51
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Gao A, Chen Z, Amitai A, Doelger J, Mallajosyula V, Sundquist E, Pereyra Segal F, Carrington M, Davis MM, Streeck H, Chakraborty AK, Julg B. Learning from HIV-1 to predict the immunogenicity of T cell epitopes in SARS-CoV-2. iScience 2021; 24:102311. [PMID: 33748696 PMCID: PMC7956900 DOI: 10.1016/j.isci.2021.102311] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/22/2021] [Accepted: 03/10/2021] [Indexed: 12/18/2022] Open
Abstract
We describe a physics-based learning model for predicting the immunogenicity of cytotoxic T lymphocyte (CTL) epitopes derived from diverse pathogens including SARS-CoV-2. The model was trained and optimized on the relative immunodominance of CTL epitopes in human immunodeficiency virus infection. Its accuracy was tested against experimental data from patients with COVID-19. Our model predicts that only some SARS-CoV-2 epitopes predicted to bind to HLA molecules are immunogenic. The immunogenic CTL epitopes across all SARS-CoV-2 proteins are predicted to provide broad population coverage, but those from the SARS-CoV-2 spike protein alone are unlikely to do so. Our model also predicts that several immunogenic SARS-CoV-2 CTL epitopes are identical to seasonal coronaviruses circulating in the population and such cross-reactive CD8+ T cells can indeed be detected in prepandemic blood donors, suggesting that some level of CTL immunity against COVID-19 may be present in some individuals before SARS-CoV-2 infection.
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Affiliation(s)
- Ang Gao
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zhilin Chen
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, 400 Technology Sq., Cambridge, MA 02139, USA
| | - Assaf Amitai
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Julia Doelger
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Vamsee Mallajosyula
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Emily Sundquist
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, 400 Technology Sq., Cambridge, MA 02139, USA
| | | | - Mary Carrington
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, 400 Technology Sq., Cambridge, MA 02139, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mark M. Davis
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hendrik Streeck
- Institut für Virologie, Universitätsklinikum Bonn, 53127 Bonn, Germany
| | - Arup K. Chakraborty
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, 400 Technology Sq., Cambridge, MA 02139, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Boris Julg
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, 400 Technology Sq., Cambridge, MA 02139, USA
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52
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Lo WL, Weiss A. Adapting T Cell Receptor Ligand Discrimination Capability via LAT. Front Immunol 2021; 12:673196. [PMID: 33936119 PMCID: PMC8085316 DOI: 10.3389/fimmu.2021.673196] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 03/29/2021] [Indexed: 12/19/2022] Open
Abstract
Self- and non-self ligand discrimination is a core principle underlying T cell-mediated immunity. Mature αβ T cells can respond to a foreign peptide ligand presented by major histocompatibility complex molecules (pMHCs) on antigen presenting cells, on a background of continuously sensed self-pMHCs. How αβ T cells can properly balance high sensitivity and high specificity to foreign pMHCs, while surrounded by a sea of self-peptide ligands is not well understood. Such discrimination cannot be explained solely by the affinity parameters of T cell antigen receptor (TCR) and pMHC interaction. In this review, we will discuss how T cell ligand discrimination may be molecularly defined by events downstream of the TCR-pMHC interaction. We will discuss new evidence in support of the kinetic proofreading model of TCR ligand discrimination, and in particular how the kinetics of specific phosphorylation sites within the adaptor protein linker for activation of T cells (LAT) determine the outcome of TCR signaling. In addition, we will discuss emerging data regarding how some kinases, including ZAP-70 and LCK, may possess scaffolding functions to more efficiently direct their kinase activities.
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Affiliation(s)
- Wan-Lin Lo
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Arthur Weiss
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, United States
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53
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Prasad M, Wojciech L, Brzostek J, Hu J, Chua YL, Tung DWH, Yap J, Rybakin V, Gascoigne NRJ. Expansion of an Unusual Virtual Memory CD8 + Subpopulation Bearing Vα3.2 TCR in Themis-Deficient Mice. Front Immunol 2021; 12:644483. [PMID: 33897691 PMCID: PMC8058184 DOI: 10.3389/fimmu.2021.644483] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/19/2021] [Indexed: 11/23/2022] Open
Abstract
Deletion of the gene for Themis affects T cell selection in the thymus, which would be expected to affect the TCR repertoire. We found an increased proportion of cells expressing Vα3.2 (TRAV9N-3) in the peripheral CD8+ T cell population in mice with germline Themis deficiency. Analysis of the TCRα repertoire indicated it was generally reduced in diversity in the absence of Themis, whereas the diversity of sequences using the TRAV9N-3 V-region element was increased. In wild type mice, Vα3.2+ cells showed higher CD5, CD6 and CD44 expression than non-Vα3-expressing cells, and this was more marked in cells from Themis-deficient mice. This suggested a virtual memory phenotype, as well as a stronger response to self-pMHC. The Vα3.2+ cells responded more strongly to IL-15, as well as showing bystander effector capability in a Listeria infection. Thus, the unusually large population of Vα3.2+ CD8+ T cells found in the periphery of Themis-deficient mice reflects not only altered thymic selection, but also allowed identification of a subset of bystander-competent cells that are also present in wild-type mice.
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Affiliation(s)
- Mukul Prasad
- Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Lukasz Wojciech
- Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Joanna Brzostek
- Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Jianfang Hu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Yen Leong Chua
- Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Desmond Wai Hon Tung
- Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jiawei Yap
- Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Vasily Rybakin
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Nicholas R J Gascoigne
- Immunology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
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54
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Mhanna V, Fourcade G, Barennes P, Quiniou V, Pham HP, Ritvo PG, Brimaud F, Gouritin B, Churlaud G, Six A, Mariotti-Ferrandiz E, Klatzmann D. Impaired Activated/Memory Regulatory T Cell Clonal Expansion Instigates Diabetes in NOD Mice. Diabetes 2021; 70:976-985. [PMID: 33479057 DOI: 10.2337/db20-0896] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/19/2021] [Indexed: 11/13/2022]
Abstract
Regulatory T cell (Treg) insufficiency licenses the destruction of insulin-producing pancreatic β-cells by autoreactive effector T cells (Teffs), causing spontaneous autoimmune diabetes in NOD mice. We investigated the contribution to diabetes of the T-cell receptor (TCR) repertoires of naive regulatory T cells (nTregs), activated/memory Tregs (amTregs), and CD4+ Teffs from prediabetic NOD mice and normal C57BL/6 (B6) mice. NOD mice amTreg and Teff repertoire diversity was unexpectedly higher than that of B6 mice. This was due to the presence of highly expanded clonotypes in B6 amTregs and Teffs that were largely lost in their NOD counterparts. Interleukin-2 (IL-2) administration to NOD mice restored such amTreg clonotype expansions and prevented diabetes development. In contrast, IL-2 administration only led to few or no clonotype expansions in nTregs and Teffs, respectively. Noteworthily, IL-2-expanded amTreg and nTreg clonotypes were markedly enriched in islet-antigen specific TCRs. Altogether, our results highlight the link between a reduced clonotype expansion within the activated Treg repertoire and the development of an autoimmune disease. They also indicate that the repertoire of amTregs is amenable to rejuvenation by IL-2.
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Affiliation(s)
- Vanessa Mhanna
- Sorbonne Universite, INSERM, UMRS959 Immunology-Immunopathology-Immunotherapy Laboratory, Paris, France
| | - Gwladys Fourcade
- Sorbonne Universite, INSERM, UMRS959 Immunology-Immunopathology-Immunotherapy Laboratory, Paris, France
| | - Pierre Barennes
- Sorbonne Universite, INSERM, UMRS959 Immunology-Immunopathology-Immunotherapy Laboratory, Paris, France
| | - Valentin Quiniou
- Sorbonne Universite, INSERM, UMRS959 Immunology-Immunopathology-Immunotherapy Laboratory, Paris, France
- Clinical Investigation Center in Biotherapy and Inflammation-Immunopathology-Biotherapy Department, Assistance Publique-Hôpitaux de Paris, Hôpital Universitaire Pitié-Salpêtrière, Paris, France
| | - Hang P Pham
- Statistics Department, ILTOO Pharma, Paris, France
| | - Paul-Gydeon Ritvo
- Sorbonne Universite, INSERM, UMRS959 Immunology-Immunopathology-Immunotherapy Laboratory, Paris, France
| | - Faustine Brimaud
- Sorbonne Universite, INSERM, UMRS959 Immunology-Immunopathology-Immunotherapy Laboratory, Paris, France
| | - Bruno Gouritin
- Sorbonne Universite, INSERM, UMRS959 Immunology-Immunopathology-Immunotherapy Laboratory, Paris, France
| | - Guillaume Churlaud
- Sorbonne Universite, INSERM, UMRS959 Immunology-Immunopathology-Immunotherapy Laboratory, Paris, France
- Clinical Investigation Center in Biotherapy and Inflammation-Immunopathology-Biotherapy Department, Assistance Publique-Hôpitaux de Paris, Hôpital Universitaire Pitié-Salpêtrière, Paris, France
| | - Adrien Six
- Sorbonne Universite, INSERM, UMRS959 Immunology-Immunopathology-Immunotherapy Laboratory, Paris, France
| | | | - David Klatzmann
- Sorbonne Universite, INSERM, UMRS959 Immunology-Immunopathology-Immunotherapy Laboratory, Paris, France
- Clinical Investigation Center in Biotherapy and Inflammation-Immunopathology-Biotherapy Department, Assistance Publique-Hôpitaux de Paris, Hôpital Universitaire Pitié-Salpêtrière, Paris, France
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55
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Grimsholm O, Piano Mortari E, Davydov AN, Shugay M, Obraztsova AS, Bocci C, Marasco E, Marcellini V, Aranburu A, Farroni C, Silvestris DA, Cristofoletti C, Giorda E, Scarsella M, Cascioli S, Barresi S, Lougaris V, Plebani A, Cancrini C, Finocchi A, Moschese V, Valentini D, Vallone C, Signore F, de Vincentiis G, Zaffina S, Russo G, Gallo A, Locatelli F, Tozzi AE, Tartaglia M, Chudakov DM, Carsetti R. The Interplay between CD27 dull and CD27 bright B Cells Ensures the Flexibility, Stability, and Resilience of Human B Cell Memory. Cell Rep 2021; 30:2963-2977.e6. [PMID: 32130900 DOI: 10.1016/j.celrep.2020.02.022] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/23/2019] [Accepted: 02/05/2020] [Indexed: 10/24/2022] Open
Abstract
Memory B cells (MBCs) epitomize the adaptation of the immune system to the environment. We identify two MBC subsets in peripheral blood, CD27dull and CD27bright MBCs, whose frequency changes with age. Heavy chain variable region (VH) usage, somatic mutation frequency replacement-to-silent ratio, and CDR3 property changes, reflecting consecutive selection of highly antigen-specific, low cross-reactive antibody variants, all demonstrate that CD27dull and CD27bright MBCs represent sequential MBC developmental stages, and stringent antigen-driven pressure selects CD27dull into the CD27bright MBC pool. Dynamics of human MBCs are exploited in pregnancy, when 50% of maternal MBCs are lost and CD27dull MBCs transit to the more differentiated CD27bright stage. In the postpartum period, the maternal MBC pool is replenished by the expansion of persistent CD27dull clones. Thus, the stability and flexibility of human B cell memory is ensured by CD27dull MBCs that expand and differentiate in response to change.
