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Cheng TY, Praveena T, Govindarajan S, Almeida CF, Pellicci DG, Arkins WC, Van Rhijn I, Venken K, Elewaut D, Godfrey DI, Rossjohn J, Moody DB. Lipidomic scanning of self-lipids identifies headless antigens for natural killer T cells. Proc Natl Acad Sci U S A 2024; 121:e2321686121. [PMID: 39141352 PMCID: PMC11348285 DOI: 10.1073/pnas.2321686121] [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: 01/08/2024] [Accepted: 06/12/2024] [Indexed: 08/15/2024] Open
Abstract
To broadly measure the spectrum of cellular self-antigens for natural killer T cells (NKT), we developed a sensitive lipidomics system to analyze lipids trapped between CD1d and NKT T cell receptors (TCRs). We captured diverse antigen complexes formed in cells from natural endogenous lipids, with or without inducing endoplasmic reticulum (ER) stress. After separating protein complexes with no, low, or high CD1d-TCR interaction, we eluted lipids to establish the spectrum of self-lipids that facilitate this interaction. Although this unbiased approach identified fifteen molecules, they clustered into only two related groups: previously known phospholipid antigens and unexpected neutral lipid antigens. Mass spectrometry studies identified the neutral lipids as ceramides, deoxyceramides, and diacylglycerols, which can be considered headless lipids because they lack polar headgroups that usually form the TCR epitope. The crystal structure of the TCR-ceramide-CD1d complex showed how the missing headgroup allowed the TCR to predominantly contact CD1d, supporting a model of CD1d autoreactivity. Ceramide and related headless antigens mediated physiological TCR binding affinity, weak NKT cell responses, and tetramer binding to polyclonal human and mouse NKT cells. Ceramide and sphingomyelin are oppositely regulated components of the "sphingomyelin cycle" that are altered during apoptosis, transformation, and ER stress. Thus, the unique molecular link of ceramide to NKT cell response, along with the recent identification of sphingomyelin blockers of NKT cell activation, provide two mutually reinforcing links for NKT cell response to sterile cellular stress conditions.
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Affiliation(s)
- Tan-Yun Cheng
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA02210
| | - T. Praveena
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
| | - Srinath Govindarajan
- Molecular Immunology and Inflammation Unit, Vlaams Instituut voor Biotechnologie, Center for Inflammation Research, Ghent University, 9052Ghent, Belgium
- Faculty of Medicine and Health Sciences, Department of Internal Medicine and Pediatrics (Rheumatology unit), Ghent University, 9000Ghent, Belgium
| | - Catarina F. Almeida
- Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC3010, Australia
| | - Daniel G. Pellicci
- Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC3010, Australia
| | - Wellington C. Arkins
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA02210
| | - Ildiko Van Rhijn
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA02210
| | - Koen Venken
- Molecular Immunology and Inflammation Unit, Vlaams Instituut voor Biotechnologie, Center for Inflammation Research, Ghent University, 9052Ghent, Belgium
- Faculty of Medicine and Health Sciences, Department of Internal Medicine and Pediatrics (Rheumatology unit), Ghent University, 9000Ghent, Belgium
| | - Dirk Elewaut
- Molecular Immunology and Inflammation Unit, Vlaams Instituut voor Biotechnologie, Center for Inflammation Research, Ghent University, 9052Ghent, Belgium
- Faculty of Medicine and Health Sciences, Department of Internal Medicine and Pediatrics (Rheumatology unit), Ghent University, 9000Ghent, Belgium
| | - Dale I. Godfrey
- Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC3010, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, CardiffCF14 4XN, UK
| | - D. Branch Moody
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA02210
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2
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Rogers J, Bajur AT, Salaita K, Spillane KM. Mechanical control of antigen detection and discrimination by T and B cell receptors. Biophys J 2024; 123:2234-2255. [PMID: 38794795 PMCID: PMC11331051 DOI: 10.1016/j.bpj.2024.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/10/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024] Open
Abstract
The adaptive immune response is orchestrated by just two cell types, T cells and B cells. Both cells possess the remarkable ability to recognize virtually any antigen through their respective antigen receptors-the T cell receptor (TCR) and B cell receptor (BCR). Despite extensive investigations into the biochemical signaling events triggered by antigen recognition in these cells, our ability to predict or control the outcome of T and B cell activation remains elusive. This challenge is compounded by the sensitivity of T and B cells to the biophysical properties of antigens and the cells presenting them-a phenomenon we are just beginning to understand. Recent insights underscore the central role of mechanical forces in this process, governing the conformation, signaling activity, and spatial organization of TCRs and BCRs within the cell membrane, ultimately eliciting distinct cellular responses. Traditionally, T cells and B cells have been studied independently, with researchers working in parallel to decipher the mechanisms of activation. While these investigations have unveiled many overlaps in how these cell types sense and respond to antigens, notable differences exist. To fully grasp their biology and harness it for therapeutic purposes, these distinctions must be considered. This review compares and contrasts the TCR and BCR, placing emphasis on the role of mechanical force in regulating the activity of both receptors to shape cellular and humoral adaptive immune responses.
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Affiliation(s)
- Jhordan Rogers
- Department of Chemistry, Emory University, Atlanta, Georgia
| | - Anna T Bajur
- Department of Physics, King's College London, London, United Kingdom; Randall Centre for Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Khalid Salaita
- Department of Chemistry, Emory University, Atlanta, Georgia; Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia.
| | - Katelyn M Spillane
- Department of Physics, King's College London, London, United Kingdom; Randall Centre for Cell and Molecular Biophysics, King's College London, London, United Kingdom; Department of Life Sciences, Imperial College London, London, United Kingdom.
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3
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Sim MJW, Hanada KI, Stotz Z, Yu Z, Lu J, Brennan P, Quastel M, Gillespie GM, Long EO, Yang JC, Sun PD. Identification and structural characterization of a mutant KRAS-G12V specific TCR restricted by HLA-A3. Eur J Immunol 2024:e2451079. [PMID: 39030753 DOI: 10.1002/eji.202451079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/17/2024] [Accepted: 06/21/2024] [Indexed: 07/22/2024]
Abstract
Mutations in KRAS are some of the most common across multiple cancer types and are thus attractive targets for therapy. Recent studies demonstrated that mutant KRAS generates immunogenic neoantigens that are targetable by adoptive T-cell therapy in metastatic diseases. To expand mutant KRAS-specific immunotherapies, it is critical to identify additional HLA-I allotypes that can present KRAS neoantigens and their cognate T-cell receptors (TCR). Here, we identified a murine TCR specific to a KRAS-G12V neoantigen (7VVVGAVGVGK16) using a vaccination approach with transgenic mice expressing HLA-A*03:01 (HLA-A3). This TCR demonstrated exquisite specificity for mutant G12V and not WT KRAS peptides. To investigate the molecular basis for neoantigen recognition by this TCR, we determined its structure in complex with HLA-A3(G12V). G12V-TCR CDR3β and CDR1β formed a hydrophobic pocket to interact with p6 Val of the G12V but not the WT KRAS peptide. To improve the tumor sensitivity of this TCR, we designed rational substitutions to improve TCR:HLA-A3 contacts. Two substitutions exhibited modest improvements in TCR binding avidity to HLA-A3 (G12V) but did not sufficiently improve T-cell sensitivity for further clinical development. Our study provides mechanistic insight into how TCRs detect neoantigens and reveals the challenges in targeting KRAS-G12V mutations.
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Affiliation(s)
- Malcolm J W Sim
- Division of Intramural Research (DIR), Laboratory of Immunogenetics, NIAID, NIH, Bethesda, Maryland, USA
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | | | - Zachary Stotz
- Division of Intramural Research (DIR), Laboratory of Immunogenetics, NIAID, NIH, Bethesda, Maryland, USA
| | - Zhiya Yu
- Surgery Branch, NCI, NIH, Bethesda, Maryland, USA
| | - Jinghua Lu
- Division of Intramural Research (DIR), Laboratory of Immunogenetics, NIAID, NIH, Bethesda, Maryland, USA
| | - Paul Brennan
- Division of Intramural Research (DIR), Laboratory of Immunogenetics, NIAID, NIH, Bethesda, Maryland, USA
| | - Max Quastel
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Geraldine M Gillespie
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Eric O Long
- Division of Intramural Research (DIR), Laboratory of Immunogenetics, NIAID, NIH, Bethesda, Maryland, USA
| | - James C Yang
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Peter D Sun
- Division of Intramural Research (DIR), Laboratory of Immunogenetics, NIAID, NIH, Bethesda, Maryland, USA
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4
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Bai Z, Hao J, Chen M, Yao K, Zheng L, Liu L, Hu J, Guo K, Lv Y, Li F. Integrating plasma proteomics with genome-wide association data to identify novel drug targets for inflammatory bowel disease. Sci Rep 2024; 14:16251. [PMID: 39009667 PMCID: PMC11250821 DOI: 10.1038/s41598-024-66780-w] [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: 02/27/2024] [Accepted: 07/03/2024] [Indexed: 07/17/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic disease that includes Crohn's disease (CD) and ulcerative colitis (UC). Although genome-wide association studies (GWASs) have identified many relevant genetic risk loci, the impact of these loci on protein abundance and their potential utility as clinical therapeutic targets remain uncertain. Therefore, this study aimed to investigate the pathogenesis of IBD and identify effective therapeutic targets through a comprehensive and integrated analysis. We systematically integrated GWAS data related to IBD, UC and CD (N = 25,305) by the study of de Lange KM with the human blood proteome (N = 7213) by the Atherosclerosis Risk in Communities (ARIC) study. Proteome-wide association study (PWAS), mendelian randomisation (MR) and Bayesian colocalisation analysis were used to identify proteins contributing to the risk of IBD. Integrative analysis revealed that genetic variations in IBD, UC and CD affected the abundance of five (ERAP2, RIPK2, TALDO1, CADM2 and RHOC), three (VSIR, HGFAC and CADM2) and two (MST1 and FLRT3) cis-regulated plasma proteins, respectively (P < 0.05). Among the proteins identified via Bayesian colocalisation analysis, CADM2 was found to be an important common protein between IBD and UC. A drug and five druggable target genes were identified from DGIdb after Bayesian colocalisation analysis. Our study's findings from genetic and proteomic approaches have identified compelling proteins that may serve as important leads for future functional studies and potential drug targets for IBD (UC and CD).
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Affiliation(s)
- Zhongyuan Bai
- First Clinical Medical School, Shanxi Medical University, Taiyuan, China
| | - Jiawei Hao
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Miaoran Chen
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Kaixin Yao
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Leilei Zheng
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Liu Liu
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Jingxi Hu
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Kaiqing Guo
- Hepatobiliary Pancreatogastric Surgery, Shanxi Province Cancer Hospital, Taiyuan, China.
- Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Taiyuan, China.
- Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China.
| | - Yongqiang Lv
- Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Taiyuan, China.
- Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China.
- Department of Scientific Research, Shanxi Province Cancer Hospital, Taiyuan, China.
| | - Feng Li
- Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences, Taiyuan, China.
- Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China.
- Central Laboratory, Shanxi Province Cancer Hospital, Taiyuan, China.
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5
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Rosenberg AM, Ayres CM, Medina-Cucurella AV, Whitehead TA, Baker BM. Enhanced T cell receptor specificity through framework engineering. Front Immunol 2024; 15:1345368. [PMID: 38545094 PMCID: PMC10967027 DOI: 10.3389/fimmu.2024.1345368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/15/2024] [Indexed: 04/12/2024] Open
Abstract
Development of T cell receptors (TCRs) as immunotherapeutics is hindered by inherent TCR cross-reactivity. Engineering more specific TCRs has proven challenging, as unlike antibodies, improving TCR affinity does not usually improve specificity. Although various protein design approaches have been explored to surmount this, mutations in TCR binding interfaces risk broadening specificity or introducing new reactivities. Here we explored if TCR specificity could alternatively be tuned through framework mutations distant from the interface. Studying the 868 TCR specific for the HIV SL9 epitope presented by HLA-A2, we used deep mutational scanning to identify a framework mutation above the mobile CDR3β loop. This glycine to proline mutation had no discernable impact on binding affinity or functional avidity towards the SL9 epitope but weakened recognition of SL9 escape variants and led to fewer responses in a SL9-derived positional scanning library. In contrast, an interfacial mutation near the tip of CDR3α that also did not impact affinity or functional avidity towards SL9 weakened specificity. Simulations indicated that the specificity-enhancing mutation functions by reducing the range of loop motions, limiting the ability of the TCR to adjust to different ligands. Although our results are likely to be TCR dependent, using framework engineering to control TCR loop motions may be a viable strategy for improving the specificity of TCR-based immunotherapies.
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Affiliation(s)
- Aaron M. Rosenberg
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
| | - Cory M. Ayres
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
| | | | - Timothy A. Whitehead
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, United States
| | - Brian M. Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
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6
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Holehouse AS, Kragelund BB. The molecular basis for cellular function of intrinsically disordered protein regions. Nat Rev Mol Cell Biol 2024; 25:187-211. [PMID: 37957331 PMCID: PMC11459374 DOI: 10.1038/s41580-023-00673-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2023] [Indexed: 11/15/2023]
Abstract
Intrinsically disordered protein regions exist in a collection of dynamic interconverting conformations that lack a stable 3D structure. These regions are structurally heterogeneous, ubiquitous and found across all kingdoms of life. Despite the absence of a defined 3D structure, disordered regions are essential for cellular processes ranging from transcriptional control and cell signalling to subcellular organization. Through their conformational malleability and adaptability, disordered regions extend the repertoire of macromolecular interactions and are readily tunable by their structural and chemical context, making them ideal responders to regulatory cues. Recent work has led to major advances in understanding the link between protein sequence and conformational behaviour in disordered regions, yet the link between sequence and molecular function is less well defined. Here we consider the biochemical and biophysical foundations that underlie how and why disordered regions can engage in productive cellular functions, provide examples of emerging concepts and discuss how protein disorder contributes to intracellular information processing and regulation of cellular function.
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Affiliation(s)
- Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA.
- Center for Biomolecular Condensates, Washington University in St Louis, St Louis, MO, USA.
| | - Birthe B Kragelund
- REPIN, Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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7
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Srivastava PK. Cancer neoepitopes viewed through negative selection and peripheral tolerance: a new path to cancer vaccines. J Clin Invest 2024; 134:e176740. [PMID: 38426497 PMCID: PMC10904052 DOI: 10.1172/jci176740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Abstract
A proportion of somatic mutations in tumors create neoepitopes that can prime T cell responses that target the MHC I-neoepitope complexes on tumor cells, mediating tumor control or rejection. Despite the compelling centrality of neoepitopes to cancer immunity, we know remarkably little about what constitutes a neoepitope that can mediate tumor control in vivo and what distinguishes such a neoepitope from the vast majority of similar candidate neoepitopes that are inefficacious in vivo. Studies in mice as well as clinical trials have begun to reveal the unexpected paradoxes in this area. Because cancer neoepitopes straddle that ambiguous ground between self and non-self, some rules that are fundamental to immunology of frankly non-self antigens, such as viral or model antigens, do not appear to apply to neoepitopes. Because neoepitopes are so similar to self-epitopes, with only small changes that render them non-self, immune response to them is regulated at least partially the way immune response to self is regulated. Therefore, neoepitopes are viewed and understood here through the clarifying lens of negative thymic selection. Here, the emergent questions in the biology and clinical applications of neoepitopes are discussed critically and a mechanistic and testable framework that explains the complexity and translational potential of these wonderful antigens is proposed.
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8
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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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9
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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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10
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Liu L, Yoon CW, Yuan Z, Guo T, Qu Y, He P, Yu X, Zhu Z, Limsakul P, Wang Y. Cellular and molecular imaging of CAR-T cell-based immunotherapy. Adv Drug Deliv Rev 2023; 203:115135. [PMID: 37931847 PMCID: PMC11052581 DOI: 10.1016/j.addr.2023.115135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/18/2023] [Accepted: 11/03/2023] [Indexed: 11/08/2023]
Abstract
Chimeric Antigen Receptor T cell (CAR-T) therapy has emerged as a transformative therapeutic strategy for hematological malignancies. However, its efficacy in treating solid tumors remains limited. An in-depth and comprehensive understanding of CAR-T cell signaling pathways and the ability to track CAR-T cell biodistribution and activation in real-time within the tumor microenvironment will be instrumental in designing the next generation of CAR-T cells for solid tumor therapy. This review summarizes the signaling network and the cellular and molecular imaging tools and platforms that are utilized in CAR-T cell-based immune therapies, covering both in vitro and in vivo studies. Firstly, we provide an overview of the existing understanding of the activation and cytotoxic mechanisms of CAR-T cells, compared to the mechanism of T cell receptor (TCR) signaling pathways. We further describe the commonly employed tools for live cell imaging, coupled with recent research progress, with a focus on genetically encoded fluorescent proteins (FPs) and biosensors. We then discuss the utility of diverse in vivo imaging modalities, including fluorescence and bioluminescence imaging, Magnetic Resonance Imaging (MRI), Positron Emission Tomography (PET), and photoacoustic (PA) imaging, for noninvasive monitoring of CAR-T cell dynamics within tumor tissues, thereby providing critical insights into therapy's strengths and weaknesses. Lastly, we discuss the current challenges and future directions of CAR-T cell therapy from the imaging perspective. We foresee that a comprehensive and integrative approach to CAR-T cell imaging will enable the development of more effective treatments for solid tumors in the future.
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Affiliation(s)
- Longwei Liu
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA.
| | - Chi Woo Yoon
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA
| | - Zhou Yuan
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA
| | - Tianze Guo
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA
| | - Yunjia Qu
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Peixiang He
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Xi Yu
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA
| | - Ziyue Zhu
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA
| | - Praopim Limsakul
- Division of Physical Science, Faculty of Science and Center of Excellence for Trace Analysis and Biosensor, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Yingxiao Wang
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA; Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA.
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11
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Levi R, Levi L, Louzoun Y. Bw4 ligand and direct T-cell receptor binding induced selection on HLA A and B alleles. Front Immunol 2023; 14:1236080. [PMID: 38077375 PMCID: PMC10703150 DOI: 10.3389/fimmu.2023.1236080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/26/2023] [Indexed: 12/18/2023] Open
Abstract
Introduction The HLA region is the hallmark of balancing selection, argued to be driven by the pressure to present a wide variety of viral epitopes. As such selection on the peptide-binding positions has been proposed to drive HLA population genetics. MHC molecules also directly binds to the T-Cell Receptor and killer cell immunoglobulin-like receptors (KIR). Methods We here combine the HLA allele frequencies in over six-million Hematopoietic Stem Cells (HSC) donors with a novel machine-learning-based method to predict allele frequency. Results We show for the first time that allele frequency can be predicted from their sequences. This prediction yields a natural measure for selection. The strongest selection is affecting KIR binding regions, followed by the peptide-binding cleft. The selection from the direct interaction with the KIR and TCR is centered on positively charged residues (mainly Arginine), and some positions in the peptide-binding cleft are not associated with the allele frequency, especially Tyrosine residues. Discussion These results suggest that the balancing selection for peptide presentation is combined with a positive selection for KIR and TCR binding.
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Affiliation(s)
| | | | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan, Israel
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12
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Choy C, Chen J, Li J, Gallagher DT, Lu J, Wu D, Zou A, Hemani H, Baptiste BA, Wichmann E, Yang Q, Ciffelo J, Yin R, McKelvy J, Melvin D, Wallace T, Dunn C, Nguyen C, Chia CW, Fan J, Ruffolo J, Zukley L, Shi G, Amano T, An Y, Meirelles O, Wu WW, Chou CK, Shen RF, Willis RA, Ko MSH, Liu YT, De S, Pierce BG, Ferrucci L, Egan J, Mariuzza R, Weng NP. SARS-CoV-2 infection establishes a stable and age-independent CD8 + T cell response against a dominant nucleocapsid epitope using restricted T cell receptors. Nat Commun 2023; 14:6725. [PMID: 37872153 PMCID: PMC10593757 DOI: 10.1038/s41467-023-42430-z] [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: 04/04/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023] Open
Abstract
The resolution of SARS-CoV-2 replication hinges on cell-mediated immunity, wherein CD8+ T cells play a vital role. Nonetheless, the characterization of the specificity and TCR composition of CD8+ T cells targeting non-spike protein of SARS-CoV-2 before and after infection remains incomplete. Here, we analyzed CD8+ T cells recognizing six epitopes from the SARS-CoV-2 nucleocapsid (N) protein and found that SARS-CoV-2 infection slightly increased the frequencies of N-recognizing CD8+ T cells but significantly enhanced activation-induced proliferation compared to that of the uninfected donors. The frequencies of N-specific CD8+ T cells and their proliferative response to stimulation did not decrease over one year. We identified the N222-230 peptide (LLLDRLNQL, referred to as LLL thereafter) as a dominant epitope that elicited the greatest proliferative response from both convalescent and uninfected donors. Single-cell sequencing of T cell receptors (TCR) from LLL-specific CD8+ T cells revealed highly restricted Vα gene usage (TRAV12-2) with limited CDR3α motifs, supported by structural characterization of the TCR-LLL-HLA-A2 complex. Lastly, transcriptome analysis of LLL-specific CD8+ T cells from donors who had expansion (expanders) or no expansion (non-expanders) after in vitro stimulation identified increased chromatin modification and innate immune functions of CD8+ T cells in non-expanders. These results suggests that SARS-CoV-2 infection induces LLL-specific CD8+ T cell responses with a restricted TCR repertoire.
