1
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O’Reilly RJ, Prockop S, Oved JH. Virus-specific T-cells from third party or transplant donors for treatment of EBV lymphoproliferative diseases arising post hematopoietic cell or solid organ transplantation. Front Immunol 2024; 14:1290059. [PMID: 38274824 PMCID: PMC10808771 DOI: 10.3389/fimmu.2023.1290059] [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: 09/06/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
EBV+ lymphomas constitute a significant cause of morbidity and mortality in recipients of allogeneic hematopoietic cell (HCT) and solid organ transplants (SOT). Phase I and II trials have shown that in HCT recipients, adoptive transfer of EBV-specific T-cells from the HCT donor can safely induce durable remissions of EBV+ lymphomas including 70->90% of patients who have failed to respond to treatment with Rituximab. More recently, EBV-specific T-cells generated from allogeneic 3rd party donors have also been shown to induce durable remission of EBV+ lymphomas in Rituximab refractory HCT and SOT recipients. In this review, we compare results of phase I and II trials of 3rd party and donor derived EBV-specific T-cells. We focus on the attributes and limitations of each product in terms of access, safety, responses achieved and durability. The limited data available regarding donor and host factors contributing to T cell persistence is also described. We examine factors contributing to treatment failures and approaches to prevent or salvage relapse. Lastly, we summarize strategies to further improve results for virus-specific immunotherapies for post-transplant EBV lymphomas.
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Affiliation(s)
- Richard J. O’Reilly
- Department of Pediatrics, Stem Cell Transplantation and Cellular Therapies Service, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Susan Prockop
- Pediatric Stem Cell Transplantation, Boston Children’s Hospital/Dana-Farber Cancer Institute, Boston, MA, United States
| | - Joseph H. Oved
- Department of Pediatrics, Stem Cell Transplantation and Cellular Therapies Service, Memorial Sloan Kettering Cancer Center, New York, NY, United States
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2
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Angelakakis G, Serraneau KS, Barker VR, Callahan BM, Tong WL, Zaman S, Huda TI, Blanck G. TCR gene segment usage and HLA alleles that are associated with cancer survival rates also represent racial disparities. Int J Immunogenet 2023; 50:41-47. [PMID: 36585798 DOI: 10.1111/iji.12610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 01/01/2023]
Abstract
Understanding racial disparities in cancer outcomes continues to be a challenge, with likely many factors at play, including socioeconomic factors and genetic polymorphisms impacting basic cellular and molecular functions. Additionally, it is possible that specific combinations of environment and genetics have specific impacts. T-cell receptor (TCR) gene segment usage, HLA allele combinations have been associated with autoimmune and infectious disease courses, and more recently, TCR gene segment usage, HLA allele combinations have been associated with distinct survival outcomes in cancer as well. We examined several such, previously reported cancer-related TCR gene segment usage, HLA allele combinations for evidence of racial disparities, with regard to the prevalence of the combination in different racial groups. Results indicated that TCR gene segment usage, potentially reflecting environmental factors related to previous pathogen exposure, in combination with certain HLA alleles or independently, may represent a novel explanation for racial disparities in cancer outcomes. Overall, at this point, a genetic connection to racial disparities in cancer outcomes is detectable but remains modest, suggesting that other factors, such as socioeconomic factors, remain as important considerations.
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Affiliation(s)
- George Angelakakis
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Karisa S Serraneau
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Vayda R Barker
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Blake M Callahan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Wei Lue Tong
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Saif Zaman
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Taha I Huda
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA.,Immunology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
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3
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Morita D, Asa M, Sugita M. Engagement with the TCR induces plasticity in antigenic ligands bound to MHC class I and CD1 molecules. Int Immunol 2023; 35:7-17. [PMID: 36053252 DOI: 10.1093/intimm/dxac046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 08/31/2022] [Indexed: 01/25/2023] Open
Abstract
Complementarity-determining regions (CDRs) of αβ T-cell receptors (TCRs) sense peptide-bound MHC (pMHC) complexes via chemical interactions, thereby mediating antigen specificity and MHC restriction. Flexible finger-like movement of CDR loops contributes to the establishment of optimal interactions with pMHCs. In contrast, peptide ligands captured in MHC molecules are considered more static because of the rigid hydrogen-bond network that stabilizes peptide ligands in the antigen-binding groove of MHC molecules. An array of crystal structures delineating pMHC complexes in TCR-docked and TCR-undocked forms is now available, which enables us to assess TCR engagement-induced conformational changes in peptide ligands. In this short review, we overview conformational changes in MHC class I-bound peptide ligands upon TCR docking, followed by those for CD1-bound glycolipid ligands. Finally, we analyze the co-crystal structure of the TCR:lipopeptide-bound MHC class I complex that we recently reported. We argue that TCR engagement-induced conformational changes markedly occur in lipopeptide ligands, which are essential for exposure of a primary T-cell epitope to TCRs. These conformational changes are affected by amino acid residues, such as glycine, that do not interact directly with TCRs. Thus, ligand recognition by specific TCRs involves not only T-cell epitopes but also non-epitopic amino acid residues. In light of their critical function, we propose to refer to these residues as non-epitopic residues affecting ligand plasticity and antigenicity (NR-PA).
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Affiliation(s)
- Daisuke Morita
- Laboratory of Cell Regulation, Institute for Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.,Laboratory of Cell Regulation and Molecular Network, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Minori Asa
- Laboratory of Cell Regulation, Institute for Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.,Laboratory of Cell Regulation and Molecular Network, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masahiko Sugita
- Laboratory of Cell Regulation, Institute for Life and Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.,Laboratory of Cell Regulation and Molecular Network, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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4
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Ma K, Chai Y, Guan J, Tan S, Qi J, Kawana-Tachikawa A, Dong T, Iwamoto A, Shi Y, Gao GF. Molecular Basis for the Recognition of HIV Nef138-8 Epitope by a Pair of Human Public T Cell Receptors. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:1652-1661. [PMID: 36130828 DOI: 10.4049/jimmunol.2200191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 08/30/2022] [Indexed: 11/07/2022]
Abstract
Cross-recognized public TCRs against HIV epitopes have been proposed to be important for the control of AIDS disease progression and HIV variants. The overlapping Nef138-8 and Nef138-10 peptides from the HIV Nef protein are HLA-A24-restricted immunodominant T cell epitopes, and an HIV mutant strain with a Y139F substitution in Nef protein can result in immune escape and is widespread in Japan. Here, we identified a pair of public TCRs specific to the HLA-A24-restricted Nef-138-8 epitope using PBMCs from White and Japanese patients, respectively, namely TD08 and H25-11. The gene use of the variable domain for TD08 and H25-11 is TRAV8-3, TRAJ10 for the α-chain and TRBV7-9, TRBD1*01, TRBJ2-5 for the β-chain. Both TCRs can recognize wild-type and Y2F-mutated Nef138-8 epitopes. We further determined three complex structures, including TD08/HLA-A24-Nef138-8, H25-11/HLA-A24-Nef138-8, and TD08/HLA-A24-Nef138-8 (2F). Then, we revealed the molecular basis of the public TCR binding to the peptide HLA, which mostly relies on the interaction between the TCR and HLA and can tolerate the mutation in the Nef138-8 peptide. These findings promote the molecular understanding of T cell immunity against HIV epitopes and provide an important basis for the engineering of TCRs to develop T cell-based immunotherapy against HIV infection.
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Affiliation(s)
- Keke Ma
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.,Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yan Chai
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jiawei Guan
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuguang Tan
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jianxun Qi
- Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ai Kawana-Tachikawa
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tao Dong
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, UK; and
| | - Aikichi Iwamoto
- Department of Research Promotion, Japan Agency for Medical Research and Development, Tokyo, Japan
| | - Yi Shi
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China; .,Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - George F Gao
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China; .,Chinese Academy of Sciences Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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5
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T. RR, Smith JC. Structural patterns in class 1 major histocompatibility complex‐restricted nonamer peptide binding to T‐cell receptors. Proteins 2022; 90:1645-1654. [DOI: 10.1002/prot.26343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/12/2022] [Accepted: 03/27/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Rajitha Rajeshwar T.
- Department of Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville Tennessee USA
- UT/ORNL Center for Molecular Biophysics Oak Ridge National Laboratory Oak Ridge Tennessee USA
| | - Jeremy C. Smith
- Department of Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville Tennessee USA
- UT/ORNL Center for Molecular Biophysics Oak Ridge National Laboratory Oak Ridge Tennessee USA
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6
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Clonotype pattern in T-cell lymphomas map the cell of origin to immature lymphoid precursors. Blood Adv 2022; 6:2334-2345. [PMID: 35015812 PMCID: PMC9006294 DOI: 10.1182/bloodadvances.2021005884] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/07/2021] [Indexed: 11/20/2022] Open
Abstract
Mature T-cell lymphomas (TCLs) are rare, clinically heterogeneous hematologic cancers of high medical need. TCLs have inferior prognosis which is attributed to poor understanding of their pathogenesis. Based on phenotypic similarities between normal and neoplastic lymphocytes it has been assumed that TCLs develop in the periphery, directly from various subtypes of normal T-cells. To address the debated question of the cell of origin in TCLs we analyzed to identify the highly variable complementarity determining regions (CDR3) regions of T-cell receptor (TCR) to trace the clonal history of the T-cells. We have collected previously published whole genome -exome, and -transcriptome sequencing data from 574 TCL patients. TCR clonotypes were identified by de novo assembly of CDR3 regions of TCR γ, β and α. We have found that the vast majority of TCLs are clonotypically oligoclonal, although the pattern oligoclonality varied. Anaplastic large cell lymphoma was most diverse comprising multiple clonotypes of TCRγ, β and α whereas adult T-cell lymphoma/leukemia and peripheral T-cell lymphomas often showed monoclonality for TCRγ and β but had diverse TCRα clonotypes. These patterns of rearrangements indicated that TCLs are initiated at the level of the lymphoid precursor. In keeping with this hypothesis, TCR rearrangements in TCLs resembled the pattern seen in the human thymus showing biased usage of V and J segments of high combinatorial probability resulting in recurrent, "public" CDR3 sequences shared across unrelated patients and different clinical TCL entities. Clonotypically diverse initiating cells may seed target tissues being responsible for disease relapses after therapy.