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Affiliation(s)
- Ola Grimsholm
- B Cell Pathophysiology Unit, Immunology Research Area, Bambino Gesù Children's Hospital IRCCS, 00146 Rome, Italy; Department of Rheumatology and Inflammation Research, University of Gothenburg, Box 480, 405 30 Gothenburg, Sweden
| | - Eva Piano Mortari
- B Cell Pathophysiology Unit, Immunology Research Area, Bambino Gesù Children's Hospital IRCCS, 00146 Rome, Italy
| | - Alexey N Davydov
- Central European Institute of Technology, 625 00 Brno, Czech Republic
| | - Mikhail Shugay
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, 101000 Moscow, Russia
| | - Anna S Obraztsova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, 101000 Moscow, Russia
| | - Chiara Bocci
- B Cell Pathophysiology Unit, Immunology Research Area, Bambino Gesù Children's Hospital IRCCS, 00146 Rome, Italy
| | - Emiliano Marasco
- Division of Rheumatology, Bambino Gesù Children's Hospital IRCCS, 00146 Roma, Italy
| | - Valentina Marcellini
- B Cell Pathophysiology Unit, Immunology Research Area, Bambino Gesù Children's Hospital IRCCS, 00146 Rome, Italy
| | - Alaitz Aranburu
- Department of Rheumatology and Inflammation Research, University of Gothenburg, Box 480, 405 30 Gothenburg, Sweden
| | - Chiara Farroni
- B Cell Pathophysiology Unit, Immunology Research Area, Bambino Gesù Children's Hospital IRCCS, 00146 Rome, Italy
| | | | | | - Ezio Giorda
- B Cell Pathophysiology Unit, Immunology Research Area, Bambino Gesù Children's Hospital IRCCS, 00146 Rome, Italy
| | - Marco Scarsella
- B Cell Pathophysiology Unit, Immunology Research Area, Bambino Gesù Children's Hospital IRCCS, 00146 Rome, Italy
| | - Simona Cascioli
- B Cell Pathophysiology Unit, Immunology Research Area, Bambino Gesù Children's Hospital IRCCS, 00146 Rome, Italy
| | - Sabina Barresi
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, 00146 Rome, Italy
| | - Vassilios Lougaris
- Department of Experimental and Clinical Sciences, University of Brescia, 25121 Brescia, Italy
| | - Alessandro Plebani
- DPUO, Division of Immuno-Infectivology, University Department of Pediatrics, 00146 Bambino Gesù Children's Hospital, Rome, Italy
| | - Caterina Cancrini
- DPUO, Division of Immuno-Infectivology, University Department of Pediatrics, 00146 Bambino Gesù Children's Hospital, Rome, Italy; School of Medicine, University of Tor Vergata, 00133 Rome, Italy
| | - Andrea Finocchi
- DPUO, Division of Immuno-Infectivology, University Department of Pediatrics, 00146 Bambino Gesù Children's Hospital, Rome, Italy; School of Medicine, University of Tor Vergata, 00133 Rome, Italy
| | - Viviana Moschese
- Pediatric Immunology Unit, Policlinico Tor Vergata, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Diletta Valentini
- Pediatric and Infectious Disease Unit, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Cristina Vallone
- Department of Obstetrics and Gynaecology, Misericordia Hospital Grosseto, Usl Toscana Sud-est, 58100 Grosseto, Italy
| | - Fabrizio Signore
- Department of Obstetrics and Gynaecology, Misericordia Hospital Grosseto, Usl Toscana Sud-est, 58100 Grosseto, Italy
| | | | - Salvatore Zaffina
- Occupational Medicine/Health Technology Assessment and Safety Research Unit, Clinical-Technological Innovations Research Area, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | | | - Angela Gallo
- Oncohaematology Department, Bambino Gesù Children's Hospital IRCCS, 00146 Rome, Italy
| | - Franco Locatelli
- Oncohaematology Department, Bambino Gesù Children's Hospital IRCCS, 00146 Rome, Italy; Department of Pediatrics, Sapienza, University of Rome, 00161 Rome, Italy
| | - Alberto E Tozzi
- Multifactorial Disease and Complex Phenotype Research Area, Bambino Gesù Children's Hospital, IRCSS, 00146 Rome, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, 00146 Rome, Italy
| | - Dmitriy M Chudakov
- Central European Institute of Technology, 625 00 Brno, Czech Republic; Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, 101000 Moscow, Russia
| | - Rita Carsetti
- B Cell Pathophysiology Unit, Immunology Research Area, Bambino Gesù Children's Hospital IRCCS, 00146 Rome, Italy; Diagnostic Immunology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy.
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56
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Genetic Bias, Diversity Indices, Physiochemical Properties and CDR3 Motifs Divide Auto-Reactive from Allo-Reactive T-Cell Repertoires. Int J Mol Sci 2021; 22:ijms22041625. [PMID: 33562731 PMCID: PMC7915266 DOI: 10.3390/ijms22041625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/30/2021] [Accepted: 01/31/2021] [Indexed: 12/26/2022] Open
Abstract
The distinct properties of allo-reactive T-cell repertoires are not well understood. To investigate whether auto-reactive and allo-reactive T-cell repertoires encoded distinct properties, we used dextramer enumeration, enrichment, single-cell T-cell receptor (TCR) sequencing and multiparameter analysis. We found auto-reactive and allo-reactive T-cells differed in mean ex vivo frequency which was antigen dependent. Allo-reactive T-cells showed clear differences in TCR architecture, with enriched usage of specific T-cell receptor variable (TRBJ) genes and broader use of T-cell receptor variable joining (TRBJ) genes. Auto-reactive T-cell repertoires exhibited complementary determining regions three (CDR3) lengths using a Gaussian distribution whereas allo-reactive T-cell repertoires exhibited distorted patterns in CDR3 length. CDR3 loops from allo-reactive T-cells showed distinct physical-chemical properties, tending to encode loops that were more acidic in charge. Allo-reactive T-cell repertoires differed in diversity metrics, tending to show increased overall diversity and increased homogeneity between repertoires. Motif analysis of CDR3 loops showed allo-reactive T-cell repertoires differed in motif preference which included broader motif use. Collectively, these data conclude that allo-reactive T-cell repertoires are indeed different to auto-reactive repertoires and provide tangible metrics for further investigations and validation. Given that the antigens studied here are overexpressed on multiple cancers and that allo-reactive TCRs often show increased ligand affinity, this new TCR bank also has translational potential for adoptive cell therapy, soluble TCR-based therapy and rational TCR design.
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57
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Izraelson M, Metsger M, Davydov AN, Shagina IA, Dronina MA, Obraztsova AS, Miskevich DA, Mamedov IZ, Volchkova LN, Nakonechnaya TO, Shugay M, Bolotin DA, Staroverov DB, Sharonov GV, Kondratyuk EY, Zagaynova EV, Lukyanov S, Shams I, Britanova OV, Chudakov DM. Distinct organization of adaptive immunity in the long-lived rodent Spalax galili. NATURE AGING 2021; 1:179-189. [PMID: 37118630 DOI: 10.1038/s43587-021-00029-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/08/2021] [Indexed: 04/30/2023]
Abstract
A balanced immune response is a cornerstone of healthy aging. Here, we uncover distinctive features of the long-lived blind mole-rat (Spalax spp.) adaptive immune system, relative to humans and mice. The T-cell repertoire remains diverse throughout the Spalax lifespan, suggesting a paucity of large long-lived clones of effector-memory T cells. Expression of master transcription factors of T-cell differentiation, as well as checkpoint and cytotoxicity genes, remains low as Spalax ages. The thymus shrinks as in mice and humans, while interleukin-7 and interleukin-7 receptor expression remains high, potentially reflecting the sustained homeostasis of naive T cells. With aging, immunoglobulin hypermutation level does not increase and the immunoglobulin-M repertoire remains diverse, suggesting shorter B-cell memory and sustained homeostasis of innate-like B cells. The Spalax adaptive immune system thus appears biased towards sustained functional and receptor diversity over specialized, long-lived effector-memory clones-a unique organizational strategy that potentially underlies this animal's extraordinary longevity and healthy aging.
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Affiliation(s)
- M Izraelson
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - M Metsger
- Central European Institute of Technology, Brno, Czech Republic
| | - A N Davydov
- Central European Institute of Technology, Brno, Czech Republic
| | - I A Shagina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - M A Dronina
- Institute of Evolution & Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
| | - A S Obraztsova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - D A Miskevich
- Institute of Evolution & Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
| | - I Z Mamedov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Central European Institute of Technology, Brno, Czech Republic
| | - L N Volchkova
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - T O Nakonechnaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - M Shugay
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - D A Bolotin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - D B Staroverov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - G V Sharonov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - E Y Kondratyuk
- Institute of Systematics and Ecology of Animals SB RAS, Novosibirsk, Russia
| | - E V Zagaynova
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - S Lukyanov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - I Shams
- Institute of Evolution & Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
| | - O V Britanova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
| | - D M Chudakov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia.
- Pirogov Russian National Research Medical University, Moscow, Russia.
- Central European Institute of Technology, Brno, Czech Republic.
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58
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Kasatskaya SA, Ladell K, Egorov ES, Miners KL, Davydov AN, Metsger M, Staroverov DB, Matveyshina EK, Shagina IA, Mamedov IZ, Izraelson M, Shelyakin PV, Britanova OV, Price DA, Chudakov DM. Functionally specialized human CD4 + T-cell subsets express physicochemically distinct TCRs. eLife 2020; 9:57063. [PMID: 33289628 PMCID: PMC7773335 DOI: 10.7554/elife.57063] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 12/04/2020] [Indexed: 12/26/2022] Open
Abstract
The organizational integrity of the adaptive immune system is determined by functionally discrete subsets of CD4+ T cells, but it has remained unclear to what extent lineage choice is influenced by clonotypically expressed T-cell receptors (TCRs). To address this issue, we used a high-throughput approach to profile the αβ TCR repertoires of human naive and effector/memory CD4+ T-cell subsets, irrespective of antigen specificity. Highly conserved physicochemical and recombinatorial features were encoded on a subset-specific basis in the effector/memory compartment. Clonal tracking further identified forbidden and permitted transition pathways, mapping effector/memory subsets related by interconversion or ontogeny. Public sequences were largely confined to particular effector/memory subsets, including regulatory T cells (Tregs), which also displayed hardwired repertoire features in the naive compartment. Accordingly, these cumulative repertoire portraits establish a link between clonotype fate decisions in the complex world of CD4+ T cells and the intrinsic properties of somatically rearranged TCRs.
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Affiliation(s)
- Sofya A Kasatskaya
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russian Federation.,Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Evgeniy S Egorov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Kelly L Miners
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Alexey N Davydov
- Adaptive Immunity Group, Central European Institute of Technology, Brno, Czech Republic
| | - Maria Metsger
- Adaptive Immunity Group, Central European Institute of Technology, Brno, Czech Republic
| | - Dmitry B Staroverov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.,Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Elena K Matveyshina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Irina A Shagina
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.,Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Ilgar Z Mamedov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.,Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Mark Izraelson
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.,Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Pavel V Shelyakin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russian Federation.,Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Olga V Britanova
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.,Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom.,Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Dmitriy M Chudakov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russian Federation.,Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.,Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
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59
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Lee CH, Salio M, Napolitani G, Ogg G, Simmons A, Koohy H. Predicting Cross-Reactivity and Antigen Specificity of T Cell Receptors. Front Immunol 2020; 11:565096. [PMID: 33193332 PMCID: PMC7642207 DOI: 10.3389/fimmu.2020.565096] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022] Open
Abstract
Adaptive immune recognition is mediated by specific interactions between heterodimeric T cell receptors (TCRs) and their cognate peptide-MHC (pMHC) ligands, and the methods to accurately predict TCR:pMHC interaction would have profound clinical, therapeutic and pharmaceutical applications. Herein, we review recent developments in predicting cross-reactivity and antigen specificity of TCR recognition. We discuss current experimental and computational approaches to investigate cross-reactivity and antigen-specificity of TCRs and highlight how integrating kinetic, biophysical and structural features may offer valuable insights in modeling immunogenicity. We further underscore the close inter-relationship of these two interconnected notions and the need to investigate each in the light of the other for a better understanding of T cell responsiveness for the effective clinical applications.
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Affiliation(s)
- Chloe H. Lee
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- MRC WIMM Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Mariolina Salio
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Giorgio Napolitani
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Graham Ogg
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Alison Simmons
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, United Kingdom
| | - Hashem Koohy
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- MRC WIMM Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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60
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Levinson M, Khass M, Burrows PD, Schroeder HW. Replacement of TCR Dβ With Immunoglobulin D H DSP2.3 Imposes a Tyrosine-Enriched TCR Repertoire and Adversely Affects T Cell Development. Front Immunol 2020; 11:573413. [PMID: 33133088 PMCID: PMC7550431 DOI: 10.3389/fimmu.2020.573413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/07/2020] [Indexed: 11/13/2022] Open
Abstract
Enrichment for tyrosine in immunoglobulin CDR-H3 is due in large part to natural selection of germline immunoglobulin DH sequence. We have previously shown that when DH sequence is modified to reduce the contribution of tyrosine codons, epitope recognition is altered and B cell development, antibody production, autoantibody production, and morbidity and mortality following pathogen challenge are adversely affected. TCRβ diversity (Dβ) gene segment sequences are even more highly conserved than DH, with trout Dβ1 identical to human and mouse Dβ1. We hypothesized that natural selection of Dβ sequence also shapes CDR-B3 diversity and influences T cell development and T cell function. To test this, we used a mouse strain that lacked Dβ2 and contained a novel Dβ1 allele (DβYTL) that replaces Dβ1 with an immunoglobulin DH, DSP2.3. Unlike Dβ1, wherein glycine predominates in all three reading frames (RFs), in DSP2.3 there is enrichment for tyrosine in RF1, threonine in RF2, and leucine in RF3. Mature T cells using DβYTL expressed TCRs enriched at particular CDR-B3 positions for tyrosine but depleted of leucine. Changing Dβ sequence altered thymocyte and peripheral T cell numbers and the T cell response to an ovalbumin immunodominant epitope. The differences in tyrosine content might explain, at least in part, why TCRs are more polyspecific and of lower affinity for their cognate antigens than their immunoglobulin counterparts.
