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Liu Q, Yang S, Tan Y, Feng W, Wang Q, Qiao J, Yang B, Wang C, Tao J, Wang H, Cui L. Bulk T-cell receptor sequencing confirms clonality in obstetric antiphospholipid syndrome and may as a potential biomarker. Autoimmunity 2024; 57:2360490. [PMID: 38836341 DOI: 10.1080/08916934.2024.2360490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 05/16/2024] [Indexed: 06/06/2024]
Abstract
The heterogeneity of the T cell receptor (TCR) repertoire critically influences the autoimmune response in obstetric antiphospholipid syndrome (OAPS) and is intimately associated with the prophylaxis of autoimmune disorders. Investigating the TCR diversity patterns in patients with OAPS is thus of paramount clinical importance. This investigation procured peripheral blood specimens from 31 individuals with OAPS, 21 patients diagnosed with systemic lupus erythematosus (SLE), and 22 healthy controls (HC), proceeding with TCR repertoire sequencing. Concurrently, adverse pregnancy outcomes in the OAPS cohort were monitored and documented over an 18-month timeframe. We paid particular attention to disparities in V/J gene utilisation and the prevalence of shared clonotypes amongst OAPS patients and the comparative groups. When juxtaposed with observations from healthy controls and SLE patients, immune repertoire sequencing disclosed irregular T- and B-cell profiles and a contraction of diversity within the OAPS group. Marked variances were found in the genomic rearrangements of the V gene, J gene, and V/J combinations. Utilising a specialised TCRβ repertoire, we crafted a predictive model for OAPS classification with robust discriminative capability (AUC = 0.852). Our research unveils alterations in the TCR repertoire among OAPS patients for the first time, positing potential covert autoimmune underpinnings. These findings nominate the TCR repertoire as a prospective peripheral blood biomarker for the clinical diagnosis of OAPS and may offer valuable insights for advancing the understanding of OAPS immunologic mechanisms and prognostic outcomes.
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Affiliation(s)
- Qi Liu
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
- Department of Clinical Laboratory, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Shuo Yang
- Department of Clinical Laboratory, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Yuan Tan
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
- Department of Clinical Laboratory, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Weimin Feng
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
- Department of Clinical Laboratory, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Qingchen Wang
- Department of Clinical Laboratory, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Jiao Qiao
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
- Department of Clinical Laboratory, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Boxing Yang
- Department of Clinical Laboratory, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Chong Wang
- Department of Clinical Laboratory, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Jingjin Tao
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
- Department of Clinical Laboratory, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - He Wang
- Department of Clinical Laboratory, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Liyan Cui
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
- Department of Clinical Laboratory, Peking University Third Hospital, Beijing, China
- Core Unit of National Clinical Research Center for Laboratory Medicine, Peking University Third Hospital, Beijing, China
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Syed S, Boland BS, Bourke LT, Chen LA, Churchill L, Dobes A, Greene A, Heller C, Jayson C, Kostiuk B, Moss A, Najdawi F, Plung L, Rioux JD, Rosen MJ, Torres J, Zulqarnain F, Satsangi J. Challenges in IBD Research 2024: Precision Medicine. Inflamm Bowel Dis 2024; 30:S39-S54. [PMID: 38778628 DOI: 10.1093/ibd/izae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Indexed: 05/25/2024]
Abstract
Precision medicine is part of 5 focus areas of the Challenges in IBD Research 2024 research document, which also includes preclinical human IBD mechanisms, environmental triggers, novel technologies, and pragmatic clinical research. Building on Challenges in IBD Research 2019, the current Challenges aims to provide a comprehensive overview of current gaps in inflammatory bowel diseases (IBDs) research and deliver actionable approaches to address them with a focus on how these gaps can lead to advancements in interception, remission, and restoration for these diseases. The document is the result of multidisciplinary input from scientists, clinicians, patients, and funders, and represents a valuable resource for patient-centric research prioritization. In particular, the precision medicine section is focused on the main research gaps in elucidating how to bring the best care to the individual patient in IBD. Research gaps were identified in biomarker discovery and validation for predicting disease progression and choosing the most appropriate treatment for each patient. Other gaps were identified in making the best use of existing patient biosamples and clinical data, developing new technologies to analyze large datasets, and overcoming regulatory and payer hurdles to enable clinical use of biomarkers. To address these gaps, the Workgroup suggests focusing on thoroughly validating existing candidate biomarkers, using best-in-class data generation and analysis tools, and establishing cross-disciplinary teams to tackle regulatory hurdles as early as possible. Altogether, the precision medicine group recognizes the importance of bringing basic scientific biomarker discovery and translating it into the clinic to help improve the lives of IBD patients.
