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Khorki ME, Shi T, Cianciolo EE, Burg AR, Chukwuma PC, Picarsic JL, Morrice MK, Woodle ES, Maltzman JS, Ferguson A, Katz JD, Baker BM, Hildeman DA. Prior viral infection primes cross-reactive CD8+ T cells that respond to mouse heart allografts. Front Immunol 2023; 14:1287546. [PMID: 38143762 PMCID: PMC10748599 DOI: 10.3389/fimmu.2023.1287546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/14/2023] [Indexed: 12/26/2023] Open
Abstract
Introduction Significant evidence suggests a connection between transplant rejection and the presence of high levels of pre-existing memory T cells. Viral infection can elicit viral-specific memory T cells that cross-react with allo-MHC capable of driving allograft rejection in mice. Despite these advances, and despite their critical role in transplant rejection, a systematic study of allo-reactive memory T cells, their specificities, and the role of cross-reactivity with viral antigens has not been performed. Methods Here, we established a model to identify, isolate, and characterize cross-reactive T cells using Nur77 reporter mice (C57BL/6 background), which transiently express GFP exclusively upon TCR engagement. We infected Nur77 mice with lymphocytic choriomeningitis virus (LCMV-Armstrong) to generate a robust memory compartment, where quiescent LCMV-specific memory CD8+ T cells could be readily tracked with MHC tetramer staining. Then, we transplanted LCMV immune mice with allogeneic hearts and monitored expression of GFP within MHC-tetramer defined viral-specific T cells as an indicator of their ability to cross-react with alloantigens. Results Strikingly, prior LCMV infection significantly increased the kinetics and magnitude of rejection as well as CD8+ T cell recruitment into allogeneic, but not syngeneic, transplanted hearts, relative to non-infected controls. Interestingly, as early as day 1 after allogeneic heart transplant an average of ~8% of MHC-tetramer+ CD8+ T cells expressed GFP, in contrast to syngeneic heart transplants, where the frequency of viral-specific CD8+ T cells that were GFP+ was <1%. These data show that a significant percentage of viral-specific memory CD8+ T cells expressed T cell receptors that also recognized alloantigens in vivo. Notably, the frequency of cross-reactive CD8+ T cells differed depending upon the viral epitope. Further, TCR sequences derived from cross-reactive T cells harbored distinctive motifs that may provide insight into cross-reactivity and allo-specificity. Discussion In sum, we have established a mouse model to track viral-specific, allo-specific, and cross-reactive T cells; revealing that prior infection elicits substantial numbers of viral-specific T cells that cross-react to alloantigen, respond very early after transplant, and may promote rapid rejection.
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Affiliation(s)
- M. Eyad Khorki
- Division of Nephrology & Hypertension, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Tiffany Shi
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Eileen E. Cianciolo
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Ashley R. Burg
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - P. Chukwunalu Chukwuma
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
| | - Jennifer L. Picarsic
- Division of Pathology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pathology, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Mary K. Morrice
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - E. Steve Woodle
- Division of Transplantation, Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Jonathan S. Maltzman
- Department of Medicine, Stanford University, Palo Alto, CA, United States
- Geriatric Research and Education Clinical Center, Veterans Affairs (VA) Palo Alto Health Care System, Palo Alto, CA, United States
| | - Autumn Ferguson
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
| | - Jonathan D. Katz
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Brian M. Baker
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
| | - David A. Hildeman
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, United States
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2
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Danilkovich AV, Turobov VI, Palikov VA, Palikova YA, Shepelyakovskaya AO, Mikhaylov ES, Slashcheva GA, Shadrina TE, Shaykhutdinova ER, Rasskazova EA, Tukhovskaya EA, Khokhlova ON, Dyachenko IA, Ismailova AM, Zinchenko DV, Navolotskaya EV, Lipkin VM, Murashev AN, Udovichenko IP. C-Terminal Region of Caveolin-3 Contains a Stretch of Amino Acid Residues Capable of Diminishing Symptoms of Experimental Autoimmune Encephalomyelitis but Not Rheumatoid Arthritis Modeled in Rats. Biomedicines 2023; 11:2855. [PMID: 37893228 PMCID: PMC10603933 DOI: 10.3390/biomedicines11102855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/24/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
A short synthetic peptide from the C-terminal part of the caveolin-3 structure was tested for experimental autoimmune encephalomyelitis (EAE) treatment in rats. The structure-function similarity established between the novel synthetic peptide of pCav3 and the well-known immunomodulator immunocortin determined pCav3's ability to reduce EAE symptoms in Dark Agouti (DA) rats injected with pCav3 (500 µg/kg). pCav3 was found to interfere with the proliferation of lymphocytes extracted from the LNs of DA rats primed with homogenate injection, with IC50 = 0.42 μM (2.35 mcg/mL). pCav3 affected EAE in a very similar manner as immunocortin. The high degree of homology between the amino acid sequences of pCav3 and immunocortin corresponded well with the therapeutic activities of both peptides, as demonstrated on EAE. The latter peptide, possessing a homologous structure to pCav3, was also tested on EAE to explore whether there were structural restrictions between these peptides implied by the MHC-involved cell machinery. Consequently, immunocortin was further examined with a different autoimmune disease model, collagen-induced arthritis (CIA), established in Sprague-Dawley rats. CIA was established using an intentionally different genetic platform than EAE. Based on the results, it was concluded that the effectiveness of pCav3 and immunocortin peptides in EAE rat model was almost identical, but differed in the rat model of rheumatoid arthritis; thus, efficacy may be sensitive to the MHC type of animals used to establish the autoimmune disease model.
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Affiliation(s)
- Alexey V. Danilkovich
- State Center for Sciences by Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (BIBCh RAS), 6 Prospekt Nauki, 142290 Pushchino, Russia (O.N.K.); (D.V.Z.)
- Fundamental Biotechnology Department, RosBioTech University at Pushchino, 3 Prospekt Nauki, 142290 Pushchino, Russia
| | - Valery I. Turobov
- State Center for Sciences by Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (BIBCh RAS), 6 Prospekt Nauki, 142290 Pushchino, Russia (O.N.K.); (D.V.Z.)
| | - Victor A. Palikov
- State Center for Sciences by Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (BIBCh RAS), 6 Prospekt Nauki, 142290 Pushchino, Russia (O.N.K.); (D.V.Z.)
| | - Yulia A. Palikova
- State Center for Sciences by Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (BIBCh RAS), 6 Prospekt Nauki, 142290 Pushchino, Russia (O.N.K.); (D.V.Z.)
| | - Anna O. Shepelyakovskaya
- State Center for Sciences by Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (BIBCh RAS), 6 Prospekt Nauki, 142290 Pushchino, Russia (O.N.K.); (D.V.Z.)
| | - Evgeniy S. Mikhaylov
- State Center for Sciences by Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (BIBCh RAS), 6 Prospekt Nauki, 142290 Pushchino, Russia (O.N.K.); (D.V.Z.)
| | - Gulsara A. Slashcheva
- State Center for Sciences by Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (BIBCh RAS), 6 Prospekt Nauki, 142290 Pushchino, Russia (O.N.K.); (D.V.Z.)
| | - Tatiana E. Shadrina
- State Center for Sciences by Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (BIBCh RAS), 6 Prospekt Nauki, 142290 Pushchino, Russia (O.N.K.); (D.V.Z.)
| | - Elvira R. Shaykhutdinova
- State Center for Sciences by Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (BIBCh RAS), 6 Prospekt Nauki, 142290 Pushchino, Russia (O.N.K.); (D.V.Z.)
| | - Ekaterina A. Rasskazova
- State Center for Sciences by Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (BIBCh RAS), 6 Prospekt Nauki, 142290 Pushchino, Russia (O.N.K.); (D.V.Z.)
| | - Elena A. Tukhovskaya
- State Center for Sciences by Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (BIBCh RAS), 6 Prospekt Nauki, 142290 Pushchino, Russia (O.N.K.); (D.V.Z.)
| | - Oksana N. Khokhlova
- State Center for Sciences by Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (BIBCh RAS), 6 Prospekt Nauki, 142290 Pushchino, Russia (O.N.K.); (D.V.Z.)
| | - Igor A. Dyachenko
- State Center for Sciences by Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (BIBCh RAS), 6 Prospekt Nauki, 142290 Pushchino, Russia (O.N.K.); (D.V.Z.)
- Fundamental Biotechnology Department, RosBioTech University at Pushchino, 3 Prospekt Nauki, 142290 Pushchino, Russia
| | - Alina M. Ismailova
- State Center for Sciences by Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (BIBCh RAS), 6 Prospekt Nauki, 142290 Pushchino, Russia (O.N.K.); (D.V.Z.)
| | - Dmitry V. Zinchenko
- State Center for Sciences by Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (BIBCh RAS), 6 Prospekt Nauki, 142290 Pushchino, Russia (O.N.K.); (D.V.Z.)
| | - Elena V. Navolotskaya
- State Center for Sciences by Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (BIBCh RAS), 6 Prospekt Nauki, 142290 Pushchino, Russia (O.N.K.); (D.V.Z.)
| | - Valery M. Lipkin
- State Center for Sciences by Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (BIBCh RAS), 6 Prospekt Nauki, 142290 Pushchino, Russia (O.N.K.); (D.V.Z.)
| | - Arkady N. Murashev
- State Center for Sciences by Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (BIBCh RAS), 6 Prospekt Nauki, 142290 Pushchino, Russia (O.N.K.); (D.V.Z.)
- Fundamental Biotechnology Department, RosBioTech University at Pushchino, 3 Prospekt Nauki, 142290 Pushchino, Russia
| | - Igor. P. Udovichenko
- State Center for Sciences by Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (BIBCh RAS), 6 Prospekt Nauki, 142290 Pushchino, Russia (O.N.K.); (D.V.Z.)
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3
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Fahad AS, Chung CY, López Acevedo SN, Boyle N, Madan B, Gutiérrez-González MF, Matus-Nicodemos R, Laflin AD, Ladi RR, Zhou J, Wolfe J, Llewellyn-Lacey S, Koup RA, Douek DC, Balfour HH, Price DA, DeKosky BJ. Cell activation-based screening of natively paired human T cell receptor repertoires. Sci Rep 2023; 13:8011. [PMID: 37198258 PMCID: PMC10192375 DOI: 10.1038/s41598-023-31858-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 03/20/2023] [Indexed: 05/19/2023] Open
Abstract
Adoptive immune therapies based on the transfer of antigen-specific T cells have been used successfully to treat various cancers and viral infections, but improved techniques are needed to identify optimally protective human T cell receptors (TCRs). Here we present a high-throughput approach to the identification of natively paired human TCRα and TCRβ (TCRα:β) genes encoding heterodimeric TCRs that recognize specific peptide antigens bound to major histocompatibility complex molecules (pMHCs). We first captured and cloned TCRα:β genes from individual cells, ensuring fidelity using a suppression PCR. We then screened TCRα:β libraries expressed in an immortalized cell line using peptide-pulsed antigen-presenting cells and sequenced activated clones to identify the cognate TCRs. Our results validated an experimental pipeline that allows large-scale repertoire datasets to be annotated with functional specificity information, facilitating the discovery of therapeutically relevant TCRs.
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Affiliation(s)
- Ahmed S Fahad
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | - Cheng Yu Chung
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | - Sheila N López Acevedo
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | - Nicoleen Boyle
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | - Bharat Madan
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | | | - Rodrigo Matus-Nicodemos
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Amy D Laflin
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | - Rukmini R Ladi
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | - John Zhou
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | - Jacy Wolfe
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | - Sian Llewellyn-Lacey
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, CF14 4XN, UK
| | - Richard A Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Henry H Balfour
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, CF14 4XN, UK
- Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, CF14 4XN, UK
| | - Brandon J DeKosky
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA.
- Department of Chemical Engineering, The University of Kansas, Lawrence, KS, 66044, USA.
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
- The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA.
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4
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Souter MN, Awad W, Li S, Pediongco TJ, Meehan BS, Meehan LJ, Tian Z, Zhao Z, Wang H, Nelson A, Le Nours J, Khandokar Y, Praveena T, Wubben J, Lin J, Sullivan LC, Lovrecz GO, Mak JY, Liu L, Kostenko L, Kedzierska K, Corbett AJ, Fairlie DP, Brooks AG, Gherardin NA, Uldrich AP, Chen Z, Rossjohn J, Godfrey DI, McCluskey J, Pellicci DG, Eckle SB. CD8 coreceptor engagement of MR1 enhances antigen responsiveness by human MAIT and other MR1-reactive T cells. J Exp Med 2022; 219:213423. [PMID: 36018322 PMCID: PMC9424912 DOI: 10.1084/jem.20210828] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/24/2022] [Accepted: 07/21/2022] [Indexed: 11/04/2022] Open
Abstract
Mucosal-associated invariant T (MAIT) cells detect microbial infection via recognition of riboflavin-based antigens presented by the major histocompatibility complex class I (MHC-I)-related protein 1 (MR1). Most MAIT cells in human peripheral blood express CD8αα or CD8αβ coreceptors, and the binding site for CD8 on MHC-I molecules is relatively conserved in MR1. Yet, there is no direct evidence of CD8 interacting with MR1 or the functional consequences thereof. Similarly, the role of CD8αα in lymphocyte function remains ill-defined. Here, using newly developed MR1 tetramers, mutated at the CD8 binding site, and by determining the crystal structure of MR1-CD8αα, we show that CD8 engaged MR1, analogous to how it engages MHC-I molecules. CD8αα and CD8αβ enhanced MR1 binding and cytokine production by MAIT cells. Moreover, the CD8-MR1 interaction was critical for the recognition of folate-derived antigens by other MR1-reactive T cells. Together, our findings suggest that both CD8αα and CD8αβ act as functional coreceptors for MAIT and other MR1-reactive T cells.