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MESH Headings
- Animals
- Complementarity Determining Regions
- Genes, Immunoglobulin Heavy Chain
- Genes, T-Cell Receptor beta
- Immunization
- Immunodominant Epitopes
- Immunoglobulin Heavy Chains/genetics
- Immunoglobulin Heavy Chains/metabolism
- Lymphocyte Activation
- Mice, Inbred C57BL
- Mice, Knockout
- Ovalbumin/administration & dosage
- Ovalbumin/immunology
- Phenotype
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Thymocytes/immunology
- Thymocytes/metabolism
- Tyrosine
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Affiliation(s)
- Michael Levinson
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Mohamed Khass
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Division of Genetic Engineering and Biotechnology, National Research Center, Cairo, Egypt
| | - Peter D. Burrows
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Harry W. Schroeder
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
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61
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Crean RM, MacLachlan BJ, Madura F, Whalley T, Rizkallah PJ, Holland CJ, McMurran C, Harper S, Godkin A, Sewell AK, Pudney CR, van der Kamp MW, Cole DK. Molecular Rules Underpinning Enhanced Affinity Binding of Human T Cell Receptors Engineered for Immunotherapy. Mol Ther Oncolytics 2020; 18:443-456. [PMID: 32913893 PMCID: PMC7452143 DOI: 10.1016/j.omto.2020.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 07/27/2020] [Indexed: 10/25/2022] Open
Abstract
Immuno-oncology approaches that utilize T cell receptors (TCRs) are becoming highly attractive because of their potential to target virtually all cellular proteins, including cancer-specific epitopes, via the recognition of peptide-human leukocyte antigen (pHLA) complexes presented at the cell surface. However, because natural TCRs generally recognize cancer-derived pHLAs with very weak affinities, efforts have been made to enhance their binding strength, in some cases by several million-fold. In this study, we investigated the mechanisms underpinning human TCR affinity enhancement by comparing the crystal structures of engineered enhanced affinity TCRs with those of their wild-type progenitors. Additionally, we performed molecular dynamics simulations to better understand the energetic mechanisms driving the affinity enhancements. These data demonstrate that supra-physiological binding affinities can be achieved without altering native TCR-pHLA binding modes via relatively subtle modifications to the interface contacts, often driven through the addition of buried hydrophobic residues. Individual energetic components of the TCR-pHLA interaction governing affinity enhancements were distinct and highly variable for each TCR, often resulting from additive, or knock-on, effects beyond the mutated residues. This comprehensive analysis of affinity-enhanced TCRs has important implications for the future rational design of engineered TCRs as efficacious and safe drugs for cancer treatment.
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Affiliation(s)
- Rory M. Crean
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
- Doctoral Training Centre in Sustainable Chemical Technologies, University of Bath, Bath, BA2 7AY, UK
| | | | - Florian Madura
- Division of Infection & Immunity, Cardiff University, Cardiff, CF14 4XN, UK
| | - Thomas Whalley
- Division of Infection & Immunity, Cardiff University, Cardiff, CF14 4XN, UK
| | | | | | | | | | - Andrew Godkin
- Division of Infection & Immunity, Cardiff University, Cardiff, CF14 4XN, UK
| | - Andrew K. Sewell
- Division of Infection & Immunity, Cardiff University, Cardiff, CF14 4XN, UK
| | - Christopher R. Pudney
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
- Centre for Therapeutic Innovation, University of Bath, Bath, BA2 7AY, UK
| | - Marc W. van der Kamp
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, UK
| | - David K. Cole
- Division of Infection & Immunity, Cardiff University, Cardiff, CF14 4XN, UK
- Immunocore, Ltd., Abingdon, OX14 4RY, UK
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62
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Immune dysregulation in patients with RAG deficiency and other forms of combined immune deficiency. Blood 2020; 135:610-619. [PMID: 31942628 DOI: 10.1182/blood.2019000923] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/25/2019] [Indexed: 12/12/2022] Open
Abstract
Traditionally, primary immune deficiencies have been defined based on increased susceptibility to recurrent and/or severe infections. However, immune dysregulation, manifesting with autoimmunity or hyperinflammatory disease, has emerged as a common feature. This is especially true in patients affected by combined immune deficiency (CID), a group of disorders caused by genetic defects that impair, but do not completely abolish, T-cell function. Hypomorphic mutations in the recombination activating genes RAG1 and RAG2 represent the prototype of the broad spectrum of clinical and immunological phenotypes associated with CID. The study of patients with RAG deficiency and with other forms of CID has revealed distinct abnormalities in central and peripheral T- and B-cell tolerance as the key mechanisms involved in immune dysregulation. Understanding the pathophysiology of autoimmunity and hyperinflammation in these disorders may also permit more targeted therapeutic interventions.
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63
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Darrigues J, Santamaria JC, Galindo-Albarrán A, Robey EA, Joffre OP, van Meerwijk JPM, Romagnoli P. Robust intrathymic development of regulatory T cells in young NOD mice is rapidly restrained by recirculating cells. Eur J Immunol 2020; 51:580-593. [PMID: 32730634 DOI: 10.1002/eji.202048743] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/03/2020] [Accepted: 07/28/2020] [Indexed: 12/11/2022]
Abstract
Regulatory T lymphocytes (Treg) play a vital role in the protection of the organism against autoimmune pathology. It is therefore paradoxical that comparatively large numbers of Treg were found in the thymus of type I diabetes-prone NOD mice. The Treg population in the thymus is composed of newly developing cells and cells that had recirculated from the periphery back to the thymus. We here demonstrate that exceptionally large numbers of Treg develop in the thymus of young, but not adult, NOD mice. Once emigrated from the thymus, an unusually large proportion of these Treg is activated in the periphery, which causes a particularly abundant accumulation of recirculating Treg in the thymus. These cells then rapidly inhibit de novo development of Treg. The proportions of developing Treg thus reach levels similar to or lower than those found in most other, type 1 diabetes-resistant, inbred mouse strains. Thus, in adult NOD mice the particularly large Treg-niche is actually composed of mostly recirculating cells and only few newly developing Treg.
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Affiliation(s)
- Julie Darrigues
- Centre de Physiopathologie Toulouse Purpan (CPTP), Inserm U1043, CNRS UMR 5282, Université de Toulouse III (UPS), Toulouse, France
| | - Jeremy C Santamaria
- Centre de Physiopathologie Toulouse Purpan (CPTP), Inserm U1043, CNRS UMR 5282, Université de Toulouse III (UPS), Toulouse, France
| | - Ariel Galindo-Albarrán
- Centre de Physiopathologie Toulouse Purpan (CPTP), Inserm U1043, CNRS UMR 5282, Université de Toulouse III (UPS), Toulouse, France.,Station d'Ecologie Théorique et Expérimentale, CNRS, Moulis, France, Université Paul Sabatier, Moulis, France
| | - Ellen A Robey
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA
| | - Olivier P Joffre
- Centre de Physiopathologie Toulouse Purpan (CPTP), Inserm U1043, CNRS UMR 5282, Université de Toulouse III (UPS), Toulouse, France
| | - Joost P M van Meerwijk
- Centre de Physiopathologie Toulouse Purpan (CPTP), Inserm U1043, CNRS UMR 5282, Université de Toulouse III (UPS), Toulouse, France
| | - Paola Romagnoli
- Centre de Physiopathologie Toulouse Purpan (CPTP), Inserm U1043, CNRS UMR 5282, Université de Toulouse III (UPS), Toulouse, France
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64
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Gowthaman R, Pierce BG. TCR3d: The T cell receptor structural repertoire database. Bioinformatics 2020; 35:5323-5325. [PMID: 31240309 PMCID: PMC6954642 DOI: 10.1093/bioinformatics/btz517] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/31/2019] [Accepted: 06/20/2019] [Indexed: 12/31/2022] Open
Abstract
Summary T cell receptors (TCRs) are critical molecules of the adaptive immune system, capable of recognizing diverse antigens, including peptides, lipids and small molecules, and represent a rapidly growing class of therapeutics. Determining the structural and mechanistic basis of TCR targeting of antigens is a major challenge, as each individual has a vast and diverse repertoire of TCRs. Despite shared general recognition modes, diversity in TCR sequence and recognition represents a challenge to predictive modeling and computational techniques being developed to predict antigen specificity and mechanistic basis of TCR targeting. To this end, we have developed the TCR3d database, a resource containing all known TCR structures, with a particular focus on antigen recognition. TCR3d provides key information on antigen binding mode, interface features, loop sequences and germline gene usage. Users can interactively view TCR complex structures, search sequences of interest against known structures and sequences, and download curated datasets of structurally characterized TCR complexes. This database is updated on a weekly basis, and can serve the community as a centralized resource for those studying T cell receptors and their recognition. Availability and implementation The TCR3d database is available at https://tcr3d.ibbr.umd.edu/.
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Affiliation(s)
- Ragul Gowthaman
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA.,University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | - Brian G Pierce
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA.,University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
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65
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Gonçalves P, El Daker S, Vasseur F, Serafini N, Lim A, Azogui O, Decaluwe H, Guy-Grand D, Freitas AA, Di Santo JP, Rocha B. Microbiota stimulation generates LCMV-specific memory CD8 + T cells in SPF mice and determines their TCR repertoire during LCMV infection. Mol Immunol 2020; 124:125-141. [PMID: 32563081 DOI: 10.1016/j.molimm.2020.05.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/16/2020] [Accepted: 05/11/2020] [Indexed: 12/15/2022]
Abstract
Both mouse and human harbour memory phenotype CD8+ T cells specific for antigens in hosts that have not been previously exposed to these antigens. The origin and the nature of the stimuli responsible for generation of CD44hi CD8+ T cells in specific pathogen-free (SPF) mice remain controversial. It is known that microbiota plays a crucial role in the prevention and resolution of systemic infections by influencing myelopoiesis, regulating dendritic cells, inflammasome activation and promoting the production of type I and II interferons. By contrast, here we suggest that microbiota has a direct effect on generation of memory phenotype CD44hiGP33+CD8+ T cells. In SPF mice, it generates a novel GP33+CD44hiCD8+ T cell sub-population associating the properties of innate and genuine memory cells. These cells are highly enriched in the bone marrow, proliferate rapidly and express immediate effector functions. They dominate the response to LCMV and express particular TCRβ chains. The sequence of these selected TCRβ chains overlaps with that of GP33+CD8+ T cells directly selected by microbiota in the gut epithelium of SPF mice, demonstrating a common selection mechanism in gut and peripheral CD8+ T cell pool. Therefore microbiota has a direct role in priming T cell immunity in SPF mice and in the selection of TCRβ repertoires during systemic infection. We identify a mechanism that primes T cell immunity in SPF mice and may have a major role in colonization resistance and protection from infection.
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Affiliation(s)
- Pedro Gonçalves
- Population Biology Unit, CNRS URA 196, Institut Pasteur, Paris 75015, France; INSERM, U1151, CNRS, UMR8253, Institut Necker Enfants Malades, Université Paris Descartes, Paris 75015, France; Innate Immunity Unit, INSERM, U668, Institut Pasteur, Paris 75015, France.
| | - Sary El Daker
- Population Biology Unit, CNRS URA 196, Institut Pasteur, Paris 75015, France
| | - Florence Vasseur
- INSERM, U1151, CNRS, UMR8253, Institut Necker Enfants Malades, Université Paris Descartes, Paris 75015, France
| | - Nicolas Serafini
- Innate Immunity Unit, INSERM, U668, Institut Pasteur, Paris 75015, France; INSERM U1223, Paris 75015, France
| | | | - Orly Azogui
- INSERM, U1151, CNRS, UMR8253, Institut Necker Enfants Malades, Université Paris Descartes, Paris 75015, France
| | - Helene Decaluwe
- Population Biology Unit, CNRS URA 196, Institut Pasteur, Paris 75015, France
| | - Delphine Guy-Grand
- INSERM U1223, Paris 75015, France; Lymphopoiesis Unit, INSERM U668, University Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Institut Pasteur, Paris 75015, France
| | - Antonio A Freitas
- Population Biology Unit, CNRS URA 196, Institut Pasteur, Paris 75015, France
| | - James P Di Santo
- Innate Immunity Unit, INSERM, U668, Institut Pasteur, Paris 75015, France; INSERM U1223, Paris 75015, France
| | - Benedita Rocha
- Population Biology Unit, CNRS URA 196, Institut Pasteur, Paris 75015, France; INSERM, U1151, CNRS, UMR8253, Institut Necker Enfants Malades, Université Paris Descartes, Paris 75015, France.
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66
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MHC-II alleles shape the CDR3 repertoires of conventional and regulatory naïve CD4 + T cells. Proc Natl Acad Sci U S A 2020; 117:13659-13669. [PMID: 32482872 DOI: 10.1073/pnas.2003170117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
T cell maturation and activation depend upon T cell receptor (TCR) interactions with a wide variety of antigenic peptides displayed in a given major histocompatibility complex (MHC) context. Complementarity-determining region 3 (CDR3) is the most variable part of the TCRα and -β chains, which govern interactions with peptide-MHC complexes. However, it remains unclear how the CDR3 landscape is shaped by individual MHC context during thymic selection of naïve T cells. We established two mouse strains carrying distinct allelic variants of H2-A and analyzed thymic and peripheral production and TCR repertoires of naïve conventional CD4+ T (Tconv) and naïve regulatory CD4+ T (Treg) cells. Compared with tuberculosis-resistant C57BL/6 (H2-Ab) mice, the tuberculosis-susceptible H2-Aj mice had fewer CD4+ T cells of both subsets in the thymus. In the periphery, this deficiency was only apparent for Tconv and was compensated for by peripheral reconstitution for Treg We show that H2-Aj favors selection of a narrower and more convergent repertoire with more hydrophobic and strongly interacting amino acid residues in the middle of CDR3α and CDR3β, suggesting more stringent selection against a narrower peptide-MHC-II context. H2-Aj and H2-Ab mice have prominent reciprocal differences in CDR3α and CDR3β features, probably reflecting distinct modes of TCR fitting to MHC-II variants. These data reveal the mechanics and extent of how MHC-II shapes the naïve CD4+ T cell CDR3 landscape, which essentially defines adaptive response to infections and self-antigens.
