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Wu Y, Liang X, Sun Y, Ning J, Dai Y, Jin S, Xu Y, Chen S, Pan L. A general pHLA-CD80 scaffold fusion protein to promote efficient antigen-specific T cell-based immunotherapy. MOLECULAR THERAPY. ONCOLOGY 2024; 32:200827. [PMID: 39027379 PMCID: PMC11255371 DOI: 10.1016/j.omton.2024.200827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/23/2024] [Accepted: 06/07/2024] [Indexed: 07/20/2024]
Abstract
Inadequate antigen-specific T cells activation hampers immunotherapy due to complex antigen presentation. In addition, therapeutic in vivo T cell expansion is constrained by slow expansion rates and limited functionality. Herein, we introduce a model fusion protein termed antigen-presenting cell-mimic fusion protein (APC-mimic), designed to greatly mimicking the natural antigen presentation pattern of antigen-presenting cells and directly expand T cells both in vitro and in vivo. The APC-mimic comprises the cognate peptide-human leukocyte antigen (pHLA) complex and the co-stimulatory marker CD80, which are natural ligands on APCs. Following a single stimulation, APC-mimic leads to an approximately 400-fold increase in the polyclonal expansion of antigen-specific T cells compared with the untreated group in vitro without the requirement for specialized antigen-presenting cells. Through the combination of single-cell TCR sequencing (scTCR-seq) and single-cell RNA sequencing (scRNA-seq), we identify an approximately 600-fold monoclonal expansion clonotype among these polyclonal clonotypes. It also exhibits suitability for in vivo applications confirmed in the OT-1 mouse model. Furthermore, T cells expanded by APC-mimic effectively inhibits tumor growth in adoptive cell transfer (ACT) murine models. These findings pave the way for the versatile APC-mimic platform for personalized therapeutics, enabling direct expansion of polyfunctional antigen-specific T cell subsets in vitro and in vivo.
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Affiliation(s)
- Yue Wu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiao Liang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yanping Sun
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jiangtao Ning
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yukun Dai
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shijie Jin
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yingchun Xu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shuqing Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Department of Precision Medicine on Tumor Therapeutics, ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Liqiang Pan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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2
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Boyd LF, Jiang J, Ahmad J, Natarajan K, Margulies DH. Experimental Structures of Antibody/MHC-I Complexes Reveal Details of Epitopes Overlooked by Computational Prediction. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1366-1380. [PMID: 38456672 PMCID: PMC10982845 DOI: 10.4049/jimmunol.2300839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/14/2024] [Indexed: 03/09/2024]
Abstract
mAbs to MHC class I (MHC-I) molecules have proved to be crucial reagents for tissue typing and fundamental studies of immune recognition. To augment our understanding of epitopic sites seen by a set of anti-MHC-I mAb, we determined X-ray crystal structures of four complexes of anti-MHC-I Fabs bound to peptide/MHC-I/β2-microglobulin (pMHC-I). An anti-H2-Dd mAb, two anti-MHC-I α3 domain mAbs, and an anti-β2-microglobulin mAb bind pMHC-I at sites consistent with earlier mutational and functional experiments, and the structures explain allelomorph specificity. Comparison of the experimentally determined structures with computationally derived models using AlphaFold Multimer showed that although predictions of the individual pMHC-I heterodimers were quite acceptable, the computational models failed to properly identify the docking sites of the mAb on pMHC-I. The experimental and predicted structures provide insight into strengths and weaknesses of purely computational approaches and suggest areas that merit additional attention.
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Affiliation(s)
- Lisa F. Boyd
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Jiansheng Jiang
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Javeed Ahmad
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Kannan Natarajan
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - David H. Margulies
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
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3
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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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4
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Chang-Gonzalez AC, Mallis RJ, Lang MJ, Reinherz EL, Hwang W. Asymmetric framework motion of TCRαβ controls load-dependent peptide discrimination. eLife 2024; 13:e91881. [PMID: 38167271 PMCID: PMC10869138 DOI: 10.7554/elife.91881] [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: 08/14/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024] Open
Abstract
Mechanical force is critical for the interaction between an αβ T cell receptor (TCR) and a peptide-bound major histocompatibility complex (pMHC) molecule to initiate productive T-cell activation. However, the underlying mechanism remains unclear. We use all-atom molecular dynamics simulations to examine the A6 TCR bound to HLA-A*02:01 presenting agonist or antagonist peptides under different extensions to simulate the effects of applied load on the complex, elucidating their divergent biological responses. We found that TCR α and β chains move asymmetrically, which impacts the interface with pMHC, in particular the peptide-sensing CDR3 loops. For the wild-type agonist, the complex stabilizes in a load-dependent manner while antagonists destabilize it. Simulations of the Cβ FG-loop deletion, which reduces the catch bond response, and simulations with in silico mutant peptides further support the observed behaviors. The present results highlight the combined role of interdomain motion, fluctuating forces, and interfacial contacts in determining the mechanical response and fine peptide discrimination by a TCR, thereby resolving the conundrum of nearly identical crystal structures of TCRαβ-pMHC agonist and antagonist complexes.
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Affiliation(s)
- Ana C Chang-Gonzalez
- Department of Biomedical Engineering, Texas A&M UniversityCollege StationUnited States
| | - Robert J Mallis
- Department of Dermatology, Harvard Medical SchoolBostonUnited States
- Laboratory of Immunobiology, Dana-Farber Cancer InstituteBostonUnited States
- Department of Medicine, Oncology, Dana-Farber Cancer InstituteBostonUnited States
| | - Matthew J Lang
- Department of Chemistry and Biomolecular Engineering, Vanderbilt UniversityNashvilleUnited States
- Department of Molecular Physiology and Biophysics, Vanderbilt UniversityNashvilleUnited States
| | - Ellis L Reinherz
- Laboratory of Immunobiology, Dana-Farber Cancer InstituteBostonUnited States
- Department of Medicine, Oncology, Dana-Farber Cancer InstituteBostonUnited States
- Department of Medicine, Harvard Medical SchoolBostonUnited States
| | - Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M UniversityCollege StationUnited States
- Department of Materials Science & Engineering, Texas A&M UniversityCollege StationUnited States
- Department of Physics & Astronomy, Texas A&M UniversityCollege StationUnited States
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5
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Boyd LF, Jiang J, Ahmad J, Natarajan K, Margulies DH. Experimental structures of antibody/MHC-I complexes reveal details of epitopes overlooked by computational prediction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569627. [PMID: 38106040 PMCID: PMC10723347 DOI: 10.1101/2023.12.01.569627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Monoclonal antibodies (mAb) to major histocompatibility complex class I (MHC-I) molecules have proved to be crucial reagents for tissue typing and fundamental studies of immune recognition. To augment our understanding of epitopic sites seen by a set of anti-MHC-I mAb, we determined X-ray crystal structures of four complexes of anti-MHC-I antigen-binding fragments (Fab) bound to peptide/MHC-I/β2m (pMHC-I). An anti-H2-Dd mAb, two anti-MHC-I α3 domain mAb, and an anti-β2-microglobulin (β2m) mAb bind pMHC-I at sites consistent with earlier mutational and functional experiments, and the structures explain allelomorph specificity. Comparison of the experimentally determined structures with computationally derived models using AlphaFold Multimer (AF-M) showed that although predictions of the individual pMHC-I heterodimers were quite acceptable, the computational models failed to properly identify the docking sites of the mAb on pMHC-I. The experimental and predicted structures provide insight into strengths and weaknesses of purely computational approaches and suggest areas that merit additional attention.
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Affiliation(s)
| | | | - Javeed Ahmad
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD, 20892-1892
| | - Kannan Natarajan
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD, 20892-1892
| | - David H. Margulies
- Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD, 20892-1892
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6
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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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7
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Chang-Gonzalez AC, Mallis RJ, Lang MJ, Reinherz EL, Hwang W. Asymmetric framework motion of TCR αβ controls load-dependent peptide discrimination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.10.557064. [PMID: 37745603 PMCID: PMC10515854 DOI: 10.1101/2023.09.10.557064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Mechanical force is critical for the interaction between an αβT cell receptor (TCR) and a peptide-bound major histocompatibility complex (pMHC) molecule to initiate productive T-cell activation. However, the underlying mechanism remains unclear. We use all-atom molecular dynamics simulations to examine the A6 TCR bound to HLA-A*02:01 presenting agonist or antagonist peptides under different extensions to simulate the effects of applied load on the complex, elucidating their divergent biological responses. We found that TCR α and β chains move asymmetrically, which impacts the interface with pMHC, in particular the peptide-sensing CDR3 loops. For the wild-type agonist, the complex stabilizes in a load-dependent manner while antagonists destabilize it. Simulations of the Cβ FG-loop deletion, which reduces the catch bond response, and simulations with in silico mutant peptides further support the observed behaviors. The present results highlight the combined role of interdomain motion, fluctuating forces, and interfacial contacts in determining the mechanical response and fine peptide discrimination by a TCR, thereby resolving the conundrum of nearly identical crystal structures of TCRαβ-pMHC agonist and antagonist complexes.
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Affiliation(s)
- Ana C. Chang-Gonzalez
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
| | - Robert J. Mallis
- Dept. Dermatology, Harvard Medical School, Boston, MA, USA
- Lab. of Immunobio., Dana-Farber Cancer Inst., Boston, MA, USA
- Dept. Med. Oncology, Dana-Farber Cancer Inst., Boston, MA, USA
| | - Matthew J. Lang
- Dept. Chem. and Biomolec. Eng., Vanderbilt Univ., Nashville, TN, USA
- Dept. Molec. Physiology and Biophys., Vanderbilt Univ., Nashville, TN, USA
| | - Ellis L. Reinherz
- Dept. Medicine, Harvard Medical School, Boston, MA, USA
- Lab. of Immunobio., Dana-Farber Cancer Inst., Boston, MA, USA
- Dept. Med. Oncology, Dana-Farber Cancer Inst., Boston, MA, USA
| | - Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
- Department of Materials Science & Engineering, Texas A&M University, College Station, TX, USA
- Dept. Phys. & Astronomy, Texas A&M Univ., College Station, TX, USA
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8
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Ghoreyshi ZS, George JT. Quantitative approaches for decoding the specificity of the human T cell repertoire. Front Immunol 2023; 14:1228873. [PMID: 37781387 PMCID: PMC10539903 DOI: 10.3389/fimmu.2023.1228873] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/17/2023] [Indexed: 10/03/2023] Open
Abstract
T cell receptor (TCR)-peptide-major histocompatibility complex (pMHC) interactions play a vital role in initiating immune responses against pathogens, and the specificity of TCRpMHC interactions is crucial for developing optimized therapeutic strategies. The advent of high-throughput immunological and structural evaluation of TCR and pMHC has provided an abundance of data for computational approaches that aim to predict favorable TCR-pMHC interactions. Current models are constructed using information on protein sequence, structures, or a combination of both, and utilize a variety of statistical learning-based approaches for identifying the rules governing specificity. This review examines the current theoretical, computational, and deep learning approaches for identifying TCR-pMHC recognition pairs, placing emphasis on each method's mathematical approach, predictive performance, and limitations.
