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Tippalagama R, Chihab LY, Kearns K, Lewis S, Panda S, Willemsen L, Burel JG, Lindestam Arlehamn CS. Antigen-specificity measurements are the key to understanding T cell responses. Front Immunol 2023; 14:1127470. [PMID: 37122719 PMCID: PMC10140422 DOI: 10.3389/fimmu.2023.1127470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/30/2023] [Indexed: 05/02/2023] Open
Abstract
Antigen-specific T cells play a central role in the adaptive immune response and come in a wide range of phenotypes. T cell receptors (TCRs) mediate the antigen-specificities found in T cells. Importantly, high-throughput TCR sequencing provides a fingerprint which allows tracking of specific T cells and their clonal expansion in response to particular antigens. As a result, many studies have leveraged TCR sequencing in an attempt to elucidate the role of antigen-specific T cells in various contexts. Here, we discuss the published approaches to studying antigen-specific T cells and their specific TCR repertoire. Further, we discuss how these methods have been applied to study the TCR repertoire in various diseases in order to characterize the antigen-specific T cells involved in the immune control of disease.
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Mijnheer G, Servaas NH, Leong JY, Boltjes A, Spierings E, Chen P, Lai L, Petrelli A, Vastert S, de Boer RJ, Albani S, Pandit A, van Wijk F. Compartmentalization and persistence of dominant (regulatory) T cell clones indicates antigen skewing in juvenile idiopathic arthritis. eLife 2023; 12:79016. [PMID: 36688525 PMCID: PMC9995115 DOI: 10.7554/elife.79016] [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: 03/29/2022] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
Autoimmune inflammation is characterized by tissue infiltration and expansion of antigen-specific T cells. Although this inflammation is often limited to specific target tissues, it remains yet to be explored whether distinct affected sites are infiltrated with the same, persistent T cell clones. Here, we performed CyTOF analysis and T cell receptor (TCR) sequencing to study immune cell composition and (hyper-)expansion of circulating and joint-derived Tregs and non-Tregs in juvenile idiopathic arthritis (JIA). We studied different joints affected at the same time, as well as over the course of relapsing-remitting disease. We found that the composition and functional characteristics of immune infiltrates are strikingly similar between joints within one patient, and observed a strong overlap between dominant T cell clones, especially Treg, of which some could also be detected in circulation and persisted over the course of relapsing-remitting disease. Moreover, these T cell clones were characterized by a high degree of sequence similarity, indicating the presence of TCR clusters responding to the same antigens. These data suggest that in localized autoimmune disease, there is autoantigen-driven expansion of both Teffector and Treg clones that are highly persistent and are (re)circulating. These dominant clones might represent interesting therapeutic targets.
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Affiliation(s)
- Gerdien Mijnheer
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht UniversityUtrechtNetherlands
| | - Nila Hendrika Servaas
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht UniversityUtrechtNetherlands
| | - Jing Yao Leong
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the AcademiaSingaporeSingapore
| | - Arjan Boltjes
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht UniversityUtrechtNetherlands
| | - Eric Spierings
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht UniversityUtrechtNetherlands
| | - Phyllis Chen
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the AcademiaSingaporeSingapore
| | - Liyun Lai
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the AcademiaSingaporeSingapore
| | - Alessandra Petrelli
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht UniversityUtrechtNetherlands
| | - Sebastiaan Vastert
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht UniversityUtrechtNetherlands
- Pediatric Immunology & Rheumatology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht UniversityUtrechtNetherlands
| | - Rob J de Boer
- Theoretical Biology, Utrecht UniversityUtrechtNetherlands
| | - Salvatore Albani
- Translational Immunology Institute, Singhealth/Duke-NUS Academic Medical Centre, the AcademiaSingaporeSingapore
| | - Aridaman Pandit
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht UniversityUtrechtNetherlands
| | - Femke van Wijk
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht UniversityUtrechtNetherlands
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Safra M, Werner L, Peres A, Polak P, Salamon N, Schvimer M, Weiss B, Barshack I, Shouval DS, Yaari G. A somatic hypermutation-based machine learning model stratifies individuals with Crohn's disease and controls. Genome Res 2023; 33:71-79. [PMID: 36526432 PMCID: PMC9977146 DOI: 10.1101/gr.276683.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022]
Abstract
Crohn's disease (CD) is a chronic relapsing-remitting inflammatory disorder of the gastrointestinal tract that is characterized by altered innate and adaptive immune function. Although massively parallel sequencing studies of the T cell receptor repertoire identified oligoclonal expansion of unique clones, much less is known about the B cell receptor (BCR) repertoire in CD. Here, we present a novel BCR repertoire sequencing data set from ileal biopsies from pediatric patients with CD and controls, and identify CD-specific somatic hypermutation (SHM) patterns, revealed by a machine learning (ML) algorithm trained on BCR repertoire sequences. Moreover, ML classification of a different data set from blood samples of adults with CD versus controls identified that V gene usage, clusters, or mutation frequencies yielded excellent results in classifying the disease (F1 > 90%). In summary, we show that an ML algorithm enables the classification of CD based on unique BCR repertoire features with high accuracy.
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Affiliation(s)
- Modi Safra
- The Alexander Kofkin Faculty of Engineering, Bar Ilan University, 5290002, Ramat Gan, Israel;,Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Lael Werner
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center of Israel, Petah Tikva 4920235, Israel;,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Ayelet Peres
- The Alexander Kofkin Faculty of Engineering, Bar Ilan University, 5290002, Ramat Gan, Israel;,Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Pazit Polak
- The Alexander Kofkin Faculty of Engineering, Bar Ilan University, 5290002, Ramat Gan, Israel;,Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002, Ramat Gan, Israel
| | - Naomi Salamon
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan 5262100, Israel
| | - Michael Schvimer
- Institute of Pathology, Sheba Medical Center, Ramat Gan 5262100, Israel
| | - Batia Weiss
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel;,Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan 5262100, Israel
| | - Iris Barshack
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel;,Institute of Pathology, Sheba Medical Center, Ramat Gan 5262100, Israel
| | - Dror S. Shouval
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center of Israel, Petah Tikva 4920235, Israel;,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Gur Yaari
- The Alexander Kofkin Faculty of Engineering, Bar Ilan University, 5290002, Ramat Gan, Israel;,Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, 5290002, Ramat Gan, Israel
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4
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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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Hong SN, Park JY, Yang SY, Lee C, Kim YH, Joung JG. Reduced diversity of intestinal T-cell receptor repertoire in patients with Crohn’s disease. Front Cell Infect Microbiol 2022; 12:932373. [PMID: 36034703 PMCID: PMC9401206 DOI: 10.3389/fcimb.2022.932373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/12/2022] [Indexed: 11/29/2022] Open
Abstract
Background The intestinal microenvironment directly determines the human T-cell receptor (TCR) repertoire. Despite its extreme diversity, TCR repertoire analysis may provide a better understanding of the immune system in patients with inflammatory bowel disease. Methods To investigate TCR repertoires in the intestinal mucosa, RNA sequencing was performed for inflamed and non-inflamed intestinal mucosa samples obtained from 13 patients with Crohn’s disease (CD) and healthy mucosa from nine non-IBD controls. Results The gene expression frequency of the TCR repertoire showed a clear separation between inflamed mucosa of patients with CD and healthy mucosa of non-IBD controls in the hierarchical clustering heatmap. The richness of TCR repertoires measured by the Chao1 index did not show a significant difference among groups, whereas diversity measured by the D50 diversity index was decreased in the inflamed mucosa of CD patients. Rare/small TCR clonotypes occupied a large proportion of TCR repertoires in healthy mucosa of controls, whereas expanded clonotypes were common in inflamed mucosa of patients with CD. Segment usages of TRAV2, TRAV22, TRAV40, TRJ14, TRAJ51, TRBV1, TRBV21.1, and TRBJ1.5 were significantly decreased in CD patients. KEGG enrichment analysis identified the enrichment of several KEGG pathways, including inflammatory bowel disease (p = 0.0012), Th1 and Th2 cell differentiation (p = 0.0011), and intestinal immune network for IgA production (p = 0.0468). Conclusions The diversity of the TCR repertoire is reduced in inflamed mucosa of CD patients, which might contribute to intestinal inflammation.