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67
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Gao A, Chen Z, Segal FP, Carrington M, Streeck H, Chakraborty AK, Julg B. Predicting the Immunogenicity of T cell epitopes: From HIV to SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.05.14.095885. [PMID: 32511339 PMCID: PMC7241102 DOI: 10.1101/2020.05.14.095885] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We describe a physics-based learning model for predicting the immunogenicity of Cytotoxic T Lymphocyte (CTL) epitopes derived from diverse pathogens, given a Human Leukocyte Antigen (HLA) genotype. The model was trained and tested on experimental data on the relative immunodominance of CTL epitopes in Human Immunodeficiency Virus infection. The method is more accurate than publicly available models. Our model predicts that only a fraction of SARS-CoV-2 epitopes that have been predicted to bind to HLA molecules is immunogenic. The immunogenic CTL epitopes across all SARS-CoV-2 proteins are predicted to provide broad population coverage, but the immunogenic epitopes in the SARS-CoV-2 spike protein alone are unlikely to do so. Our model predicts that several immunogenic SARS-CoV-2 CTL epitopes are identical to those contained in low-pathogenicity coronaviruses circulating in the population. Thus, we suggest that some level of CTL immunity against COVID-19 may be present in some individuals prior to SARS-CoV-2 infection.
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Affiliation(s)
- Ang Gao
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology Cambridge, MA 02139, USA
| | - Zhilin Chen
- Ragon Insitute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA 02139, USA
| | | | - Mary Carrington
- Ragon Insitute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA 02139, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Hendrik Streeck
- Institut für Virologie, Universitätsklinikum Bonn, 53127 Bonn, Germany
| | - Arup K. Chakraborty
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Insitute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology Cambridge, MA 02139, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Boris Julg
- Ragon Insitute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA 02139, USA
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68
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Spidale NA, Malhotra N, Frascoli M, Sylvia K, Miu B, Freeman C, Stadinski BD, Huseby E, Kang J. Neonatal-derived IL-17 producing dermal γδ T cells are required to prevent spontaneous atopic dermatitis. eLife 2020; 9:e51188. [PMID: 32065580 PMCID: PMC7025821 DOI: 10.7554/elife.51188] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 02/11/2020] [Indexed: 01/01/2023] Open
Abstract
Atopic Dermatitis (AD) is a T cell-mediated chronic skin disease and is associated with altered skin barrier integrity. Infants with mutations in genes involved in tissue barrier fitness are predisposed towards inflammatory diseases, but most do not develop or sustain the diseases, suggesting that there exist regulatory immune mechanisms to prevent aberrant inflammation. The absence of one single murine dermal cell type, the innate neonatal-derived IL-17 producing γδ T (Tγδ17) cells, from birth resulted in spontaneous, highly penetrant AD with many of the major hallmarks of human AD. In Tγδ17 cell-deficient mice, basal keratinocyte transcriptome was altered months in advance of AD induction. Tγδ17 cells respond to skin commensal bacteria and the fulminant disease in their absence was driven by skin commensal bacteria dysbiosis. AD in this model was characterized by highly expanded dermal αβ T clonotypes that produce the type three cytokines, IL-17 and IL-22. These results demonstrate that neonatal Tγδ17 cells are innate skin regulatory T cells that are critical for skin homeostasis, and that IL-17 has dual homeostatic and inflammatory function in the skin.
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MESH Headings
- Animals
- Animals, Newborn
- Autoantigens/genetics
- Cell Differentiation
- Dermatitis, Atopic/genetics
- Dermatitis, Atopic/immunology
- Dermatitis, Atopic/prevention & control
- Disease Models, Animal
- Gene Expression
- Interleukin-17/biosynthesis
- Interleukins/biosynthesis
- Keratinocytes/cytology
- Keratinocytes/metabolism
- Lymphocyte Activation
- Mice
- Mice, Knockout
- Receptors, Antigen, T-Cell, gamma-delta/immunology
- Receptors, Antigen, T-Cell, gamma-delta/metabolism
- Skin/metabolism
- Skin/microbiology
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Interleukin-22
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Affiliation(s)
- Nicholas A Spidale
- Department of PathologyUniversity of Massachusetts Medical SchoolWorcesterUnited States
| | - Nidhi Malhotra
- Department of PathologyUniversity of Massachusetts Medical SchoolWorcesterUnited States
| | - Michela Frascoli
- Department of PathologyUniversity of Massachusetts Medical SchoolWorcesterUnited States
| | - Katelyn Sylvia
- Department of PathologyUniversity of Massachusetts Medical SchoolWorcesterUnited States
| | - Bing Miu
- Department of PathologyUniversity of Massachusetts Medical SchoolWorcesterUnited States
| | - Coral Freeman
- Department of PathologyUniversity of Massachusetts Medical SchoolWorcesterUnited States
| | - Brian D Stadinski
- Department of PathologyUniversity of Massachusetts Medical SchoolWorcesterUnited States
| | - Eric Huseby
- Department of PathologyUniversity of Massachusetts Medical SchoolWorcesterUnited States
| | - Joonsoo Kang
- Department of PathologyUniversity of Massachusetts Medical SchoolWorcesterUnited States
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69
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Ko A, Watanabe M, Nguyen T, Shi A, Achour A, Zhang B, Sun X, Wang Q, Zhuang Y, Weng NP, Hodes RJ. TCR Repertoires of Thymic Conventional and Regulatory T Cells: Identification and Characterization of Both Unique and Shared TCR Sequences. THE JOURNAL OF IMMUNOLOGY 2020; 204:858-867. [PMID: 31924652 DOI: 10.4049/jimmunol.1901006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/10/2019] [Indexed: 11/19/2022]
Abstract
Thymic regulatory T cells (tTreg) are critical in the maintenance of normal T cell immunity and tolerance. The role of TCR in tTreg selection remains incompletely understood. In this study, we assessed TCRα and TCRβ sequences of mouse tTreg and thymic conventional CD4+ T cells (Tconv) by high-throughput sequencing. We identified αβ TCR sequences that were unique to either tTreg or Tconv and found that these were distinct as recognized by machine learning algorithm and by preferentially used amino acid trimers in αβ CDR3 of tTreg. In addition, a proportion of αβ TCR sequences expressed by tTreg were also found in Tconv, and machine learning classified the great majority of these shared αβ TCR sequences as characteristic of Tconv and not tTreg. These findings identify two populations of tTreg, one in which the regulatory T cell fate is associated with unique properties of the TCR and another with TCR properties characteristic of Tconv for which tTreg fate is determined by factors beyond TCR sequence.
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Affiliation(s)
- Annette Ko
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Bethesda, MD 21224
| | - Masashi Watanabe
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Thomas Nguyen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Bethesda, MD 21224
| | - Alvin Shi
- Department of Systems and Computational Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; and
| | - Achouak Achour
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Bethesda, MD 21224
| | - Baojun Zhang
- Department of Immunology, Duke University, Durham, NC 27710
| | - Xiaoping Sun
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Bethesda, MD 21224
| | - Qun Wang
- Department of Immunology, Duke University, Durham, NC 27710
| | - Yuan Zhuang
- Department of Immunology, Duke University, Durham, NC 27710
| | - Nan-Ping Weng
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Bethesda, MD 21224;
| | - Richard J Hodes
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892;
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70
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Werner L, Lee YN, Rechavi E, Lev A, Yerushalmi B, Ling G, Shah N, Uhlig HH, Weiss B, Somech R, Snapper SB, Shouval DS. Alterations in T and B Cell Receptor Repertoires Patterns in Patients With IL10 Signaling Defects and History of Infantile-Onset IBD. Front Immunol 2020; 11:109. [PMID: 32117262 PMCID: PMC7017840 DOI: 10.3389/fimmu.2020.00109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/15/2020] [Indexed: 01/04/2023] Open
Abstract
Patients with loss-of-function mutations in IL10 or IL10 receptor (IL10R) genes develop severe, medical-refractory, infantile-onset inflammatory bowel disease (IBD). We have previously reported significant alterations in innate and adaptive immune responses in these patients. Next generation sequencing platforms enable a comprehensive assessment of T cell receptor (TCR) and B cell receptor (BCR) repertoire patterns. We aimed to characterize TCR and BCR features in peripheral blood of patients with deleterious IL10 signaling defects. DNA was isolated from blood of seven patients with IL10R mutations and one with an IL10 mutation, along with eight controls, and subjected to next generation sequencing of TRB and IgH loci. A significant increase in clonality was observed in both TCR and BCR repertoires in circulating lymphocytes of IL10/IL10R-deficient patients, but to a much greater extent in T cells. Furthermore, short CDR3β length and altered hydrophobicity were demonstrated in T cells of patients, but not in B cells, secondary to lower rates of insertions of nucleotides, but not deletions, at the V-, D-, or J-junctions. We were unable to observe specific T or B clones that were limited only to the patients or among controls. Moreover, the expanded T cells clones were unique to each patient. In conclusion, next generation sequencing of the TCR and BCR is a powerful tool for characterizing the adaptive immune cell phenotype and function in immune-mediated disorders. The oligoclonality observed among IL10/IL10R-deficient patients may suggest specialization of unique clones that likely have a role in mediating tissue damage. Nevertheless, the lack of shared clones between patients provides another piece of evidence that the adaptive immune response in IBD is not triggered against common antigens. Additional studies are required to define the specific antigens that interact with the expanded IL10/IL10R-deficient clones.
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Affiliation(s)
- Lael Werner
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yu Nee Lee
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel
| | - Erez Rechavi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel
| | - Atar Lev
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel
| | - Baruch Yerushalmi
- Pediatric Gastroenterology Unit, Soroka University Medical Center, Ben Gurion University of the Negev, Be'er Sheva, Israel
| | - Galina Ling
- Pediatric Gastroenterology Unit, Soroka University Medical Center, Ben Gurion University of the Negev, Be'er Sheva, Israel
| | - Neil Shah
- Department of Gastroenterology, Great Ormond Street Hospital, London, United Kingdom
| | - Holm H Uhlig
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom.,Department of Pediatrics, University of Oxford, Oxford, United Kingdom.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Batia Weiss
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Raz Somech
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Dror S Shouval
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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71
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Tanno H, Gould TM, McDaniel JR, Cao W, Tanno Y, Durrett RE, Park D, Cate SJ, Hildebrand WH, Dekker CL, Tian L, Weyand CM, Georgiou G, Goronzy JJ. Determinants governing T cell receptor α/β-chain pairing in repertoire formation of identical twins. Proc Natl Acad Sci U S A 2020; 117:532-540. [PMID: 31879353 PMCID: PMC6955297 DOI: 10.1073/pnas.1915008117] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The T cell repertoire in each individual includes T cell receptors (TCRs) of enormous sequence diversity through the pairing of diverse TCR α- and β-chains, each generated by somatic recombination of paralogous gene segments. Whether the TCR repertoire contributes to susceptibility to infectious or autoimmune diseases in concert with disease-associated major histocompatibility complex (MHC) polymorphisms is unknown. Due to a lack in high-throughput technologies to sequence TCR α-β pairs, current studies on whether the TCR repertoire is shaped by host genetics have so far relied only on single-chain analysis. Using a high-throughput single T cell sequencing technology, we obtained the largest paired TCRαβ dataset so far, comprising 965,523 clonotypes from 15 healthy individuals including 6 monozygotic twin pairs. Public TCR α- and, to a lesser extent, TCR β-chain sequences were common in all individuals. In contrast, sharing of entirely identical TCRαβ amino acid sequences was very infrequent in unrelated individuals, but highly increased in twins, in particular in CD4 memory T cells. Based on nucleotide sequence identity, a subset of these shared clonotypes appeared to be the progeny of T cells that had been generated during fetal development and had persisted for more than 50 y. Additional shared TCRαβ in twins were encoded by different nucleotide sequences, implying that genetic determinants impose structural constraints on thymic selection that favor the selection of TCR α-β pairs with entire sequence identities.
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Affiliation(s)
- Hidetaka Tanno
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
| | - Timothy M Gould
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA 94304
| | - Jonathan R McDaniel
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712
| | - Wenqiang Cao
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA 94304
| | - Yuri Tanno
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712
| | - Russell E Durrett
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712
| | - Daechan Park
- Department of Life Sciences, Ajou University, Suwon 16499, South Korea
| | - Steven J Cate
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - William H Hildebrand
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
| | - Cornelia L Dekker
- Department of Pediatrics (Infectious Diseases), Stanford University School of Medicine, Stanford, CA 94305
| | - Lu Tian
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305
| | - Cornelia M Weyand
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA 94304
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712;
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712
| | - Jörg J Goronzy
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305;
- Department of Medicine, Palo Alto Veterans Administration Healthcare System, Palo Alto, CA 94304
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72
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De Simone G, Mazza EMC, Cassotta A, Davydov AN, Kuka M, Zanon V, De Paoli F, Scamardella E, Metsger M, Roberto A, Pilipow K, Colombo FS, Tenedini E, Tagliafico E, Gattinoni L, Mavilio D, Peano C, Price DA, Singh SP, Farber JM, Serra V, Cucca F, Ferrari F, Orrù V, Fiorillo E, Iannacone M, Chudakov DM, Sallusto F, Lugli E. CXCR3 Identifies Human Naive CD8 + T Cells with Enhanced Effector Differentiation Potential. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2019; 203:3179-3189. [PMID: 31740485 PMCID: PMC6900484 DOI: 10.4049/jimmunol.1901072] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 10/16/2019] [Indexed: 01/19/2023]
Abstract
In mice, the ability of naive T (TN) cells to mount an effector response correlates with TCR sensitivity for self-derived Ags, which can be quantified indirectly by measuring surface expression levels of CD5. Equivalent findings have not been reported previously in humans. We identified two discrete subsets of human CD8+ TN cells, defined by the absence or presence of the chemokine receptor CXCR3. The more abundant CXCR3+ TN cell subset displayed an effector-like transcriptional profile and expressed TCRs with physicochemical characteristics indicative of enhanced interactions with peptide-HLA class I Ags. Moreover, CXCR3+ TN cells frequently produced IL-2 and TNF in response to nonspecific activation directly ex vivo and differentiated readily into Ag-specific effector cells in vitro. Comparative analyses further revealed that human CXCR3+ TN cells were transcriptionally equivalent to murine CXCR3+ TN cells, which expressed high levels of CD5. These findings provide support for the notion that effector differentiation is shaped by heterogeneity in the preimmune repertoire of human CD8+ T cells.