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Affiliation(s)
- Sana Syed
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
- Patient representative for Crohn's & Colitis Foundation, New York, NY, USA
| | - Brigid S Boland
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lauren T Bourke
- Precision Medicine Drug Development, Early Respiratory and Immunology, AstraZeneca, Boston, MA, USA
| | - Lea Ann Chen
- Division of Gastroenterology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Laurie Churchill
- Leona M. and Harry B. Helmsley Charitable Trust, New York, NY, USA
| | | | - Adam Greene
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | | | | | | | - Alan Moss
- Crohn's & Colitis Foundation, New York, NY, USA
| | | | - Lori Plung
- Patient representative for Crohn's & Colitis Foundation, New York, NY, USA
| | - John D Rioux
- Research Center, Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Michael J Rosen
- Division of Pediatric Gastroenterology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Joana Torres
- Division of Gastroenterology, Hospital Beatriz Ângelo, Hospital da Luz, Lisbon, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Fatima Zulqarnain
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | - Jack Satsangi
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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3
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Xiong H, Ji L, Yang J, Wan J, Song M, Liu G, Yang L, Dong X. Analysis of CD8 + TCRβ Chain repertoire in peripheral blood of vitiligo via high-throughput sequencing. Mol Immunol 2023; 160:112-120. [PMID: 37421821 DOI: 10.1016/j.molimm.2023.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 06/11/2023] [Accepted: 06/24/2023] [Indexed: 07/10/2023]
Abstract
Vitiligo is an autoimmune depigmentation dermatosis induced by melanocyte destruction, and CD8+ T cells play a pivotal role in melanocyte destruction. However, an accurate profile of the CD8+ T cell receptor (TCR) repertoire in vitiligo patients has not been reported, and the clonotype features of the involved CD8+ T cells remain largely unknown. This study aimed to assess the TCRβ chain repertoire diversity and composition of blood in nine nonsegmental vitiligo patients via high-throughput sequencing. Vitiligo patients manifested a low TCRβ repertoire diversity with highly expanded clones. Differential usage of TRBV, the TRBJ gene, and the TRBV/TRBJ combination were compared between patients with vitiligo and healthy controls. A set of TRBV/TRBJ combinations could differentiate patients with vitiligo from healthy controls (area under the curve = 0.9383, 95% CI: 0.8167-1.00). Our study revealed distinct TCRβ repertoires of CD8+ T cells in patients with vitiligo and will help explore novel immune biomarkers and potential therapeutic targets for vitiligo.
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Affiliation(s)
- Hao Xiong
- Department of Dermatology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Liyan Ji
- Beijing GenePlus Genomics Institute, China
| | - Jin Yang
- Department of Allergy and Immunology, Huashan Hospital, Fudan University, Shanghai, China; Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jianji Wan
- Department of Dermatology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | | | - Guangren Liu
- Department of Dermatology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Ling Yang
- Beijing GenePlus Genomics Institute, China
| | - Xiuqin Dong
- Department of Dermatology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China.
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Boardman DA, Wong MQ, Rees WD, Wu D, Himmel ME, Orban PC, Vent-Schmidt J, Zachos NC, Steiner TS, Levings MK. Flagellin-specific human CAR Tregs for immune regulation in IBD. J Autoimmun 2023; 134:102961. [PMID: 36470208 PMCID: PMC9908852 DOI: 10.1016/j.jaut.2022.102961] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/04/2022]
Abstract
Regulatory T cell (Treg) therapy is a promising strategy to treat inflammatory bowel disease (IBD). Data from animal models has shown that Tregs specific for intestinal antigens are more potent than polyclonal Tregs at inhibiting colitis. Flagellins, the major structural proteins of bacterial flagella, are immunogenic antigens frequently targeted in IBD subjects, leading to the hypothesis that flagellin-specific Tregs could be an effective cell therapy for IBD. We developed a novel chimeric antigen receptor (CAR) specific for flagellin derived from Escherichia coli H18 (FliC). We used this CAR to confer FliC-specificity to human Tregs and investigated their therapeutic potential. FliC-CAR Tregs were activated by recombinant FliC protein but not a control flagellin protein, demonstrating CAR specificity and functionality. In a humanized mouse model, expression of the FliC-CAR drove preferential migration to the colon and expression of the activation marker PD1. In the presence of recombinant FliC protein in vitro, FliC-CAR Tregs were significantly more suppressive than control Tregs and promoted the establishment of colon-derived epithelial cell monolayers. These results demonstrate the potential of FliC-CAR Tregs to treat IBD and more broadly show the therapeutic potential of CARs targeting microbial-derived antigens.
