic compounds and drugs, where an immune response needs to be prevented or inhibited. In this Forum Article, we aimed to revisit the issue of immunogenicity to discuss a series of simple questions relevant to the concept that are frequently rephrased but incompletely resolved in the immunologic literature.
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36
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Coeliac disease and rheumatoid arthritis: similar mechanisms, different antigens. Nat Rev Rheumatol 2015; 11:450-61. [PMID: 25986717 DOI: 10.1038/nrrheum.2015.59] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Rheumatoid arthritis (RA) and coeliac disease are inflammatory diseases that both have a strong association with class II HLAs: individuals carrying HLA-DQ2.5 and/or HLA-DQ8 alleles have an increased risk of developing coeliac disease, whereas those carrying HLA-DR shared epitope alleles exhibit an increased risk of developing RA. Although the molecular basis of the association with specific HLA molecules in RA remains poorly defined, an immune response against post-translationally modified protein antigens is a hallmark of each disease. In RA, understanding of the pathogenetic role of B-cell responses to citrullinated antigens, including vimentin, fibrinogen and α-enolase, is rapidly growing. Moreover, insight into the role of HLAs in the pathogenesis of coeliac disease has been considerably advanced by the identification of T-cell responses to deamidated gluten antigens presented in conjunction with predisposing HLA-DQ2.5 molecules. This article briefly reviews these advances and draws parallels between the immune mechanisms leading to RA and coeliac disease, which point to a crucial role for T-cell-B-cell cooperation in the development of full-blown disease. Finally, the ways in which these novel insights are being exploited therapeutically to re-establish tolerance in patients with RA and coeliac disease are described.
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37
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Rist MJ, Hibbert KM, Croft NP, Smith C, Neller MA, Burrows JM, Miles JJ, Purcell AW, Rossjohn J, Gras S, Burrows SR. T Cell Cross-Reactivity between a Highly Immunogenic EBV Epitope and a Self-Peptide Naturally Presented by HLA-B*18:01+ Cells. THE JOURNAL OF IMMUNOLOGY 2015; 194:4668-75. [PMID: 25855358 DOI: 10.4049/jimmunol.1500233] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 03/12/2015] [Indexed: 01/06/2023]
Abstract
T cell cross-reactivity underpins the molecular mimicry hypothesis in which microbial peptides sharing structural features with host peptides stimulate T cells that cross-react with self-peptides, thereby initiating and/or perpetuating autoimmune disease. EBV represents a potentially important factor in the pathogenesis of several T cell-mediated autoimmune disorders, with molecular mimicry a likely mechanism. In this study, we describe a human self-peptide (DELEIKAY) that is a homolog of a highly immunogenic EBV T cell epitope (SELEIKRY) presented by HLA-B*18:01. This self-peptide was shown to bind stably to HLA-B*18:01, and peptide elution/mass spectrometric studies showed it is naturally presented by this HLA molecule on the surface of human cells. A significant proportion of CD8(+) T cells raised from some healthy individuals against this EBV epitope cross-reacted with the self-peptide. A diverse array of TCRs was expressed by the cross-reactive T cells, with variable functional avidity for the self-peptide, including some T cells that appeared to avoid autoreactivity by a narrow margin, with only 10-fold more of the self-peptide required for equivalent activation as compared with the EBV peptide. Structural studies revealed that the self-peptide-HLA-B*18:01 complex is a structural mimic of the EBV peptide-HLA-B*18:01 complex, and that the strong antiviral T cell response is primarily dependent on the alanine/arginine mismatch at position 7. To our knowledge, this is the first report confirming the natural presentation of a self-peptide cross-recognized in the context of self-HLA by EBV-reactive CD8(+) T cells. These results illustrate how aberrant immune responses and immunopathological diseases could be generated by EBV infection.
