151
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Chiou SH, Tseng D, Reuben A, Mallajosyula V, Molina IS, Conley S, Wilhelmy J, McSween AM, Yang X, Nishimiya D, Sinha R, Nabet BY, Wang C, Shrager JB, Berry MF, Backhus L, Lui NS, Wakelee HA, Neal JW, Padda SK, Berry GJ, Delaidelli A, Sorensen PH, Sotillo E, Tran P, Benson JA, Richards R, Labanieh L, Klysz DD, Louis DM, Feldman SA, Diehn M, Weissman IL, Zhang J, Wistuba II, Futreal PA, Heymach JV, Garcia KC, Mackall CL, Davis MM. Global analysis of shared T cell specificities in human non-small cell lung cancer enables HLA inference and antigen discovery. Immunity 2021; 54:586-602.e8. [PMID: 33691136 PMCID: PMC7960510 DOI: 10.1016/j.immuni.2021.02.014] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/08/2020] [Accepted: 02/11/2021] [Indexed: 12/12/2022]
Abstract
To identify disease-relevant T cell receptors (TCRs) with shared antigen specificity, we analyzed 778,938 TCRβ chain sequences from 178 non-small cell lung cancer patients using the GLIPH2 (grouping of lymphocyte interactions with paratope hotspots 2) algorithm. We identified over 66,000 shared specificity groups, of which 435 were clonally expanded and enriched in tumors compared to adjacent lung. The antigenic epitopes of one such tumor-enriched specificity group were identified using a yeast peptide-HLA A∗02:01 display library. These included a peptide from the epithelial protein TMEM161A, which is overexpressed in tumors and cross-reactive epitopes from Epstein-Barr virus and E. coli. Our findings suggest that this cross-reactivity may underlie the presence of virus-specific T cells in tumor infiltrates and that pathogen cross-reactivity may be a feature of multiple cancers. The approach and analytical pipelines generated in this work, as well as the specificity groups defined here, present a resource for understanding the T cell response in cancer.
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Affiliation(s)
- Shin-Heng Chiou
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Diane Tseng
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Alexandre Reuben
- Department of Thoracic Head and Neck Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Vamsee Mallajosyula
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Irene S Molina
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Stephanie Conley
- Institute for Stem Cell Biology and Regenerative Medicine Institute, Stanford University, Stanford, CA 94305, USA
| | - Julie Wilhelmy
- Stanford Genome Technology Center, Stanford University, Stanford, CA 94305, USA
| | - Alana M McSween
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Xinbo Yang
- Department of Molecular and Cellular Physiology and Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Daisuke Nishimiya
- Department of Molecular and Cellular Physiology and Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine Institute, Stanford University, Stanford, CA 94305, USA
| | - Barzin Y Nabet
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA
| | - Chunlin Wang
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Joseph B Shrager
- Department of Cardiothoracic Surgery - Thoracic Surgery, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Mark F Berry
- Department of Cardiothoracic Surgery - Thoracic Surgery, Stanford University, Stanford, CA 94305, USA
| | - Leah Backhus
- Department of Cardiothoracic Surgery - Thoracic Surgery, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Natalie S Lui
- Department of Cardiothoracic Surgery - Thoracic Surgery, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Heather A Wakelee
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Joel W Neal
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Sukhmani K Padda
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Gerald J Berry
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Alberto Delaidelli
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
| | - Poul H Sorensen
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
| | - Elena Sotillo
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Patrick Tran
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Jalen A Benson
- Department of Cardiothoracic Surgery - Thoracic Surgery, Stanford University, Stanford, CA 94305, USA
| | - Rebecca Richards
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Louai Labanieh
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Dorota D Klysz
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - David M Louis
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Steven A Feldman
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Maximilian Diehn
- Institute for Stem Cell Biology and Regenerative Medicine Institute, Stanford University, Stanford, CA 94305, USA; Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine Institute, Stanford University, Stanford, CA 94305, USA
| | - Jianjun Zhang
- Department of Thoracic Head and Neck Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John V Heymach
- Department of Thoracic Head and Neck Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology and Structural Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Crystal L Mackall
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
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152
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Heikkilä N, Sormunen S, Mattila J, Härkönen T, Knip M, Ihantola EL, Kinnunen T, Mattila IP, Saramäki J, Arstila TP. Generation of self-reactive, shared T-cell receptor α chains in the human thymus. J Autoimmun 2021; 119:102616. [PMID: 33652347 DOI: 10.1016/j.jaut.2021.102616] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/04/2021] [Accepted: 02/07/2021] [Indexed: 11/26/2022]
Abstract
The T-cell receptor (TCR) repertoire is generated in a semistochastic process of gene recombination and pairing of TCRα to TCRβ chains with the estimated total TCR diversity of >108. Despite this high diversity, similar or identical TCR chains are found to recur in immune responses. Here, we analyzed the thymic generation of TCR sequences previously associated with recognition of self- and nonself-antigens, represented by sequences associated with autoimmune diabetes and HIV, respectively. Unexpectedly, in the CD4+ compartment TCRα chains associated with the recognition of self-antigens were generated in significantly higher numbers than TCRα chains associated with the recognition of nonself-antigens. The analysis of the circulating repertoire further showed that these chains are not lost in negative selection nor predominantly converted to the regulatory T-cell lineage. The high abundance of self-reactive TCRα chains in multiple individuals suggests that the human thymus has a predilection to generate self-reactive TCRα chains independently of the HLA-type and that the individual risk of autoimmunity may be modulated by the TCRβ repertoire associated with these chains.
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Affiliation(s)
- Nelli Heikkilä
- Research Programs Unit, Translational Immunology, and Medicum, University of Helsinki, Haartmaninkatu 3, 00290, Helsinki, Finland.
| | - Silja Sormunen
- Department of Computer Science, Aalto University, Konemiehenkatu 2, 02150, Espoo, Finland
| | - Joonatan Mattila
- Research Programs Unit, Translational Immunology, and Medicum, University of Helsinki, Haartmaninkatu 3, 00290, Helsinki, Finland
| | - Taina Härkönen
- Pediatric Research Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Stenbäckinkatu 9, 00290, Helsinki, Finland
| | - Mikael Knip
- Pediatric Research Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Stenbäckinkatu 9, 00290, Helsinki, Finland; Research Program for Clinical and Molecular Metabolism, University of Helsinki, Haartmaninkatu 8, 00290, Helsinki, Finland; Folkhälsan Research Center, Topeliuksenkatu 25, 00250, Helsinki, Finland; Department of Pediatrics, Tampere University Hospital, Elämänaukio 2, 33520, Tampere, Finland
| | - Emmi-Leena Ihantola
- Department of Clinical Microbiology, Institute of Clinical Medicine, University of Eastern Finland, Puijonlaaksontie 2, 70210, Kuopio, Finland
| | - Tuure Kinnunen
- Department of Clinical Microbiology, Institute of Clinical Medicine, University of Eastern Finland, Puijonlaaksontie 2, 70210, Kuopio, Finland; Eastern Finland Laboratory Centre (ISLAB), Puijonlaaksontie 2, 70210, Kuopio, Finland
| | - Ilkka P Mattila
- Department of Pediatric Cardiac and Transplantation Surgery, Hospital for Children and Adolescents, Helsinki University Central Hospital, Stenbäckinkatu 9, 00290, Helsinki, Finland
| | - Jari Saramäki
- Department of Computer Science, Aalto University, Konemiehenkatu 2, 02150, Espoo, Finland
| | - T Petteri Arstila
- Research Programs Unit, Translational Immunology, and Medicum, University of Helsinki, Haartmaninkatu 3, 00290, Helsinki, Finland
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153
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Holland CJ, Crean RM, Pentier JM, de Wet B, Lloyd A, Srikannathasan V, Lissin N, Lloyd KA, Blicher TH, Conroy PJ, Hock M, Pengelly RJ, Spinner TE, Cameron B, Potter EA, Jeyanthan A, Molloy PE, Sami M, Aleksic M, Liddy N, Robinson RA, Harper S, Lepore M, Pudney CR, van der Kamp MW, Rizkallah PJ, Jakobsen BK, Vuidepot A, Cole DK. Specificity of bispecific T cell receptors and antibodies targeting peptide-HLA. J Clin Invest 2021; 130:2673-2688. [PMID: 32310221 DOI: 10.1172/jci130562] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 02/11/2020] [Indexed: 01/09/2023] Open
Abstract
Tumor-associated peptide-human leukocyte antigen complexes (pHLAs) represent the largest pool of cell surface-expressed cancer-specific epitopes, making them attractive targets for cancer therapies. Soluble bispecific molecules that incorporate an anti-CD3 effector function are being developed to redirect T cells against these targets using 2 different approaches. The first achieves pHLA recognition via affinity-enhanced versions of natural TCRs (e.g., immune-mobilizing monoclonal T cell receptors against cancer [ImmTAC] molecules), whereas the second harnesses an antibody-based format (TCR-mimic antibodies). For both classes of reagent, target specificity is vital, considering the vast universe of potential pHLA molecules that can be presented on healthy cells. Here, we made use of structural, biochemical, and computational approaches to investigate the molecular rules underpinning the reactivity patterns of pHLA-targeting bispecifics. We demonstrate that affinity-enhanced TCRs engage pHLA using a comparatively broad and balanced energetic footprint, with interactions distributed over several HLA and peptide side chains. As ImmTAC molecules, these TCRs also retained a greater degree of pHLA selectivity, with less off-target activity in cellular assays. Conversely, TCR-mimic antibodies tended to exhibit binding modes focused more toward hot spots on the HLA surface and exhibited a greater degree of crossreactivity. Our findings extend our understanding of the basic principles that underpin pHLA selectivity and exemplify a number of molecular approaches that can be used to probe the specificity of pHLA-targeting molecules, aiding the development of future reagents.
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Affiliation(s)
| | - Rory M Crean
- Department of Biology and Biochemistry and.,Doctoral Training Centre in Sustainable Chemical Technologies, University of Bath, Bath, United Kingdom
| | | | - Ben de Wet
- Immunocore Ltd., Milton Park, Abingdon, United Kingdom
| | | | | | | | - Katy A Lloyd
- Immunocore Ltd., Milton Park, Abingdon, United Kingdom
| | | | - Paul J Conroy
- Immunocore Ltd., Milton Park, Abingdon, United Kingdom
| | - Miriam Hock
- Immunocore Ltd., Milton Park, Abingdon, United Kingdom
| | | | | | - Brian Cameron
- Immunocore Ltd., Milton Park, Abingdon, United Kingdom
| | | | | | | | - Malkit Sami
- Immunocore Ltd., Milton Park, Abingdon, United Kingdom
| | - Milos Aleksic
- Immunocore Ltd., Milton Park, Abingdon, United Kingdom
| | | | | | | | - Marco Lepore
- Immunocore Ltd., Milton Park, Abingdon, United Kingdom
| | | | | | - Pierre J Rizkallah
- Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
| | | | | | - David K Cole
- Immunocore Ltd., Milton Park, Abingdon, United Kingdom.,Cardiff University School of Medicine, Heath Park, Cardiff, United Kingdom
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154
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Droplet-based mRNA sequencing of fixed and permeabilized cells by CLInt-seq allows for antigen-specific TCR cloning. Proc Natl Acad Sci U S A 2021; 118:2021190118. [PMID: 33431692 PMCID: PMC7826406 DOI: 10.1073/pnas.2021190118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
T cell receptors (TCRs) surveil cellular environment by recognizing peptides presented by the major histocompatibility complex. TCR sequencing allows for understanding the scope of T cell reactivity in health and disease. Specific TCR clones can be used as therapeutics in cancer and autoimmune disease. We present a technique that allows for TCR sequencing based on intracellular signaling molecules, such as cytokines and transcription factors. The core concept is highly generalizable and should be applicable to global gene expression analysis where intracellular marker-based cell isolation is required. T cell receptors (TCRs) are generated by somatic recombination of V/D/J segments to produce up to 1015 unique sequences. Highly sensitive and specific techniques are required to isolate and identify the rare TCR sequences that respond to antigens of interest. Here, we describe the use of mRNA sequencing via cross-linker regulated intracellular phenotype (CLInt-Seq) for efficient recovery of antigen-specific TCRs in cells stained for combinations of intracellular proteins such as cytokines or transcription factors. This method enables high-throughput identification and isolation of low-frequency TCRs specific for any antigen. As a proof of principle, intracellular staining for TNFα and IFNγ identified cytomegalovirus (CMV)- and Epstein-Barr virus (EBV)-reactive TCRs with efficiencies similar to state-of-the-art peptide-MHC multimer methodology. In a separate experiment, regulatory T cells were profiled based on intracellular FOXP3 staining, demonstrating the ability to examine phenotypes based on transcription factors. We further optimized the intracellular staining conditions to use a chemically cleavable primary amine cross-linker compatible with current single-cell sequencing technology. CLInt-Seq for TNFα and IFNγ performed similarly to isolation with multimer staining for EBV-reactive TCRs. We anticipate CLInt-Seq will enable droplet-based single-cell mRNA analysis from any tissue where minor populations need to be isolated by intracellular markers.