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Affiliation(s)
- Michael N.T. Souter
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Wael Awad
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Shihan Li
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Troi J. Pediongco
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Bronwyn S. Meehan
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Lucy J. Meehan
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Zehua Tian
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Zhe Zhao
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Huimeng Wang
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia,State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Adam Nelson
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Jérôme Le Nours
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Yogesh Khandokar
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - T. Praveena
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Jacinta Wubben
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Jie Lin
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Lucy C. Sullivan
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - George O. Lovrecz
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Melbourne, Australia
| | - Jeffrey Y.W. Mak
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Ligong Liu
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Lyudmila Kostenko
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Alexandra J. Corbett
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Andrew G. Brooks
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Nicholas A. Gherardin
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Adam P. Uldrich
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Zhenjun Chen
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia,Institute of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Dale I. Godfrey
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Daniel G. Pellicci
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia,Murdoch Children’s Research Institute, Parkville, Melbourne, Australia
| | - Sidonia B.G. Eckle
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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Katayama Y, Kobayashi TJ. Comparative Study of Repertoire Classification Methods Reveals Data Efficiency of k-mer Feature Extraction. Front Immunol 2022; 13:797640. [PMID: 35936014 PMCID: PMC9346074 DOI: 10.3389/fimmu.2022.797640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 06/20/2022] [Indexed: 01/18/2023] Open
Abstract
The repertoire of T cell receptors encodes various types of immunological information. Machine learning is indispensable for decoding such information from repertoire datasets measured by next-generation sequencing (NGS). In particular, the classification of repertoires is the most basic task, which is relevant for a variety of scientific and clinical problems. Supported by the recent appearance of large datasets, efficient but data-expensive methods have been proposed. However, it is unclear whether they can work efficiently when the available sample size is severely restricted as in practical situations. In this study, we demonstrate that their performances can be impaired substantially below critical sample sizes. To complement this drawback, we propose MotifBoost, which exploits the information of short k-mer motifs of TCRs. MotifBoost can perform the classification as efficiently as a deep learning method on large datasets while providing more stable and reliable results on small datasets. We tested MotifBoost on the four small datasets which consist of various conditions such as Cytomegalovirus (CMV), HIV, α-chain, β-chain and it consistently preserved the stability. We also clarify that the robustness of MotifBoost can be attributed to the efficiency of k-mer motifs as representation features of repertoires. Finally, by comparing the predictions of these methods, we show that the whole sequence identity and sequence motifs encode partially different information and that a combination of such complementary information is necessary for further development of repertoire analysis.
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Affiliation(s)
- Yotaro Katayama
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
- *Correspondence: Yotaro Katayama,
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6
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Heterologous Immunity of Virus-Specific T Cells Leading to Alloreactivity: Possible Implications for Solid Organ Transplantation. Viruses 2021; 13:v13122359. [PMID: 34960628 PMCID: PMC8706157 DOI: 10.3390/v13122359] [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: 10/31/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 12/18/2022] Open
Abstract
Exposure of the adaptive immune system to a pathogen can result in the activation and expansion of T cells capable of recognizing not only the specific antigen but also different unrelated antigens, a process which is commonly referred to as heterologous immunity. While such cross-reactivity is favourable in amplifying protective immune responses to pathogens, induction of T cell-mediated heterologous immune responses to allo-antigens in the setting of solid organ transplantation can potentially lead to allograft rejection. In this review, we provide an overview of murine and human studies investigating the incidence and functional properties of virus-specific memory T cells cross-reacting with allo-antigens and discuss their potential relevance in the context of solid organ transplantation.
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7
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Ma Y, Ou J, Lin T, Chen L, Chen J, Wang M. Next Generation Sequencing-Based Identification of T-Cell Receptors for Immunotherapy Against Hepatocellular Carcinoma. Hepatol Commun 2021; 5:1106-1119. [PMID: 34141993 PMCID: PMC8183181 DOI: 10.1002/hep4.1697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/19/2021] [Accepted: 02/04/2021] [Indexed: 01/02/2023] Open
Abstract
Hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) remains a global health concern, and HBV proteins may be ideal targets for T cell-based immunotherapy for HCC. There is a need for fast and efficient identification of HBV-specific T cell receptors (TCRs) for the development of TCR-transduced T (TCR-T) cell-based immunotherapy. Two widely employed TCR identification approaches, T cell clonal expansion and single-cell sequencing, involve a TCR singularization process for the direct identification of Vα and Vβ pairs of TCR chains. Clonal expansion of T cells is well known to have tedious time and effort requirements due to the use of T cell cultures, whereas single-cell sequencing is limited by the requirements of cell sorting and the preparation of a single-cell immune-transcriptome library as well as the massive cost of the whole procedure. Here, we present a next-generation sequencing (NGS)-based HBV-specific TCR identification that does not require the TCR singularization process. Conclusion: Two pairing strategies, ranking-based strategy and α-β chain mixture-based strategy, have proved to be useful for NGS-based TCR identification, particularly for polyclonal T cells purified by a peptide-major histocompatibility complex (pMHC) multimer-based approach. Functional evaluation confirmed the specificity and avidity of two identified HBV-specific TCRs, which may potentially be used to produce TCR-T cells to treat patients with HBV-related HCC.
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Affiliation(s)
- Yipeng Ma
- Department of Research and DevelopmentShenzhen Institute for Innovation and Translational MedicineShenzhen International Biological Valley-Life Science Industrial ParkShenzhenChina
| | - Jiayu Ou
- Department of Research and DevelopmentShenzhen Institute for Innovation and Translational MedicineShenzhen International Biological Valley-Life Science Industrial ParkShenzhenChina
| | - Tong Lin
- Department of Research and DevelopmentShenzhen Institute for Innovation and Translational MedicineShenzhen International Biological Valley-Life Science Industrial ParkShenzhenChina
| | - Lei Chen
- Department of Research and DevelopmentShenzhen Institute for Innovation and Translational MedicineShenzhen International Biological Valley-Life Science Industrial ParkShenzhenChina
| | - Junhui Chen
- Intervention and Cell Therapy CenterPeking University Shenzhen HospitalShenzhenChina
| | - Mingjun Wang
- Department of Research and DevelopmentShenzhen Institute for Innovation and Translational MedicineShenzhen International Biological Valley-Life Science Industrial ParkShenzhenChina
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8
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Sullivan LC, Nguyen THO, Harpur CM, Stankovic S, Kanagarajah AR, Koutsakos M, Saunders PM, Cai Z, Gray JA, Widjaja JML, Lin J, Pietra G, Mingari MC, Moretta L, Samir J, Luciani F, Westall GP, Malmberg KJ, Kedzierska K, Brooks AG. Natural killer cell receptors regulate responses of HLA-E-restricted T cells. Sci Immunol 2021; 6:eabe9057. [PMID: 33893172 DOI: 10.1126/sciimmunol.abe9057] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 03/25/2021] [Indexed: 12/11/2022]
Abstract
Human cytomegalovirus (CMV) infection can stimulate robust human leukocyte antigen (HLA)-E-restricted CD8+ T cell responses. These T cells recognize a peptide from UL40, which differs by as little as a single methyl group from self-peptides that also bind HLA-E, challenging their capacity to avoid self-reactivity. Unexpectedly, we showed that the UL40/HLA-E T cell receptor (TCR) repertoire included TCRs that had high affinities for HLA-E/self-peptide. However, paradoxically, lower cytokine responses were observed from UL40/HLA-E T cells bearing TCRs with high affinity for HLA-E. RNA sequencing and flow cytometric analysis revealed that these T cells were marked by the expression of inhibitory natural killer cell receptors (NKRs) KIR2DL1 and KIR2DL2/L3. On the other hand, UL40/HLA-E T cells bearing lower-affinity TCRs expressed the activating receptor NKG2C. Activation of T cells bearing higher-affinity TCRs was regulated by the interaction between KIR2D receptors and HLA-C. These findings identify a role for NKR signaling in regulating self/non-self discrimination by HLA-E-restricted T cells, allowing for antiviral responses while avoiding contemporaneous self-reactivity.
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Affiliation(s)
- Lucy C Sullivan
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia.
- Lung Transplant Service, The Alfred Hospital and Monash University Melbourne, Victoria 3000, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Christopher M Harpur
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Sanda Stankovic
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Abbie R Kanagarajah
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Marios Koutsakos
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Philippa M Saunders
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Zhangying Cai
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - James A Gray
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Jacqueline M L Widjaja
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Jie Lin
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Gabriella Pietra
- Department of Experimental Medicine (DiMES). University of Genoa, Genoa 16132, Italy
- Unità Operativa Complessa Immunologia, Ospedale Policlinico San Martino, Genoa 16132, Italy
| | - Maria Cristina Mingari
- Department of Experimental Medicine (DiMES). University of Genoa, Genoa 16132, Italy
- Unità Operativa Complessa Immunologia, Ospedale Policlinico San Martino, Genoa 16132, Italy
- Center of Excellence for Biomedical Research, University of Genoa, Genoa 16132, Italy
| | - Lorenzo Moretta
- Istituto di Ricovero e Cura a Carattere Scientifico Ospedale Pediatrico Bambino Gesù, 00165 Roma, Italy
| | - Jerome Samir
- School of Medical Sciences and The Kirby Institute, UNSW, Sydney, New South Wales, Australia
| | - Fabio Luciani
- School of Medical Sciences and The Kirby Institute, UNSW, Sydney, New South Wales, Australia
| | - Glen P Westall
- Lung Transplant Service, The Alfred Hospital and Monash University Melbourne, Victoria 3000, Australia
| | - Karl J Malmberg
- KG Jebsen Center for Cancer Immunotherapy, Institute of Clinical Medicine, University of Oslo, Oslo 0318, Norway
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo 0310, Norway
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, 14186 Stockholm, Sweden
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia
| | - Andrew G Brooks
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Parkville, Victoria 3010, Australia.
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9
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Dahal-Koirala S, Risnes LF, Neumann RS, Christophersen A, Lundin KEA, Sandve GK, Qiao SW, Sollid LM. Comprehensive Analysis of CDR3 Sequences in Gluten-Specific T-Cell Receptors Reveals a Dominant R-Motif and Several New Minor Motifs. Front Immunol 2021; 12:639672. [PMID: 33927715 PMCID: PMC8076556 DOI: 10.3389/fimmu.2021.639672] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/17/2021] [Indexed: 12/20/2022] Open
Abstract
Gluten-specific CD4+ T cells are drivers of celiac disease (CeD). Previous studies of gluten-specific T-cell receptor (TCR) repertoires have found public TCRs shared across multiple individuals, biased usage of particular V-genes and conserved CDR3 motifs. The CDR3 motifs within the gluten-specific TCR repertoire, however, have not been systematically investigated. In the current study, we analyzed the largest TCR database of gluten-specific CD4+ T cells studied so far consisting of TCRs of 3122 clonotypes from 63 CeD patients. We established a TCR database from CD4+ T cells isolated with a mix of HLA-DQ2.5:gluten tetramers representing four immunodominant gluten epitopes. In an unbiased fashion we searched by hierarchical clustering for common CDR3 motifs among 2764 clonotypes. We identified multiple CDR3α, CDR3β, and paired CDR3α:CDR3β motif candidates. Among these, a previously known conserved CDR3β R-motif used by TRAV26-1/TRBV7-2 TCRs specific for the DQ2.5-glia-α2 epitope was the most prominent motif. Furthermore, we identified the epitope specificity of altogether 16 new CDR3α:CDR3β motifs by comparing with TCR sequences of 231 T-cell clones with known specificity and TCR sequences of cells sorted with single HLA-DQ2.5:gluten tetramers. We identified 325 public TCRα and TCRβ sequences of which 145, 102 and 78 belonged to TCRα, TCRβ and paired TCRαβ sequences, respectively. While the number of public sequences was depended on the number of clonotypes in each patient, we found that the proportion of public clonotypes from the gluten-specific TCR repertoire of given CeD patients appeared to be stable (median 37%). Taken together, we here demonstrate that the TCR repertoire of CD4+ T cells specific to immunodominant gluten epitopes in CeD is diverse, yet there is clearly biased V-gene usage, presence of public TCRs and existence of conserved motifs of which R-motif is the most prominent.