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Affiliation(s)
- Zahra S. Ghoreyshi
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, United States
| | - Jason T. George
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, United States
- Engineering Medicine Program, Texas A&M University, Houston, TX, United States
- Center for Theoretical Biological Physics, Rice University, Houston, TX, United States
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9
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Aran A, Lázaro G, Marco V, Molina E, Abancó F, Peg V, Gión M, Garrigós L, Pérez-García J, Cortés J, Martí M. Analysis of tumor infiltrating CD4+ and CD8+ CDR3 sequences reveals shared features putatively associated to the anti-tumor immune response. Front Immunol 2023; 14:1227766. [PMID: 37600765 PMCID: PMC10436466 DOI: 10.3389/fimmu.2023.1227766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/20/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Tumor-infiltrating lymphocytes (TILs) have predictive and prognostic value in breast cancer (BC) and exert a protective function against tumor growth, indicating that it is susceptible to treatment using adoptive cell transfer of TILs or T cell receptor (TCR)-based therapies. TCR can be used to identify naturally tumor-reactive T cells, but little is known about the differences in the TCR repertoires of CD4+ and CD8+ TILs. Methods TCR high-throughput sequencing was performed using TILs derived from the initial cultures of 11 BC biopsies and expanded and sorted CD4+ and CD8+ TILs as well as using PBMCs from healthy donors expanded and sorted using the same methodology. Results Physicochemical TCR differences between T cell subsets were observed, as CD4+ TILs presented larger N(D)Nnt TRB sequences and with a higher usage of positively charged residues, although only the latest was also observed in peripheral T cells from healthy individuals. Moreover, in CD4+ TILs, a more restricted TCR repertoire with a higher abundance of similar sequences containing certain amino acid motifs was observed. Discussion Some differences between CD4+ and CD8+ TCRs were intrinsic to T cell subsets as can also be observed in peripheral T cells from healthy individuals, while other were only found in TILs samples and therefore may be tumor-driven. Notably, the higher similarity among CD4+ TCRs suggests a higher TCR promiscuity in this subset.
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Affiliation(s)
- Andrea Aran
- Immunology Unit, Department of Cell Biology, Physiology, and Immunology, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Gonzalo Lázaro
- Immunology Unit, Department of Cell Biology, Physiology, and Immunology, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Vicente Marco
- Pathology, Hospital Quironsalud Barcelona, Barcelona, Spain
| | - Elisa Molina
- Immunology Unit, Department of Cell Biology, Physiology, and Immunology, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Ferran Abancó
- Immunology Unit, Department of Cell Biology, Physiology, and Immunology, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Vicente Peg
- Pathology Department, Vall d’Hebron University Hospital, Barcelona, Spain
- Department of Morphological Sciences, Universidad Autónoma de Barcelona, Bellaterra, Spain
- Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Madrid, Spain
| | - María Gión
- Medical Oncology Department, Ramón y Cajal University Hospital, Madrid, Spain
| | - Laia Garrigós
- International Breast Cancer Center (IBCC), Pangaea Oncology, Quironsalud Group, Barcelona, Spain
| | - José Pérez-García
- International Breast Cancer Center (IBCC), Pangaea Oncology, Quironsalud Group, Barcelona, Spain
- Medical Scientia Innovation Research (MedSIR), Barcelona, Spain
| | - Javier Cortés
- International Breast Cancer Center (IBCC), Pangaea Oncology, Quironsalud Group, Barcelona, Spain
- Medical Scientia Innovation Research (MedSIR), Barcelona, Spain
- Department of Medicine, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Madrid, Spain
| | - Mercè Martí
- Immunology Unit, Department of Cell Biology, Physiology, and Immunology, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- Biosensing and Bioanalysis Group, Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Spain
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10
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Ng Chau K, George JT, Onuchic JN, Lin X, Levine H. Contact map dependence of a T-cell receptor binding repertoire. Phys Rev E 2022; 106:014406. [PMID: 35974642 DOI: 10.1103/physreve.106.014406] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
The T-cell arm of the adaptive immune system provides the host protection against unknown pathogens by discriminating between host and foreign material. This discriminatory capability is achieved by the creation of a repertoire of cells each carrying a T-cell receptor (TCR) specific to non-self-antigens displayed as peptides bound to the major histocompatibility complex (pMHC). The understanding of the dynamics of the adaptive immune system at a repertoire level is complex, due to both the nuanced interaction of a TCR-pMHC pair and to the number of different possible TCR-pMHC pairings, making computationally exact solutions currently unfeasible. To gain some insight into this problem, we study an affinity-based model for TCR-pMHC binding in which a crystal structure is used to generate a distance-based contact map that weights the pairwise amino acid interactions. We find that the TCR-pMHC binding energy distribution strongly depends both on the number of contacts and the repeat structure allowed by the topology of the contact map of choice; this in turn influences T-cell recognition probability during negative selection, with higher variances leading to higher survival probabilities. In addition, we quantify the degree to which neoantigens with mutations in sites with higher contacts are recognized at a higher rate.
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Affiliation(s)
- Kevin Ng Chau
- Physics Department, Northeastern University, Boston, Massachusetts 02115, USA
| | - Jason T George
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
| | - José N Onuchic
- Center for Theoretical Biological Physics and Departments of Physics and Astronomy, Chemistry and Biosciences, Rice University, Houston, Texas 77005, USA
| | - Xingcheng Lin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Herbert Levine
- Center for Theoretical Biological Physics and Departments of Physics and Bioengineering, Northeastern University, Boston, Massachusetts 02115, USA
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11
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Pishesha N, Harmand TJ, Ploegh HL. A guide to antigen processing and presentation. Nat Rev Immunol 2022; 22:751-764. [PMID: 35418563 DOI: 10.1038/s41577-022-00707-2] [Citation(s) in RCA: 223] [Impact Index Per Article: 111.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2022] [Indexed: 12/13/2022]
Abstract
Antigen processing and presentation are the cornerstones of adaptive immunity. B cells cannot generate high-affinity antibodies without T cell help. CD4+ T cells, which provide such help, use antigen-specific receptors that recognize major histocompatibility complex (MHC) molecules in complex with peptide cargo. Similarly, eradication of virus-infected cells often depends on cytotoxic CD8+ T cells, which rely on the recognition of peptide-MHC complexes for their action. The two major classes of glycoproteins entrusted with antigen presentation are the MHC class I and class II molecules, which present antigenic peptides to CD8+ T cells and CD4+ T cells, respectively. This Review describes the essentials of antigen processing and presentation. These pathways are divided into six discrete steps that allow a comparison of the various means by which antigens destined for presentation are acquired and how the source proteins for these antigens are tagged for degradation, destroyed and ultimately displayed as peptides in complex with MHC molecules for T cell recognition.
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Affiliation(s)
- Novalia Pishesha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.,Society of Fellows, Harvard University, Cambridge, MA, USA.,Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Thibault J Harmand
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
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12
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Zhang A, Piechocka-Trocha A, Li X, Walker BD. A Leucine Zipper Dimerization Strategy to Generate Soluble T Cell Receptors Using the Escherichia coli Expression System. Cells 2022; 11:cells11030312. [PMID: 35159122 PMCID: PMC8834513 DOI: 10.3390/cells11030312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/13/2022] [Accepted: 01/14/2022] [Indexed: 12/10/2022] Open
Abstract
T cell-mediated adaptive immunity plays a key role in immunological surveillance and host control of infectious diseases. A better understanding of T cell receptor (TCR) recognition of pathogen-derived epitopes or cancer-associated neoantigens is the basis for developing T cell-based vaccines and immunotherapies. Studies on the interaction between soluble TCR α:β heterodimers and peptide-bound major histocompatibility complexes (pMHCs) inform underlying mechanisms driving TCR recognition, but not every isolated TCR can be prepared in soluble form for structural and functional studies using conventional methods. Here, taking a challenging HIV-specific TCR as a model, we designed a general leucine zipper (LZ) dimerization strategy for soluble TCR preparation using the Escherichia coli expression system. We report details of TCR construction, inclusion body expression and purification, and protein refolding and purification. Measurements of binding affinity between the TCR and its specific pMHC using surface plasmon resonance (SPR) verify its activity. We conclude that this is a feasible approach to produce challenging TCRs in soluble form, needed for studies related to T cell recognition.
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Affiliation(s)
- Angela Zhang
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; (A.Z.); (A.P.-T.)
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Alicja Piechocka-Trocha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; (A.Z.); (A.P.-T.)
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Xiaolong Li
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; (A.Z.); (A.P.-T.)
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Correspondence: (X.L.); (B.D.W.)
| | - Bruce D. Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; (A.Z.); (A.P.-T.)
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Institute for Medical Engineering and Science (IMES) and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Correspondence: (X.L.); (B.D.W.)
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13
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Barbosa CRR, Barton J, Shepherd AJ, Mishto M. Mechanistic diversity in MHC class I antigen recognition. Biochem J 2021; 478:4187-4202. [PMID: 34940832 PMCID: PMC8786304 DOI: 10.1042/bcj20200910] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/20/2022]
Abstract
Throughout its evolution, the human immune system has developed a plethora of strategies to diversify the antigenic peptide sequences that can be targeted by the CD8+ T cell response against pathogens and aberrations of self. Here we provide a general overview of the mechanisms that lead to the diversity of antigens presented by MHC class I complexes and their recognition by CD8+ T cells, together with a more detailed analysis of recent progress in two important areas that are highly controversial: the prevalence and immunological relevance of unconventional antigen peptides; and cross-recognition of antigenic peptides by the T cell receptors of CD8+ T cells.