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Affiliation(s)
- Dominic A Boardman
- Department of Surgery, University of British Columbia, Canada; BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - May Q Wong
- BC Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Medicine, University of British Columbia, Canada
| | - William D Rees
- BC Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Medicine, University of British Columbia, Canada
| | - Dan Wu
- Department of Surgery, University of British Columbia, Canada; BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Megan E Himmel
- BC Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Medicine, University of British Columbia, Canada
| | - Paul C Orban
- Department of Surgery, University of British Columbia, Canada; BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Jens Vent-Schmidt
- BC Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Medicine, University of British Columbia, Canada
| | - Nicholas C Zachos
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Theodore S Steiner
- BC Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Medicine, University of British Columbia, Canada
| | - Megan K Levings
- Department of Surgery, University of British Columbia, Canada; BC Children's Hospital Research Institute, Vancouver, BC, Canada; School of Biomedical Engineering, University of British Columbia, Canada.
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5
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Morgan NN, Duck LW, Wu J, Rujani M, Thomes PG, Elson CO, Mannon PJ. Crohn's Disease Patients Uniquely Contain Inflammatory Responses to Flagellin in a CD4 Effector Memory Subset. Inflamm Bowel Dis 2022; 28:1893-1903. [PMID: 35931421 DOI: 10.1093/ibd/izac146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Indexed: 12/09/2022]
Abstract
BACKGROUND Specific microbial antigens stimulate production of antibodies indicative of the aberrant immune response in Crohn's disease (CD). We tested for T cell reactivity linkage to B cell responses and now report on the prevalence, functionality, and phenotypic differences of flagellin-specific T cells among CD patients, ulcerative colitis (UC) patients, and control subjects and association with clinical features and flagellin seropositivity within CD patients. METHODS Sera from non-inflammatory bowel disease control subjects, CD patients, and UC patients were probed for antibody reactivity to gut bacterial recombinant flagellin antigens. Peripheral blood mononuclear cells were measured for flagellin antigen (CBir1, A4 Fla2, FlaX) or control (Candida albicans, and CytoStim) reactivity analyzed by flow cytometry for CD154 and cytokine expression on CD4+ T cells. Supernatants from post-flagellin-stimulated and unstimulated cells were used to measure effects on epithelial barrier function. RESULTS CD patients had a significantly higher percentage of flagellin-specific CD154+ CD4+ cells that have an effector memory T helper 1 and T helper 17 phenotype compared with UC patients and healthy control subjects. There was a positive correlation between the frequency of flagellin-specific CD154+ CD4+ effector memory T cells and serum levels of anti-flagellin immunoglobulin G in the CD patients. In addition, A4 Fla2-reactive T cells from active CD patients produced cytokines that can decrease barrier function in a gut epithelium. CONCLUSIONS These findings demonstrate a Crohn's-associated flagellin-reactive CD4 cell subset distinct from UC patients and control subjects. There is a link between these cells and flagellin seropositivity. This CD4 cell subset could reflect a particular endophenotype of CD, leading to novel insight into its pathology and treatment.
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Affiliation(s)
- Nadine N Morgan
- Program in Immunology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Lennard W Duck
- Program in Immunology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jiongru Wu
- Division of Gastroenterology and Hepatology, Paustian IBD Center, University of Nebraska Medical Center, Omaha, NE, USA.,Medical Service and Department of Medicine, Omaha VA Medical Center, Omaha, NE, USA
| | - Mahmud Rujani
- Medical Service and Department of Medicine, Omaha VA Medical Center, Omaha, NE, USA
| | - Paul G Thomes
- Division of Gastroenterology and Hepatology, Paustian IBD Center, University of Nebraska Medical Center, Omaha, NE, USA.,Medical Service and Department of Medicine, Omaha VA Medical Center, Omaha, NE, USA
| | - Charles O Elson
- Division of Gastroenterology and Hepatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Peter J Mannon
- Division of Gastroenterology and Hepatology, Paustian IBD Center, University of Nebraska Medical Center, Omaha, NE, USA.,Medical Service and Department of Medicine, Omaha VA Medical Center, Omaha, NE, USA
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6
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Rosati E, Rios Martini G, Pogorelyy MV, Minervina AA, Degenhardt F, Wendorff M, Sari S, Mayr G, Fazio A, Dowds CM, Hauser C, Tran F, von Schönfels W, Pochhammer J, Salnikova MA, Jaeckel C, Gigla JB, Sabet SS, Hübenthal M, Schiminsky E, Schreiber S, Rosenstiel PC, Scheffold A, Thomas PG, Lieb W, Bokemeyer B, Witte M, Aden K, Hendricks A, Schafmayer C, Egberts JH, Mamedov IZ, Bacher P, Franke A. A novel unconventional T cell population enriched in Crohn's disease. Gut 2022; 71:2194-2204. [PMID: 35264446 PMCID: PMC9554086 DOI: 10.1136/gutjnl-2021-325373] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 02/22/2022] [Indexed: 12/12/2022]