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155
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Shinkawa T, Tokita S, Nakatsugawa M, Kikuchi Y, Kanaseki T, Torigoe T. Characterization of CD8 + T-cell responses to non-anchor-type HLA class I neoantigens with single amino-acid substitutions. Oncoimmunology 2021; 10:1870062. [PMID: 33537174 PMCID: PMC7833734 DOI: 10.1080/2162402x.2020.1870062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
CD8+ T cells are capable of recognizing mutation-derived neoantigens displayed by HLA class I molecules, thereby exhibiting the ability to distinguish between cancer and normal cells. However, accumulating evidence has shown that only a small fraction of nonsynonymous somatic mutations give rise to clinically relevant neoantigens. The properties of such neoantigens, which must be presented by HLA and immunogenic to induce a T-cell response, remain elusive. In this study, we explored the HLA class I ligandome of a human cancer cell line with microsatellite instability using a proteogenomic approach. The results demonstrated that neoantigens accounted for only 0.34% of the HLA class I ligandome, and most neoantigens were encoded by genes with abundant expression. Thereafter, T-cell responses were prioritized, and immunodominant neoantigens were defined using naive CD8+ T cells derived from healthy donors. AKF9, an immunogenic neoantigen with a mutation at a non-anchor position, formed a stable peptide-HLA complex. T-cell responses were analyzed against a panel of AKF9 variants with single amino-acid substitutions, in which mutations did not alter the high HLA-binding affinity and stability. The responses varied across individuals, demonstrating the impact of heterogeneous T-cell repertoires in this human cancer model. Moreover, responses were biased toward a variant group with large structural changes compared to the wild-type peptide. Thus, naive T-cell induction can be attributed to multiple determinants. Combining structural dissimilarity with gene-expression levels, HLA-binding affinity, and stability may further help prioritize the immunogenicity of non-anchor-type neoantigens.
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Affiliation(s)
- Tomoyo Shinkawa
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | - Serina Tokita
- Academic center, Sapporo Dohto Hospital, Sapporo, Japan.,Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | - Munehide Nakatsugawa
- Department of Pathology, Tokyo Medical University Hachioji Medical Center, Tokyo, Japan.,Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | - Yasuhiro Kikuchi
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
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156
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Cueno ME, Imai K. Structural Comparison of the SARS CoV 2 Spike Protein Relative to Other Human-Infecting Coronaviruses. Front Med (Lausanne) 2021; 7:594439. [PMID: 33585502 PMCID: PMC7874069 DOI: 10.3389/fmed.2020.594439] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/14/2020] [Indexed: 12/19/2022] Open
Abstract
Coronaviruses (CoV) are enveloped positive-stranded RNA viruses and, historically, there are seven known human-infecting CoVs with varying degrees of virulence. CoV attachment to the host is the first step of viral pathogenesis and mainly relies on the spike glycoprotein located on the viral surface. Among the human-infecting CoVs, only the infection of SARS CoV 2 (SARS2) among humans resulted to a pandemic which would suggest that the protein structural conformation of SARS2 spike protein is distinct as compared to other human-infecting CoVs. Surprisingly, the possible differences and similarities in the protein structural conformation between the various human-infecting CoV spike proteins have not been fully elucidated. In this study, we utilized a computational approach to generate models and analyze the seven human-infecting CoV spike proteins, namely: HCoV 229E, HCoV OC43, HCoV NL63, HCoV HKU1, SARS CoV, MERS CoV, and SARS2. Model quality assessment of all CoV models generated, structural superimposition of the whole protein model and selected S1 domains (S1-CTD and S1-NTD), and structural comparison based on RMSD values, Tm scores, and contact mapping were all performed. We found that the structural orientation of S1-CTD is a potential structural feature associated to both the CoV phylogenetic cluster and lineage. Moreover, we observed that spike models in the same phylogenetic cluster or lineage could potentially have similar protein structure. Additionally, we established that there are potentially three distinct S1-CTD orientation (Pattern I, Pattern II, Pattern III) among the human-infecting CoVs. Furthermore, we postulate that human-infecting CoVs in the same phylogenetic cluster may have similar S1-CTD and S1-NTD structural orientation. Taken together, we propose that the SARS2 spike S1-CTD follows a Pattern III orientation which has a higher degree of similarity with SARS1 and some degree of similarity with both OC43 and HKU1 which coincidentally are in the same phylogenetic cluster and lineage, whereas, the SARS2 spike S1-NTD has some degree of similarity among human-infecting CoVs that are either in the same phylogenetic cluster or lineage.
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Affiliation(s)
- Marni E Cueno
- Department of Microbiology, Nihon University School of Dentistry, Tokyo, Japan
| | - Kenichi Imai
- Department of Microbiology, Nihon University School of Dentistry, Tokyo, Japan
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157
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The burgeoning role of MR1-restricted T-cells in infection, cancer and autoimmune disease. Curr Opin Immunol 2021; 69:10-17. [PMID: 33434741 DOI: 10.1016/j.coi.2020.12.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/22/2020] [Accepted: 12/14/2020] [Indexed: 12/16/2022]
Abstract
MR1 is a ubiquitously expressed, monomorphic antigen presenting molecule that has been largely preserved throughout mammalian evolution. The primary role of MR1 is to present conserved microbial metabolites to highly abundant mucosal-associated invariant T (MAIT) cells. The role of MAIT cells and other MR1-restricted T cells (MR1T) has been recently extended to immunomodulation during cancer. MR1Ts have also been implicated in autoimmune disease. The highly conserved nature of MR1 across the human population is in stark contrast to the MHC molecules recognised by conventional αβ T-cells, therefore MR1Ts may form fertile ground for the development of pan-population T-cell immunotherapeutics for a wide range of important morbidities.
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158
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Velardi E, Clave E, Arruda LCM, Benini F, Locatelli F, Toubert A. The role of the thymus in allogeneic bone marrow transplantation and the recovery of the peripheral T-cell compartment. Semin Immunopathol 2021; 43:101-117. [PMID: 33416938 DOI: 10.1007/s00281-020-00828-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/14/2020] [Indexed: 12/11/2022]
Abstract
As the thymus represents the primary site of T-cell development, optimal thymic function is of paramount importance for the successful reconstitution of the adaptive immunity after allogeneic hematopoietic stem cell transplantation. Thymus involutes as part of the aging process and several factors, including previous chemotherapy treatments, conditioning regimen used in preparation to the allograft, occurrence of graft-versus-host disease, and steroid therapy that impair the integrity of the thymus, thus affecting its role in supporting T-cell neogenesis. Although the pathways governing its regeneration are still poorly understood, the thymus has a remarkable capacity to recover its function after damage. Measurement of both recent thymic emigrants and T-cell receptor excision circles is valuable tools to assess thymic output and gain insights on its function. In this review, we will extensively discuss available data on factors regulating thymic function after allogeneic hematopoietic stem cell transplantation, as well as the strategies and therapeutic approaches under investigation to promote thymic reconstitution and accelerate immune recovery in transplanted patients, including the use of cytokines, sex-steroid ablation, precursor T-cells, and thymus bioengineering. Although none of them is routinely used in the clinic, these approaches have the potential to enhance thymic function and immune recovery, not only in patients given an allograft but also in other conditions characterized by immune deficiencies related to a defective function of the thymus.
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Affiliation(s)
- Enrico Velardi
- Department of Pediatric Hematology and Oncology, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy.
| | - Emmanuel Clave
- Université de Paris, Institut de Recherche Saint Louis, EMiLy, Inserm U1160, F-75010, Paris, France
| | - Lucas C M Arruda
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Francesca Benini
- Department of Maternal and Child Health, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Franco Locatelli
- Department of Pediatric Hematology and Oncology, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy.,Department of Maternal and Child Health, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Antoine Toubert
- Université de Paris, Institut de Recherche Saint Louis, EMiLy, Inserm U1160, F-75010, Paris, France.,Laboratoire d'Immunologie et d'Histocompatibilité, AP-HP, Hopital Saint-Louis, F-75010, Paris, France
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159
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Affiliation(s)
- Luigi Buonaguro
- Innovative Immunological Models, Istituto Nazionale per lo Studio e la Cura dei Tumori, "Fondazione Pascale"-IRCCS, Via Mariano Semmola, 52, 80131 Naples, Italy.
| | - Vincenzo Cerullo
- Drug Research Program ImmunoViroTherapy Lab (IVTLAb), Faculty of Pharmacy, University of Helsinki, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland; Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland; Translational Immunology Program (TRIMM), University of Helsinki, Helsinki, Finland; Department of Molecular Medicine and Medical Biotechnology, Naples University "Federico II," S. Pansini 5, Italy.
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160
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Martini A, Fallara G, Pellegrino F, Cirulli GO, Larcher A, Necchi A, Montorsi F, Capitanio U. Neoadjuvant and adjuvant immunotherapy in renal cell carcinoma. World J Urol 2021; 39:1369-1376. [PMID: 33386494 DOI: 10.1007/s00345-020-03550-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 11/30/2020] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE The treatment landscape for renal cell carcinoma (RCC) is rapidly evolving. The aim of this review is to summarize the randomized-controlled trials evaluating the role of immunotherapy in neoadjuvant or adjuvant setting. MATERIALS AND METHODS We searched PubMed, Cochrane Central Register of Controlled Trials, and ClinicalTrials.gov for studies including neoadjuvant or adjuvant immunotherapy, and provided a brief overview of the pharmacodynamics of immunotherapy for RCC. RESULTS Several drugs are currently under investigation. In the neoadjuvant setting, four studies are evaluating the role of single-agent immunotherapy, one of dual-agent immunotherapy, and four studies the role of immunotherapy in combination with tyrosine kinase inhibitors or anti-interleukin-1 beta. In the adjuvant setting, two studies are evaluating the role of single-agent immunotherapy and two of dual-agent immunotherapy. CONCLUSIONS The approval of immune checkpoint inhibition as a front-line therapeutic strategy for advanced RCC has also ultimately led to the investigation of these agents first in the adjuvant and then in the neoadjuvant setting. Currently, there are nine studies aimed to evaluate the role of immunotherapy in the neoadjuvant setting and four studies in the adjuvant setting.
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Affiliation(s)
- Alberto Martini
- Unit of Urology, University Vita-Salute, San Raffaele Scientific Institute, Milan, Italy
- Division of Experimental Oncology, URI, Urological Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giuseppe Fallara
- Unit of Urology, University Vita-Salute, San Raffaele Scientific Institute, Milan, Italy
- Division of Experimental Oncology, URI, Urological Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesco Pellegrino
- Unit of Urology, University Vita-Salute, San Raffaele Scientific Institute, Milan, Italy
- Division of Experimental Oncology, URI, Urological Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giuseppe Ottone Cirulli
- Unit of Urology, University Vita-Salute, San Raffaele Scientific Institute, Milan, Italy
- Division of Experimental Oncology, URI, Urological Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alessandro Larcher
- Unit of Urology, University Vita-Salute, San Raffaele Scientific Institute, Milan, Italy
- Division of Experimental Oncology, URI, Urological Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Necchi
- Unit of Urology, University Vita-Salute, San Raffaele Scientific Institute, Milan, Italy
- Division of Experimental Oncology, URI, Urological Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesco Montorsi
- Unit of Urology, University Vita-Salute, San Raffaele Scientific Institute, Milan, Italy
- Division of Experimental Oncology, URI, Urological Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Umberto Capitanio
- Unit of Urology, University Vita-Salute, San Raffaele Scientific Institute, Milan, Italy.
- Division of Experimental Oncology, URI, Urological Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy.
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161
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Tracking the Genetic Susceptibility Background of B-Cell Non-Hodgkin's Lymphomas from Genome-Wide Association Studies. Int J Mol Sci 2020; 22:ijms22010122. [PMID: 33374413 PMCID: PMC7795678 DOI: 10.3390/ijms22010122] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/10/2020] [Accepted: 12/18/2020] [Indexed: 12/31/2022] Open
Abstract
B-cell non-Hodgkin’s lymphoma (NHL) risk associations had been mainly attributed to family history of the disease, inflammation, and immune components including human leukocyte antigen (HLA) genetic variations. Nevertheless, a broad range of genome-wide association studies (GWAS) have shed light into the identification of several genetic variants presumptively associated with B-cell NHL etiologies, survival or shared genetic risk with other diseases. The present review aims to overview HLA structure and diversity and summarize the evidence of genetic variations, by GWAS, on five NHL subtypes (diffuse large B-cell lymphoma DLBCL, follicular lymphoma FL, chronic lymphocytic leukemia CLL, marginal zone lymphoma MZL, and primary central nervous system lymphoma PCNSL). Evidence indicates that the HLA zygosity status in B-cell NHL might promote immune escape and that genome-wide significance variants can give biological insight but also potential therapeutic markers such as WEE1 in DLBCL. However, additional studies are needed, especially for non-DLBCL, to replicate the associations found to date.