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Affiliation(s)
- Sung Noh Hong
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
- Stem Cell & Regenerative Medicine Center, Samsung Medical Center, Seoul, South Korea
- *Correspondence: Sung Noh Hong, ; ; Je-Gun Joung,
| | - Joo-Young Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - So-Yun Yang
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Chansu Lee
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
- Stem Cell & Regenerative Medicine Center, Samsung Medical Center, Seoul, South Korea
| | - Young-Ho Kim
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Je-Gun Joung
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam, South Korea
- *Correspondence: Sung Noh Hong, ; ; Je-Gun Joung,
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Hu M, Chen Z, Liao Y, Wu J, Zheng D, Zhang H. Clinical value of the expression levels of protein tyrosine phosphatase non-receptor type 22.6 mRNA in peripheral blood mononuclear cells in Crohn's disease. Clin Exp Immunol 2022; 209:311-315. [PMID: 35751647 PMCID: PMC9521657 DOI: 10.1093/cei/uxac061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/16/2022] [Accepted: 06/24/2022] [Indexed: 01/23/2023] Open
Abstract
OBJECTIVE To explore the relationship between the expression levels of protein tyrosine phosphatase non-receptor type (PTPN) 22.6 mRNA in peripheral blood mononuclear cells (PBMCs) and the disease activity as well as clinical characteristics in Crohn's disease (CD) patients. METHODS A total of 480 subjects were enrolled. Data were collected including baseline information, expression levels of PTPN22.6 mRNA in PBMCs for all subjects, C-reactive protein (CRP) levels in serum, clinical characteristics, and disease activity for all patients. Expression levels of PTPN22.6 mRNA in PBMCs, CRP levels in serum, clinical characteristics according to Montreal Classification [8], and Crohn's disease activity index (CDAI) were the primary observation outcomes. RESULTS The expression levels of PTPN22.6 mRNA (P = 0.032) in PBMCs and serum CRP levels (P < 0.001) were significantly higher in active CD patients than in inactive CD patients (P = 0.032). Correlation analysis showed that there was a positive correlation between expression levels of PTPN22.6 mRNA and CDAI value (r = 0.512, P = 0.003), as well as expression levels of PTPN22.6 mRNA and CRP levels in the CD group (r = 0.456, P = 0.006). There were significantly higher expression levels of PTPN22.6 mRNA in PBMCs in patients with structuring behavior than that in patients with non-stricturing and non-penetrating (NSNP) behaviors (P = 0.018) and penetrating behaviors (P = 0.024). CONCLUSIONS The expression levels of PTPN22.6 mRNA can be used as an indicator to help predict CD diagnosis, disease activity, serum CRP level, and behavior type of CD disease.
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Affiliation(s)
| | | | - Yusheng Liao
- Department of Gastroenterology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology; Key Laboratory for Molecular Diagnosis of Hubei Province, Wuhan, People’s Republic of China
| | - Jie Wu
- Department of Gastroenterology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology; Key Laboratory for Molecular Diagnosis of Hubei Province, Wuhan, People’s Republic of China
| | - Dan Zheng
- Department of Gastroenterology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology; Key Laboratory for Molecular Diagnosis of Hubei Province, Wuhan, People’s Republic of China
| | - Heng Zhang
- Correspondence: Heng Zhang, Department of Gastroenterology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology Sheng Li Street 26, Wuhan 430014, Hubei Province, People’s Republic of China.
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7
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Bachour SP, Shah RS, Rieder F, Qazi T, Achkar JP, Philpott J, Lashner B, Holubar SD, Lightner AL, Barnes EL, Axelrad J, Regueiro M, Click B, Cohen BL. Intra-abdominal septic complications after ileocolic resection increases risk for endoscopic and surgical postoperative Crohn's disease recurrence. J Crohns Colitis 2022; 16:1696-1705. [PMID: 35705188 PMCID: PMC9924045 DOI: 10.1093/ecco-jcc/jjac078] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND Postoperative recurrence [POR] of Crohn's disease following ileocolonic resection is common. The impact of immediate postoperative intra-abdominal septic complications [IASC] on endoscopic and surgical recurrence has not been elucidated. AIMS To evaluate if IASC is associated with an increased risk for endoscopic and surgical POR. METHODS This was a retrospective study of adult Crohn's disease patients undergoing ileocolonic resection with primary anastomosis between 2009 and 2020. IASC was defined as anastomotic leak or intra-abdominal abscess within 90 days of the date of surgery. Multivariable logistic and Cox proportional hazard modelling were performed to assess the impact of IASC on endoscopic POR [modified Rutgeerts' score ≥ i2b] at index postoperative ileocolonoscopy and long-term surgical recurrence. RESULTS In 535 Crohn's disease patients [median age 35 years, 22.1% active smokers, 35.7% one or more prior resection] had an ileocolonic resection with primary anastomosis. A minority of patients [N = 47; 8.8%] developed postoperative IASC. In total, 422 [78.9%] patients had one or more postoperative ileocolonoscopies, of whom 163 [38.6%] developed endoscopic POR. After adjusting for other risk factors for postoperative recurrence, postoperative IASC was associated with significantly greater odds (adjusted odds ratio [aOR]: 2.45 [1.23-4.97]; p = 0.01) and decreased time (adjusted hazards ratio [aHR]: 1.60 [1.04-2.45]; p = 0.03] to endoscopic POR. Furthermore, IASC was associated with increased risk (aOR: 2.3 [1.04-4.87] p = 0.03) and decreased survival-free time [aHR: 2.53 [1.31-4.87]; p = 0.006] for surgical recurrence. CONCLUSION IASC is associated with an increased risk for endoscopic and surgical POR of Crohn's disease. Preoperative optimization to prevent IASC, in addition to postoperative biological prophylaxis, may help reduce the risk for endoscopic and surgical POR.
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Affiliation(s)
- Salam P Bachour
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA
| | - Ravi S Shah
- Cleveland Clinic Department of Gastroenterology, Hepatology, and Nutrition, Cleveland, OH, USA
| | - Florian Rieder
- Cleveland Clinic Department of Gastroenterology, Hepatology, and Nutrition, Cleveland, OH, USA,Department of Inflammation and Immunity, Lerner Research Institute, Cleveland, OH, USA
| | - Taha Qazi
- Cleveland Clinic Department of Gastroenterology, Hepatology, and Nutrition, Cleveland, OH, USA
| | - Jean Paul Achkar
- Cleveland Clinic Department of Gastroenterology, Hepatology, and Nutrition, Cleveland, OH, USA
| | - Jessica Philpott
- Cleveland Clinic Department of Gastroenterology, Hepatology, and Nutrition, Cleveland, OH, USA
| | - Bret Lashner
- Cleveland Clinic Department of Gastroenterology, Hepatology, and Nutrition, Cleveland, OH, USA
| | - Stefan D Holubar
- Cleveland Clinic Department of Colorectal Surgery, Cleveland, OH, USA
| | - Amy L Lightner
- Cleveland Clinic Department of Colorectal Surgery, Cleveland, OH, USA
| | - Edward L Barnes
- University of North Carolina at Chapel Hill, Division of Gastroenterology and Hepatology, Chapel Hill, NC, USA
| | - Jordan Axelrad
- New York University Department of Gastroenterology and Hepatology, New York, NY, USA
| | - Miguel Regueiro
- Cleveland Clinic Department of Gastroenterology, Hepatology, and Nutrition, Cleveland, OH, USA
| | - Benjamin Click
- Cleveland Clinic Department of Gastroenterology, Hepatology, and Nutrition, Cleveland, OH, USA
| | - Benjamin L Cohen
- Correspondence: Benjamin L. Cohen, MD, MAS, Cleveland Clinic Department of Gastroenterology, Hepatology, and Nutrition, 9500 Euclid Ave., A30, Cleveland, OH, 44195, USA.