Abstract
OBJECTIVE One of the current hypotheses to explain the proinflammatory immune response in IBD is a dysregulated T cell reaction to yet unknown intestinal antigens. As such, it may be possible to identify disease-associated T cell clonotypes by analysing the peripheral and intestinal T-cell receptor (TCR) repertoire of patients with IBD and controls. DESIGN We performed bulk TCR repertoire profiling of both the TCR alpha and beta chains using high-throughput sequencing in peripheral blood samples of a total of 244 patients with IBD and healthy controls as well as from matched blood and intestinal tissue of 59 patients with IBD and disease controls. We further characterised specific T cell clonotypes via single-cell RNAseq. RESULTS We identified a group of clonotypes, characterised by semi-invariant TCR alpha chains, to be significantly enriched in the blood of patients with Crohn's disease (CD) and particularly expanded in the CD8+ T cell population. Single-cell RNAseq data showed an innate-like phenotype of these cells, with a comparable gene expression to unconventional T cells such as mucosal associated invariant T and natural killer T (NKT) cells, but with distinct TCRs. CONCLUSIONS We identified and characterised a subpopulation of unconventional Crohn-associated invariant T (CAIT) cells. Multiple evidence suggests these cells to be part of the NKT type II population. The potential implications of this population for CD or a subset thereof remain to be elucidated, and the immunophenotype and antigen reactivity of CAIT cells need further investigations in future studies.
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Affiliation(s)
- Elisa Rosati
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany .,Institute of Immunology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Gabriela Rios Martini
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany,Institute of Immunology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Mikhail V Pogorelyy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation,Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Anastasia A Minervina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation,Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Mareike Wendorff
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Soner Sari
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Gabriele Mayr
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Antonella Fazio
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Christel Marie Dowds
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Charlotte Hauser
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany,Department of Internal Medicine I, Universitätsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Witigo von Schönfels
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Julius Pochhammer
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Maria A Salnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Charlot Jaeckel
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Johannes Boy Gigla
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Sanaz Sedghpour Sabet
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Matthias Hübenthal
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany,Department of Dermatology, University Hospital Schleswig Holstein, Kiel, Schleswig-Holstein, Germany
| | - Esther Schiminsky
- Institute of Immunology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Stefan Schreiber
- Department of Internal Medicine I, Universitätsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Philip C Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Alexander Scheffold
- Institute of Immunology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank POPGEN, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Bernd Bokemeyer
- Interdisciplinary Crohn Colitis Centre Minden, Minden, Germany
| | - Maria Witte
- Department of General Surgery, Rostock University Medical Center, Rostock, Mecklenburg-Vorpommern, Germany
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany,Department of Internal Medicine I, Universitätsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Alexander Hendricks
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany,Department of General Surgery, Rostock University Medical Center, Rostock, Mecklenburg-Vorpommern, Germany
| | - Clemens Schafmayer
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany,Department of General Surgery, Rostock University Medical Center, Rostock, Mecklenburg-Vorpommern, Germany
| | - Jan-Hendrick Egberts
- Department of Visceral and Thoracic Surgery, Universitatsklinikum Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Ilgar Z Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation,CEITEC, Masaryk University, Brno, Czech Republic,Dmitry Rogachev National Research Center of Pediatric Hematology, Moscow, Russian Federation,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow, Russian Federation
| | - Petra Bacher