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Affiliation(s)
- Camila R. R. Barbosa
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL London, U.K
- Francis Crick Institute, NW1 1AT London, U.K
| | - Justin Barton
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck, University of London, WC1E 7HX London, U.K
| | - Adrian J. Shepherd
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck, University of London, WC1E 7HX London, U.K
| | - Michele Mishto
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) & Peter Gorer Department of Immunobiology, King's College London, SE1 1UL London, U.K
- Francis Crick Institute, NW1 1AT London, U.K
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14
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Riedel F, Aparicio-Soto M, Curato C, Thierse HJ, Siewert K, Luch A. Immunological Mechanisms of Metal Allergies and the Nickel-Specific TCR-pMHC Interface. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:10867. [PMID: 34682608 PMCID: PMC8535423 DOI: 10.3390/ijerph182010867] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/03/2021] [Accepted: 10/11/2021] [Indexed: 12/19/2022]
Abstract
Besides having physiological functions and general toxic effects, many metal ions can cause allergic reactions in humans. We here review the immune events involved in the mediation of metal allergies. We focus on nickel (Ni), cobalt (Co) and palladium (Pd), because these allergens are among the most prevalent sensitizers (Ni, Co) and immediate neighbors in the periodic table of the chemical elements. Co-sensitization between Ni and the other two metals is frequent while the knowledge on a possible immunological cross-reactivity using in vivo and in vitro approaches remains limited. At the center of an allergic reaction lies the capability of a metal allergen to form T cell epitopes that are recognized by specific T cell receptors (TCR). Technological advances such as activation-induced marker assays and TCR high-throughput sequencing recently provided new insights into the interaction of Ni2+ with the αβ TCR-peptide-major histocompatibility complex (pMHC) interface. Ni2+ functionally binds to the TCR gene segment TRAV9-2 or a histidine in the complementarity determining region 3 (CDR3), the main antigen binding region. Thus, we overview known, newly identified and hypothesized mechanisms of metal-specific T cell activation and discuss current knowledge on cross-reactivity.
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Affiliation(s)
- Franziska Riedel
- Department for Chemicals and Product Safety, Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany; (M.A.-S.); (C.C.); (H.-J.T.); (K.S.); (A.L.)
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2, 14195 Berlin, Germany
| | - Marina Aparicio-Soto
- Department for Chemicals and Product Safety, Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany; (M.A.-S.); (C.C.); (H.-J.T.); (K.S.); (A.L.)
| | - Caterina Curato
- Department for Chemicals and Product Safety, Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany; (M.A.-S.); (C.C.); (H.-J.T.); (K.S.); (A.L.)
| | - Hermann-Josef Thierse
- Department for Chemicals and Product Safety, Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany; (M.A.-S.); (C.C.); (H.-J.T.); (K.S.); (A.L.)
| | - Katherina Siewert
- Department for Chemicals and Product Safety, Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany; (M.A.-S.); (C.C.); (H.-J.T.); (K.S.); (A.L.)
| | - Andreas Luch
- Department for Chemicals and Product Safety, Federal Institute for Risk Assessment, Max-Dohrn-Straße 8-10, 10589 Berlin, Germany; (M.A.-S.); (C.C.); (H.-J.T.); (K.S.); (A.L.)
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2, 14195 Berlin, Germany
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15
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Lanz AL, Masi G, Porciello N, Cohnen A, Cipria D, Prakaash D, Bálint Š, Raggiaschi R, Galgano D, Cole DK, Lepore M, Dushek O, Dustin ML, Sansom MSP, Kalli AC, Acuto O. Allosteric activation of T cell antigen receptor signaling by quaternary structure relaxation. Cell Rep 2021; 36:109375. [PMID: 34260912 PMCID: PMC8293630 DOI: 10.1016/j.celrep.2021.109375] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 05/05/2021] [Accepted: 06/18/2021] [Indexed: 01/05/2023] Open
Abstract
The mechanism of T cell antigen receptor (TCR-CD3) signaling remains elusive. Here, we identify mutations in the transmembrane region of TCRβ or CD3ζ that augment peptide T cell antigen receptor (pMHC)-induced signaling not explicable by enhanced ligand binding, lateral diffusion, clustering, or co-receptor function. Using a biochemical assay and molecular dynamics simulation, we demonstrate that the gain-of-function mutations loosen the interaction between TCRαβ and CD3ζ. Similar to the activating mutations, pMHC binding reduces TCRαβ cohesion with CD3ζ. This event occurs prior to CD3ζ phosphorylation and at 0°C. Moreover, we demonstrate that soluble monovalent pMHC alone induces signaling and reduces TCRαβ cohesion with CD3ζ in membrane-bound or solubilised TCR-CD3. Our data provide compelling evidence that pMHC binding suffices to activate allosteric changes propagating from TCRαβ to the CD3 subunits, reconfiguring interchain transmembrane region interactions. These dynamic modifications could change the arrangement of TCR-CD3 boundary lipids to license CD3ζ phosphorylation and initiate signal propagation. Mutations in TCRβ and CD3ζ TMRs that reduce their interaction augment signaling pMHC and anti-CD3 binding to TCR-CD3 induce similar quaternary structure relaxation Soluble monovalent pMHC alone signals and reduces TCRαβ cohesion with CD3ζ Allosteric changes in TCR-CD3 dynamics instigate T cell activation
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Affiliation(s)
- Anna-Lisa Lanz
- T-cell signalling laboratory, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Giulia Masi
- T-cell signalling laboratory, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Nicla Porciello
- T-cell signalling laboratory, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - André Cohnen
- T-cell signalling laboratory, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Deborah Cipria
- T-cell signalling laboratory, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Dheeraj Prakaash
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Štefan Bálint
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, UK
| | - Roberto Raggiaschi
- T-cell signalling laboratory, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Donatella Galgano
- T-cell signalling laboratory, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - David K Cole
- Division Infection & Immunity, Cardiff University, Cardiff CF14 4XN, UK; Immunocore Ltd., Abingdon OX14 4RY, UK
| | | | - Omer Dushek
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Michael L Dustin
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
| | - Antreas C Kalli
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds LS2 9JT, UK; Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
| | - Oreste Acuto
- T-cell signalling laboratory, Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
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16
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Yan D, Yang J, Ji Z, Wang J, Lu X, Huang Y, Zhong C, Li L. Profiling T cell receptor β-chain in responders after immunization with recombinant hepatitis B vaccine. J Gene Med 2021; 23:e3367. [PMID: 34048625 DOI: 10.1002/jgm.3367] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/22/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND T cells with edited T cell receptor β-chain variable (TRBV) are involved in the immune response to recombinant hepatitis B surface antigen (rHBsAg) vaccine and the production of hepatitis B surface antibody (HBsAb). The immune repertoire (IR) profile and mechanism of vaccination positive responders (VPR) with rHBsAg are not fully understood. METHODS The IR of six VPRs (HBsAb+, HbsAg-) with rHBsAg vaccination was established by the high throughput sequencing technique and bioinformatics analysis and compared with those in five vaccination negative responders (VNRs) (HbsAb-, HbsAg-) who were also inoculated with rHBsAg. The repertoire features of the BV, BJ and V (CDR3) J genes and immune diversity in peripheral blood mononuclear cells, respectively, were analyzed for each subject. RESULTS There was no significant difference in sequencing amplification indices of each sample. However, TRBV15/BJ2-3 demonstrated significantly high expression levels in VPR compared to those in the VNR group (both p < 0.05). Further results showed that the BV15/BJ2-5 level was significantly increased for VPR compared to that of VNR group. Interestingly, the motif of CDR3 in TRBV15/BJ2-5 was mostly expressed as "GGETQ" or "GETQ". Additionally, there was no remarkable difference between the two groups of distribution with respect to the different clone expression levels of V (CDR3) J. CONCLUSIONS The features of IR in the VPR and VNR will contribute to the exploration of the mechanism of the positive response to rHBsAg, and also contribute to development of optimized hepatitis B vaccine, in addition to providing a partial interpretation of the VNR who has a relatively low infection with HBV.
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Affiliation(s)
- Dong Yan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiezuan Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhongkang Ji
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ju Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoqing Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yandi Huang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chengli Zhong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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17
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Bingöl EN, Serçinoğlu O, Ozbek P. Unraveling the Allosteric Communication Mechanisms in T-Cell Receptor-Peptide-Loaded Major Histocompatibility Complex Dynamics Using Molecular Dynamics Simulations: An Approach Based on Dynamic Cross Correlation Maps and Residue Interaction Energy Calculations. J Chem Inf Model 2021; 61:2444-2453. [PMID: 33930270 DOI: 10.1021/acs.jcim.1c00338] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Antigen presentation by major histocompatibility complex (MHC) proteins to T-cell receptors (TCRs) plays a crucial role in triggering the adaptive immune response. Most of our knowledge on TCR-peptide-loaded major histocompatibility complex (pMHC) interaction stemmed from experiments yielding static structures, yet the dynamic aspects of this molecular interaction are equally important to understand the underlying molecular mechanisms and to develop treatment strategies against diseases such as cancer and autoimmune diseases. To this end, computational biophysics studies including all-atom molecular dynamics simulations have provided useful insights; however, we still lack a basic understanding of an overall allosteric mechanism that results in conformational changes in the TCR and subsequent T-cell activation. Previous hydrogen-deuterium exchange and nuclear magnetic resonance studies provided clues regarding these molecular mechanisms, including global rigidification and allosteric effects on the constant domain of TCRs away from the pMHC interaction site. Here, we show that molecular dynamics simulations can be used to identify how this overall rigidification may be related to the allosteric communication within TCRs upon pMHC interaction via essential dynamics and nonbonded residue-residue interaction energy analyses. The residues taking part in the rigidification effect are highlighted with an intricate analysis on residue interaction changes, which lead to a detailed outline of the complex formation event. Our results indicate that residues of the Cβ domain of TCRs show significant differences in their nonbonded interactions upon complex formation. Moreover, the dynamic cross correlations between these residues are also increased, in line with their nonbonded interaction energy changes. Altogether, our approach may be valuable for elucidating intramolecular allosteric changes in the TCR structure upon pMHC interaction in molecular dynamics simulations.