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Affiliation(s)
- Cecily Choy
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Joseph Chen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Jiangyuan Li
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - D Travis Gallagher
- National Institute of Standards and Technology (NIST), Gaithersburg, MD, USA
| | - Jian Lu
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Daichao Wu
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | - Ainslee Zou
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Humza Hemani
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Beverly A Baptiste
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Emily Wichmann
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Qian Yang
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Jeffrey Ciffelo
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Rui Yin
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | - Julia McKelvy
- Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Denise Melvin
- Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Tonya Wallace
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Christopher Dunn
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Cuong Nguyen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Chee W Chia
- Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Jinshui Fan
- Computational Biology and Genomics Core, Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Jeannie Ruffolo
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Linda Zukley
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | | | | | - Yang An
- Laboratory of Behavioral Neuroscience, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Osorio Meirelles
- Laboratory of Epidemiology & Population Sciences, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Wells W Wu
- Facility for Biotechnology Resources, CBER, Food and Drug Administration, Silver Spring, MD, USA
| | - Chao-Kai Chou
- Facility for Biotechnology Resources, CBER, Food and Drug Administration, Silver Spring, MD, USA
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, CBER, Food and Drug Administration, Silver Spring, MD, USA
| | - Richard A Willis
- NIH Tetramer Core Facility at Emory University, Atlanta, GA, USA
| | | | | | - Supriyo De
- Computational Biology and Genomics Core, Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Brian G Pierce
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Josephine Egan
- Laboratory of Clinical Investigation, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Roy Mariuzza
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | - Nan-Ping Weng
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD, USA.
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13
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Linsley P, Nakayama M, Balmas E, Chen J, Pour F, Bansal S, Serti E, Speake C, Pugliese A, Cerosaletti K. Self-reactive germline-like TCR alpha chains shared between blood and pancreas. RESEARCH SQUARE 2023:rs.3.rs-3446917. [PMID: 37886513 PMCID: PMC10602137 DOI: 10.21203/rs.3.rs-3446917/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Human islet antigen reactive CD4 + memory T cells (IAR T cells) from peripheral blood have been studied extensively for their role in the pathogenesis of autoimmune type 1 diabetes (T1D). However, IAR T cells are rare, and it remains poorly understood how they affect T1D progression in the pancreas. Using single cell RNA-sequencing coupled with a multiplexed activation induced marker (AIM) enrichment assay, we identified paired TCR alpha/beta (TRA/TRB) T cell receptors (TCRs) in IAR T cells from the blood of healthy, at-risk, new onset, and established T1D donors. Using TCR sequences as barcodes, we measured infiltration of IAR T cells from blood into pancreas of organ donors with and without T1D. We detected extensive TCR sharing between IAR T cells from peripheral blood and pancreatic infiltrating T cells (PIT), with perfectly matched or single mismatched TRA junctions and J gene regions, comprising ~ 34% of unique IAR TCRs. PIT-matching IAR T cells had public TRA chains that showed increased use of germline-encoded residues in epitope engagement and a propensity for cross-reactivity. The link with T cells in the pancreas implicates autoreactive IAR T cells with shared TRA junctions and increased levels in blood with the prediabetic and new onset phases of T1D progression.
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14
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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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15
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Huang S, Shahine A, Cheng TY, Chen YL, Ng SW, Balaji GR, Farquhar R, Gras S, Hardman CS, Altman JD, Tahiri N, Minnaard AJ, Ogg GS, Mayfield JA, Rossjohn J, Moody DB. CD1 lipidomes reveal lipid-binding motifs and size-based antigen-display mechanisms. Cell 2023; 186:4583-4596.e13. [PMID: 37725977 PMCID: PMC10591967 DOI: 10.1016/j.cell.2023.08.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 05/05/2023] [Accepted: 08/21/2023] [Indexed: 09/21/2023]
Abstract
The CD1 system binds lipid antigens for display to T cells. Here, we solved lipidomes for the four human CD1 antigen-presenting molecules, providing a map of self-lipid display. Answering a basic question, the detection of >2,000 CD1-lipid complexes demonstrates broad presentation of self-sphingolipids and phospholipids. Whereas peptide antigens are chemically processed, many lipids are presented in an unaltered form. However, each type of CD1 protein differentially edits the self-lipidome to show distinct capture motifs based on lipid length and chemical composition, suggesting general antigen display mechanisms. For CD1a and CD1d, lipid size matches the CD1 cleft volume. CD1c cleft size is more variable, and CD1b is the outlier, where ligands and clefts show an extreme size mismatch that is explained by uniformly seating two small lipids in one cleft. Furthermore, the list of compounds that comprise the integrated CD1 lipidome supports the ongoing discovery of lipid blockers and antigens for T cells.
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Affiliation(s)
- Shouxiong Huang
- Division of Rheumatology, Immunity and Inflammation, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Adam Shahine
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Tan-Yun Cheng
- Division of Rheumatology, Immunity and Inflammation, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yi-Ling Chen
- Human Immunology Unit, Weatherall Institute for Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Soo Weei Ng
- Human Immunology Unit, Weatherall Institute for Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK
| | - Gautham R. Balaji
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Rachel Farquhar
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Stephanie Gras
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Clare S. Hardman
- Human Immunology Unit, Weatherall Institute for Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK
| | - John D. Altman
- Emory Vaccine Center, Emory School of Medicine, Atlanta, GA 30322, USA
| | - Nabil Tahiri
- Department of Chemical Biology, Stratingh Institute for Chemistry, Groningen, Netherlands
| | - Adriaan J. Minnaard
- Department of Chemical Biology, Stratingh Institute for Chemistry, Groningen, Netherlands
| | - Graham S. Ogg
- Human Immunology Unit, Weatherall Institute for Molecular Medicine, University of Oxford, Headington, Oxford OX3 9DS, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Jacob A. Mayfield
- Division of Rheumatology, Immunity and Inflammation, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
- Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - D. Branch Moody
- Division of Rheumatology, Immunity and Inflammation, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Lead contact
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16
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Fast E, Dhar M, Chen B. TAPIR: a T-cell receptor language model for predicting rare and novel targets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557285. [PMID: 37745475 PMCID: PMC10515850 DOI: 10.1101/2023.09.12.557285] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
T-cell receptors (TCRs) are involved in most human diseases, but linking their sequences with their targets remains an unsolved grand challenge in the field. In this study, we present TAPIR (T-cell receptor and Peptide Interaction Recognizer), a T-cell receptor (TCR) language model that predicts TCR-target interactions, with a focus on novel and rare targets. TAPIR employs deep convolutional neural network (CNN) encoders to process TCR and target sequences across flexible representations (e.g., beta-chain only, unknown MHC allele, etc.) and learns patterns of interactivity via several training tasks. This flexibility allows TAPIR to train on more than 50k either paired (alpha and beta chain) or unpaired TCRs (just alpha or beta chain) from public and proprietary databases against 1933 unique targets. TAPIR demonstrates state-of-the-art performance when predicting TCR interactivity against common benchmark targets and is the first method to demonstrate strong performance when predicting TCR interactivity against novel targets, where no examples are provided in training. TAPIR is also capable of predicting TCR interaction against MHC alleles in the absence of target information. Leveraging these capabilities, we apply TAPIR to cancer patient TCR repertoires and identify and validate a novel and potent anti-cancer T-cell receptor against a shared cancer neoantigen target (PIK3CA H1047L). We further show how TAPIR, when extended with a generative neural network, is capable of directly designing T-cell receptor sequences that interact with a target of interest.
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Affiliation(s)
- Ethan Fast
- Vcreate, Inc., Menlo Park, CA, 94025, USA
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17
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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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18
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Buonaguro L, Tagliamonte M. Peptide-based vaccine for cancer therapies. Front Immunol 2023; 14:1210044. [PMID: 37654484 PMCID: PMC10467431 DOI: 10.3389/fimmu.2023.1210044] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/31/2023] [Indexed: 09/02/2023] Open
Abstract
Different strategies based on peptides are available for cancer treatment, in particular to counter-act the progression of tumor growth and disease relapse. In the last decade, in the context of therapeutic strategies against cancer, peptide-based vaccines have been evaluated in different tumor models. The peptides selected for cancer vaccine development can be classified in two main type: tumor-associated antigens (TAAs) and tumor-specific antigens (TSAs), which are captured, internalized, processed and presented by antigen-presenting cells (APCs) to cell-mediated immunity. Peptides loaded onto MHC class I are recognized by a specific TCR of CD8+ T cells, which are activated to exert their cytotoxic activity against tumor cells presenting the same peptide-MHC-I complex. This process is defined as active immunotherapy as the host's immune system is either de novo activated or restimulated to mount an effective, tumor-specific immune reaction that may ultimately lead to tu-mor regression. However, while the preclinical data have frequently shown encouraging results, therapeutic cancer vaccines clinical trials, including those based on peptides have not provided satisfactory data to date. The limited efficacy of peptide-based cancer vaccines is the consequence of several factors, including the identification of specific target tumor antigens, the limited immunogenicity of peptides and the highly immunosuppressive tumor microenvironment (TME). An effective cancer vaccine can be developed only by addressing all such different aspects. The present review describes the state of the art for each of such factors.
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Affiliation(s)
| | - Maria Tagliamonte
- Innovative Immunological Models Unit, Istituto Nazionale Tumori - IRCCS - “Fond G. Pascale”, Naples, Italy
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19
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Amaya-Ramirez D, Martinez-Enriquez LC, Parra-López C. Usefulness of Docking and Molecular Dynamics in Selecting Tumor Neoantigens to Design Personalized Cancer Vaccines: A Proof of Concept. Vaccines (Basel) 2023; 11:1174. [PMID: 37514989 PMCID: PMC10386133 DOI: 10.3390/vaccines11071174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 07/30/2023] Open
Abstract
Personalized cancer vaccines based on neoantigens are a new and promising treatment for cancer; however, there are still multiple unresolved challenges to using this type of immunotherapy. Among these, the effective identification of immunogenic neoantigens stands out, since the in silico tools used generate a significant portion of false positives. Inclusion of molecular simulation techniques can refine the results these tools produce. In this work, we explored docking and molecular dynamics to study the association between the stability of peptide-HLA complexes and their immunogenicity, using as a proof of concept two HLA-A2-restricted neoantigens that were already evaluated in vitro. The results obtained were in accordance with the in vitro immunogenicity, since the immunogenic neoantigen ASTN1 remained bound at both ends to the HLA-A2 molecule. Additionally, molecular dynamic simulation suggests that position 1 of the peptide has a more relevant role in stabilizing the N-terminus than previously proposed. Likewise, the mutations may have a "delocalized" effect on the peptide-HLA interaction, which means that the mutated amino acid influences the intensity of the interactions of distant amino acids of the peptide with the HLA. These findings allow us to propose the inclusion of molecular simulation techniques to improve the identification of neoantigens for cancer vaccines.