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Borrman T, Pierce BG, Vreven T, Baker BM, Weng Z. High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides. Bioinformatics 2020; 36:5377-5385. [PMID: 33355667 PMCID: PMC8016493 DOI: 10.1093/bioinformatics/btaa1050] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 11/23/2020] [Accepted: 12/08/2020] [Indexed: 01/14/2023] Open
Abstract
MOTIVATION The binding of T cell receptors (TCRs) to their target peptide MHC (pMHC) ligands initializes the cell-mediated immune response. In autoimmune diseases such as multiple sclerosis, the TCR erroneously recognizes self-peptides as foreign and activates an immune response against healthy cells. Such responses can be triggered by cross-recognition of the autoreactive TCR with foreign peptides. Hence, it would be desirable to identify such foreign-antigen triggers to provide a mechanistic understanding of autoimmune diseases. However, the large sequence space of foreign antigens presents an obstacle in the identification of cross-reactive peptides. RESULTS Here, we present an in silico modeling and scoring method which exploits the structural properties of TCR-pMHC complexes to predict the binding of cross-reactive peptides. We analyzed three mouse TCRs and one human TCR isolated from a patient with multiple sclerosis. Cross-reactive peptides for these TCRs were previously identified via yeast display coupled with deep sequencing, providing a robust dataset for evaluating our method. Modeling query peptides in their associated TCR-pMHC crystal structures, our method accurately selected the top binding peptides from sets containing more than a hundred thousand unique peptides. AVAILABILITY AND IMPLEMENTATION Analyses were performed using custom Python and R scripts available at https://github.com/tborrman/antigen-predict. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tyler Borrman
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Brian G Pierce
- University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Thom Vreven
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA.,Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
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163
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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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164
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Qiu CX, Bai XF, Shen Y, Zhou Z, Pan LQ, Xu YC, Zhao WB, Chen SQ. Specific Inhibition of Tumor Growth by T Cell Receptor-Drug Conjugates Targeting Intracellular Cancer-Testis Antigen NY-ESO-1/LAGE-1. Bioconjug Chem 2020; 31:2767-2778. [PMID: 33237767 DOI: 10.1021/acs.bioconjchem.0c00548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite the significant therapeutic advances in T-cell immunotherapy, many malignancies remain unresponsive, which might be because of the negative regulation of T cells by the tumor microenvironment (TME). T cells discriminate tumor cells and normal cells through T-cell receptors (TCRs); therefore, we generated a novel type of TCR-drug conjugates (TDCs) by referring antibody-drug conjugations (ADCs) to overcome the effects of the TME on T cells while preserving the specificity of TCR for tumor recognition. We selected HLA-A2/NY-ESO-1157-165 (peptide NY-ESO-1157-165 in complex with human leukocyte antigen serotype HLA-A*02:01) as the antigen and the antigen-specific TCR (1G4113) as the carrier. By sortase A-mediated ligation, we obtained three NY-TCR-vcMMAEs and further studied their properties, antitumor activity, and toxicity in vitro and in vivo. We found that all the NY-TCR-vcMMAEs had high endocytosis efficiency and specifically killed HLA-A2/NY-ESO-1157-165 positive tumor cells. In xenograft models, one of the TDCs, NY-TCR-2M, was effectively and specifically distributed into tumor tissues and inhibited tumor growth without inducing obvious toxicity. Our results demonstrated that TCRs can be carriers of toxic payloads and that the TDCs thus formed can specifically inhibit tumor growth, neglecting the immune microenvironment.
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Affiliation(s)
- Chi-Xiao Qiu
- Institute of Drug Metabolism and Pharmaceutical Analysis & Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xue-Fei Bai
- Institute of Drug Metabolism and Pharmaceutical Analysis & Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ying Shen
- Institute of Drug Metabolism and Pharmaceutical Analysis & Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhan Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis & Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Li-Qiang Pan
- Institute of Drug Metabolism and Pharmaceutical Analysis & Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ying-Chun Xu
- Institute of Drug Metabolism and Pharmaceutical Analysis & Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wen-Bin Zhao
- Institute of Drug Metabolism and Pharmaceutical Analysis & Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shu-Qing Chen
- Institute of Drug Metabolism and Pharmaceutical Analysis & Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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165
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Bacher P, Rosati E, Esser D, Martini GR, Saggau C, Schiminsky E, Dargvainiene J, Schröder I, Wieters I, Khodamoradi Y, Eberhardt F, Vehreschild MJGT, Neb H, Sonntagbauer M, Conrad C, Tran F, Rosenstiel P, Markewitz R, Wandinger KP, Augustin M, Rybniker J, Kochanek M, Leypoldt F, Cornely OA, Koehler P, Franke A, Scheffold A. Low-Avidity CD4 + T Cell Responses to SARS-CoV-2 in Unexposed Individuals and Humans with Severe COVID-19. Immunity 2020; 53:1258-1271.e5. [PMID: 33296686 PMCID: PMC7689350 DOI: 10.1016/j.immuni.2020.11.016] [Citation(s) in RCA: 211] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/08/2020] [Accepted: 11/19/2020] [Indexed: 01/08/2023]
Abstract
CD4+ T cells reactive against SARS-CoV-2 can be found in unexposed individuals, and these are suggested to arise in response to common cold coronavirus (CCCoV) infection. Here, we utilized SARS-CoV-2-reactive CD4+ T cell enrichment to examine the antigen avidity and clonality of these cells, as well as the relative contribution of CCCoV cross-reactivity. SARS-CoV-2-reactive CD4+ memory T cells were present in virtually all unexposed individuals examined, displaying low functional avidity and multiple, highly variable cross-reactivities that were not restricted to CCCoVs. SARS-CoV-2-reactive CD4+ T cells from COVID-19 patients lacked cross-reactivity to CCCoVs, irrespective of strong memory T cell responses against CCCoV in all donors analyzed. In severe but not mild COVID-19, SARS-CoV-2-specific T cells displayed low functional avidity and clonality, despite increased frequencies. Our findings identify low-avidity CD4+ T cell responses as a hallmark of severe COVID-19 and argue against a protective role for CCCoV-reactive T cells in SARS-CoV-2 infection.
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Affiliation(s)
- Petra Bacher
- Institute of Immunology, Christian-Albrechts-University of Kiel & UKSH Schleswig-Holstein, Kiel, Germany; Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany.
| | - Elisa Rosati
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Daniela Esser
- Institute of Clinical Chemistry, University Hospital Schleswig-Holstein, Kiel/ Lübeck, Germany
| | - Gabriela Rios Martini
- Institute of Immunology, Christian-Albrechts-University of Kiel & UKSH Schleswig-Holstein, Kiel, Germany; Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Carina Saggau
- Institute of Immunology, Christian-Albrechts-University of Kiel & UKSH Schleswig-Holstein, Kiel, Germany
| | - Esther Schiminsky
- Institute of Immunology, Christian-Albrechts-University of Kiel & UKSH Schleswig-Holstein, Kiel, Germany
| | - Justina Dargvainiene
- Institute of Clinical Chemistry, University Hospital Schleswig-Holstein, Kiel/ Lübeck, Germany
| | - Ina Schröder
- Institute of Clinical Chemistry, University Hospital Schleswig-Holstein, Kiel/ Lübeck, Germany
| | - Imke Wieters
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt & Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Yascha Khodamoradi
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt & Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Fabian Eberhardt
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt & Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Maria J G T Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt & Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Holger Neb
- Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Michael Sonntagbauer
- Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Claudio Conrad
- Department of Internal Medicine, Hospital of Preetz, Preetz, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany; Department of Internal Medicine I, UKSH Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Robert Markewitz
- Institute of Clinical Chemistry, University Hospital Schleswig-Holstein, Kiel/ Lübeck, Germany
| | - Klaus-Peter Wandinger
- Institute of Clinical Chemistry, University Hospital Schleswig-Holstein, Kiel/ Lübeck, Germany
| | - Max Augustin
- University of Cologne, Medical Faculty and University Hospital Cologne, Department I of Internal Medicine, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; University of Cologne, Medical Faculty and University Hospital Cologne, German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Jan Rybniker
- University of Cologne, Medical Faculty and University Hospital Cologne, Department I of Internal Medicine, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; University of Cologne, Medical Faculty and University Hospital Cologne, German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Matthias Kochanek
- University of Cologne, Medical Faculty and University Hospital Cologne, Department I of Internal Medicine, Cologne, Germany
| | - Frank Leypoldt
- Institute of Clinical Chemistry, University Hospital Schleswig-Holstein, Kiel/ Lübeck, Germany; Department of Neurology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Oliver A Cornely
- University of Cologne, Medical Faculty and University Hospital Cologne, Department I of Internal Medicine, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; University of Cologne, Medical Faculty and University Hospital Cologne, German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany; Clinical Trials Centre Cologne, ZKS Köln, Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Philipp Koehler
- University of Cologne, Medical Faculty and University Hospital Cologne, Department I of Internal Medicine, Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Cologne, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Alexander Scheffold
- Institute of Immunology, Christian-Albrechts-University of Kiel & UKSH Schleswig-Holstein, Kiel, Germany
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166
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Kaufman J. From Chickens to Humans: The Importance of Peptide Repertoires for MHC Class I Alleles. Front Immunol 2020; 11:601089. [PMID: 33381122 PMCID: PMC7767893 DOI: 10.3389/fimmu.2020.601089] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/30/2020] [Indexed: 12/21/2022] Open
Abstract
In humans, killer immunoglobulin-like receptors (KIRs), expressed on natural killer (NK) and thymus-derived (T) cells, and their ligands, primarily the classical class I molecules of the major histocompatibility complex (MHC) expressed on nearly all cells, are both polymorphic. The variation of this receptor-ligand interaction, based on which alleles have been inherited, is known to play crucial roles in resistance to infectious disease, autoimmunity, and reproduction in humans. However, not all the variation in response is inherited, since KIR binding can be affected by a portion of the peptide bound to the class I molecules, with the particular peptide presented affecting the NK response. The extent to which the large multigene family of chicken immunoglobulin-like receptors (ChIRs) is involved in functions similar to KIRs is suspected but not proven. However, much is understood about the two MHC-I molecules encoded in the chicken MHC. The BF2 molecule is expressed at a high level and is thought to be the predominant ligand of cytotoxic T lymphocytes (CTLs), while the BF1 molecule is expressed at a much lower level if at all and is thought to be primarily a ligand for NK cells. Recently, a hierarchy of BF2 alleles with a suite of correlated properties has been defined, from those expressed at a high level on the cell surface but with a narrow range of bound peptides to those expressed at a lower level on the cell surface but with a very wide repertoire of bound peptides. Interestingly, there is a similar hierarchy for human class I alleles, although the hierarchy is not as wide. It is a question whether KIRs and ChIRs recognize class I molecules with bound peptide in a similar way, and whether fastidious to promiscuous hierarchy of class I molecules affect both T and NK cell function. Such effects might be different from those predicted by the similarities of peptide-binding based on peptide motifs, as enshrined in the idea of supertypes. Since the size of peptide repertoire can be very different for alleles with similar peptide motifs from the same supertype, the relative importance of these two properties may be testable.
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Affiliation(s)
- Jim Kaufman
- School of Biological Sciences, Institute for Immunology and Infection Research, University of Edinburgh, Edinburgh, United Kingdom.,Department of Pathology, University of Cambridge, Cambridge, United Kingdom
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167
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Tfh Cells in Health and Immunity: Potential Targets for Systems Biology Approaches to Vaccination. Int J Mol Sci 2020; 21:ijms21228524. [PMID: 33198297 PMCID: PMC7696930 DOI: 10.3390/ijms21228524] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/16/2022] Open
Abstract
T follicular helper (Tfh) cells are a specialised subset of CD4+ T cells that play a significant role in the adaptive immune response, providing critical help to B cells within the germinal centres (GC) of secondary lymphoid organs. The B cell receptors of GC B cells undergo multiple rounds of somatic hypermutation and affinity maturation within the GC response, a process dependent on cognate interactions with Tfh cells. B cells that receive sufficient help from Tfh cells form antibody-producing long-lived plasma and memory B cells that provide the basis of decades of effective and efficient protection and are considered the gold standard in correlates of protection post-vaccination. However, the T cell response to vaccination has been understudied, and over the last 10 years, exponential improvements in the technological underpinnings of sampling techniques, experimental and analytical tools have allowed multidisciplinary characterisation of the role of T cells and the immune system as a whole. Of particular interest to the field of vaccinology are GCs and Tfh cells, representing a unique target for improving immunisation strategies. Here, we discuss recent insights into the unique journey of Tfh cells from thymus to lymph node during differentiation and their role in the production of high-quality antibody responses as well as their journey back to the periphery as a population of memory cells. Further, we explore their function in health and disease and the power of next-generation sequencing techniques to uncover their potential as modulators of vaccine-induced immunity.
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168
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D’Ippolito E, Wagner KI, Busch DH. Needle in a Haystack: The Naïve Repertoire as a Source of T Cell Receptors for Adoptive Therapy with Engineered T Cells. Int J Mol Sci 2020; 21:E8324. [PMID: 33171940 PMCID: PMC7664211 DOI: 10.3390/ijms21218324] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/27/2020] [Accepted: 11/02/2020] [Indexed: 12/11/2022] Open
Abstract
T cell engineering with antigen-specific T cell receptors (TCRs) has allowed the generation of increasingly specific, reliable, and versatile T cell products with near-physiological features. However, a broad applicability of TCR-based therapies in cancer is still limited by the restricted number of TCRs, often also of suboptimal potency, available for clinical use. In addition, targeting of tumor neoantigens with TCR-engineered T cell therapy moves the field towards a highly personalized treatment, as tumor neoantigens derive from somatic mutations and are extremely patient-specific. Therefore, relevant TCRs have to be de novo identified for each patient and within a narrow time window. The naïve repertoire of healthy donors would represent a reliable source due to its huge diverse TCR repertoire, which theoretically entails T cells for any antigen specificity, including tumor neoantigens. As a challenge, antigen-specific naïve T cells are of extremely low frequency and mostly of low functionality, making the identification of highly functional TCRs finding a "needle in a haystack." In this review, we present the technological advancements achieved in high-throughput mapping of patient-specific neoantigens and corresponding cognate TCRs and how these platforms can be used to interrogate the naïve repertoire for a fast and efficient identification of rare but therapeutically valuable TCRs for personalized adoptive T cell therapy.
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MESH Headings
- Antigens, Neoplasm/genetics
- CD4-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/immunology
- Humans
- Immunotherapy, Adoptive/methods
- Immunotherapy, Adoptive/trends
- Neoplasms/genetics
- Precision Medicine/methods
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell/physiology
- Receptors, Chimeric Antigen/genetics
- Receptors, Chimeric Antigen/immunology
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Affiliation(s)
- Elvira D’Ippolito
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), 81675 Munich, Germany; (E.D.); (K.I.W.)
| | - Karolin I. Wagner
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), 81675 Munich, Germany; (E.D.); (K.I.W.)
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), 81675 Munich, Germany; (E.D.); (K.I.W.)