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Affiliation(s)
- Elif Naz Bingöl
- Department of Bioengineering, Institute of Pure and Applied Sciences, Marmara University, 34722 Istanbul, Turkey
| | - Onur Serçinoğlu
- Department of Bioengineering, Faculty of Engineering, Gebze Technical University, Kocaeli 41400, Turkey
| | - Pemra Ozbek
- Department of Bioengineering, Faculty of Engineering, Marmara University, Istanbul 34722, Turkey
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18
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Merkle PS, Trabjerg E, Hongjian S, Ferber M, Cuendet MA, Jørgensen TJD, Luescher I, Irving M, Zoete V, Michielin O, Rand KD. Probing the Conformational Dynamics of Affinity-Enhanced T Cell Receptor Variants upon Binding the Peptide-Bound Major Histocompatibility Complex by Hydrogen/Deuterium Exchange Mass Spectrometry. Biochemistry 2021; 60:859-872. [PMID: 33689297 DOI: 10.1021/acs.biochem.1c00035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Binding of the T cell receptor (TCR) to its cognate, peptide antigen-loaded major histocompatibility complex (pMHC) is a key interaction for triggering T cell activation and ultimately elimination of the target cell. Despite the importance of this interaction for cellular immunity, a comprehensive molecular understanding of TCR specificity and affinity is lacking. We conducted hydrogen/deuterium exchange mass spectrometry (HDX-MS) analyses of individual affinity-enhanced TCR variants and clinically relevant pMHC class I molecules (HLA-A*0201/NY-ESO-1157-165) to investigate the causality between increased binding affinity and conformational dynamics in TCR-pMHC complexes. Differential HDX-MS analyses of TCR variants revealed that mutations for affinity enhancement in TCR CDRs altered the conformational response of TCR to pMHC ligation. Improved pMHC binding affinity was in general observed to correlate with greater differences in HDX upon pMHC binding in modified TCR CDR loops, thereby providing new insights into the TCR-pMHC interaction. Furthermore, a specific point mutation in the β-CDR3 loop of the NY-ESO-1 TCR associated with a substantial increase in binding affinity resulted in a substantial change in pMHC binding kinetics (i.e., very slow kon, revealed by the detection of EX1 HDX kinetics), thus providing experimental evidence for a slow induced-fit binding mode. We also examined the conformational impact of pMHC binding on an unrelated TRAV12-2 gene-encoded TCR directed against the immunodominant MART-126-35 cancer antigen restricted by HLA-A*0201. Our findings provide a molecular basis for the observed TRAV12-2 gene bias in natural CD8+ T cell-based immune responses against the MART-1 antigen, with potential implications for general ligand discrimination and TCR cross-reactivity processes.
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MESH Headings
- Humans
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/immunology
- HLA-A2 Antigen/chemistry
- HLA-A2 Antigen/immunology
- HLA-A2 Antigen/metabolism
- HLA-A2 Antigen/genetics
- Protein Conformation
- Hydrogen Deuterium Exchange-Mass Spectrometry
- Protein Binding
- Peptides/chemistry
- Peptides/metabolism
- Peptides/immunology
- Major Histocompatibility Complex
- Antigens, Neoplasm/chemistry
- Antigens, Neoplasm/metabolism
- Antigens, Neoplasm/immunology
- Antigens, Neoplasm/genetics
- Peptide Fragments/chemistry
- Peptide Fragments/metabolism
- Peptide Fragments/genetics
- Peptide Fragments/immunology
- Deuterium Exchange Measurement
- Mutation
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Affiliation(s)
- Patrick S Merkle
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Esben Trabjerg
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Song Hongjian
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Mathias Ferber
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Michel A Cuendet
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
- Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, United States
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Immanuel Luescher
- Ludwig Branch for Cancer Research of the University of Lausanne, 8001 Zurich, Switzerland
| | - Melita Irving
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
- Ludwig Branch for Cancer Research of the University of Lausanne, 8001 Zurich, Switzerland
| | - Vincent Zoete
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Olivier Michielin
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Kasper D Rand
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
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19
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Zhu Y, Huang C, Su M, Ge Z, Gao L, Shi Y, Wang X, Chen J. Characterization of amino acid residues of T-cell receptors interacting with HLA-A*02-restricted antigen peptides. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:495. [PMID: 33850892 PMCID: PMC8039679 DOI: 10.21037/atm-21-835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background The present study aimed to explore residues’ properties interacting with HLA-A*02-restricted peptides on T-cell receptors (TCRs) and their effects on bond types of interaction and binding free energy. Methods We searched the crystal structures of HLA-A*02-restricted peptide-TCR complexes from the Protein Data Bank (PDB) database and subsequently collected relevant parameters. We then employed Schrodinger to analyze the bond types of interaction and Gromacs 2019 to evaluate the TCR-antigen peptide complex’s molecular dynamics simulation. Finally, we compared the changes of bond types of interaction and binding free energy before and after residue substitution to ensure consistency of the conditions before and after residue substitution. Results The main sites on the antigen peptides that formed the intermolecular interaction [hydrogen bond (HB) and pi stack] with TCRs were P4, P8, P2, and P6. The hydrophobicity of the amino acids inside or outside the disulfide bond of TCRs may be related to the intermolecular interaction and binding free energy between TCRs and peptides. Residues located outside the disulfide bond of TCR α or β chains and forming pi stack force played favorable roles in the complex intermolecular interaction and binding free energy. The residues of the TCR α or β chains that interacted with peptides were replaced by alanine (Ala) or glycine (Gly), and their intermolecular binding free energy of the complex had been improved. However, it had nothing to do with the formation of HB. Conclusions The findings of this study suggest that the hydrophobic nature of the amino acids inside or outside the disulfide bonds on the TCR may be associated with the intermolecular interaction and binding between the TCR and polypeptide. The residues located outside the TCR α or β single-chain disulfide bond and forming the pi-stack force showed a beneficial effect on the intermolecular interaction and binding of the complex. In addition, the part of the residues on the TCR α or β single chain that produced bond types of interaction with the polypeptide after being replaced by Ala or Gly, the intermolecular binding free energy of the complex was increased, regardless of whether HB was formed.
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Affiliation(s)
- Ying Zhu
- Department of Oncology, First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Changxin Huang
- Department of Oncology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Meng Su
- Master Class, Zhejiang Chinese Medical University, Fourth School of Clinical Medicine, Hangzhou, China
| | - Zuanmin Ge
- Master Class, Hangzhou Normal University, School of Medicine, Hangzhou, China
| | - Lanlan Gao
- Master Class, Hangzhou Normal University, School of Medicine, Hangzhou, China
| | - Yanfei Shi
- Master Class, Hangzhou Normal University, School of Medicine, Hangzhou, China
| | - Xuechun Wang
- Master Class, Zhejiang Chinese Medical University, Fourth School of Clinical Medicine, Hangzhou, China
| | - Jianfeng Chen
- Department of Proctology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
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20
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Gordin M, Philip H, Zilberberg A, Gidoni M, Margalit R, Clouser C, Adams K, Vigneault F, Cohen IR, Yaari G, Efroni S. Breast cancer is marked by specific, Public T-cell receptor CDR3 regions shared by mice and humans. PLoS Comput Biol 2021; 17:e1008486. [PMID: 33465095 PMCID: PMC7846026 DOI: 10.1371/journal.pcbi.1008486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 01/29/2021] [Accepted: 11/03/2020] [Indexed: 11/19/2022] Open
Abstract
The partial success of tumor immunotherapy induced by checkpoint blockade, which is not antigen-specific, suggests that the immune system of some patients contain antigen receptors able to specifically identify tumor cells. Here we focused on T-cell receptor (TCR) repertoires associated with spontaneous breast cancer. We studied the alpha and beta chain CDR3 domains of TCR repertoires of CD4 T cells using deep sequencing of cell populations in mice and applied the results to published TCR sequence data obtained from human patients. We screened peripheral blood T cells obtained monthly from individual mice spontaneously developing breast tumors by 5 months. We then looked at identical TCR sequences in published human studies; we used TCGA data from tumors and healthy tissues of 1,256 breast cancer resections and from 4 focused studies including sequences from tumors, lymph nodes, blood and healthy tissues, and from single cell dataset of 3 breast cancer subjects. We now report that mice spontaneously developing breast cancer manifest shared, Public CDR3 regions in both their alpha and beta and that a significant number of women with early breast cancer manifest identical CDR3 sequences. These findings suggest that the development of breast cancer is associated, across species, with biomarker, exclusive TCR repertoires.
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Affiliation(s)
- Miri Gordin
- The Mina & Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Hagit Philip
- The Mina & Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Alona Zilberberg
- The Mina & Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
| | - Moriah Gidoni
- Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
| | | | | | - Kristofor Adams
- Juno Therapeutics, Seattle, Washington, United States of America
| | | | - Irun R. Cohen
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
| | - Gur Yaari
- Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
- * E-mail: (GY); (SE)
| | - Sol Efroni
- The Mina & Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel
- * E-mail: (GY); (SE)
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21
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Singh NK, Alonso JA, Harris DT, Anderson SD, Ma J, Hellman LM, Rosenberg AM, Kolawole EM, Evavold BD, Kranz DM, Baker BM. An Engineered T Cell Receptor Variant Realizes the Limits of Functional Binding Modes. Biochemistry 2020; 59:4163-4175. [PMID: 33074657 DOI: 10.1021/acs.biochem.0c00689] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
T cell receptors (TCRs) orchestrate cellular immunity by recognizing peptides presented by a range of major histocompatibility complex (MHC) proteins. Naturally occurring TCRs bind the composite peptide/MHC surface, recognizing peptides that are structurally and chemically compatible with the TCR binding site. Here we describe a molecularly evolved TCR variant that binds the human class I MHC protein HLA-A2 independent of the bound peptide, achieved by a drastic perturbation of the TCR binding geometry that places the molecule far from the peptide binding groove. This unique geometry is unsupportive of normal T cell signaling. A substantial divergence between affinity measurements in solution and in two dimensions between proximal cell membranes leads us to attribute the lack of signaling to steric hindrance that limits binding in the confines of a cell-cell interface. Our results provide an example of how receptor binding geometry can impact T cell function and provide further support for the view that germline-encoded residues in TCR binding loops evolved to drive productive TCR recognition and signaling.
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Affiliation(s)
- Nishant K Singh
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jesus A Alonso
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Daniel T Harris
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, Illinois 61801, United States
| | - Scott D Anderson
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, Illinois 61801, United States
| | - Jiaqi Ma
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Lance M Hellman
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Aaron M Rosenberg
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Elizabeth M Kolawole
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, Utah 84112, United States
| | - Brian D Evavold
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, Utah 84112, United States
| | - David M Kranz
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, Illinois 61801, United States
| | - Brian M Baker
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
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22
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Tarbe M, Miles JJ, Edwards ESJ, Miles KM, Sewell AK, Baker BM, Quideau S. Synthesis and Biological Evaluation of Hapten-Clicked Analogues of The Antigenic Peptide Melan-A/MART-1 26(27L)-35. ChemMedChem 2020; 15:799-807. [PMID: 32162475 PMCID: PMC7473458 DOI: 10.1002/cmdc.202000038] [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: 01/22/2020] [Revised: 03/03/2020] [Indexed: 11/12/2022]
Abstract
A click-chemistry-based approach was implemented to prepare peptidomimetics designed in silico and made from aromatic azides and a propargylated GIGI-mimicking platform derived from the altered Melan-A/MART-126(27L)-35 antigenic peptide ELAGIGILTV. The CuI -catalyzed Huisgen cycloaddition was carried out on solid support to generate rapidly a first series of peptidomimetics, which were evaluated for their capacity to dock at the interface between the major histocompatibility complex class-I (MHC-I) human leucocyte antigen (HLA)-A2 and T-cell receptors (TCRs). Despite being a weak HLA-A2 ligand, one of these 11 first synthetic compounds bearing a p-nitrobenzyl-triazole side chain was recognized by the receptor proteins of Melan-A/MART-1-specific T-cells. After modification of the N and C termini of this agonist, which was intended to enhance HLA-A2 binding, one of the resulting seven additional compounds triggered significant T-cell responses. Thus, these results highlight the capacity of naturally circulating human TCRs that are specific for the native Melan-A/MART-126-35 peptide to cross-react with peptidomimetics bearing organic motifs structurally different from the native central amino acids.