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany,Institute of Immunology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel, Kiel, Schleswig-Holstein, Germany
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7
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Alexander KL, Zhao Q, Reif M, Rosenberg AF, Mannon PJ, Duck LW, Elson CO. Human Microbiota Flagellins Drive Adaptive Immune Responses in Crohn's Disease. Gastroenterology 2021; 161:522-535.e6. [PMID: 33844987 PMCID: PMC8489510 DOI: 10.1053/j.gastro.2021.03.064] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 03/26/2021] [Accepted: 03/30/2021] [Indexed: 12/22/2022]
Abstract
BACKGROUND AND AIMS Crohn's disease and ulcerative colitis are characterized by dysregulated adaptive immune responses to the microbiota in genetically susceptible individuals, but the specificity of these responses remains largely undefined. Therefore, we developed a microbiota antigen microarray to characterize microbial antibody reactivity, particularly to human-derived microbiota flagellins, in inflammatory bowel disease. METHODS Sera from healthy volunteers (n = 87) at the University of Alabama at Birmingham and from patients recruited from the Kirklin Clinic of University of Alabama at Birmingham Hospital, including patients with Crohn's disease (n = 152) and ulcerative colitis (n = 170), were individually probed against microbiota bacterial flagellins of both mouse and human origin and analyzed for IgG and IgA antibody responses. Circulating flagellin-reactive T effector (CD4+CD154+) and T regulatory (CD4+CD137+) cells were isolated and evaluated in selected patients. Resulting adaptive immune responses were compared with corresponding clinical data to determine relevancy to disease behavior. RESULTS We show that patients with IBD express selective patterns of antibody reactivity to microbiota flagellins. Patients with Crohn's disease, but not patients with ulcerative colitis, display augmented serum IgG to human ileal-localized Lachnospiraceae flagellins, with a subset of patients having high responses to more than 10 flagellins. Elevated responses to CBir1, a mouse Lachnospiraceae flagellin used clinically to diagnose CD, correlated with multi-Lachnospiraceae flagellin reactivity. In this subset of patients with CD, multi-flagellin reactivity was associated with elevated flagellin-specific CD154+CD45RA- T memory cells, a reduced ratio of flagellin-reactive CD4+ T regulatory to T effector cells, and a high frequency of disease complications. CONCLUSIONS Patients with Crohn's disease display strong adaptive immune response to human-derived Lachnospiraceae flagellins, which may be targeted for prognosis and future personalized therapies.
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Affiliation(s)
- Katie L. Alexander
- Department of Medicine, University of Alabama at
Birmingham, Birmingham, Alabama
| | - Qing Zhao
- Department of Medicine, University of Alabama at
Birmingham, Birmingham, Alabama
| | - Meagan Reif
- Department of Medicine, University of Alabama at
Birmingham, Birmingham, Alabama
| | - Alexander F. Rosenberg
- Department of Microbiology, University of Alabama at
Birmingham, Birmingham, Alabama,Informatics Institute, University of Alabama at Birmingham,
Birmingham, Alabama
| | - Peter J. Mannon
- Department of Medicine, University of Alabama at
Birmingham, Birmingham, Alabama,Birmingham Veterans Affairs Medical Center, Medical
Service, Birmingham, Alabama
| | - Lennard Wayne Duck
- Department of Medicine, University of Alabama at
Birmingham, Birmingham, Alabama
| | - Charles O. Elson
- Department of Medicine, University of Alabama at
Birmingham, Birmingham, Alabama,Department of Microbiology, University of Alabama at
Birmingham, Birmingham, Alabama
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8
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Song R, Jia X, Zhao J, Du P, Zhang JA. T cell receptor revision and immune repertoire changes in autoimmune diseases. Int Rev Immunol 2021; 41:517-533. [PMID: 34243694 DOI: 10.1080/08830185.2021.1929954] [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] [Indexed: 10/20/2022]
Abstract
Autoimmune disease (AID) is a condition in which the immune system breaks down and starts to attack the body. Some common AIDs include systemic lupus erythematosus, rheumatoid arthritis, type 1 diabetes mellitus and so forth. The changes in T-cell receptor (TCR) repertoire have been found in several autoimmune diseases, and may be responsible for the breakdown of peripheral immune tolerance. In this review, we discussed the processes of TCR revision in peripheral immune environment, the changes in TCR repertoire that occurred in various AIDs, and the specifically expanded T cell clones. We hope our discussion can provide insights for the future studies, helping with the discovery of disease biomarkers and expanding the strategies of immune-targeted therapy. HighlightsRestricted TCR repertoire and biased TCR-usage are found in a variety of AIDs.TCR repertoire shows tissue specificity in a variety of AID diseases.The relationship between TCR repertoire diversity and disease activity is still controversial in AIDs.Dominant TCR clonotypes may help to discover new disease biomarkers and expand the strategies of immune-targeted therapy.