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Affiliation(s)
- Shiva Dahal-Koirala
- K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway.,Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Louise Fremgaard Risnes
- K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway.,Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Ralf Stefan Neumann
- K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway
| | - Asbjørn Christophersen
- K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway.,Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Knut E A Lundin
- K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway.,Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway.,Department of Gastroenterology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Geir Kjetil Sandve
- Biomedical Informatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Shuo-Wang Qiao
- K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway.,Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Ludvig M Sollid
- K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway.,Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, Oslo, Norway
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10
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Granadier D, Iovino L, Kinsella S, Dudakov JA. Dynamics of thymus function and T cell receptor repertoire breadth in health and disease. Semin Immunopathol 2021; 43:119-134. [PMID: 33608819 PMCID: PMC7894242 DOI: 10.1007/s00281-021-00840-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/12/2021] [Indexed: 12/26/2022]
Abstract
T cell recognition of unknown antigens relies on the tremendous diversity of the T cell receptor (TCR) repertoire; generation of which can only occur in the thymus. TCR repertoire breadth is thus critical for not only coordinating the adaptive response against pathogens but also for mounting a response against malignancies. However, thymic function is exquisitely sensitive to negative stimuli, which can come in the form of acute insult, such as that caused by stress, infection, or common cancer therapies; or chronic damage such as the progressive decline in thymic function with age. Whether it be prolonged T cell deficiency after hematopoietic cell transplantation (HCT) or constriction in the breadth of the peripheral TCR repertoire with age; these insults result in poor adaptive immune responses. In this review, we will discuss the importance of thymic function for generation of the TCR repertoire and how acute and chronic thymic damage influences immune health. We will also discuss methods that are used to measure thymic function in patients and strategies that have been developed to boost thymic function.
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Affiliation(s)
- David Granadier
- Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
- Department of Molecular and Cellular Biology, University of Washington, Seattle, WA, USA
| | - Lorenzo Iovino
- Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sinéad Kinsella
- Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jarrod A Dudakov
- Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Immunotherapy Integrated Research Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Department of Immunology, University of Washington, Seattle, WA, USA.
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11
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Attaf M, Roider J, Malik A, Rius Rafael C, Dolton G, Prendergast AJ, Leslie A, Ndung'u T, Kløverpris HN, Sewell AK, Goulder PJ. Cytomegalovirus-Mediated T Cell Receptor Repertoire Perturbation Is Present in Early Life. Front Immunol 2020; 11:1587. [PMID: 33101265 PMCID: PMC7554308 DOI: 10.3389/fimmu.2020.01587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/15/2020] [Indexed: 12/14/2022] Open
Abstract
Human cytomegalovirus (CMV) is a highly prevalent herpesvirus, particularly in sub-Saharan Africa, where it is endemic from infancy. The T cell response against CMV is important in keeping the virus in check, with CD8 T cells playing a major role in the control of CMV viraemia. Human leukocyte antigen (HLA) B*44:03-positive individuals raise a robust response against the NEGVKAAW (NW8) epitope, derived from the immediate-early-2 (IE-2) protein. We previously showed that the T cell receptor (TCR) repertoire raised against the NW8-HLA-B*44:03 complex was oligoclonal and characterised by superdominant clones, which were shared amongst unrelated individuals (i.e., "public"). Here, we address the question of how stable the CMV-specific TCR repertoire is over the course of infection, and whether substantial differences are evident in TCR repertoires in children, compared with adults. We present a longitudinal study of four HIV/CMV co-infected mother-child pairs, who in each case express HLA-B*44:03 and make responses to the NW8 epitope, and analyse their TCR repertoire over a period spanning more than 10 years. Using high-throughput sequencing, the paediatric CMV-specific repertoire was found to be highly diverse. In addition, paediatric repertoires were remarkably similar to adults, with public TCR responses being shared amongst children and adults alike. The CMV-specific repertoire in both adults and children displayed strong fluctuations in TCR clonality and repertoire architecture over time. Previously characterised superdominant clonotypes were readily identifiable in the children at high frequency, suggesting that the distortion of the CMV-specific repertoire is incurred as a direct result of CMV infection rather than a product of age-related "memory inflation." Early distortion of the TCR repertoire was particularly apparent in the case of the TCR-β chain, where oligoclonality was low in children and positively correlated with age, a feature we did not observe for TCR-α. This discrepancy between TCR-α and -β chain repertoire may reflect differential contribution to NW8 recognition. Altogether, the results of the present study provide insight into the formation of the TCR repertoire in early life and pave the way to better understanding of CD8 T cell responses to CMV at the molecular level.
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MESH Headings
- Adolescent
- Adult
- Age Factors
- Antigens, Viral/immunology
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- Child
- Child, Preschool
- Coinfection
- Cytomegalovirus/immunology
- Cytomegalovirus Infections/immunology
- Cytomegalovirus Infections/metabolism
- Cytomegalovirus Infections/virology
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/immunology
- Female
- HIV Infections/immunology
- HIV Infections/virology
- HLA Antigens/immunology
- High-Throughput Nucleotide Sequencing
- Humans
- Infant
- Leukocytes, Mononuclear/immunology
- Leukocytes, Mononuclear/metabolism
- Peptides/chemistry
- Peptides/immunology
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- T-Cell Antigen Receptor Specificity
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Viral Load
- Young Adult
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Affiliation(s)
- Meriem Attaf
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Julia Roider
- Human Immunodeficiency Virus Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- German Centre for Infection Research, Munich, Germany
- Department of Infectious Diseases, Ludwig-Maximilians-University, Munich, Germany
| | - Amna Malik
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Cristina Rius Rafael
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Garry Dolton
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Andrew J. Prendergast
- Zvitambo Institute for Maternal and Child Health Research, Harare, Zimbabwe
- Centre for Genomics and Child Health, Blizard Institute, Queen Mary University of London, London, United Kingdom
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Alasdair Leslie
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Infection and Immunity, University College London, London, United Kingdom
| | - Thumbi Ndung'u
- Human Immunodeficiency Virus Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Infection and Immunity, University College London, London, United Kingdom
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA, United States
- Virology and Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Henrik N. Kløverpris
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Infection and Immunity, University College London, London, United Kingdom
| | - Andrew K. Sewell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
- Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Philip J. Goulder
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA, United States
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12
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Watkins TS, Miles JJ. The human T-cell receptor repertoire in health and disease and potential for omics integration. Immunol Cell Biol 2020; 99:135-145. [PMID: 32677130 DOI: 10.1111/imcb.12377] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/07/2020] [Accepted: 07/12/2020] [Indexed: 12/11/2022]
Abstract
The adaptive immune system arose 600 million years ago in a cold-blooded fish. Over countless generations, our antecedents tuned the function of the T-cell receptor (TCR). The TCR system is arguably the most complex known to science. The TCR evolved hypervariability to fight the hypervariability of pathogens and cancers that look to consume our resources. This review describes the genetics and architecture of the human TCR and highlights surprising new discoveries over the past years that have disproved very old dogmas. The standardization of TCR sequencing data is discussed in preparation for big data bioinformatics and predictive analysis. We next catalogue new signatures and phenomenon discovered by TCR next generation sequencing (NGS) in health and disease and work that remain to be done in this space. Finally, we discuss how TCR NGS can add to immunodiagnostics and integrate with other omics platforms for both a deeper understanding of TCR biology and its use in the clinical setting.
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Affiliation(s)
- Thomas S Watkins
- The Australian Institute of Tropical Health and Medicine (AITHM), James Cook University, Cairns, QLD, Australia.,Centre for Molecular Therapeutics, James Cook University, Cairns, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, QLD, Australia
| | - John J Miles
- The Australian Institute of Tropical Health and Medicine (AITHM), James Cook University, Cairns, QLD, Australia.,Centre for Molecular Therapeutics, James Cook University, Cairns, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, QLD, Australia
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13
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Escherichiacoli-Specific CD4+ T Cells Have Public T-Cell Receptors and Low Interleukin 10 Production in Crohn's Disease. Cell Mol Gastroenterol Hepatol 2020; 10:507-526. [PMID: 32361018 PMCID: PMC7385044 DOI: 10.1016/j.jcmgh.2020.04.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 01/07/2023]
Abstract
BACKGROUND & AIMS Crohn's disease (CD) likely represents decreased immune tolerance to intestinal bacterial antigens. Most CD patients have high titers of antibodies to intestinal commensal proteins, including the outer membrane porin C (OmpC) of Escherichia coli. METHODS By using major histocompatibility complex II tetramers, we identified an HLA-DRB1∗15:01-restricted peptide epitope of OmpC recognized by CD4+ T cells in peripheral blood mononuclear cells from HLA-DRB1∗15:01+ healthy control (HC) and CD patients. RESULTS The precursor frequency of these cells in CD correlated with anti-OmpC IgA titers, but did not differ from that of HCs. In both cohorts, they showed a CD161+, integrin α4β7+ phenotype ex vivo by flow cytometry, distinct from the C-X-C Motif Chemokine Receptor 3 phenotype of autologous influenza hemagglutinin (Flu) peptide-specific T cells. The T-cell receptor α and β chains of in vitro-expanded OmpC-specific T-cell clones often contained public amino acid sequences that were identical in cells from different patients. Expanded T-cell clones from CD subjects produced significantly less interleukin (IL)10 (P < .0001) than those from HCs, and a trend toward decreased production of the T helper 2 cell-associated IL4, IL5, and IL13 by CD clones also was seen. CONCLUSIONS Both HCs and CD patients have detectable OmpC-specific T cells in circulation, with similar immunophenotypes and often identical T-cell-receptor sequences. However, expanded clones from patients with CD produce less of the immunoregulatory cytokine IL10, showing a selective defect in the regulatory function of intestinal microbial antigen-specific T cells in patients with CD.
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14
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Gil A, Kamga L, Chirravuri-Venkata R, Aslan N, Clark F, Ghersi D, Luzuriaga K, Selin LK. Epstein-Barr Virus Epitope-Major Histocompatibility Complex Interaction Combined with Convergent Recombination Drives Selection of Diverse T Cell Receptor α and β Repertoires. mBio 2020; 11:e00250-20. [PMID: 32184241 PMCID: PMC7078470 DOI: 10.1128/mbio.00250-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 02/11/2020] [Indexed: 01/07/2023] Open
Abstract
Recognition modes of individual T cell receptors (TCRs) are well studied, but factors driving the selection of TCR repertoires from primary through persistent human virus infections are less well understood. Using deep sequencing, we demonstrate a high degree of diversity of Epstein-Barr virus (EBV)-specific clonotypes in acute infectious mononucleosis (AIM). Only 9% of unique clonotypes detected in AIM persisted into convalescence; the majority (91%) of unique clonotypes detected in AIM were not detected in convalescence and were seeming replaced by equally diverse "de novo" clonotypes. The persistent clonotypes had a greater probability of being generated than nonpersistent clonotypes due to convergence recombination of multiple nucleotide sequences to encode the same amino acid sequence, as well as the use of shorter complementarity-determining regions 3 (CDR3s) with fewer nucleotide additions (i.e., sequences closer to germ line). Moreover, the two most immunodominant HLA-A2-restricted EBV epitopes, BRLF1109 and BMLF1280, show highly distinct antigen-specific public (i.e., shared between individuals) features. In fact, TCRα CDR3 motifs played a dominant role, while TCRβ played a minimal role, in the selection of TCR repertoire to an immunodominant EBV epitope, BRLF1. This contrasts with the majority of previously reported repertoires, which appear to be selected either on TCRβ CDR3 interactions with peptide/major histocompatibility complex (MHC) or in combination with TCRα CDR3. Understanding of how TCR-peptide-MHC complex interactions drive repertoire selection can be used to develop optimal strategies for vaccine design or generation of appropriate adoptive immunotherapies for viral infections in transplant settings or for cancer.IMPORTANCE Several lines of evidence suggest that TCRα and TCRβ repertoires play a role in disease outcomes and treatment strategies during viral infections in transplant patients and in cancer and autoimmune disease therapy. Our data suggest that it is essential that we understand the basic principles of how to drive optimum repertoires for both TCR chains, α and β. We address this important issue by characterizing the CD8 TCR repertoire to a common persistent human viral infection (EBV), which is controlled by appropriate CD8 T cell responses. The ultimate goal would be to determine if the individuals who are infected asymptomatically develop a different TCR repertoire than those that develop the immunopathology of AIM. Here, we begin by doing an in-depth characterization of both CD8 T cell TCRα and TCRβ repertoires to two immunodominant EBV epitopes over the course of AIM, identifying potential factors that may be driving their selection.