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7
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Wu D, Kolesnikov A, Yin R, Guest JD, Gowthaman R, Shmelev A, Serdyuk Y, Dianov DV, Efimov GA, Pierce BG, Mariuzza RA. Structural assessment of HLA-A2-restricted SARS-CoV-2 spike epitopes recognized by public and private T-cell receptors. Nat Commun 2022; 13:19. [PMID: 35013235 PMCID: PMC8748687 DOI: 10.1038/s41467-021-27669-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 12/02/2021] [Indexed: 12/23/2022] Open
Abstract
T cells play a vital role in combatting SARS-CoV-2 and forming long-term memory responses. Whereas extensive structural information is available on neutralizing antibodies against SARS-CoV-2, such information on SARS-CoV-2-specific T-cell receptors (TCRs) bound to their peptide-MHC targets is lacking. Here we determine the structures of a public and a private TCR from COVID-19 convalescent patients in complex with HLA-A2 and two SARS-CoV-2 spike protein epitopes (YLQ and RLQ). The structures reveal the basis for selection of particular TRAV and TRBV germline genes by the public but not the private TCR, and for the ability of the TCRs to recognize natural variants of RLQ but not YLQ. Neither TCR recognizes homologous epitopes from human seasonal coronaviruses. By elucidating the mechanism for TCR recognition of an immunodominant yet variable epitope (YLQ) and a conserved but less commonly targeted epitope (RLQ), this study can inform prospective efforts to design vaccines to elicit pan-coronavirus immunity.
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MESH Headings
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/metabolism
- CD4-Positive T-Lymphocytes/virology
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- CD8-Positive T-Lymphocytes/virology
- COVID-19/immunology
- COVID-19/virology
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/metabolism
- HLA-A2 Antigen/chemistry
- HLA-A2 Antigen/immunology
- HLA-A2 Antigen/metabolism
- Humans
- Immunodominant Epitopes/immunology
- Immunodominant Epitopes/metabolism
- Jurkat Cells
- K562 Cells
- Peptides/chemistry
- Peptides/immunology
- Peptides/metabolism
- Protein Binding
- Protein Conformation
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- SARS-CoV-2/immunology
- SARS-CoV-2/metabolism
- SARS-CoV-2/physiology
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
- Surface Plasmon Resonance/methods
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Affiliation(s)
- Daichao Wu
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, USA
- Department of Histology and Embryology, Hengyang Medical School, University of South China, Hengyang, Hunan, 421001, China
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Alexander Kolesnikov
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Rui Yin
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Johnathan D Guest
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Ragul Gowthaman
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, USA
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Anton Shmelev
- National Research Center for Hematology, Moscow, Russia
| | - Yana Serdyuk
- National Research Center for Hematology, Moscow, Russia
| | | | | | - Brian G Pierce
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, USA.
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA.
| | - Roy A Mariuzza
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, 20850, USA.
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA.
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8
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Clark F, Gil A, Thapa I, Aslan N, Ghersi D, Selin LK. Cross-reactivity influences changes in human influenza A virus and Epstein Barr virus specific CD8 memory T cell receptor alpha and beta repertoires between young and old. Front Immunol 2022; 13:1011935. [PMID: 36923729 PMCID: PMC10009332 DOI: 10.3389/fimmu.2022.1011935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 12/30/2022] [Indexed: 03/03/2023] Open
Abstract
Older people have difficulty controlling infection with common viruses such as influenza A virus (IAV), RNA virus which causes recurrent infections due to a high rate of genetic mutation, and Epstein Barr virus (EBV), DNA virus which persists in B cells for life in the 95% of people that become acutely infected. We questioned whether changes in epitope-specific memory CD8 T cell receptor (TCR) repertoires to these two common viruses could occur with increasing age and contribute to waning immunity. We compared CD8 memory TCR alpha and beta repertoires in two HLA-A2+ EBV- and IAV-immune donors, young (Y) and older (O) donors to three immunodominant epitopes known to be cross-reactive, IAV-M158-66 (IAV-M1), EBV-BMLF1280-288 (EBV-BM), and EBV-BRLF1109-117 (EBV-BR). We, therefore, also designed these studies to examine if TCR cross-reactivity could contribute to changes in repertoire with increasing age. TCR high throughput sequencing showed a significant difference in the pattern of TRBV usage between Y and O. However, there were many more differences in AV and AJ usage, between the age groups suggesting that changes in TCRα usage may play a greater role in evolution of the TCR repertoire emphasizing the importance of studying TRAV repertoires. With increasing age there was a preferential retention of TCR for all three epitopes with features in their complementarity-determining region (CDR3) that increased their ease of generation, and their cross-reactive potential. Young and older donors differed in the patterns of AV/AJ and BV/BJ pairings and usage of dominant CDR3 motifs specific to all three epitopes. Both young and older donors had cross-reactive responses between these 3 epitopes, which were unique and differed from the cognate responses having features that suggested they could interact with either ligand. There was an increased tendency for the classic IAV-M1 specific clone BV19-IRSS-JB2.7/AV27-CAGGGSQGNLIF-AJ42 to appear among the cross-reactive clones, suggesting that the dominance of this clone may relate to its cross-reactivity with EBV. These results suggest that although young and older donors retain classic TCR features for each epitope their repertoires are gradually changing with age, maintaining TCRs that are cross-reactive between these two common human viruses, one with recurrent infections and the other a persistent virus which frequently reactivates.
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Affiliation(s)
- Fransenio Clark
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Anna Gil
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Ishwor Thapa
- School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, NE, United States
| | - Nuray Aslan
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Dario Ghersi
- School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, NE, United States
| | - Liisa K Selin
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, United States
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9
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Abstract
Grouping TCRs on the similarity of CDR3 sequences could effectively cluster them by specificity. Three versions of the GLIPH algorithm are described briefly here, with instructions to use GLIPH algorithms to cluster TCRs by specificity.
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Affiliation(s)
- Chunlin Wang
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA.
| | - Huang Huang
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark M Davis
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
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10
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Patel DN, Yeagley M, Arturo JF, Falasiri S, Chobrutskiy BI, Gozlan EC, Blanck G. A comparison of immune receptor recombination databases sourced from tumour exome or RNAseq files: Verifications of immunological distinctions between primary and metastatic melanoma. Int J Immunogenet 2021; 48:409-418. [PMID: 34298587 DOI: 10.1111/iji.12550] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 07/11/2021] [Indexed: 02/07/2023]
Abstract
It became apparent several years ago that RNAseq and exome files prepared from tissue could be mined for adaptive immune receptor (IR) recombinations, which has given extra value to datasets originally intended for gene expression or mutation studies. For example, recovery of IR recombination reads from tumour specimen genomics files can correlate with survival rates. In particular, many benchmarking processes have been applied to the two sets of the IR recombination reads obtained from the cancer genome atlas files, but these two sets have never been directly compared. Here we show that both sets largely agree regarding several parameters. For example, recovery of TRB recombination reads from both WXS and RNAseq files representing metastatic melanoma was associated with a better outcome (p < .0004 in both cases); and T-cell receptor recombination read recovery, for both genomics file types, associated very strongly with T-cell gene expression markers. However, the use of CDR3 chemical features for survival distinctions was not consistent. This topic, and the surprising result that both datasets indicated that primary melanoma with recovery of IR recombination reads, in stark contrast to metastatic melanoma, represents a worse outcome, are discussed.
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Affiliation(s)
- Dhruv N Patel
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Michelle Yeagley
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Juan F Arturo
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Shayan Falasiri
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Boris I Chobrutskiy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Etienne C Gozlan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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11
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Zhang W, Hawkins PG, He J, Gupta NT, Liu J, Choonoo G, Jeong SW, Chen CR, Dhanik A, Dillon M, Deering R, Macdonald LE, Thurston G, Atwal GS. A framework for highly multiplexed dextramer mapping and prediction of T cell receptor sequences to antigen specificity. SCIENCE ADVANCES 2021; 7:7/20/eabf5835. [PMID: 33990328 PMCID: PMC8121425 DOI: 10.1126/sciadv.abf5835] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/25/2021] [Indexed: 05/04/2023]
Abstract
T cell receptor (TCR) antigen-specific recognition is essential for the adaptive immune system. However, building a TCR-antigen interaction map has been challenging due to the staggering diversity of TCRs and antigens. Accordingly, highly multiplexed dextramer-TCR binding assays have been recently developed, but the utility of the ensuing large datasets is limited by the lack of robust computational methods for normalization and interpretation. Here, we present a computational framework comprising a novel method, ICON (Integrative COntext-specific Normalization), for identifying reliable TCR-pMHC (peptide-major histocompatibility complex) interactions and a neural network-based classifier TCRAI that outperforms other state-of-the-art methods for TCR-antigen specificity prediction. We further demonstrated that by combining ICON and TCRAI, we are able to discover novel subgroups of TCRs that bind to a given pMHC via different mechanisms. Our framework facilitates the identification and understanding of TCR-antigen-specific interactions for basic immunological research and clinical immune monitoring.
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Affiliation(s)
- Wen Zhang
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA.
| | - Peter G Hawkins
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Jing He
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Namita T Gupta
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Jinrui Liu
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Gabrielle Choonoo
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Se W Jeong
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Calvin R Chen
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Ankur Dhanik
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Myles Dillon
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Raquel Deering
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Lynn E Macdonald
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Gavin Thurston
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Gurinder S Atwal
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA.
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12
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Yiu HH, Schoettle LN, Garcia‐Neuer M, Blattman JN, Johnson PLF. Selection influences naive CD8+ TCR-β repertoire sharing. Immunology 2021; 162:464-475. [PMID: 33345304 PMCID: PMC7968400 DOI: 10.1111/imm.13299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 11/22/2020] [Accepted: 11/29/2020] [Indexed: 11/28/2022] Open
Abstract
Within each individual, the adaptive immune system generates a repertoire of cells expressing receptors capable of recognizing diverse potential pathogens. The theoretical diversity of the T-cell receptor (TCR) repertoire exceeds the actual size of the T-cell population in an individual by several orders of magnitude - making the observation of identical TCRs in different individuals extremely improbable if all receptors were equally likely. Despite this disparity between the theoretical and the realized diversity of the repertoire, these 'public' receptor sequences have been identified in autoimmune, cancer and pathogen interaction contexts. Biased generation processes explain the presence of public TCRs in the naive repertoire, but do not adequately explain the different abundances of these public TCRs. We investigate and characterize the distribution of genomic TCR-β sequences of naive CD8+ T cells from three genetically identical mice, comparing non-productive (non-functional sequences) and productive sequences. We find public TCR-β sequences at higher abundances compared with unshared sequences in the productive, but not in the non-productive, repertoire. We show that neutral processes such as recombination biases, codon degeneracy and generation probability do not fully account for these differences, and conclude that thymic or peripheral selection plays an important role in increasing the abundances of public TCR-β sequences.