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8
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Jia X, Zhai TY, Wang B, Zhang JA, Song RH. High-throughput T cell receptor sequencing reveals differential immune repertoires in autoimmune thyroid diseases. Mol Cell Endocrinol 2022; 550:111644. [PMID: 35429598 DOI: 10.1016/j.mce.2022.111644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/30/2022] [Accepted: 04/03/2022] [Indexed: 01/16/2023]
Abstract
BACKGROUND Autoimmune thyroid diseases (AITDs) are chronic autoimmune diseases specific to thyroid and mainly include Graves' disease (GD) and Hashimoto' thyroiditis (HT). The adaptive immunoreactivity of CD4+ T cells plays a crucial role in the pathogenesis of AITDs, but very little has been known about its changes in disease status. METHODS We collected peripheral CD4+ T cells from 12 GD patients, including 6 newly diagnosed GD (NGD) and 6 refractory GD (RGD) patients, 6 HT patients and 6 healthy controls, and examined the gene expression profiles and colon types of T cells receptor (TCR) β chain complementarity determining region 3 (CDR3) using high-throughput sequencing. RESULTS The TCR repertoire were significantly expanded in AITDs groups, and some TCR genes were expressed more preferentially in AITDs group than in the healthy control group, including TRBV15 (P = 0.001), TRBV4-2 (P = 0.003), TRBV9 (P = 0.007), TRBV3-2 (P = 0.012), TRBV7-8 (P = 0.015), TRBV25-1 (P = 0.019), TRBV12-4 (P = 0.019) and TRBV27 (P = 0.02) in GD patients as well as TRBV29-1 (P = 0.004), TRBV12-4 (P = 0.004), TRBV6-5 (P = 0.011), TRBV7-2 (P = 0.012), TRBV27 (P = 0.012), TRBV9 (P = 0.031) and TRBV4-2 (P = 0.032) in HT patients. Moreover, subgroup analysis showed that the difference in the TCR spectrum between the normal group and NGD was not obvious, but a large number of differential genes appeared in the RGD group. CONCLUSION TCR spectrum has changed in patients with AITDs with expanded repertoire and many upregulated TRBV genes. Moreover, this difference is not apparent in GD patients at the initial stage, but as the disease progresses, the differences in TCR profiles became more pronounced.
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Affiliation(s)
- Xi Jia
- Department of Endocrinology and Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, China
| | - Tian-Yu Zhai
- Department of Endocrinology, Zhongshan Hospital of Fudan University, China
| | - Bing Wang
- Department of Endocrinology and Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, China
| | - Jin-An Zhang
- Department of Endocrinology and Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, China.
| | - Rong-Hua Song
- Department of Endocrinology and Rheumatology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, China.
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9
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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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10
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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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11
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Foth S, Völkel S, Bauersachs D, Zemlin M, Skevaki C. T Cell Repertoire During Ontogeny and Characteristics in Inflammatory Disorders in Adults and Childhood. Front Immunol 2021; 11:611573. [PMID: 33633732 PMCID: PMC7899981 DOI: 10.3389/fimmu.2020.611573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/22/2020] [Indexed: 12/17/2022] Open
Abstract
Since the first day of life, a newborn has to deal with various pathogens from the environment. While passive immune protection is provided by diaplacental maternal antibodies, the development of cellular immunity is ongoing. A mature immune system should be able not only to defend against pathogens, but should also be able to differentiate between self- and non-self-antigens. Dysregulation in the development of cellular immunity can lead to severe disorders like immunodeficiency, autoimmunity and chronic inflammation. In this review, we explain the role of T cell immunity in antigen detection and summarize the characteristics of a mature TCR repertoire as well as the current state of knowledge about the development of the TCR repertoire in ontogenesis. In addition, methods of assessments are outlined, with a focus on the advantages and disadvantages of advanced methods such as next generation sequencing. Subsequently, we provide an overview of various disorders occuring in early childhood like immunodeficiencies, autoimmunity, allergic diseases and chronic infections and outline known changes in the TCR repertoire. Finally, we summarize the latest findings and discuss current research gaps as well as potential future developments.
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Affiliation(s)
- Svenja Foth
- German Center for Lung Research (DZL), Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, Marburg, Germany
| | - Sara Völkel
- German Center for Lung Research (DZL), Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, Marburg, Germany
| | - Daniel Bauersachs
- German Center for Lung Research (DZL), Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, Marburg, Germany
| | - Michael Zemlin
- Department of General Pediatrics and Neonatology, Saarland University Medical School, Homburg, Germany
| | - Chrysanthi Skevaki
- German Center for Lung Research (DZL), Institute of Laboratory Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, Marburg, Germany
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12
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Immune and TRG repertoire signature of the thymus in Down syndrome patients. Pediatr Res 2021; 89:102-109. [PMID: 32231346 DOI: 10.1038/s41390-020-0857-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 01/10/2020] [Accepted: 03/11/2020] [Indexed: 11/08/2022]
Abstract
BACKGROUND Patients with Down syndrome (DS) are at increased risk for infections and autoimmune disorders. Although several immunological abnormalities were previously found, differences in T cell receptor repertoire have never been shown. Thus we compared the T cell receptor gamma (TRG) repertoire in DS and non-syndromic pediatric patients by next-generation sequencing, in addition to other immunological markers. METHODS Genomic DNA was extracted from thymuses of pediatric patients who underwent heart surgery, where six were with DS and six were non-syndromic patients. Peripheral blood counts, T cell subpopulations, thymus TCR excision circles (TRECs), spectratyping, and next-generation sequencing for TRG were analyzed. RESULTS The mean age of the patients was 7 months and the mean lymphocyte count was slightly lower in patients with DS, whereas thymus TREC results were similar to non-syndromic patients (p = 0.197). The TRG repertoire analysis showed that patients with DS had a significantly larger number of unique TRG sequences, together with decreased clonal expansion. Lastly, the V and J gene usages in the thymus were similar in DS and non-syndromic patients. CONCLUSIONS Patients with DS showed increased TRG repertoire diversity with decreased clonal expansion compared to non-syndromic patients. IMPACT Alterations in T cell receptor gamma repertoire were found in patients with Down syndrome using next-generation sequencing (NGS) technique. Patients showed increased repertoire diversity and decreased clonal expansion compared to controls. These findings add to previous reports on abnormalities of other immune system components in patients with Down syndrome. NGS technique may point out differences not seen by previous methods. Repertoire abnormalities may contribute to those patients' predisposition to infections and autoimmune diseases.
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13
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The Role of Inflammation in Crohn's Disease Recurrence after Surgical Treatment. J Immunol Res 2020; 2020:8846982. [PMID: 33426097 PMCID: PMC7781709 DOI: 10.1155/2020/8846982] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/04/2020] [Accepted: 12/08/2020] [Indexed: 02/08/2023] Open
Abstract
Introduction Postoperative recurrence after surgery for Crohn's disease (CD) is virtually inevitable, and its mechanism is poorly known. Aim To review the numerous factors involved in CD postoperative recurrence (POR) pathogenesis, focusing on single immune system components as well as the immune system as a whole and highlighting the clinical significance in terms of preventive strategies and future perspectives. Methods A systematic literature search on CD POR, followed by a review of the main findings. Results The immune system plays a pivotal role in CD POR, with many different factors involved. Memory T-lymphocytes retained in mesenteric lymph nodes seem to represent the main driving force. New pathophysiology-based preventive strategies in the medical and surgical fields may help reduce POR rates. In particular, surgical strategies have already been developed and are currently under investigation. Conclusions POR is a complex phenomenon, whose driving mechanisms are gradually being unraveled. New preventive strategies addressing these mechanisms seem promising.
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Gamliel A, Werner L, Pinsker M, Salamon N, Weiss B, Shouval DS. Circulating α4β7 + Memory T Cells in Pediatric IBD Patients Express a Polyclonal T Cell Receptor Repertoire. Clin Exp Gastroenterol 2020; 13:439-447. [PMID: 33061522 PMCID: PMC7537844 DOI: 10.2147/ceg.s271565] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 08/21/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The integrin α4β7 is highly expressed on activated T cells and is thought to direct homing of lymphocytes to the intestine. Since ulcerative colitis (UC) and Crohn's disease (CD) are characterized by mucosal oligoclonal T cells' expansion, we aimed to assess whether similar repertoire features are identified in circulating gut-specific memory T cells. METHODS Memory CD3+ T cells were isolated from blood samples of control subjects and patients with active UC or CD and then FACS-sorted into α4β7+ and α4β7- populations. DNA was extracted from each subset and subjected to next-generation sequencing of the TCRβ. Different repertoire characteristics were compared between α4β7+ and α4β7- subsets for each subject, and between groups. RESULTS The percentages of memory T cells and α4β7+ cells were comparable between groups. α4β7+ memory T cells displayed a polyclonal distribution, in control subjects and in UC or CD patients, with similar indices of diversity. Strikingly, the clonal overlap between α4β7+ and α4β7- T cells for each subject in all three groups was high, ranging between 20%-50%. We were unable to identify shared T cell clones that were specific to one of the groups. CONCLUSION α4β7+ memory T cells exhibited a polyclonal repertoire in both control subjects and patients with active inflammatory bowel disease, with high rates of overlap with α4β7- memory T cells. Our study, along with additional recent reports, may suggest that the suppression of intestinal inflammation by vedolizumab is independent of the drug's effect on T cell migration to the gut.
