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Genolet R, Bobisse S, Chiffelle J, Arnaud M, Petremand R, Queiroz L, Michel A, Reichenbach P, Cesbron J, Auger A, Baumgaertner P, Guillaume P, Schmidt J, Irving M, Kandalaft LE, Speiser DE, Coukos G, Harari A. TCR sequencing and cloning methods for repertoire analysis and isolation of tumor-reactive TCRs. CELL REPORTS METHODS 2023; 3:100459. [PMID: 37159666 PMCID: PMC10163020 DOI: 10.1016/j.crmeth.2023.100459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/27/2023] [Accepted: 03/27/2023] [Indexed: 05/11/2023]
Abstract
T cell receptor (TCR) technologies, including repertoire analyses and T cell engineering, are increasingly important in the clinical management of cellular immunity in cancer, transplantation, and other immune diseases. However, sensitive and reliable methods for repertoire analyses and TCR cloning are still lacking. Here, we report on SEQTR, a high-throughput approach to analyze human and mouse repertoires that is more sensitive, reproducible, and accurate as compared with commonly used assays, and thus more reliably captures the complexity of blood and tumor TCR repertoires. We also present a TCR cloning strategy to specifically amplify TCRs from T cell populations. Positioned downstream of single-cell or bulk TCR sequencing, it allows time- and cost-effective discovery, cloning, screening, and engineering of tumor-specific TCRs. Together, these methods will accelerate TCR repertoire analyses in discovery, translational, and clinical settings and permit fast TCR engineering for cellular therapies.
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Affiliation(s)
- Raphael Genolet
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
- Corresponding author
| | - Sara Bobisse
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Johanna Chiffelle
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Marion Arnaud
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Rémy Petremand
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Lise Queiroz
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Alexandra Michel
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Patrick Reichenbach
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
| | - Julien Cesbron
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Aymeric Auger
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Petra Baumgaertner
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Philippe Guillaume
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Julien Schmidt
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Melita Irving
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
| | - Lana E. Kandalaft
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital, Lausanne, Switzerland
| | - Daniel E. Speiser
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
| | - George Coukos
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Corresponding author
| | - Alexandre Harari
- Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
- Corresponding author
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Zhi Y, Li M, Lv G. Into the multi-omics era: Progress of T cells profiling in the context of solid organ transplantation. Front Immunol 2023; 14:1058296. [PMID: 36798139 PMCID: PMC9927650 DOI: 10.3389/fimmu.2023.1058296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/20/2023] [Indexed: 02/04/2023] Open
Abstract
T cells are the common type of lymphocyte to mediate allograft rejection, remaining long-term allograft survival impeditive. However, the heterogeneity of T cells, in terms of differentiation and activation status, the effector function, and highly diverse T cell receptors (TCRs) have thus precluded us from tracking these T cells and thereby comprehending their fate in recipients due to the limitations of traditional detection approaches. Recently, with the widespread development of single-cell techniques, the identification and characterization of T cells have been performed at single-cell resolution, which has contributed to a deeper comprehension of T cell heterogeneity by relevant detections in a single cell - such as gene expression, DNA methylation, chromatin accessibility, surface proteins, and TCR. Although these approaches can provide valuable insights into an individual cell independently, a comprehensive understanding can be obtained when applied joint analysis. Multi-omics techniques have been implemented in characterizing T cells in health and disease, including transplantation. This review focuses on the thesis, challenges, and advances in these technologies and highlights their application to the study of alloreactive T cells to improve the understanding of T cell heterogeneity in solid organ transplantation.
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Affiliation(s)
- Yao Zhi
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
| | - Mingqian Li
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
| | - Guoyue Lv
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
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3
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Thieme CJ, Schulz M, Wehler P, Anft M, Amini L, Blàzquez-Navarro A, Stervbo U, Hecht J, Nienen M, Stittrich AB, Choi M, Zgoura P, Viebahn R, Schmueck-Henneresse M, Reinke P, Westhoff TH, Roch T, Babel N. In vitro and in vivo evidence that the switch from calcineurin to mTOR inhibitors may be a strategy for immunosuppression in Epstein-Barr virus-associated post-transplant lymphoproliferative disorder. Kidney Int 2022; 102:1392-1408. [PMID: 36103953 DOI: 10.1016/j.kint.2022.08.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 08/02/2022] [Accepted: 08/12/2022] [Indexed: 01/12/2023]
Abstract
Post-transplant lymphoproliferative disorder is a life-threatening complication of immunosuppression following transplantation mediated by failure of T cells to control Epstein-Barr virus (EBV)-infected and transformed B cells. Typically, a modification or reduction of immunosuppression is recommended, but insufficiently defined thus far. In order to help delineate this, we characterized EBV-antigen-specific T cells and lymphoblastoid cell lines from healthy donors and in patients with a kidney transplant in the absence or presence of the standard immunosuppressants tacrolimus, cyclosporin A, prednisolone, rapamycin, and mycophenolic acid. Phenotypes of lymphoblastoid cell-lines and T cells, T cell-receptor-repertoire diversity, and T-cell reactivity upon co-culture with autologous lymphoblastoid cell lines were analyzed. Rapamycin and mycophenolic acid inhibited lymphoblastoid cell-line proliferation. T cells treated with prednisolone and rapamycin showed nearly normal cytokine production. Proliferation and the viability of T cells were decreased by mycophenolic acid, while tacrolimus and cyclosporin A were strong suppressors of T-cell function including their killing activity. Overall, our study provides a basis for the clinical decision for the modification and reduction of immunosuppression and adds information to the complex balance of maintaining anti-viral immunity while preventing acute rejection. Thus, an immunosuppressive regime based on mTOR inhibition and reduced or withdrawn calcineurin inhibitors could be a promising strategy for patients with increased risk of or manifested EBV-associated post-transplant lymphoproliferative disorder.