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Affiliation(s)
- Ronghua Song
- Department of Endocrinology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Xi Jia
- Department of Endocrinology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Jing Zhao
- Department of Endocrinology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Peng Du
- Department of Endocrinology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Jin-An Zhang
- Department of Endocrinology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
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9
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Morgan NN, Mannon PJ. Flagellin-Specific CD4 Cytokine Production in Crohn Disease and Controls Is Limited to a Small Subset of Antigen-Induced CD40L + T Cells. THE JOURNAL OF IMMUNOLOGY 2021; 206:345-354. [PMID: 33298614 DOI: 10.4049/jimmunol.2000918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/12/2020] [Indexed: 01/19/2023]
Abstract
Flagellin is an immunodominant Ag in Crohn disease, with many patients showing anti-flagellin Abs. To study the clonality of flagellin-reactive CD4 cells in Crohn patients, we used a common CD154-based enrichment method following short-term Ag exposure to identify Ag-reactive CD4 cells. CD154 expression and cytokine production following Ag exposure compared with negative control responses (no Ag exposure) revealed that only a small fraction of CD154-enriched cells could be defined by Ag-reactive cytokine responses. This was especially true for low-frequency flagellin-reactive CD4 cells compared with polyclonal stimulation or Candida albicans Ag exposure. Moreover, we found that culture conditions used for the assay contributed to background CD40L (CD154) expression in the CD154-enriched CD4 cells. Using a cut-off rule based on flow cytometry results of the negative control CD154-enriched CD4 cells, we could reliably find the fraction of Ag-reactive cells in the CD154-enriched population. Ag-reactive CD4 cytokine production was restricted to CD4 cells with an effector memory phenotype and the highest levels of induced CD154 expression. This has important implications for identifying Ag-specific T cells of interest for single cell cloning, phenotyping, and transcriptomics.
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Affiliation(s)
- Nadine N Morgan
- Department of Medicine and Program in Immunology, University of Alabama at Birmingham, Birmingham, AL 35294; and
| | - Peter J Mannon
- Birmingham VA Medical Center, Medical Service and Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233
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10
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Niu X, Li S, Li P, Pan W, Wang Q, Feng Y, Mo X, Yan Q, Ye X, Luo J, Qu L, Weber D, Byrne-Steele ML, Wang Z, Yu F, Li F, Myers RM, Lotze MT, Zhong N, Han J, Chen L. Longitudinal Analysis of T and B Cell Receptor Repertoire Transcripts Reveal Dynamic Immune Response in COVID-19 Patients. Front Immunol 2020; 11:582010. [PMID: 33117392 PMCID: PMC7561365 DOI: 10.3389/fimmu.2020.582010] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 09/15/2020] [Indexed: 01/08/2023] Open
Abstract
Severe COVID-19 is associated with profound lymphopenia and an elevated neutrophil to lymphocyte ratio. We applied a novel dimer avoidance multiplexed polymerase chain reaction next-generation sequencing assay to analyze T (TCR) and B cell receptor (BCR) repertoires. Surprisingly, TCR repertoires were markedly diminished during the early onset of severe disease but recovered during the convalescent stage. Monitoring TCR repertoires could serve as an indicative biomarker to predict disease progression and recovery. Panoramic concurrent assessment of BCR repertoires demonstrated isotype switching and a transient but dramatic early IgA expansion. Dominant B cell clonal expansion with decreased diversity occurred following recovery from infection. Profound changes in T cell homeostasis raise critical questions about the early events in COVID-19 infection and demonstrate that immune repertoire analysis is a promising method for evaluating emergent host immunity to SARS-CoV-2 viral infection, with great implications for assessing vaccination and other immunological therapies.
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Affiliation(s)
- Xuefeng Niu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Song Li
- Jiangsu Industrial Technology Research Institute (JITRI), Applied Adaptome Immunology Institute, Nanjing, China.,iRepertoire Inc., Huntsville, AL, United States
| | - Pingchao Li
- Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Wenjing Pan
- iRepertoire Inc., Huntsville, AL, United States.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Qian Wang
- Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ying Feng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaoneng Mo
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Qihong Yan
- Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xianmiao Ye
- Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jia Luo
- Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Linbing Qu
- Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | | | | | - Zhe Wang
- Jiangsu Industrial Technology Research Institute (JITRI), Applied Adaptome Immunology Institute, Nanjing, China
| | - Fengjia Yu
- Jiangsu Industrial Technology Research Institute (JITRI), Applied Adaptome Immunology Institute, Nanjing, China
| | - Fang Li
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Michael T Lotze
- Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jian Han
- Jiangsu Industrial Technology Research Institute (JITRI), Applied Adaptome Immunology Institute, Nanjing, China.,iRepertoire Inc., Huntsville, AL, United States.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Ling Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
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11
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Ye X, Wang Z, Ye Q, Zhang J, Huang P, Song J, Li Y, Zhang H, Song F, Xuan Z, Wang K. High-Throughput Sequencing-Based Analysis of T Cell Repertoire in Lupus Nephritis. Front Immunol 2020; 11:1618. [PMID: 32849548 PMCID: PMC7423971 DOI: 10.3389/fimmu.2020.01618] [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: 02/24/2020] [Accepted: 06/17/2020] [Indexed: 12/22/2022] Open
Abstract
T cell receptor (TCR)-mediated immune functions are closely related to autoimmune diseases, such as systemic lupus erythematosus (SLE). However, technical challenges used to limit the accurate profiling of TCR diversity in SLE and the characteristics of SLE patients remain largely unknown. In this study, we collected peripheral blood samples from 10 SLE patients with lupus nephritis (LN) who were confirmed by renal biopsy, as well as 10 healthy controls. The TCR repertoire of each sample was assessed by high-throughput sequencing to examine the distinction between SLE subjects and healthy controls. Our results showed statistically significant differences in TCR diversity and usage of TRBV/TRBJ genes between the two groups. A set of signature V–J combinations enabled efficient identification of SLE cases, yielding an area under the curve (AUC) of 0.89 (95% CI: 0.74–1.00). Taken together, our results revealed the potential correlation between the TCR repertoire and SLE status, which may facilitate the development of novel immune biomarkers.