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MESH Headings
- Animals
- CD8-Positive T-Lymphocytes/physiology
- Cells, Cultured
- Clonal Selection, Antigen-Mediated
- Codon Usage
- Genes, T-Cell Receptor beta/genetics
- Humans
- Mice
- Mice, Inbred C57BL
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Recombination, Genetic
- Thymus Gland/immunology
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Affiliation(s)
- Hao H. Yiu
- Department of BiologyUniversity of MarylandCollege ParkMDUSA
| | - Louis N. Schoettle
- School of Life SciencesThe Biodesign InstituteArizona State UniversityTempeAZUSA
| | - Marlene Garcia‐Neuer
- School of Life SciencesThe Biodesign InstituteArizona State UniversityTempeAZUSA
| | - Joseph N. Blattman
- School of Life SciencesThe Biodesign InstituteArizona State UniversityTempeAZUSA
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13
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DeepTCR is a deep learning framework for revealing sequence concepts within T-cell repertoires. Nat Commun 2021; 12:1605. [PMID: 33707415 PMCID: PMC7952906 DOI: 10.1038/s41467-021-21879-w] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 02/15/2021] [Indexed: 01/31/2023] Open
Abstract
Deep learning algorithms have been utilized to achieve enhanced performance in pattern-recognition tasks. The ability to learn complex patterns in data has tremendous implications in immunogenomics. T-cell receptor (TCR) sequencing assesses the diversity of the adaptive immune system and allows for modeling its sequence determinants of antigenicity. We present DeepTCR, a suite of unsupervised and supervised deep learning methods able to model highly complex TCR sequencing data by learning a joint representation of a TCR by its CDR3 sequences and V/D/J gene usage. We demonstrate the utility of deep learning to provide an improved 'featurization' of the TCR across multiple human and murine datasets, including improved classification of antigen-specific TCRs and extraction of antigen-specific TCRs from noisy single-cell RNA-Seq and T-cell culture-based assays. Our results highlight the flexibility and capacity for deep neural networks to extract meaningful information from complex immunogenomic data for both descriptive and predictive purposes.
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14
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Zhu Y, Huang C, Su M, Ge Z, Gao L, Shi Y, Wang X, Chen J. Characterization of amino acid residues of T-cell receptors interacting with HLA-A*02-restricted antigen peptides. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:495. [PMID: 33850892 PMCID: PMC8039679 DOI: 10.21037/atm-21-835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background The present study aimed to explore residues’ properties interacting with HLA-A*02-restricted peptides on T-cell receptors (TCRs) and their effects on bond types of interaction and binding free energy. Methods We searched the crystal structures of HLA-A*02-restricted peptide-TCR complexes from the Protein Data Bank (PDB) database and subsequently collected relevant parameters. We then employed Schrodinger to analyze the bond types of interaction and Gromacs 2019 to evaluate the TCR-antigen peptide complex’s molecular dynamics simulation. Finally, we compared the changes of bond types of interaction and binding free energy before and after residue substitution to ensure consistency of the conditions before and after residue substitution. Results The main sites on the antigen peptides that formed the intermolecular interaction [hydrogen bond (HB) and pi stack] with TCRs were P4, P8, P2, and P6. The hydrophobicity of the amino acids inside or outside the disulfide bond of TCRs may be related to the intermolecular interaction and binding free energy between TCRs and peptides. Residues located outside the disulfide bond of TCR α or β chains and forming pi stack force played favorable roles in the complex intermolecular interaction and binding free energy. The residues of the TCR α or β chains that interacted with peptides were replaced by alanine (Ala) or glycine (Gly), and their intermolecular binding free energy of the complex had been improved. However, it had nothing to do with the formation of HB. Conclusions The findings of this study suggest that the hydrophobic nature of the amino acids inside or outside the disulfide bonds on the TCR may be associated with the intermolecular interaction and binding between the TCR and polypeptide. The residues located outside the TCR α or β single-chain disulfide bond and forming the pi-stack force showed a beneficial effect on the intermolecular interaction and binding of the complex. In addition, the part of the residues on the TCR α or β single chain that produced bond types of interaction with the polypeptide after being replaced by Ala or Gly, the intermolecular binding free energy of the complex was increased, regardless of whether HB was formed.
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Affiliation(s)
- Ying Zhu
- Department of Oncology, First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Changxin Huang
- Department of Oncology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Meng Su
- Master Class, Zhejiang Chinese Medical University, Fourth School of Clinical Medicine, Hangzhou, China
| | - Zuanmin Ge
- Master Class, Hangzhou Normal University, School of Medicine, Hangzhou, China
| | - Lanlan Gao
- Master Class, Hangzhou Normal University, School of Medicine, Hangzhou, China
| | - Yanfei Shi
- Master Class, Hangzhou Normal University, School of Medicine, Hangzhou, China
| | - Xuechun Wang
- Master Class, Zhejiang Chinese Medical University, Fourth School of Clinical Medicine, Hangzhou, China
| | - Jianfeng Chen
- Department of Proctology, Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
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15
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Genetic Bias, Diversity Indices, Physiochemical Properties and CDR3 Motifs Divide Auto-Reactive from Allo-Reactive T-Cell Repertoires. Int J Mol Sci 2021; 22:ijms22041625. [PMID: 33562731 PMCID: PMC7915266 DOI: 10.3390/ijms22041625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/30/2021] [Accepted: 01/31/2021] [Indexed: 12/26/2022] Open
Abstract
The distinct properties of allo-reactive T-cell repertoires are not well understood. To investigate whether auto-reactive and allo-reactive T-cell repertoires encoded distinct properties, we used dextramer enumeration, enrichment, single-cell T-cell receptor (TCR) sequencing and multiparameter analysis. We found auto-reactive and allo-reactive T-cells differed in mean ex vivo frequency which was antigen dependent. Allo-reactive T-cells showed clear differences in TCR architecture, with enriched usage of specific T-cell receptor variable (TRBJ) genes and broader use of T-cell receptor variable joining (TRBJ) genes. Auto-reactive T-cell repertoires exhibited complementary determining regions three (CDR3) lengths using a Gaussian distribution whereas allo-reactive T-cell repertoires exhibited distorted patterns in CDR3 length. CDR3 loops from allo-reactive T-cells showed distinct physical-chemical properties, tending to encode loops that were more acidic in charge. Allo-reactive T-cell repertoires differed in diversity metrics, tending to show increased overall diversity and increased homogeneity between repertoires. Motif analysis of CDR3 loops showed allo-reactive T-cell repertoires differed in motif preference which included broader motif use. Collectively, these data conclude that allo-reactive T-cell repertoires are indeed different to auto-reactive repertoires and provide tangible metrics for further investigations and validation. Given that the antigens studied here are overexpressed on multiple cancers and that allo-reactive TCRs often show increased ligand affinity, this new TCR bank also has translational potential for adoptive cell therapy, soluble TCR-based therapy and rational TCR design.
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16
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TCR Recognition of Peptide-MHC-I: Rule Makers and Breakers. Int J Mol Sci 2020; 22:ijms22010068. [PMID: 33374673 PMCID: PMC7793522 DOI: 10.3390/ijms22010068] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 12/15/2022] Open
Abstract
T cells are a critical part of the adaptive immune system that are able to distinguish between healthy and unhealthy cells. Upon recognition of protein fragments (peptides), activated T cells will contribute to the immune response and help clear infection. The major histocompatibility complex (MHC) molecules, or human leukocyte antigens (HLA) in humans, bind these peptides to present them to T cells that recognise them with their surface T cell receptors (TCR). This recognition event is the first step that leads to T cell activation, and in turn can dictate disease outcomes. The visualisation of TCR interaction with pMHC using structural biology has been crucial in understanding this key event, unravelling the parameters that drive this interaction and their impact on the immune response. The last five years has been the most productive within the field, wherein half of current unique TCR-pMHC-I structures to date were determined within this time. Here, we review the new insights learned from these recent TCR-pMHC-I structures and their impact on T cell activation.
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17
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Smith NL, Nahrendorf W, Sutherland C, Mooney JP, Thompson J, Spence PJ, Cowan GJM. A Conserved TCRβ Signature Dominates a Highly Polyclonal T-Cell Expansion During the Acute Phase of a Murine Malaria Infection. Front Immunol 2020; 11:587756. [PMID: 33329568 PMCID: PMC7719809 DOI: 10.3389/fimmu.2020.587756] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/27/2020] [Indexed: 01/31/2023] Open
Abstract
CD4+ αβ T-cells are key mediators of the immune response to a first Plasmodium infection, undergoing extensive activation and splenic expansion during the acute phase of an infection. However, the clonality and clonal composition of this expansion has not previously been described. Using a comparative infection model, we sequenced the splenic CD4+ T-cell receptor repertoires generated over the time-course of a Plasmodium chabaudi infection. We show through repeat replicate experiments, single-cell RNA-seq, and analyses of independent RNA-seq data, that following a first infection - within a highly polyclonal expansion - T-effector repertoires are consistently dominated by TRBV3 gene usage. Clustering by sequence similarity, we find the same dominant clonal signature is expanded across replicates in the acute phase of an infection, revealing a conserved pathogen-specific T-cell response that is consistently a hallmark of a first infection, but not expanded upon re-challenge. Determining the host or parasite factors driving this conserved response may uncover novel immune targets for malaria therapeutic purposes.
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Affiliation(s)
- Natasha L. Smith
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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18
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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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19
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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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20
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Coles CH, McMurran C, Lloyd A, Hock M, Hibbert L, Raman MCC, Hayes C, Lupardus P, Cole DK, Harper S. T cell receptor interactions with human leukocyte antigen govern indirect peptide selectivity for the cancer testis antigen MAGE-A4. J Biol Chem 2020; 295:11486-11494. [PMID: 32532817 PMCID: PMC7450119 DOI: 10.1074/jbc.ra120.014016] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/11/2020] [Indexed: 12/18/2022] Open
Abstract
T cell-mediated immunity is governed primarily by T cell receptor (TCR) recognition of peptide-human leukocyte antigen (pHLA) complexes and is essential for immunosurveillance and disease control. This interaction is generally stabilized by interactions between the HLA surface and TCR germline-encoded complementarity-determining region (CDR) loops 1 and 2, whereas peptide selectivity is guided by direct interactions with the TCR CDR3 loops. Here, we solved the structure of a newly identified TCR in complex with a clinically relevant peptide derived from the cancer testis antigen melanoma antigen-A4 (MAGE-A4). The TCR bound pHLA in a position shifted toward the peptide's N terminus. This enabled the TCR to achieve peptide selectivity via an indirect mechanism, whereby the TCR sensed the first residue of the peptide through HLA residue Trp-167, which acted as a tunable gateway. Amino acid substitutions at peptide position 1 predicted to alter the HLA Trp-167 side-chain conformation abrogated TCR binding, indicating that this indirect binding mechanism is essential for peptide recognition. These findings extend our understanding of the molecular rules that underpin antigen recognition by TCRs and have important implications for the development of TCR-based therapies.