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Affiliation(s)
- Gabriele De Simone
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
| | - Emilia M C Mazza
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
| | - Antonino Cassotta
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - Alexey N Davydov
- Central European Institute of Technology, 621 00 Brno, Czech Republic
| | - Mirela Kuka
- Division of Immunology, Transplantation and Infectious Diseases and Experimental Imaging Center, IRCCS, San Raffaele Scientific Institute and Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Veronica Zanon
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
| | - Federica De Paoli
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
| | - Eloise Scamardella
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
| | - Maria Metsger
- Central European Institute of Technology, 621 00 Brno, Czech Republic
| | - Alessandra Roberto
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
| | - Karolina Pilipow
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
| | - Federico S Colombo
- Humanitas Flow Cytometry Core, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
| | - Elena Tenedini
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Enrico Tagliafico
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Luca Gattinoni
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
- Regensburg Center for Interventional Immunology, University Regensburg and University Hospital Regensburg, 93053 Regensburg, Germany
| | - Domenico Mavilio
- Unit of Clinical and Experimental Immunology, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, 20122 Milan, Italy
| | - Clelia Peano
- Division of Genetic and Biomedical Research, UoS Milan, National Research Council, 20089 Rozzano, Milan, Italy
- Genomic Unit, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, United Kingdom
- Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff CF14 4XN, United Kingdom
| | - Satya P Singh
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Joshua M Farber
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | | | | | | | - Valeria Orrù
- IRGB, National Research Council, 09042 Monserrato, Italy
| | | | - Matteo Iannacone
- Division of Immunology, Transplantation and Infectious Diseases and Experimental Imaging Center, IRCCS, San Raffaele Scientific Institute and Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Dmitriy M Chudakov
- Central European Institute of Technology, 621 00 Brno, Czech Republic
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; and
- Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Federica Sallusto
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, USI, 6500 Bellinzona, Switzerland
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - Enrico Lugli
- Laboratory of Translational Immunology, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy;
- Humanitas Flow Cytometry Core, Humanitas Clinical and Research Center, 20089 Rozzano, Milan, Italy
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73
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Ritmahan W, Kesmir C, Vroomans RMA. Revealing factors determining immunodominant responses against dominant epitopes. Immunogenetics 2019; 72:109-118. [PMID: 31811313 PMCID: PMC6971151 DOI: 10.1007/s00251-019-01134-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 10/04/2019] [Indexed: 12/20/2022]
Abstract
Upon recognition of peptide-MHC complexes by T cell receptors (TCR), the cognate T cells expand and differentiate into effector T cells to generate protective immunity. Despite the fact that any immune response generates a diverse set of TCR clones against a particular epitope, only a few clones are highly expanded in any immune response. Previous studies observed that the highest frequency clones usually control viral infections better than subdominant clones, but the reasons for this dominance among T cell clones are still unclear. Here, we used publicly available TCR amino acid sequences to study which factors determine whether a response becomes immunodominance (ID) per donor; we classified the largest T cell clone as the epitope-specific dominant clone and all the other clones as subdominant responses (SD). We observed a distinctively hydrophobic CDR3 in ID responses against a dominant epitope from influenza A virus, compared to the SD responses. The common V-J combinations were shared between ID and SD responses, suggesting that the biased V-J recombination events are restricted by epitope specificity; thus, the immunodominance is not directly determined by a bias combination of V and J genetic segments. Our findings reveal a close similarity of global sequence properties between dominant and subdominant clones of epitope-specific responses but detectable distinctive amino acid enrichments in ID. Taken together, we believe this first comparative study of immunodominant and subdominant TCR sequences can guide further studies to resolve factors determining the immunodominance of antiviral as well as tumor-specific T cell responses.
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Affiliation(s)
- Wannisa Ritmahan
- The Centre for Integrative Bioinformatics VU, Vrije Universiteit, Amsterdam, The Netherlands. .,Theoretical Biology, Utrecht University, Utrecht, The Netherlands.
| | - Can Kesmir
- Theoretical Biology, Utrecht University, Utrecht, The Netherlands
| | - Renske M A Vroomans
- Theoretical Biology, Utrecht University, Utrecht, The Netherlands.,Institute for Advanced Study, University of Amsterdam, Amsterdam, The Netherlands
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74
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Bertoli D, Sottini A, Capra R, Scarpazza C, Bresciani R, Notarangelo LD, Imberti L. Lack of specific T- and B-cell clonal expansions in multiple sclerosis patients with progressive multifocal leukoencephalopathy. Sci Rep 2019; 9:16605. [PMID: 31719595 PMCID: PMC6851145 DOI: 10.1038/s41598-019-53010-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 10/26/2019] [Indexed: 01/11/2023] Open
Abstract
Progressive multifocal leukoencephalopathy (PML) is a rare, potentially devastating myelin-degrading disease caused by the JC virus. PML occurs preferentially in patients with compromised immune system, but has been also observed in multiple sclerosis (MS) patients treated with disease-modifying drugs. We characterized T and B cells in 5 MS patients that developed PML, 4 during natalizumab therapy and one after alemtuzumab treatment, and in treated patients who did not develop the disease. Results revealed that: i) thymic and bone marrow output was impaired in 4 out 5 patients at the time of PML development; ii) T-cell repertoire was restricted; iii) clonally expanded T cells were present in all patients. However, common usage or pairings of T-cell receptor beta variable or joining genes, specific clonotypes or obvious “public” T-cell response were not detected at the moment of PML onset. Similarly, common restrictions were not found in the immunoglobulin heavy chain repertoire. The data indicate that no JCV-related specific T- and B-cell expansions were mounted at the time of PML. The current results enhance our understanding of JC virus infection and PML, and should be taken into account when choosing targeted therapies.
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Affiliation(s)
- Diego Bertoli
- Centro di Ricerca Emato-oncologica AIL (CREA), Diagnostic Department, ASST Spedali Civili, Brescia, Italy.,Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Alessandra Sottini
- Centro di Ricerca Emato-oncologica AIL (CREA), Diagnostic Department, ASST Spedali Civili, Brescia, Italy
| | - Ruggero Capra
- Multiple Sclerosis Center, ASST Spedali Civili, Brescia, Italy
| | - Cristina Scarpazza
- Multiple Sclerosis Center, ASST Spedali Civili, Brescia, Italy.,Department of General Psychology, University of Padova, Padova, Italy
| | - Roberto Bresciani
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Luisa Imberti
- Centro di Ricerca Emato-oncologica AIL (CREA), Diagnostic Department, ASST Spedali Civili, Brescia, Italy.
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75
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Abstract
The repertoire of αβ T cell antigen receptors (TCRs) on mature T cells is selected in the thymus where it is rendered both self-tolerant and restricted to the recognition of major histocompatibility complex molecules presenting peptide antigens (pMHC). It remains unclear whether germline TCR sequences exhibit an inherent bias to interact with pMHC prior to selection. Here, we isolated TCR libraries from unselected thymocytes and upon reexpression of these random TCR repertoires in recipient T cell hybridomas, interrogated their reactivities to antigen-presenting cell lines. While these random TCR combinations could potentially have reacted with any surface molecule on the cell lines, the hybridomas were stimulated most frequently by pMHC ligands. The nature and CDR3 loop composition of the TCRβ chain played a dominant role in determining pMHC-reactivity. Replacing the germline regions of mouse TCRβ chains with those of other jawed vertebrates preserved reactivity to mouse pMHC. Finally, introducing the CD4 coreceptor into the hybridomas increased the proportion of cells that could respond to pMHC ligands. Thus, αβ TCRs display an intrinsic and evolutionary conserved bias for pMHC molecules in the absence of any selective pressure, which is further strengthened in the presence of coreceptors.
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76
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Abstract
Given the many cell types and molecular components of the human immune system, along with vast variations across individuals, how should we go about developing causal and predictive explanations of immunity? A central strategy in human studies is to leverage natural variation to find relationships among variables, including DNA variants, epigenetic states, immune phenotypes, clinical descriptors, and others. Here, we focus on how natural variation is used to find patterns, infer principles, and develop predictive models for two areas: (a) immune cell activation-how single-cell profiling boosts our ability to discover immune cell types and states-and (b) antigen presentation and recognition-how models can be generated to predict presentation of antigens on MHC molecules and their detection by T cell receptors. These are two examples of a shift in how we find the drivers and targets of immunity, especially in the human system in the context of health and disease.
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Affiliation(s)
- Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02129, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA;
| | - Siranush Sarkizova
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA; .,Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02142, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Harvard Medical School, Boston, Massachusetts 02115, USA; .,Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
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77
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A temporal thymic selection switch and ligand binding kinetics constrain neonatal Foxp3 + T reg cell development. Nat Immunol 2019; 20:1046-1058. [PMID: 31209405 DOI: 10.1038/s41590-019-0414-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 04/29/2019] [Indexed: 12/21/2022]
Abstract
The neonatal thymus generates Foxp3+ regulatory T (tTreg) cells that are critical in controlling immune homeostasis and preventing multiorgan autoimmunity. The role of antigen specificity on neonatal tTreg cell selection is unresolved. Here we identify 17 self-peptides recognized by neonatal tTreg cells, and reveal ligand specificity patterns that include self-antigens presented in an age- and inflammation-dependent manner. Fate-mapping studies of neonatal peptidyl arginine deiminase type IV (Padi4)-specific thymocytes reveal disparate fate choices. Neonatal thymocytes expressing T cell receptors that engage IAb-Padi4 with moderate dwell times within a conventional docking orientation are exported as tTreg cells. In contrast, Padi4-specific T cell receptors with short dwell times are expressed on CD4+ T cells, while long dwell times induce negative selection. Temporally, Padi4-specific thymocytes are subject to a developmental stage-specific change in negative selection, which precludes tTreg cell development. Thus, a temporal switch in negative selection and ligand binding kinetics constrains the neonatal tTreg selection window.
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78
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Ruscher R, Hogquist KA. Development, ontogeny, and maintenance of TCRαβ + CD8αα IEL. Curr Opin Immunol 2019; 58:83-88. [PMID: 31146182 DOI: 10.1016/j.coi.2019.04.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 04/19/2019] [Indexed: 02/07/2023]
Abstract
The intestinal epithelium is the outermost cellular layer that separates the body from the gut lumen. The integrity of this protective mucosal barrier is crucial and maintained by specialized cells-intraepithelial lymphocytes (IEL). Much research has been conducted on these cells and our overall understanding of them is increasing rapidly. In this review we focus on the TCRαβ+ subset of CD8αα IEL. We discuss recent studies that shed light on the development, ontogeny, maintenance, and functional characteristics of CD8αα IEL, and highlight yet unanswered questions for future studies.
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Affiliation(s)
- Roland Ruscher
- Center for Immunology and Department of Laboratory Medicine & Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Kristin A Hogquist
- Center for Immunology and Department of Laboratory Medicine & Pathology, University of Minnesota, Minneapolis, MN, USA.
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79
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La Cava A. Human T cell repertoire: what happens in thymus does not stay in thymus. J Clin Invest 2019; 129:2195-2197. [PMID: 31081801 DOI: 10.1172/jci128371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The T cell receptor (TCR) repertoire is diverse, thus allowing recognition of a wide range of pathogens by T cells. In humans, the study of the formation of TCR repertoires is problematic because of the difficulty in performing investigations in vivo. In this issue of the JCI, Khosravi-Maharlooei and colleagues describe a new humanized mouse model that allows direct investigations on this topic. Using high-throughput and single-cell TCR-complementarity-determining region 3 β (TCR-CDR3β) sequencing, the authors were able to demonstrate that human thymic selection is a major driver of TCR sequence sharing, also implicating a preferential selection of shared cross-reactive CDR3βs during repertoire formation.