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Affiliation(s)
- Anna Gil
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Larisa Kamga
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | | | - Nuray Aslan
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Fransenio Clark
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Dario Ghersi
- School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, Nebraska, USA
| | - Katherine Luzuriaga
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Liisa K Selin
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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15
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Enterovirus 71 Infection Shapes Host T Cell Receptor Repertoire and Presumably Expands VP1-Specific TCRβ CDR3 Cluster. Pathogens 2020; 9:pathogens9020121. [PMID: 32075096 PMCID: PMC7169398 DOI: 10.3390/pathogens9020121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/03/2020] [Accepted: 02/11/2020] [Indexed: 11/17/2022] Open
Abstract
Enterovirus 71 (EV71) has become an important public health problem in the Asia-Pacific region in the past decades. EV71 infection might cause neurological and psychiatric complications and even death. Although an EV71 vaccine has been currently approved, there is no effective therapy for treating EV71-infected patients. Virus infections have been reported to shape host T cell receptor (TCR) repertoire. Therefore, understanding of host TCR repertoire in EV71 infection could better the knowledge in viral pathogenesis and further benefit the anti-viral therapy development. In this study, we used a mouse-adapted EV71 (mEV71) model to observe changes of host TCR repertoire in an EV71-infected central nervous system. Neonate mice were infected with mEV71 and mouse brainstem TCRβ repertoires were explored. Here, we reported that mEV71 infection impacted host brainstem TCRβ repertoire, where mEV71 infection skewed TCRβ diversity, changed VJ combination usages, and further expanded specific TCRβ CDR3 clones. Using bioinformatics analysis and ligand-binding prediction, we speculated the expanded TCRβ CDR3 clone harboring CASSLGANSDYTF sequence was capable of binding cleaved EV71 VP1 peptides in concert with major histocompatibility complex (MHC) molecules. We observed that mEV71 infection shaped host TCRβ repertoire and presumably expanded VP1-specific TCRβ CDR3 in mEV71-infected mouse brainstem that integrated EV71 pathogenesis in central nervous system.
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16
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Gate D, Saligrama N, Leventhal O, Yang AC, Unger MS, Middeldorp J, Chen K, Lehallier B, Channappa D, De Los Santos MB, McBride A, Pluvinage J, Elahi F, Tam GKY, Kim Y, Greicius M, Wagner AD, Aigner L, Galasko DR, Davis MM, Wyss-Coray T. Clonally expanded CD8 T cells patrol the cerebrospinal fluid in Alzheimer's disease. Nature 2020; 577:399-404. [PMID: 31915375 PMCID: PMC7445078 DOI: 10.1038/s41586-019-1895-7] [Citation(s) in RCA: 462] [Impact Index Per Article: 115.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 12/02/2019] [Indexed: 11/08/2022]
Abstract
Alzheimer's disease is an incurable neurodegenerative disorder in which neuroinflammation has a critical function1. However, little is known about the contribution of the adaptive immune response in Alzheimer's disease2. Here, using integrated analyses of multiple cohorts, we identify peripheral and central adaptive immune changes in Alzheimer's disease. First, we performed mass cytometry of peripheral blood mononuclear cells and discovered an immune signature of Alzheimer's disease that consists of increased numbers of CD8+ T effector memory CD45RA+ (TEMRA) cells. In a second cohort, we found that CD8+ TEMRA cells were negatively associated with cognition. Furthermore, single-cell RNA sequencing revealed that T cell receptor (TCR) signalling was enhanced in these cells. Notably, by using several strategies of single-cell TCR sequencing in a third cohort, we discovered clonally expanded CD8+ TEMRA cells in the cerebrospinal fluid of patients with Alzheimer's disease. Finally, we used machine learning, cloning and peptide screens to demonstrate the specificity of clonally expanded TCRs in the cerebrospinal fluid of patients with Alzheimer's disease to two separate Epstein-Barr virus antigens. These results reveal an adaptive immune response in the blood and cerebrospinal fluid in Alzheimer's disease and provide evidence of clonal, antigen-experienced T cells patrolling the intrathecal space of brains affected by age-related neurodegeneration.
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Affiliation(s)
- David Gate
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.
- Veterans Administration Palo Alto Healthcare System, Palo Alto, CA, USA.
| | - Naresha Saligrama
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Olivia Leventhal
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Andrew C Yang
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Chemistry, Engineering and Medicine for Human Health, Stanford University, Stanford, CA, USA
| | - Michael S Unger
- Institute of Molecular Regenerative Medicine, Paracelsus Medical University, Salzburg, Austria
- Spinal Cord Injury and Tissue Regeneration Center Salzburg, Paracelsus Medical University, Salzburg, Austria
| | - Jinte Middeldorp
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Veterans Administration Palo Alto Healthcare System, Palo Alto, CA, USA
- Department of Translational Neuroscience, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Kelly Chen
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Benoit Lehallier
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Veterans Administration Palo Alto Healthcare System, Palo Alto, CA, USA
| | - Divya Channappa
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark B De Los Santos
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Alisha McBride
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Veterans Administration Palo Alto Healthcare System, Palo Alto, CA, USA
| | - John Pluvinage
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
- Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Fanny Elahi
- Department of Neurology, Memory and Aging Center, University of California at San Francisco, San Francisco, CA, USA
| | - Grace Kyin-Ye Tam
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Functional Imaging in Neuropsychiatric Disorders Laboratory, Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Yongha Kim
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Functional Imaging in Neuropsychiatric Disorders Laboratory, Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael Greicius
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Functional Imaging in Neuropsychiatric Disorders Laboratory, Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Anthony D Wagner
- Department of Psychology, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Ludwig Aigner
- Institute of Molecular Regenerative Medicine, Paracelsus Medical University, Salzburg, Austria
- Spinal Cord Injury and Tissue Regeneration Center Salzburg, Paracelsus Medical University, Salzburg, Austria
| | - Douglas R Galasko
- Department of Neurosciences, University of California at San Diego, La Jolla, CA, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA, USA
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.
- Veterans Administration Palo Alto Healthcare System, Palo Alto, CA, USA.
- Chemistry, Engineering and Medicine for Human Health, Stanford University, Stanford, CA, USA.
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA.
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17
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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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18
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Attaf M, Malik A, Severinsen MC, Roider J, Ogongo P, Buus S, Ndung'u T, Leslie A, Kløverpris HN, Matthews PC, Sewell AK, Goulder P. Major TCR Repertoire Perturbation by Immunodominant HLA-B *44:03-Restricted CMV-Specific T Cells. Front Immunol 2018; 9:2539. [PMID: 30487790 PMCID: PMC6246681 DOI: 10.3389/fimmu.2018.02539] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 10/15/2018] [Indexed: 12/12/2022] Open
Abstract
Lack of disease during chronic human cytomegalovirus (CMV) infection depends on the maintenance of a high-frequency CMV-specific T cell response. The composition of the T cell receptor (TCR) repertoire underlying this response remains poorly characterised, especially within African populations in which CMV is endemic from infancy. Here we focus on the immunodominant CD8+ T cell response to the immediate-early 2 (IE-2)-derived epitope NEGVKAAW (NW8) restricted by HLA-B*44:03, a highly prevalent response in African populations, which in some subjects represents >10% of the circulating CD8+ T cells. Using pMHC multimer staining and sorting of NW8-specific T cells, the TCR repertoire raised against NW8 was characterised here using high-throughput sequencing in 20 HLA-B*44:03 subjects. We found that the CD8+ T cell repertoire raised in response to NW8 was highly skewed and featured preferential use of a restricted set of V and J gene segments. Furthermore, as often seen in immunity against ancient viruses like CMV and Epstein-Barr virus (EBV), the response was strongly dominated by identical TCR sequences shared by multiple individuals, or “public” TCRs. Finally, we describe a pair “superdominant” TCR clonotypes, which were germline or nearly germline-encoded and produced at remarkably high frequencies in certain individuals, with a single CMV-specific clonotype representing up to 17% of all CD8+ T cells. Given the magnitude of the NW8 response, we propose that this major skewing of CMV-specific immunity leads to massive perturbations in the overall TCR repertoire in HLA-B*44:03 individuals.
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Affiliation(s)
- Meriem Attaf
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom.,Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Amna Malik
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Mai C Severinsen
- Africa Health Research Institute, Durban, South Africa.,Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Julia Roider
- Africa Health Research Institute, Durban, South Africa.,Department of infectious diseases, Medizinische Klinik IV, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Paul Ogongo
- Africa Health Research Institute, Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.,Department of Tropical and Infectious Diseases, Institute of Primate Research, Nairobi, Kenya
| | - Søren Buus
- Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thumbi Ndung'u
- Africa Health Research Institute, Durban, South Africa.,Department of Infection and Immunity, University College London, London, United Kingdom
| | - Alasdair Leslie
- Africa Health Research Institute, Durban, South Africa.,Department of Infection and Immunity, University College London, London, United Kingdom
| | - Henrik N Kløverpris
- Africa Health Research Institute, Durban, South Africa.,Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Infection and Immunity, University College London, London, United Kingdom
| | - Philippa C Matthews
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Andrew K Sewell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom.,Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Philip Goulder
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
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19
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Simon S, Wu Z, Cruard J, Vignard V, Fortun A, Khammari A, Dreno B, Lang F, Rulli SJ, Labarriere N. TCR Analyses of Two Vast and Shared Melanoma Antigen-Specific T Cell Repertoires: Common and Specific Features. Front Immunol 2018; 9:1962. [PMID: 30214446 PMCID: PMC6125394 DOI: 10.3389/fimmu.2018.01962] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/09/2018] [Indexed: 12/11/2022] Open
Abstract
Among Immunotherapeutic approaches for cancer treatment, the adoptive transfer of antigen specific T cells is still a relevant approach, that could have higher efficacy when further combined with immune check-point blockade. A high number of adoptive transfer trials have been performed in metastatic melanoma, due to its high immunogenic potential, either with polyclonal TIL or antigen-specific polyclonal populations. In this setting, the extensive characterization of T cell functions and receptor diversity of infused polyclonal T cells is required, notably for monitoring purposes. We developed a clinical grade procedure for the selection and amplification of polyclonal CD8 T cells, specific for two shared and widely expressed melanoma antigens: Melan-A and MELOE-1. This procedure is currently used in a clinical trial for HLA-A2 metastatic melanoma patients. In this study, we characterized the T-cell diversity (T-cell repertoire) of such T cell populations using a new RNAseq strategy. We first assessed the added-value of TCR receptor sequencing, in terms of sensitivity and specificity, by direct comparison with cytometry analysis of the T cell populations labeled with anti-Vß-specific antibodies. Results from these analyzes also confirmed specific features already reported for Melan-A and MELOE-1 specific T cell repertoires in terms of V-alpha recurrence usage, on a very high number of T cell clonotypes. Furthermore, these analyses also revealed undescribed features, such as the recurrence of a specific motif in the CDR3α region for MELOE-1 specific T cell repertoire. Finally, the analysis of a large number of T cell clonotypes originating from various patients revealed the existence of public CDR3α and ß clonotypes for Melan-A and MELOE-1 specific T cells. In conclusion, this method of high throughput TCR sequencing is a reliable and powerful approach to deeply characterize polyclonal T cell repertoires, and to reveal specific features of a given TCR repertoire, that would be useful for immune follow-up of cancer patients treated by immunotherapeutic approaches.
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Affiliation(s)
- Sylvain Simon
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France
| | - Zhong Wu
- Qiagen Sciences, Frederick, MD, United States
| | - J Cruard
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France
| | - Virginie Vignard
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France.,Centre Hospitalier Universitaire Nantes, Nantes, France
| | - Agnes Fortun
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France
| | - Amir Khammari
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France.,Department of Dermato-Cancerology of Nantes Hospital, Nantes, France
| | - Brigitte Dreno
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France.,Department of Dermato-Cancerology of Nantes Hospital, Nantes, France
| | - Francois Lang
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France
| | | | - Nathalie Labarriere
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France.,Centre Hospitalier Universitaire Nantes, Nantes, France
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20
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Elhanati Y, Sethna Z, Callan CG, Mora T, Walczak AM. Predicting the spectrum of TCR repertoire sharing with a data-driven model of recombination. Immunol Rev 2018; 284:167-179. [PMID: 29944757 PMCID: PMC6033145 DOI: 10.1111/imr.12665] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Despite the extreme diversity of T-cell repertoires, many identical T-cell receptor (TCR) sequences are found in a large number of individual mice and humans. These widely shared sequences, often referred to as "public," have been suggested to be over-represented due to their potential immune functionality or their ease of generation by V(D)J recombination. Here, we show that even for large cohorts, the observed degree of sharing of TCR sequences between individuals is well predicted by a model accounting for the known quantitative statistical biases in the generation process, together with a simple model of thymic selection. Whether a sequence is shared by many individuals is predicted to depend on the number of queried individuals and the sampling depth, as well as on the sequence itself, in agreement with the data. We introduce the degree of publicness conditional on the queried cohort size and the size of the sampled repertoires. Based on these observations, we propose a public/private sequence classifier, "PUBLIC" (Public Universal Binary Likelihood Inference Classifier), based on the generation probability, which performs very well even for small cohort sizes.