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Affiliation(s)
- Marion Tarbe
- Université de Bordeaux, ISM (CNRS-UMR 5255), 351 cours de la Libération, 33405, Talence Cedex, France
| | - John J Miles
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Emily S J Edwards
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
- Department of Immunology and Pathology, Central Clinical School, Monash University, Level 6, 89 Commercial Road, Melbourne, Victoria, 3004, Australia
| | - Kim M Miles
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
| | - Andrew K Sewell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
| | - Brian M Baker
- Department of Chemistry & Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Stéphane Quideau
- Université de Bordeaux, ISM (CNRS-UMR 5255), 351 cours de la Libération, 33405, Talence Cedex, France
- Institut Universitaire de France, 1 rue Descartes, 75231, Paris Cedex 05, France
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23
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Tripathi SK, Salunke DM. Exploring the different states of wild-type T-cell receptor and mutant conformational changes towards understanding the antigen recognition. J Biomol Struct Dyn 2020; 39:188-201. [PMID: 31870204 DOI: 10.1080/07391102.2019.1708795] [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] [Indexed: 10/25/2022]
Abstract
Recognition of proteolytic peptide fragments presented by major histocompatibility complex (MHC) on target cells by T-cell receptor (TCR) is among the most important interactions in the adaptive immune system. Several computational studies have been performed to investigate conformational and dynamical properties of TCRs for enhanced immunogenicity. Here, we present the large-scale molecular dynamics (MD) simulation studies of the two comprehensive systems consisting of the wild-type and mutant IG4 TCR in complex with the tumor epitope NY-ESO peptide (SLLMWITQC) and analyzed for mapping conformational changes of TCR in the states prior to antigen binding, upon antigen binding and after the antigen was released. All of the simulations were performed with different states of TCRs for each 1000 ns of simulation time, providing six simulations for time duration of 6000 ns (6µs). We show that rather than undergoing most critical conformational changes upon antigen binding, the high proportion of complementarity-determining region (CDR) loops change by comparatively small amount. The hypervariable CDRα3 and CDRβ3 loops showed significant structural changes. Interestingly, the TCR β chain loops showed the least changes, which is reliable with recent implications that β domain of TCR may propel antigen interaction. The mutant shows higher rigidity than wild-type even in released state; expose an induced fit mechanism occurring from the re-structuring of CDRα3 loop and can allow enhanced binding affinity of the peptide antigen. Additionally, we show that CDRα3 loop and peptide contacts are an adaptive feature of affinity enhanced mutant TCR.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sunil Kumar Tripathi
- Structural Immunology Group, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Dinakar M Salunke
- Structural Immunology Group, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India.,Structural Immunology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
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24
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Mösch A, Raffegerst S, Weis M, Schendel DJ, Frishman D. Machine Learning for Cancer Immunotherapies Based on Epitope Recognition by T Cell Receptors. Front Genet 2019; 10:1141. [PMID: 31798635 PMCID: PMC6878726 DOI: 10.3389/fgene.2019.01141] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/21/2019] [Indexed: 12/30/2022] Open
Abstract
In the last years, immunotherapies have shown tremendous success as treatments for multiple types of cancer. However, there are still many obstacles to overcome in order to increase response rates and identify effective therapies for every individual patient. Since there are many possibilities to boost a patient's immune response against a tumor and not all can be covered, this review is focused on T cell receptor-mediated therapies. CD8+ T cells can detect and destroy malignant cells by binding to peptides presented on cell surfaces by MHC (major histocompatibility complex) class I molecules. CD4+ T cells can also mediate powerful immune responses but their peptide recognition by MHC class II molecules is more complex, which is why the attention has been focused on CD8+ T cells. Therapies based on the power of T cells can, on the one hand, enhance T cell recognition by introducing TCRs that preferentially direct T cells to tumor sites (so called TCR-T therapy) or through vaccination to induce T cells in vivo. On the other hand, T cell activity can be improved by immune checkpoint inhibition or other means that help create a microenvironment favorable for cytotoxic T cell activity. The manifold ways in which the immune system and cancer interact with each other require not only the use of large omics datasets from gene, to transcript, to protein, and to peptide but also make the application of machine learning methods inevitable. Currently, discovering and selecting suitable TCRs is a very costly and work intensive in vitro process. To facilitate this process and to additionally allow for highly personalized therapies that can simultaneously target multiple patient-specific antigens, especially neoepitopes, breakthrough computational methods for predicting antigen presentation and TCR binding are urgently required. Particularly, potential cross-reactivity is a major consideration since off-target toxicity can pose a major threat to patient safety. The current speed at which not only datasets grow and are made available to the public, but also at which new machine learning methods evolve, is assuring that computational approaches will be able to help to solve problems that immunotherapies are still facing.
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Affiliation(s)
- Anja Mösch
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
- Medigene Immunotherapies GmbH, a subsidiary of Medigene AG, Planegg, Germany
| | - Silke Raffegerst
- Medigene Immunotherapies GmbH, a subsidiary of Medigene AG, Planegg, Germany
| | - Manon Weis
- Medigene Immunotherapies GmbH, a subsidiary of Medigene AG, Planegg, Germany
| | - Dolores J. Schendel
- Medigene Immunotherapies GmbH, a subsidiary of Medigene AG, Planegg, Germany
| | - Dmitrij Frishman
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
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25
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Yu K, Shi J, Lu D, Yang Q. Comparative analysis of CDR3 regions in paired human αβ CD8 T cells. FEBS Open Bio 2019; 9:1450-1459. [PMID: 31237075 PMCID: PMC6668380 DOI: 10.1002/2211-5463.12690] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 05/23/2019] [Accepted: 06/21/2019] [Indexed: 01/21/2023] Open
Abstract
The majority of human CD8 cytotoxic T lymphocytes express αβ T-cell receptors that recognize peptide-MHC class I complexes. Considerable attention has been devoted to TCR β repertoires, but study of TCR α chains has been limited. To gain a better understanding of the features of CDR3α and CDR3β in paired samples, we comprehensively analyzed 776 unique paired αβ TCR CDR3 regions in this study. We found that (I) the CDR3 length among paired αβ TCRs had a fairly narrow distribution due to random assortment of CDR3 length in alpha and beta chains; (II) nucleotide deletions among CDR3 regions were positively correlated with insertions in both α and β TCRs; (III) the CDR3 loops of both α and β chains contained an abundance of charged/polar residues and the CDR3 base regions contained a conserved motif; and (IV) the occurrence of Gly was CDR3 length- and position-dependent in both chains, whereas the frequency of Ser at positions 106 and 107 was positively correlated with CDR3 length in TCR β. Overall, the amino acids in CDR3 loop regions were significantly different between TCR α and β, which suggests a distinct role for each chain in the recognition of antigen-MHC complexes. Here, we have provided detailed information on CDR3 in paired TCRs expressed on human CD8+ T cells and established the basis of a reference set for αβ TCR repertoires in healthy humans.
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MESH Headings
- Amino Acid Sequence
- CD8-Positive T-Lymphocytes/immunology
- Complementarity Determining Regions/chemistry
- Histocompatibility Antigens Class I/metabolism
- Humans
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- T-Lymphocytes, Cytotoxic/immunology
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Affiliation(s)
- Kun Yu
- Department of Breast and Thyroid SurgeryZhejiang Provincial People's HospitalPeople's Hospital of Hangzhou Medical CollegeHangzhouChina
| | - Ji Shi
- Department of Breast and Thyroid SurgeryTongDe Hospital of Zhejiang ProvinceHangzhouChina
| | - Dan Lu
- Department of RehabilitationTongDe Hospital of Zhejiang ProvinceHangzhouChina
| | - Qiong Yang
- Department of Breast and Thyroid SurgeryZhejiang Provincial People's HospitalPeople's Hospital of Hangzhou Medical CollegeHangzhouChina
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Karch R, Stocsits C, Ilieva N, Schreiner W. Intramolecular Domain Movements of Free and Bound pMHC and TCR Proteins: A Molecular Dynamics Simulation Study. Cells 2019; 8:cells8070720. [PMID: 31337065 PMCID: PMC6678086 DOI: 10.3390/cells8070720] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/02/2019] [Accepted: 07/12/2019] [Indexed: 12/11/2022] Open
Abstract
The interaction of antigenic peptides (p) and major histocompatibility complexes (pMHC) with T-cell receptors (TCR) is one of the most important steps during the immune response. Here we present a molecular dynamics simulation study of bound and unbound TCR and pMHC proteins of the LC13-HLA-B*44:05-pEEYLQAFTY complex to monitor differences in relative orientations and movements of domains between bound and unbound states of TCR-pMHC. We generated local coordinate systems for MHC α1- and MHC α2-helices and the variable T-cell receptor regions TCR Vα and TCR Vβ and monitored changes in the distances and mutual orientations of these domains. In comparison to unbound states, we found decreased inter-domain movements in the simulations of bound states. Moreover, increased conformational flexibility was observed for the MHC α2-helix, the peptide, and for the complementary determining regions of the TCR in TCR-unbound states as compared to TCR-bound states.
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Affiliation(s)
- Rudolf Karch
- Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, A-1090 Vienna, Austria
| | - Claudia Stocsits
- Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, A-1090 Vienna, Austria
| | - Nevena Ilieva
- Institute of Information and Communication Technologies (IICT), Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 25A, 1113 Sofia, Bulgaria
- CERN-TH, Esplanade des Particules 1, 1211 Geneva, Switzerland
| | - Wolfgang Schreiner
- Section of Biosimulation and Bioinformatics, Center for Medical Statistics, Informatics and Intelligent Systems (CeMSIIS), Medical University of Vienna, Spitalgasse 23, A-1090 Vienna, Austria.
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27
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Sleep Matters: CD4 + T Cell Memory Formation and the Central Nervous System. Trends Immunol 2019; 40:674-686. [PMID: 31262652 DOI: 10.1016/j.it.2019.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 06/05/2019] [Accepted: 06/05/2019] [Indexed: 11/23/2022]
Abstract
The mechanisms of CD4+ T-cell memory formation in the immune system are debated. With the well-established concept of memory formation in the central nervous system (CNS), we propose that formation of CD4+ T-cell memory depends on the interaction of two different cell systems handling two types of stored information. First, information about antigen (event) and challenge (context) is taken up by antigen-presenting cells, as initial storage. Second, event and context information is transferred to CD4+ T cells. During activation, two categories of CD4+ T cell develop: effector CD4+ T cells, carrying event and context information, enabling them to efficiently focus their response to tissues under attack; and persisting CD4+ T cells, providing context-independent antigen-specific memories and long-term storage. This novel hypothesis is supported by the observation that mammalian sleep can improve both CNS and CD4+ T-cell memory.