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80
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Hou X, Yang Y, Chen J, Jia H, Zeng P, Lv L, Lu Y, Liu X, Diao H. TCRβ repertoire of memory T cell reveals potential role for Escherichia coli in the pathogenesis of primary biliary cholangitis. Liver Int 2019; 39:956-966. [PMID: 30721553 DOI: 10.1111/liv.14066] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/19/2018] [Accepted: 11/28/2018] [Indexed: 12/24/2022]
Abstract
BACKGROUND Primary biliary cholangitis (PBC) is an organ-specific, T cell-mediated autoimmune disease which is characterized by the breakdown of self-tolerance to the highly conserved pyruvate dehydrogenase complex, especially the pyruvate dehydrogenase E2 complex (PDC-E2). However, the molecular mechanism of breakdown of self-tolerance is still unclear. METHODS A combination of multiplex-PCR and immune repertoire sequencing (IR-seq) was used for a standardized analysis of memory T cell receptor (TCR) β-chain repertoire of PBC patient and healthy volunteers. In vitro induction and expansion of human PDC-E2163-176 (human PDC-E2)-specific T cells and E coli PDC-E231-44/134-147/235-248 (E coli PDC-E2)-specific T cells, and identified the human (and E coli) PDC-E2-specific TCRβ repertoire by IR-seq. RESULTS Primary biliary cholangitis patients have shorter complementarity-determining region 3s (CDR3s), and higher degree of sequence overlap in the TCRβ repertoire of memory T cell. Moreover, altered insertion patterns and skewed TRBV segment usage were observed in PBC patients. With regard to the pathogenesis, the concentration of E coli was higher in PBC patients' faecal. The frequency of E coli (and human)-specific TCRs was higher in the memory TCRβ repertoire of PBC patients compared with healthy controls. Importantly, the TCRβ repertoire characteristics were almost identical between E coli PDC-E2-related TCRs and human PDC-E2-related TCRs, including the patterns of TRBV usage, CDR3 length and amino acid composition. CONCLUSION Our findings comprehensively revealed the TCRβ repertoire characterization of PBC patients, and provided a TCR molecular basis to understand the mechanism of cross-recognition between human PDC-E2 and E coli PDC-E2, and the imbalance of immune tolerance in PBC.
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Affiliation(s)
- Xianliang Hou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yida Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jianing Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Hongyu Jia
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ping Zeng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Longxian Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yingfeng Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xiangdong Liu
- College of Materials and Textile, Zhejiang Sci-Tech University, Xiasha Higher Education Zone, Hangzhou, China
| | - Hongyan Diao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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81
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Daley SR, Koay HF, Dobbs K, Bosticardo M, Wirasinha RC, Pala F, Castagnoli R, Rowe JH, Ott de Bruin LM, Keles S, Lee YN, Somech R, Holland SM, Delmonte OM, Draper D, Maxwell S, Niemela J, Stoddard J, Rosenzweig SD, Poliani PL, Capo V, Villa A, Godfrey DI, Notarangelo LD. Cysteine and hydrophobic residues in CDR3 serve as distinct T-cell self-reactivity indices. J Allergy Clin Immunol 2019; 144:333-336. [PMID: 31053347 DOI: 10.1016/j.jaci.2019.03.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Stephen R Daley
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia.
| | - Hui-Fern Koay
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, Australia
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Rushika C Wirasinha
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Francesca Pala
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Riccardo Castagnoli
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Jared H Rowe
- Division of Hematology-Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, Mass
| | - Lisa M Ott de Bruin
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, Mass
| | - Sevgi Keles
- Division of Pediatric Immunology and Allergy, Meram Medical Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Yu Nee Lee
- Immunology Service, Edmond and Lily Safra Children's Hospital Sheba Medical Center, Tel Hashomer, Israel
| | - Raz Somech
- Immunology Service, Edmond and Lily Safra Children's Hospital Sheba Medical Center, Tel Hashomer, Israel
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Debbie Draper
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Sandra Maxwell
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Julie Niemela
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Md
| | - Jennifer Stoddard
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Md
| | - Sergio D Rosenzweig
- Immunology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Md
| | - Pietro Luigi Poliani
- Department of Molecular and Translational Medicine, Pathology Unit, University of Brescia, Brescia, Italy
| | - Valentina Capo
- San Raffaele Telethon Institute for Gene Therapy, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Anna Villa
- San Raffaele Telethon Institute for Gene Therapy, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy; Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Milan Unit, Milan, Italy
| | - Dale I Godfrey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, Australia
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
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82
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Deletion of self-reactive CCR7- thymocytes in the absence of MHC expression on thymic epithelial cells. Cell Death Differ 2019; 26:2727-2739. [PMID: 31019259 DOI: 10.1038/s41418-019-0331-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 03/18/2019] [Accepted: 04/05/2019] [Indexed: 12/11/2022] Open
Abstract
The selection of αβ T cells in the thymus is punctuated by checkpoints at which thymocytes differentiate or undergo apoptosis. Wave 1 deletion is defined as apoptosis within nascent αβ T-cell antigen receptor (TCR)-signalled thymocytes that lack CCR7 expression. The antigen-presenting cell (APC) types that mediate wave 1 deletion are unclear. To measure wave 1 deletion, we compared the frequencies of TCRβ + CD5 + Helios + CCR7- cells in nascent thymocyte cohorts in mice with normal or defective apoptosis. This thymocyte population is small in mice lacking major histocompatibility complex (MHC) expression. The scale of wave 1 deletion was increased by transgenic expression of the self-reactive Yae62 TCRβ chain, was almost halved when haemopoietic APCs lacked MHC expression and, surprisingly, was unchanged when epithelial cells lacked MHC expression. These findings demonstrate efficiency, and some redundancy, in the APC types that mediate wave 1 deletion in the normal mouse thymus.
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83
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Xu J, Jo J. Broad cross-reactivity of the T-cell repertoire achieves specific and sufficiently rapid target searching. J Theor Biol 2019; 466:119-127. [PMID: 30699327 DOI: 10.1016/j.jtbi.2019.01.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 12/20/2018] [Accepted: 01/24/2019] [Indexed: 11/29/2022]
Abstract
The molecular recognition of T-cell receptors is the hallmark of the adaptive immunity. Given the finiteness of the T-cell repertoire, individual T-cell receptors are necessary to be cross-reactive to multiple antigenic peptides. In this study, we quantify the variability of the cross-reactivity by using a string model that estimates the binding affinity between two sequences of amino acids. We examine sequences of 10,000 human T-cell receptors and 10,000 antigenic peptides, and obtain a full spectrum of cross-reactivity of the receptor-peptide binding. Then, we find that the cross-reactivity spectrum is broad. Some T-cells are reactive to 1000 peptides, but some T-cells are reactive to only one or two peptides. Since the degree of cross-reactivity has a correlation with the (un)binding affinity of receptors, we further investigate how the broad cross-reactivity affects the target searching of T-cells. High cross-reactive T-cells may not require many trials for searching correct targets, but they may spend long time to unbind from incorrect targets. In contrast, low cross-reactive T-cells may not spend long time to ignore incorrect targets, but they require many trials for screening correct targets. We evaluate this hypothesis, and show that the broad cross-reactivity of the natural T-cell repertoire can balance the trade-off between the rapid screening and unbinding penalty.
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Affiliation(s)
- Jin Xu
- Asia Pacific Center for Theoretical Physics (APCTP), 67 Cheongam-ro, Pohang, 37673, South Korea; Department of Physics, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Pohang, 37673, South Korea
| | - Junghyo Jo
- Asia Pacific Center for Theoretical Physics (APCTP), 67 Cheongam-ro, Pohang, 37673, South Korea; Department of Physics, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Pohang, 37673, South Korea; School of Computational Sciences, Korea Institute for Advanced Study (KIAS), 85 Hoegiro, Seoul, 02455, South Korea; Department of Statistics, Keimyung University, 1095 Dalgubeol-daero, Daegu, 42601, South Korea.
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84
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Khosravi-Maharlooei M, Obradovic A, Misra A, Motwani K, Holzl M, Seay HR, DeWolf S, Nauman G, Danzl N, Li H, Ho SH, Winchester R, Shen Y, Brusko TM, Sykes M. Crossreactive public TCR sequences undergo positive selection in the human thymic repertoire. J Clin Invest 2019; 129:2446-2462. [PMID: 30920391 DOI: 10.1172/jci124358] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We investigated human T-cell repertoire formation using high throughput TCRβ CDR3 sequencing in immunodeficient mice receiving human hematopoietic stem cells (HSCs) and human thymus grafts. Replicate humanized mice generated diverse and highly divergent repertoires. Repertoire narrowing and increased CDR3β sharing was observed during thymocyte selection. While hydrophobicity analysis implicated self-peptides in positive selection of the overall repertoire, positive selection favored shorter shared sequences that had reduced hydrophobicity at positions 6 and 7 of CDR3βs, suggesting weaker interactions with self-peptides than unshared sequences, possibly allowing escape from negative selection. Sharing was similar between autologous and allogeneic thymi and occurred between different cell subsets. Shared sequences were enriched for allo-crossreactive CDR3βs and for Type 1 diabetes-associated autoreactive CDR3βs. Single-cell TCR-sequencing showed increased sharing of CDR3αs compared to CDR3βs between mice. Our data collectively implicate preferential positive selection for shared human CDR3βs that are highly cross-reactive. While previous studies suggested a role for recombination bias in producing "public" sequences in mice, our study is the first to demonstrate a role for thymic selection. Our results implicate positive selection for promiscuous TCRβ sequences that likely evade negative selection, due to their low affinity for self-ligands, in the abundance of "public" human TCRβ sequences.
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Affiliation(s)
- Mohsen Khosravi-Maharlooei
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, Columbia University, New York, New York, USA
| | - Aleksandar Obradovic
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, Columbia University, New York, New York, USA
| | - Aditya Misra
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, Columbia University, New York, New York, USA
| | - Keshav Motwani
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Markus Holzl
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, Columbia University, New York, New York, USA
| | - Howard R Seay
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Susan DeWolf
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, Columbia University, New York, New York, USA
| | - Grace Nauman
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, Columbia University, New York, New York, USA.,Department of Microbiology and Immunology, Columbia University Medical Center, Columbia University, New York, New York, USA
| | - Nichole Danzl
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, Columbia University, New York, New York, USA
| | - Haowei Li
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, Columbia University, New York, New York, USA
| | - Siu-Hong Ho
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, Columbia University, New York, New York, USA
| | | | - Yufeng Shen
- Center for Computational Biology and Bioinformatics, and
| | - Todd M Brusko
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Megan Sykes
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, Columbia University, New York, New York, USA.,Department of Microbiology and Immunology, Columbia University Medical Center, Columbia University, New York, New York, USA.,Department of Surgery, Columbia University Medical Center, Columbia University, New York, New York, USA
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85
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Molecular constraints on CDR3 for thymic selection of MHC-restricted TCRs from a random pre-selection repertoire. Nat Commun 2019; 10:1019. [PMID: 30833553 PMCID: PMC6399321 DOI: 10.1038/s41467-019-08906-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 02/07/2019] [Indexed: 12/19/2022] Open
Abstract
The αβ T cell receptor (TCR) repertoire on mature T cells is selected in the thymus, but the basis for thymic selection of MHC-restricted TCRs from a randomly generated pre-selection repertoire is not known. Here we perform comparative repertoire sequence analyses of pre-selection and post-selection TCR from multiple MHC-sufficient and MHC-deficient mouse strains, and find that MHC-restricted and MHC-independent TCRs are primarily distinguished by features in their non-germline CDR3 regions, with many pre-selection CDR3 sequences not compatible with MHC-binding. Thymic selection of MHC-independent TCR is largely unconstrained, but the selection of MHC-specific TCR is restricted by both CDR3 length and specific amino acid usage. MHC-restriction disfavors TCR with CDR3 longer than 13 amino acids, limits positively charged and hydrophobic amino acids in CDR3β, and clonally deletes TCRs with cysteines in their CDR3 peptide-binding regions. Together, these MHC-imposed structural constraints form the basis to shape VDJ recombination sequences into MHC-restricted repertoires. For T cells, functional antigen receptors are selected in the thymus from a pre-selection repertoire by interaction with self MHCs. Here the authors show that specific, non-germline coded features located in the complementarity determining region 3 of the pre-selection antigen receptors are essential for the selection of MHC-restricted repertoire.
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86
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Abstract
Recombination-activating genes (
RAG)
1 and
RAG2 initiate the molecular processes that lead to lymphocyte receptor formation through VDJ recombination. Nonsense mutations in
RAG1/
RAG2 cause the most profound immunodeficiency syndrome, severe combined immunodeficiency (SCID). Other severe and less-severe clinical phenotypes due to mutations in
RAG genes are now recognized. The degree of residual protein function may permit some lymphocyte receptor formation, which confers a less-severe clinical phenotype. Many of the non-SCID phenotypes are associated with autoimmunity. New findings into the effect of mutations in
RAG1/2 on the developing T- and B-lymphocyte receptor give insight into the development of autoimmunity. This article summarizes recent findings and places the genetic and molecular findings in a clinical context.
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Affiliation(s)
- Andrew Gennery
- Paediatric Immunology and Haematopoietic Stem Cell Transplantation, Great North Childrens' Hospital, Newcastle upon Tyne, UK.,Primary Immunodeficiency Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
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87
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Villa A, Notarangelo LD. RAG gene defects at the verge of immunodeficiency and immune dysregulation. Immunol Rev 2019; 287:73-90. [PMID: 30565244 PMCID: PMC6309314 DOI: 10.1111/imr.12713] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 08/21/2018] [Indexed: 12/18/2022]
Abstract
Mutations of the recombinase activating genes (RAG) in humans underlie a broad spectrum of clinical and immunological phenotypes that reflect different degrees of impairment of T- and B-cell development and alterations of mechanisms of central and peripheral tolerance. Recent studies have shown that this phenotypic heterogeneity correlates, albeit imperfectly, with different levels of recombination activity of the mutant RAG proteins. Furthermore, studies in patients and in newly developed animal models carrying hypomorphic RAG mutations have disclosed various mechanisms underlying immune dysregulation in this condition. Careful annotation of clinical outcome and immune reconstitution in RAG-deficient patients who have received hematopoietic stem cell transplantation has shown that progress has been made in the treatment of this disease, but new approaches remain to be tested to improve stem cell engraftment and durable immune reconstitution. Finally, initial attempts have been made to treat RAG deficiency with gene therapy.