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Affiliation(s)
| | - Laura Camila Martinez-Enriquez
- Grupo de Inmunología y Medicina Traslacional, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Carlos Parra-López
- Grupo de Inmunología y Medicina Traslacional, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá 111321, Colombia
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20
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Saotome K, Dudgeon D, Colotti K, Moore MJ, Jones J, Zhou Y, Rafique A, Yancopoulos GD, Murphy AJ, Lin JC, Olson WC, Franklin MC. Structural analysis of cancer-relevant TCR-CD3 and peptide-MHC complexes by cryoEM. Nat Commun 2023; 14:2401. [PMID: 37100770 PMCID: PMC10132440 DOI: 10.1038/s41467-023-37532-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 03/21/2023] [Indexed: 04/28/2023] Open
Abstract
The recognition of antigenic peptide-MHC (pMHC) molecules by T-cell receptors (TCR) initiates the T-cell mediated immune response. Structural characterization is key for understanding the specificity of TCR-pMHC interactions and informing the development of therapeutics. Despite the rapid rise of single particle cryoelectron microscopy (cryoEM), x-ray crystallography has remained the preferred method for structure determination of TCR-pMHC complexes. Here, we report cryoEM structures of two distinct full-length α/β TCR-CD3 complexes bound to their pMHC ligand, the cancer-testis antigen HLA-A2/MAGEA4 (230-239). We also determined cryoEM structures of pMHCs containing MAGEA4 (230-239) peptide and the closely related MAGEA8 (232-241) peptide in the absence of TCR, which provided a structural explanation for the MAGEA4 preference displayed by the TCRs. These findings provide insights into the TCR recognition of a clinically relevant cancer antigen and demonstrate the utility of cryoEM for high-resolution structural analysis of TCR-pMHC interactions.
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Affiliation(s)
- Kei Saotome
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA.
| | - Drew Dudgeon
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | | | | | - Jennifer Jones
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | - Yi Zhou
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
| | | | | | | | - John C Lin
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, 10591, USA
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21
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Fitzpatrick KS, Degefu HN, Poljakov K, Bibby MG, Remington AJ, Searles TG, Gray MD, Boonyaratanakornkit J, Rosato PC, Taylor JJ. Validation of Ligand Tetramers for the Detection of Antigen-Specific Lymphocytes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:1156-1165. [PMID: 36883850 PMCID: PMC10073333 DOI: 10.4049/jimmunol.2200934] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/07/2023] [Indexed: 03/09/2023]
Abstract
The study of Ag-specific lymphocytes has been a key advancement in immunology over the past few decades. The development of multimerized probes containing Ags, peptide:MHC complexes, or other ligands was one innovation allowing the direct study of Ag-specific lymphocytes by flow cytometry. Although these types of study are now common and performed by thousands of laboratories, quality control and assessment of probe quality are often minimal. In fact, many of these types of probe are made in-house, and protocols vary between laboratories. Although peptide:MHC multimers can often be obtained from commercial sources or core facilities, few such services exist for Ag multimers. To ensure high quality and consistency with ligand probes, we have developed an easy and robust multiplexed approach using commercially available beads able to bind Abs specific for the ligand of interest. Using this assay, we have sensitively assessed the performance of peptide:MHC and Ag tetramers and have found considerable batch-to-batch variability in performance and stability over time more easily than using murine or human cell-based assays. This bead-based assay can also reveal common production errors such as miscalculation of Ag concentration. This work could set the stage for the development of standardized assays for all commonly used ligand probes to limit laboratory-to-laboratory technical variation and experimental failure caused by probe underperformance.
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Affiliation(s)
- Kristin S Fitzpatrick
- Immunology and Vaccine Development Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
- Molecular Medicine and Mechanisms of Disease PhD Program, University of Washington, Seattle, WA
| | - Hanna N Degefu
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Lebanon, NH
| | - Katrina Poljakov
- Immunology and Vaccine Development Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Madeleine G Bibby
- Immunology and Vaccine Development Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Allison J Remington
- Immunology and Vaccine Development Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
- Division of Dermatology, Department of Medicine, University of Washington, Seattle, WA
| | - Tyler G Searles
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Lebanon, NH
| | - Matthew D Gray
- Immunology and Vaccine Development Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Jim Boonyaratanakornkit
- Immunology and Vaccine Development Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Pamela C Rosato
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Lebanon, NH
| | - Justin J Taylor
- Immunology and Vaccine Development Program, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA
- Department of Immunology, University of Washington, Seattle, WA
- Department of Global Health, University of Washington, Seattle, WA
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22
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Tippalagama R, Chihab LY, Kearns K, Lewis S, Panda S, Willemsen L, Burel JG, Lindestam Arlehamn CS. Antigen-specificity measurements are the key to understanding T cell responses. Front Immunol 2023; 14:1127470. [PMID: 37122719 PMCID: PMC10140422 DOI: 10.3389/fimmu.2023.1127470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/30/2023] [Indexed: 05/02/2023] Open
Abstract
Antigen-specific T cells play a central role in the adaptive immune response and come in a wide range of phenotypes. T cell receptors (TCRs) mediate the antigen-specificities found in T cells. Importantly, high-throughput TCR sequencing provides a fingerprint which allows tracking of specific T cells and their clonal expansion in response to particular antigens. As a result, many studies have leveraged TCR sequencing in an attempt to elucidate the role of antigen-specific T cells in various contexts. Here, we discuss the published approaches to studying antigen-specific T cells and their specific TCR repertoire. Further, we discuss how these methods have been applied to study the TCR repertoire in various diseases in order to characterize the antigen-specific T cells involved in the immune control of disease.
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23
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Peng X, Lei Y, Feng P, Jia L, Ma J, Zhao D, Zeng J. Characterizing the interaction conformation between T-cell receptors and epitopes with deep learning. NAT MACH INTELL 2023. [DOI: 10.1038/s42256-023-00634-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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24
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Thomas C, Tampé R. Structure and mechanism of immunoreceptors: New horizons in T cell and B cell receptor biology and beyond. Curr Opin Struct Biol 2023; 80:102570. [PMID: 36940642 DOI: 10.1016/j.sbi.2023.102570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 01/15/2023] [Accepted: 02/07/2023] [Indexed: 03/23/2023]
Abstract
Immunoreceptors, also named non-catalytic tyrosine-phosphorylated receptors, are a large class of leukocyte cell-surface proteins critically involved in innate and adaptive immune responses. Their most characteristic defining feature is a shared signal transduction machinery where binding events of cell surface-anchored ligands to the small extracellular receptor domains are translated into phosphorylation of conserved tyrosine-containing cytosolic sequence motifs initiating downstream signal transduction cascades. Despite their central importance to immunology, the molecular mechanism of how ligand binding activates the receptors and results in robust intracellular signaling has remained enigmatic. Recent breakthroughs in our understanding of the architecture and triggering mechanism of immunoreceptors come from cryogenic electron microscopy studies of the B cell and T cell antigen receptors.
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Affiliation(s)
- Christoph Thomas
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt/Main, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue Str. 9, 60438 Frankfurt/Main, Germany.
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25
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Non-random Codon Usage of Synonymous and Non-synonymous Mutations in the Human HLA-A Gene. J Mol Evol 2023; 91:169-191. [PMID: 36809491 DOI: 10.1007/s00239-023-10093-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 01/13/2023] [Indexed: 02/23/2023]
Abstract
The structure and function of human leucocyte antigen (HLA-A) is well known and is an extremely variable protein. From the public HLA-A database, we chose 26 high frequency HLA-A alleles (45% of sequenced alleles). Using five arbitrary references from these alleles, we analyzed synonymous mutations at the third codon position (sSNP3) and non-synonymous mutations (NSM). Both mutation types showed non-random locations of 29 sSNP3 codons and 71 NSM codons in the five reference lists. Most sSNP3 codons show identical mutation types with many mutations resulting from cytosine deamination. We proposed 23 ancestral parents of sSNP3 in five reference sequences using conserved parents in five unidirectional codons and 18 majority parents in reciprocal codons. These 23 proposed ancestral parents show exclusive codon usage of G3 or C3 parents located on both DNA strands that mutate to A3 or T3 variants mostly (76%) by cytosine deamination The sSNP3 and NSM show clear separation of the two variant types with most sSNP3 located in conserved areas in exons 2, 3 and 4, compared to most NSM appearing in two Variable Areas with no sSNP3 in the latter parts of exons 2 (α1) and 3 (α2). The Variable Areas contain NSM (polymorphic) residues at the center of the groove that bind the foreign peptide. We find distinctly different mutation patterns in NSM codons from those of sSNP3. Namely, G-C to A-T mutation frequency was much smaller, suggesting that evolutional pressures of deamination and other mechanisms applied to the two areas are significantly different.
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26
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Morita D, Asa M, Sugita M. Engagement with the TCR induces plasticity in antigenic ligands bound to MHC class I and CD1 molecules. Int Immunol 2023; 35:7-17. [PMID: 36053252 DOI: 10.1093/intimm/dxac046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 08/31/2022] [Indexed: 01/25/2023] Open
Abstract
Complementarity-determining regions (CDRs) of αβ T-cell receptors (TCRs) sense peptide-bound MHC (pMHC) complexes via chemical interactions, thereby mediating antigen specificity and MHC restriction. Flexible finger-like movement of CDR loops contributes to the establishment of optimal interactions with pMHCs. In contrast, peptide ligands captured in MHC molecules are considered more static because of the rigid hydrogen-bond network that stabilizes peptide ligands in the antigen-binding groove of MHC molecules. An array of crystal structures delineating pMHC complexes in TCR-docked and TCR-undocked forms is now available, which enables us to assess TCR engagement-induced conformational changes in peptide ligands. In this short review, we overview conformational changes in MHC class I-bound peptide ligands upon TCR docking, followed by those for CD1-bound glycolipid ligands. Finally, we analyze the co-crystal structure of the TCR:lipopeptide-bound MHC class I complex that we recently reported. We argue that TCR engagement-induced conformational changes markedly occur in lipopeptide ligands, which are essential for exposure of a primary T-cell epitope to TCRs. These conformational changes are affected by amino acid residues, such as glycine, that do not interact directly with TCRs. Thus, ligand recognition by specific TCRs involves not only T-cell epitopes but also non-epitopic amino acid residues. In light of their critical function, we propose to refer to these residues as non-epitopic residues affecting ligand plasticity and antigenicity (NR-PA).