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28
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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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29
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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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30
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Crooks JE, Boughter CT, Scott LR, Adams EJ. The Hypervariable Loops of Free TCRs Sample Multiple Distinct Metastable Conformations in Solution. Front Mol Biosci 2018; 5:95. [PMID: 30483515 PMCID: PMC6243104 DOI: 10.3389/fmolb.2018.00095] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/22/2018] [Indexed: 01/12/2023] Open
Abstract
CD4+ and CD8+ αβ T cell antigen recognition is determined by the interaction between the TCR Complementarity Determining Region (CDR) loops and the peptide-presenting MHC complex. These T cells are known for their ability to recognize multiple pMHC complexes, and for a necessary promiscuity that is required for their selection and function in the periphery. Crystallographic studies have previously elucidated the role of structural interactions in TCR engagement, but our understanding of the dynamic process that occurs during TCR binding is limited. To better understand the dynamic states that exist for TCR CDR loops in solution, and how this relates to their states when in complex with pMHC, we simulated the 2C T cell receptor in solution using all-atom molecular dynamics in explicit water and constructed a Markov State Model for each of the CDR3α and CDR3β loops. These models reveal multiple metastable states for the CDR3 loops in solution. Simulation data and metastable states reproduce known CDR3β crystal conformations, and reveal several novel conformations suggesting that CDR3β bound states are the result of search processes from nearby pre-existing equilibrium conformational states. Similar simulations of the invariant, Type I Natural Killer T cell receptor NKT15, which engages the monomorphic, MHC-like CD1d ligand, demonstrate that iNKT TCRs also have distinct states, but comparatively restricted degrees of motion.
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Affiliation(s)
- James E Crooks
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, United States
| | - Christopher T Boughter
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, United States
| | - L Ridgway Scott
- Department of Computer Science, University of Chicago, Chicago, IL, United States
| | - Erin J Adams
- Committee on Immunology University of Chicago, Chicago, IL, United States
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31
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Chen H, Chakraborty AK, Kardar M. How nonuniform contact profiles of T cell receptors modulate thymic selection outcomes. Phys Rev E 2018; 97:032413. [PMID: 29776088 DOI: 10.1103/physreve.97.032413] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Indexed: 11/07/2022]
Abstract
T cell receptors (TCRs) bind foreign or self-peptides attached to major histocompatibility complex (MHC) molecules, and the strength of this interaction determines T cell activation. Optimizing the ability of T cells to recognize a diversity of foreign peptides yet be tolerant of self-peptides is crucial for the adaptive immune system to properly function. This is achieved by selection of T cells in the thymus, where immature T cells expressing unique, stochastically generated TCRs interact with a large number of self-peptide-MHC; if a TCR does not bind strongly enough to any self-peptide-MHC, or too strongly with at least one self-peptide-MHC, the T cell dies. Past theoretical work cast thymic selection as an extreme value problem and characterized the statistical enrichment or depletion of amino acids in the postselection TCR repertoire, showing how T cells are selected to be able to specifically recognize peptides derived from diverse pathogens yet have limited self-reactivity. Here, we investigate how the diversity of the postselection TCR repertoire is modified when TCRs make nonuniform contacts with peptide-MHC. Specifically, we were motivated by recent experiments showing that amino acids at certain positions of a TCR sequence have large effects on thymic selection outcomes, and crystal structure data that reveal a nonuniform contact profile between a TCR and its peptide-MHC ligand. Using a representative TCR contact profile as an illustration, we show via simulations that the statistical enrichment or depletion of amino acids now varies by position according to the contact profile, and, importantly, it depends on the implementation of nonuniform contacts during thymic selection. We explain these nontrivial results analytically. Our study has implications for understanding the selection forces that shape the functionality of the postselection TCR repertoire.
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Affiliation(s)
- Hanrong Chen
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Arup K Chakraborty
- Departments of Chemical Engineering, Chemistry, and Biological Engineering, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Mehran Kardar
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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32
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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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33
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Negroni MP, Stern LJ. The N-terminal region of photocleavable peptides that bind HLA-DR1 determines the kinetics of fragment release. PLoS One 2018; 13:e0199704. [PMID: 29965980 PMCID: PMC6028098 DOI: 10.1371/journal.pone.0199704] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 06/12/2018] [Indexed: 12/15/2022] Open
Abstract
Major Histocompatibility Complex class II (MHC-II) molecules bind peptides and present them to receptors on CD4+ T cells as part of the immune system's surveillance of pathogens and malignancy. In the absence of peptide, MHC-II equilibrates between peptide-receptive and peptide-averse conformations. The conversion between these forms has been postulated to be important in regulating cellular antigen presentation but has been difficult to study. In order to generate the MHC-II molecule HLA-DR1 in the peptide-receptive form, we designed and tested a series of photocleavable peptides that included the UV-sensitive 3-amino-3-(2-nitrophenyl)-propionate amino acid analog. They were intended to bind tightly to the HLA-DR1 MHC molecule, but to generate low-affinity fragments after UV exposure that would be released to yield HLA-DR1 in the peptide-receptive conformation. We were able to identify photocleavable peptides that bound tightly to HLA-DR1 and generated the peptide-receptive conformation after UV exposure. However, slow release of photocleaved peptide fragments from the binding site limited the rate of binding of an incoming labeled peptide and complicated kinetic measurements of the individual steps of the overall peptide binding reaction. Modification of the N-terminal region of the photocleavable peptide to reduce MHC-II pocket or H-bonding interactions allowed for generation of the peptide receptive form immediately after UV exposure with peptide fragments neither retained within the site nor interfering with binding of an incoming peptide. However this was achieved only at the expense of a substantial reduction in overall peptide binding affinity, and these peptides had such weak interaction with HLA-DR1 that they were easily exchanged by incoming peptide without UV exposure. These results show that photocleavable peptides can be used to generate peptide-receptive HLA-DR1 and to facilitate peptide exchange in generation of specific peptide-MHC-II complexes, but that usage of these peptides for kinetic studies can be constrained by slow fragment release.
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Affiliation(s)
- Maria Pia Negroni
- Program in Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Lawrence J. Stern
- Program in Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
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34
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Chancellor A, Gadola SD, Mansour S. The versatility of the CD1 lipid antigen presentation pathway. Immunology 2018; 154:196-203. [PMID: 29460282 DOI: 10.1111/imm.12912] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 02/12/2018] [Accepted: 02/14/2018] [Indexed: 12/19/2022] Open
Abstract
The family of non-classical major histocompatibility complex (MHC) class-I like CD1 molecules has an emerging role in human disease. Group 1 CD1 includes CD1a, CD1b and CD1c, which function to display lipids on the cell surface of antigen-presenting cells for direct recognition by T-cells. The recent advent of CD1 tetramers and the identification of novel lipid ligands has contributed towards the increasing number of CD1-restricted T-cell clones captured. These advances have helped to identify novel donor unrestricted and semi-invariant T-cell populations in humans and new mechanisms of T-cell recognition. However, although there is an opportunity to design broadly acting lipids and harness the therapeutic potential of conserved T-cells, knowledge of their role in health and disease is lacking. We briefly summarize the current evidence implicating group 1 CD1 molecules in infection, cancer and autoimmunity and show that although CD1 are not as diverse as MHC, recent discoveries highlight their versatility as they exhibit intricate mechanisms of antigen presentation.
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Affiliation(s)
- Andrew Chancellor
- Faculty of Medicine, Academic Unit of Clinical and Experimental Sciences, Southampton, UK
| | - Stephan D Gadola
- Faculty of Medicine, Academic Unit of Clinical and Experimental Sciences, Southampton, UK.,F.Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Salah Mansour
- Faculty of Medicine, Academic Unit of Clinical and Experimental Sciences, Southampton, UK
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35
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Marrack P, Krovi SH, Silberman D, White J, Kushnir E, Nakayama M, Crooks J, Danhorn T, Leach S, Anselment R, Scott-Browne J, Gapin L, Kappler J. The somatically generated portion of T cell receptor CDR3α contributes to the MHC allele specificity of the T cell receptor. eLife 2017; 6:30918. [PMID: 29148973 PMCID: PMC5701794 DOI: 10.7554/elife.30918] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 11/16/2017] [Indexed: 01/24/2023] Open
Abstract
Mature T cells bearing αβ T cell receptors react with foreign antigens bound to alleles of major histocompatibility complex proteins (MHC) that they were exposed to during their development in the thymus, a phenomenon known as positive selection. The structural basis for positive selection has long been debated. Here, using mice expressing one of two different T cell receptor β chains and various MHC alleles, we show that positive selection-induced MHC bias of T cell receptors is affected both by the germline encoded elements of the T cell receptor α and β chain and, surprisingly, dramatically affected by the non germ line encoded portions of CDR3 of the T cell receptor α chain. Thus, in addition to determining specificity for antigen, the non germline encoded elements of T cell receptors may help the proteins cope with the extremely polymorphic nature of major histocompatibility complex products within the species.
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Affiliation(s)
- Philippa Marrack
- Howard Hughes Medical Institute, Denver, United States.,Department of Biomedical Research, National Jewish Health, Denver, United States.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States
| | - Sai Harsha Krovi
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States
| | - Daniel Silberman
- Department of Biomedical Research, National Jewish Health, Denver, United States.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States
| | - Janice White
- Department of Biomedical Research, National Jewish Health, Denver, United States
| | - Eleanor Kushnir
- Department of Biomedical Research, National Jewish Health, Denver, United States
| | - Maki Nakayama
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States.,Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, United States
| | - James Crooks
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, United States
| | - Thomas Danhorn
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, United States
| | - Sonia Leach
- Department of Biomedical Research, National Jewish Health, Denver, United States.,Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, United States
| | - Randy Anselment
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, United States
| | | | - Laurent Gapin
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States
| | - John Kappler
- Howard Hughes Medical Institute, Denver, United States.,Department of Biomedical Research, National Jewish Health, Denver, United States.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States
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36
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Structural basis of a novel PD-L1 nanobody for immune checkpoint blockade. Cell Discov 2017; 3:17004. [PMID: 28280600 PMCID: PMC5341541 DOI: 10.1038/celldisc.2017.4] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/05/2017] [Indexed: 12/12/2022] Open
Abstract
The use of antibodies to target immune checkpoints, particularly PD-1/PD-L1, has made a profound impact in the field of cancer immunotherapy. Here, we identified KN035, an anti-PD-L1 nanobody that can strongly induce T-cell responses and inhibit tumor growth. The crystal structures of KN035 complexed with PD-L1 and free PD-L1, solved here at 1.7 and 2.7 Å resolution, respectively, show that KN035 competes with PD-1 (programmed death protein 1) for the same flat surface on PD-L1, mainly through a single surface loop of 21 amino acids. This loop forms two short helices and develops key hydrophobic and ionic interactions with PD-L1 residues, such as Ile54, Tyr56 and Arg113, which are also involved in PD-1 binding. The detailed mutagenesis study identified the hotspot residues of the PD-L1 surface and provides an explanation for the stronger (~1 000-fold) binding of KN035 to PD-L1 than PD-1 and its lack of binding to PD-L2. Overall, this study reveals how a single immunoglobulin-variable scaffold of KN035 or PD-1 can bind to a flat protein surface through either a single surface loop or beta-sheet strands; and provides a basis for designing new immune checkpoint blockers and generating bi-specific antibodies for combination therapy.