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Affiliation(s)
- Yuval Elhanati
- Joseph Henry LaboratoriesPrinceton UniversityPrincetonNJUSA
| | - Zachary Sethna
- Joseph Henry LaboratoriesPrinceton UniversityPrincetonNJUSA
| | | | - Thierry Mora
- Laboratoire de physique statistiqueCNRSSorbonne UniversitéUniversité Paris‐Diderot, and École Normale Supérieure (PSL University)ParisFrance
| | - Aleksandra M. Walczak
- Laboratoire de physique théoriqueCNRSSorbonne Université, and École Normale Supérieure (PSL University)ParisFrance
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21
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Di Carluccio AR, Triffon CF, Chen W. Perpetual complexity: predicting human CD8 + T-cell responses to pathogenic peptides. Immunol Cell Biol 2018; 96:358-369. [PMID: 29424002 DOI: 10.1111/imcb.12019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 01/17/2023]
Abstract
The accurate prediction of human CD8+ T-cell epitopes has great potential clinical and translational implications in the context of infection, cancer and autoimmunity. Prediction algorithms have traditionally focused on calculated peptide affinity for the binding groove of MHC-I. However, over the years it has become increasingly clear that the ultimate T-cell recognition of MHC-I-bound peptides is governed by many contributing factors within the complex antigen presentation pathway. Recent advances in next-generation sequencing and immunnopeptidomics have increased the precision of HLA-I sub-allele classification, and have led to the discovery of peptide processing events and individual allele-specific binding preferences. Here, we review some of the discoveries that initiated the development of peptide prediction algorithms, and outline some of the current available online tools for CD8+ T-cell epitope prediction.
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Affiliation(s)
- Anthony R Di Carluccio
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Cristina F Triffon
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Weisan Chen
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
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22
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Liu X, Wu J. History, applications, and challenges of immune repertoire research. Cell Biol Toxicol 2018; 34:441-457. [PMID: 29484527 DOI: 10.1007/s10565-018-9426-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 02/14/2018] [Indexed: 12/19/2022]
Abstract
The diversity of T and B cells in terms of their receptor sequences is huge in the vertebrate's immune system and provides broad protection against the vast diversity of pathogens. Immune repertoire is defined as the sum of T cell receptors and B cell receptors (also named immunoglobulin) that makes the organism's adaptive immune system. Before the emergence of high-throughput sequencing, the studies on immune repertoire were limited by the underdeveloped methodologies, since it was impossible to capture the whole picture by the low-throughput tools. The massive paralleled sequencing technology suits perfectly the researches on immune repertoire. In this article, we review the history of immune repertoire studies, in terms of technologies and research applications. Particularly, we discuss several aspects of challenges in this field and highlight the efforts to develop potential solutions, in the era of high-throughput sequencing of the immune repertoire.
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Affiliation(s)
- Xiao Liu
- BGI-Shenzhen, Shenzhen, 518083, China.
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23
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A Unique T-Cell Receptor Amino Acid Sequence Selected by Human T-Cell Lymphotropic Virus Type 1 Tax 301-309-Specific Cytotoxic T Cells in HLA-A24:02-Positive Asymptomatic Carriers and Adult T-Cell Leukemia/Lymphoma Patients. J Virol 2017; 91:JVI.00974-17. [PMID: 28724766 DOI: 10.1128/jvi.00974-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Accepted: 07/06/2017] [Indexed: 11/20/2022] Open
Abstract
We previously reported that the T-cell receptor (TCR) repertoire of human T-cell lymphotropic virus type 1 (HTLV-1) Tax301-309-specific CD8+ cytotoxic T cells (Tax301-309-CTLs) was highly restricted and a particular amino acid sequence motif, the PDR motif, was conserved among HLA-A*24:02-positive (HLA-A*24:02+) adult T-cell leukemia/lymphoma (ATL) patients who had undergone allogeneic hematopoietic cell transplantation (allo-HSCT). Furthermore, we found that donor-derived PDR+ CTLs selectively expanded in ATL long-term HSCT survivors with strong CTL activity against HTLV-1. On the other hand, the TCR repertoires in Tax301-309-CTLs of asymptomatic HTLV-1 carriers (ACs) remain unclear. In this study, we directly identified the DNA sequence of complementarity-determining region 3 (CDR3) of the TCR-β chain of Tax301-309-CTLs at the single-cell level and compared not only the TCR repertoires but also the frequencies and phenotypes of Tax301-309-CTLs between ACs and ATL patients. We did not observe any essential difference in the frequencies of Tax301-309-CTLs between ACs and ATL patients. In the single-cell TCR repertoire analysis of Tax301-309-CTLs, 1,458 Tax301-309-CTLs and 140 clones were identified in this cohort. Tax301-309-CTLs showed highly restricted TCR repertoires with a strongly biased usage of BV7, and PDR, the unique motif in TCR-β CDR3, was exclusively observed in all ACs and ATL patients. However, there was no correlation between PDR+ CTL frequencies and HTLV-1 proviral load (PVL). In conclusion, we have identified, for the first time, a unique amino acid sequence, PDR, as a public TCR-CDR3 motif against Tax in HLA-A*24:02+ HTLV-1-infected individuals. Further investigations are warranted to elucidate the role of the PDR+ CTL response in the progression from carrier state to ATL.IMPORTANCE ATL is an aggressive T-cell malignancy caused by HTLV-1 infection. The HTLV-1 regulatory protein Tax aggressively promotes the proliferation of HTLV-1-infected lymphocytes and is also a major target antigen for CD8+ CTLs. In our previous evaluation of Tax301-309-CTLs, we found that a unique amino acid sequence motif, PDR, in CDR3 of the TCR-β chain of Tax301-309-CTLs was conserved among ATL patients after allo-HSCT. Furthermore, the PDR+ Tax301-309-CTL clones selectively expanded and showed strong cytotoxic activities against HTLV-1. On the other hand, it remains unclear how Tax301-309-CTL repertoire exists in ACs. In this study, we comprehensively compared Tax-specific TCR repertoires at the single-cell level between ACs and ATL patients. Tax301-309-CTLs showed highly restricted TCR repertoires with a strongly biased usage of BV7, and PDR, the unique motif in TCR-β CDR3, was conserved in all ACs and ATL patients, regardless of clinical subtype in HTLV-1 infection.
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24
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van den Heuvel H, Heutinck KM, van der Meer-Prins EMW, Yong SL, van Miert PPMC, Anholts JDH, Franke-van Dijk MEI, Zhang XQ, Roelen DL, Ten Berge RJM, Claas FHJ. Allo-HLA Cross-Reactivities of Cytomegalovirus-, Influenza-, and Varicella Zoster Virus-Specific Memory T Cells Are Shared by Different Healthy Individuals. Am J Transplant 2017; 17:2033-2044. [PMID: 28332333 DOI: 10.1111/ajt.14279] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 02/23/2017] [Accepted: 03/11/2017] [Indexed: 01/25/2023]
Abstract
Virus-specific T cells can recognize allogeneic HLA (allo-HLA) through TCR cross-reactivity. The allospecificity often differs by individual (private cross-reactivity) but also can be shared by multiple individuals (public cross-reactivity); however, only a few examples of the latter have been described. Because these could facilitate alloreactivity prediction in transplantation, we aimed to identify novel public cross-reactivities of human virus-specific CD8+ T cells directed against allo-HLA by assessing their reactivity in mixed-lymphocyte reactions. Further characterization was done by studying TCR usage with primer-based DNA sequencing, cytokine production with ELISAs, and cytotoxicity with 51 chromium-release assays. We identified three novel public allo-HLA cross-reactivities of human virus-specific CD8+ T cells. CMV B35/IPS CD8+ T cells cross-reacted with HLA-B51 and/or HLA-B58/B57 (23% of tetramer-positive individuals), FLU A2/GIL (influenza IMP[58-66] HLA-A*02:01/GILGFVFTL) CD8+ T cells with HLA-B38 (90% of tetramer-positive individuals), and VZV A2/ALW (varicella zoster virus IE62[593-601] HLA-A*02:01/ALWALPHAA) CD8+ T cells with HLA-B55 (two unrelated individuals). Cross-reactivity was tested against different cell types including endothelial and epithelial cells. All cross-reactive T cells expressed a memory phenotype, emphasizing the importance for transplantation. We conclude that public allo-HLA cross-reactivity of virus-specific memory T cells is not uncommon and may create novel opportunities for alloreactivity prediction and risk estimation in transplantation.
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Affiliation(s)
- H van den Heuvel
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - K M Heutinck
- Department of Experimental Immunology, Academic Medical Centre, Amsterdam, The Netherlands.,Renal Transplant Unit, Department of Internal Medicine, Division of Internal Medicine, Academic Medical Centre, Amsterdam, The Netherlands
| | - E M W van der Meer-Prins
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - S L Yong
- Department of Experimental Immunology, Academic Medical Centre, Amsterdam, The Netherlands.,Renal Transplant Unit, Department of Internal Medicine, Division of Internal Medicine, Academic Medical Centre, Amsterdam, The Netherlands
| | - P P M C van Miert
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - J D H Anholts
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - M E I Franke-van Dijk
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - X Q Zhang
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - D L Roelen
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - R J M Ten Berge
- Renal Transplant Unit, Department of Internal Medicine, Division of Internal Medicine, Academic Medical Centre, Amsterdam, The Netherlands
| | - F H J Claas
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
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25
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Comprehensive assessment of peripheral blood TCRβ repertoire in infectious mononucleosis and chronic active EBV infection patients. Ann Hematol 2017; 96:665-680. [PMID: 28091735 DOI: 10.1007/s00277-016-2911-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 12/22/2016] [Indexed: 10/20/2022]
Abstract
Epstein-Barr virus (EBV) primary infection is usually asymptomatic, but it sometimes progresses to infectious mononucleosis (IM). Occasionally, some people develop chronic active EBV infection (CAEBV) with underlying immunodeficiency, which belongs to a continuous spectrum of EBV-associated lymphoproliferative disorders (EBV+ LPD) with heterogeneous clinical presentations and high mortality. It has been well established that T cell-mediated immune response plays a critical role in the disease evolution of EBV infection. Recently, high-throughput sequencing of the hypervariable complementarity-determining region 3 (CDR3) segments of the T cell receptor (T cell receptor β (TCRβ)) has emerged as a sensitive approach to assess the T cell repertoire. In this study, we fully characterized the diversity of peripheral blood TCRβ repertoire in IM (n = 6) and CAEBV patients (n = 5) and EBV-seropositive controls (n = 5). Compared with the healthy EBV-seropositive controls, both IM and CAEBV patients demonstrate a significant decrease in peripheral blood TCRβ repertoire diversity, basically, including narrowed repertoire breadth, highly expanded clones, and skewed CDR3 length distribution. However, there is no significant difference between IM and CAEBV patients. Furthermore, we observed some disease-related preferences in TRBV/TRBJ usage and combinations, as well as lots of T cell clones shared by different groups (unique or overlapped) involved in public T cell responses, which provide more detailed insights into the divergent disease evolution.
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26
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Dockree T, Holland CJ, Clement M, Ladell K, McLaren JE, van den Berg HA, Gostick E, L Miners K, Llewellyn-Lacey S, Bridgeman JS, Man S, Bailey M, Burrows SR, Price DA, Wooldridge L. CD8 + T-cell specificity is compromised at a defined MHCI/CD8 affinity threshold. Immunol Cell Biol 2017; 95:68-76. [PMID: 27670790 PMCID: PMC5215125 DOI: 10.1038/icb.2016.85] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 07/27/2016] [Accepted: 07/28/2016] [Indexed: 12/12/2022]
Abstract
The CD8 co-receptor engages peptide-major histocompatibility complex class I (pMHCI) molecules at a largely invariant site distinct from the T-cell receptor (TCR)-binding platform and enhances the sensitivity of antigen-driven activation to promote effective CD8+ T-cell immunity. A small increase in the strength of the pMHCI/CD8 interaction (~1.5-fold) can disproportionately amplify this effect, boosting antigen sensitivity by up to two orders of magnitude. However, recognition specificity is lost altogether with more substantial increases in pMHCI/CD8 affinity (~10-fold). In this study, we used a panel of MHCI mutants with altered CD8-binding properties to show that TCR-mediated antigen specificity is delimited by a pMHCI/CD8 affinity threshold. Our findings suggest that CD8 can be engineered within certain biophysical parameters to enhance the therapeutic efficacy of adoptive T-cell transfer irrespective of antigen specificity.