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Affiliation(s)
- Constantin J Thieme
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Malissa Schulz
- Hochschule für Technik und Wirtschaft Berlin (HTW), Berlin, Germany
| | - Patrizia Wehler
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Moritz Anft
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | - Leila Amini
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Arturo Blàzquez-Navarro
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | - Ulrik Stervbo
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | - Jochen Hecht
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain; Experimental and Health Sciences Department, Universitat Pompeu Fabra, Barcelona, Spain
| | - Mikalai Nienen
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Mira Choi
- Department of Nephrology and Medical Intensive Care, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Panagiota Zgoura
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | - Richard Viebahn
- Department of Surgery, University Hospital Knappschaftskrankenhaus Bochum, Ruhr-University Bochum, Bochum, Germany
| | - Michael Schmueck-Henneresse
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Petra Reinke
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Timm H Westhoff
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | - Toralf Roch
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | - Nina Babel
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany.
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Gerdemann U, Fleming RA, Kaminski J, McGuckin C, Rui X, Lane JF, Keskula P, Cagnin L, Shalek AK, Tkachev V, Kean LS. Identification and Tracking of Alloreactive T Cell Clones in Rhesus Macaques Through the RM-scTCR-Seq Platform. Front Immunol 2022; 12:804932. [PMID: 35154078 PMCID: PMC8825351 DOI: 10.3389/fimmu.2021.804932] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/22/2021] [Indexed: 01/14/2023] Open
Abstract
T cell receptor (TCR) clonotype tracking is a powerful tool for interrogating T cell mediated immune processes. New methods to pair a single cell's transcriptional program with its TCR identity allow monitoring of T cell clonotype-specific transcriptional dynamics. While these technologies have been available for human and mouse T cells studies, they have not been developed for Rhesus Macaques (RM), a critical translational organism for autoimmune diseases, vaccine development and transplantation. We describe a new pipeline, 'RM-scTCR-Seq', which, for the first time, enables RM specific single cell TCR amplification, reconstruction and pairing of RM TCR's with their transcriptional profiles. We apply this method to a RM model of GVHD, and identify and track in vitro detected alloreactive clonotypes in GVHD target organs and explore their GVHD driven cytotoxic T cell signature. This novel, state-of-the-art platform fundamentally advances the utility of RM to study protective and pathogenic T cell responses.
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Affiliation(s)
- Ulrike Gerdemann
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
| | - Ryan A Fleming
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
| | - James Kaminski
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States.,Broad Institute of MIT and Harvard, Cambridge, MA, United States.,Department of Chemistry, Institute for Medical Engineering and Science (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, United States.,Ragon Institute of Massachusetts General Hospital (MGH), MIT and Harvard, Cambridge, MA, United States
| | - Connor McGuckin
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
| | - Xianliang Rui
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
| | - Jennifer F Lane
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
| | - Paula Keskula
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
| | - Lorenzo Cagnin
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
| | - Alex K Shalek
- Broad Institute of MIT and Harvard, Cambridge, MA, United States.,Department of Chemistry, Institute for Medical Engineering and Science (IMES), and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, United States.,Ragon Institute of Massachusetts General Hospital (MGH), MIT and Harvard, Cambridge, MA, United States
| | - Victor Tkachev
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
| | - Leslie S Kean
- Division of Pediatric Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, United States
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AIRR Community Guide to Planning and Performing AIRR-Seq Experiments. Methods Mol Biol 2022; 2453:261-278. [PMID: 35622331 PMCID: PMC9761540 DOI: 10.1007/978-1-0716-2115-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The development of high-throughput sequencing of adaptive immune receptor repertoires (AIRR-seq of IG and TR rearrangements) has provided a new frontier for in-depth analysis of the immune system. The last decade has witnessed an explosion in protocols, experimental methodologies, and computational tools. In this chapter, we discuss the major considerations in planning a successful AIRR-seq experiment together with basic strategies for controlling and evaluating the outcome of the experiment. Members of the AIRR Community have authored several chapters in this edition, which cover step-by-step instructions to successfully conduct, analyze, and share an AIRR-seq project.