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Affiliation(s)
- Daisuke Morita
- Laboratory of Cell Regulation, Institute for Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.,Laboratory of Cell Regulation and Molecular Network, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Minori Asa
- Laboratory of Cell Regulation, Institute for Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.,Laboratory of Cell Regulation and Molecular Network, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masahiko Sugita
- Laboratory of Cell Regulation, Institute for Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.,Laboratory of Cell Regulation and Molecular Network, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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27
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Mehta NM, Li Y, Patel V, Li W, Morningstar-Kywi N, Pospiech M, Alachkar H, Haworth IS. Prediction of Peptide and TCR CDR3 Loops in Formation of Class I MHC-Peptide-TCR Complexes Using Molecular Models with Solvation. Methods Mol Biol 2023; 2673:273-287. [PMID: 37258921 PMCID: PMC11059237 DOI: 10.1007/978-1-0716-3239-0_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Formation of major histocompatibility (MHC)-peptide-T cell receptor (TCR) complexes is central to initiation of an adaptive immune response. These complexes form through initial stabilization of the MHC fold via binding of a short peptide, and subsequent interaction of the TCR to form a ternary complex, with contacts made predominantly through the complementarity-determining region (CDR) loops of the TCR. Stimulation of an immune response is central to cancer immunotherapy. This approach depends on identification of the appropriate combinations of MHC molecules, peptides, and TCRs to elicit an antitumor immune response. This prediction is a current challenge in computational biochemistry. In this chapter, we introduce a predictive method that involves generation of multiple peptides and TCR CDR 3 loop conformations, solvation of these conformers in the context of the MHC-peptide-TCR ternary complex, extraction of parameters from the generated complexes, and use of an AI model to evaluate the potential for the assembled ternary complex to support an immune response.
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Affiliation(s)
- Nairuti Milan Mehta
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Yuhui Li
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Vini Patel
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Wanning Li
- Titus Family Department of Clinical Pharmacy, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Noam Morningstar-Kywi
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Mateusz Pospiech
- Titus Family Department of Clinical Pharmacy, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Houda Alachkar
- Titus Family Department of Clinical Pharmacy, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Ian S Haworth
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA.
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28
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Yang X, Garner LI, Zvyagin IV, Paley MA, Komech EA, Jude KM, Zhao X, Fernandes RA, Hassman LM, Paley GL, Savvides CS, Brackenridge S, Quastel MN, Chudakov DM, Bowness P, Yokoyama WM, McMichael AJ, Gillespie GM, Garcia KC. Autoimmunity-associated T cell receptors recognize HLA-B*27-bound peptides. Nature 2022; 612:771-777. [PMID: 36477533 PMCID: PMC10511244 DOI: 10.1038/s41586-022-05501-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 11/01/2022] [Indexed: 12/12/2022]
Abstract
Human leucocyte antigen B*27 (HLA-B*27) is strongly associated with inflammatory diseases of the spine and pelvis (for example, ankylosing spondylitis (AS)) and the eye (that is, acute anterior uveitis (AAU))1. How HLA-B*27 facilitates disease remains unknown, but one possible mechanism could involve presentation of pathogenic peptides to CD8+ T cells. Here we isolated orphan T cell receptors (TCRs) expressing a disease-associated public β-chain variable region-complementary-determining region 3β (BV9-CDR3β) motif2-4 from blood and synovial fluid T cells from individuals with AS and from the eye in individuals with AAU. These TCRs showed consistent α-chain variable region (AV21) chain pairing and were clonally expanded in the joint and eye. We used HLA-B*27:05 yeast display peptide libraries to identify shared self-peptides and microbial peptides that activated the AS- and AAU-derived TCRs. Structural analysis revealed that TCR cross-reactivity for peptide-MHC was rooted in a shared binding motif present in both self-antigens and microbial antigens that engages the BV9-CDR3β TCRs. These findings support the hypothesis that microbial antigens and self-antigens could play a pathogenic role in HLA-B*27-associated disease.
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Affiliation(s)
- Xinbo Yang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lee I Garner
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ivan V Zvyagin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Michael A Paley
- Rheumatology Division, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Ekaterina A Komech
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Kevin M Jude
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Xiang Zhao
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ricardo A Fernandes
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lynn M Hassman
- Department of Ophthalmology, Washington University School of Medicine, St Louis, MO, USA
| | - Grace L Paley
- Department of Ophthalmology, Washington University School of Medicine, St Louis, MO, USA
| | - Christina S Savvides
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Simon Brackenridge
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Max N Quastel
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Dmitriy M Chudakov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Paul Bowness
- Nuffield Department of Orthopaedics Rheumatology and Muscuoskeletal Science (NDORMS), Botnar Research Center, University of Oxford, Oxford, UK
| | - Wayne M Yokoyama
- Rheumatology Division, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
- Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA.
| | - Andrew J McMichael
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Geraldine M Gillespie
- NDM Research Building, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Centre for Immuno-oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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29
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Immunoinformatics Approach for Epitope-Based Vaccine Design: Key Steps for Breast Cancer Vaccine. Diagnostics (Basel) 2022; 12:diagnostics12122981. [PMID: 36552988 PMCID: PMC9777080 DOI: 10.3390/diagnostics12122981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Vaccines are an upcoming medical intervention for breast cancer. By targeting the tumor antigen, cancer vaccines can be designed to train the immune system to recognize tumor cells. Therefore, along with technological advances, the vaccine design process is now starting to be carried out with more rational methods such as designing epitope-based peptide vaccines using immunoinformatics methods. Immunoinformatics methods can assist vaccine design in terms of antigenicity and safety. Common protocols used to design epitope-based peptide vaccines include tumor antigen identification, protein structure analysis, T cell epitope prediction, epitope characterization, and evaluation of protein-epitope interactions. Tumor antigen can be divided into two types: tumor associated antigen and tumor specific antigen. We will discuss the identification of tumor antigens using high-throughput technologies. Protein structure analysis comprises the physiochemical, hydrochemical, and antigenicity of the protein. T cell epitope prediction models are widely available with various prediction parameters as well as filtering tools for the prediction results. Epitope characterization such as allergenicity and toxicity can be done in silico as well using allergenicity and toxicity predictors. Evaluation of protein-epitope interactions can also be carried out in silico with molecular simulation. We will also discuss current and future developments of breast cancer vaccines using an immunoinformatics approach. Finally, although prediction models have high accuracy, the opposite can happen after being tested in vitro and in vivo. Therefore, further studies are needed to ensure the effectiveness of the vaccine to be developed. Although epitope-based peptide vaccines have the disadvantage of low immunogenicity, the addition of adjuvants can be a solution.
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30
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Huisman W, de Gier M, Hageman L, Shomuradova AS, Leboux DA, Amsen D, Falkenburg JF, Jedema I. Amino acids at position 5 in the peptide/MHC binding region of a public virus-specific TCR are completely inter-changeable without loss of function. Eur J Immunol 2022; 52:1819-1828. [PMID: 36189878 PMCID: PMC9828479 DOI: 10.1002/eji.202249975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/25/2022] [Accepted: 09/28/2022] [Indexed: 01/12/2023]
Abstract
Anti-viral T-cell responses are usually directed against a limited set of antigens, but often contain many T cells expressing different T-cell receptors (TCRs). Identical TCRs found within virus-specific T-cell populations in different individuals are known as public TCRs, but also TCRs highly-similar to these public TCRs, with only minor variations in amino acids on specific positions in the Complementary Determining Regions (CDRs), are frequently found. However, the degree of freedom at these positions was not clear. In this study, we used the HLA-A*02:01-restricted EBV-LMP2FLY -specific public TCR as model and modified the highly-variable position 5 of the CDR3β sequence with all 20 amino acids. Our results demonstrate that amino acids at this particular position in the CDR3β region of this TCR are completely inter-changeable, without loss of TCR function. We show that the inability to find certain variants in individuals is explained by their lower recombination probability rather than by steric hindrance.
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Affiliation(s)
- Wesley Huisman
- Department of HematologyLeiden University Medical CenterThe Netherlands,Department of HematopoiesisSanquin Research and Landsteiner Laboratory for Blood Cell ResearchAmsterdamThe Netherlands
| | - Melanie de Gier
- Department of HematologyLeiden University Medical CenterThe Netherlands
| | - Lois Hageman
- Department of HematologyLeiden University Medical CenterThe Netherlands
| | - Alina S. Shomuradova
- Laboratory for Transplantation ImmunologyNational Research Center for HematologyMoscowRussia
| | | | - Derk Amsen
- Department of HematopoiesisSanquin Research and Landsteiner Laboratory for Blood Cell ResearchAmsterdamThe Netherlands
| | | | - Inge Jedema
- Department of HematologyLeiden University Medical CenterThe Netherlands
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31
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Abstract
Single-pass transmembrane receptors (SPTMRs) represent a diverse group of integral membrane proteins that are involved in many essential cellular processes, including signal transduction, cell adhesion, and transmembrane transport of materials. Dysregulation of the SPTMRs is linked with many human diseases. Despite extensive efforts in past decades, the mechanisms of action of the SPTMRs remain incompletely understood. One major hurdle is the lack of structures of the full-length SPTMRs in different functional states. Such structural information is difficult to obtain by traditional structural biology methods such as X-ray crystallography and nuclear magnetic resonance (NMR). The recent rapid development of single-particle cryo-electron microscopy (cryo-EM) has led to an exponential surge in the number of high-resolution structures of integral membrane proteins, including SPTMRs. Cryo-EM structures of SPTMRs solved in the past few years have tremendously improved our understanding of how SPTMRs function. In this review, we will highlight these progresses in the structural studies of SPTMRs by single-particle cryo-EM, analyze important structural details of each protein involved, and discuss their implications on the underlying mechanisms. Finally, we also briefly discuss remaining challenges and exciting opportunities in the field.
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Affiliation(s)
- Kai Cai
- Departments of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
| | - Xuewu Zhang
- Departments of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Departments of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Corresponding Author: Xuewu Zhang, Department of pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA;
| | - Xiao-chen Bai
- Departments of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Departments of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75231, USA
- Corresponding Author: Xiao-chen Bai, Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390, USA;
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32
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Sušac L, Vuong MT, Thomas C, von Bülow S, O'Brien-Ball C, Santos AM, Fernandes RA, Hummer G, Tampé R, Davis SJ. Structure of a fully assembled tumor-specific T cell receptor ligated by pMHC. Cell 2022; 185:3201-3213.e19. [PMID: 35985289 PMCID: PMC9630439 DOI: 10.1016/j.cell.2022.07.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/05/2022] [Accepted: 07/15/2022] [Indexed: 12/12/2022]
Abstract
The T cell receptor (TCR) expressed by T lymphocytes initiates protective immune responses to pathogens and tumors. To explore the structural basis of how TCR signaling is initiated when the receptor binds to peptide-loaded major histocompatibility complex (pMHC) molecules, we used cryogenic electron microscopy to determine the structure of a tumor-reactive TCRαβ/CD3δγε2ζ2 complex bound to a melanoma-specific human class I pMHC at 3.08 Å resolution. The antigen-bound complex comprises 11 subunits stabilized by multivalent interactions across three structural layers, with clustered membrane-proximal cystines stabilizing the CD3-εδ and CD3-εγ heterodimers. Extra density sandwiched between transmembrane helices reveals the involvement of sterol lipids in TCR assembly. The geometry of the pMHC/TCR complex suggests that efficient TCR scanning of pMHC requires accurate pre-positioning of T cell and antigen-presenting cell membranes. Comparisons of the ligand-bound and unliganded receptors, along with molecular dynamics simulations, indicate that TCRs can be triggered in the absence of spontaneous structural rearrangements.