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Affiliation(s)
- Adir Gamliel
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lael Werner
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Marina Pinsker
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat Gan, Israel
- Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Naomi Salamon
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat Gan, Israel
| | - Batia Weiss
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Dror S Shouval
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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15
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Rosati E, Pogorelyy MV, Dowds CM, Moller FT, Sorensen SB, Lebedev YB, Frey N, Schreiber S, Spehlmann ME, Andersen V, Mamedov IZ, Franke A. Identification of Disease-associated Traits and Clonotypes in the T Cell Receptor Repertoire of Monozygotic Twins Affected by Inflammatory Bowel Diseases. J Crohns Colitis 2020; 14:778-790. [PMID: 31711184 PMCID: PMC7346890 DOI: 10.1093/ecco-jcc/jjz179] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND AND AIMS Intestinal inflammation in inflammatory bowel diseases [IBD] is thought to be T cell mediated and therefore dependent on the interaction between the T cell receptor [TCR] and human leukocyte antigen [HLA] proteins expressed on antigen presenting cells. The collection of all TCRs in one individual, known as the TCR repertoire, is characterised by enormous diversity and inter-individual variability. It was shown that healthy monozygotic [MZ] twins are more similar in their TCR repertoire than unrelated individuals. Therefore MZ twins, concordant or discordant for IBD, may be useful to identify disease-related and non-genetic factors in the TCR repertoire which could potentially be used as disease biomarkers. METHODS Employing unique molecular barcoding that can distinguish between polymerase chain reaction [PCR] artefacts and true sequence variation, we performed deep TCRα and TCRβ repertoire profiling of the peripheral blood of 28 MZ twin pairs from Denmark and Germany, 24 of whom were discordant and four concordant for IBD. RESULTS We observed disease- and smoking-associated traits such as sharing, diversity and abundance of specific clonotypes in the TCR repertoire of IBD patients, and particularly in patients with active disease, compared with their healthy twins. CONCLUSIONS Our findings identified TCR repertoire features specific for smokers and IBD patients, particularly when signs of disease activity were present. These findings are a first step towards the application of TCR repertoire analyses as a valuable tool to characterise inflammatory bowel diseases and to identify potential biomarkers and true disease causes.
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MESH Headings
- Adult
- C-Reactive Protein/analysis
- Colitis, Ulcerative/diagnosis
- Colitis, Ulcerative/immunology
- Colitis, Ulcerative/physiopathology
- Crohn Disease/diagnosis
- Crohn Disease/immunology
- Crohn Disease/physiopathology
- Denmark
- Feces
- Female
- Genes, T-Cell Receptor alpha
- Genes, T-Cell Receptor beta
- Germany
- Humans
- Leukocyte L1 Antigen Complex/analysis
- Male
- Patient Acuity
- Receptors, Antigen, T-Cell, alpha-beta/blood
- Sequence Analysis, DNA
- Smoking/immunology
- Twins, Monozygotic
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Affiliation(s)
- Elisa Rosati
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Mikhail V Pogorelyy
- Laboratory of comparative and functional genomic, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
- Department of Translational Medicine, Pirogov Russian National Research Medical University [RNRMU], Moscow, Russian Federation
| | - C Marie Dowds
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Frederik T Moller
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Signe B Sorensen
- Focused Research Unit for Molecular Diagnostic and Clinical Research, University Hospital of Southern Denmark, Aabenraa, Denmark
- Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Yuri B Lebedev
- Laboratory of comparative and functional genomic, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Norbert Frey
- Department of Internal Medicine III, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Stefan Schreiber
- Department of Internal Medicine I, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Martina E Spehlmann
- Department of Internal Medicine III, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Vibeke Andersen
- Focused Research Unit for Molecular Diagnostic and Clinical Research, University Hospital of Southern Denmark, Aabenraa, Denmark
- Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
- IRS-Center Sønderjylland, University of Southern Denmark, Odense, Denmark
| | - Ilgar Z Mamedov
- Laboratory of comparative and functional genomic, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
- Department of Translational Medicine, Pirogov Russian National Research Medical University [RNRMU], Moscow, Russian Federation
- Laboratory of molecular biology, Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
- CEITEC, Masaryk University, Brno, Czech Republic
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- Corresponding author: Andre Franke, Dr. rer. nat.., Institute of Clinical Molecular Biology,Christian-Albrechts-University of Kiel,Rosalind-Franklin-Str. 12,D- 24105 Kiel,Germany. Tel,: 49 179 485 1891;
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16
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Multiple sevoflurane exposures don't disturb the T-cell receptor repertoire in infant rhesus monkeys' thymus. Life Sci 2020; 248:117457. [PMID: 32092334 DOI: 10.1016/j.lfs.2020.117457] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/10/2020] [Accepted: 02/19/2020] [Indexed: 12/11/2022]
Abstract
AIMS Multiple surgical procedures and anesthesia increase the risk of the development in children. However, the influence of such exposures on the developing childhood immunity organs is rarely reported. MATERIALS AND METHODS High-throughput sequencing of T-cell receptor (TCR) repertoires (TCRseq) from rhesus monkeys' thymus was performed to investigate whether anesthetics could induce de novo antigen recognition via TCR or TCR development impairments. KEY FINDINGS No significant difference between sevoflurane and control groups regarding VJ gene combinations and diversity of V and J gene was seen, nor was there an obvious change in similar average number of Complementarity Determining Region 3 (CDR3) aa clonotypes. Our analysis of Rank abundance, Gini coefficient, Simpson index, Normalized Shannon Diversity Entropy (NSDE), Morisita-Horn Similarity Index (MHSI) and Bhattacharyya Distance (BD) indicated there is no difference in TCR diversity and similarity. SIGNIFICANCE These results suggest early events in thymic T cell development and repertoire generation are not abnormality after multiple sevoflurane exposure during childhood. The stabilization of the immune repertoires suggested the safety of sevoflurane in host immune response in children.
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17
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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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Kakuta Y, Nakano T, Naito T, Watanabe K, Izumiyama Y, Okamoto D, Ichikawa R, Moroi R, Kuroha M, Kanazawa Y, Kimura T, Shiga H, Naitoh T, Kinouchi Y, Unno M, Masamune A. Repertoire analysis of memory T-cell receptors in Japanese patients with inflammatory bowel disease. JGH OPEN 2020; 4:624-631. [PMID: 32782948 PMCID: PMC7411559 DOI: 10.1002/jgh3.12305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 01/11/2020] [Indexed: 01/07/2023]
Abstract
Background and Aim The T‐cell receptor (TCR) repertoire was assessed in response to various antigens and was considered to be associated with the pathogenesis of inflammatory bowel disease (IBD). Thus, we performed TCR repertoire analysis to examine the pathology of IBD from changes in the TCR repertoire of memory T cells in the intestinal lamina propria mononuclear cells (LPMCs) and peripheral blood mononuclear cells (PBMCs) of patients with IBD. Methods LPMCs in the surgical specimens and PBMCs were isolated from 12 patients with IBD (5 patients with ulcerative colitis [UC] and 7 patients with Crohn's disease [CD]). PBMCs were collected from 10 healthy individuals as controls. Comprehensive TCR sequence analyses of adaptor‐ligation polymerase chain reaction (PCR) products were performed using MiSeq. Results The diversity of TCR‐α and TCR‐β in PBMCs was significantly lower in patients with IBD than that in controls (P = 0.00084 and 0.0013, respectively). Comparisons of TCR diversity in LPMCs and PBMCs between CD and UC showed that the diversity in LPMC was not affected by diseases, whereas that in PBMCs was significantly lower in CD than in UC (P = 0.045 and 0.049, respectively). Some TCR clones may have shown a specific increase or decrease in CD and UC, and many clones were common to both LPMCs and PBMCs in the same patients. Conclusion The diversity of TCR clones in LPMCs and PBMCs in patients with IBD was significantly lower than that of PBMCs in controls. TCR diversity in PBMCs was particularly low in patients with CD.