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Abstract
Single-cell RNA sequencing (scRNA-seq) is a comprehensive technical tool to analyze intracellular and intercellular interaction data by whole transcriptional profile analysis. Here, we describe the application in biomedical research, focusing on the immune system during organ transplantation and rejection. Unlike conventional transcriptome analysis, this method provides a full map of multiple cell populations in one specific tissue and presents a dynamic and transient unbiased method to explore the progression of allograft dysfunction, starting from the stress response to final graft failure. This promising sequencing technology remarkably improves individualized organ rejection treatment by identifying decisive cellular subgroups and cell-specific interactions.
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Yan D, Yang J, Ji Z, Wang J, Lu X, Huang Y, Zhong C, Li L. Profiling T cell receptor β-chain in responders after immunization with recombinant hepatitis B vaccine. J Gene Med 2021; 23:e3367. [PMID: 34048625 DOI: 10.1002/jgm.3367] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/22/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND T cells with edited T cell receptor β-chain variable (TRBV) are involved in the immune response to recombinant hepatitis B surface antigen (rHBsAg) vaccine and the production of hepatitis B surface antibody (HBsAb). The immune repertoire (IR) profile and mechanism of vaccination positive responders (VPR) with rHBsAg are not fully understood. METHODS The IR of six VPRs (HBsAb+, HbsAg-) with rHBsAg vaccination was established by the high throughput sequencing technique and bioinformatics analysis and compared with those in five vaccination negative responders (VNRs) (HbsAb-, HbsAg-) who were also inoculated with rHBsAg. The repertoire features of the BV, BJ and V (CDR3) J genes and immune diversity in peripheral blood mononuclear cells, respectively, were analyzed for each subject. RESULTS There was no significant difference in sequencing amplification indices of each sample. However, TRBV15/BJ2-3 demonstrated significantly high expression levels in VPR compared to those in the VNR group (both p < 0.05). Further results showed that the BV15/BJ2-5 level was significantly increased for VPR compared to that of VNR group. Interestingly, the motif of CDR3 in TRBV15/BJ2-5 was mostly expressed as "GGETQ" or "GETQ". Additionally, there was no remarkable difference between the two groups of distribution with respect to the different clone expression levels of V (CDR3) J. CONCLUSIONS The features of IR in the VPR and VNR will contribute to the exploration of the mechanism of the positive response to rHBsAg, and also contribute to development of optimized hepatitis B vaccine, in addition to providing a partial interpretation of the VNR who has a relatively low infection with HBV.
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Affiliation(s)
- Dong Yan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiezuan Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhongkang Ji
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ju Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoqing Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yandi Huang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chengli Zhong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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8
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Stervbo U, Rahmann S, Roch T, Westhoff TH, Babel N. Epitope similarity cannot explain the pre-formed T cell immunity towards structural SARS-CoV-2 proteins. Sci Rep 2020; 10:18995. [PMID: 33149224 PMCID: PMC7642385 DOI: 10.1038/s41598-020-75972-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/18/2020] [Indexed: 01/08/2023] Open
Abstract
The current pandemic is caused by the SARS-CoV-2 virus and large progress in understanding the pathology of the virus has been made since its emergence in late 2019. Several reports indicate short lasting immunity against endemic coronaviruses, which contrasts studies showing that biobanked venous blood contains T cells reactive to SARS-CoV-2 S-protein even before the outbreak in Wuhan. This suggests a preformed T cell memory towards structural proteins in individuals not exposed to SARS-CoV-2. Given the similarity of SARS-CoV-2 to other members of the Coronaviridae family, the endemic coronaviruses appear likely candidates to generate this T cell memory. However, given the apparent poor immunological memory created by the endemic coronaviruses, immunity against other common pathogens might offer an alternative explanation. Here, we utilize a combination of epitope prediction and similarity to common human pathogens to identify potential sources of the SARS-CoV-2 T cell memory. Although beta-coronaviruses are the most likely candidates to explain the pre-existing SARS-CoV-2 reactive T cells in uninfected individuals, the SARS-CoV-2 epitopes with the highest similarity to those from beta-coronaviruses are confined to replication associated proteins-not the host interacting S-protein. Thus, our study suggests that the observed SARS-CoV-2 pre-formed immunity to structural proteins is not driven by near-identical epitopes.
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Affiliation(s)
- Ulrik Stervbo
- Center for Translational Medicine, University Hospital Marien Hospital Herne, Ruhr-University, Bochum, Germany.