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Affiliation(s)
- Tamsin Dockree
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | | | - Mathew Clement
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Kristin Ladell
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - James E McLaren
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | | | - Emma Gostick
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Kelly L Miners
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Sian Llewellyn-Lacey
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - John S Bridgeman
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Stephen Man
- Institute of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Mick Bailey
- Faculty of Health Sciences, University of Bristol, Bristol, UK
| | - Scott R Burrows
- Cellular Immunology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - David A Price
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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27
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Heutinck KM, Yong SL, Tonneijck L, van den Heuvel H, van der Weerd NC, van der Pant KAMI, Bemelman FJ, Claas FHJ, Ten Berge IJM. Virus-Specific CD8(+) T Cells Cross-Reactive to Donor-Alloantigen Are Transiently Present in the Circulation of Kidney Transplant Recipients Infected With CMV and/or EBV. Am J Transplant 2016; 16:1480-91. [PMID: 26603974 DOI: 10.1111/ajt.13618] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/05/2015] [Accepted: 10/24/2015] [Indexed: 01/25/2023]
Abstract
T cells play a dual role in transplantation: They mediate transplant rejection and are crucial for virus control. Memory T cells generated in response to pathogens can cross-react to alloantigen, a phenomenon called heterologous immunity. Virus-specific CD8(+) T cells cross-reacting to donor-alloantigen might affect alloimmune responses and hamper tolerance induction following transplantation. Here, we longitudinally studied these cross-reactive cells in peripheral blood of 25 kidney transplant recipients with a cytomegalovirus and/or Epstein-Barr virus infection. Cross-reactive T cells were identified by flow cytometry as virus-specific T cells that proliferate in response to donor cells in a mixed-lymphocyte reaction. In 13 of 25 patients, we found cross-reactivity to donor cells for at least 1 viral epitope before (n = 7) and/or after transplantation (n = 8). Cross-reactive T cells were transiently present in the circulation, and their precursor frequency did not increase following transplantation or viral infection. Cross-reactive T cells expressed interferon-γ and CD107a in response to both alloantigen and viral peptide and resembled virus-specific T cells in phenotype and function. Their presence was not associated with impaired renal function, proteinuria, or rejection. In conclusion, virus-specific T cells that cross-react to donor-alloantigen are transiently detectable in the circulation of kidney transplant recipients.
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Affiliation(s)
- K M Heutinck
- Department of Experimental Immunology, Academic Medical Center, Amsterdam, The Netherlands.,Renal Transplant Unit, Department of Nephrology, Division of Internal Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - S L Yong
- Department of Experimental Immunology, Academic Medical Center, Amsterdam, The Netherlands.,Renal Transplant Unit, Department of Nephrology, Division of Internal Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - L Tonneijck
- Department of Experimental Immunology, Academic Medical Center, Amsterdam, The Netherlands
| | - H van den Heuvel
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - N C van der Weerd
- Renal Transplant Unit, Department of Nephrology, Division of Internal Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - K A M I van der Pant
- Renal Transplant Unit, Department of Nephrology, Division of Internal Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - F J Bemelman
- Renal Transplant Unit, Department of Nephrology, Division of Internal Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - F H J Claas
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - I J M Ten Berge
- Renal Transplant Unit, Department of Nephrology, Division of Internal Medicine, Academic Medical Center, Amsterdam, The Netherlands
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28
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Kanakry CG, Coffey DG, Towlerton AMH, Vulic A, Storer BE, Chou J, Yeung CCS, Gocke CD, Robins HS, O'Donnell PV, Luznik L, Warren EH. Origin and evolution of the T cell repertoire after posttransplantation cyclophosphamide. JCI Insight 2016; 1. [PMID: 27213183 DOI: 10.1172/jci.insight.86252] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Posttransplantation cyclophosphamide (PTCy) effectively prevents graft-versus-host disease (GVHD), but its immunologic impact is poorly understood. We assessed lymphocyte reconstitution via flow cytometry (n = 74) and antigen receptor sequencing (n = 35) in recipients of myeloablative, HLA-matched allogeneic BM transplantation using PTCy. Recovering T cells were primarily phenotypically effector memory with lower T cell receptor β (TRB) repertoire diversity than input donor repertoires. Recovering B cells were predominantly naive with immunoglobulin heavy chain locus (IGH) repertoire diversity similar to donors. Numerical T cell reconstitution and TRB diversity were strongly associated with recipient cytomegalovirus seropositivity. Global similarity between input donor and recipient posttransplant repertoires was uniformly low at 1-2 months after transplant but increased over the balance of the first posttransplant year. Blood TRB repertoires at ≥3 months after transplant were often dominated by clones present in the donor blood/marrow memory CD8+ compartment. Limited overlap was observed between the TRB repertoires of T cells infiltrating the skin or gastrointestinal tract versus the blood. Although public TRB sequences associated with herpesvirus- or alloantigen-specific CD8+ T cells were detected in some patients, posttransplant TRB and IGH repertoires were unique to each individual. These data define the immune dynamics occurring after PTCy and establish a benchmark against which immune recovery after other transplantation approaches can be compared.
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Affiliation(s)
- Christopher G Kanakry
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - David G Coffey
- Clinical Research Division, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, Washington, USA; Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Andrea M H Towlerton
- Clinical Research Division, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, Washington, USA
| | - Ante Vulic
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Barry E Storer
- Clinical Research Division, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, Washington, USA
| | - Jeffrey Chou
- Clinical Research Division, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, Washington, USA; Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Cecilia C S Yeung
- Clinical Research Division, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, Washington, USA; Department of Pathology, University of Washington, Seattle, Washington, USA
| | - Christopher D Gocke
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Harlan S Robins
- Public Health Sciences Division, FHCRC, Seattle, Washington, USA
| | - Paul V O'Donnell
- Clinical Research Division, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, Washington, USA; Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Leo Luznik
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Edus H Warren
- Clinical Research Division, Fred Hutchinson Cancer Research Center (FHCRC), Seattle, Washington, USA; Department of Medicine, University of Washington, Seattle, Washington, USA
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29
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WANG CHUNYAN, YU PEIFA, HE XIAOBING, FANG YONGXIANG, CHENG WENYU, JING ZHIZHONG. αβ T-cell receptor bias in disease and therapy (Review). Int J Oncol 2016; 48:2247-56. [DOI: 10.3892/ijo.2016.3492] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 03/21/2016] [Indexed: 11/06/2022] Open
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30
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CD8(+) T-cell pathogenicity in Rasmussen encephalitis elucidated by large-scale T-cell receptor sequencing. Nat Commun 2016; 7:11153. [PMID: 27040081 PMCID: PMC4822013 DOI: 10.1038/ncomms11153] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 02/25/2016] [Indexed: 11/29/2022] Open
Abstract
Rasmussen encephalitis (RE) is a rare paediatric epilepsy with uni-hemispheric inflammation and progressive neurological deficits. To elucidate RE immunopathology, we applied T-cell receptor (TCR) sequencing to blood (n=23), cerebrospinal fluid (n=2) and brain biopsies (n=5) of RE patients, and paediatric controls. RE patients present with peripheral CD8+ T-cell expansion and its strength correlates with disease severity. In addition, RE is the only paediatric epilepsy with prominent T-cell expansions in the CNS. Consistently, common clones are shared between RE patients, who also share MHC-I alleles. Public RE clones share Vβ genes and length of the CDR3. Rituximab/natalizumab/basiliximab treatment does not change TCR diversity, stem cell transplantation replaces the TCR repertoire with minimal overlap between donor and recipient, as observed in individual cases. Our study supports the hypothesis of an antigen-specific attack of peripherally expanded CD8+ lymphocytes against CNS structures in RE, which might be ameliorated by restricting access to the CNS. Rasmussen Encephalitis is a rare neurological disease accompanied by inflammation and T cell infiltration in the brain. Here the authors show that the severity of this disease correlates with clonal CD8 T cell expansion.
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31
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Covacu R, Philip H, Jaronen M, Almeida J, Kenison JE, Darko S, Chao CC, Yaari G, Louzoun Y, Carmel L, Douek DC, Efroni S, Quintana FJ. System-wide Analysis of the T Cell Response. Cell Rep 2016; 14:2733-44. [PMID: 26972015 PMCID: PMC4805488 DOI: 10.1016/j.celrep.2016.02.056] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 01/12/2016] [Accepted: 02/02/2016] [Indexed: 01/01/2023] Open
Abstract
The T cell receptor (TCR) controls the cellular adaptive immune response to antigens, but our understanding of TCR repertoire diversity and response to challenge is still incomplete. For example, TCR clones shared by different individuals with minimal alteration to germline gene sequences (public clones) are detectable in all vertebrates, but their significance is unknown. Although small in size, the zebrafish TCR repertoire is controlled by processes similar to those operating in mammals. Thus, we studied the zebrafish TCR repertoire and its response to stimulation with self and foreign antigens. We found that cross-reactive public TCRs dominate the T cell response, endowing a limited TCR repertoire with the ability to cope with diverse antigenic challenges. These features of vertebrate public TCRs might provide a mechanism for the rapid generation of protective T cell immunity, allowing a short temporal window for the development of more specific private T cell responses.
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Affiliation(s)
- Ruxandra Covacu
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Hagit Philip
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Merja Jaronen
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Jorge Almeida
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, MD 20892, USA
| | - Jessica E Kenison
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Samuel Darko
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, MD 20892, USA
| | - Chun-Cheih Chao
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Gur Yaari
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan 52900, Israel; Gonda Brain Research Center, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Liran Carmel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, MD 20892, USA.
| | - Sol Efroni
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel.
| | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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32
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Van Rhijn I, Moody DB. Donor Unrestricted T Cells: A Shared Human T Cell Response. THE JOURNAL OF IMMUNOLOGY 2015; 195:1927-32. [PMID: 26297792 DOI: 10.4049/jimmunol.1500943] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The now-famous term "restriction" derived from experiments in which T cells from Donor A failed to recognize Ags presented by cells from Donor B. Restriction results from interdonor variation in MHC genes. Donor restriction dominates immunologists' thinking about the T cell response because it governs organ transplantation and hinders the discovery of disease-associated Ags. However, other T cells can be considered "donor unrestricted" because their targets, CD1a, CD1b, CD1c, CD1d, or MR1, are expressed in a similar form among all humans. A striking feature of donor unrestricted T cells is the expression of invariant TCRs with nearly species-wide distribution. In this article, we review new evidence that donor unrestricted T cells are common in humans. NKT cells, mucosa-associated invariant T cells, and germline-encoded mycolyl-reactive T cells operate outside of the familiar principles of the MHC system, providing a broader picture of T cell function and new opportunities for therapy.
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Affiliation(s)
- Ildiko Van Rhijn
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115; and Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584CL Utrecht, the Netherlands
| | - D Branch Moody
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115; and
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33
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Multiplex Identification of Antigen-Specific T Cell Receptors Using a Combination of Immune Assays and Immune Receptor Sequencing. PLoS One 2015; 10:e0141561. [PMID: 26509579 PMCID: PMC4624875 DOI: 10.1371/journal.pone.0141561] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/10/2015] [Indexed: 01/05/2023] Open
Abstract
Monitoring antigen-specific T cells is critical for the study of immune responses and development of biomarkers and immunotherapeutics. We developed a novel multiplex assay that combines conventional immune monitoring techniques and immune receptor repertoire sequencing to enable identification of T cells specific to large numbers of antigens simultaneously. We multiplexed 30 different antigens and identified 427 antigen-specific clonotypes from 5 individuals with frequencies as low as 1 per million T cells. The clonotypes identified were validated several ways including repeatability, concordance with published clonotypes, and high correlation with ELISPOT. Applying this technology we have shown that the vast majority of shared antigen-specific clonotypes identified in different individuals display the same specificity. We also showed that shared antigen-specific clonotypes are simpler sequences and are present at higher frequencies compared to non-shared clonotypes specific to the same antigen. In conclusion this technology enables sensitive and quantitative monitoring of T cells specific for hundreds or thousands of antigens simultaneously allowing the study of T cell responses with an unprecedented resolution and scale.