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Affiliation(s)
- Anna Villa
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), Division of Regenerative Medicine, Stem Cell and Gene Therapy, San Raffaele Scientific Institute, Milan, Italy
- Milan Unit, Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Milan, Italy
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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88
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Huth A, Liang X, Krebs S, Blum H, Moosmann A. Antigen-Specific TCR Signatures of Cytomegalovirus Infection. THE JOURNAL OF IMMUNOLOGY 2018; 202:979-990. [PMID: 30587531 DOI: 10.4049/jimmunol.1801401] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 11/19/2018] [Indexed: 11/19/2022]
Abstract
CMV is a prevalent human pathogen. The virus cannot be eliminated from the body, but is kept in check by CMV-specific T cells. Patients with an insufficient T cell response, such as transplant recipients, are at high risk of developing CMV disease. However, the CMV-specific T cell repertoire is complex, and it is not yet clear which T cells protect best against virus reactivation and disease. In this study, we present a highly resolved characterization of CMV-specific human CD8+ T cells based on enrichment by specific peptide stimulation and mRNA sequencing of their TCR β-chains (TCRβ). Our analysis included recently identified T cell epitopes restricted through HLA-C, whose presentation is resistant to viral immunomodulation, and well-studied HLA-B-restricted epitopes. In eight healthy virus carriers, we identified a total of 1052 CMV-specific TCRβ sequences. HLA-C-restricted, CMV-specific TCRβ clonotypes dominated the ex vivo T cell response and contributed the highest-frequency clonotype of the entire repertoire in two of eight donors. We analyzed sharing and similarity of CMV-specific TCRβ sequences and identified 63 public or related sequences belonging to 17 public TCRβ families. In our cohort, and in an independent cohort of 352 donors, the cumulative frequency of these public TCRβ family members was a highly discriminatory indicator of carrying both CMV infection and the relevant HLA type. Based on these findings, we propose CMV-specific TCRβ signatures as a biomarker for an antiviral T cell response to identify patients in need of treatment and to guide future development of immunotherapy.
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Affiliation(s)
- Alina Huth
- German Center for Infection Research Group Host Control of Viral Latency and Reactivation, Research Unit Gene Vectors, Helmholtz Center Munich, 81377 Munich, Germany.,Deutsches Zentrum für Infektionsforschung, 81377 Munich, Germany; and
| | - Xiaoling Liang
- German Center for Infection Research Group Host Control of Viral Latency and Reactivation, Research Unit Gene Vectors, Helmholtz Center Munich, 81377 Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilian University of Munich, 81377 Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig Maximilian University of Munich, 81377 Munich, Germany
| | - Andreas Moosmann
- German Center for Infection Research Group Host Control of Viral Latency and Reactivation, Research Unit Gene Vectors, Helmholtz Center Munich, 81377 Munich, Germany; .,Deutsches Zentrum für Infektionsforschung, 81377 Munich, Germany; and
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89
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Broad CD8 + T cell cross-recognition of distinct influenza A strains in humans. Nat Commun 2018; 9:5427. [PMID: 30575715 PMCID: PMC6303473 DOI: 10.1038/s41467-018-07815-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/23/2018] [Indexed: 11/29/2022] Open
Abstract
Newly-emerged and vaccine-mismatched influenza A viruses (IAVs) result in a rapid global spread of the virus due to minimal antibody-mediated immunity. In that case, established CD8+ T-cells can reduce disease severity. However, as mutations occur sporadically within immunogenic IAV-derived T-cell peptides, understanding of T-cell receptor (TCRαβ) cross-reactivity towards IAV variants is needed for a vaccine design. Here, we investigate TCRαβ cross-strain recognition across IAV variants within two immunodominant human IAV-specific CD8+ T-cell epitopes, HLA-B*37:01-restricted NP338-346 (B37-NP338) and HLA-A*01:01-restricted NP44-52 (A1-NP44). We find high abundance of cross-reactive TCRαβ clonotypes recognizing distinct IAV variants. Structures of the wild-type and variant peptides revealed preserved conformation of the bound peptides. Structures of a cross-reactive TCR-HLA-B37-NP338 complex suggest that the conserved conformation of the variants underpins TCR cross-reactivity. Overall, cross-reactive CD8+ T-cell responses, underpinned by conserved epitope structure, facilitates recognition of distinct IAV variants, thus CD8+ T-cell-targeted vaccines could provide protection across different IAV strains. Mutations within immunological epitope containing regions of influenza A virus can impair the established immune response between influenza strains and could impact rational vaccine design. Here Grant et al. examine the presence, structural impact and cross reactivity of two human immunodominant influenza epitope variants.
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90
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Banerjee S, Chapman SJ. Influence of correlated antigen presentation on T-cell negative selection in the thymus. J R Soc Interface 2018; 15:rsif.2018.0311. [PMID: 30404905 PMCID: PMC6283997 DOI: 10.1098/rsif.2018.0311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 10/08/2018] [Indexed: 11/12/2022] Open
Abstract
The thymus is the primary organ for the generation of naive T cells, a key component of the immune system. Tolerance of T cells to self is achieved primarily in the thymic medulla, where immature T cells (thymocytes) sample self-peptides presented by medullary thymic epithelial cells (mTECs). A sufficiently strong interaction activates the thymocytes leading to negative selection. A key question of current interest is whether there is any structure in the manner in which mTECs present peptides: can any mTEC present any peptide at any time, or are there particular patterns of correlated peptide presentation? We investigate this question using a mathematical model of negative selection. We find that correlated patterns of peptide presentation may be advantageous in negatively selecting low-degeneracy thymocytes (that is, those thymocytes which respond to relatively few peptides). We also quantify the probability that an auto-reactive thymocyte exits the thymus before it encounters a cognate antigen. The results suggest that heterogeneity of gene co-expression in mTECs has an effect on the probability of escape of autoreactive thymocytes.
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91
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Evolution of weak cooperative interactions for biological specificity. Proc Natl Acad Sci U S A 2018; 115:E11053-E11060. [PMID: 30404915 PMCID: PMC6255166 DOI: 10.1073/pnas.1815912115] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Functional specificity in biology is mediated by two classes of mechanisms, “lock–key” interactions and multivalent weak cooperative interactions (WCI). Despite growing evidence that WCI are widely prevalent in higher organisms, little is known about the selection forces that drove its evolution and repeated positive selection for mediating biological specificity in metazoa. We report that multivalent WCI for mediating biological specificity evolved as the number of tasks that organisms had to perform with functional specificity became large (e.g., multicellular organisms). We find that the evolution of multivalent WCI confer enhanced and robust evolvability to organisms, and thus it has been repeatedly positively selected. Thus, we provide insights on the evolution of WCI and, more broadly, on the evolution of evolvability. A hallmark of biological systems is that particular functions and outcomes are realized in specific contexts, such as when particular signals are received. One mechanism for mediating specificity is described by Fisher’s “lock and key” metaphor, exemplified by enzymes that bind selectively to a particular substrate via specific finely tuned interactions. Another mechanism, more prevalent in multicellular organisms, relies on multivalent weak cooperative interactions. Its importance has recently been illustrated by the recognition that liquid-liquid phase transitions underlie the formation of membraneless condensates that perform specific cellular functions. Based on computer simulations of an evolutionary model, we report that the latter mechanism likely became evolutionarily prominent when a large number of tasks had to be performed specifically for organisms to function properly. We find that the emergence of weak cooperative interactions for mediating specificity results in organisms that can evolve to accomplish new tasks with fewer, and likely less lethal, mutations. We argue that this makes the system more capable of undergoing evolutionary changes robustly, and thus this mechanism has been repeatedly positively selected in increasingly complex organisms. Specificity mediated by weak cooperative interactions results in some useful cross-reactivity for related tasks, but at the same time increases susceptibility to misregulation that might lead to pathologies.
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92
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DiToro D, Winstead CJ, Pham D, Witte S, Andargachew R, Singer JR, Wilson CG, Zindl CL, Luther RJ, Silberger DJ, Weaver BT, Kolawole EM, Martinez RJ, Turner H, Hatton RD, Moon JJ, Way SS, Evavold BD, Weaver CT. Differential IL-2 expression defines developmental fates of follicular versus nonfollicular helper T cells. Science 2018; 361:361/6407/eaao2933. [PMID: 30213884 DOI: 10.1126/science.aao2933] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 03/25/2018] [Accepted: 08/06/2018] [Indexed: 12/12/2022]
Abstract
In response to infection, naïve CD4+ T cells differentiate into two subpopulations: T follicular helper (TFH) cells, which support B cell antibody production, and non-TFH cells, which enhance innate immune cell functions. Interleukin-2 (IL-2), the major cytokine produced by naïve T cells, plays an important role in the developmental divergence of these populations. However, the relationship between IL-2 production and fate determination remains unclear. Using reporter mice, we found that differential production of IL-2 by naïve CD4+ T cells defined precursors fated for different immune functions. IL-2 producers, which were fated to become TFH cells, delivered IL-2 to nonproducers destined to become non-TFH cells. Because IL-2 production was limited to cells receiving the strongest T cell receptor (TCR) signals, a direct link between TCR-signal strength, IL-2 production, and T cell fate determination has been established.
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Affiliation(s)
- Daniel DiToro
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35203, USA
| | - Colleen J Winstead
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35203, USA
| | - Duy Pham
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35203, USA
| | - Steven Witte
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35203, USA
| | - Rakieb Andargachew
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Jeffrey R Singer
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35203, USA
| | - C Garrett Wilson
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35203, USA
| | - Carlene L Zindl
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35203, USA
| | - Rita J Luther
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35203, USA
| | - Daniel J Silberger
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35203, USA
| | | | - E Motunrayo Kolawole
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Ryan J Martinez
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Henrietta Turner
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35203, USA
| | - Robin D Hatton
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35203, USA
| | - James J Moon
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Sing Sing Way
- Division of Infectious Diseases and Perinatal Institute, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Brian D Evavold
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Casey T Weaver
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35203, USA.
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93
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Chen H, Chakraborty AK, Kardar M. How nonuniform contact profiles of T cell receptors modulate thymic selection outcomes. Phys Rev E 2018; 97:032413. [PMID: 29776088 DOI: 10.1103/physreve.97.032413] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Indexed: 11/07/2022]
Abstract
T cell receptors (TCRs) bind foreign or self-peptides attached to major histocompatibility complex (MHC) molecules, and the strength of this interaction determines T cell activation. Optimizing the ability of T cells to recognize a diversity of foreign peptides yet be tolerant of self-peptides is crucial for the adaptive immune system to properly function. This is achieved by selection of T cells in the thymus, where immature T cells expressing unique, stochastically generated TCRs interact with a large number of self-peptide-MHC; if a TCR does not bind strongly enough to any self-peptide-MHC, or too strongly with at least one self-peptide-MHC, the T cell dies. Past theoretical work cast thymic selection as an extreme value problem and characterized the statistical enrichment or depletion of amino acids in the postselection TCR repertoire, showing how T cells are selected to be able to specifically recognize peptides derived from diverse pathogens yet have limited self-reactivity. Here, we investigate how the diversity of the postselection TCR repertoire is modified when TCRs make nonuniform contacts with peptide-MHC. Specifically, we were motivated by recent experiments showing that amino acids at certain positions of a TCR sequence have large effects on thymic selection outcomes, and crystal structure data that reveal a nonuniform contact profile between a TCR and its peptide-MHC ligand. Using a representative TCR contact profile as an illustration, we show via simulations that the statistical enrichment or depletion of amino acids now varies by position according to the contact profile, and, importantly, it depends on the implementation of nonuniform contacts during thymic selection. We explain these nontrivial results analytically. Our study has implications for understanding the selection forces that shape the functionality of the postselection TCR repertoire.
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Affiliation(s)
- Hanrong Chen
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Arup K Chakraborty
- Departments of Chemical Engineering, Chemistry, and Biological Engineering, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Mehran Kardar
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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94
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Venturi V, Thomas PG. The expanding role of systems immunology in decoding the T cell receptor repertoire. ACTA ACUST UNITED AC 2018; 12:37-45. [PMID: 31106281 DOI: 10.1016/j.coisb.2018.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
T cells play a crucial role in the immune system's defense against many infectious diseases, including persistent infections for which no effective vaccines currently exist. The T cell component of the adaptive immune system is highly complex involving a constantly evolving landscape of various inter-related T cell populations. These T cell populations are characterized by their phenotypic and functional properties as well as the collection, or repertoire, of T cell receptors (TCR) that mediate T cell recognition of antigenic peptides derived from pathogens. Understanding the various processes and factors that impact the development and evolution of the broader T cell repertoire available to recognize and respond to pathogens and the characteristics of antigen-experienced T cell repertoires associated with effective immune control of pathogens is critical to the rational design of T cell-based vaccines and therapies. In this article we discuss, using examples of recent research, the promise that systems immunology approaches, involving quantitative analysis and mathematical and computational modeling of immunological data, hold for decoding the complex TCR repertoire system in the current era of advancing technologies.