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Affiliation(s)
- Lukas Sušac
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Mai T Vuong
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Christoph Thomas
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Sören von Bülow
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany
| | - Caitlin O'Brien-Ball
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Ana Mafalda Santos
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Ricardo A Fernandes
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt am Main, Germany; Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany.
| | - Simon J Davis
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK; Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.
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33
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Dolton G, Rius C, Hasan MS, Wall A, Szomolay B, Behiry E, Whalley T, Southgate J, Fuller A, Morin T, Topley K, Tan LR, Goulder PJR, Spiller OB, Rizkallah PJ, Jones LC, Connor TR, Sewell AK. Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope. Cell 2022; 185:2936-2951.e19. [PMID: 35931021 PMCID: PMC9279490 DOI: 10.1016/j.cell.2022.07.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 05/08/2022] [Accepted: 07/07/2022] [Indexed: 01/06/2023]
Abstract
We studied the prevalent cytotoxic CD8 T cell response mounted against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike glycoprotein269-277 epitope (sequence YLQPRTFLL) via the most frequent human leukocyte antigen (HLA) class I worldwide, HLA A∗02. The Spike P272L mutation that has arisen in at least 112 different SARS-CoV-2 lineages to date, including in lineages classified as "variants of concern," was not recognized by the large CD8 T cell response seen across cohorts of HLA A∗02+ convalescent patients and individuals vaccinated against SARS-CoV-2, despite these responses comprising of over 175 different individual T cell receptors. Viral escape at prevalent T cell epitopes restricted by high frequency HLAs may be particularly problematic when vaccine immunity is focused on a single protein such as SARS-CoV-2 Spike, providing a strong argument for inclusion of multiple viral proteins in next generation vaccines and highlighting the need for monitoring T cell escape in new SARS-CoV-2 variants.
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Affiliation(s)
- Garry Dolton
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK
| | - Cristina Rius
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK
| | - Md Samiul Hasan
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK
| | - Aaron Wall
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK
| | - Barbara Szomolay
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK; Systems Immunology Research Institute, Cardiff University, CF14 4XN Cardiff, Wales, UK
| | - Enas Behiry
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK
| | - Thomas Whalley
- School of Biosciences, Cardiff University, CF10 3AX Cardiff, Wales, UK
| | - Joel Southgate
- School of Biosciences, Cardiff University, CF10 3AX Cardiff, Wales, UK
| | - Anna Fuller
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK
| | - Théo Morin
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK
| | - Katie Topley
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK
| | - Li Rong Tan
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK
| | - Philip J R Goulder
- Department of Paediatrics, University of Oxford, OX3 9DU Oxford, England, UK
| | - Owen B Spiller
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK
| | - Pierre J Rizkallah
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK
| | - Lucy C Jones
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK; Centre for Clinical Research, Royal Glamorgan Hospital, Ynysmaerdy CF72 8XR, UK
| | - Thomas R Connor
- Systems Immunology Research Institute, Cardiff University, CF14 4XN Cardiff, Wales, UK; School of Biosciences, Cardiff University, CF10 3AX Cardiff, Wales, UK; Pathogen genomics Unit, Public Health Wales NHS Trust, CF14 4XW Cardiff, Wales, UK.
| | - Andrew K Sewell
- Division of Infection and Immunity, Cardiff University School of Medicine, CF14 4XN Cardiff, Wales, UK; Systems Immunology Research Institute, Cardiff University, CF14 4XN Cardiff, Wales, UK.
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34
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Erausquin E, Serra P, Parras D, Santamaria P, López-Sagaseta J. Structural plasticity in I-Ag7 links autoreactivity to hybrid insulin peptides in type I diabetes. Front Immunol 2022; 13:924311. [PMID: 35967292 PMCID: PMC9365947 DOI: 10.3389/fimmu.2022.924311] [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: 04/20/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
We recently provided evidence for promiscuous recognition of several different hybrid insulin peptides (HIPs) by the highly diabetogenic, I-Ag7-restricted 4.1-T cell receptor (TCR). To understand the structural determinants of this phenomenon, we solved the structure of an agonistic HIP/I-Ag7 complex, both in isolation as well as bound to the 4.1-TCR. We find that HIP promiscuity of the 4.1-TCR is dictated, on the one hand, by an amino acid sequence pattern that ensures I-Ag7 binding and, on the other hand, by the presence of three acidic residues at positions P5, P7 and P8 that favor an optimal engagement by the 4.1-TCR’s complementary determining regions. Surprisingly, comparison of the TCR-bound and unbound HIP/I-Ag7 structures reveals that 4.1-TCR binding triggers several novel and unique structural motions in both the I-Ag7 molecule and the peptide that are essential for docking. This observation indicates that the type 1 diabetes-associated I-Ag7 molecule is structurally malleable and that this plasticity allows the recognition of multiple peptides by individual TCRs that would otherwise be unable to do so.
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Affiliation(s)
- Elena Erausquin
- Unit of Protein Crystallography and Structural Immunology, Navarrabiomed, Navarra, Spain
- Public University of Navarra (UPNA), Pamplona, Spain
- Navarra University Hospital, Pamplona, Spain
| | - Pau Serra
- Institut D’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Daniel Parras
- Institut D’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Pere Santamaria
- Institut D’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Julia McFarlane Diabetes Research Centre (JMDRC) and Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- *Correspondence: Jacinto López-Sagaseta, ; Pere Santamaria,
| | - Jacinto López-Sagaseta
- Unit of Protein Crystallography and Structural Immunology, Navarrabiomed, Navarra, Spain
- Public University of Navarra (UPNA), Pamplona, Spain
- Navarra University Hospital, Pamplona, Spain
- *Correspondence: Jacinto López-Sagaseta, ; Pere Santamaria,
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35
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Wegrecki M, Ocampo TA, Gunasinghe SD, von Borstel A, Tin SY, Reijneveld JF, Cao TP, Gully BS, Le Nours J, Moody DB, Van Rhijn I, Rossjohn J. Atypical sideways recognition of CD1a by autoreactive γδ T cell receptors. Nat Commun 2022; 13:3872. [PMID: 35790773 PMCID: PMC9256601 DOI: 10.1038/s41467-022-31443-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 06/16/2022] [Indexed: 01/04/2023] Open
Abstract
CD1a is a monomorphic antigen-presenting molecule on dendritic cells that presents lipids to αβ T cells. Whether CD1a represents a ligand for other immune receptors remains unknown. Here we use CD1a tetramers to show that CD1a is a ligand for Vδ1+ γδ T cells. Functional studies suggest that two γδ T cell receptors (TCRs) bound CD1a in a lipid-independent manner. The crystal structures of three Vγ4Vδ1 TCR-CD1a-lipid complexes reveal that the γδ TCR binds at the extreme far side and parallel to the long axis of the β-sheet floor of CD1a's antigen-binding cleft. Here, the γδ TCR co-recognises the CD1a heavy chain and β2 microglobulin in a manner that is distinct from all other previously observed γδ TCR docking modalities. The 'sideways' and lipid antigen independent mode of autoreactive CD1a recognition induces TCR clustering on the cell surface and proximal T cell signalling as measured by CD3ζ phosphorylation. In contrast with the 'end to end' binding of αβ TCRs that typically contact carried antigens, autoreactive γδ TCRs support geometrically diverse approaches to CD1a, as well as antigen independent recognition.
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Affiliation(s)
- Marcin Wegrecki
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Tonatiuh A Ocampo
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, US
| | - Sachith D Gunasinghe
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- European Molecular Biology Laboratory (EMBL) Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Anouk von Borstel
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Shin Yi Tin
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Josephine F Reijneveld
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, US
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Thinh-Phat Cao
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Benjamin S Gully
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jérôme Le Nours
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - D Branch Moody
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, US.
| | - Ildiko Van Rhijn
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, US.
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
- Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff, UK.
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36
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Ayres CM, Baker BM. Peptide-dependent tuning of major histocompatibility complex motional properties and the consequences for cellular immunity. Curr Opin Immunol 2022; 76:102184. [PMID: 35550277 PMCID: PMC10052791 DOI: 10.1016/j.coi.2022.102184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/15/2022] [Accepted: 04/05/2022] [Indexed: 12/22/2022]
Abstract
T cell receptors (TCRs) and other receptors of the immune system recognize peptides presented by class I or class II major histocompatibility complex (MHC) proteins. Although we generally distinguish between the MHC protein and its peptide, at an atomic level the two form a structural composite, which allows peptides to influence MHC properties and vice versa. One consequence is the peptide-dependent tuning of MHC structural dynamics, which contributes to protein structural adaptability and influences how receptors identify and bind targets. Peptide-dependent tuning of MHC protein dynamics can impact processes such as antigenicity, TCR cross-reactivity, and T cell repertoire selection. Motional tuning extends beyond the binding groove, influencing peptide selection and exchange, as well as interactions with other immune receptors. Here, we review recent findings showing how peptides can affect the dynamic and adaptable nature of MHC proteins. We highlight consequences for immunity and demonstrate how MHC proteins have evolved to be highly sensitive dynamic reporters, with broad immunological consequences.
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Affiliation(s)
- Cory M Ayres
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Brian M Baker
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA.
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37
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Huisman W, Hageman L, Leboux DAT, Khmelevskaya A, Efimov GA, Roex MCJ, Amsen D, Falkenburg JHF, Jedema I. Public T-Cell Receptors (TCRs) Revisited by Analysis of the Magnitude of Identical and Highly-Similar TCRs in Virus-Specific T-Cell Repertoires of Healthy Individuals. Front Immunol 2022; 13:851868. [PMID: 35401538 PMCID: PMC8987591 DOI: 10.3389/fimmu.2022.851868] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/04/2022] [Indexed: 01/11/2023] Open
Abstract
Since multiple different T-cell receptor (TCR) sequences can bind to the same peptide-MHC combination and the number of TCR-sequences that can theoretically be generated even exceeds the number of T cells in a human body, the likelihood that many public identical (PUB-I) TCR-sequences frequently contribute to immune responses has been estimated to be low. Here, we quantitatively analyzed the TCR-repertoires of 190 purified virus-specific memory T-cell populations, directed against 21 epitopes of Cytomegalovirus, Epstein-Barr virus and Adenovirus isolated from 29 healthy individuals, and determined the magnitude, defined as prevalence within the population and frequencies within individuals, of PUB-I TCR and of TCR-sequences that are highly-similar (PUB-HS) to these PUB-I TCR-sequences. We found that almost one third of all TCR nucleotide-sequences represented PUB-I TCR amino-acid (AA) sequences and found an additional 12% of PUB-HS TCRs differing by maximally 3 AAs. We illustrate that these PUB-I and PUB-HS TCRs were structurally related and contained shared core-sequences in their TCR-sequences. We found a prevalence of PUB-I and PUB-HS TCRs of up to 50% among individuals and showed frequencies of virus-specific PUB-I and PUB-HS TCRs making up more than 10% of each virus-specific T-cell population. These findings were confirmed by using an independent TCR-database of virus-specific TCRs. We therefore conclude that the magnitude of the contribution of PUB-I and PUB-HS TCRs to these virus-specific T-cell responses is high. Because the T cells from these virus-specific memory TCR-repertoires were the result of successful control of the virus in these healthy individuals, these PUB-HS TCRs and PUB-I TCRs may be attractive candidates for immunotherapy in immunocompromised patients that lack virus-specific T cells to control viral reactivation.