- German Center for Infection Research (DZIF), Partner Site Munich, 81675 Munich, Germany
- Focus Group ‘‘Clinical Cell Processing and Purification”, Institute for Advanced Study, Technische Universität München (TUM), 81675 Munich, Germany
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169
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Kamath SD, Scheiblhofer S, Johnson CM, Machado Y, McLean T, Taki AC, Ramsland PA, Iyer S, Joubert I, Hofer H, Wallner M, Thalhamer J, Rolland J, O’Hehir R, Briza P, Ferreira F, Weiss R, Lopata AL. Effect of structural stability on endolysosomal degradation and T-cell reactivity of major shrimp allergen tropomyosin. Allergy 2020; 75:2909-2919. [PMID: 32436591 PMCID: PMC7687109 DOI: 10.1111/all.14410] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/21/2020] [Accepted: 04/30/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Tropomyosins are highly conserved proteins, an attribute that forms the molecular basis for their IgE antibody cross-reactivity. Despite sequence similarities, their allergenicity varies greatly between ingested and inhaled invertebrate sources. In this study, we investigated the relationship between the structural stability of different tropomyosins, their endolysosomal degradation patterns, and T-cell reactivity. METHODS We investigated the differences between four tropomyosins-the major shrimp allergen Pen m 1 and the minor allergens Der p 10 (dust mite), Bla g 7 (cockroach), and Ani s 3 (fish parasite)-in terms of IgE binding, structural stability, endolysosomal degradation and subsequent peptide generation, and T-cell cross-reactivity in a BALB/c murine model. RESULTS Tropomyosins displayed different melting temperatures, which did not correlate with amino acid sequence similarities. Endolysosomal degradation experiments demonstrated differential proteolytic digestion, as a function of thermal stability, generating different peptide repertoires. Pen m 1 (Tm 42°C) and Der p 10 (Tm 44°C) elicited similar patterns of endolysosomal degradation, but not Bla g 7 (Tm 63°C) or Ani s 3 (Tm 33°C). Pen m 1-specific T-cell clones, with specificity for regions highly conserved in all four tropomyosins, proliferated weakly to Der p 10, but did not proliferate to Bla g 7 and Ani s 3, indicating lack of T-cell epitope cross-reactivity. CONCLUSIONS Tropomyosin T-cell cross-reactivity, unlike IgE cross-reactivity, is dependent on structural stability rather than amino acid sequence similarity. These findings contribute to our understanding of cross-sensitization among different invertebrates and design of suitable T-cell peptide-based immunotherapies for shrimp and related allergies.
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Affiliation(s)
- Sandip D. Kamath
- Australian Institute of Tropical Health and MedicineJames Cook UniversityTownsvilleQldAustralia
| | | | | | - Yoan Machado
- Department of BiosciencesUniversity of SalzburgSalzburgAustria
- Centre of Blood ResearchUniversity of British ColumbiaVancouverBCCanada
| | - Thomas McLean
- School of ScienceRMIT UniversityMelbourneVic.Australia
| | - Aya C. Taki
- Faculty of Veterinary and Agricultural SciencesUniversity of MelbourneMelbourneVic.Australia
| | | | - Swati Iyer
- Department of PhysiologyUniversity of MelbourneMelbourneVic.Australia
| | | | - Heidi Hofer
- Department of BiosciencesUniversity of SalzburgSalzburgAustria
| | - Michael Wallner
- Department of BiosciencesUniversity of SalzburgSalzburgAustria
| | - Josef Thalhamer
- Department of BiosciencesUniversity of SalzburgSalzburgAustria
| | - Jennifer Rolland
- Department of Immunology and PathologyCentral Clinical SchoolMonash UniversityMelbourneVic.Australia
- Department of Allergy, Immunology and Respiratory MedicineCentral Clinical SchoolMonash UniversityMelbourneVic.Australia
- Alfred HospitalMelbourneVic.Australia
| | - Robyn O’Hehir
- Department of Immunology and PathologyCentral Clinical SchoolMonash UniversityMelbourneVic.Australia
- Department of Allergy, Immunology and Respiratory MedicineCentral Clinical SchoolMonash UniversityMelbourneVic.Australia
- Alfred HospitalMelbourneVic.Australia
| | - Peter Briza
- Department of BiosciencesUniversity of SalzburgSalzburgAustria
| | - Fatima Ferreira
- Department of BiosciencesUniversity of SalzburgSalzburgAustria
| | - Richard Weiss
- Department of BiosciencesUniversity of SalzburgSalzburgAustria
| | - Andreas L. Lopata
- Australian Institute of Tropical Health and MedicineJames Cook UniversityTownsvilleQldAustralia
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170
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Scheffold A, Bacher P, LeibundGut-Landmann S. T cell immunity to commensal fungi. Curr Opin Microbiol 2020; 58:116-123. [PMID: 33120172 DOI: 10.1016/j.mib.2020.09.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/12/2020] [Accepted: 09/15/2020] [Indexed: 02/07/2023]
Abstract
Fungi are an important part of the microbiota in healthy barrier tissues. Fungal dysbiosis in turn is associated with local and distal inflammatory diseases. Recent advances have shed light on the antigen-specific IL-17-dependent mechanisms that regulate fungal commensalism and prevent fungal overgrowth during homeostasis. Progress in our understanding of species-specific differences in fungus-host interactions provides new hypotheses of why Candida albicans-targeting T cells exceed those directed against other fungal species in the human T cell repertoire. Importantly, C. albicans-specific Th17 cells can also contribute to immune pathology in distant organs such as the lung via cross-reaction with heterologous antigens.
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Affiliation(s)
- Alexander Scheffold
- Institute of Immunology, Christian-Albrechts Universität zu Kiel and Universitätsklinik Schleswig-Holstein, Kiel, Germany
| | - Petra Bacher
- Institute of Immunology, Christian-Albrechts Universität zu Kiel and Universitätsklinik Schleswig-Holstein, Kiel, Germany; Institute of Clinical Molecular Biology, Christian-Albrechts Universität zu Kiel, Kiel, Germany
| | - Salomé LeibundGut-Landmann
- Section of Immunology, Vetsuisse Faculty, University of Zürich, Switzerland; Institute of Experimental Immunology, University of Zürich, Switzerland.
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171
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Lee CH, Salio M, Napolitani G, Ogg G, Simmons A, Koohy H. Predicting Cross-Reactivity and Antigen Specificity of T Cell Receptors. Front Immunol 2020; 11:565096. [PMID: 33193332 PMCID: PMC7642207 DOI: 10.3389/fimmu.2020.565096] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022] Open
Abstract
Adaptive immune recognition is mediated by specific interactions between heterodimeric T cell receptors (TCRs) and their cognate peptide-MHC (pMHC) ligands, and the methods to accurately predict TCR:pMHC interaction would have profound clinical, therapeutic and pharmaceutical applications. Herein, we review recent developments in predicting cross-reactivity and antigen specificity of TCR recognition. We discuss current experimental and computational approaches to investigate cross-reactivity and antigen-specificity of TCRs and highlight how integrating kinetic, biophysical and structural features may offer valuable insights in modeling immunogenicity. We further underscore the close inter-relationship of these two interconnected notions and the need to investigate each in the light of the other for a better understanding of T cell responsiveness for the effective clinical applications.
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Affiliation(s)
- Chloe H. Lee
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- MRC WIMM Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Mariolina Salio
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Giorgio Napolitani
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Graham Ogg
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Alison Simmons
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, United Kingdom
| | - Hashem Koohy
- MRC Human Immunology Unit, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine (WIMM), John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- MRC WIMM Centre for Computational Biology, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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172
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Singh NK, Alonso JA, Harris DT, Anderson SD, Ma J, Hellman LM, Rosenberg AM, Kolawole EM, Evavold BD, Kranz DM, Baker BM. An Engineered T Cell Receptor Variant Realizes the Limits of Functional Binding Modes. Biochemistry 2020; 59:4163-4175. [PMID: 33074657 DOI: 10.1021/acs.biochem.0c00689] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
T cell receptors (TCRs) orchestrate cellular immunity by recognizing peptides presented by a range of major histocompatibility complex (MHC) proteins. Naturally occurring TCRs bind the composite peptide/MHC surface, recognizing peptides that are structurally and chemically compatible with the TCR binding site. Here we describe a molecularly evolved TCR variant that binds the human class I MHC protein HLA-A2 independent of the bound peptide, achieved by a drastic perturbation of the TCR binding geometry that places the molecule far from the peptide binding groove. This unique geometry is unsupportive of normal T cell signaling. A substantial divergence between affinity measurements in solution and in two dimensions between proximal cell membranes leads us to attribute the lack of signaling to steric hindrance that limits binding in the confines of a cell-cell interface. Our results provide an example of how receptor binding geometry can impact T cell function and provide further support for the view that germline-encoded residues in TCR binding loops evolved to drive productive TCR recognition and signaling.
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Affiliation(s)
- Nishant K Singh
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jesus A Alonso
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Daniel T Harris
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, Illinois 61801, United States
| | - Scott D Anderson
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, Illinois 61801, United States
| | - Jiaqi Ma
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Lance M Hellman
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Aaron M Rosenberg
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Elizabeth M Kolawole
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, Utah 84112, United States
| | - Brian D Evavold
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, Utah 84112, United States
| | - David M Kranz
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, Illinois 61801, United States
| | - Brian M Baker
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
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173
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Crean RM, MacLachlan BJ, Madura F, Whalley T, Rizkallah PJ, Holland CJ, McMurran C, Harper S, Godkin A, Sewell AK, Pudney CR, van der Kamp MW, Cole DK. Molecular Rules Underpinning Enhanced Affinity Binding of Human T Cell Receptors Engineered for Immunotherapy. Mol Ther Oncolytics 2020; 18:443-456. [PMID: 32913893 PMCID: PMC7452143 DOI: 10.1016/j.omto.2020.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 07/27/2020] [Indexed: 10/25/2022] Open
Abstract
Immuno-oncology approaches that utilize T cell receptors (TCRs) are becoming highly attractive because of their potential to target virtually all cellular proteins, including cancer-specific epitopes, via the recognition of peptide-human leukocyte antigen (pHLA) complexes presented at the cell surface. However, because natural TCRs generally recognize cancer-derived pHLAs with very weak affinities, efforts have been made to enhance their binding strength, in some cases by several million-fold. In this study, we investigated the mechanisms underpinning human TCR affinity enhancement by comparing the crystal structures of engineered enhanced affinity TCRs with those of their wild-type progenitors. Additionally, we performed molecular dynamics simulations to better understand the energetic mechanisms driving the affinity enhancements. These data demonstrate that supra-physiological binding affinities can be achieved without altering native TCR-pHLA binding modes via relatively subtle modifications to the interface contacts, often driven through the addition of buried hydrophobic residues. Individual energetic components of the TCR-pHLA interaction governing affinity enhancements were distinct and highly variable for each TCR, often resulting from additive, or knock-on, effects beyond the mutated residues. This comprehensive analysis of affinity-enhanced TCRs has important implications for the future rational design of engineered TCRs as efficacious and safe drugs for cancer treatment.
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Affiliation(s)
- Rory M. Crean
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
- Doctoral Training Centre in Sustainable Chemical Technologies, University of Bath, Bath, BA2 7AY, UK
| | | | - Florian Madura
- Division of Infection & Immunity, Cardiff University, Cardiff, CF14 4XN, UK
| | - Thomas Whalley
- Division of Infection & Immunity, Cardiff University, Cardiff, CF14 4XN, UK
| | | | | | | | | | - Andrew Godkin
- Division of Infection & Immunity, Cardiff University, Cardiff, CF14 4XN, UK
| | - Andrew K. Sewell
- Division of Infection & Immunity, Cardiff University, Cardiff, CF14 4XN, UK
| | - Christopher R. Pudney
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
- Centre for Therapeutic Innovation, University of Bath, Bath, BA2 7AY, UK
| | - Marc W. van der Kamp
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, UK
| | - David K. Cole
- Division of Infection & Immunity, Cardiff University, Cardiff, CF14 4XN, UK
- Immunocore, Ltd., Abingdon, OX14 4RY, UK
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174
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Apavaloaei A, Hardy MP, Thibault P, Perreault C. The Origin and Immune Recognition of Tumor-Specific Antigens. Cancers (Basel) 2020; 12:E2607. [PMID: 32932620 PMCID: PMC7565792 DOI: 10.3390/cancers12092607] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/09/2020] [Accepted: 09/11/2020] [Indexed: 02/07/2023] Open
Abstract
The dominant paradigm holds that spontaneous and therapeutically induced anti-tumor responses are mediated mainly by CD8 T cells and directed against tumor-specific antigens (TSAs). The presence of specific TSAs on cancer cells can only be proven by mass spectrometry analyses. Bioinformatic predictions and reverse immunology studies cannot provide this type of conclusive evidence. Most TSAs are coded by unmutated non-canonical transcripts that arise from cancer-specific epigenetic and splicing aberrations. When searching for TSAs, it is therefore important to perform mass spectrometry analyses that interrogate not only the canonical reading frame of annotated exome but all reading frames of the entire translatome. The majority of aberrantly expressed TSAs (aeTSAs) derive from unstable short-lived proteins that are good substrates for direct major histocompatibility complex (MHC) I presentation but poor substrates for cross-presentation. This is an important caveat, because cancer cells are poor antigen-presenting cells, and the immune system, therefore, depends on cross-presentation by dendritic cells (DCs) to detect the presence of TSAs. We, therefore, postulate that, in the untreated host, most aeTSAs are undetected by the immune system. We present evidence suggesting that vaccines inducing direct aeTSA presentation by DCs may represent an attractive strategy for cancer treatment.
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Affiliation(s)
| | | | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; (A.A.); (M.-P.H.)
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; (A.A.); (M.-P.H.)