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Affiliation(s)
| | | | | | | | | | | | | | | | - David K Cole
- Immunocore Ltd., Abingdon, United Kingdom .,Cardiff University School of Medicine, Cardiff, United Kingdom
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21
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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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22
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Kamga L, Gil A, Song I, Brody R, Ghersi D, Aslan N, Stern LJ, Selin LK, Luzuriaga K. CDR3α drives selection of the immunodominant Epstein Barr virus (EBV) BRLF1-specific CD8 T cell receptor repertoire in primary infection. PLoS Pathog 2019; 15:e1008122. [PMID: 31765434 PMCID: PMC6901265 DOI: 10.1371/journal.ppat.1008122] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/09/2019] [Accepted: 10/03/2019] [Indexed: 12/20/2022] Open
Abstract
The T cell receptor (TCR) repertoire is an essential component of the CD8 T-cell immune response. Here, we seek to investigate factors that drive selection of TCR repertoires specific to the HLA-A2-restricted immunodominant epitope BRLF1109-117 (YVLDHLIVV) over the course of primary Epstein Barr virus (EBV) infection. Using single-cell paired TCRαβ sequencing of tetramer sorted CD8 T cells ex vivo, we show at the clonal level that recognition of the HLA-A2-restricted BRLF1 (YVL-BR, BRLF-1109) epitope is mainly driven by the TCRα chain. For the first time, we identify a CDR3α (complementarity determining region 3 α) motif, KDTDKL, resulting from an obligate AV8.1-AJ34 pairing that was shared by all four individuals studied. This observation coupled with the fact that this public AV8.1-KDTDKL-AJ34 TCR pairs with multiple different TCRβ chains within the same donor (median 4; range: 1–9), suggests that there are some unique structural features of the interaction between the YVL-BR/MHC and the AV8.1-KDTDKL-AJ34 TCR that leads to this high level of selection. Newly developed TCR motif algorithms identified a lysine at position 1 of the CDR3α motif that is highly conserved and likely important for antigen recognition. Crystal structure analysis of the YVL-BR/HLA-A2 complex revealed that the MHC-bound peptide bulges at position 4, exposing a negatively charged aspartic acid that may interact with the positively charged lysine of CDR3α. TCR cloning and site-directed mutagenesis of the CDR3α lysine ablated YVL-BR-tetramer staining and substantially reduced CD69 upregulation on TCR mutant-transduced cells following antigen-specific stimulation. Reduced activation of T cells expressing this CDR3 motif was also observed following exposure to mutated (D4A) peptide. In summary, we show that a highly public TCR repertoire to an immunodominant epitope of a common human virus is almost completely selected on the basis of CDR3α and provide a likely structural basis for the selection. These studies emphasize the importance of examining TCRα, as well as TCRβ, in understanding the CD8 T cell receptor repertoire. EBV is a ubiquitous human virus that has been linked to several diseases, including cancers and post-transplant lymphoproliferative disorders. CD8 T cells are important for controlling EBV replication. Generation and maintenance of virus-specific CD8 T cells is dependent on specific interaction between MHC-peptide complexes on the infected cell and the TCR. In this study, we performed single cell sequencing of paired TCR α and β chains from EBV-specific CD8 T cells isolated at two time points (primary infection and convalescence) from four individuals undergoing acute EBV infection. We describe a TCRα sequence that was shared by all four individuals and identify conserved residues within this sequence that likely contribute to viral recognition. Examination of the crystal structure of the peptide-MHC complex and subsequent experimental data suggest that a specific interaction between a negatively charged aspartic acid at position 4 of the peptide and a positively charged lysine in the TCR may be particularly important. These findings are highly relevant to current efforts to understand how the TCR repertoire may contribute to or protect against disease, the development of TCR diagnostics for diseases, and at improving the efficacy of T cell based therapies.
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MESH Headings
- Amino Acid Sequence
- CD8-Positive T-Lymphocytes/immunology
- Complementarity Determining Regions/genetics
- Complementarity Determining Regions/immunology
- Complementarity Determining Regions/metabolism
- Epitopes, T-Lymphocyte/immunology
- Epstein-Barr Virus Infections/immunology
- Epstein-Barr Virus Infections/virology
- HLA-A2 Antigen/immunology
- Herpesvirus 4, Human/immunology
- Humans
- Immediate-Early Proteins/genetics
- Immediate-Early Proteins/immunology
- Immediate-Early Proteins/metabolism
- Immunodominant Epitopes/immunology
- Peptide Fragments/immunology
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- T-Lymphocytes, Cytotoxic/immunology
- Trans-Activators/genetics
- Trans-Activators/immunology
- Trans-Activators/metabolism
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Affiliation(s)
- Larisa Kamga
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Anna Gil
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Inyoung Song
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Robin Brody
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Dario Ghersi
- School of Interdisciplinary Informatics, University of Nebraska at Omaha, Nebraska, United States of America
| | - Nuray Aslan
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Lawrence J. Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Liisa K. Selin
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail: (LKS); (KL)
| | - Katherine Luzuriaga
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail: (LKS); (KL)
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23
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Meckiff BJ, Ladell K, McLaren JE, Ryan GB, Leese AM, James EA, Price DA, Long HM. Primary EBV Infection Induces an Acute Wave of Activated Antigen-Specific Cytotoxic CD4 + T Cells. THE JOURNAL OF IMMUNOLOGY 2019; 203:1276-1287. [PMID: 31308093 PMCID: PMC6697742 DOI: 10.4049/jimmunol.1900377] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/20/2019] [Indexed: 12/14/2022]
Abstract
Primary EBV infection drives highly cytotoxic virus-specific CD4+ T cell responses. EBV-specific memory CD4+ T cells are polyfunctional but lack cytotoxic activity. Acute EBV-specific CD4-CTLs differ transcriptionally from classical memory CD4-CTLs.
CD4+ T cells are essential for immune protection against viruses, yet their multiple roles remain ill-defined at the single-cell level in humans. Using HLA class II tetramers, we studied the functional properties and clonotypic architecture of EBV-specific CD4+ T cells in patients with infectious mononucleosis, a symptomatic manifestation of primary EBV infection, and in long-term healthy carriers of EBV. We found that primary infection elicited oligoclonal expansions of TH1-like EBV-specific CD4+ T cells armed with cytotoxic proteins that responded immediately ex vivo to challenge with EBV-infected B cells. Importantly, these acutely generated cytotoxic CD4+ T cells were highly activated and transcriptionally distinct from classically described cytotoxic CD4+ memory T cells that accumulate during other persistent viral infections, including CMV and HIV. In contrast, EBV-specific memory CD4+ T cells displayed increased cytokine polyfunctionality but lacked cytotoxic activity. These findings suggested an important effector role for acutely generated cytotoxic CD4+ T cells that could potentially be harnessed to improve the efficacy of vaccines against EBV.
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Affiliation(s)
- Benjamin J Meckiff
- Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, United Kingdom; and
| | - James E McLaren
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, United Kingdom; and
| | - Gordon B Ryan
- Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Alison M Leese
- Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Eddie A James
- Tetramer Core Laboratory, Diabetes Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, United Kingdom; and
| | - Heather M Long
- Institute of Immunology and Immunotherapy, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom;
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24
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Wehr P, Purvis H, Law S, Thomas R. Dendritic cells, T cells and their interaction in rheumatoid arthritis. Clin Exp Immunol 2019; 196:12-27. [PMID: 30589082 PMCID: PMC6422662 DOI: 10.1111/cei.13256] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2018] [Indexed: 12/27/2022] Open
Abstract
Dendritic cells (DCs) are the key professional antigen-presenting cells which bridge innate and adaptive immune responses, inducing the priming and differentiation of naive to effector CD4+ T cells, the cross-priming of CD8+ T cells and the promotion of B cell antibody responses. DCs also play a critical role in the maintenance of immune homeostasis and tolerance. DC-T cell interactions underpin the generation of an autoimmune response in rheumatoid arthritis (RA). Here we describe the function of DCs and review evidence for DC and T cell involvement in RA pathogenesis, in particular through the presentation of self-peptide by DCs that triggers differentiation and activation of autoreactive T cells. Finally, we discuss the emerging field of targeting the DC-T cell interaction for antigen-specific immunotherapy of RA.
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Affiliation(s)
- P. Wehr
- The University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra HospitalBrisbaneAustralia
| | - H. Purvis
- King's College London, Academic Department of Rheumatology, Centre for Inflammation Biology and Cancer Immunology, School of Immunology and Microbial Sciences, Faculty of Life Sciences and MedicineLondonUK
| | - S.‐C. Law
- The University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra HospitalBrisbaneAustralia
| | - R. Thomas
- The University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra HospitalBrisbaneAustralia
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25
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T cell receptor-β J usage, in combination with particular HLA class II alleles, correlates with better cancer survival rates. Immunol Res 2019; 66:219-223. [PMID: 29594966 DOI: 10.1007/s12026-018-8990-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
T cell receptor (TCR) β V and J usage correlates with either the HLA class I or HLA class II major histocompatibility subtypes, and in both infectious diseases and autoimmune settings, the use of particular TCR-β V and J's, in persons with specific HLA alleles, represents either better outcomes or certain clinical features. However, the relationship of TCR V and J usage, HLA alleles, and clinical parameters in the cancer setting has been less well studied. Here, we have evaluated the relationship of what is likely dominant TCR-β V and J usage among tissue-resident lymphocytes for lung, head and neck, kidney, stomach, ovarian, and endometrial cancers, with patient HLA class II alleles. The most striking indication is that TCR-β J subgroup usage, in combination with particular patient HLA class II alleles, correlated with either better or worse outcomes for lung cancer. One combination, TCR-β J2 segment usage and the HLA-DRB1*1501 allele, correlated with a better survival rate for both lung and head and neck cancers. These results fill a gap in knowledge regarding the relevance of HLA typing to cancer and indicate that HLA typing, along with an indication of dominant TCR-β J usage among tissue-resident lymphocytes, can be useful for prognosis.
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26
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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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27
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Heather JM, Ismail M, Oakes T, Chain B. High-throughput sequencing of the T-cell receptor repertoire: pitfalls and opportunities. Brief Bioinform 2018; 19:554-565. [PMID: 28077404 PMCID: PMC6054146 DOI: 10.1093/bib/bbw138] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/21/2016] [Indexed: 02/06/2023] Open
Abstract
T-cell specificity is determined by the T-cell receptor, a heterodimeric protein coded for by an extremely diverse set of genes produced by imprecise somatic gene recombination. Massively parallel high-throughput sequencing allows millions of different T-cell receptor genes to be characterized from a single sample of blood or tissue. However, the extraordinary heterogeneity of the immune repertoire poses significant challenges for subsequent analysis of the data. We outline the major steps in processing of repertoire data, considering low-level processing of raw sequence files and high-level algorithms, which seek to extract biological or pathological information. The latest generation of bioinformatics tools allows millions of DNA sequences to be accurately and rapidly assigned to their respective variable V and J gene segments, and to reconstruct an almost error-free representation of the non-templated additions and deletions that occur. High-level processing can measure the diversity of the repertoire in different samples, quantify V and J usage and identify private and public T-cell receptors. Finally, we discuss the major challenge of linking T-cell receptor sequence to function, and specifically to antigen recognition. Sophisticated machine learning algorithms are being developed that can combine the paradoxical degeneracy and cross-reactivity of individual T-cell receptors with the specificity of the overall T-cell immune response. Computational analysis will provide the key to unlock the potential of the T-cell receptor repertoire to give insight into the fundamental biology of the adaptive immune system and to provide powerful biomarkers of disease.