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34
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Tscharke DC, Croft NP, Doherty PC, La Gruta NL. Sizing up the key determinants of the CD8+ T cell response. Nat Rev Immunol 2015; 15:705-16. [DOI: 10.1038/nri3905] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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35
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Ruggiero E, Nicolay JP, Fronza R, Arens A, Paruzynski A, Nowrouzi A, Ürenden G, Lulay C, Schneider S, Goerdt S, Glimm H, Krammer PH, Schmidt M, von Kalle C. High-resolution analysis of the human T-cell receptor repertoire. Nat Commun 2015; 6:8081. [PMID: 26324409 PMCID: PMC4569693 DOI: 10.1038/ncomms9081] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 07/15/2015] [Indexed: 02/06/2023] Open
Abstract
Unbiased dissection of T-cell receptor (TCR) repertoire diversity at the nucleotide level could provide important insights into human immunity. Here we show that TCR ligation-anchored-magnetically captured PCR (TCR-LA-MC PCR) identifies TCR α- and β-chain diversity without sequence-associated or quantitative restrictions in healthy and diseased conditions. TCR-LA-MC PCR identifies convergent recombination events, classifies different stages of cutaneous T-cell lymphoma in vivo and demonstrates TCR reactivation after in vitro cytomegalovirus stimulation. TCR-LA-MC PCR allows ultra-deep data access to both physiological TCR diversity and mechanisms influencing clonality in all clinical settings with restricted or distorted TCR repertoires. Immune system diversity is generated by V(D)J recombination, leading to clonal T-cell lineages. Here the authors investigate the events leading to T-cell diversity through the use of a modified PCR technique combined with deep sequencing.
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Affiliation(s)
- Eliana Ruggiero
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Jan P Nicolay
- Division of Immunogenetics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.,Department of Dermatology, Venereology and Allergology, University Medical Center, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Raffaele Fronza
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Anne Arens
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Anna Paruzynski
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Ali Nowrouzi
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Gökçe Ürenden
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Christina Lulay
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Sven Schneider
- Institute for Clinical Chemistry, University Medical Center, Ruprecht-Karls-University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Sergij Goerdt
- Department of Dermatology, Venereology and Allergology, University Medical Center, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Hanno Glimm
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Peter H Krammer
- Division of Immunogenetics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Manfred Schmidt
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Christof von Kalle
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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36
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Cukalac T, Kan WT, Dash P, Guan J, Quinn KM, Gras S, Thomas PG, La Gruta NL. Paired TCRαβ analysis of virus-specific CD8(+) T cells exposes diversity in a previously defined 'narrow' repertoire. Immunol Cell Biol 2015; 93:804-14. [PMID: 25804828 DOI: 10.1038/icb.2015.44] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/18/2015] [Accepted: 03/19/2015] [Indexed: 02/07/2023]
Abstract
T-cell receptor (TCR) usage has an important role in determining the outcome of CD8(+) cytotoxic T-lymphocyte responses to viruses and other pathogens. However, the characterization of TCR usage from which such conclusions are drawn is based on exclusive analysis of either the TCRα chain or, more commonly, the TCRβ chain. Here, we have used a multiplexed reverse transcription-PCR protocol to analyse the CDR3 regions of both TCRα and β chains from single naive or immune epitope-specific cells to provide a comprehensive picture of epitope-specific TCR usage and selection into the immune response. Analysis of TCR repertoires specific for three influenza-derived epitopes (D(b)NP(366), D(b)PA(224) and D(b)PB1-F2(62)) showed preferential usage of particular TCRαβ proteins in the immune repertoire relative to the naive repertoire, in some cases, resulting in a complete shift in TRBV preference or CDR3 length, and restricted repertoire diversity. The NP(366)-specific TCRαβ repertoire, previously defined as clonally restricted based on TCRβ analysis, was similarly diverse as the PA(224)- and PB1-F2(62)-specific repertoires. Intriguingly, preferred TCR characteristics (variable gene usage, CDR3 length and junctional gene usage) appeared to be able to confer specificity either independently or in concert with one another, depending on the epitope specificity. These data have implications for established correlations between the nature of the TCR repertoire and response outcomes after infection, and suggest that analysis of a subset of cells or a single TCR chain does not accurately depict the nature of the antigen-specific TCRαβ repertoire.
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Affiliation(s)
- Tania Cukalac
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute of Infection and Immunity, Melbourne, VIC, Australia
| | - Wan-Ting Kan
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute of Infection and Immunity, Melbourne, VIC, Australia
| | - Pradyot Dash
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jing Guan
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute of Infection and Immunity, Melbourne, VIC, Australia
| | - Kylie M Quinn
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute of Infection and Immunity, Melbourne, VIC, Australia
| | - Stephanie Gras
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, VIC, Australia
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Nicole L La Gruta
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute of Infection and Immunity, Melbourne, VIC, Australia
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37
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Narrowing of human influenza A virus-specific T cell receptor α and β repertoires with increasing age. J Virol 2015; 89:4102-16. [PMID: 25609818 DOI: 10.1128/jvi.03020-14] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
UNLABELLED Alterations in memory CD8 T cell responses may contribute to the high morbidity and mortality caused by seasonal influenza A virus (IAV) infections in older individuals. We questioned whether memory CD8 responses to this nonpersistent virus, to which recurrent exposure with new strains is common, changed over time with increasing age. Here, we show a direct correlation between increasing age and narrowing of the HLA-A2-restricted IAV Vα and Vβ T cell repertoires specific to M1 residues 58 to 66 (M158-66), which simultaneously lead to oligoclonal expansions, including the usage of a single identical VA12-JA29 clonotype in all eight older donors. The Vα repertoire of older individuals also had longer CDR3 regions with increased usage of G/A runs, whose molecular flexibility may enhance T cell receptor (TCR) promiscuity. Collectively, these results suggest that CD8 memory T cell responses to nonpersistent viruses like IAV in humans are dynamic, and with aging there is a reduced diversity but a preferential retention of T cell repertoires with features of enhanced cross-reactivity. IMPORTANCE With increasing age, the immune system undergoes drastic changes, and older individuals have declined resistance to infections. Vaccinations become less effective, and infection with influenza A virus in older individuals is associated with higher morbidity and mortality. Here, we questioned whether T cell responses directed against the highly conserved HLA-A2-restricted M158-66 peptide of IAV evolves with increasing age. Specifically, we postulated that CD8 T cell repertoires narrow with recurrent exposure and may thus be less efficient in response to new infections with new strains of IAV. Detailed analyses of the VA and VB TCR repertoires simultaneously showed a direct correlation between increasing age and narrowing of the TCR repertoire. Features of the TCRs indicated potentially enhanced cross-reactivity in all older donors. In summary, T cell repertoire analysis in older individuals may be useful as one of the predictors of protection after vaccination.
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Miles JJ, McCluskey J, Rossjohn J, Gras S. Understanding the complexity and malleability of T-cell recognition. Immunol Cell Biol 2015; 93:433-41. [PMID: 25582337 DOI: 10.1038/icb.2014.112] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 11/21/2014] [Accepted: 11/23/2014] [Indexed: 12/15/2022]
Abstract
T cells are the master regulators of immune system function, continually walking the biological tightrope between adequate host defence and accidental host pathology. Tolerance is maintained or broken through an intricate structural interplay between the T-cell receptor (TCR) and major histocompatibility complex (MHC) molecule cradling peptide antigens (p). Recent advances in structural biology have shown that the TCR/pMHC interface is surprising precise and extraordinarily malleable. We have seen that seemingly minor changes in the TCR/pMHC interface can abrogate function, as well as substantial conformational changes before and after TCR docking. Our understanding of T-cell biology has also been altered with the knowledge that MHC molecules can bind not only peptides, but also an array of natural and synthetic compounds. Here, we review some examples of the precision and flexibility intrinsic to the TCR/p/MHCI axis.
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Affiliation(s)
- John J Miles
- 1] QIMR Berghofer Medical Research Institute and QIMR Berghofer Centre for Immunotherapy and Vaccine Development, Brisbane, Queensland, Australia [2] School of Medicine, The University of Queensland, Brisbane, Queensland, Australia [3] Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales, UK
| | - James McCluskey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Jamie Rossjohn
- 1] Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales, UK [2] Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia [3] ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Stephanie Gras
- 1] Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria, Australia [2] ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
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Abstract
The unbiased, paired analysis of T-cell receptor (TCR) α- and β-chain usage at the single-cell level provides a valuable window of understanding into the TCR repertoire and the nature of the immune response. Earlier technologies for TCR repertoire analysis were often limited to examining TCR complementarity-determining region 3 (CDR3) β expression or required in vitro cloning procedures that can artificially skew the TCR repertoire from its in vivo state. We describe here a direct ex vivo, single-cell-based strategy for the clonotypic analysis of TCRαβ repertoires that utilizes multiplexed panels of TCRα and TCRβ-specific primers in a nested PCR to amplify expressed transcripts from individual, epitope-specific T cells. This strategy yields the paired TCRαβ sequences of any given population of αβ T cells of interest.
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Affiliation(s)
- Pradyot Dash
- Department of Immunology, St. Jude Children's Research Hospital, 262 Danny Thomas Place/MS 351, Memphis, TN, 38105, USA.
| | - George C Wang
- Department of Immunology, St. Jude Children's Research Hospital, 262 Danny Thomas Place/MS 351, Memphis, TN, 38105, USA.,Center of Excellence in Geriatric Medicine, Newton Medical Center, Sparta, NJ, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, 262 Danny Thomas Place/MS 351, Memphis, TN, 38105, USA.
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40
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Defining the alloreactive T cell repertoire using high-throughput sequencing of mixed lymphocyte reaction culture. PLoS One 2014; 9:e111943. [PMID: 25365040 PMCID: PMC4218856 DOI: 10.1371/journal.pone.0111943] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 10/02/2014] [Indexed: 12/20/2022] Open
Abstract
The cellular immune response is the most important mediator of allograft rejection and is a major barrier to transplant tolerance. Delineation of the depth and breadth of the alloreactive T cell repertoire and subsequent application of the technology to the clinic may improve patient outcomes. As a first step toward this, we have used MLR and high-throughput sequencing to characterize the alloreactive T cell repertoire in healthy adults at baseline and 3 months later. Our results demonstrate that thousands of T cell clones proliferate in MLR, and that the alloreactive repertoire is dominated by relatively high-abundance T cell clones. This clonal make up is consistently reproducible across replicates and across a span of three months. These results indicate that our technology is sensitive and that the alloreactive TCR repertoire is broad and stable over time. We anticipate that application of this approach to track donor-reactive clones may positively impact clinical management of transplant patients.
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41
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Madi A, Shifrut E, Reich-Zeliger S, Gal H, Best K, Ndifon W, Chain B, Cohen IR, Friedman N. T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity. Genome Res 2014; 24:1603-12. [PMID: 25024161 PMCID: PMC4199372 DOI: 10.1101/gr.170753.113] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The T-cell receptor (TCR) repertoire is formed by random recombinations of genomic precursor elements; the resulting combinatorial diversity renders unlikely extensive TCR sharing between individuals. Here, we studied CDR3β amino acid sequence sharing in a repertoire-wide manner, using high-throughput TCR-seq in 28 healthy mice. We uncovered hundreds of public sequences shared by most mice. Public CDR3 sequences, relative to private sequences, are two orders of magnitude more abundant on average, express restricted V/J segments, and feature high convergent nucleic acid recombination. Functionally, public sequences are enriched for MHC-diverse CDR3 sequences that were previously associated with autoimmune, allograft, and tumor-related reactions, but not with anti-pathogen-related reactions. Public CDR3 sequences are shared between mice of different MHC haplotypes, but are associated with different, MHC-dependent, V genes. Thus, despite their random generation process, TCR repertoires express a degree of uniformity in their post-genomic organization. These results, together with numerical simulations of TCR genomic rearrangements, suggest that biases and convergence in TCR recombination combine with ongoing selection to generate a restricted subset of self-associated, public CDR3 TCR sequences, and invite reexamination of the basic mechanisms of T-cell repertoire formation.
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Affiliation(s)
- Asaf Madi
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eric Shifrut
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Hilah Gal
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Katharine Best
- Division of Infection and Immunity, The Cruciform Building, UCL, London WC1 6BT, United Kingdom
| | - Wilfred Ndifon
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Benjamin Chain
- Division of Infection and Immunity, The Cruciform Building, UCL, London WC1 6BT, United Kingdom
| | - Irun R Cohen
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel;
| | - Nir Friedman
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel;
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42
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Cárdenas Sierra D, Vélez Colmenares G, Orfao de Matos A, Fiorentino Gómez S, Quijano Gómez SM. Age-associated Epstein-Barr virus-specific T cell responses in seropositive healthy adults. Clin Exp Immunol 2014; 177:320-32. [PMID: 24666437 PMCID: PMC4089182 DOI: 10.1111/cei.12337] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2014] [Indexed: 12/13/2022] Open
Abstract
Epstein-Barr virus (EBV) is present in 95% of the world's adult population. The immune response participates in immune vigilance and persistent infection control, and this condition is maintained by both a good quality (functionality) and quantity of specific T cells throughout life. In the present study, we evaluated EBV-specific CD4(+) and CD8(+) T lymphocyte responses in seropositive healthy individuals younger and older than 50 years of age. The assessment comprised the frequency, phenotype, functionality and clonotypic distribution of T lymphocytes. We found that in both age groups a similar EBV-specific T cell response was found, with overlapping numbers of tumour necrosis factor (TNF)-α(+) T lymphocytes (CD4(+) and CD8(+)) within the memory and effector cell compartments, in addition to monofunctional and multi-functional T cells producing interleukin (IL)-2 and/or interferon (IFN)-γ. However, individuals aged more than 50 years showed significantly higher frequencies of IL-2-producing CD4(+) T lymphocytes in association with greater production of soluble IFN-γ, TNF-α and IL-6 than subjects younger than 50 years. A polyclonal T cell receptor (TCR)-variable beta region (Vβ) repertoire exists in both age groups under basal conditions and in response to EBV; the major TCR families found in TNF-α(+) /CD4(+) T lymphocytes were Vβ1, Vβ2, Vβ17 and Vβ22 in both age groups, and the major TCR family in TNF-α(+) /CD8(+) T cells was Vβ13·1 for individuals younger than 50 years and Vβ9 for individuals aged more than 50 years. Our findings suggest that the EBV-specific T cell response (using a polyclonal stimulation model) is distributed throughout several T cell differentiation compartments in an age-independent manner and includes both monofunctional and multi-functional T lymphocytes.