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175
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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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176
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Mannie MD, DeOca KB, Bastian AG, Moorman CD. Tolerogenic vaccines: Targeting the antigenic and cytokine niches of FOXP3 + regulatory T cells. Cell Immunol 2020; 355:104173. [PMID: 32712270 PMCID: PMC7444458 DOI: 10.1016/j.cellimm.2020.104173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/06/2020] [Accepted: 07/10/2020] [Indexed: 02/06/2023]
Abstract
FOXP3+ regulatory T cells (Tregs) constitute a critical barrier that enforces tolerance to both the self-peptidome and the extended-self peptidome to ensure tissue-specific resistance to autoimmune, allergic, and other inflammatory disorders. Here, we review intuitive models regarding how T cell antigen receptor (TCR) specificity and antigen recognition efficiency shape the Treg and conventional T cell (Tcon) repertoires to adaptively regulate T cell maintenance, tissue-residency, phenotypic stability, and immune function in peripheral tissues. Three zones of TCR recognition efficiency are considered, including Tcon recognition of specific low-efficiency self MHC-ligands, Treg recognition of intermediate-efficiency agonistic self MHC-ligands, and Tcon recognition of cross-reactive high-efficiency agonistic foreign MHC-ligands. These respective zones of TCR recognition efficiency are key to understanding how tissue-resident immune networks integrate the antigenic complexity of local environments to provide adaptive decisions setting the balance of suppressive and immunogenic responses. Importantly, deficiencies in the Treg repertoire appear to be an important cause of chronic inflammatory disease. Deficiencies may include global deficiencies in Treg numbers or function, subtle 'holes in the Treg repertoire' in tissue-resident Treg populations, or simply Treg insufficiencies that are unable to counter an overwhelming molecular mimicry stimulus. Tolerogenic vaccination and Treg-based immunotherapy are two therapeutic modalities meant to restore dominance of Treg networks to reverse chronic inflammatory disease. Studies of these therapeutic modalities in a preclinical setting have provided insight into the Treg niche, including the concept that intermediate-efficiency TCR signaling, high IFN-β concentrations, and low IL-2 concentrations favor Treg responses and active dominant mechanisms of immune tolerance. Overall, the purpose here is to assimilate new and established concepts regarding how cognate TCR specificity of the Treg repertoire and the contingent cytokine networks provide a foundation for understanding Treg suppressive strategy.
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Affiliation(s)
- Mark D Mannie
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, United States.
| | - Kayla B DeOca
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, United States
| | - Alexander G Bastian
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, United States
| | - Cody D Moorman
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, United States
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177
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Springer I, Besser H, Tickotsky-Moskovitz N, Dvorkin S, Louzoun Y. Prediction of Specific TCR-Peptide Binding From Large Dictionaries of TCR-Peptide Pairs. Front Immunol 2020; 11:1803. [PMID: 32983088 PMCID: PMC7477042 DOI: 10.3389/fimmu.2020.01803] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 07/06/2020] [Indexed: 11/13/2022] Open
Abstract
Current sequencing methods allow for detailed samples of T cell receptors (TCR) repertoires. To determine from a repertoire whether its host had been exposed to a target, computational tools that predict TCR-epitope binding are required. Currents tools are based on conserved motifs and are applied to peptides with many known binding TCRs. We employ new Natural Language Processing (NLP) based methods to predict whether any TCR and peptide bind. We combined large-scale TCR-peptide dictionaries with deep learning methods to produce ERGO (pEptide tcR matchinG predictiOn), a highly specific and generic TCR-peptide binding predictor. A set of standard tests are defined for the performance of peptide-TCR binding, including the detection of TCRs binding to a given peptide/antigen, choosing among a set of candidate peptides for a given TCR and determining whether any pair of TCR-peptide bind. ERGO reaches similar results to state of the art methods in these tests even when not trained specifically for each test. The software implementation and data sets are available at https://github.com/louzounlab/ERGO. ERGO is also available through a webserver at: http://tcr.cs.biu.ac.il/.
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Affiliation(s)
- Ido Springer
- Department of Mathematics, Bar Ilan University, Ramat Gan, Israel
| | - Hanan Besser
- Department of Mathematics, Bar Ilan University, Ramat Gan, Israel
| | | | - Shirit Dvorkin
- Department of Mathematics, Bar Ilan University, Ramat Gan, Israel
| | - Yoram Louzoun
- Department of Mathematics, Bar Ilan University, Ramat Gan, Israel
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178
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Vujovic M, Degn KF, Marin FI, Schaap-Johansen AL, Chain B, Andresen TL, Kaplinsky J, Marcatili P. T cell receptor sequence clustering and antigen specificity. Comput Struct Biotechnol J 2020; 18:2166-2173. [PMID: 32952933 PMCID: PMC7473833 DOI: 10.1016/j.csbj.2020.06.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/25/2020] [Accepted: 06/27/2020] [Indexed: 11/17/2022] Open
Abstract
There has been increasing interest in the role of T cells and their involvement in cancer, autoimmune and infectious diseases. However, the nature of T cell receptor (TCR) epitope recognition at a repertoire level is not yet fully understood. Due to technological advances a plethora of TCR sequences from a variety of disease and treatment settings has become readily available. Current efforts in TCR specificity analysis focus on identifying characteristics in immune repertoires which can explain or predict disease outcome or progression, or can be used to monitor the efficacy of disease therapy. In this context, clustering of TCRs by sequence to reflect biological similarity, and especially to reflect antigen specificity have become of paramount importance. We review the main TCR sequence clustering methods and the different similarity measures they use, and discuss their performance and possible improvement. We aim to provide guidance for non-specialists who wish to use TCR repertoire sequencing for disease tracking, patient stratification or therapy prediction, and to provide a starting point for those aiming to develop novel techniques for TCR annotation through clustering.
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Affiliation(s)
- Milena Vujovic
- DTU HealthTech, Department of Health Technology, Technical University of Denmark, Ørsteds Plads, Building 345C, DK-2800 Kgs. Lyngby, Denmark
| | - Kristine Fredlund Degn
- DTU HealthTech, Department of Health Technology, Technical University of Denmark, Ørsteds Plads, Building 345C, DK-2800 Kgs. Lyngby, Denmark
| | - Frederikke Isa Marin
- DTU HealthTech, Department of Health Technology, Technical University of Denmark, Ørsteds Plads, Building 345C, DK-2800 Kgs. Lyngby, Denmark
| | - Anna-Lisa Schaap-Johansen
- DTU HealthTech, Department of Health Technology, Technical University of Denmark, Ørsteds Plads, Building 345C, DK-2800 Kgs. Lyngby, Denmark
| | - Benny Chain
- UCL Division of Infection and Immunity, University College London, Wing 3.2, Cruciform Building, Gower Street, London WC1E 6BT, United Kingdom
| | - Thomas Lars Andresen
- DTU HealthTech, Department of Health Technology, Technical University of Denmark, Ørsteds Plads, Building 345C, DK-2800 Kgs. Lyngby, Denmark
| | - Joseph Kaplinsky
- Ludwig Institute for Cancer Research Ltd, University of Oxford, Nuffield Department of Medicine, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Paolo Marcatili
- DTU HealthTech, Department of Health Technology, Technical University of Denmark, Ørsteds Plads, Building 345C, DK-2800 Kgs. Lyngby, Denmark
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179
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Mendoza JL, Fischer S, Gee MH, Lam LH, Brackenridge S, Powrie FM, Birnbaum M, McMichael AJ, Garcia KC, Gillespie GM. Interrogating the recognition landscape of a conserved HIV-specific TCR reveals distinct bacterial peptide cross-reactivity. eLife 2020; 9:58128. [PMID: 32716298 PMCID: PMC7384859 DOI: 10.7554/elife.58128] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/01/2020] [Indexed: 11/20/2022] Open
Abstract
T cell cross-reactivity ensures that diverse pathogen-derived epitopes encountered during a lifetime are recognized by the available TCR repertoire. A feature of cross-reactivity where previous exposure to one microbe can alter immunity to subsequent, non-related pathogens has been mainly explored for viruses. Yet cross-reactivity to additional microbes is important to consider, especially in HIV infection where gut-intestinal barrier dysfunction could facilitate T cell exposure to commensal/pathogenic microbes. Here we evaluated the cross-reactivity of a ‘public’, HIV-specific, CD8 T cell-derived TCR (AGA1 TCR) using MHC class I yeast display technology. Via screening of MHC-restricted libraries comprising ~2×108 sequence-diverse peptides, AGA1 TCR specificity was mapped to a central peptide di-motif. Using the top TCR-enriched library peptides to probe the non-redundant protein database, bacterial peptides that elicited functional responses by AGA1-expressing T cells were identified. The possibility that in context-specific settings, MHC class I proteins presenting microbial peptides influence virus-specific T cell populations in vivo is discussed.
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Affiliation(s)
- Juan L Mendoza
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Suzanne Fischer
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Marvin H Gee
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Lilian H Lam
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom.,Translational Gastroenterology Unit, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Simon Brackenridge
- Nuffield Department of Medicine, University of Oxford, NDM Research Building, Old Road Campus, Headington, Oxford, United Kingdom
| | - Fiona M Powrie
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom.,Translational Gastroenterology Unit, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Michael Birnbaum
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States.,Koch Institute at MIT, Cambridge, United States
| | - Andrew J McMichael
- Nuffield Department of Medicine, University of Oxford, NDM Research Building, Old Road Campus, Headington, Oxford, United Kingdom
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States
| | - Geraldine M Gillespie
- Nuffield Department of Medicine, University of Oxford, NDM Research Building, Old Road Campus, Headington, Oxford, United Kingdom
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180
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Abstract
T cells respond to threats in an antigen-specific manner using T cell receptors (TCRs) that recognize short peptide antigens presented on major histocompatibility complex (MHC) proteins. The TCR-peptide-MHC interaction mediated between a T cell and its target cell dictates its function and thereby influences its role in disease. A lack of approaches for antigen discovery has limited the fundamental understanding of the antigenic landscape of the overall T cell response. Recent advances in high-throughput sequencing, mass cytometry, microfluidics and computational biology have led to a surge in approaches to address the challenge of T cell antigen discovery. Here, we summarize the scope of this challenge, discuss in depth the recent exciting work and highlight the outstanding questions and remaining technical hurdles in this field.
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181
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Yaqinuddin A. Cross-immunity between respiratory coronaviruses may limit COVID-19 fatalities. Med Hypotheses 2020; 144:110049. [PMID: 32758887 PMCID: PMC7326438 DOI: 10.1016/j.mehy.2020.110049] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 06/25/2020] [Indexed: 01/09/2023]
Abstract
Of the seven coronaviruses associated with disease in humans, SARS-CoV, MERS-CoV and SARS-CoV-2 cause considerable mortality but also share significant sequence homology, and potentially antigenic epitopes capable of inducing an immune response. The degree of similarity is such that perhaps prior exposure to one virus could confer partial immunity to another. Indeed, data suggests a considerable amount of cross-reactivity and recognition by the hosts immune response between different coronavirus infections. While the ongoing COVID-19 outbreak rapidly overwhelmed medical facilities of particularly Europe and North America, accounting for 78% of global deaths, only 8% of deaths have occurred in Asia where the outbreak originated. Interestingly, Asia and the Middle East have previously experienced multiple rounds of coronavirus infections, perhaps suggesting buildup of acquired immunity to the causative SARS-CoV-2 that underlies COVID-19. This article hypothesizes that a causative factor underlying such low morbidity in these regions is perhaps (at least in part) due to acquired immunity from multiple rounds of coronavirus infections and discusses the mechanisms and recent evidence to support such assertions. Further investigations of such phenomenon would allow us to examine strategies to confer protective immunity, perhaps aiding vaccine development.
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182
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Tong Y, Wang J, Zheng T, Zhang X, Xiao X, Zhu X, Lai X, Liu X. SETE: Sequence-based Ensemble learning approach for TCR Epitope binding prediction. Comput Biol Chem 2020; 87:107281. [PMID: 32623023 DOI: 10.1016/j.compbiolchem.2020.107281] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/09/2020] [Indexed: 11/30/2022]
Abstract
Predicting the binding of T cell receptors (TCRs) to epitopes plays a vital role in the immunotherapy, because it guides the development of therapeutic vaccines and cancer treatments. Many prediction methods attempted to explain the relationship between TCR repertoires from different aspects such as the V(D)J gene locus and the biophysical features of amino acids molecules, but the extraction of these features is time consuming and the performance of these models are limited. Few studies have investigated how k-mers formed by adjacent amino acids in TCR sequences direct the epitope recognition, and the specific mechanism of TCR epitope binding is still unclear. Motivated by these, we presented SETE (Sequence-based Ensemble learning approach for TCR Epitope binding prediction), a novel model to predict the TCR epitope binding accurately. The model deconstructed the CDR3β sequence to short amino acid chains as features and learned the pattern of them between different TCR repertoires with gradient boosting decision tree algorithm. Experiments have demonstrated that SETE can be helpful in predicting the TCRs' corresponding epitopes and it outperforms other state-of-the-art methods in predicting the epitope specificity of TCR on VDJdb data set. The source codes have been uploaded at https://github.com/wonanut/SETE for academic usage only.
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Affiliation(s)
- Yao Tong
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Jiayin Wang
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an, 710049, China.
| | - Tian Zheng
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Xuanping Zhang
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Xiao Xiao
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Xiaoyan Zhu
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Xin Lai
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Xiang Liu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital, University of South China, Hengyang, 421001, China.
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183
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Metaxakis A, Petratou D, Tavernarakis N. Molecular Interventions towards Multiple Sclerosis Treatment. Brain Sci 2020; 10:brainsci10050299. [PMID: 32429225 PMCID: PMC7287961 DOI: 10.3390/brainsci10050299] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 12/24/2022] Open
Abstract
Multiple sclerosis (MS) is an autoimmune life-threatening disease, afflicting millions of people worldwide. Although the disease is non-curable, considerable therapeutic advances have been achieved through molecular immunotherapeutic approaches, such as peptides vaccination, administration of monoclonal antibodies, and immunogenic copolymers. The main aims of these therapeutic strategies are to shift the MS-related autoimmune response towards a non-inflammatory T helper 2 (Th2) cells response, inactivate or ameliorate cytotoxic autoreactive T cells, induce secretion of anti-inflammatory cytokines, and inhibit recruitment of autoreactive lymphocytes to the central nervous system (CNS). These approaches can efficiently treat autoimmune encephalomyelitis (EAE), an essential system to study MS in animals, but they can only partially inhibit disease progress in humans. Nevertheless, modern immunotherapeutic techniques remain the most promising tools for the development of safe MS treatments, specifically targeting the cellular factors that trigger the initiation of the disease.