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Affiliation(s)
| | | | | | - Benny Chain
- Division of Infection and Immunity, University College of London, Bloomsbury, UK
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28
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Callahan BM, Yavorski JM, Tu YN, Tong WL, Kinskey JC, Clark KR, Fawcett TJ, Blanck G. T-cell receptor-β V and J usage, in combination with particular HLA class I and class II alleles, correlates with cancer survival patterns. Cancer Immunol Immunother 2018; 67:885-892. [PMID: 29508024 PMCID: PMC11028132 DOI: 10.1007/s00262-018-2139-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 02/21/2018] [Indexed: 12/18/2022]
Abstract
Class I and class II HLA proteins, respectively, have been associated with subsets of V(D)J usage resulting from recombination of the T-cell receptor (TCR) genes. Additionally, particular HLA alleles, in combination with dominant TCR V(D)J recombinations, have been associated with several autoimmune diseases. The recovery of TCR recombination reads from tumor specimen exome files has allowed rapid and extensive assessments of V(D)J usage, likely for cancer resident T-cells, across relatively large cancer datasets. The results from this approach, in this report, have permitted an extensive alignment of TCR-β VDJ usage and HLA class I and II alleles. Results indicate the correlation of both better and worse cancer survival rates with particular TCR-β, V and J usage-HLA allele combinations, with differences in median survival times ranging from 7 to 130 months, depending on the cancer and the specific TCR-β V and J usage/HLA class allele combination.
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Affiliation(s)
- Blake M Callahan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA
| | - John M Yavorski
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA
| | - Yaping N Tu
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA
| | - Wei Lue Tong
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA
| | - Jacob C Kinskey
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA
| | - Kendall R Clark
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA
| | | | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA.
- Immunology Program, H. Lee Moffitt Cancer and Research Institute, Tampa, FL, USA.
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29
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Cole DK, Fuller A, Dolton G, Zervoudi E, Legut M, Miles K, Blanchfield L, Madura F, Holland CJ, Bulek AM, Bridgeman JS, Miles JJ, Schauenburg AJA, Beck K, Evavold BD, Rizkallah PJ, Sewell AK. Dual Molecular Mechanisms Govern Escape at Immunodominant HLA A2-Restricted HIV Epitope. Front Immunol 2017; 8:1503. [PMID: 29209312 PMCID: PMC5701626 DOI: 10.3389/fimmu.2017.01503] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 10/25/2017] [Indexed: 12/05/2022] Open
Abstract
Serial accumulation of mutations to fixation in the SLYNTVATL (SL9) immunodominant, HIV p17 Gag-derived, HLA A2-restricted cytotoxic T lymphocyte epitope produce the SLFNTIAVL triple mutant “ultimate” escape variant. These mutations in solvent-exposed residues are believed to interfere with TCR recognition, although confirmation has awaited structural verification. Here, we solved a TCR co-complex structure with SL9 and the triple escape mutant to determine the mechanism of immune escape in this eminent system. We show that, in contrast to prevailing hypotheses, the main TCR contact residue is 4N and the dominant mechanism of escape is not via lack of TCR engagement. Instead, mutation of solvent-exposed residues in the peptide destabilise the peptide–HLA and reduce peptide density at the cell surface. These results highlight the extraordinary lengths that HIV employs to evade detection by high-affinity TCRs with a broad peptide-binding footprint and necessitate re-evaluation of this exemplar model of HIV TCR escape.
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Affiliation(s)
- David K Cole
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Anna Fuller
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Garry Dolton
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Efthalia Zervoudi
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Mateusz Legut
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Kim Miles
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Lori Blanchfield
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, United States
| | - Florian Madura
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Christopher J Holland
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Anna M Bulek
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - John S Bridgeman
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - John J Miles
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom.,James Cook University, Cairns, QLD, Australia
| | - Andrea J A Schauenburg
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Konrad Beck
- Cardiff University School of Dentistry, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Brian D Evavold
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, United States
| | - Pierre J Rizkallah
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
| | - Andrew K Sewell
- Cardiff University School of Medicine, University Hospital, Heath Park, Cardiff, United Kingdom
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30
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Abstract
PURPOSE OF REVIEW The genetic susceptibility and dominant protection for type 1 diabetes (T1D) associated with human leukocyte antigen (HLA) haplotypes, along with minor risk variants, have long been thought to shape the T cell receptor (TCR) repertoire and eventual phenotype of autoreactive T cells that mediate β-cell destruction. While autoantibodies provide robust markers of disease progression, early studies tracking autoreactive T cells largely failed to achieve clinical utility. RECENT FINDINGS Advances in acquisition of pancreata and islets from T1D organ donors have facilitated studies of T cells isolated from the target tissues. Immunosequencing of TCR α/β-chain complementarity determining regions, along with transcriptional profiling, offers the potential to transform biomarker discovery. Herein, we review recent studies characterizing the autoreactive TCR signature in T1D, emerging technologies, and the challenges and opportunities associated with tracking TCR molecular profiles during the natural history of T1D.
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Affiliation(s)
- Laura M Jacobsen
- Department of Pediatrics, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Amanda Posgai
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Howard R Seay
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Michael J Haller
- Department of Pediatrics, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Todd M Brusko
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA.
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31
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Attaf M, Sewell AK. Disease etiology and diagnosis by TCR repertoire analysis goes viral. Eur J Immunol 2017; 46:2516-2519. [PMID: 27813075 DOI: 10.1002/eji.201646649] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 09/21/2016] [Accepted: 10/10/2016] [Indexed: 12/24/2022]
Abstract
The importance of T-cell receptor (TCR) repertoire diversity is highlighted in murine models of immunodeficiency and in many human pathologies. However, the true extent of TCR diversity and how this diversity varies in health and disease is poorly understood. In a previous issue of the European Journal of Immunology, Lossius et al. [Eur. J. Immunol. 2014. 44: 3439-3452] dissected the composition of the TCR repertoire in the context of multiple sclerosis (MS) using high-throughput sequencing of TCR-β chains in cerebrospinal fluid samples and blood. The authors demonstrated that the TCR repertoire of the CSF was largely distinct from the blood and enriched in EBV-reactive CD8+ T cells in MS patients. Studies of this kind have long been hindered by technical limitations and remain scarce in the literature. However, TCR sequencing methodologies are progressing apace and will undoubtedly shed light on the genetic basis of T-cell responses and the ontogeny of T-cell-mediated diseases, such as MS.
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Affiliation(s)
- Meriem Attaf
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, UK.
| | - Andrew K Sewell
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, UK
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32
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Dash P, Fiore-Gartland AJ, Hertz T, Wang GC, Sharma S, Souquette A, Crawford JC, Clemens EB, Nguyen THO, Kedzierska K, La Gruta NL, Bradley P, Thomas PG. Quantifiable predictive features define epitope-specific T cell receptor repertoires. Nature 2017. [PMID: 28636592 DOI: 10.1038/nature22383] [Citation(s) in RCA: 519] [Impact Index Per Article: 74.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
T cells are defined by a heterodimeric surface receptor, the T cell receptor (TCR), that mediates recognition of pathogen-associated epitopes through interactions with peptide and major histocompatibility complexes (pMHCs). TCRs are generated by genomic rearrangement of the germline TCR locus, a process termed V(D)J recombination, that has the potential to generate marked diversity of TCRs (estimated to range from 1015 (ref. 1) to as high as 1061 (ref. 2) possible receptors). Despite this potential diversity, TCRs from T cells that recognize the same pMHC epitope often share conserved sequence features, suggesting that it may be possible to predictively model epitope specificity. Here we report the in-depth characterization of ten epitope-specific TCR repertoires of CD8+ T cells from mice and humans, representing over 4,600 in-frame single-cell-derived TCRαβ sequence pairs from 110 subjects. We developed analytical tools to characterize these epitope-specific repertoires: a distance measure on the space of TCRs that permits clustering and visualization, a robust repertoire diversity metric that accommodates the low number of paired public receptors observed when compared to single-chain analyses, and a distance-based classifier that can assign previously unobserved TCRs to characterized repertoires with robust sensitivity and specificity. Our analyses demonstrate that each epitope-specific repertoire contains a clustered group of receptors that share core sequence similarities, together with a dispersed set of diverse 'outlier' sequences. By identifying shared motifs in core sequences, we were able to highlight key conserved residues driving essential elements of TCR recognition. These analyses provide insights into the generalizable, underlying features of epitope-specific repertoires and adaptive immune recognition.
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Affiliation(s)
- Pradyot Dash
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Andrew J Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Tomer Hertz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - George C Wang
- Division of Geriatric Medicine and Gerontology, Biology of Healthy Aging Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21224, USA
| | - Shalini Sharma
- Department of Veterinary Physiology and Biochemistry, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004, India
| | - Aisha Souquette
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Jeremy Chase Crawford
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - E Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia
| | - Nicole L La Gruta
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Philip Bradley
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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33
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Chen G, Yang X, Ko A, Sun X, Gao M, Zhang Y, Shi A, Mariuzza RA, Weng NP. Sequence and Structural Analyses Reveal Distinct and Highly Diverse Human CD8 + TCR Repertoires to Immunodominant Viral Antigens. Cell Rep 2017; 19:569-583. [PMID: 28423320 DOI: 10.1016/j.celrep.2017.03.072] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Revised: 02/02/2017] [Accepted: 03/24/2017] [Indexed: 01/07/2023] Open
Abstract
A diverse T cell receptor (TCR) repertoire is essential for controlling viral infections. However, information about TCR repertoires to defined viral antigens is limited. We performed a comprehensive analysis of CD8+ TCR repertoires for two dominant viral epitopes: pp65495-503 (NLV) of cytomegalovirus and M158-66 (GIL) of influenza A virus. The highly individualized repertoires (87-5,533 α or β clonotypes per subject) comprised thousands of unique TCRα and TCRβ sequences and dozens of distinct complementary determining region (CDR)3α and CDR3β motifs. However, diversity is effectively restricted by preferential V-J combinations, CDR3 lengths, and CDR3α/CDR3β pairings. Structures of two GIL-specific TCRs bound to GIL-HLA-A2 provided a potential explanation for the lower diversity of GIL-specific versus NLV-specific repertoires. These anti-viral TCRs occupied up to 3.4% of the CD8+ TCRβ repertoire, ensuring broad T cell responses to single epitopes. Our portrait of two anti-viral TCR repertoires may inform the development of predictors of immune protection.