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Affiliation(s)
- Yoichi Kakuta
- Division of Gastroenterology Tohoku University Graduate School of Medicine Sendai Japan
| | - Takeru Nakano
- Division of Gastroenterology Tohoku University Graduate School of Medicine Sendai Japan
| | - Takeo Naito
- Division of Gastroenterology Tohoku University Graduate School of Medicine Sendai Japan
| | - Kazuhiro Watanabe
- Department of Surgery Tohoku University Graduate School of Medicine Sendai Japan
| | - Yasuhiro Izumiyama
- Division of Gastroenterology Tohoku University Graduate School of Medicine Sendai Japan
| | - Daisuke Okamoto
- Division of Gastroenterology Tohoku University Graduate School of Medicine Sendai Japan
| | - Ryo Ichikawa
- Division of Gastroenterology Tohoku University Graduate School of Medicine Sendai Japan
| | - Rintaro Moroi
- Division of Gastroenterology Tohoku University Graduate School of Medicine Sendai Japan
| | - Masatake Kuroha
- Division of Gastroenterology Tohoku University Graduate School of Medicine Sendai Japan
| | - Yoshitake Kanazawa
- Division of Gastroenterology Tohoku University Graduate School of Medicine Sendai Japan
| | - Tomoya Kimura
- Division of Gastroenterology Tohoku University Graduate School of Medicine Sendai Japan
| | - Hisashi Shiga
- Division of Gastroenterology Tohoku University Graduate School of Medicine Sendai Japan
| | - Takeshi Naitoh
- Department of Surgery Tohoku University Graduate School of Medicine Sendai Japan
| | - Yoshitaka Kinouchi
- Student Health Care Center, Institute for Excellence in Higher Education Tohoku University Sendai Japan
| | - Michiaki Unno
- Department of Surgery Tohoku University Graduate School of Medicine Sendai Japan
| | - Atsushi Masamune
- Division of Gastroenterology Tohoku University Graduate School of Medicine Sendai Japan
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19
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Werner L, Lee YN, Rechavi E, Lev A, Yerushalmi B, Ling G, Shah N, Uhlig HH, Weiss B, Somech R, Snapper SB, Shouval DS. Alterations in T and B Cell Receptor Repertoires Patterns in Patients With IL10 Signaling Defects and History of Infantile-Onset IBD. Front Immunol 2020; 11:109. [PMID: 32117262 PMCID: PMC7017840 DOI: 10.3389/fimmu.2020.00109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/15/2020] [Indexed: 01/04/2023] Open
Abstract
Patients with loss-of-function mutations in IL10 or IL10 receptor (IL10R) genes develop severe, medical-refractory, infantile-onset inflammatory bowel disease (IBD). We have previously reported significant alterations in innate and adaptive immune responses in these patients. Next generation sequencing platforms enable a comprehensive assessment of T cell receptor (TCR) and B cell receptor (BCR) repertoire patterns. We aimed to characterize TCR and BCR features in peripheral blood of patients with deleterious IL10 signaling defects. DNA was isolated from blood of seven patients with IL10R mutations and one with an IL10 mutation, along with eight controls, and subjected to next generation sequencing of TRB and IgH loci. A significant increase in clonality was observed in both TCR and BCR repertoires in circulating lymphocytes of IL10/IL10R-deficient patients, but to a much greater extent in T cells. Furthermore, short CDR3β length and altered hydrophobicity were demonstrated in T cells of patients, but not in B cells, secondary to lower rates of insertions of nucleotides, but not deletions, at the V-, D-, or J-junctions. We were unable to observe specific T or B clones that were limited only to the patients or among controls. Moreover, the expanded T cells clones were unique to each patient. In conclusion, next generation sequencing of the TCR and BCR is a powerful tool for characterizing the adaptive immune cell phenotype and function in immune-mediated disorders. The oligoclonality observed among IL10/IL10R-deficient patients may suggest specialization of unique clones that likely have a role in mediating tissue damage. Nevertheless, the lack of shared clones between patients provides another piece of evidence that the adaptive immune response in IBD is not triggered against common antigens. Additional studies are required to define the specific antigens that interact with the expanded IL10/IL10R-deficient clones.
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Affiliation(s)
- Lael Werner
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yu Nee Lee
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel
| | - Erez Rechavi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel
| | - Atar Lev
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel
| | - Baruch Yerushalmi
- Pediatric Gastroenterology Unit, Soroka University Medical Center, Ben Gurion University of the Negev, Be'er Sheva, Israel
| | - Galina Ling
- Pediatric Gastroenterology Unit, Soroka University Medical Center, Ben Gurion University of the Negev, Be'er Sheva, Israel
| | - Neil Shah
- Department of Gastroenterology, Great Ormond Street Hospital, London, United Kingdom
| | - Holm H Uhlig
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom.,Department of Pediatrics, University of Oxford, Oxford, United Kingdom.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Batia Weiss
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Raz Somech
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Dror S Shouval
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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20
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Allez M, Auzolle C, Ngollo M, Bottois H, Chardiny V, Corraliza AM, Salas A, Perez K, Stefanescu C, Nancey S, Buisson A, Pariente B, Fumery M, Sokol H, Tréton X, Barnich N, Seksik P, Le Bourhis L. T cell clonal expansions in ileal Crohn's disease are associated with smoking behaviour and postoperative recurrence. Gut 2019; 68:1961-1970. [PMID: 30792246 DOI: 10.1136/gutjnl-2018-317878] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 12/14/2022]
Abstract
UNLABELLED T cell clonal expansions are present in the inflamed mucosa of patients with Crohn's disease (CD) and may be implicated in postoperative recurrence after ileocolonic resection. METHODS T cell receptor (TCR) analysis was performed in 57 patients included in a prospective multicentre cohort. Endoscopic recurrence was defined by a Rutgeerts score >i0. DNA and mRNA were extracted from biopsies collected from the surgical specimen and endoscopy, and analysed by high throughput sequencing and microarray, respectively. RESULTS TCR repertoire in the mucosa of patients with CD displayed diverse clonal expansions. Active smokers at time of surgery had a significantly increased proportion of clonal expansions as compared with non-smokers (25.9%vs17.9%, p=0.02). The percentage of high frequency clones in the surgical specimen was significantly higher in patients with recurrence and correlated with postoperative endoscopic recurrence (area under the curve (AUC) 0.69, 95% CI 0.54 to 0.83). All patients with clonality above 26.8% (18/57) had an endoscopic recurrence. These patients with a high clonality were more frequently smokers than patients with a low clonality (61% vs 23%, p=0.005). The persistence of a similar TCR repertoire at postoperative endoscopy was associated with smoking and disease recurrence. Patients with high clonality showed increased expression of genes associated with CD8 T cells and reduced expression of inflammation-related genes. Expanded clones were found predominantly in the CD8 T cell compartment. CONCLUSION Clonal T cell expansions are implicated in postoperative endoscopic recurrence. CD patients with increased proportion of clonal T cell expansions in the ileal mucosa represent a subgroup associated with smoking and where pathogenesis appears as T cell driven. TRIAL REGISTRATION NUMBER NCT03458195.
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Affiliation(s)
- Matthieu Allez
- Department of Gastroenterology, Hopital Saint Louis, Paris, France.,INSERM U1160, Hôpital Saint-Louis, Paris, France
| | - Claire Auzolle
- Department of Gastroenterology, Hopital Saint Louis, Paris, France
| | | | - Hugo Bottois
- INSERM U1160, Hôpital Saint-Louis, Paris, France
| | | | | | - Azucena Salas
- Hospital Clinic Barcelona, IDIBAPS, CIBERehd, Barcelona, Spain
| | - Kevin Perez
- INSERM U1160, Hôpital Saint-Louis, Paris, France
| | - Carmen Stefanescu
- Service de Gastroentérologie, MICI et Assistance Nutritive, Hôpital Beaujon, Clichy, France
| | - Stéphane Nancey
- Department of Gastroenterology, Lyon Sud Hospital, Hospices Civils de Lyon, Pierre Benite, Lyon, France
| | - Anthony Buisson
- Gastroenterology Department, University Hospital Estaing, Clermont-Ferrand, France
| | - Benjamin Pariente
- Department of Gastroenterology, Hopital Claude huriez, Lille, France
| | - Mathurin Fumery
- Hepato-Gastroenterology Department, CHU Amiens, Amiens, France
| | - Harry Sokol
- Department of Gastroenterology, Hopital Saint-Antoine, Paris, Île-de-France, France
| | - Xavier Tréton
- Service de Gastroentérologie, MICI et Assistance Nutritive, Hopital Beaujon, Clichy, France
| | - Nicolas Barnich
- M2iSH, UMR Inserm U1071, USC INRA 2018, Université d'Auvergne, Clermont Ferrand, France
| | - Philippe Seksik
- Department of Gastroenterology, Hopital Saint-Antoine, Paris, Île-de-France, France
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21
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Werner L, Nunberg MY, Rechavi E, Lev A, Braun T, Haberman Y, Lahad A, Shteyer E, Schvimer M, Somech R, Weiss B, Lee YN, Shouval DS. Altered T cell receptor beta repertoire patterns in pediatric ulcerative colitis. Clin Exp Immunol 2019; 196:1-11. [PMID: 30556140 DOI: 10.1111/cei.13247] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2018] [Indexed: 01/06/2023] Open
Abstract
The antigenic specificity of T cells occurs via generation and rearrangement of different gene segments producing a functional T cell receptor (TCR). High-throughput sequencing (HTS) allows in-depth assessment of TCR repertoire patterns. There are limited data concerning whether TCR repertoires are altered in inflammatory bowel disease. We hypothesized that pediatric ulcerative colitis (UC) patients possess unique TCR repertoires, resulting from clonotypical expansions in the gut. Paired blood and rectal samples were collected from nine newly diagnosed treatment-naive pediatric UC patients and four healthy controls. DNA was isolated to determine the TCR-β repertoire by HTS. Significant clonal expansion was demonstrated in UC patients, with inverse correlation between clinical disease severity and repertoire diversity in the gut. Using different repertoire variables in rectal biopsies, a clear segregation was observed between patients with severe UC, those with mild-moderate disease and healthy controls. Moreover, the overlap between autologous blood-rectal samples in UC patients was significantly higher compared with overlap among controls. Finally, we identified several clonotypes that were shared in either all or the majority of UC patients in the colon. Clonal expansion of TCR-β-expressing T cells among UC patients correlates with disease severity and highlights their involvement in mediating intestinal inflammation.