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Affiliation(s)
- Athanasios Metaxakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Nikolaou Plastira 100, 70013 Heraklion, Greece; (A.M.); (D.P.)
| | - Dionysia Petratou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Nikolaou Plastira 100, 70013 Heraklion, Greece; (A.M.); (D.P.)
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Nikolaou Plastira 100, 70013 Heraklion, Greece; (A.M.); (D.P.)
- Department of Basic Sciences, Faculty of Medicine, University of Crete, 71110 Heraklion, Greece
- Correspondence: ; Tel.: +30-2810-391066
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184
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Tarbe M, Miles JJ, Edwards ESJ, Miles KM, Sewell AK, Baker BM, Quideau S. Synthesis and Biological Evaluation of Hapten-Clicked Analogues of The Antigenic Peptide Melan-A/MART-1 26(27L)-35. ChemMedChem 2020; 15:799-807. [PMID: 32162475 PMCID: PMC7473458 DOI: 10.1002/cmdc.202000038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/03/2020] [Indexed: 11/12/2022]
Abstract
A click-chemistry-based approach was implemented to prepare peptidomimetics designed in silico and made from aromatic azides and a propargylated GIGI-mimicking platform derived from the altered Melan-A/MART-126(27L)-35 antigenic peptide ELAGIGILTV. The CuI -catalyzed Huisgen cycloaddition was carried out on solid support to generate rapidly a first series of peptidomimetics, which were evaluated for their capacity to dock at the interface between the major histocompatibility complex class-I (MHC-I) human leucocyte antigen (HLA)-A2 and T-cell receptors (TCRs). Despite being a weak HLA-A2 ligand, one of these 11 first synthetic compounds bearing a p-nitrobenzyl-triazole side chain was recognized by the receptor proteins of Melan-A/MART-1-specific T-cells. After modification of the N and C termini of this agonist, which was intended to enhance HLA-A2 binding, one of the resulting seven additional compounds triggered significant T-cell responses. Thus, these results highlight the capacity of naturally circulating human TCRs that are specific for the native Melan-A/MART-126-35 peptide to cross-react with peptidomimetics bearing organic motifs structurally different from the native central amino acids.
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Affiliation(s)
- Marion Tarbe
- Université de Bordeaux, ISM (CNRS-UMR 5255), 351 cours de la Libération, 33405, Talence Cedex, France
| | - John J Miles
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878, Australia
| | - Emily S J Edwards
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
- Department of Immunology and Pathology, Central Clinical School, Monash University, Level 6, 89 Commercial Road, Melbourne, Victoria, 3004, Australia
| | - Kim M Miles
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
| | - Andrew K Sewell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
| | - Brian M Baker
- Department of Chemistry & Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556, USA
| | - Stéphane Quideau
- Université de Bordeaux, ISM (CNRS-UMR 5255), 351 cours de la Libération, 33405, Talence Cedex, France
- Institut Universitaire de France, 1 rue Descartes, 75231, Paris Cedex 05, France
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185
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Uhl LFK, Gérard A. Modes of Communication between T Cells and Relevance for Immune Responses. Int J Mol Sci 2020; 21:E2674. [PMID: 32290500 PMCID: PMC7215318 DOI: 10.3390/ijms21082674] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/08/2020] [Accepted: 04/10/2020] [Indexed: 11/16/2022] Open
Abstract
T cells are essential mediators of the adaptive immune system, which constantly patrol the body in search for invading pathogens. During an infection, T cells that recognise the pathogen are recruited, expand and differentiate into subtypes tailored to the infection. In addition, they differentiate into subsets required for short and long-term control of the pathogen, i.e., effector or memory. T cells have a remarkable degree of plasticity and heterogeneity in their response, however, their overall response to a given infection is consistent and robust. Much research has focused on how individual T cells are activated and programmed. However, in order to achieve a critical level of population-wide reproducibility and robustness, neighbouring cells and surrounding tissues have to provide or amplify relevant signals to tune the overall response accordingly. The characteristics of the immune response-stochastic on the individual cell level, robust on the global level-necessitate coordinated responses on a system-wide level, which facilitates the control of pathogens, while maintaining self-tolerance. This global coordination can only be achieved by constant cellular communication between responding cells, and faults in this intercellular crosstalk can potentially lead to immunopathology or autoimmunity. In this review, we will discuss how T cells mount a global, collective response, by describing the modes of T cell-T cell (T-T) communication they use and highlighting their physiological relevance in programming and controlling the T cell response.
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Affiliation(s)
| | - Audrey Gérard
- The Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, UK;
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186
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Toptygina AP. Heterologous immune responses in health and disease. RUSSIAN JOURNAL OF INFECTION AND IMMUNITY 2020. [DOI: 10.15789/2220-7619-hir-1292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Immunological memory and tolerance represent major achievements and advantages of adaptive immunity. Organisms bearing adaptive immunity display prominent competitive advantages in the fight against infections. Memory immune cells are preserved for decades and are able to repel a second attack of an infectious agent. However, studies performed in the XXI century have shown that even unrelated pathogens may be quickly and effectively destroyed by memory cells. This type of response is called heterologous so that heterologous immune response is mainly typical to viral infections and other intracellular infections, where T-cells play a lead role in protection. This review will discuss various mechanisms involved in implementing T-cell cross-reactivity, describe molecular prerequisites for heterologous T-cell responses. Experimental evidence of memory T-cell potential to heterologous immune response in mouse models and in human infections are also discussed. Heterologous immune response is an important immune arm in adults and the elderly when the yield of naive cells to the periphery declines due to thymus involution. Along with obvious advantages, heterologous immune response leads to imbalanced memory T-cell repertoire, replacement of immunodominant epitopes with minor ones allowing viruses to evade immune response that results in virus persistence, or, conversely, fulminant infection course. Another threat of heterologous immune response due to switch in dominant repertoire of recognizable epitopes is presented by random self-epitope recognition, which can lead to development of autoimmune pathology. Heterologous immunity can also disrupt drug-induced tolerance in organ and tissue transplants and lead to graft rejection. Heterologous immune response should be taken into consideration while developing and using new vaccines, especially in adults and the elderly.
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187
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Aversa I, Malanga D, Fiume G, Palmieri C. Molecular T-Cell Repertoire Analysis as Source of Prognostic and Predictive Biomarkers for Checkpoint Blockade Immunotherapy. Int J Mol Sci 2020; 21:ijms21072378. [PMID: 32235561 PMCID: PMC7177412 DOI: 10.3390/ijms21072378] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/22/2020] [Accepted: 03/28/2020] [Indexed: 02/08/2023] Open
Abstract
The T cells are key players of the response to checkpoint blockade immunotherapy (CBI) and monitoring the strength and specificity of antitumor T-cell reactivity remains a crucial but elusive component of precision immunotherapy. The entire assembly of T-cell receptor (TCR) sequences accounts for antigen specificity and strength of the T-cell immune response. The TCR repertoire hence represents a “footprint” of the conditions faced by T cells that dynamically evolves according to the challenges that arise for the immune system, such as tumor neo-antigenic load. Hence, TCR repertoire analysis is becoming increasingly important to comprehensively understand the nature of a successful antitumor T-cell response, and to improve the success and safety of current CBI.
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Affiliation(s)
- Ilenia Aversa
- Research Center of Biochemistry and Advanced Molecular Biology, Department of Experimental and Clinical Medicine, University “Magna Græcia” of Catanzaro, 88100 Catanzaro, Italy;
| | - Donatella Malanga
- Interdepartmental Center of Services (CIS), Department of Experimental and Clinical Medicine, University “Magna Græcia” of Catanzaro, 88100 Catanzaro, Italy;
| | - Giuseppe Fiume
- Department of Experimental and Clinical Medicine, University “Magna Græcia” of Catanzaro, 88100 Catanzaro, Italy;
| | - Camillo Palmieri
- Department of Experimental and Clinical Medicine, University “Magna Græcia” of Catanzaro, 88100 Catanzaro, Italy;
- Correspondence:
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188
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Hopkins JR, Crean RM, Catici DAM, Sewell AK, Arcus VL, Van der Kamp MW, Cole DK, Pudney CR. Peptide cargo tunes a network of correlated motions in human leucocyte antigens. FEBS J 2020; 287:3777-3793. [PMID: 32134551 PMCID: PMC8651013 DOI: 10.1111/febs.15278] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 02/20/2020] [Accepted: 03/03/2020] [Indexed: 11/28/2022]
Abstract
Most biomolecular interactions are typically thought to increase the (local) rigidity of a complex, for example, in drug‐target binding. However, detailed analysis of specific biomolecular complexes can reveal a more subtle interplay between binding and rigidity. Here, we focussed on the human leucocyte antigen (HLA), which plays a crucial role in the adaptive immune system by presenting peptides for recognition by the αβ T‐cell receptor (TCR). The role that the peptide plays in tuning HLA flexibility during TCR recognition is potentially crucial in determining the functional outcome of an immune response, with obvious relevance to the growing list of immunotherapies that target the T‐cell compartment. We have applied high‐pressure/temperature perturbation experiments, combined with molecular dynamics simulations, to explore the drivers that affect molecular flexibility for a series of different peptide–HLA complexes. We find that different peptide sequences affect peptide–HLA flexibility in different ways, with the peptide cargo tuning a network of correlated motions throughout the pHLA complex, including in areas remote from the peptide‐binding interface, in a manner that could influence T‐cell antigen discrimination.
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Affiliation(s)
- Jade R Hopkins
- Division of Infection and Immunity, School of Medicine, Cardiff University, UK
| | - Rory M Crean
- Department of Biology and Biochemistry, University of Bath, UK.,Doctoral Training Centre in Sustainable Chemical Technologies, University of Bath, UK
| | | | - Andrew K Sewell
- Division of Infection and Immunity, School of Medicine, Cardiff University, UK
| | - Vickery L Arcus
- School of Science, Faculty of Science and Engineering, University of Waikato, Hamilton, New Zealand
| | | | - David K Cole
- Division of Infection and Immunity, School of Medicine, Cardiff University, UK
| | - Christopher R Pudney
- Department of Biology and Biochemistry, University of Bath, UK.,Centre for Therapeutic Innovation, University of Bath, UK
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189
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Ahmed R, Omidian Z, Giwa A, Cornwell B, Majety N, Bell DR, Lee S, Zhang H, Michels A, Desiderio S, Sadegh-Nasseri S, Rabb H, Gritsch S, Suva ML, Cahan P, Zhou R, Jie C, Donner T, Hamad ARA. A Public BCR Present in a Unique Dual-Receptor-Expressing Lymphocyte from Type 1 Diabetes Patients Encodes a Potent T Cell Autoantigen. Cell 2020; 177:1583-1599.e16. [PMID: 31150624 DOI: 10.1016/j.cell.2019.05.007] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 12/10/2018] [Accepted: 05/02/2019] [Indexed: 12/17/2022]
Abstract
T and B cells are the two known lineages of adaptive immune cells. Here, we describe a previously unknown lymphocyte that is a dual expresser (DE) of TCR and BCR and key lineage markers of both B and T cells. In type 1 diabetes (T1D), DEs are predominated by one clonotype that encodes a potent CD4 T cell autoantigen in its antigen binding site. Molecular dynamics simulations revealed that this peptide has an optimal binding register for diabetogenic HLA-DQ8. In concordance, a synthetic version of the peptide forms stable DQ8 complexes and potently stimulates autoreactive CD4 T cells from T1D patients, but not healthy controls. Moreover, mAbs bearing this clonotype are autoreactive against CD4 T cells and inhibit insulin tetramer binding to CD4 T cells. Thus, compartmentalization of adaptive immune cells into T and B cells is not absolute, and violators of this paradigm are likely key drivers of autoimmune diseases.
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Affiliation(s)
- Rizwan Ahmed
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Zahra Omidian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Adebola Giwa
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Benjamin Cornwell
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Neha Majety
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - David R Bell
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Sangyun Lee
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Aaron Michels
- Barbara Davis Center for Diabetes, University of Colorado, Aurora, CO 80045, USA
| | - Stephen Desiderio
- Department of Molecular Biology and Genetics and Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Hamid Rabb
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Simon Gritsch
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Mario L Suva
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Patrick Cahan
- Department of Molecular Biology and Genetics and Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ruhong Zhou
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA; Department of Chemistry, Columbia University, New York, NY 10027, USA.
| | - Chunfa Jie
- Department of Biochemistry and Nutrition, Des Moines University, Des Moines, IA 50312, USA
| | - Thomas Donner
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Abdel Rahim A Hamad
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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190
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de Greef PC, Oakes T, Gerritsen B, Ismail M, Heather JM, Hermsen R, Chain B, de Boer RJ. The naive T-cell receptor repertoire has an extremely broad distribution of clone sizes. eLife 2020; 9:e49900. [PMID: 32187010 PMCID: PMC7080410 DOI: 10.7554/elife.49900] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 03/03/2020] [Indexed: 12/24/2022] Open
Abstract
The clone size distribution of the human naive T-cell receptor (TCR) repertoire is an important determinant of adaptive immunity. We estimated the abundance of TCR sequences in samples of naive T cells from blood using an accurate quantitative sequencing protocol. We observe most TCR sequences only once, consistent with the enormous diversity of the repertoire. However, a substantial number of sequences were observed multiple times. We detect abundant TCR sequences even after exclusion of methodological confounders such as sort contamination, and multiple mRNA sampling from the same cell. By combining experimental data with predictions from models we describe two mechanisms contributing to TCR sequence abundance. TCRα abundant sequences can be primarily attributed to many identical recombination events in different cells, while abundant TCRβ sequences are primarily derived from large clones, which make up a small percentage of the naive repertoire, and could be established early in the development of the T-cell repertoire.