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Affiliation(s)
- Guobing Chen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Xinbo Yang
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Annette Ko
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Xiaoping Sun
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Mingming Gao
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Yongqing Zhang
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Alvin Shi
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Roy A Mariuzza
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Nan-Ping Weng
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD 21224, USA.
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34
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Tickotsky N, Sagiv T, Prilusky J, Shifrut E, Friedman N. McPAS-TCR: a manually curated catalogue of pathology-associated T cell receptor sequences. Bioinformatics 2017; 33:2924-2929. [DOI: 10.1093/bioinformatics/btx286] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 05/02/2017] [Indexed: 11/14/2022] Open
Affiliation(s)
- Nili Tickotsky
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Sagiv
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Jaime Prilusky
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Eric Shifrut
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Nir Friedman
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
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35
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MacLachlan BJ, Greenshields-Watson A, Mason GH, Schauenburg AJ, Bianchi V, Rizkallah PJ, Sewell AK, Fuller A, Cole DK. Using X-ray Crystallography, Biophysics, and Functional Assays to Determine the Mechanisms Governing T-cell Receptor Recognition of Cancer Antigens. J Vis Exp 2017:54991. [PMID: 28287509 PMCID: PMC5408581 DOI: 10.3791/54991] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Human CD8+ cytotoxic T lymphocytes (CTLs) are known to play an important role in tumor control. In order to carry out this function, the cell surface-expressed T-cell receptor (TCR) must functionally recognize human leukocyte antigen (HLA)-restricted tumor-derived peptides (pHLA). However, we and others have shown that most TCRs bind sub-optimally to tumor antigens. Uncovering the molecular mechanisms that define this poor recognition could aid in the development of new targeted therapies that circumnavigate these shortcomings. Indeed, present therapies that lack this molecular understanding have not been universally effective. Here, we describe methods that we commonly employ in the laboratory to determine how the nature of the interaction between TCRs and pHLA governs T-cell functionality. These methods include the generation of soluble TCRs and pHLA and the use of these reagents for X-ray crystallography, biophysical analysis, and antigen-specific T-cell staining with pHLA multimers. Using these approaches and guided by structural analysis, it is possible to modify the interaction between TCRs and pHLA and to then test how these modifications impact T-cell antigen recognition. These findings have already helped to clarify the mechanism of T-cell recognition of a number of cancer antigens and could direct the development of altered peptides and modified TCRs for new cancer therapies.
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Affiliation(s)
- Bruce J MacLachlan
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University
| | | | - Georgina H Mason
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University
| | - Andrea J Schauenburg
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University
| | - Valentina Bianchi
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University; Department of Oncology, University Hospital of Lausanne (CHUV); Ludwig Insitutue for Cancer Research, Lausanne Branch, University of Lausanne
| | - Pierre J Rizkallah
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University
| | - Andrew K Sewell
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University
| | - Anna Fuller
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University
| | - David K Cole
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University;
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36
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Maintenance of the EBV-specific CD8 + TCRαβ repertoire in immunosuppressed lung transplant recipients. Immunol Cell Biol 2016; 95:77-86. [PMID: 27507557 PMCID: PMC5214975 DOI: 10.1038/icb.2016.71] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 07/04/2016] [Accepted: 08/01/2016] [Indexed: 12/12/2022]
Abstract
Epstein-Barr virus (EBV) is one of the most common viruses in humans, capable of causing life-threatening infections and cancers in immunocompromised individuals. Although CD8+ T cells provide key protection against EBV, the persistence and dynamics of specific T-cell receptor (TCR) clones during immunosuppression in transplant patients is largely unknown. For the first time, we used a novel single-cell TCRαβ multiplex-nested reverse transcriptase PCR to dissect TCRαβ clonal diversity within GLCTLVAML (GLC)-specific CD8+ T cells in healthy individuals and immunocompromised lung transplant recipients. The GLC peptide presented by HLA-A*02:01 is one of the most immunogenic T-cell targets from the EBV proteome. We found that the GLC-specific TCRαβ repertoire was heavily biased toward TRAV5 and encompassed five classes of public TCRαβs, suggesting that these clonotypes are preferentially utilized following infection. We identified that a common TRAV5 was diversely paired with different TRAJ and TRBV/TRBJ genes, in both immunocompetent and immunocompromised individuals, with an average of 12 different TCRαβ clonotypes/donor. Moreover, pre-transplant GLC-specific TCRαβ repertoires were relatively stable over 1 year post transplant under immunosuppression in the absence or presence of EBV reactivation. In addition, we provide the first evidence of early GLC-specific CD8+ T cells at 87 days post transplant, which preceded clinical EBV detection at 242 days in an EBV-seronegative patient receiving a lung allograft from an EBV-seropositive donor. This was associated with a relatively stable TCRαβ repertoire after CD8+ T-cell expansion. Our findings provide insights into the composition and temporal dynamics of the EBV-specific TCRαβ repertoire in immunocompromised transplant patients and suggest that the early detection of EBV-specific T cells might be a predictor of ensuing EBV blood viremia.
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37
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Grant EJ, Josephs TM, Valkenburg SA, Wooldridge L, Hellard M, Rossjohn J, Bharadwaj M, Kedzierska K, Gras S. Lack of Heterologous Cross-reactivity toward HLA-A*02:01 Restricted Viral Epitopes Is Underpinned by Distinct αβT Cell Receptor Signatures. J Biol Chem 2016; 291:24335-24351. [PMID: 27645996 DOI: 10.1074/jbc.m116.753988] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/11/2016] [Indexed: 11/06/2022] Open
Abstract
αβT cell receptor (TCR) genetic diversity is outnumbered by the quantity of pathogenic epitopes to be recognized. To provide efficient protective anti-viral immunity, a single TCR ideally needs to cross-react with a multitude of pathogenic epitopes. However, the frequency, extent, and mechanisms of TCR cross-reactivity remain unclear, with conflicting results on anti-viral T cell cross-reactivity observed in humans. Namely, both the presence and lack of T cell cross-reactivity have been reported with HLA-A*02:01-restricted epitopes from the Epstein-Barr and influenza viruses (BMLF-1 and M158, respectively) or with the hepatitis C and influenza viruses (NS31073 and NA231, respectively). Given the high sequence similarity of these paired viral epitopes (56 and 88%, respectively), the ubiquitous nature of the three viruses, and the high frequency of the HLA-A*02:01 allele, we selected these epitopes to establish the extent of T cell cross-reactivity. We combined ex vivo and in vitro functional assays, single-cell αβTCR repertoire sequencing, and structural analysis of these four epitopes in complex with HLA-A*02:01 to determine whether they could lead to heterologous T cell cross-reactivity. Our data show that sequence similarity does not translate to structural mimicry of the paired epitopes in complexes with HLA-A*02:01, resulting in induction of distinct αβTCR repertoires. The differences in epitope architecture might be an obstacle for TCR recognition, explaining the lack of T cell cross-reactivity observed. In conclusion, sequence similarity does not necessarily result in structural mimicry, and despite the need for cross-reactivity, antigen-specific TCR repertoires can remain highly specific.
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Affiliation(s)
- Emma J Grant
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia
| | - Tracy M Josephs
- the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, and; the Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Sophie A Valkenburg
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia
| | - Linda Wooldridge
- the Faculty of Health Sciences, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Margaret Hellard
- the Center for Research Excellence in Injecting Drug Use, Burnet Institute, Melbourne, Victoria 3004, Australia, and
| | - Jamie Rossjohn
- the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, and; the Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia,; the Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Mandvi Bharadwaj
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia
| | - Katherine Kedzierska
- From the Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia,.
| | - Stephanie Gras
- the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, and; the Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia,.
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38
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Lu IN, Farinelle S, Sausy A, Muller CP. Identification of a CD4 T-cell epitope in the hemagglutinin stalk domain of pandemic H1N1 influenza virus and its antigen-driven TCR usage signature in BALB/c mice. Cell Mol Immunol 2016; 14:511-520. [PMID: 27157498 PMCID: PMC5518815 DOI: 10.1038/cmi.2016.20] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 02/17/2016] [Accepted: 03/08/2016] [Indexed: 01/31/2023] Open
Abstract
The stalk region of the influenza virus hemagglutinin is relatively well conserved compared with the globular head domain, which makes it a potential target for use as a universal vaccine against influenza. However, the role of CD4 T cells in the hemagglutinin stalk-specific immune response is not clear. Here we identified a mouse CD4 T-cell epitope that encompasses residues HA2113-131 from the hemagglutinin stalk domain after a sub-lethal infection of influenza. In response to stimulation with the identified epitope, splenocytes derived from the infected mice showed significant polyfunctionality as shown by IL-2, TNF-α and IFN-γ production as well as degranulation. Moreover, mice immunized with the peptide corresponding to this CD4 T-cell epitope exhibited interindividual sharing of the CD4 T-cell receptor β sequences, and they had a higher survival rate following a challenge with a lethal dose of pandemic H1N1 influenza virus. Thus, our data demonstrated a crucial role of hemagglutinin stalk-specific CD4 T cells in the host immune response against influenza virus infection.
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Affiliation(s)
- I-Na Lu
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette L-4354, Luxembourg
| | - Sophie Farinelle
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette L-4354, Luxembourg
| | - Aurélie Sausy
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette L-4354, Luxembourg
| | - Claude P Muller
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette L-4354, Luxembourg
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39
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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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40
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How structural adaptability exists alongside HLA-A2 bias in the human αβ TCR repertoire. Proc Natl Acad Sci U S A 2016; 113:E1276-85. [PMID: 26884163 DOI: 10.1073/pnas.1522069113] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
How T-cell receptors (TCRs) can be intrinsically biased toward MHC proteins while simultaneously display the structural adaptability required to engage diverse ligands remains a controversial puzzle. We addressed this by examining αβ TCR sequences and structures for evidence of physicochemical compatibility with MHC proteins. We found that human TCRs are enriched in the capacity to engage a polymorphic, positively charged "hot-spot" region that is almost exclusive to the α1-helix of the common human class I MHC protein, HLA-A*0201 (HLA-A2). TCR binding necessitates hot-spot burial, yielding high energetic penalties that must be offset via complementary electrostatic interactions. Enrichment of negative charges in TCR binding loops, particularly the germ-line loops encoded by the TCR Vα and Vβ genes, provides this capacity and is correlated with restricted positioning of TCRs over HLA-A2. Notably, this enrichment is absent from antibody genes. The data suggest a built-in TCR compatibility with HLA-A2 that biases receptors toward, but does not compel, particular binding modes. Our findings provide an instructional example for how structurally pliant MHC biases can be encoded within TCRs.