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Affiliation(s)
- L Werner
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - M Y Nunberg
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - E Rechavi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - A Lev
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - T Braun
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Y Haberman
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - A Lahad
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - E Shteyer
- Juliet Keidan Institute of Pediatric Gastroenterology, Hepatology and Nutrition, Shaare Zedek Medical Center and The Hebrew University of Jerusalem, Jerusalem, Israel
| | - M Schvimer
- Institute of Pathology, Sheba Medical Center, Tel Hashomer, Israel
| | - R Somech
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - B Weiss
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Y N Lee
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - D S Shouval
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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22
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Zeissig S, Rosati E, Dowds CM, Aden K, Bethge J, Schulte B, Pan WH, Mishra N, Zuhayra M, Marx M, Paulsen M, Strigli A, Conrad C, Schuldt D, Sinha A, Ebsen H, Kornell SC, Nikolaus S, Arlt A, Kabelitz D, Ellrichmann M, Lützen U, Rosenstiel PC, Franke A, Schreiber S. Vedolizumab is associated with changes in innate rather than adaptive immunity in patients with inflammatory bowel disease. Gut 2019; 68:25-39. [PMID: 29730603 DOI: 10.1136/gutjnl-2018-316023] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 04/03/2018] [Accepted: 04/17/2018] [Indexed: 01/10/2023]
Abstract
OBJECTIVE Vedolizumab, a monoclonal antibody directed against the integrin heterodimer α4β7, is approved for the treatment of Crohn's disease and ulcerative colitis. The efficacy of vedolizumab has been suggested to result from inhibition of intestinal T cell trafficking although human data to support this conclusion are scarce. We therefore performed a comprehensive analysis of vedolizumab-induced alterations in mucosal and systemic immunity in patients with inflammatory bowel disease (IBD), using anti-inflammatory therapy with the TNFα antibody infliximab as control. DESIGN Immunophenotyping, immunohistochemistry, T cell receptor profiling and RNA sequencing were performed using blood and colonic biopsies from patients with IBD before and during treatment with vedolizumab (n=18) or, as control, the anti-TNFα antibody infliximab (n=20). Leucocyte trafficking in vivo was assessed using single photon emission computed tomography and endomicroscopy. RESULTS Vedolizumab was not associated with alterations in the abundance or phenotype of lamina propria T cells and did not affect the mucosal T cell repertoire or leucocyte trafficking in vivo. Surprisingly, however, α4β7 antibody treatment was associated with substantial effects on innate immunity including changes in macrophage populations and pronounced alterations in the expression of molecules involved in microbial sensing, chemoattraction and regulation of the innate effector response. These effects were specific to vedolizumab, not observed in response to the TNFα antibody infliximab, and associated with inhibition of intestinal inflammation. CONCLUSION Our findings suggest that modulation of innate immunity contributes to the therapeutic efficacy of vedolizumab in IBD. TRIAL REGISTRATION NUMBER NCT02694588.
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Affiliation(s)
- Sebastian Zeissig
- Department of Medicine I, Universitätsklinikum Carl Gustav Carus Dresden, Technische Universität (TU) Dresden, Dresden, Germany.,Center for Regenerative Therapies Dresden, Technische Universität (TU) Dresden, Dresden, Germany.,Department of Internal Medicine I, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Elisa Rosati
- Institute of Clinical Molecular Biology, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - C Marie Dowds
- Department of Internal Medicine I, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany.,Institute of Clinical Molecular Biology, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Konrad Aden
- Department of Internal Medicine I, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany.,Institute of Clinical Molecular Biology, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Johannes Bethge
- Department of Internal Medicine I, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Berenice Schulte
- Department of Internal Medicine I, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Wei Hung Pan
- Institute of Clinical Molecular Biology, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Neha Mishra
- Institute of Clinical Molecular Biology, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Maaz Zuhayra
- Department of Nuclear Medicine, Molecular Diagnostic Imaging and Therapy, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Marlies Marx
- Department of Nuclear Medicine, Molecular Diagnostic Imaging and Therapy, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Maren Paulsen
- Institute of Clinical Molecular Biology, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Anne Strigli
- Department of Medicine I, Universitätsklinikum Carl Gustav Carus Dresden, Technische Universität (TU) Dresden, Dresden, Germany.,Center for Regenerative Therapies Dresden, Technische Universität (TU) Dresden, Dresden, Germany
| | - Claudio Conrad
- Department of Internal Medicine I, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Dörthe Schuldt
- Department of Internal Medicine I, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Anupam Sinha
- Institute of Clinical Molecular Biology, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Henriette Ebsen
- Institute of Immunology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Sabin-Christin Kornell
- Department of Internal Medicine I, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany.,Institute of Clinical Molecular Biology, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Susanna Nikolaus
- Department of Internal Medicine I, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Alexander Arlt
- Department of Internal Medicine I, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Dieter Kabelitz
- Institute of Immunology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Mark Ellrichmann
- Department of Internal Medicine I, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Ulf Lützen
- Department of Nuclear Medicine, Molecular Diagnostic Imaging and Therapy, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Philip C Rosenstiel
- Institute of Clinical Molecular Biology, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Stefan Schreiber
- Department of Internal Medicine I, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany.,Institute of Clinical Molecular Biology, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
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23
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Jia X, Wang B, Zhai T, Yao Q, Li Q, Zhang JA. WITHDRAWN: T cell receptor revision and immune repertoire changes in autoimmune diseases. Clin Immunol 2018:S1521-6616(18)30724-1. [PMID: 30543918 DOI: 10.1016/j.clim.2018.12.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
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Affiliation(s)
- Xi Jia
- Department of Endocrinology, Jinshan Hospital of Fudan University, Shanghai 201508, China
| | - Bing Wang
- Department of Endocrinology, Jinshan Hospital of Fudan University, Shanghai 201508, China
| | - Tianyu Zhai
- Department of Endocrinology, Zhongshan Hospital of Fudan University, Shanghai 201508, China
| | - Qiuming Yao
- Department of Endocrinology, Jinshan Hospital of Fudan University, Shanghai 201508, China
| | - Qian Li
- Department of Endocrinology, Jinshan Hospital of Fudan University, Shanghai 201508, China
| | - Jin-An Zhang
- Department of Endocrinology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201318, China.
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24
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Bai Y, Wang D, Li W, Huang Y, Ye X, Waite J, Barry T, Edelmann KH, Levenkova N, Guo C, Skokos D, Wei Y, Macdonald LE, Fury W. Evaluation of the capacities of mouse TCR profiling from short read RNA-seq data. PLoS One 2018; 13:e0207020. [PMID: 30439982 PMCID: PMC6237323 DOI: 10.1371/journal.pone.0207020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/22/2018] [Indexed: 11/18/2022] Open
Abstract
Profiling T cell receptor (TCR) repertoire via short read transcriptome sequencing (RNA-Seq) has a unique advantage of probing simultaneously TCRs and the genome-wide RNA expression of other genes. However, compared to targeted amplicon approaches, the shorter read length is more prone to mapping error. In addition, only a small percentage of the genome-wide reads may cover the TCR loci and thus the repertoire could be significantly under-sampled. Although this approach has been applied in a few studies, the utility of transcriptome sequencing in probing TCR repertoires has not been evaluated extensively. Here we present a systematic assessment of RNA-Seq in TCR profiling. We evaluate the power of both Fluidigm C1 full-length single cell RNA-Seq and bulk RNA-Seq in characterizing the repertoires of different diversities under either naïve conditions or after immunogenic challenges. Standard read length and sequencing coverage were employed so that the evaluation was conducted in accord with the current RNA-Seq practices. Despite high sequencing depth in bulk RNA-Seq, we encountered difficulty quantifying TCRs with low transcript abundance (<1%). Nevertheless, top enriched TCRs with an abundance of 1–3% or higher can be faithfully detected and quantified. When top TCR sequences are of interest and transcriptome sequencing is available, it is worthwhile to conduct a TCR profiling using the RNA-Seq data.