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MESH Headings
- Adaptive Immunity
- Algorithms
- Antigens/immunology
- Clonal Evolution/genetics
- Computational Biology/methods
- High-Throughput Nucleotide Sequencing
- Humans
- Immunologic Memory
- Models, Biological
- Organ Specificity/genetics
- Organ Specificity/immunology
- 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-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- V(D)J Recombination
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Affiliation(s)
- Peter C de Greef
- Theoretical Biology and Bioinformatics, Utrecht UniversityUtrechtNetherlands
| | - Theres Oakes
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Bram Gerritsen
- Theoretical Biology and Bioinformatics, Utrecht UniversityUtrechtNetherlands
- Department of Pathology, Yale School of MedicineNew HavenUnited States
| | - Mazlina Ismail
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - James M Heather
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Rutger Hermsen
- Theoretical Biology and Bioinformatics, Utrecht UniversityUtrechtNetherlands
| | - Benjamin Chain
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht UniversityUtrechtNetherlands
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191
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Comprehensive analysis of structural and sequencing data reveals almost unconstrained chain pairing in TCRαβ complex. PLoS Comput Biol 2020; 16:e1007714. [PMID: 32163410 PMCID: PMC7093030 DOI: 10.1371/journal.pcbi.1007714] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 03/24/2020] [Accepted: 02/04/2020] [Indexed: 11/19/2022] Open
Abstract
Antigen recognition by T-cells is guided by the T-cell receptor (TCR) heterodimer formed by α and β chains. A huge diversity of TCR sequences should be maintained by the immune system in order to be able to mount an effective response towards foreign pathogens, so, due to cooperative binding of α and β chains to the pathogen, any constraints on chain pairing can have a profound effect on immune repertoire structure, diversity and antigen specificity. By integrating available structural data and paired chain sequencing results we were able to show that there are almost no constraints on pairing in TCRαβ complexes, allowing naive T-cell repertoire to reach the highest possible diversity. Additional analysis reveals that the specific choice of contacting amino acids can still have a profound effect on complex conformation. Moreover, antigen-driven selection can distort the uniform landscape of chain pairing, while small, yet significant, differences in the pairing can be attributed to various specialized T-cell subsets such as MAIT and iNKT T-cells, as well as other TCR sets specific to certain antigens. In the present paper we study chain pairing preferences in the T-cell receptor (TCR) heterodimer complex. The TCR molecule is formed by α and β chains and binding of both of these chains to an antigen presented by the major histocompatibility complex (MHC) molecule is required in order to trigger an immune response against foreign pathogens and neoantigens. We show that chain pairing in the TCR complex is nearly random ensuring a highly diverse set of TCRs required for recognition of a vast set of antigens. Our results also show that chain pairing preferences can nevertheless influence TCR complex geometry and biases in TCR chain pairing can be used to identify antigen-driven selection or selection towards specialized subsets of T-cells such as mucosal-associated and natural killer invariant T-cells.
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192
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Is T Cell Negative Selection a Learning Algorithm? Cells 2020; 9:cells9030690. [PMID: 32168897 PMCID: PMC7140671 DOI: 10.3390/cells9030690] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/06/2020] [Accepted: 03/07/2020] [Indexed: 11/28/2022] Open
Abstract
Our immune system can destroy most cells in our body, an ability that needs to be tightly controlled. To prevent autoimmunity, the thymic medulla exposes developing T cells to normal “self” peptides and prevents any responders from entering the bloodstream. However, a substantial number of self-reactive T cells nevertheless reaches the periphery, implying that T cells do not encounter all self peptides during this negative selection process. It is unclear if T cells can still discriminate foreign peptides from self peptides they haven’t encountered during negative selection. We use an “artificial immune system”—a machine learning model of the T cell repertoire—to investigate how negative selection could alter the recognition of self peptides that are absent from the thymus. Our model reveals a surprising new role for T cell cross-reactivity in this context: moderate T cell cross-reactivity should skew the post-selection repertoire towards peptides that differ systematically from self. Moreover, even some self-like foreign peptides can be distinguished provided that the peptides presented in the thymus are not too similar to each other. Thus, our model predicts that negative selection on a well-chosen subset of self peptides would generate a repertoire that tolerates even “unseen” self peptides better than foreign peptides. This effect would resemble a “generalization” process as it is found in learning systems. We discuss potential experimental approaches to test our theory.
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193
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Whalley T, Dolton G, Brown PE, Wall A, Wooldridge L, van den Berg H, Fuller A, Hopkins JR, Crowther MD, Attaf M, Knight RR, Cole DK, Peakman M, Sewell AK, Szomolay B. GPU-Accelerated Discovery of Pathogen-Derived Molecular Mimics of a T-Cell Insulin Epitope. Front Immunol 2020; 11:296. [PMID: 32184781 PMCID: PMC7058665 DOI: 10.3389/fimmu.2020.00296] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 02/05/2020] [Indexed: 01/09/2023] Open
Abstract
The strong links between (Human Leukocyte Antigen) HLA, infection and autoimmunity combine to implicate T-cells as primary triggers of autoimmune disease (AD). T-cell crossreactivity between microbially-derived peptides and self-peptides has been shown to break tolerance and trigger AD in experimental animal models. Detailed examination of the potential for T-cell crossreactivity to trigger human AD will require means of predicting which peptides might be recognised by autoimmune T-cell receptors (TCRs). Recent developments in high throughput sequencing and bioinformatics mean that it is now possible to link individual TCRs to specific pathologies for the first time. Deconvolution of TCR function requires knowledge of TCR specificity. Positional Scanning Combinatorial Peptide Libraries (PS-CPLs) can be used to predict HLA-restriction and define antigenic peptides derived from self and pathogen proteins. In silico search of the known terrestrial proteome with a prediction algorithm that ranks potential antigens in order of recognition likelihood requires complex, large-scale computations over several days that are infeasible on a personal computer. We decreased the time required for peptide searching to under 30 min using multiple blocks on graphics processing units (GPUs). This time-efficient, cost-effective hardware accelerator was used to screen bacterial and fungal human pathogens for peptide sequences predicted to activate a T-cell clone, InsB4, that was isolated from a patient with type 1 diabetes and recognised the insulin B-derived epitope HLVEALYLV in the context of disease-risk allele HLA A*0201. InsB4 was shown to kill HLA A*0201+ human insulin producing β-cells demonstrating that T-cells with this specificity might contribute to disease. The GPU-accelerated algorithm and multispecies pathogen proteomic databases were validated to discover pathogen-derived peptide sequences that acted as super-agonists for the InsB4 T-cell clone. Peptide-MHC tetramer binding and surface plasmon resonance were used to confirm that the InsB4 TCR bound to the highest-ranked peptide agonists derived from infectious bacteria and fungi. Adoption of GPU-accelerated prediction of T-cell agonists has the capacity to revolutionise our understanding of AD by identifying potential targets for autoimmune T-cells. This approach has further potential for dissecting T-cell responses to infectious disease and cancer.
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Affiliation(s)
- Thomas Whalley
- Cardiff University School of Medicine, Cardiff, United Kingdom.,Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Garry Dolton
- Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Paul E Brown
- Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick Coventry, Coventry, United Kingdom
| | - Aaron Wall
- Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Linda Wooldridge
- Faculty of Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Hugo van den Berg
- Mathematics Institute, University of Warwick, Coventry, United Kingdom
| | - Anna Fuller
- Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Jade R Hopkins
- Cardiff University School of Medicine, Cardiff, United Kingdom
| | | | - Meriem Attaf
- Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Robin R Knight
- Peter Gorer Department of Immunobiology, Guy's Hospital, London, United Kingdom
| | - David K Cole
- Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Mark Peakman
- Peter Gorer Department of Immunobiology, Guy's Hospital, London, United Kingdom
| | - Andrew K Sewell
- Cardiff University School of Medicine, Cardiff, United Kingdom.,Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Barbara Szomolay
- Cardiff University School of Medicine, Cardiff, United Kingdom.,Systems Immunity Research Institute, Cardiff University, Cardiff, United Kingdom
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194
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Rakebrandt N, Joller N. Infection History Determines Susceptibility to Unrelated Diseases. Bioessays 2020; 41:e1800191. [PMID: 31132173 DOI: 10.1002/bies.201800191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 04/04/2019] [Indexed: 12/11/2022]
Abstract
Epidemiological data suggest that previous infections can alter an individual's susceptibility to unrelated diseases. Nevertheless, the underlying mechanisms are not completely understood. Substantial research efforts have expanded the classical concept of immune memory to also include long-lasting changes in innate immunity and antigen-independent reactivation of adaptive immunity. Collectively, these processes provide possible explanations on how acute infections might induce long-term changes that also affect immunity to unrelated diseases. Here, we review lasting changes the immune compartment undergoes upon infection and how infection experience alters the responsiveness of immune cells towards universal signals. This heightened state of alert enhances the ability of the immune system to combat even unrelated infections but may also increase susceptibility to autoimmunity. At the same time, infection-induced changes in the regulatory compartment may dampen subsequent immune responses and promote pathogen persistence. The concepts presented here outline how infection-induced changes in the immune system may affect human health.
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Affiliation(s)
- Nikolas Rakebrandt
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Nicole Joller
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
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195
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Rushdi M, Li K, Yuan Z, Travaglino S, Grakoui A, Zhu C. Mechanotransduction in T Cell Development, Differentiation and Function. Cells 2020; 9:E364. [PMID: 32033255 PMCID: PMC7072571 DOI: 10.3390/cells9020364] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 01/16/2020] [Accepted: 01/17/2020] [Indexed: 02/07/2023] Open
Abstract
Cells in the body are actively engaging with their environments that include both biochemical and biophysical aspects. The process by which cells convert mechanical stimuli from their environment to intracellular biochemical signals is known as mechanotransduction. Exemplifying the reliance on mechanotransduction for their development, differentiation and function are T cells, which are central to adaptive immune responses. T cell mechanoimmunology is an emerging field that studies how T cells sense, respond and adapt to the mechanical cues that they encounter throughout their life cycle. Here we review different stages of the T cell's life cycle where existing studies have shown important effects of mechanical force or matrix stiffness on a T cell as sensed through its surface molecules, including modulating receptor-ligand interactions, inducing protein conformational changes, triggering signal transduction, amplifying antigen discrimination and ensuring directed targeted cell killing. We suggest that including mechanical considerations in the immunological studies of T cells would inform a more holistic understanding of their development, differentiation and function.
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Affiliation(s)
- Muaz Rushdi
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; (M.R.); (K.L.); (S.T.)
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA;
| | - Kaitao Li
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; (M.R.); (K.L.); (S.T.)
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA;
| | - Zhou Yuan
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA;
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30313, USA
| | - Stefano Travaglino
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; (M.R.); (K.L.); (S.T.)
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA;
| | - Arash Grakoui
- Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes Research Primate Center, Emory University School of Medicine, Atlanta, GA 30329, USA;
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Cheng Zhu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; (M.R.); (K.L.); (S.T.)
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA;
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30313, USA
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196
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Onishi KG, Maneval AC, Cable EC, Tuohy MC, Scasny AJ, Sterina E, Love JA, Riggle JP, Malamut LK, Mukerji A, Novo JS, Appah-Sampong A, Gary JB, Prendergast BJ. Circadian and circannual timescales interact to generate seasonal changes in immune function. Brain Behav Immun 2020; 83:33-43. [PMID: 31351184 DOI: 10.1016/j.bbi.2019.07.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/14/2019] [Accepted: 07/23/2019] [Indexed: 12/22/2022] Open
Abstract
Annual changes in day length enhance or suppress diverse aspects of immune function, giving rise to seasonal cycles of illness and mortality. The daily light-dark cycle also entrains circadian rhythms in immunity. Most published reports on immunological seasonality rely on measurements or interventions performed only at one point in the day. Because there can be no perfect matching of circadian phase across photoperiods of different duration, the manner in which these timescales interact to affect immunity is not understood. We examined whether photoperiodic changes in immune function reflect phenotypic changes that persist throughout the daily cycle, or merely reflect photoperiodic shifts in the circadian phase alignment of immunological rhythms. Diurnal rhythms in blood leukocyte trafficking, infection induced sickness responses, and delayed-type hypersensitivity skin inflammatory responses were examined at high-frequency sampling intervals (every 3 h) in Siberian hamsters (Phodopus sungorus) following immunological adaptation to summer or winter photoperiods. Photoperiod profoundly enhanced or suppressed immune function, in a trait-specific manner, and we were unable to identify a phase alignment of diurnal waveforms which eliminated these enhancing and suppressing effects of photoperiod. These results support the hypothesis that seasonal timescales affect immunity via mechanisms independent of circadian entrainment of the immunological circadian waveform.