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Affiliation(s)
- Melissa J Rist
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia; School of Medicine, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Kelly M Hibbert
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia; and
| | - Nathan P Croft
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Corey Smith
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Michelle A Neller
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | | | - John J Miles
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia; School of Medicine, University of Queensland, Brisbane, Queensland 4072, Australia; Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Jamie Rossjohn
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia; and Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Stephanie Gras
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia; and
| | - Scott R Burrows
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia; School of Medicine, University of Queensland, Brisbane, Queensland 4072, Australia;
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38
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Knapp B, Demharter S, Esmaielbeiki R, Deane CM. Current status and future challenges in T-cell receptor/peptide/MHC molecular dynamics simulations. Brief Bioinform 2015; 16:1035-44. [DOI: 10.1093/bib/bbv005] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Indexed: 11/12/2022] Open
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39
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God JM, Cameron C, Figueroa J, Amria S, Hossain A, Kempkes B, Bornkamm GW, Stuart RK, Blum JS, Haque A. Elevation of c-MYC disrupts HLA class II-mediated immune recognition of human B cell tumors. THE JOURNAL OF IMMUNOLOGY 2015; 194:1434-45. [PMID: 25595783 DOI: 10.4049/jimmunol.1402382] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Elevated levels of the transcription factor c-myc are strongly associated with various cancers, and in particular B cell lymphomas. Although many of c-MYC's functions have been elucidated, its effect on the presentation of Ag through the HLA class II pathway has not been reported previously. This is an issue of considerable importance, given the low immunogenicity of many c-MYC-positive tumors. We report in this paper that increased c-MYC expression has a negative effect on the ability of B cell lymphomas to functionally present Ags/peptides to CD4(+) T cells. This defect was associated with alterations in the expression of distinct cofactors as well as interactions of antigenic peptides with class II molecules required for the presentation of class II-peptide complexes and T cell engagement. Using early passage Burkitt's lymphoma (BL) tumors and transformed cells, we show that compared with B lymphoblasts, BL cells express decreased levels of the class II editor HLA-DM, lysosomal thiol-reductase GILT, and a 47-kDa enolase-like protein. Functional Ag presentation was partially restored in BL cells treated with a c-MYC inhibitor, demonstrating the impact of this oncogene on Ag recognition. This restoration of HLA class II-mediated Ag presentation in early passage BL tumors/cells was linked to enhanced HLA-DM expression and a concurrent decrease in HLA-DO in BL cells. Taken together, these results reveal c-MYC exerts suppressive effects at several critical checkpoints in Ag presentation, which contribute to the immunoevasive properties of BL tumors.
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Affiliation(s)
- Jason M God
- Department of Microbiology and Immunology, Hollings Cancer Center and Children's Research Institute, Medical University of South Carolina, Charleston, SC 29425
| | - Christine Cameron
- Department of Microbiology and Immunology, Hollings Cancer Center and Children's Research Institute, Medical University of South Carolina, Charleston, SC 29425
| | - Janette Figueroa
- Department of Microbiology and Immunology, Hollings Cancer Center and Children's Research Institute, Medical University of South Carolina, Charleston, SC 29425
| | - Shereen Amria
- Department of Microbiology and Immunology, Hollings Cancer Center and Children's Research Institute, Medical University of South Carolina, Charleston, SC 29425
| | - Azim Hossain
- Department of Microbiology and Immunology, Hollings Cancer Center and Children's Research Institute, Medical University of South Carolina, Charleston, SC 29425
| | - Bettina Kempkes
- Department of Gene Vectors, German Research Center for Environmental Health, 81377 Munich, Germany
| | - Georg W Bornkamm
- Institute of Clinical Molecular Biology and Tumor Genetics, German Research Center for Environmental Health, 81377 Munich, Germany
| | - Robert K Stuart
- Department of Hematology and Oncology, Medical University of South Carolina, Charleston, SC 29425; and
| | - Janice S Blum
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Azizul Haque
- Department of Microbiology and Immunology, Hollings Cancer Center and Children's Research Institute, Medical University of South Carolina, Charleston, SC 29425;
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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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Sun Y, Liu Q. Differential structural dynamics and antigenicity of two similar influenza H5N1 virus HA-specific HLA-A*0201-restricted CLT epitopes. RSC Adv 2015. [DOI: 10.1039/c4ra08874c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The free RI-10 and KI-10 peptides showed bent rather than extended conformations as binding in the cleft of the HLA-A*0201 molecule, and KI-10–HLA-A*0201 processed a much higher flexibility than RI-10–HLA-A*0201.