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Affiliation(s)
- Xiaolan Ye
- Department of Pharmacy, People's Hospital of Hangzhou Medical College, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Zhe Wang
- National Engineering Research Center for Protein Drugs, Beijing, China.,GS Medical (Beijing) Technology Development LLC, Beijing, China.,JITRI Applied Adaptome Immunology Institute, Nanjing, China
| | - Qiang Ye
- Department of Pharmacy, People's Hospital of Hangzhou Medical College, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Jing Zhang
- National Engineering Research Center for Protein Drugs, Beijing, China.,GS Medical (Beijing) Technology Development LLC, Beijing, China
| | - Ping Huang
- Department of Pharmacy, People's Hospital of Hangzhou Medical College, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Jingying Song
- Department of Nephrology, Changed Central Hospital, Chengde, China
| | - Yiwen Li
- Department of Nephrology, People's Hospital of Hangzhou Medical College, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Hongjuan Zhang
- Department of Nephrology, People's Hospital of Hangzhou Medical College, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Feifeng Song
- Department of Pharmacy, People's Hospital of Hangzhou Medical College, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Zixue Xuan
- Department of Pharmacy, People's Hospital of Hangzhou Medical College, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Kejian Wang
- Lin He's Academician Workstation of New Medicine and Clinical Translation at The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
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12
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Sethna Z, Elhanati Y, Callan CG, Walczak AM, Mora T. OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs. Bioinformatics 2020; 35:2974-2981. [PMID: 30657870 PMCID: PMC6735909 DOI: 10.1093/bioinformatics/btz035] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 11/10/2018] [Accepted: 01/13/2019] [Indexed: 01/08/2023] Open
Abstract
MOTIVATION High-throughput sequencing of large immune repertoires has enabled the development of methods to predict the probability of generation by V(D)J recombination of T- and B-cell receptors of any specific nucleotide sequence. These generation probabilities are very non-homogeneous, ranging over 20 orders of magnitude in real repertoires. Since the function of a receptor really depends on its protein sequence, it is important to be able to predict this probability of generation at the amino acid level. However, brute-force summation over all the nucleotide sequences with the correct amino acid translation is computationally intractable. The purpose of this paper is to present a solution to this problem. RESULTS We use dynamic programming to construct an efficient and flexible algorithm, called OLGA (Optimized Likelihood estimate of immunoGlobulin Amino-acid sequences), for calculating the probability of generating a given CDR3 amino acid sequence or motif, with or without V/J restriction, as a result of V(D)J recombination in B or T cells. We apply it to databases of epitope-specific T-cell receptors to evaluate the probability that a typical human subject will possess T cells responsive to specific disease-associated epitopes. The model prediction shows an excellent agreement with published data. We suggest that OLGA may be a useful tool to guide vaccine design. AVAILABILITY AND IMPLEMENTATION Source code is available at https://github.com/zsethna/OLGA. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zachary Sethna
- Joseph Henry Laboratories, Princeton University, Princeton, NJ, USA
| | - Yuval Elhanati
- Joseph Henry Laboratories, Princeton University, Princeton, NJ, USA
| | - Curtis G Callan
- Joseph Henry Laboratories, Princeton University, Princeton, NJ, USA.,Laboratoire de physique de l'Ecole normale supérieure (PSL University), Centre national de la recherche scientifique, Sorbonne University, University Paris-Diderot, Paris, France
| | - Aleksandra M Walczak
- Laboratoire de physique de l'Ecole normale supérieure (PSL University), Centre national de la recherche scientifique, Sorbonne University, University Paris-Diderot, Paris, France
| | - Thierry Mora
- Laboratoire de physique de l'Ecole normale supérieure (PSL University), Centre national de la recherche scientifique, Sorbonne University, University Paris-Diderot, Paris, France
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13
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Clough JN, Omer OS, Tasker S, Lord GM, Irving PM. Regulatory T-cell therapy in Crohn's disease: challenges and advances. Gut 2020; 69:942-952. [PMID: 31980447 PMCID: PMC7229901 DOI: 10.1136/gutjnl-2019-319850] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/21/2019] [Accepted: 12/19/2019] [Indexed: 12/12/2022]
Abstract
The prevalence of IBD is rising in the Western world. Despite an increasing repertoire of therapeutic targets, a significant proportion of patients suffer chronic morbidity. Studies in mice and humans have highlighted the critical role of regulatory T cells in immune homeostasis, with defects in number and suppressive function of regulatory T cells seen in patients with Crohn's disease. We review the function of regulatory T cells and the pathways by which they exert immune tolerance in the intestinal mucosa. We explore the principles and challenges of manufacturing a cell therapy, and discuss clinical trial evidence to date for their safety and efficacy in human disease, with particular focus on the development of a regulatory T-cell therapy for Crohn's disease.