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Affiliation(s)
- Kenneth G Onishi
- Department of Psychology and Institute for Mind and Biology, University of Chicago, Chicago, IL 60637, United States.
| | - Andrew C Maneval
- Department of Psychology and Institute for Mind and Biology, University of Chicago, Chicago, IL 60637, United States
| | - Erin C Cable
- Department of Psychology and Institute for Mind and Biology, University of Chicago, Chicago, IL 60637, United States
| | - Mary Claire Tuohy
- Department of Psychology and Institute for Mind and Biology, University of Chicago, Chicago, IL 60637, United States
| | - Andrew J Scasny
- Department of Psychology and Institute for Mind and Biology, University of Chicago, Chicago, IL 60637, United States
| | - Evelina Sterina
- Department of Psychology and Institute for Mind and Biology, University of Chicago, Chicago, IL 60637, United States
| | - Jharnae A Love
- Department of Psychology and Institute for Mind and Biology, University of Chicago, Chicago, IL 60637, United States
| | - Jonathan P Riggle
- Department of Psychology and Institute for Mind and Biology, University of Chicago, Chicago, IL 60637, United States
| | - Leah K Malamut
- Department of Psychology and Institute for Mind and Biology, University of Chicago, Chicago, IL 60637, United States
| | - Aashna Mukerji
- Department of Psychology and Institute for Mind and Biology, University of Chicago, Chicago, IL 60637, United States
| | - Jennifer S Novo
- Department of Psychology and Institute for Mind and Biology, University of Chicago, Chicago, IL 60637, United States
| | - Abena Appah-Sampong
- Department of Psychology and Institute for Mind and Biology, University of Chicago, Chicago, IL 60637, United States
| | - Joseph B Gary
- Department of Psychology and Institute for Mind and Biology, University of Chicago, Chicago, IL 60637, United States
| | - Brian J Prendergast
- Department of Psychology and Institute for Mind and Biology, University of Chicago, Chicago, IL 60637, United States; Committee on Neurobiology, University of Chicago, Chicago, IL 60637, United States; Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, University of Chicago, Chicago, IL 60637, United States
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197
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Hardy MP, Vincent K, Perreault C. The Genomic Landscape of Antigenic Targets for T Cell-Based Leukemia Immunotherapy. Front Immunol 2019; 10:2934. [PMID: 31921187 PMCID: PMC6933603 DOI: 10.3389/fimmu.2019.02934] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/29/2019] [Indexed: 12/30/2022] Open
Abstract
Intensive fundamental and clinical research in cancer immunotherapy has led to the emergence and evolution of two parallel universes with surprisingly little interactions: the realm of hematologic malignancies and that of solid tumors. Treatment of hematologic cancers using allogeneic hematopoietic cell transplantation (AHCT) serendipitously led to the discovery that T cells specific for minor histocompatibility antigens (MiHAs) could cure hematopoietic cancers. Besides, studies based on treatment of solid tumor with ex vivo-expanded tumor infiltrating lymphocytes or immune checkpoint therapy demonstrated that anti-tumor responses could be achieved by targeting tumor-specific antigens (TSAs). It is our contention that much insight can be gained by sharing the tremendous amount of data generated in the two-abovementioned universes. Our perspective article has two specific goals. First, to discuss the value of methods currently used for MiHA and TSA discovery and to explain the key role of mass spectrometry analyses in this process. Second, to demonstrate the importance of broadening the scope of TSA discovery efforts beyond classic annotated protein-coding genomic sequences.
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Affiliation(s)
- Marie-Pierre Hardy
- Department of Immunobiology, Institute for Research in Immunology and Cancer, Montreal, QC, Canada
| | - Krystel Vincent
- Department of Immunobiology, Institute for Research in Immunology and Cancer, Montreal, QC, Canada
| | - Claude Perreault
- Department of Immunobiology, Institute for Research in Immunology and Cancer, Montreal, QC, Canada
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198
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Gross CC, Meyer C, Bhatia U, Yshii L, Kleffner I, Bauer J, Tröscher AR, Schulte-Mecklenbeck A, Herich S, Schneider-Hohendorf T, Plate H, Kuhlmann T, Schwaninger M, Brück W, Pawlitzki M, Laplaud DA, Loussouarn D, Parratt J, Barnett M, Buckland ME, Hardy TA, Reddel SW, Ringelstein M, Dörr J, Wildemann B, Kraemer M, Lassmann H, Höftberger R, Beltrán E, Dornmair K, Schwab N, Klotz L, Meuth SG, Martin-Blondel G, Wiendl H, Liblau R. CD8 + T cell-mediated endotheliopathy is a targetable mechanism of neuro-inflammation in Susac syndrome. Nat Commun 2019; 10:5779. [PMID: 31852955 PMCID: PMC6920411 DOI: 10.1038/s41467-019-13593-5] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 11/11/2019] [Indexed: 12/19/2022] Open
Abstract
Neuroinflammation is often associated with blood-brain-barrier dysfunction, which contributes to neurological tissue damage. Here, we reveal the pathophysiology of Susac syndrome (SuS), an enigmatic neuroinflammatory disease with central nervous system (CNS) endotheliopathy. By investigating immune cells from the blood, cerebrospinal fluid, and CNS of SuS patients, we demonstrate oligoclonal expansion of terminally differentiated activated cytotoxic CD8+ T cells (CTLs). Neuropathological data derived from both SuS patients and a newly-developed transgenic mouse model recapitulating the disease indicate that CTLs adhere to CNS microvessels in distinct areas and polarize granzyme B, which most likely results in the observed endothelial cell injury and microhemorrhages. Blocking T-cell adhesion by anti-α4 integrin-intervention ameliorates the disease in the preclinical model. Similarly, disease severity decreases in four SuS patients treated with natalizumab along with other therapy. Our study identifies CD8+ T-cell-mediated endotheliopathy as a key disease mechanism in SuS and highlights therapeutic opportunities.
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Affiliation(s)
- Catharina C Gross
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany.
| | - Céline Meyer
- Centre de Physiopathologie Toulouse-Purpan (CPTP), Université de Toulouse, CNRS, Inserm, UPS, CHU Purpan - BP 3028 - 31024, Toulouse Cedex 3, Toulouse, France
| | - Urvashi Bhatia
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Lidia Yshii
- Centre de Physiopathologie Toulouse-Purpan (CPTP), Université de Toulouse, CNRS, Inserm, UPS, CHU Purpan - BP 3028 - 31024, Toulouse Cedex 3, Toulouse, France
| | - Ilka Kleffner
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
- Department of Neurology, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, In der Schornau 23-25, 44892, Bochum, Germany
| | - Jan Bauer
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090, Vienna, Austria
| | - Anna R Tröscher
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090, Vienna, Austria
| | - Andreas Schulte-Mecklenbeck
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Sebastian Herich
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Tilman Schneider-Hohendorf
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Henrike Plate
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Tanja Kuhlmann
- Institute of Neuropathology, University Hospital Münster, University of Münster, Pottkamp 2, 48149, Münster, Germany
| | - Markus Schwaninger
- Institute of Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Wolfgang Brück
- Institute of Neuropathology, University Medical Center Göttingen, Robert-Koch-Straße 40, 37099, Göttingen, Germany
| | - Marc Pawlitzki
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - David-Axel Laplaud
- UMR 1064, INSERM, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, CHU Nantes - Hôtel Dieu Bd Jean Monnet, 44093, Nantes Cedex 01, France
- Service Neurologie, CHU Nantes, Nantes, France
| | - Delphine Loussouarn
- Service d'Anatomo-Pathologie, CHU Nantes, Hôtel-Dieu, rez-de-jardin, 44093, Nantes Cedex 1, France
| | - John Parratt
- Department of Neurology, Royal North Shore Hospital, Sydney, Australia
- Australia Northern Clinical School, University of Sydney, Reserve Road, St Leonards, Sydney, NSW, 2065, Australia
| | - Michael Barnett
- Brain and Mind Centre, Medical Faculty, University of Sydney, Mallett Street, Camperdown, Sydney, NSW, 2050, Australia
| | - Michael E Buckland
- Brain and Mind Centre, Medical Faculty, University of Sydney, Mallett Street, Camperdown, Sydney, NSW, 2050, Australia
- Department of Neuropathology, Royal Prince Alfred Hospital, 94, Mallett Street, Camperdown, Sydney, NSW, 2050, Australia
| | - Todd A Hardy
- Brain and Mind Centre, Medical Faculty, University of Sydney, Mallett Street, Camperdown, Sydney, NSW, 2050, Australia
- Department of Neurology, Concord Hospital, University of Sydney, Sydney, NSW, 2139, Australia
| | - Stephen W Reddel
- Brain and Mind Centre, Medical Faculty, University of Sydney, Mallett Street, Camperdown, Sydney, NSW, 2050, Australia
- Department of Neurology, Concord Hospital, University of Sydney, Sydney, NSW, 2139, Australia
| | - Marius Ringelstein
- Department of Neurology, Medical Faculty, Heinrich Heine University, Moorenstraße 5, 40225, Düsseldorf, Germany
- Department of Neurology, Center of Neurology und Neuropsychiatry, LVR-Klinikum, Heinrich Heine University Düsseldorf, Bergische Landstraße 2, 40629, Düsseldorf, Germany
| | - Jan Dörr
- Max Delbrueck Center for Molecular Medicine and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, NeuroCure, Experimental and Clinical Research Center, Charitéplatz 1, 10117, Berlin, Germany
| | - Brigitte Wildemann
- Molecular Neuroimmunology Group, Department of Neurology, University of Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
| | - Markus Kraemer
- Department of Neurology, Medical Faculty, Heinrich Heine University, Moorenstraße 5, 40225, Düsseldorf, Germany
- Department of Neurology, Alfried Krupp Hospital, Alfried-Krupp-Strasse 21, 45130, Essen, Germany
| | - Hans Lassmann
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090, Vienna, Austria
| | - Romana Höftberger
- Institute of Neurology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Eduardo Beltrán
- Institute of Clinical Neuroimmunology, Biomedical Center and Hospital of the Ludwig-Maximilians-University Munich, Großhaderner Straße 9, Martinsried, 82152, Munich, Germany
| | - Klaus Dornmair
- Institute of Clinical Neuroimmunology, Biomedical Center and Hospital of the Ludwig-Maximilians-University Munich, Großhaderner Straße 9, Martinsried, 82152, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Nicholas Schwab
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Luisa Klotz
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Sven G Meuth
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
- Cells in Motion (CiM), Münster, Germany
| | - Guillaume Martin-Blondel
- Centre de Physiopathologie Toulouse-Purpan (CPTP), Université de Toulouse, CNRS, Inserm, UPS, CHU Purpan - BP 3028 - 31024, Toulouse Cedex 3, Toulouse, France
- Department of Infectious and Tropical Diseases, Toulouse University Hospital, Toulouse, France
| | - Heinz Wiendl
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany.
- Australia Northern Clinical School, University of Sydney, Reserve Road, St Leonards, Sydney, NSW, 2065, Australia.
- Cells in Motion (CiM), Münster, Germany.
| | - Roland Liblau
- Centre de Physiopathologie Toulouse-Purpan (CPTP), Université de Toulouse, CNRS, Inserm, UPS, CHU Purpan - BP 3028 - 31024, Toulouse Cedex 3, Toulouse, France.
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199
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Sanderson JP, Crowley DJ, Wiedermann GE, Quinn LL, Crossland KL, Tunbridge HM, Cornforth TV, Barnes CS, Ahmed T, Howe K, Saini M, Abbott RJ, Anderson VE, Tavano B, Maroto M, Gerry AB. Preclinical evaluation of an affinity-enhanced MAGE-A4-specific T-cell receptor for adoptive T-cell therapy. Oncoimmunology 2019; 9:1682381. [PMID: 32002290 PMCID: PMC6959444 DOI: 10.1080/2162402x.2019.1682381] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/12/2019] [Accepted: 10/14/2019] [Indexed: 12/13/2022] Open
Abstract
A substantial obstacle to the success of adoptive T cell-based cancer immunotherapy is the sub-optimal affinity of T-cell receptors (TCRs) for most tumor antigens. Genetically engineered TCRs that have enhanced affinity for specific tumor peptide-MHC complexes may overcome this barrier. However, this enhancement risks increasing weak TCR cross-reactivity to other antigens expressed by normal tissues, potentially leading to clinical toxicities. To reduce the risk of such adverse clinical outcomes, we have developed an extensive preclinical testing strategy, involving potency testing using 2D and 3D human cell cultures and primary tumor material, and safety testing using human primary cell and cell-line cross-reactivity screening and molecular analysis to predict peptides recognized by the affinity-enhanced TCR. Here, we describe this strategy using a developmental T-cell therapy, ADP-A2M4, which recognizes the HLA-A2-restricted MAGE-A4 peptide GVYDGREHTV. ADP-A2M4 demonstrated potent anti-tumor activity in the absence of major off-target cross-reactivity against a range of human primary cells and cell lines. Identification and characterization of peptides recognized by the affinity-enhanced TCR also revealed no cross-reactivity. These studies demonstrated that this TCR is highly potent and without major safety concerns, and as a result, this TCR is now being investigated in two clinical trials (NCT03132922, NCT04044768).
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Affiliation(s)
| | | | | | | | | | | | | | | | - Tina Ahmed
- Preclinical Research, Adaptimmune, Abingdon, UK
| | - Karen Howe
- Target Validation, Adaptimmune, Abingdon, UK
| | - Manoj Saini
- Preclinical Research, Adaptimmune, Abingdon, UK
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200
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Wang G, Yu Y, Cai X, Zhou EM, Zimmerman JJ. Effects of PRRSV Infection on the Porcine Thymus. Trends Microbiol 2019; 28:212-223. [PMID: 31744664 DOI: 10.1016/j.tim.2019.10.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 10/15/2019] [Accepted: 10/17/2019] [Indexed: 12/13/2022]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) dramatically affects the thymus and its ability to carry out its normal functions. In particular, infection incapacitates PRRSV-susceptible CD14pos antigen-presenting cells (APCs) in the thymus and throughout the body. PRRSV-induced autophagy in thymic epithelial cells modulates the development of T cells, and PRRSV-induced apoptosis in CD4posCD8pos thymocytes modulates cellular immunity against PRRSV and other pathogens. Pigs are less able to resist and/or eliminate secondary infectious agents due the effect of PRRSV on the thymus, and this susceptibility phenomenon is long recognized as a primary characteristic of PRRSV infection.
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Affiliation(s)
- Gang Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China; Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
| | - Ying Yu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China; College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Xuehui Cai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - En-Min Zhou
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Jeffrey J Zimmerman
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
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