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37
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Lam C, Liu WF, Bel RD, Chan K, Miller L, Brown MC, Chen Z, Cheng D, Patel D, Xu W, Darling GE, Liu G. Polymorphisms of the FOXF1 and MHC locus genes in individuals undergoing esophageal acid reflux assessments. Dis Esophagus 2017; 30:1-7. [PMID: 26822871 DOI: 10.1111/dote.12456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Gastroesophageal reflux disease (GERD) may lead to Barrett's esophagus (BE). Previously, a large genome-wide association study found two germline markers to be associated with BE, FOXF1 rs9936833 (C allele) and MHC rs9257809 (A allele). This study evaluated whether these two polymorphisms are associated with gastroesphageal acid reflux as measured by 24-hour pH testing. Patients with acid reflux symptoms referred for esophageal manometry and 24-hour pH monitoring at University Health Network (Toronto, ON) were enrolled. DNA extracted from blood was genotyped using a Taqman Polymerase Chain Reaction (PCR) assay. DeMeester scores of ≥14.7 or prior evidence of reflux esophagitis on endoscopy defined individuals with esophageal acid reflux. Logistic regression analysis, adjusted for clinical risk factors, was used to calculate odds ratios with 95% confidence intervals for each polymorphism in relation to the presence of acid reflux. Of 182 patients, the median age was 50 years and 62% were female; 95 (52%) met the definition of GERD. In the multivariable analysis, both FOXF1 rs9936833 (OR = 1.82; 95%CI: 1.12-2.96; P = 0.02) and MHC rs9257809 (OR = 9.36; 95%CI: 2.92-29.99; P < 0.001) remained significantly associated with presence of acid reflux. When both polymorphisms were placed in the same model, the adjusted ORs were 2.10 (95%CI: 1.24-3.53; P = 0.005) and 10.95 (95%CI: 3.32-36.09; P < 0.001), respectively. The association for risk allele C in FOXF1 rs9936833 and risk allele A in MHC rs9257809 with the presence of acid reflux suggests a potential pathophysiologic mechanism for the role of genetic influences in BE development.
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Affiliation(s)
- C Lam
- Department of Medical Biophysics and Medicine, Princess Margaret Hospital-University Health Network, University of Toronto, Toronto, Ontario, Canada.,School of Medicine, University of Nottingham, Nottingham, UK
| | - W F Liu
- Department of Medical Biophysics and Medicine, Princess Margaret Hospital-University Health Network, University of Toronto, Toronto, Ontario, Canada.,Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - R D Bel
- Biostatistics Department, Princess Margaret Hospital-University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - K Chan
- Department of Medical Biophysics and Medicine, Princess Margaret Hospital-University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - L Miller
- Department of Surgery (Thoracic Surgery), Toronto General Hospital-University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - M C Brown
- Department of Medical Biophysics and Medicine, Princess Margaret Hospital-University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Z Chen
- Department of Medical Biophysics and Medicine, Princess Margaret Hospital-University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - D Cheng
- Department of Medical Biophysics and Medicine, Princess Margaret Hospital-University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - D Patel
- Department of Medical Biophysics and Medicine, Princess Margaret Hospital-University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - W Xu
- Biostatistics Department, Princess Margaret Hospital-University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - G E Darling
- Department of Surgery (Thoracic Surgery), Toronto General Hospital-University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - G Liu
- Department of Medical Biophysics and Medicine, Princess Margaret Hospital-University Health Network, University of Toronto, Toronto, Ontario, Canada
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38
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Riley TP, Ayres CM, Hellman LM, Singh NK, Cosiano M, Cimons JM, Anderson MJ, Piepenbrink KH, Pierce BG, Weng Z, Baker BM. A generalized framework for computational design and mutational scanning of T-cell receptor binding interfaces. Protein Eng Des Sel 2016; 29:595-606. [PMID: 27624308 PMCID: PMC5181382 DOI: 10.1093/protein/gzw050] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/19/2016] [Accepted: 08/23/2016] [Indexed: 11/13/2022] Open
Abstract
T-cell receptors (TCRs) have emerged as a new class of therapeutics, most prominently for cancer where they are the key components of new cellular therapies as well as soluble biologics. Many studies have generated high affinity TCRs in order to enhance sensitivity. Recent outcomes, however, have suggested that fine manipulation of TCR binding, with an emphasis on specificity may be more valuable than large affinity increments. Structure-guided design is ideally suited for this role, and here we studied the generality of structure-guided design as applied to TCRs. We found that a previous approach, which successfully optimized the binding of a therapeutic TCR, had poor accuracy when applied to a broader set of TCR interfaces. We thus sought to develop a more general purpose TCR design framework. After assembling a large dataset of experimental data spanning multiple interfaces, we trained a new scoring function that accounted for unique features of each interface. Together with other improvements, such as explicit inclusion of molecular flexibility, this permitted the design new affinity-enhancing mutations in multiple TCRs, including those not used in training. Our approach also captured the impacts of mutations and substitutions in the peptide/MHC ligand, and recapitulated recent findings regarding TCR specificity, indicating utility in more general mutational scanning of TCR-pMHC interfaces.
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Affiliation(s)
- Timothy P Riley
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Cory M Ayres
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Lance M Hellman
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Nishant K Singh
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Michael Cosiano
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Jennifer M Cimons
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Michael J Anderson
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Kurt H Piepenbrink
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Brian G Pierce
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Brian M Baker
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
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39
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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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40
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Zhang H, Lim HS, Knapp B, Deane CM, Aleksic M, Dushek O, van der Merwe PA. The contribution of major histocompatibility complex contacts to the affinity and kinetics of T cell receptor binding. Sci Rep 2016; 6:35326. [PMID: 27734930 PMCID: PMC5062128 DOI: 10.1038/srep35326] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/28/2016] [Indexed: 11/09/2022] Open
Abstract
The interaction between the T cell antigen receptor (TCR) and antigenic peptide in complex with major histocompatibility complex (MHC) molecules is a crucial step in T cell activation. The relative contributions of TCR:peptide and TCR:MHC contacts to the overall binding energy remain unclear. This has important implications for our understanding of T cell development and function. In this study we used site directed mutagenesis to estimate the contribution of HLA-A2 side-chains to the binding of four TCRs. Our results show that these TCRs have very different energetic ‘footprints’ on HLA-A2, with no residues contributing to all TCR interactions. The estimated overall contribution of MHC side-chains to the total interaction energy was variable, with lower limits ranging from 11% to 50%. Kinetic analysis suggested a minor and variable contribution of MHC side-chains to the transition state complex, arguing against a two-step mechanism for TCR binding.
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Affiliation(s)
- Hao Zhang
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom
| | - Hong-Sheng Lim
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom
| | - Berhard Knapp
- Department of Statistics, University of Oxford, United Kingdom
| | | | - Milos Aleksic
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom
| | - Omer Dushek
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom
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41
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An Engineered Switch in T Cell Receptor Specificity Leads to an Unusual but Functional Binding Geometry. Structure 2016; 24:1142-1154. [PMID: 27238970 DOI: 10.1016/j.str.2016.04.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Revised: 03/31/2016] [Accepted: 04/19/2016] [Indexed: 11/21/2022]
Abstract
Utilizing a diverse binding site, T cell receptors (TCRs) specifically recognize a composite ligand comprised of a foreign peptide and a major histocompatibility complex protein (MHC). To help understand the determinants of TCR specificity, we studied a parental and engineered receptor whose peptide specificity had been switched via molecular evolution. Altered specificity was associated with a significant change in TCR-binding geometry, but this did not impact the ability of the TCR to signal in an antigen-specific manner. The determinants of binding and specificity were distributed among contact and non-contact residues in germline and hypervariable loops, and included disruption of key TCR-MHC interactions that bias αβ TCRs toward particular binding modes. Sequence-fitness landscapes identified additional mutations that further enhanced specificity. Our results demonstrate that TCR specificity arises from the distributed action of numerous sites throughout the interface, with significant implications for engineering therapeutic TCRs with novel and functional recognition properties.
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42
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Differential utilization of binding loop flexibility in T cell receptor ligand selection and cross-reactivity. Sci Rep 2016; 6:25070. [PMID: 27118724 PMCID: PMC4846865 DOI: 10.1038/srep25070] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 04/11/2016] [Indexed: 12/27/2022] Open
Abstract
Complementarity determining region (CDR) loop flexibility has been suggested to play an important role in the selection and binding of ligands by T cell receptors (TCRs) of the cellular immune system. However, questions remain regarding the role of loop motion in TCR binding, and crystallographic structures have raised questions about the extent to which generalizations can be made. Here we studied the flexibility of two structurally well characterized αβ TCRs, A6 and DMF5. We found that the two receptors utilize loop motion very differently in ligand binding and cross-reactivity. While the loops of A6 move rapidly in an uncorrelated fashion, those of DMF5 are substantially less mobile. Accordingly, the mechanisms of binding and cross-reactivity are very different between the two TCRs: whereas A6 relies on conformational selection to select and bind different ligands, DMF5 uses a more rigid, permissive architecture with greater reliance on slower motions or induced-fit. In addition to binding site flexibility, we also explored whether ligand-binding resulted in common dynamical changes in A6 and DMF5 that could contribute to TCR triggering. Although binding-linked motional changes propagated throughout both receptors, no common features were observed, suggesting that changes in nanosecond-level TCR structural dynamics do not contribute to T cell signaling.