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41
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Raman MCC, Rizkallah PJ, Simmons R, Donnellan Z, Dukes J, Bossi G, Le Provost GS, Todorov P, Baston E, Hickman E, Mahon T, Hassan N, Vuidepot A, Sami M, Cole DK, Jakobsen BK. Direct molecular mimicry enables off-target cardiovascular toxicity by an enhanced affinity TCR designed for cancer immunotherapy. Sci Rep 2016; 6:18851. [PMID: 26758806 PMCID: PMC4725365 DOI: 10.1038/srep18851] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/27/2015] [Indexed: 12/11/2022] Open
Abstract
Natural T-cell responses generally lack the potency to eradicate cancer. Enhanced affinity T-cell receptors (TCRs) provide an ideal approach to target cancer cells, with emerging clinical data showing significant promise. Nevertheless, the risk of off target reactivity remains a key concern, as exemplified in a recent clinical report describing fatal cardiac toxicity, following administration of MAGE-A3 specific TCR-engineered T-cells, mediated through cross-reactivity with an unrelated epitope from the Titin protein presented on cardiac tissue. Here, we investigated the structural mechanism enabling TCR cross-recognition of MAGE-A3 and Titin, and applied the resulting data to rationally design mutants with improved antigen discrimination, providing a proof-of-concept strategy for altering the fine specificity of a TCR towards an intended target antigen. This study represents the first example of direct molecular mimicry leading to clinically relevant fatal toxicity, mediated by a modified enhanced affinity TCR designed for cancer immunotherapy. Furthermore, these data demonstrate that self-antigens that are expressed at high levels on healthy tissue should be treated with extreme caution when designing immuno-therapeutics.
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MESH Headings
- Antigen Presentation
- Antigen-Presenting Cells/immunology
- Antigen-Presenting Cells/metabolism
- Antigens, Neoplasm/chemistry
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/immunology
- Antigens, Neoplasm/metabolism
- Cardiotoxicity
- Cell Line
- Connectin/chemistry
- Connectin/immunology
- Connectin/metabolism
- Cross Reactions/immunology
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/immunology
- Genetic Engineering
- Humans
- Immunotherapy/adverse effects
- Immunotherapy/methods
- Models, Molecular
- Molecular Mimicry
- Mutation
- Neoplasm Proteins/genetics
- Neoplasm Proteins/immunology
- Neoplasm Proteins/metabolism
- Peptide Fragments/chemistry
- Peptide Fragments/immunology
- Protein Binding/immunology
- Protein Conformation
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- T-Cell Antigen Receptor Specificity/immunology
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
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Affiliation(s)
- Marine C C Raman
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
| | - Pierre J Rizkallah
- Division of Infection and Immunity, Cardiff University School of Medicine, Henry Wellcome building, Heath Park, Cardiff, CF14 4XN, United Kingdom
| | - Ruth Simmons
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
| | - Zoe Donnellan
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
| | - Joseph Dukes
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
| | - Giovanna Bossi
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
| | - Gabrielle S Le Provost
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
| | - Penio Todorov
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
| | - Emma Baston
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
| | - Emma Hickman
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
| | - Tara Mahon
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
| | - Namir Hassan
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
| | - Annelise Vuidepot
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
| | - Malkit Sami
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
| | - David K Cole
- Division of Infection and Immunity, Cardiff University School of Medicine, Henry Wellcome building, Heath Park, Cardiff, CF14 4XN, United Kingdom
| | - Bent K. Jakobsen
- Immunocore Limited, 101 Park Drive, Milton Park, Abingdon, Oxon, OX14 4RX, United Kingdom
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42
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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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43
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Yang X, Gao M, Chen G, Pierce BG, Lu J, Weng NP, Mariuzza RA. Structural Basis for Clonal Diversity of the Public T Cell Response to a Dominant Human Cytomegalovirus Epitope. J Biol Chem 2015; 290:29106-19. [PMID: 26429912 DOI: 10.1074/jbc.m115.691311] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Indexed: 11/06/2022] Open
Abstract
Cytomegalovirus (CMV) is a ubiquitous and persistent human pathogen that is kept in check by CD8(+) cytotoxic T lymphocytes. Individuals expressing the major histocompatibility complex (MHC) class I molecule HLA-A2 produce cytotoxic T lymphocytes bearing T cell receptors (TCRs) that recognize the immunodominant CMV epitope NLVPMVATV (NLV). The NLV-specific T cell repertoire is characterized by a high prevalence of TCRs that are frequently observed in multiple unrelated individuals. These public TCRs feature identical, or nearly identical, complementarity-determining region 3α (CDR3α) and/or CDR3β sequences. The TCRs may express public CDR3α motifs alone, public CDR3β motifs alone, or dual public CDR3αβ motifs. In addition, the same public CDR3α motif may pair with different CDR3β motifs (and the reverse), giving rise to highly diverse NLV-specific TCR repertoires. To investigate the structural underpinnings of this clonal diversity, we determined crystal structures of two public TCRs (C7 and C25) in complex with NLV·HLA-A2. These TCRs utilize completely different CDR3α and CDR3β motifs that, in addition, can associate with multiple variable α and variable β regions in NLV-specific T cell repertoires. The C7·NLV·HLA-A2 and C25·NLV·HLA-A2 complexes exhibit divergent TCR footprints on peptide-MHC such that C25 is more focused on the central portion of the NLV peptide than is C7. These structures combined with molecular modeling show how the public CDR3α motif of C25 may associate with different variable α regions and how the public CDR3α motif of C7 may pair with different CDR3β motifs. This interchangeability of TCR V regions and CDR3 motifs permits multiple structural solutions to binding an identical peptide-MHC ligand and thereby the generation of a clonally diverse public T cell response to CMV.
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Affiliation(s)
- Xinbo Yang
- From the University of Maryland Institute for Bioscience and Biotechnology Research, W. M. Keck Laboratory for Structural Biology, Rockville, Maryland 20850, Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Mingming Gao
- From the University of Maryland Institute for Bioscience and Biotechnology Research, W. M. Keck Laboratory for Structural Biology, Rockville, Maryland 20850, Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742
| | - Guobing Chen
- Lymphocyte Differentiation Section, Laboratory of Molecular Biology and Immunology, NIA, National Institutes of Health, Baltimore, Maryland 21224, and
| | - Brian G Pierce
- From the University of Maryland Institute for Bioscience and Biotechnology Research, W. M. Keck Laboratory for Structural Biology, Rockville, Maryland 20850
| | - Jinghua Lu
- Structural Immunology Section, Laboratory of Immunogenetics, NIAID, National Institutes of Health, Rockville, Maryland 20852
| | - Nan-Ping Weng
- Lymphocyte Differentiation Section, Laboratory of Molecular Biology and Immunology, NIA, National Institutes of Health, Baltimore, Maryland 21224, and
| | - Roy A Mariuzza
- From the University of Maryland Institute for Bioscience and Biotechnology Research, W. M. Keck Laboratory for Structural Biology, Rockville, Maryland 20850, Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742,
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44
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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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45
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Pauza CD, Cairo C. Evolution and function of the TCR Vgamma9 chain repertoire: It's good to be public. Cell Immunol 2015; 296:22-30. [PMID: 25769734 PMCID: PMC4466227 DOI: 10.1016/j.cellimm.2015.02.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 02/11/2015] [Accepted: 02/17/2015] [Indexed: 01/17/2023]
Abstract
Lymphocytes expressing a T cell receptor (TCR) composed of Vgamma9 and Vdelta2 chains represent a minor fraction of human thymocytes. Extrathymic selection throughout post-natal life causes the proportion of cells with a Vgamma9-JP rearrangement to increase and elevates the capacity for responding to non-peptidic phosphoantigens. Extrathymic selection is so powerful that phosphoantigen-reactive cells comprise about 1 in 40 circulating memory T cells in healthy adults and the subset expands rapidly upon infection or in response to malignancy. Skewing of the gamma delta TCR repertoire is accompanied by selection for public gamma chain sequences such that many unrelated individuals overlap extensive in their circulating repertoire. This type of selection implies the presence of a monomorphic antigen-presenting molecule that is an object of current research but remains incompletely defined. While selection on a monomorphic presenting molecule may seem unusual, similar mechanisms shape the alpha beta T cell repertoire including the extreme examples of NKT or mucosal-associated invariant T cells (MAIT) and the less dramatic amplification of public Vbeta chain rearrangements driven by individual MHC molecules and associated with resistance to viral pathogens. Selecting and amplifying public T cell receptors whether alpha beta or gamma delta, are important steps in developing an anticipatory TCR repertoire. Cell clones expressing public TCR can accelerate the kinetics of response to pathogens and impact host survival.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- CD4-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/immunology
- Evolution, Molecular
- Humans
- Immunologic Memory/immunology
- Natural Killer T-Cells/immunology
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, gamma-delta/genetics
- Receptors, Antigen, T-Cell, gamma-delta/immunology
- Sequence Homology
- T-Lymphocyte Subsets/immunology
- Thymocytes/immunology
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Affiliation(s)
- C David Pauza
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Cristiana Cairo
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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46
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Attaf M, Huseby E, Sewell AK. αβ T cell receptors as predictors of health and disease. Cell Mol Immunol 2015; 12:391-9. [PMID: 25619506 PMCID: PMC4496535 DOI: 10.1038/cmi.2014.134] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 12/17/2014] [Indexed: 02/08/2023] Open
Abstract
The diversity of antigen receptors and the specificity it underlies are the hallmarks of the cellular arm of the adaptive immune system. T and B lymphocytes are indeed truly unique in their ability to generate receptors capable of recognizing virtually any pathogen. It has been known for several decades that T lymphocytes recognize short peptides derived from degraded proteins presented by major histocompatibility complex (MHC) molecules at the cell surface. Interaction between peptide-MHC (pMHC) and the T cell receptor (TCR) is central to both thymic selection and peripheral antigen recognition. It is widely assumed that TCR diversity is required, or at least highly desirable, to provide sufficient immune coverage. However, a number of immune responses are associated with the selection of predictable, narrow, or skewed repertoires and public TCR chains. Here, we summarize the current knowledge on the formation of the TCR repertoire and its maintenance in health and disease. We also outline the various molecular mechanisms that govern the composition of the pre-selection, naive and antigen-specific TCR repertoires. Finally, we suggest that with the development of high-throughput sequencing, common TCR 'signatures' raised against specific antigens could provide important diagnostic biomarkers and surrogate predictors of disease onset, progression and outcome.