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Affiliation(s)
- Yeping Sun
- CAS Key Laboratory of Pathogenic Microbiology and Immunology
- Institute of Microbiology
- Chinese Academy of Sciences
- Beijing 100101
- P. R. China
| | - Qian Liu
- Supercomputing Center
- Chinese Academy of Sciences
- Beijing 100101
- P. R. China
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42
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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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43
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Saunders PM, Vivian JP, Baschuk N, Beddoe T, Widjaja J, O'Connor GM, Hitchen C, Pymm P, Andrews DM, Gras S, McVicar DW, Rossjohn J, Brooks AG. The interaction of KIR3DL1*001 with HLA class I molecules is dependent upon molecular microarchitecture within the Bw4 epitope. THE JOURNAL OF IMMUNOLOGY 2014; 194:781-789. [PMID: 25480565 DOI: 10.4049/jimmunol.1402542] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The killer cell Ig-like receptor 3DL1 (KIR3DL1) inhibits activation of NK cells upon interaction with HLA class I molecules such as HLA-B*57:01, which contains the Bw4 epitope spanning residues 77-83 (e.g., NLRIALR), and not with HLA allomorphs that possess the Bw6 motif (e.g., HLA-B*08:01), which differ at residues 77, 80, 81, 82, and 83. Although Bw4 residues Ile(80) and Arg(83) directly interact with KIR3DL1*001, their precise role in determining KIR3DL1-HLA-Bw4 specificity remains unclear. Recognition of HLA-B*57:01 by either KIR3DL1(+) NK cells or the NK cell line YTS transfected with KIR3DL1*001 was impaired by mutation of residues 80 and 83 of HLA-B*57:01 to the corresponding amino acids within the Bw6 motif. Conversely, the simultaneous introduction of three Bw4 residues at positions 80, 82, and 83 into HLA-B*08:01 conferred an interaction with KIR3DL1*001. Structural analysis of HLA-B*57:01, HLA-B*08:01, and mutants of each bearing substitutions at positions 80 and 83 revealed that Ile(80) and Arg(83) within the Bw4 motif constrain the conformation of Glu(76), primarily through a salt bridge between Arg(83) and Glu(76). This salt bridge was absent in HLA-Bw6 molecules as well as position 83 mutants of HLA-B*57:01. Mutation of the Bw4 residue Ile(80) also disrupted this salt bridge, providing further insight into the role that position 80 plays in mediating KIR3DL1 recognition. Thus, the strict conformation of HLA-Bw4 allotypes, held in place by the Glu(76)-Arg(83) interaction, facilitates KIR3DL1 binding, whereas Bw6 allotypes present a platform on the α1 helix that is less permissive for KIR3DL1 binding.
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Affiliation(s)
- Philippa M Saunders
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Julian P Vivian
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Nikola Baschuk
- Cancer Immunology Program, Peter McCallum Cancer Institute, Melbourne, 3002 Australia
| | - Travis Beddoe
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Jacqueline Widjaja
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Geraldine M O'Connor
- Cancer and Inflammation Program, National Cancer Institute-Frederick, Frederick, MD 21702, USA
| | - Corinne Hitchen
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Phillip Pymm
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Daniel M Andrews
- Cancer Immunology Program, Peter McCallum Cancer Institute, Melbourne, 3002 Australia
| | - Stephanie Gras
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Daniel W McVicar
- Cancer and Inflammation Program, National Cancer Institute-Frederick, Frederick, MD 21702, USA
| | - Jamie Rossjohn
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia.,Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff, CF14 4XN, UK.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Andrew G Brooks
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria 3010, Australia
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44
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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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45
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Reiser JB, Legoux F, Gras S, Trudel E, Chouquet A, Léger A, Le Gorrec M, Machillot P, Bonneville M, Saulquin X, Housset D. Analysis of relationships between peptide/MHC structural features and naive T cell frequency in humans. THE JOURNAL OF IMMUNOLOGY 2014; 193:5816-26. [PMID: 25392532 DOI: 10.4049/jimmunol.1303084] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The structural rules governing peptide/MHC (pMHC) recognition by T cells remain unclear. To address this question, we performed a structural characterization of several HLA-A2/peptide complexes and assessed in parallel their antigenicity, by analyzing the frequency of the corresponding Ag-specific naive T cells in A2(+) and A2(-) individuals, as well as within CD4(+) and CD8(+) subsets. We were able to find a correlation between specific naive T cell frequency and peptide solvent accessibility and/or mobility for a subset of moderately prominent peptides. However, one single structural parameter of the pMHC complexes could not be identified to explain each peptide antigenicity. Enhanced pMHC antigenicity was associated with both highly biased TRAV usage, possibly reflecting favored interaction between particular pMHC complexes and germline TRAV loops, and peptide structural features allowing interactions with a broad range of permissive CDR3 loops. In this context of constrained TCR docking mode, an optimal peptide solvent exposed surface leading to an optimal complementarity with TCR interface may constitute one of the key features leading to high frequency of specific T cells. Altogether our results suggest that frequency of specific T cells depends on the fine-tuning of several parameters, the structural determinants governing TCR-pMHC interaction being just one of them.