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Affiliation(s)
- D Cárdenas Sierra
- Grupo de Inmunobiología y Biología Celular, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia
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43
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Eugster A, Lindner A, Heninger AK, Wilhelm C, Dietz S, Catani M, Ziegler AG, Bonifacio E. Measuring T cell receptor and T cell gene expression diversity in antigen-responsive human CD4+ T cells. J Immunol Methods 2013; 400-401:13-22. [PMID: 24239865 DOI: 10.1016/j.jim.2013.11.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 11/11/2013] [Indexed: 12/25/2022]
Abstract
T cells have diversity in TCR, epitope recognition, and cytokine production, and can be used for immune monitoring. Furthermore, clonal expansion of TCR families in disease may provide opportunities for TCR-directed therapies. We developed methodology for sequencing expressed genes of TCR alpha and beta chains from single cells and applied this to vaccine (tetanus-toxoid)-responsive CD4(+) T cells. TCR alpha and beta chains were both successfully sequenced in 1309 (43%) of 3038 CD4(+) T cells yielding 677 different receptors. TRAV and TRBV gene usage differed between tetanus-toxoid-responsive and non-responsive cells (p=0.004 and 0.0002), and there was extensive TCR diversity in tetanus-toxoid-responsive cells within individuals. Identical TCRs could be recovered in different samples from the same subject: TCRs identified after booster vaccination were frequent in pre-booster memory T cells (31% of pre-booster TCR), and also identified in pre-booster vaccination naïve cells (6.5%). No TCR was shared between subjects, but tetanus toxoid-responsive cells sharing one of their TCR chains were observed within and between subjects. Coupling single-cell gene expression profiling to TCR sequencing revealed examples of distinct cytokine profiles in cells bearing identical TCR. Novel molecular methodology demonstrates extensive diversity of Ag-responsive CD4(+) T cells within and between individuals.
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Affiliation(s)
- Anne Eugster
- DFG Research Center for Regenerative Therapies Dresden, Technische Universität Dresden, Germany; Paul Langerhans Institute Dresden, German Center for Diabetes Research (DZD).
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44
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Kobayashi E, Mizukoshi E, Kishi H, Ozawa T, Hamana H, Nagai T, Nakagawa H, Jin A, Kaneko S, Muraguchi A. A new cloning and expression system yields and validates TCRs from blood lymphocytes of patients with cancer within 10 days. Nat Med 2013; 19:1542-6. [PMID: 24121927 DOI: 10.1038/nm.3358] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 04/08/2013] [Indexed: 12/19/2022]
Abstract
Antigen-specific T cell therapy, or T cell receptor (TCR) gene therapy, is a promising immunotherapy for infectious diseases and cancers. However, a suitable rapid and direct screening system for antigen-specific TCRs is not available. Here, we report an efficient cloning and functional evaluation system to determine the antigen specificity of TCR cDNAs derived from single antigen-specific human T cells within 10 d. Using this system, we cloned and analyzed 380 Epstein-Barr virus-specific TCRs from ten healthy donors with latent Epstein-Barr virus infection and assessed the activity of cytotoxic T lymphocytes (CTLs) carrying these TCRs against antigenic peptide-bearing target cells. We also used this system to clone tumor antigen-specific TCRs from peptide-vaccinated patients with cancer. We obtained 210 tumor-associated antigen-specific TCRs and demonstrated the cytotoxic activity of CTLs carrying these TCRs against peptide-bearing cells. This system may provide a fast and powerful approach for TCR gene therapy for infectious diseases and cancers.
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Affiliation(s)
- Eiji Kobayashi
- 1] Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan. [2]
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45
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Jackson KJL, Kidd MJ, Wang Y, Collins AM. The shape of the lymphocyte receptor repertoire: lessons from the B cell receptor. Front Immunol 2013; 4:263. [PMID: 24032032 PMCID: PMC3759170 DOI: 10.3389/fimmu.2013.00263] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/19/2013] [Indexed: 11/13/2022] Open
Abstract
Both the B cell receptor (BCR) and the T cell receptor (TCR) repertoires are generated through essentially identical processes of V(D)J recombination, exonuclease trimming of germline genes, and the random addition of non-template encoded nucleotides. The naïve TCR repertoire is constrained by thymic selection, and TCR repertoire studies have therefore focused strongly on the diversity of MHC-binding complementarity determining region (CDR) CDR3. The process of somatic point mutations has given B cell studies a major focus on variable (IGHV, IGLV, and IGKV) genes. This in turn has influenced how both the naïve and memory BCR repertoires have been studied. Diversity (D) genes are also more easily identified in BCR VDJ rearrangements than in TCR VDJ rearrangements, and this has allowed the processes and elements that contribute to the incredible diversity of the immunoglobulin heavy chain CDR3 to be analyzed in detail. This diversity can be contrasted with that of the light chain where a small number of polypeptide sequences dominate the repertoire. Biases in the use of different germline genes, in gene processing, and in the addition of non-template encoded nucleotides appear to be intrinsic to the recombination process, imparting "shape" to the repertoire of rearranged genes as a result of differences spanning many orders of magnitude in the probabilities that different BCRs will be generated. This may function to increase the precursor frequency of naïve B cells with important specificities, and the likely emergence of such B cell lineages upon antigen exposure is discussed with reference to public and private T cell clonotypes.
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Affiliation(s)
- Katherine J. L. Jackson
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Marie J. Kidd
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Yan Wang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Andrew M. Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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46
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Burrows SR, Miles JJ. Immune parameters to consider when choosing T-cell receptors for therapy. Front Immunol 2013; 4:229. [PMID: 23935599 PMCID: PMC3733007 DOI: 10.3389/fimmu.2013.00229] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2013] [Accepted: 07/22/2013] [Indexed: 11/13/2022] Open
Abstract
T-cell receptor (TCR) therapy has arrived as a realistic treatment option for many human diseases. TCR gene therapy allows for the mass redirection of T-cells against a defined antigen while high affinity TCR engineering allows for the creation of a new class of soluble drugs. However, deciding which TCR blueprint to take forward for gene therapy or engineering is difficult. More than one quintillion TCR combinations can be generated by somatic recombination and we are only now beginning to appreciate that not all are functionally equal. TCRs can exhibit high or low degrees of HLA-restricted cross-reactivity and alloreact against one or a combination of HLA alleles. Identifying TCR candidates with high specificity and minimal cross-reactivity/alloreactivity footprints before engineering is obviously highly desirable. Here we will summarize what we currently know about TCR biology with regard to immunoengineering.
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Affiliation(s)
- Scott R Burrows
- Human Immunity Laboratory and Cellular Immunology Laboratory, Queensland Institute of Medical Research , Brisbane, QLD , Australia ; School of Medicine, The University of Queensland , Brisbane, QLD , Australia
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47
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Frigstad T, Løset GÅ, Sandlie I, Bogen B. A public T cell receptor recognized by a monoclonal antibody specific for the D-J junction of the β-chain. Scand J Immunol 2013; 78:345-51. [PMID: 23841814 DOI: 10.1111/sji.12098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 06/27/2013] [Indexed: 11/30/2022]
Abstract
It is becoming increasingly clear that T cell responses against many antigens are dominated by public α/β T cell receptors (TCRs) with restricted heterogeneity. Because expression of public TCRs may be related to resistance, or predisposition to diseases, it is relevant to measure their frequencies. Although staining with tetrameric peptide/major histocompatibility complex (pMHC) molecules gives information about specificity, it does not give information about the TCR composition of the individual T cells that stain. Moreover, next-generation sequencing of TCR does not yield information on pairing of α- and β-chains in single T cells. In an effort to overcome these limitations, we have here investigated the possibility of raising a monoclonal antibody (moAb) that recognizes a public TCR. As a model system, we have used T cells responding to the 91-101 CDR3 peptide of an Ig L-chain (λ2³¹⁵), presented by the MHC class II molecule I-E(d). The CD4⁺ T cell responses against this pMHC are dominated by a receptor composed of Vα3Jα1;Vβ6DβJβ1.1. Even the V(D)J junctions are to a large extent shared between T cell clones derived from different BALB/c mice. We here describe a murine moAb (AB10) of B10.D2 origin that recognizes this public TCR, while binding to peripheral T cells is negligible. Binding of the moAb is abrogated by introduction of two Gly residues in the D-J junction of the CDR3 of the β-chain. A model for the public TCR determinant is presented.
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Affiliation(s)
- T Frigstad
- Centre for Immune Regulation and Institute of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
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48
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Eckle SBG, Rossjohn J, McCluskey J. Alloreactivity. Methods Mol Biol 2013; 1034:3-39. [PMID: 23775729 DOI: 10.1007/978-1-62703-493-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
The alloimmune response between individuals genetically disparate for antigens encoded within the major histocompatibility complex (MHC) remains a substantial barrier to transplantation of solid organs, tissues, and hematopoietic stem cells. Alloreactivity has been an immunological paradox because of its apparent contradiction to the requirement of MHC restriction for the induction of normal T lymphocyte mediated immune responses. Through crystallographic analyses and experimental systems utilizing murine CD8(+) cytolytic T cell clones, major advances have been achieved in understanding the molecular and structural basis of T cell receptor recognition of MHC-peptide complexes and the basis of T cell mediated alloreactivity. These studies have further provided an explanation for the relatively high frequencies of alloreactive T cells compared to the frequencies of T cells for microbial derived antigens.
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Affiliation(s)
- Sidonia B G Eckle
- Department of Microbiology & Immunology, University of Melbourne, Parkville, VIC, Australia
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49
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Koning D, Costa AI, Hoof I, Miles JJ, Nanlohy NM, Ladell K, Matthews KK, Venturi V, Schellens IMM, Borghans JAM, Keşmir C, Price DA, van Baarle D. CD8+ TCR Repertoire Formation Is Guided Primarily by the Peptide Component of the Antigenic Complex. THE JOURNAL OF IMMUNOLOGY 2012; 190:931-9. [DOI: 10.4049/jimmunol.1202466] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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50
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D'Orsogna LJ, van den Heuvel H, van der Meer-Prins EMW, Roelen DL, Doxiadis IIN, Claas FHJ. Stimulation of human EBV- and CMV-specific cytolytic effector function using allogeneic HLA molecules. THE JOURNAL OF IMMUNOLOGY 2012; 189:4825-31. [PMID: 23077240 DOI: 10.4049/jimmunol.1201034] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Viral infection is a major cause of morbidity and mortality, and there are few therapeutic options available to augment a virus-specific T cell response. Although allo-HLA cross-reactivity from virus-specific memory T cells is common, it is unclear whether priming with specific allogeneic cells could conversely elicit a viral peptide/self-HLA restricted cytotoxic T cell response in humans. First, we used the previously described allo-HLA-B*44:02 cross-reactivity of EBV peptide/HLA-B8 restricted T cells, to determine whether allogeneic HLA stimulation can elicit a cytolytic immune response against EBV. HLA-B8(+) HLA-B44(-) EBV-seropositive PBMCs were stimulated with either HLA-B*44:02(+) or HLA-B*44:03(+) mismatched irradiated PBMCs in a 7-10 d MLR. The allo-HLA stimulated responder cells were then evaluated for cytotoxicity using EBV peptide loaded autologous target cells and unloaded HLA-B8(+) EBV LCL target cells. PBMCs from EBV-seropositive donors gained EBV-specific cytolytic effector function following specific allo-HLA stimulation. Finally, we also elicited cytolytic CMV-specific responses using specific allogeneic cell stimulation, to confirm that this technique can be used to elicit viral peptide/self-HLA restricted responses even from nonpublic TCR responses. Allogeneic cell stimulation used as a cell therapy may be a potential tool to augment an antiviral T cell response in patients with EBV or CMV infection.
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Affiliation(s)
- Lloyd J D'Orsogna
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre, Leiden 2300 RC, The Netherlands.
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