- Berlin-Brandenburg Center for Regenerative Therapies, and Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin Institute of Health, Berlin, Germany.
| | - Sven Rahmann
- Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen, Duisburg, Germany.
| | - Toralf Roch
- Center for Translational Medicine, University Hospital Marien Hospital Herne, Ruhr-University, Bochum, Germany
- Berlin-Brandenburg Center for Regenerative Therapies, and Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin Institute of Health, Berlin, Germany
| | - Timm H Westhoff
- Center for Translational Medicine, University Hospital Marien Hospital Herne, Ruhr-University, Bochum, Germany
| | - Nina Babel
- Center for Translational Medicine, University Hospital Marien Hospital Herne, Ruhr-University, Bochum, Germany
- Berlin-Brandenburg Center for Regenerative Therapies, and Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin Institute of Health, Berlin, Germany
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9
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Moore C, Gao B, Roskin KM, Vasilescu ERM, Addonizio L, Givertz MM, Madsen JC, Zorn E. B cell clonal expansion within immune infiltrates in human cardiac allograft vasculopathy. Am J Transplant 2020; 20:1431-1438. [PMID: 31811777 PMCID: PMC7238293 DOI: 10.1111/ajt.15737] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/21/2019] [Accepted: 11/24/2019] [Indexed: 01/25/2023]
Abstract
Cardiac allograft vasculopathy (CAV) is associated with intragraft B cell infiltrates. Here, we studied the clonal composition of B cell infiltrates using 4 graft specimens with CAV. Using deep sequencing, we analyzed the immunoglobulin heavy chain variable region repertoire in both graft and blood. Results showed robust B cell clonal expansion in the graft but not in the blood for all cases. Several expanded B cell clones, characterized by their uniquely rearranged complementarity-determining region 3, were detected in different locations in the graft. Sequences from intragraft B cells also showed elevated levels of mutated rearrangements in the graft compared to blood B cells. The number of somatic mutations per rearrangement was also higher in the graft than in the blood, suggesting that B cells continued maturing in situ. Overall, our studies demonstrated B cell clonal expansion in human cardiac allografts with CAV. This local B cell response may contribute to the pathophysiology of CAV through a mechanism that needs to be identified.
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Affiliation(s)
- Carolina Moore
- Center for Transplantation Science, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts,Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio,Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Baoshan Gao
- Center for Transplantation Science, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts,Transplant Center, The First Hospital of Jilin University, Changchun, China
| | - Krishna M. Roskin
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio,Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio,Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, Ohio
| | | | - Linda Addonizio
- Division of Cardiothoracic Surgery, Department of Surgery, Columbia University Medical Center, New York, New York
| | - Michael M. Givertz
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Joren C. Madsen
- Center for Transplantation Science, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts,Division of Cardiac Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Emmanuel Zorn
- Center for Transplantation Science, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts,Columbia Center for Translational Immunology, Columbia University Medical Center, New York, New York
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10
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Differential Diagnosis of Interstitial Allograft Rejection and BKV Nephropathy by T-cell Receptor Sequencing. Transplantation 2020; 104:e107-e108. [PMID: 32224816 DOI: 10.1097/tp.0000000000003054] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Gupta S, Witas R, Voigt A, Semenova T, Nguyen CQ. Single-Cell Sequencing of T cell Receptors: A Perspective on the Technological Development and Translational Application. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:29-50. [PMID: 32949388 DOI: 10.1007/978-981-15-4494-1_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
T cells recognize peptides bound to major histocompatibility complex (MHC) class I and class II molecules at the cell surface. This recognition is accomplished by the expression of T cell receptors (TCR) which are required to be diverse and adaptable in order to accommodate the various and vast number of antigens presented on the MHCs. Thus, determining TCR repertoires of effector T cells is necessary to understand the immunological process in responding to cancer progression, infection, and autoimmune development. Furthermore, understanding the TCR repertoires will provide a solid framework to predict and test the antigen which is more critical in autoimmunity. However, it has been a technical challenge to sequence the TCRs and provide a conceptual context in correlation to the vast number of TCR repertoires in the immunological system. The exploding field of single-cell sequencing has changed how the repertoires are being investigated and analyzed. In this review, we focus on the biology of TCRs, TCR signaling and its implication in autoimmunity. We discuss important methods in bulk sequencing of many cells. Lastly, we explore the most pertinent platforms in single-cell sequencing and its application in autoimmunity.
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Affiliation(s)
- Shivai Gupta
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Richard Witas
- Department of Oral Biology, College of Dentistry, Gainesville, FL, USA
| | - Alexandria Voigt
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Touyana Semenova
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Cuong Q Nguyen
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA. .,Department of Oral Biology, College of Dentistry, Gainesville, FL, USA. .,Center of Orphaned Autoimmune Diseases, University of Florida, Gainesville, FL, USA.
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