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Affiliation(s)
- Jean-Baptiste Reiser
- Université de Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France; Commissariat à l'énergie atomique et aux énergies alternatives, Direction des sciences du vivant, Institut de Biologie Structurale, F-38044 Grenoble, France; Centre national de la recherche scientifique, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - François Legoux
- Institut national de la santé et de la recherche médicale, Unité mixte de recherche 892, Centre de Recherche en Cancérologie Nantes Angers, F-44000 Nantes, France; and
| | - Stéphanie Gras
- Université de Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France; Commissariat à l'énergie atomique et aux énergies alternatives, Direction des sciences du vivant, Institut de Biologie Structurale, F-38044 Grenoble, France; Centre national de la recherche scientifique, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Eric Trudel
- Université de Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France; Commissariat à l'énergie atomique et aux énergies alternatives, Direction des sciences du vivant, Institut de Biologie Structurale, F-38044 Grenoble, France; Centre national de la recherche scientifique, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Anne Chouquet
- Université de Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France; Commissariat à l'énergie atomique et aux énergies alternatives, Direction des sciences du vivant, Institut de Biologie Structurale, F-38044 Grenoble, France; Centre national de la recherche scientifique, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Alexandra Léger
- Institut national de la santé et de la recherche médicale, Unité mixte de recherche 892, Centre de Recherche en Cancérologie Nantes Angers, F-44000 Nantes, France; and
| | - Madalen Le Gorrec
- Université de Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France; Commissariat à l'énergie atomique et aux énergies alternatives, Direction des sciences du vivant, Institut de Biologie Structurale, F-38044 Grenoble, France; Centre national de la recherche scientifique, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Paul Machillot
- Université de Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France; Commissariat à l'énergie atomique et aux énergies alternatives, Direction des sciences du vivant, Institut de Biologie Structurale, F-38044 Grenoble, France; Centre national de la recherche scientifique, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Marc Bonneville
- Institut national de la santé et de la recherche médicale, Unité mixte de recherche 892, Centre de Recherche en Cancérologie Nantes Angers, F-44000 Nantes, France; and
| | - Xavier Saulquin
- Institut national de la santé et de la recherche médicale, Unité mixte de recherche 892, Centre de Recherche en Cancérologie Nantes Angers, F-44000 Nantes, France; and Université de Nantes, F-44000 Nantes, France
| | - Dominique Housset
- Université de Grenoble Alpes, Institut de Biologie Structurale, F-38044 Grenoble, France; Commissariat à l'énergie atomique et aux énergies alternatives, Direction des sciences du vivant, Institut de Biologie Structurale, F-38044 Grenoble, France; Centre national de la recherche scientifique, Institut de Biologie Structurale, F-38044 Grenoble, France;
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46
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Law SC, Benham H, Reid HH, Rossjohn J, Thomas R. Identification of Self-antigen–specific T Cells Reflecting Loss of Tolerance in Autoimmune Disease Underpins Preventative Immunotherapeutic Strategies in Rheumatoid Arthritis. Rheum Dis Clin North Am 2014; 40:735-52. [DOI: 10.1016/j.rdc.2014.07.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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47
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Nivarthi UK, Gras S, Kjer-Nielsen L, Berry R, Lucet IS, Miles JJ, Tracy SL, Purcell AW, Bowden DS, Hellard M, Rossjohn J, McCluskey J, Bharadwaj M. An extensive antigenic footprint underpins immunodominant TCR adaptability against a hypervariable viral determinant. THE JOURNAL OF IMMUNOLOGY 2014; 193:5402-13. [PMID: 25355921 DOI: 10.4049/jimmunol.1401357] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Mutations in T cell epitopes are implicated in hepatitis C virus (HCV) persistence and can impinge on vaccine development. We recently demonstrated a narrow bias in the human TCR repertoire targeted at an immunodominant, but highly mutable, HLA-B*0801-restricted epitope ((1395)HSKKKCDEL(1403) [HSK]). To investigate if the narrow TCR repertoire facilitates CTL escape, structural and biophysical studies were undertaken, alongside comprehensive functional analysis of T cells targeted at the natural variants of HLA-B*0801-HSK in different HCV genotypes and quasispecies. Interestingly, within the TCR-HLA-B*0801-HSK complex, the TCR contacts all available surface-exposed residues of the HSK determinant. This broad epitope coverage facilitates cross-genotypic reactivity and recognition of common mutations reported in HCV quasispecies, albeit to a varying degree. Certain mutations did abrogate T cell reactivity; however, natural variants comprising these mutations are reportedly rare and transient in nature, presumably due to fitness costs. Overall, despite a narrow bias, the TCR accommodated frequent mutations by acting like a blanket over the hypervariable epitope, thereby providing effective viral immunity. Our findings simultaneously advance the understanding of anti-HCV immunity and indicate the potential for cross-genotype HCV vaccines.