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Affiliation(s)
- Wesley Huisman
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands.,Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory for Blood Cell Research, Amsterdam, Netherlands
| | - Lois Hageman
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Didier A T Leboux
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Alexandra Khmelevskaya
- Laboratory of Transplantation Immunology, National Research Center for Hematology, Moscow, Russia
| | - Grigory A Efimov
- Laboratory of Transplantation Immunology, National Research Center for Hematology, Moscow, Russia
| | - Marthe C J Roex
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Derk Amsen
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory for Blood Cell Research, Amsterdam, Netherlands
| | | | - Inge Jedema
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
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38
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Boettcher M, Joechner A, Li Z, Yang SF, Schlegel P. Development of CAR T Cell Therapy in Children-A Comprehensive Overview. J Clin Med 2022; 11:2158. [PMID: 35456250 PMCID: PMC9024694 DOI: 10.3390/jcm11082158] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 01/27/2023] Open
Abstract
CAR T cell therapy has revolutionized immunotherapy in the last decade with the successful establishment of chimeric antigen receptor (CAR)-expressing cellular therapies as an alternative treatment in relapsed and refractory CD19-positive leukemias and lymphomas. There are fundamental reasons why CAR T cell therapy has been approved by the Food and Drug administration and the European Medicines Agency for pediatric and young adult patients first. Commonly, novel therapies are developed for adult patients and then adapted for pediatric use, due to regulatory and commercial reasons. Both strategic and biological factors have supported the success of CAR T cell therapy in children. Since there is an urgent need for more potent and specific therapies in childhood malignancies, efforts should also include the development of CAR therapeutics and expand applicability by introducing new technologies. Basic aspects, the evolution and the drawbacks of childhood CAR T cell therapy are discussed as along with the latest clinically relevant information.
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Affiliation(s)
- Michael Boettcher
- Department of Pediatric Surgery, University Medical Centre Mannheim, University of Heidelberg, 69117 Heidelberg, Germany;
| | - Alexander Joechner
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney 2006, Australia;
- Cellular Cancer Therapeutics Unit, Children’s Medical Research Institute, Sydney 2145, Australia; (Z.L.); (S.F.Y.)
| | - Ziduo Li
- Cellular Cancer Therapeutics Unit, Children’s Medical Research Institute, Sydney 2145, Australia; (Z.L.); (S.F.Y.)
| | - Sile Fiona Yang
- Cellular Cancer Therapeutics Unit, Children’s Medical Research Institute, Sydney 2145, Australia; (Z.L.); (S.F.Y.)
| | - Patrick Schlegel
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney 2006, Australia;
- Cellular Cancer Therapeutics Unit, Children’s Medical Research Institute, Sydney 2145, Australia; (Z.L.); (S.F.Y.)
- Department of Pediatric Hematology and Oncology, Westmead Children’s Hospital, Sydney 2145, Australia
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39
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Dao T, Mun S, Korontsvit T, Khan AG, Pohl MA, White T, Klatt MG, Andrew D, Lorenz IC, Scheinberg DA. A TCR mimic monoclonal antibody for the HPV-16 E7-epitope p11-19/HLA-A*02:01 complex. PLoS One 2022; 17:e0265534. [PMID: 35298559 PMCID: PMC8929633 DOI: 10.1371/journal.pone.0265534] [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: 09/21/2021] [Accepted: 03/03/2022] [Indexed: 11/19/2022] Open
Abstract
More effective treatments are needed for human papilloma virus (HPV)-induced cancers despite HPV virus vaccination. The oncogenic HPV protein targets are currently undruggable and intracellular and therefore there are no antibodies to these targets. Here we report the discovery of TCR mimic monoclonal antibodies (TCRm mAb) specific for the HPV E7 protein p11-19, YMLDLQPET, when presented on the cell surface in the context of HLA-A*02:01 by use of human phage display libraries. One of the mAbs, 3F8, was able to specifically mediate T cell- redirected cytotoxicity, in a bispecific T cell engager (BiTE) form. While further studies are required to assess the therapeutic potential of this approach, the study provided the proof of concept that TCRm mAb could be a therapeutic strategy for HPV-induced human cancers.
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Affiliation(s)
- Tao Dao
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Sungsoo Mun
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Tatyana Korontsvit
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Abdul G. Khan
- Tri-Institutional Therapeutics Discovery Institute, New York, New York, United States of America
| | - Mary Ann Pohl
- Tri-Institutional Therapeutics Discovery Institute, New York, New York, United States of America
| | - Thomas White
- Tri-Institutional Therapeutics Discovery Institute, New York, New York, United States of America
| | - Martin G. Klatt
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - David Andrew
- Tri-Institutional Therapeutics Discovery Institute, New York, New York, United States of America
| | - Ivo C. Lorenz
- Tri-Institutional Therapeutics Discovery Institute, New York, New York, United States of America
| | - David A. Scheinberg
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Weill Cornell Medicine, New York, New York, United States of America
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40
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Dao T, Mun SS, Molvi Z, Korontsvit T, Klatt MG, Khan AG, Nyakatura EK, Pohl MA, White TE, Balderes PJ, Lorenz IC, O'Reilly RJ, Scheinberg DA. A TCR mimic monoclonal antibody reactive with the "public" phospho-neoantigen pIRS2/HLA-A*02:01 complex. JCI Insight 2022; 7:151624. [PMID: 35260532 PMCID: PMC8983142 DOI: 10.1172/jci.insight.151624] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 01/26/2022] [Indexed: 02/06/2023] Open
Abstract
Phosphopeptides derived from dysregulated protein phosphorylation in cancer cells can be processed and presented by MHC class I and class II molecules and, therefore, represent an untapped class of tumor-specific antigens that could be used as widely expressed “public” cancer neoantigens (NeoAgs). We generated a TCR mimic (TCRm) mAb, 6B1, specific for a phosphopeptide derived from insulin receptor substrate 2 (pIRS2) presented by HLA-A*02:01. The pIRS2 epitope’s presentation by HLA-A*02:01 was confirmed by mass spectrometry. The TCRm 6B1 specifically bound to pIRS2/HLA-A2 complex on tumor cell lines that expressed pIRS2 in the context of HLA-A*02:01. Bispecific mAbs engaging CD3 of T cells were able to kill tumor cell lines in a pIRS2- and HLA-A*02:01–restricted manner. Structure modeling shows a prerequisite for an arginine or lysine at the first position to bind mAb. Therefore, 6B1 could recognize phosphopeptides derived from various phosphorylated proteins with similar amino acid compositions. This raised the possibility that a TCRm specific for the pIRS2/HLA-A2 complex could target a range of phosphopeptides presented by HLA-A*02:01 in various tumor cells. This is the first TCRm mAb to our knowledge targeting a phosphopeptide/MHC class I complex; the potential of this class of agents for clinical applications warrants further investigation.
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Affiliation(s)
- Tao Dao
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Sung Soo Mun
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Zaki Molvi
- Immunology Program, Weill Cornell Medicine, New York, New York, USA
| | - Tatyana Korontsvit
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Martin G Klatt
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Abdul G Khan
- Tri-Institutional Therapeutics Discovery Institute, New York, New York, USA
| | | | - Mary Ann Pohl
- Tri-Institutional Therapeutics Discovery Institute, New York, New York, USA
| | - Thomas E White
- Tri-Institutional Therapeutics Discovery Institute, New York, New York, USA
| | - Paul J Balderes
- Tri-Institutional Therapeutics Discovery Institute, New York, New York, USA
| | - Ivo C Lorenz
- Tri-Institutional Therapeutics Discovery Institute, New York, New York, USA
| | - Richard J O'Reilly
- Immunology Program, Weill Cornell Medicine, New York, New York, USA.,Weill Cornell Medicine, New York, New York, USA
| | - David A Scheinberg
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.,Weill Cornell Medicine, New York, New York, USA
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41
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Sim MJW, Sun PD. T Cell Recognition of Tumor Neoantigens and Insights Into T Cell Immunotherapy. Front Immunol 2022; 13:833017. [PMID: 35222422 PMCID: PMC8867076 DOI: 10.3389/fimmu.2022.833017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/21/2022] [Indexed: 12/13/2022] Open
Abstract
In cancer, non-synonymous DNA base changes alter protein sequence and produce neoantigens that are detected by the immune system. For immune detection, neoantigens must first be presented on class I or II human leukocyte antigens (HLA) followed by recognition by peptide-specific receptors, exemplified by the T-cell receptor (TCR). Detection of neoantigens represents a unique challenge to the immune system due to their high similarity with endogenous 'self' proteins. Here, we review insights into how TCRs detect neoantigens from structural studies and delineate two broad mechanistic categories: 1) recognition of mutated 'self' peptides and 2) recognition of novel 'non-self' peptides generated through anchor residue modifications. While mutated 'self' peptides differ only by a single amino acid from an existing 'self' epitope, mutations that form anchor residues generate an entirely new epitope, hitherto unknown to the immune system. We review recent structural studies that highlight these structurally distinct mechanisms and discuss how they may lead to differential anti-tumor immune responses. We discuss how T cells specific for neoantigens derived from anchor mutations can be of high affinity and provide insights to their use in adoptive T cell transfer-based immunotherapy.
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Affiliation(s)
| | - Peter D. Sun
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Rockville, MD, United States
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42
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Crean RM, Pudney CR, Cole DK, van der Kamp MW. Reliable In Silico Ranking of Engineered Therapeutic TCR Binding Affinities with MMPB/GBSA. J Chem Inf Model 2022; 62:577-590. [PMID: 35049312 PMCID: PMC9097153 DOI: 10.1021/acs.jcim.1c00765] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Accurate
and efficient in silico ranking of protein–protein
binding affinities is useful for protein design with applications
in biological therapeutics. One popular approach to rank binding affinities
is to apply the molecular mechanics Poisson–Boltzmann/generalized
Born surface area (MMPB/GBSA) method to molecular dynamics (MD) trajectories.