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Affiliation(s)
- Yu Bai
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
- * E-mail: (YB); (WF)
| | - David Wang
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Wentian Li
- Robert S. Boas Center for Genomics & Human Genetics, Feinstein Institute for Medical Research, Northwell Health, Manhasset, New York, United States of America
| | - Ying Huang
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Xuan Ye
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Janelle Waite
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Thomas Barry
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Kurt H. Edelmann
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Natasha Levenkova
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Chunguang Guo
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Dimitris Skokos
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Yi Wei
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Lynn E. Macdonald
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Wen Fury
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
- * E-mail: (YB); (WF)
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25
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Chen L, He Z, Iuga AC, Martins Filho SN, Faith JJ, Clemente JC, Deshpande M, Jayaprakash A, Colombel JF, Lafaille JJ, Sachidanandam R, Furtado GC, Lira SA. Diet Modifies Colonic Microbiota and CD4 + T-Cell Repertoire to Induce Flares of Colitis in Mice With Myeloid-Cell Expression of Interleukin 23. Gastroenterology 2018; 155:1177-1191.e16. [PMID: 29909020 PMCID: PMC6174107 DOI: 10.1053/j.gastro.2018.06.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/24/2018] [Accepted: 06/11/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND & AIMS Several studies have shown that signaling via the interleukin 23 (IL23) receptor is required for development of colitis. We studied the roles of IL23, dietary factors, alterations to the microbiota, and T cells in the development and progression of colitis in mice. METHODS All mice were maintained on laboratory diet 5053, unless otherwise noted. We generated mice that express IL23 in CX3CR1-positive myeloid cells (R23FR mice) upon cyclic administration of tamoxifen dissolved in diet 2019. Diets 2019 and 5053 have minor differences in the overall composition of protein, fat, fiber, minerals, and vitamins. CX3CR1CreER mice (FR mice) were used as controls. Some mice were given antibiotics, and others were raised in a germ-free environment. Intestinal tissues were collected and analyzed by histology and flow cytometry. Feces were collected and analyzed by 16S rDNA sequencing. Feces from C57/Bl6, R23FR, or FR mice were fed to FR and R23FR germ-free mice in microbiota transplant experiments. We also performed studies with R23FR/Rag-/-, R23FR/Mu-/-, and R23FR/Tcrd-/- mice. R23FR mice were given injections of antibodies against CD4 or CD8 to deplete T cells. Mesenteric lymph nodes and large intestine CD4+ cells from R23FR or FR mice in remission from colitis were transferred into Rag-/- mice. CD4+ cells were isolated from donor R23FR mice and recipient Rag-/- mice, and T-cell receptor sequences were determined. RESULTS Expression of IL23 led to development of a relapsing-remitting colitis that was dependent on the microbiota and CD4+ T cells. The relapses were caused by switching from the conventional diet used in our facility (diet 5053) to the diet 2019 and were not dependent on tamoxifen after the first cycle. The switch in the diet modified the microbiota but did not alter levels of IL23 in intestinal tissues compared with mice that remained on the conventional diet. Mesenteric lymph nodes and large intestine CD4+ cells from R23FR mice in remission, but not from FR mice, induced colitis after transfer into Rag-/- mice, but only when these mice were placed on the diet 2019. The CD4+ T-cell receptor repertoire of Rag-/- mice with colitis (fed the 2019 diet) was less diverse than that from donor mice and Rag-/- mice without colitis (fed the 5053 diet) because of expansion of dominant T-cell clones. CONCLUSIONS We developed mice that express IL23 in CX3CR1-positive myeloid cells (R23FR mice) and found that they are more susceptible to diet-induced colitis than mice that do not express IL23. The R23FR mice have a population of CD4+ T cells that becomes activated in response to dietary changes and alterations to the intestinal microbiota. The results indicate that alterations in the diet, intestinal microbiota, and IL23 signaling can contribute to pathogenesis of inflammatory bowel disease.
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Affiliation(s)
- Lili Chen
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zhengxiang He
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alina Cornelia Iuga
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Sebastião N. Martins Filho
- Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, Brazil,Department of Pathology and Laboratory Medicine, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Jeremiah J. Faith
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jose C. Clemente
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA,Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Madhura Deshpande
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Jean-Frederic Colombel
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Juan J. Lafaille
- Department of Pathology, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Ravi Sachidanandam
- Girihlet Inc. Oakland, CA 94609, USA,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Glaucia C. Furtado
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sergio A. Lira
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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26
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Expanded TCRβ CDR3 clonotypes distinguish Crohn's disease and ulcerative colitis patients. Mucosal Immunol 2018; 11:1487-1495. [PMID: 29988119 DOI: 10.1038/s41385-018-0046-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 04/26/2018] [Accepted: 04/30/2018] [Indexed: 02/04/2023]
Abstract
We aimed to determine whether the TCR repertoires of Crohn's disease (CD) patients contain highly prevalent disease-specific T-cell clonotypes reflective of the characteristic and highly shared aberrant serum antibody reactivity to gut commensal flagellin antigens. The CD4 TCRβ CDR3 sequence repertoires from active CD (n = 20) and ulcerative colitis (UC) (n = 10) patients were significantly more diverse, and individual sequences over-represented, compared to healthy controls (HC) (n = 97). While a very small number of expanded public CDR3 sequences are highly shared between active CD and UC, the majority of significantly expanded TCRβ CDR3 clonotypes are private to CD and UC patients with equivalent prevalence among IBD patients. Further defining TCR clonotypes by Vβ-CDR3 linkage showed significant differences in the TCR repertoires between UC and CD. Flagellin antigen exposure induced expansion of several TCRβ CDR3 sequences in CD4 cells from a flagellin-seropositive subject including sequences highly shared by or relatively private to CD (and UC) patients. These data suggest that flagellin-reactivity contributes to the expansion of a small number of CD4 clonotypes but does not support flagellin antigens as predominantly driving CD4 cell proliferation in CD. Disease-specific expanded TCRβ CDR3 clonotypes characterize CD and UC and the shared exposure to the gamut of gut microbial antigens.
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27
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Zewde M, Kiyotani K, Park JH, Fang H, Yap KL, Yew PY, Alachkar H, Kato T, Mai TH, Ikeda Y, Matsuda T, Liu X, Ren L, Deng B, Harada M, Nakamura Y. The era of immunogenomics/immunopharmacogenomics. J Hum Genet 2018; 63:865-875. [PMID: 29785006 DOI: 10.1038/s10038-018-0468-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 05/01/2018] [Accepted: 05/02/2018] [Indexed: 11/09/2022]
Abstract
Although germline alterations and somatic mutations in disease cells have been extensively analyzed, molecular changes in immune cells associated with disease conditions have not been characterized in depth. It is clear that our immune system has a critical role in various biological and pathological conditions, such as infectious diseases, autoimmune diseases, drug-induced skin and liver toxicity, food allergy, and rejection of transplanted organs. The recent development of cancer immunotherapies, particularly drugs modulating the immune checkpoint molecules, has clearly demonstrated the importance of host immune cells in cancer treatments. However, the molecular mechanisms by which these new therapies kill tumor cells are still not fully understood. In this regard, we have begun to explore the role of newly developed tools such as next-generation sequencing in the genetic characterization of both cancer cells and host immune cells, a field that is called immunogenomics/ immunopharmacogenomics. This new field has enormous potential to help us better understand changes in our immune system during the course of various disease conditions. Here we report the potential of deep sequencing of T-cell and B-cell receptors in capturing the molecular contribution of the immune system, which we believe plays critical roles in the pathogenesis of various human diseases.