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Affiliation(s)
- Usha K Nivarthi
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3000, Australia
| | - Stephanie Gras
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Lars Kjer-Nielsen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3000, Australia
| | - Richard Berry
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Isabelle S Lucet
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - John J Miles
- Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom; Queensland Institute of Medical Research Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia; School of Medicine, University of Queensland, Brisbane, Queensland 4006, Australia
| | - Samantha L Tracy
- Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3000, Australia
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - David S Bowden
- Victorian Infectious Diseases Reference Laboratory, Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3000, Australia
| | - Margaret Hellard
- Centre for Population Health, Burnet Institute, Melbourne, Victoria 3004, Australia; Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria 3800, Australia; and Centre for Research Excellence into Injecting Drug Use, Burnet Institute, Melbourne, Victoria 3004, Australia
| | - Jamie Rossjohn
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia; Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom;
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3000, Australia;
| | - Mandvi Bharadwaj
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3000, Australia;
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48
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Large scale characterization of the LC13 TCR and HLA-B8 structural landscape in reaction to 172 altered peptide ligands: a molecular dynamics simulation study. PLoS Comput Biol 2014; 10:e1003748. [PMID: 25101830 PMCID: PMC4125040 DOI: 10.1371/journal.pcbi.1003748] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 05/28/2014] [Indexed: 12/29/2022] Open
Abstract
The interplay between T cell receptors (TCRs) and peptides bound by major histocompatibility complexes (MHCs) is one of the most important interactions in the adaptive immune system. Several previous studies have computationally investigated their structural dynamics. On the basis of these simulations several structural and dynamical properties have been proposed as effectors of the immunogenicity. Here we present the results of a large scale Molecular Dynamics simulation study consisting of 100 ns simulations of 172 different complexes. These complexes consisted of all possible point mutations of the Epstein Barr Virus peptide FLRGRAYGL bound by HLA-B*08:01 and presented to the LC13 TCR. We compare the results of these 172 structural simulations with experimental immunogenicity data. We found that simulations with more immunogenic peptides and those with less immunogenic peptides are in fact highly similar and on average only minor differences in the hydrogen binding footprints, interface distances, and the relative orientation between the TCR chains are present. Thus our large scale data analysis shows that many previously suggested dynamical and structural properties of the TCR/peptide/MHC interface are unlikely to be conserved causal factors for peptide immunogenicity.