Here, we identify protocols that enable the reliable evaluation of
T-cell receptor (TCR) variants binding to their target, peptide-human
leukocyte antigens (pHLAs). We suggest different protocols for variant
sets with a few (≤4) or many mutations, with entropy corrections
important for the latter. We demonstrate how potential outliers could
be identified in advance and that just 5–10 replicas of short
(4 ns) MD simulations may be sufficient for the reproducible and accurate
ranking of TCR variants. The protocols developed here can be applied
toward in silico screening during the optimization
of therapeutic TCRs, potentially reducing both the cost and time taken
for biologic development.
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Affiliation(s)
| | | | - David K. Cole
- Immunocore Ltd., Milton Park, Abingdon OX14 4RY, U.K
- Division of Infection & Immunity, Cardiff University, Cardiff CF14 4XN, U.K
| | - Marc W. van der Kamp
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, U.K
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43
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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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44
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Novel Molecular Targets for Hepatocellular Carcinoma. Cancers (Basel) 2021; 14:cancers14010140. [PMID: 35008303 PMCID: PMC8750630 DOI: 10.3390/cancers14010140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/17/2021] [Accepted: 12/22/2021] [Indexed: 12/15/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of death from cancer globally. Indeed, only a few treatments are available, most of which are effective only for the early stages of the disease. Therefore, there is an urgent needing for potential markers for a specifically targeted therapy. Candidate proteins were selected from datasets of The Human Protein Atlas, in order to identify specific tumor-associated proteins overexpressed in HCC samples associated with poor prognosis. Potential epitopes were predicted from such proteins, and homology with peptides derived from viral proteins was assessed. A multiparametric validation was performed, including recognition by PBMCs from HCC-patients and healthy donors, showing a T-cell cross-reactivity with paired epitopes. These results provide novel HCC-specific tumor-associated antigens (TAAs) for immunotherapeutic anti-HCC strategies potentially able to expand pre-existing virus-specific CD8+ T cells with superior anticancer efficacy.
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45
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Edholm ES, Fenton CG, Mondot S, Paulssen RH, Lefranc MP, Boudinot P, Magadan S. Profiling the T Cell Receptor Alpha/Delta Locus in Salmonids. Front Immunol 2021; 12:753960. [PMID: 34733285 PMCID: PMC8559430 DOI: 10.3389/fimmu.2021.753960] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/28/2021] [Indexed: 12/17/2022] Open
Abstract
In jawed vertebrates, two major T cell populations have been characterized. They are defined as α/β or γ/δ T cells, based on the expressed T cell receptor. Salmonids (family Salmonidae) include two key teleost species for aquaculture, rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) which constitute important models for fish immunology and important targets for vaccine development. The growing interest to decipher the dynamics of adaptive immune responses against pathogens or vaccines has resulted in recent efforts to sequence the immunoglobulin (IG) or antibodies and T cell receptor (TR) repertoire in these species. In this context, establishing a comprehensive and coherent locus annotation is the fundamental basis for the analysis of high-throughput repertoire sequencing data. We therefore decided to revisit the description and annotation of TRA/TRD locus in Atlantic salmon and two strains of rainbow trout (Swanson and Arlee) using the now available high-quality genome assemblies. Phylogenetic analysis of functional TRA/TRD V genes from these three genomes led to the definition of 25 subgroups shared by both species, some with particular feature. A total of 128 TRAJ genes were identified in Salmo, the majority with a close counterpart in Oncorhynchus. Analysis of expressed TRA repertoire indicates that most TRAV gene subgroups are expressed at mucosal and systemic level. The present work on TRA/TRD locus annotation along with the analysis of TRA repertoire sequencing data show the feasibility and advantages of a common salmonid TRA/TRD nomenclature that allows an accurate annotation and analysis of high-throughput sequencing results, across salmonid T cell subsets.
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Affiliation(s)
- Eva-Stina Edholm
- Faculty of Biosciences, Fisheries & Economics, Norwegian College of Fishery Science, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Christopher Graham Fenton
- Clinical Bioinformatics Research Group, Genomics Support Centre Tromsø (GSCT), Department of Clinical Medicine, Faculty of Health Sciences, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Stanislas Mondot
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.,GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Ruth H Paulssen
- Clinical Bioinformatics Research Group, Genomics Support Centre Tromsø (GSCT), Department of Clinical Medicine, Faculty of Health Sciences, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Marie-Paule Lefranc
- IMGT®, The International ImMunoGeneTics Information System (IMGT), Laboratoire d´ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), CNRS, University of Montpellier, Montpellier Cedex, France
| | - Pierre Boudinot
- Université Paris Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Susana Magadan
- Immunology Laboratory, Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain.,Galicia Sur Health Research Institute (IIS-GS), Hospital Alvaro Cunqueiro, Vigo, Spain
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46
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Robinson RA, McMurran C, McCully ML, Cole DK. Engineering soluble T-cell receptors for therapy. FEBS J 2021; 288:6159-6173. [PMID: 33624424 PMCID: PMC8596704 DOI: 10.1111/febs.15780] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/11/2021] [Accepted: 02/22/2021] [Indexed: 12/15/2022]
Abstract
Immunotherapy approaches that target peptide-human leukocyte antigen (pHLA) complexes are becoming highly attractive because of their potential to access virtually all foreign and cellular proteins. For this reason, there has been considerable interest in the development of the natural ligand for pHLA, the T-cell receptor (TCR), as a soluble drug to target disease-associated pHLA presented at the cell surface. However, native TCR stability is suboptimal for soluble drug development, and natural TCRs generally have weak affinities for pHLAs, limiting their potential to reach efficacious receptor occupancy levels as soluble drugs. To overcome these limitations and make full use of the TCR as a soluble drug platform, several protein engineering solutions have been applied to TCRs to enhance both their stability and affinity, with a focus on retaining target specificity and selectivity. Here, we review these advances and look to the future for the next generation of soluble TCR-based therapies that can target monomorphic HLA-like proteins presenting both peptide and nonpeptide antigens.
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47
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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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48
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Wilhelm KB, Morita S, McAffee DB, Kim S, O'Dair MK, Groves JT. Height, but not binding epitope, affects the potency of synthetic TCR agonists. Biophys J 2021; 120:3869-3880. [PMID: 34453921 PMCID: PMC8511163 DOI: 10.1016/j.bpj.2021.08.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 12/27/2022] Open
Abstract
Under physiological conditions, peptide-major histocompatibility complex (pMHC) molecules can trigger T cell receptors (TCRs) as monovalent ligands that are sparsely distributed on the plasma membrane of an antigen-presenting cell. TCRs can also be triggered by artificial clustering, such as with pMHC tetramers or antibodies; however, these strategies circumvent many of the natural ligand discrimination mechanisms of the T cell and can elicit nonphysiological signaling activity. We have recently introduced a synthetic TCR agonist composed of an anti-TCRβ Fab′ antibody fragment covalently bound to a DNA oligonucleotide, which serves as a membrane anchor. This Fab′-DNA ligand efficiently triggers TCR as a monomer when membrane associated and exhibits a potency and activation profile resembling agonist pMHC. In this report, we explore the geometric requirements for efficient TCR triggering and cellular activation by Fab′-DNA ligands. We find that T cells are insensitive to the ligand binding epitope on the TCR complex but that length of the DNA tether is important. Increasing, the intermembrane distance spanned by Fab′-DNA:TCR complexes decreases TCR triggering efficiency and T cell activation potency, consistent with the kinetic-segregation model of TCR triggering. These results establish design parameters for constructing synthetic TCR agonists that are able to activate polyclonal T cell populations, such as T cells from a human patient, in a similar manner as the native pMHC ligand.
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Affiliation(s)
- Kiera B Wilhelm
- Department of Chemistry, University of California, Berkeley, California
| | - Shumpei Morita
- Department of Chemistry, University of California, Berkeley, California
| | - Darren B McAffee
- Department of Chemistry, University of California, Berkeley, California
| | - Sungi Kim
- Department of Chemistry, University of California, Berkeley, California
| | - Mark K O'Dair
- Department of Chemistry, University of California, Berkeley, California
| | - Jay T Groves
- Department of Chemistry, University of California, Berkeley, California.
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49
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Milighetti M, Shawe-Taylor J, Chain B. Predicting T Cell Receptor Antigen Specificity From Structural Features Derived From Homology Models of Receptor-Peptide-Major Histocompatibility Complexes. Front Physiol 2021; 12:730908. [PMID: 34566692 PMCID: PMC8456106 DOI: 10.3389/fphys.2021.730908] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/02/2021] [Indexed: 11/13/2022] Open
Abstract
The physical interaction between the T cell receptor (TCR) and its cognate antigen causes T cells to activate and participate in the immune response. Understanding this physical interaction is important in predicting TCR binding to a target epitope, as well as potential cross-reactivity. Here, we propose a way of collecting informative features of the binding interface from homology models of T cell receptor-peptide-major histocompatibility complex (TCR-pMHC) complexes. The information collected from these structures is sufficient to discriminate binding from non-binding TCR-pMHC pairs in multiple independent datasets. The classifier is limited by the number of crystal structures available for the homology modelling and by the size of the training set. However, the classifier shows comparable performance to sequence-based classifiers requiring much larger training sets.
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Affiliation(s)
- Martina Milighetti
- Division of Infection and Immunity, University College London, London, United Kingdom
- Cancer Institute, University College London, London, United Kingdom
| | - John Shawe-Taylor
- Department of Computer Science, University College London, London, United Kingdom
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, United Kingdom
- Department of Computer Science, University College London, London, United Kingdom
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50
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Zhovmer AS, Chandler M, Manning A, Afonin KA, Tabdanov ED. Programmable DNA-augmented hydrogels for controlled activation of human lymphocytes. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2021; 37:102442. [PMID: 34284132 DOI: 10.1016/j.nano.2021.102442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/25/2021] [Accepted: 07/07/2021] [Indexed: 12/25/2022]
Abstract
Contractile forces within the planar interface between T cell and antigen-presenting surface mechanically stimulate T cell receptors (TCR) in the mature immune synapses. However, the origin of mechanical stimulation during the initial, i.e., presynaptic, microvilli-based TCR activation in the course of immune surveillance remains unknown and new tools to help address this problem are needed. In this work, we develop nucleic acid nanoassembly (NAN)-based technology for functionalization of hydrogels using isothermal toehold-mediated reassociation of RNA/DNA heteroduplexes. Resulting platform allows for regulation with NAN linkers of 3D force momentum along the TCR mechanical axis, whereas hydrogels contribute to modulation of 2D shear modulus. By utilizing different lengths of NAN linkers conjugated to polyacrylamide gels of different shear moduli, we demonstrate an efficient capture of human T lymphocytes and tunable activation of TCR, as confirmed by T-cell spreading and pY foci.
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Affiliation(s)
- Alexander S Zhovmer
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA.
| | - Morgan Chandler
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Alexis Manning
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Kirill A Afonin
- Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC, USA.
| | - Erdem D Tabdanov
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA.
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