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Affiliation(s)
- Jennie N Clough
- School of Immunology and Microbial Sciences, King's College London, London, UK
- NIHR Biomedical Research Centre at Guy's and Saint Thomas' NHS Foundation Trust and King's College, London, UK
| | - Omer S Omer
- School of Immunology and Microbial Sciences, King's College London, London, UK
- Department of Gastroenterology, Guy's and Saint Thomas' Hospitals NHS Trust, London, UK
| | - Scott Tasker
- Division of Transplantation Immunology and Mucosal Biology, King's College London, London, UK
| | - Graham M Lord
- School of Immunology and Microbial Sciences, King's College London, London, UK
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Peter M Irving
- School of Immunology and Microbial Sciences, King's College London, London, UK
- Department of Gastroenterology, Guy's and Saint Thomas' Hospitals NHS Trust, London, UK
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14
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Genomic profiling of intestinal T-cell receptor repertoires in inflammatory bowel disease. Genes Immun 2020; 21:109-118. [PMID: 32029881 DOI: 10.1038/s41435-020-0092-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 01/11/2020] [Accepted: 01/21/2020] [Indexed: 12/11/2022]
Abstract
Growing evidence shows that inflammatory bowel disease (IBD) results from dysregulation of immune responses to gut microbes. T-cell receptors (TCRs) expressed on the T-cell surface play critical roles in discriminating pathogens from commensal intestinal microorganisms at the front line of the adaptive immune system. The breakdown of this interaction may trigger persistent inflammatory responses to gut bacteria, resulting in IBD. Taking advantage of high-throughput sequencing, we developed an integrated approach to dissect the intestinal TCR repertoires underlying IBD by collecting peripheral blood and inflamed intestine from the same set of 11 IBD cases. The intestinal TCR repertoires show lower clonotype diversity (p < 0.05) and stronger clonal expansion (p < 0.02) than those in the blood. This pattern becomes more profound in TCRs unique to the inflamed tissue compared with shared TCRs. Our approach further identified the increased usage of TRAV12-3 (false discovery rate, FDR < 5%), which biases its choices of J genes towards the reduction of TRAJ37 and TRAJ43 usage (FDR < 20%) in the inflamed intestine. Our genomic profiling suggests that this selective bias of V and J gene usage may lead to a loss of diversity in the intestinal TCR repertoires and result in mucosal inflammation in IBD.
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15
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Graham DB, Xavier RJ. Pathway paradigms revealed from the genetics of inflammatory bowel disease. Nature 2020; 578:527-539. [PMID: 32103191 PMCID: PMC7871366 DOI: 10.1038/s41586-020-2025-2] [Citation(s) in RCA: 354] [Impact Index Per Article: 88.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/10/2019] [Indexed: 12/13/2022]
Abstract
Inflammatory bowel disease (IBD) is a complex genetic disease that is instigated and amplified by the confluence of multiple genetic and environmental variables that perturb the immune-microbiome axis. The challenge of dissecting pathological mechanisms underlying IBD has led to the development of transformative approaches in human genetics and functional genomics. Here we describe IBD as a model disease in the context of leveraging human genetics to dissect interactions in cellular and molecular pathways that regulate homeostasis of the mucosal immune system. Finally, we synthesize emerging insights from multiple experimental approaches into pathway paradigms and discuss future prospects for disease-subtype classification and therapeutic intervention.
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Affiliation(s)
- Daniel B. Graham
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.,Corresponding authors. ,
| | - Ramnik J. Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.,Corresponding authors. ,
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