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Affiliation(s)
- Meriem Attaf
- Cardiff University School of Medicine, Cardiff, UK
| | - Eric Huseby
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
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47
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Attaf M, Legut M, Cole DK, Sewell AK. The T cell antigen receptor: the Swiss army knife of the immune system. Clin Exp Immunol 2015; 181:1-18. [PMID: 25753381 PMCID: PMC4469151 DOI: 10.1111/cei.12622] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2015] [Indexed: 01/01/2023] Open
Abstract
The mammalian T cell receptor (TCR) orchestrates immunity by responding to many billions of different ligands that it has never encountered before and cannot adapt to at the protein sequence level. This remarkable receptor exists in two main heterodimeric isoforms: αβ TCR and γδ TCR. The αβ TCR is expressed on the majority of peripheral T cells. Most αβ T cells recognize peptides, derived from degraded proteins, presented at the cell surface in molecular cradles called major histocompatibility complex (MHC) molecules. Recent reports have described other αβ T cell subsets. These 'unconventional' T cells bear TCRs that are capable of recognizing lipid ligands presented in the context of the MHC-like CD1 protein family or bacterial metabolites bound to the MHC-related protein 1 (MR1). γδ T cells constitute a minority of the T cell pool in human blood, but can represent up to half of total T cells in tissues such as the gut and skin. The identity of the preferred ligands for γδ T cells remains obscure, but it is now known that this receptor can also functionally engage CD1-lipid, or immunoglobulin (Ig) superfamily proteins called butyrophilins in the presence of pyrophosphate intermediates of bacterial lipid biosynthesis. Interactions between TCRs and these ligands allow the host to discriminate between self and non-self and co-ordinate an attack on the latter. Here, we describe how cells of the T lymphocyte lineage and their antigen receptors are generated and discuss the various modes of antigen recognition by these extraordinarily versatile receptors.
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Affiliation(s)
- M Attaf
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - M Legut
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - D K Cole
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - A K Sewell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
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48
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Kløverpris HN, McGregor R, McLaren JE, Ladell K, Harndahl M, Stryhn A, Carlson JM, Koofhethile C, Gerritsen B, Keşmir C, Chen F, Riddell L, Luzzi G, Leslie A, Walker BD, Ndung'u T, Buus S, Price DA, Goulder PJ. CD8+ TCR Bias and Immunodominance in HIV-1 Infection. THE JOURNAL OF IMMUNOLOGY 2015; 194:5329-45. [PMID: 25911754 DOI: 10.4049/jimmunol.1400854] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 02/25/2015] [Indexed: 12/25/2022]
Abstract
Immunodominance describes a phenomenon whereby the immune system consistently targets only a fraction of the available Ag pool derived from a given pathogen. In the case of CD8(+) T cells, these constrained epitope-targeting patterns are linked to HLA class I expression and determine disease progression. Despite the biological importance of these predetermined response hierarchies, little is known about the factors that control immunodominance in vivo. In this study, we conducted an extensive analysis of CD8(+) T cell responses restricted by a single HLA class I molecule to evaluate the mechanisms that contribute to epitope-targeting frequency and antiviral efficacy in HIV-1 infection. A clear immunodominance hierarchy was observed across 20 epitopes restricted by HLA-B*42:01, which is highly prevalent in populations of African origin. Moreover, in line with previous studies, Gag-specific responses and targeting breadth were associated with lower viral load set-points. However, peptide-HLA-B*42:01 binding affinity and stability were not significantly linked with targeting frequencies. Instead, immunodominance correlated with epitope-specific usage of public TCRs, defined as amino acid residue-identical TRB sequences that occur in multiple individuals. Collectively, these results provide important insights into a potential link between shared TCR recruitment, immunodominance, and antiviral efficacy in a major human infection.
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Affiliation(s)
- Henrik N Kløverpris
- Department of Paediatrics, University of Oxford, Oxford OX1 3SY, United Kingdom; Department of International Health, Immunology, and Microbiology, University of Copenhagen, 2200-Copenhagen N, Denmark; KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa;
| | - Reuben McGregor
- Department of Paediatrics, University of Oxford, Oxford OX1 3SY, United Kingdom
| | - James E McLaren
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, United Kingdom
| | - Kristin Ladell
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, United Kingdom
| | - Mikkel Harndahl
- Department of International Health, Immunology, and Microbiology, University of Copenhagen, 2200-Copenhagen N, Denmark
| | - Anette Stryhn
- Department of International Health, Immunology, and Microbiology, University of Copenhagen, 2200-Copenhagen N, Denmark
| | | | - Catherine Koofhethile
- HIV Pathogenesis Program, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4013, South Africa
| | - Bram Gerritsen
- Theoretical Biology Group, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Can Keşmir
- Theoretical Biology Group, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Fabian Chen
- Department of Sexual Health, Royal Berkshire Hospital, Reading RG1 5AN, United Kingdom
| | - Lynn Riddell
- Department of Genitourinary Medicine, Northamptonshire Healthcare National Health Service Trust, Northampton General Hospital, Cliftonville, Northampton NN1 5BD, United Kingdom
| | - Graz Luzzi
- Department of Sexual Health, Wycombe Hospital, High Wycombe HP11 2TT, United Kingdom
| | - Alasdair Leslie
- KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
| | - Bruce D Walker
- Ragon Institute of MGH, MIT, and Harvard, Boston, MA 02129; Howard Hughes Medical Institute, Chevy Chase, MD 20815; and
| | - Thumbi Ndung'u
- KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa; HIV Pathogenesis Program, Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban 4013, South Africa; Max Planck Institute for Infection Biology, D-10117 Berlin, Germany
| | - Søren Buus
- Department of International Health, Immunology, and Microbiology, University of Copenhagen, 2200-Copenhagen N, Denmark
| | - David A Price
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, United Kingdom
| | - Philip J Goulder
- Department of Paediatrics, University of Oxford, Oxford OX1 3SY, United Kingdom
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49
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Neller MA, Ladell K, McLaren JE, Matthews KK, Gostick E, Pentier JM, Dolton G, Schauenburg AJA, Koning D, Fontaine Costa AICA, Watkins TS, Venturi V, Smith C, Khanna R, Miners K, Clement M, Wooldridge L, Cole DK, van Baarle D, Sewell AK, Burrows SR, Price DA, Miles JJ. Naive CD8⁺ T-cell precursors display structured TCR repertoires and composite antigen-driven selection dynamics. Immunol Cell Biol 2015; 93:625-33. [PMID: 25801351 PMCID: PMC4533101 DOI: 10.1038/icb.2015.17] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 01/04/2015] [Accepted: 01/22/2015] [Indexed: 02/07/2023]
Abstract
Basic parameters of the naive antigen (Ag)-specific T-cell repertoire in humans remain poorly defined. Systematic characterization of this ‘ground state' immunity in comparison with memory will allow a better understanding of clonal selection during immune challenge. Here, we used high-definition cell isolation from umbilical cord blood samples to establish the baseline frequency, phenotype and T-cell antigen receptor (TCR) repertoire of CD8+ T-cell precursor populations specific for a range of viral and self-derived Ags. Across the board, these precursor populations were phenotypically naive and occurred with hierarchical frequencies clustered by Ag specificity. The corresponding patterns of TCR architecture were highly ordered and displayed partial overlap with adult memory, indicating biased structuring of the T-cell repertoire during Ag-driven selection. Collectively, these results provide new insights into the complex nature and dynamics of the naive T-cell compartment.
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Affiliation(s)
- Michelle A Neller
- Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Kristin Ladell
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - James E McLaren
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Katherine K Matthews
- Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Emma Gostick
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Johanne M Pentier
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Garry Dolton
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Andrea J A Schauenburg
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Dan Koning
- Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Thomas S Watkins
- Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Vanessa Venturi
- Computational Biology Unit, Centre for Vascular Research, University of New South Wales, Kensington, NSW, Australia
| | - Corey Smith
- Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Rajiv Khanna
- Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Kelly Miners
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Mathew Clement
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Linda Wooldridge
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - David K Cole
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Debbie van Baarle
- Department of Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Andrew K Sewell
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Scott R Burrows
- 1] Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia [2] School of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - David A Price
- 1] Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK [2] Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John J Miles
- 1] Human Immunity Laboratory, Cellular Immunology Laboratory and Tumour Immunology Laboratory, Queensland Institute of Medical Research, Brisbane, QLD, Australia [2] Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK [3] School of Medicine, The University of Queensland, Brisbane, QLD, Australia
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50
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Madura F, Rizkallah PJ, Holland CJ, Fuller A, Bulek A, Godkin AJ, Schauenburg AJ, Cole DK, Sewell AK. Structural basis for ineffective T-cell responses to MHC anchor residue-improved "heteroclitic" peptides. Eur J Immunol 2015; 45:584-91. [PMID: 25471691 PMCID: PMC4357396 DOI: 10.1002/eji.201445114] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Revised: 10/03/2014] [Accepted: 11/26/2014] [Indexed: 12/11/2022]
Abstract
MHC anchor residue-modified "heteroclitic" peptides have been used in many cancer vaccine trials and often induce greater immune responses than the wild-type peptide. The best-studied system to date is the decamer MART-1/Melan-A26-35 peptide, EAAGIGILTV, where the natural alanine at position 2 has been modified to leucine to improve human leukocyte antigen (HLA)-A*0201 anchoring. The resulting ELAGIGILTV peptide has been used in many studies. We recently showed that T cells primed with the ELAGIGILTV peptide can fail to recognize the natural tumor-expressed peptide efficiently, thereby providing a potential molecular reason for why clinical trials of this peptide have been unsuccessful. Here, we solved the structure of a TCR in complex with HLA-A*0201-EAAGIGILTV peptide and compared it with its heteroclitic counterpart , HLA-A*0201-ELAGIGILTV. The data demonstrate that a suboptimal anchor residue at position 2 enables the TCR to "pull" the peptide away from the MHC binding groove, facilitating extra contacts with both the peptide and MHC surface. These data explain how a TCR can distinguish between two epitopes that differ by only a single MHC anchor residue and demonstrate how weak MHC anchoring can enable an induced-fit interaction with the TCR. Our findings constitute a novel demonstration of the extreme sensitivity of the TCR to minor alterations in peptide conformation.
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MESH Headings
- Alanine/chemistry
- Alanine/genetics
- Amino Acid Sequence
- Amino Acid Substitution
- Crystallography, X-Ray
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- HLA-A2 Antigen/chemistry
- HLA-A2 Antigen/genetics
- HLA-A2 Antigen/immunology
- Humans
- Leucine/chemistry
- Leucine/genetics
- MART-1 Antigen/chemistry
- MART-1 Antigen/genetics
- MART-1 Antigen/immunology
- Models, Molecular
- Molecular Sequence Data
- Peptides/chemistry
- Peptides/genetics
- Peptides/immunology
- Protein Binding
- Protein Interaction Domains and Motifs
- Receptors, Antigen, T-Cell, alpha-beta/chemistry
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
- T-Lymphocytes, Cytotoxic/cytology
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
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Affiliation(s)
- Florian Madura
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Pierre J Rizkallah
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Christopher J Holland
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Anna Fuller
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Anna Bulek
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Andrew J Godkin
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Andrea J Schauenburg
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - David K Cole
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
| | - Andrew K Sewell
- Division of Infection and Immunity, Cardiff University School of MedicineHeath Park, Cardiff, UK
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