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43
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Kozono H, Matsushita Y, Ogawa N, Kozono Y, Miyabe T, Sekiguchi H, Ichiyanagi K, Okimoto N, Taiji M, Kanagawa O, Sasaki YC. Single-molecule motions of MHC class II rely on bound peptides. Biophys J 2015; 108:350-9. [PMID: 25606683 DOI: 10.1016/j.bpj.2014.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 11/26/2014] [Accepted: 12/02/2014] [Indexed: 11/28/2022] Open
Abstract
The major histocompatibility complex (MHC) class II protein can bind peptides of different lengths in the region outside the peptide-binding groove. Peptide-flanking residues (PFRs) contribute to the binding affinity of the peptide for MHC and change the immunogenicity of the peptide/MHC complex with regard to T cell receptor (TCR). The mechanisms underlying these phenomena are currently unknown. The molecular flexibility of the peptide/MHC complex may be an important determinant of the structures recognized by certain T cells. We used single-molecule x-ray analysis (diffracted x-ray tracking (DXT)) and fluorescence anisotropy to investigate these mechanisms. DXT enabled us to monitor the real-time Brownian motion of the peptide/MHC complex and revealed that peptides without PFRs undergo larger rotational motions than peptides with PFRs. Fluorescence anisotropy further revealed that peptides without PFRs exhibit slightly larger motions on the nanosecond timescale. These results demonstrate that peptides without PFRs undergo dynamic motions in the groove of MHC and consequently are able to assume diverse structures that can be recognized by T cells.
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Affiliation(s)
- Haruo Kozono
- CREST Sasaki Team, Japan Science and Technology Agency, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan; Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan.
| | - Yufuku Matsushita
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Naoki Ogawa
- CREST Sasaki Team, Japan Science and Technology Agency, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan; Graduate School for Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Yuko Kozono
- Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Toshihiro Miyabe
- Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Hiroshi Sekiguchi
- CREST Sasaki Team, Japan Science and Technology Agency, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan; Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Kouhei Ichiyanagi
- CREST Sasaki Team, Japan Science and Technology Agency, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan; Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Noriaki Okimoto
- Computational Biology Research Core, Quantitative Biology Center, RIKEN, Hyogo, Japan
| | - Makoto Taiji
- Computational Biology Research Core, Quantitative Biology Center, RIKEN, Hyogo, Japan
| | - Osami Kanagawa
- CREST Sasaki Team, Japan Science and Technology Agency, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan; Centre International de Recherche en Infectiologie, INSERM U1111, Lyon, France
| | - Yuji C Sasaki
- CREST Sasaki Team, Japan Science and Technology Agency, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan; Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.
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44
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Westermann J, Lange T, Textor J, Born J. System Consolidation During Sleep – A Common Principle Underlying Psychological and Immunological Memory Formation. Trends Neurosci 2015; 38:585-597. [DOI: 10.1016/j.tins.2015.07.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/30/2015] [Accepted: 07/28/2015] [Indexed: 12/11/2022]
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45
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Arias CF, Herrero MA, Cuesta JA, Acosta FJ, Fernández-Arias C. The growth threshold conjecture: a theoretical framework for understanding T-cell tolerance. ROYAL SOCIETY OPEN SCIENCE 2015; 2:150016. [PMID: 26587263 PMCID: PMC4632576 DOI: 10.1098/rsos.150016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 06/09/2015] [Indexed: 05/15/2023]
Abstract
Adaptive immune responses depend on the capacity of T cells to target specific antigens. As similar antigens can be expressed by pathogens and host cells, the question naturally arises of how can T cells discriminate friends from foes. In this work, we suggest that T cells tolerate cells whose proliferation rates remain below a permitted threshold. Our proposal relies on well-established facts about T-cell dynamics during acute infections: T-cell populations are elastic (they expand and contract) and they display inertia (contraction is delayed relative to antigen removal). By modelling inertia and elasticity, we show that tolerance to slow-growing populations can emerge as a population-scale feature of T cells. This result suggests a theoretical framework to understand immune tolerance that goes beyond the self versus non-self dichotomy. It also accounts for currently unexplained observations, such as the paradoxical tolerance to slow-growing pathogens or the presence of self-reactive T cells in the organism.
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Affiliation(s)
- Clemente F. Arias
- Departamento de Matemática Aplicada, and, Universidad Complutense de Madrid, Madrid, Spain
- Departamento de Ecología, Universidad Complutense de Madrid, Madrid, Spain
- Author for correspondence: Clemente F. Arias e-mail:
| | - Miguel A. Herrero
- Departamento de Matemática Aplicada, and, Universidad Complutense de Madrid, Madrid, Spain
| | - José A. Cuesta
- Grupo Interdisciplinar de Sistemas Complejos, Madrid, Spain
- Departamento de Matemáticas, Universidad Carlos III de Madrid, Leganés, Madrid, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain
| | | | - Cristina Fernández-Arias
- Department of Microbiology, Division of Parasitology, New York University School of Medicine, New York, NY, USA
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Eisen HN. Affinity enhancement of antibodies: how low-affinity antibodies produced early in immune responses are followed by high-affinity antibodies later and in memory B-cell responses. Cancer Immunol Res 2014; 2:381-92. [PMID: 24795350 DOI: 10.1158/2326-6066.cir-14-0029] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The antibodies produced initially in response to most antigens are high molecular weight (MW) immunoglobulins (IgM) with low affinity for the antigen, while the antibodies produced later are lower MW classes (e.g., IgG and IgA) with, on average, orders of magnitude higher affinity for that antigen. These changes, often termed affinity maturation, take place largely in small B-cell clusters (germinal center; GC) in lymphoid tissues in which proliferating antigen-stimulated B cells express the highly mutagenic cytidine deaminase that mediates immunoglobulin class-switching and sequence diversification of the immunoglobulin variable domains of antigen-binding receptors on B cells (BCR). Of the large library of BCR-mutated B cells thus rapidly generated, a small minority with affinity-enhancing mutations are selected to survive and differentiate into long-lived antibody-secreting plasma cells and memory B cells. BCRs are also endocytic receptors; they internalize and cleave BCR-bound antigen, yielding peptide-MHC complexes that are recognized by follicular helper T cells. Imperfect correlation between BCR affinity for antigen and cognate T-cell engagement may account for the increasing affinity heterogeneity that accompanies the increasing average affinity of antibodies. Conservation of mechanisms underlying mutation and selection of high-affinity antibodies over the ≈200 million years of evolution separating bird and mammal lineages points to the crucial role of antibody affinity enhancement in adaptive immunity.
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Affiliation(s)
- Herman N Eisen
- Authors' Affiliations: Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts
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Assessing T cell clonal size distribution: a non-parametric approach. PLoS One 2014; 9:e108658. [PMID: 25275470 PMCID: PMC4183510 DOI: 10.1371/journal.pone.0108658] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 08/25/2014] [Indexed: 11/24/2022] Open
Abstract
Clonal structure of the human peripheral T-cell repertoire is shaped by a number of homeostatic mechanisms, including antigen presentation, cytokine and cell regulation. Its accurate tuning leads to a remarkable ability to combat pathogens in all their variety, while systemic failures may lead to severe consequences like autoimmune diseases. Here we develop and make use of a non-parametric statistical approach to assess T cell clonal size distributions from recent next generation sequencing data. For 41 healthy individuals and a patient with ankylosing spondylitis, who undergone treatment, we invariably find power law scaling over several decades and for the first time calculate quantitatively meaningful values of decay exponent. It has proved to be much the same among healthy donors, significantly different for an autoimmune patient before the therapy, and converging towards a typical value afterwards. We discuss implications of the findings for theoretical understanding and mathematical modeling of adaptive immunity.
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Hawse WF, Morel PA. An immunology primer for computational modelers. J Pharmacokinet Pharmacodyn 2014; 41:389-99. [PMID: 25238901 DOI: 10.1007/s10928-014-9384-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 09/09/2014] [Indexed: 11/30/2022]
Abstract
The immune system is designed to protect an organism from infection and damage caused by a pathogen. A successful immune response requires the coordinated function of multiple cell types and molecules in the innate and adaptive immune systems. Given the complexity of the immune system, it would be advantageous to build computational models to better understand immune responses and develop models to better guide the design of immunotherapies. Often, researchers with strong quantitative backgrounds do not have formal training in immunology. Therefore, the goal of this review article is to provide a brief primer on cellular immunology that is geared for computational modelers.
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Affiliation(s)
- William F Hawse
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA,
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Pedersen LE, Breum SØ, Riber U, Larsen LE, Jungersen G. Identification of swine influenza virus epitopes and analysis of multiple specificities expressed by cytotoxic T cell subsets. Virol J 2014; 11:163. [PMID: 25192825 PMCID: PMC4161877 DOI: 10.1186/1743-422x-11-163] [Citation(s) in RCA: 16] [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: 03/17/2014] [Accepted: 09/01/2014] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Major histocompatibility complex (MHC) class I peptide binding and presentation are essential for antigen-specific activation of cytotoxic T lymphocytes (CTLs) and swine MHC class I molecules, also termed swine leukocyte antigens (SLA), thus play a crucial role in the process that leads to elimination of viruses such as swine influenza virus (SwIV). This study describes the identification of SLA-presented peptide epitopes that are targets for a swine CTL response, and further analyses multiple specificities expressed by SwIV activated CTL subsets. FINDINGS Four SwIV derived peptides were identified as T cell epitopes using fluorescent influenza:SLA tetramers. In addition, multiple CTL specificities were analyzed using peptide sequence substitutions in two of the four epitope candidates analyzed. Interestingly both conserved and substituted peptides were found to stain the CD4-CD8+ T cell subsets indicating multiple specificities. CONCLUSIONS This study describes a timely and cost-effective approach for viral epitope identification in livestock animals. Analysis of T cell subsets showed multiple specificities suggesting SLA-bound epitope recognition of different conformations.
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Affiliation(s)
- Lasse E Pedersen
- National Veterinary Institute, Technical University of Denmark, Frederiksberg C, Denmark
| | - Solvej Ø Breum
- National Veterinary Institute, Technical University of Denmark, Frederiksberg C, Denmark
| | - Ulla Riber
- National Veterinary Institute, Technical University of Denmark, Frederiksberg C, Denmark
| | - Lars E Larsen
- National Veterinary Institute, Technical University of Denmark, Frederiksberg C, Denmark
| | - Gregers Jungersen
- National Veterinary Institute, Technical University of Denmark, Frederiksberg C, Denmark
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Structural Basis for the Specific Recognition of the Major Antigenic Peptide from the Japanese Cedar Pollen Allergen Cry j 1 by HLA-DP5. J Mol Biol 2014; 426:3016-27. [DOI: 10.1016/j.jmb.2014.06.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 06/26/2014] [Accepted: 06/27/2014] [Indexed: 12/20/2022]
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