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Affiliation(s)
- Vanessa Venturi
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW Australia, Sydney, NSW, Australia
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
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95
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Rowe JH, Delmonte OM, Keles S, Stadinski BD, Dobbs AK, Henderson LA, Yamazaki Y, Allende LM, Bonilla FA, Gonzalez-Granado LI, Celikbilek Celik S, Guner SN, Kapakli H, Yee C, Pai SY, Huseby ES, Reisli I, Regueiro JR, Notarangelo LD. Patients with CD3G mutations reveal a role for human CD3γ in T reg diversity and suppressive function. Blood 2018; 131:2335-2344. [PMID: 29653965 PMCID: PMC5969384 DOI: 10.1182/blood-2018-02-835561] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 04/09/2018] [Indexed: 02/05/2023] Open
Abstract
Integrity of the T-cell receptor/CD3 complex is crucial for positive and negative selection of T cells in the thymus and for effector and regulatory functions of peripheral T lymphocytes. In humans, CD3D, CD3E, and CD3Z gene defects are a cause of severe immune deficiency and present early in life with increased susceptibility to infections. By contrast, CD3G mutations lead to milder phenotypes, mainly characterized by autoimmunity. However, the role of CD3γ in establishing and maintaining immune tolerance has not been elucidated. In this manuscript, we aimed to investigate abnormalities of T-cell repertoire and function in patients with genetic defects in CD3G associated with autoimmunity. High throughput sequencing was used to study composition and diversity of the T-cell receptor β (TRB) repertoire in regulatory T cells (Tregs), conventional CD4+ (Tconv), and CD8+ T cells from 6 patients with CD3G mutations and healthy controls. Treg function was assessed by studying its ability to suppress proliferation of Tconv cells. Treg cells of patients with CD3G defects had reduced diversity, increased clonality, and reduced suppressive function. The TRB repertoire of Tconv cells from patients with CD3G deficiency was enriched for hydrophobic amino acids at positions 6 and 7 of the CDR3, a biomarker of self-reactivity. These data demonstrate that the T-cell repertoire of patients with CD3G mutations is characterized by a molecular signature that may contribute to the increased rate of autoimmunity associated with this condition.
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Affiliation(s)
- Jared H Rowe
- Division of Hematology-Oncology, Boston Children's Hospital, Boston, MA
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Sevgi Keles
- Division of Pediatric Immunology and Allergy, Meram Medical Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Brian D Stadinski
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA
| | - Adam K Dobbs
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | | | - Yasuhiro Yamazaki
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | | | | | - Luis I Gonzalez-Granado
- Primary Immunodeficiencies Unit, Department of Pediatrics, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Seyma Celikbilek Celik
- Division of Pediatric Immunology and Allergy, Meram Medical Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Sukru N Guner
- Division of Pediatric Immunology and Allergy, Meram Medical Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Hasan Kapakli
- Division of Pediatric Immunology and Allergy, Meram Medical Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Christina Yee
- Division of Immunology, Boston Children's Hospital, Boston, MA
| | - Sung-Yun Pai
- Division of Hematology-Oncology, Boston Children's Hospital, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA; and
| | - Eric S Huseby
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA
| | - Ismail Reisli
- Division of Pediatric Immunology and Allergy, Meram Medical Faculty, Necmettin Erbakan University, Konya, Turkey
| | - Jose R Regueiro
- Department of Immunology, Complutense University School of Medicine, imas12 Research Institute, Madrid, Spain
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
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96
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Wirasinha RC, Singh M, Archer SK, Chan A, Harrison PF, Goodnow CC, Daley SR. αβ T-cell receptors with a central CDR3 cysteine are enriched in CD8αα intraepithelial lymphocytes and their thymic precursors. Immunol Cell Biol 2018; 96:553-561. [PMID: 29726044 DOI: 10.1111/imcb.12047] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/09/2018] [Accepted: 03/23/2018] [Indexed: 01/04/2023]
Abstract
The thymus plays a crucial role in immune tolerance by exposing developing T cells (thymocytes) to a myriad of self-antigens. Strong T-cell receptor (TCR) engagement induces tolerance in self-reactive thymocytes by stimulating apoptosis or selection into specialized T-cell lineages, including intestinal TCRαβ+ CD8αα+ intraepithelial lymphocytes (IEL). TCR-intrinsic amino acid motifs that can be used to predict whether a TCR will be strongly self-reactive remain elusive. Here, a novel TCR sequence alignment approach revealed that T-cell lineages in C57BL/6 mice had divergent usage of cysteine within two positions of the amino acid at the apex of the complementarity-determining region 3 (CDR3) of the TCRα or TCRβ chain. Compared to pre-selection thymocytes, central CDR3 cysteine usage was increased in IEL and Type A IEL precursors (IELp) and markedly decreased in Foxp3+ regulatory T cells (T-reg) and naïve T cells. These findings reveal a TCR-intrinsic motif that distinguishes Type A IELp and IEL from T-reg and naïve T cells.
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Affiliation(s)
- Rushika C Wirasinha
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Mandeep Singh
- Immunology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Stuart K Archer
- Monash Bioinformatics Platform, Monash University, Melbourne, VIC, 3800, Australia
| | - Anna Chan
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Paul F Harrison
- Monash Bioinformatics Platform, Monash University, Melbourne, VIC, 3800, Australia
| | - Christopher C Goodnow
- Immunology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Stephen R Daley
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
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97
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Unique glandular ex-vivo Th1 and Th17 receptor motifs in Sjögren's syndrome patients using single-cell analysis. Clin Immunol 2018; 192:58-67. [PMID: 29679709 DOI: 10.1016/j.clim.2018.04.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 03/28/2018] [Accepted: 04/17/2018] [Indexed: 02/06/2023]
Abstract
Primary Sjögren's syndrome (pSS) is an autoimmune disease in which the underlying cause has yet to be elucidated. The main objective of this study was to determine the T cell receptor (TCR) repertoires of individual infiltrating T helper (Th)-1 and 17 cells of pSS patients using single-cell analysis. Single-cell analysis of ex-vivo infiltrating T cells demonstrated that pSS patients had higher frequencies of activated Th17 cells. Single-cell TCR sequencing revealed that TCRβ variable (TRBV)3-1/joint (J)1-2 (CLFLSMSACVW) and TRBV20-1/J1-1 (SVGSTAIPP*T) were expressed by activated Th1 and Th17 cells in both cohorts. Uniquely, TCRα variable (TRAV)8-2/J5 (VVSDTVLETAGE) was expressed by Th1 cells present only in patients and complementarity-determining region (CDR)3α-specific motif (LSTD*E) present in both Th1/Th17 cells. The study demonstrates that both activated Th1 and Th17 cells of pSS patients showed restricted clonal diversities of which two CDR3 motifs were present in controls and patients, with another two motifs unique to pSS.
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98
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Dendrou CA, Petersen J, Rossjohn J, Fugger L. HLA variation and disease. Nat Rev Immunol 2018; 18:325-339. [PMID: 29292391 DOI: 10.1038/nri.2017.143] [Citation(s) in RCA: 419] [Impact Index Per Article: 69.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fifty years since the first description of an association between HLA and human disease, HLA molecules have proven to be central to physiology, protective immunity and deleterious, disease-causing autoimmune reactivity. Technological advances have enabled pivotal progress in the determination of the molecular mechanisms that underpin the association between HLA genetics and functional outcome. Here, we review our current understanding of HLA molecules as the fundamental platform for immune surveillance and responsiveness in health and disease. We evaluate the scope for personalized antigen-specific disease prevention, whereby harnessing HLA-ligand interactions for clinical benefit is becoming a realistic prospect.
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Affiliation(s)
- Calliope A Dendrou
- Nuffield Department of Medicine, The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jan Petersen
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Wellington Road, Clayton, Victoria 3800, Australia.,Infection and Immunity Programme and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
| | - Jamie Rossjohn
- Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Wellington Road, Clayton, Victoria 3800, Australia.,Infection and Immunity Programme and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, Victoria 3800, Australia.,Division of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - Lars Fugger
- Danish National Research Foundation Centre PERSIMUNE, Rigshospitalet, University of Copenhagen, Copenhagen DK-2100, Denmark.,Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology and Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DS, UK
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99
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Gomez-Tourino I, Kamra Y, Baptista R, Lorenc A, Peakman M. T cell receptor β-chains display abnormal shortening and repertoire sharing in type 1 diabetes. Nat Commun 2017; 8:1792. [PMID: 29176645 PMCID: PMC5702608 DOI: 10.1038/s41467-017-01925-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 10/25/2017] [Indexed: 01/10/2023] Open
Abstract
Defects in T cell receptor (TCR) repertoire are proposed to predispose to autoimmunity. Here we show, by analyzing >2 × 108TCRB sequences of circulating naive, central memory, regulatory and stem cell-like memory CD4+ T cell subsets from patients with type 1 diabetes and healthy donors, that patients have shorter TCRB complementarity-determining region 3s (CDR3), in all cell subsets, introduced by increased deletions/reduced insertions during VDJ rearrangement. High frequency of short CDR3s is also observed in unproductive TCRB sequences, which are not subjected to thymic culling, suggesting that the shorter CDR3s arise independently of positive/negative selection. Moreover, TCRB CDR3 clonotypes expressed by autoantigen-specific CD4+ T cells are shorter compared with anti-viral T cells, and with those from healthy donors. Thus, early events in thymic T cell development and repertoire generation are abnormal in type 1 diabetes, which suggest that short CDR3s increase the potential for self-recognition, conferring heightened risk of autoimmune disease. T cell receptors are generated by somatic gene recombination, and are normally selected against autoreactivity. Here the authors show that CD4 T cells from patients with autoimmune type 1 diabetes have shorter TCRβ sequences, broader repertoire diversity, and more repertoire sharing than those from healthy individuals.
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Affiliation(s)
- Iria Gomez-Tourino
- Department of Immunobiology, Faculty of Life Sciences & Medicine, King's College London, 2nd Floor, Borough Wing, Guy's Hospital, London, SE1 9RT, UK.,National Institute for Health Research, Biomedical Research Centre at Guy's and St Thomas' Hospital Foundation Trust and King's College London, Guy's Hospital, London, SE1 9RT, UK.,Immunology Laboratory, Biomedical Research Center (CINBIO), Centro Singular de Investigación de Galicia, University of Vigo, Campus Universitario de Vigo, Pontevedra, 36310, Spain
| | - Yogesh Kamra
- Department of Immunobiology, Faculty of Life Sciences & Medicine, King's College London, 2nd Floor, Borough Wing, Guy's Hospital, London, SE1 9RT, UK
| | - Roman Baptista
- Department of Immunobiology, Faculty of Life Sciences & Medicine, King's College London, 2nd Floor, Borough Wing, Guy's Hospital, London, SE1 9RT, UK.,National Institute for Health Research, Biomedical Research Centre at Guy's and St Thomas' Hospital Foundation Trust and King's College London, Guy's Hospital, London, SE1 9RT, UK
| | - Anna Lorenc
- Department of Immunobiology, Faculty of Life Sciences & Medicine, King's College London, 2nd Floor, Borough Wing, Guy's Hospital, London, SE1 9RT, UK
| | - Mark Peakman
- Department of Immunobiology, Faculty of Life Sciences & Medicine, King's College London, 2nd Floor, Borough Wing, Guy's Hospital, London, SE1 9RT, UK. .,National Institute for Health Research, Biomedical Research Centre at Guy's and St Thomas' Hospital Foundation Trust and King's College London, Guy's Hospital, London, SE1 9RT, UK.
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100
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Marrack P, Krovi SH, Silberman D, White J, Kushnir E, Nakayama M, Crooks J, Danhorn T, Leach S, Anselment R, Scott-Browne J, Gapin L, Kappler J. The somatically generated portion of T cell receptor CDR3α contributes to the MHC allele specificity of the T cell receptor. eLife 2017; 6:30918. [PMID: 29148973 PMCID: PMC5701794 DOI: 10.7554/elife.30918] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 11/16/2017] [Indexed: 01/24/2023] Open
Abstract
Mature T cells bearing αβ T cell receptors react with foreign antigens bound to alleles of major histocompatibility complex proteins (MHC) that they were exposed to during their development in the thymus, a phenomenon known as positive selection. The structural basis for positive selection has long been debated. Here, using mice expressing one of two different T cell receptor β chains and various MHC alleles, we show that positive selection-induced MHC bias of T cell receptors is affected both by the germline encoded elements of the T cell receptor α and β chain and, surprisingly, dramatically affected by the non germ line encoded portions of CDR3 of the T cell receptor α chain. Thus, in addition to determining specificity for antigen, the non germline encoded elements of T cell receptors may help the proteins cope with the extremely polymorphic nature of major histocompatibility complex products within the species.
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Affiliation(s)
- Philippa Marrack
- Howard Hughes Medical Institute, Denver, United States.,Department of Biomedical Research, National Jewish Health, Denver, United States.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States
| | - Sai Harsha Krovi
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States
| | - Daniel Silberman
- Department of Biomedical Research, National Jewish Health, Denver, United States.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States
| | - Janice White
- Department of Biomedical Research, National Jewish Health, Denver, United States
| | - Eleanor Kushnir
- Department of Biomedical Research, National Jewish Health, Denver, United States
| | - Maki Nakayama
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States.,Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, United States
| | - James Crooks
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, United States
| | - Thomas Danhorn
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, United States
| | - Sonia Leach
- Department of Biomedical Research, National Jewish Health, Denver, United States.,Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, United States
| | - Randy Anselment
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, United States
| | | | - Laurent Gapin
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States
| | - John Kappler
- Howard Hughes Medical Institute, Denver, United States.,Department of Biomedical Research, National Jewish Health, Denver, United States.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States
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