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49
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Eckle SBG, Birkinshaw RW, Kostenko L, Corbett AJ, McWilliam HEG, Reantragoon R, Chen Z, Gherardin NA, Beddoe T, Liu L, Patel O, Meehan B, Fairlie DP, Villadangos JA, Godfrey DI, Kjer-Nielsen L, McCluskey J, Rossjohn J. A molecular basis underpinning the T cell receptor heterogeneity of mucosal-associated invariant T cells. ACTA ACUST UNITED AC 2014; 211:1585-600. [PMID: 25049336 PMCID: PMC4113946 DOI: 10.1084/jem.20140484] [Citation(s) in RCA: 217] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A novel MAIT cell antagonist, Ac-6-FP, stabilizes MR1 and can inhibit MAIT cell activation with the flexible TCR β-chain serving to fine-tune the affinity of the TCR for antigen-MR1 complexes. Mucosal-associated invariant T (MAIT) cells express an invariant T cell receptor (TCR) α-chain (TRAV1-2 joined to TRAJ33, TRAJ20, or TRAJ12 in humans), which pairs with an array of TCR β-chains. MAIT TCRs can bind folate- and riboflavin-based metabolites restricted by the major histocompatibility complex (MHC)-related class I−like molecule, MR1. However, the impact of MAIT TCR and MR1-ligand heterogeneity on MAIT cell biology is unclear. We show how a previously uncharacterized MR1 ligand, acetyl-6-formylpterin (Ac-6-FP), markedly stabilized MR1, potently up-regulated MR1 cell surface expression, and inhibited MAIT cell activation. These enhanced properties of Ac-6-FP were attributable to structural alterations in MR1 that subsequently affected MAIT TCR recognition via conformational changes within the complementarity-determining region (CDR) 3β loop. Analysis of seven TRBV6-1+ MAIT TCRs demonstrated how CDR3β hypervariability impacted on MAIT TCR recognition by altering TCR flexibility and contacts with MR1 and the Ag itself. Ternary structures of TRBV6-1, TRBV6-4, and TRBV20+ MAIT TCRs in complex with MR1 bound to a potent riboflavin-based antigen (Ag) showed how variations in TRBV gene usage exclusively impacted on MR1 contacts within a consensus MAIT TCR-MR1 footprint. Moreover, differential TRAJ gene usage was readily accommodated within a conserved MAIT TCR-MR1-Ag docking mode. Collectively, MAIT TCR heterogeneity can fine-tune MR1 recognition in an Ag-dependent manner, thereby modulating MAIT cell recognition.
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Affiliation(s)
- Sidonia B G Eckle
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Richard W Birkinshaw
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Lyudmila Kostenko
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Alexandra J Corbett
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hamish E G McWilliam
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Rangsima Reantragoon
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Zhenjun Chen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nicholas A Gherardin
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Travis Beddoe
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Ligong Liu
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Onisha Patel
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Bronwyn Meehan
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - David P Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia ARC Centre of Excellence in Advanced Molecular Imaging, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jose A Villadangos
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Dale I Godfrey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia ARC Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Lars Kjer-Nielsen
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jamie Rossjohn
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
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Thorborn G, Ploquin MJ, Eksmond U, Pike R, Bayer W, Dittmer U, Hasenkrug KJ, Pepper M, Kassiotis G. Clonotypic composition of the CD4+ T cell response to a vectored retroviral antigen is determined by its speed. THE JOURNAL OF IMMUNOLOGY 2014; 193:1567-77. [PMID: 25000983 DOI: 10.4049/jimmunol.1400667] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The mechanisms whereby different vaccines may expand distinct Ag-specific T cell clonotypes or induce disparate degrees of protection are incompletely understood. We found that several delivery modes of a model retroviral Ag, including natural infection, preferentially expanded initially rare high-avidity CD4(+) T cell clonotypes, known to mediate protection. In contrast, the same Ag vectored by human adenovirus serotype 5 induced clonotypic expansion irrespective of avidity, eliciting a predominantly low-avidity response. Nonselective clonotypic expansion was caused by relatively weak adenovirus serotype 5-vectored Ag presentation and was reproduced by replication-attenuated retroviral vaccines. Mechanistically, the potency of Ag presentation determined the speed and, consequently, completion of the CD4(+) T cell response. Whereas faster completion retained the initial advantage of high-avidity clonotypes, slower completion permitted uninhibited accumulation of low-avidity clonotypes. These results highlighted the importance of Ag presentation patterns in determining the clonotypic composition of vaccine-induced T cell responses and ultimately the efficacy of vaccination.
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Affiliation(s)
- Georgina Thorborn
- Division of Immunoregulation, Medical Research Council National Institute for Medical Research, London NW7 1AA, United Kingdom
| | - Mickaël J Ploquin
- Division of Immunoregulation, Medical Research Council National Institute for Medical Research, London NW7 1AA, United Kingdom
| | - Urszula Eksmond
- Division of Immunoregulation, Medical Research Council National Institute for Medical Research, London NW7 1AA, United Kingdom
| | - Rebecca Pike
- Division of Immunoregulation, Medical Research Council National Institute for Medical Research, London NW7 1AA, United Kingdom
| | - Wibke Bayer
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen 45147, Germany
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen 45147, Germany
| | - Kim J Hasenkrug
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840
| | - Marion Pepper
- Department of Immunology, University of Washington, Seattle, WA 98195; and
| | - George Kassiotis
- Division of Immunoregulation, Medical Research Council National Institute for Medical Research, London NW7 1AA, United Kingdom; Department of Medicine, Faculty of Medicine, Imperial College London, London W2 1PG, United Kingdom
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