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Affiliation(s)
- Makda Zewde
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Kazuma Kiyotani
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.,Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan
| | - Jae-Hyun Park
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Hua Fang
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Kai Lee Yap
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Poh Yin Yew
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Houda Alachkar
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Taigo Kato
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Tu H Mai
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Yuji Ikeda
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Tatsuo Matsuda
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Xiao Liu
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Lili Ren
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Boya Deng
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Makiko Harada
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Yusuke Nakamura
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.
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28
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Giudice V, Feng X, Kajigaya S, Young NS, Biancotto A. Optimization and standardization of fluorescent cell barcoding for multiplexed flow cytometric phenotyping. Cytometry A 2017; 91:694-703. [PMID: 28692789 DOI: 10.1002/cyto.a.23162] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 05/01/2017] [Accepted: 06/09/2017] [Indexed: 11/08/2022]
Abstract
Fluorescent cell barcoding (FCB) is a cell-based multiplexing technique for high-throughput flow cytometry. Barcoded samples can be stained and acquired collectively, minimizing staining variability and antibody consumption, and decreasing required sample volumes. Combined with functional measurements, FCB can be used for drug screening, signaling profiling, and cytokine detection, but technical issues are present. We optimized the FCB technique for routine utilization using DyLight 350, DyLight 800, Pacific Orange, and CBD500 for barcoding six, nine, or 36 human peripheral blood specimens. Working concentrations of FCB dyes ranging from 0 to 500 μg/ml were tested, and viability dye staining was optimized to increase robustness of data. A five-color staining with surface markers for Vβ usage analysis in CD4+ and CD8+ T cells was achieved in combination with nine sample barcoding. We provide improvements of the FCB technique that should be useful for multiplex drug screening and for lymphocyte characterization and perturbations in the diagnosis and during the course of disease. Published 2017 by Wiley Periodicals, Inc., on behalf of International Society for Advancement of Cytometry. This article is a US government work and as such, is in the public domain in the United States of America.
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Affiliation(s)
- Valentina Giudice
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, 20892-1202
| | - Xingmin Feng
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, 20892-1202
| | - Sachiko Kajigaya
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, 20892-1202
| | - Neal S Young
- Hematology Branch, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, 20892-1202
| | - Angélique Biancotto
- Center for Human Immunology, Autoimmunity, and Inflammation, NIH, Bethesda, Maryland, 20892-1202
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29
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Doorenspleet ME, Westera L, Peters CP, Hakvoort TBM, Esveldt RE, Vogels E, van Kampen AHC, Baas F, Buskens C, Bemelman WA, D'Haens G, Ponsioen CY, Te Velde AA, de Vries N, van den Brink GR. Profoundly Expanded T-cell Clones in the Inflamed and Uninflamed Intestine of Patients With Crohn's Disease. J Crohns Colitis 2017; 11:831-839. [PMID: 28158397 DOI: 10.1093/ecco-jcc/jjx012] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 01/30/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND AND AIM T cells are key players in the chronic intestinal inflammation that characterises Crohn's disease. Here we aim to map the intestinal T-cell receptor [TCR] repertoire in patients with Crohn's disease, using next-generation sequencing technology to examine the clonality of the T-cell compartment in relation to mucosal inflammation and response to therapy. METHODS Biopsies were taken from endoscopically inflamed and uninflamed ileum and colon of 19 patients with Crohn's disease. From this cohort, additional biopsies were taken after 8 weeks of remission induction therapy from eight responders and eight non-responders. Control biopsies from 11 patients without inflammatory bowel disease [IBD] were included. The TCRβ repertoire was analysed by next-generation sequencing of biopsy RNA. RESULTS Both in Crohn's disease patients and in non-IBD controls, a broad intestinal T-cell repertoire was found, with a considerable part consisting of expanded clones. Clones in Crohn's disease were more expanded [p = 0.008], with the largest clones representing up to as much as 58% of the total repertoire. There was a substantial overlap of the repertoire between inflamed and uninflamed tissue and between ileum and colon. Following therapy, responders showed larger changes in the T-cell repertoire than non-responders, although a considerable part of the repertoire remained unchanged in both groups. CONCLUSIONS The intestinal T-cell repertoire distribution in Crohn's disease is different from that in the normal gut, containing profoundly expanded T-cell clones that take up a large part of the repertoire. The T-cell repertoire is fairly stable regardless of endoscopic mucosal inflammation or response to therapy.
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Affiliation(s)
- M E Doorenspleet
- Amsterdam Rheumatology and immunology Center, Academic Medical Center, Amsterdam, The Netherlands.,Laboratory for Genome Analysis, Academic Medical Center, Amsterdam, The Netherlands
| | - L Westera
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, Amsterdam, The Netherlands
| | - C P Peters
- Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, The Netherlands
| | - T B M Hakvoort
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, Amsterdam, The Netherlands
| | - R E Esveldt
- Amsterdam Rheumatology and immunology Center, Academic Medical Center, Amsterdam, The Netherlands.,Laboratory for Genome Analysis, Academic Medical Center, Amsterdam, The Netherlands
| | - E Vogels
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, Amsterdam, The Netherlands
| | - A H C van Kampen
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, Amsterdam, The Netherland
| | - F Baas
- Laboratory for Genome Analysis, Academic Medical Center, Amsterdam, The Netherlands
| | - C Buskens
- Department of Surgery, Academic Medical Center, Amsterdam, The Netherlands
| | - W A Bemelman
- Department of Surgery, Academic Medical Center, Amsterdam, The Netherlands
| | - G D'Haens
- Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, The Netherlands
| | - C Y Ponsioen
- Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, The Netherlands
| | - A A Te Velde
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, Amsterdam, The Netherlands
| | - N de Vries
- Amsterdam Rheumatology and immunology Center, Academic Medical Center, Amsterdam, The Netherlands
| | - G R van den Brink
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center, Amsterdam, The Netherlands.,Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, The Netherlands
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30
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Oligoclonal T-cell Receptor Repertoire in Colonic Biopsies of Patients with Microscopic Colitis and Ulcerative Colitis. Inflamm Bowel Dis 2017; 23:932-945. [PMID: 28498152 DOI: 10.1097/mib.0000000000001127] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND Microscopic colitis (MC), comprising collagenous colitis (CC) and lymphocytic colitis (LC), is a type of variation of inflammatory bowel diseases. Local T-cell infiltration in the mucosa plays a major role in MC immunopathology. METHODS To understand diversity and clonality of infiltrating T cells, we analyzed the T-cell receptor beta (TCRβ) chains in colonic biopsies of MC, ulcerative colitis (UC), and their remission counterparts (CC/LC-HR [histological remission] or UC-R [remission]) compared with patients with noninflamed colons using next-generation sequencing. RESULTS Compared with controls and patients with CC, patients with LC had significantly lower diversity with significantly lower evenness and richness in TCRVβ-Jβ gene segments. Similarly, patients with LC-HR had lower diversity because of significantly lower TCRVβ-Jβ clone richness. Patients with UC and UC-R showed significantly higher diversity and richness. Univariate and multivariate analyses were performed to identify TCRVβ-Jβ gene segments differentiating disease types from controls or their remission counterparts. Patients with LC were discriminated from controls by 12 clones and from patients with CC by 8 clones. Neither univariate nor multivariate analyses showed significance for patients with CC or CC-HR compared with controls. Patients with UC and UC-R had 16 and 14 discriminating clones, respectively, compared with controls. CONCLUSIONS Altogether, patients with MC and UC showed an oligoclonal TCRβ distribution. TCRVβ-Jβ clone types and their diversity were distinctive between patients with CC and LC, as well as for patients with UC, suggesting different pathophysiological mechanisms according to disease type and stage. This study suggests that CC and LC are different entities because of differences in immunoregulatory responses, as mirrored by their T-cell repertoire.
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31
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Dai SX, Gu HX, Lin QY, Wu YK, Wang XY, Huang SZ, Xing TS, Chen MH, Zhang QF, Zheng ZW, Sha WH. Decreased CD8+CD28+/CD8+CD28- T cell ratio can sensitively predict poor outcome for patients with complicated Crohn disease. Medicine (Baltimore) 2017; 96:e7247. [PMID: 28658115 PMCID: PMC5500037 DOI: 10.1097/md.0000000000007247] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Crohn disease (CD) with complications such as penetrating, stricturing, and perianal disease is called complicated CD. The aim of this study is to test the efficiency with which the CD8CD28/CD8CD28 cell balance can predict a subsequent active stage in patients with newly diagnosed complicated CD.Seventeen patients with complicated CD and 48 CD patients with no complications were enrolled. Blood CD8 T cells were tested from all of the 65 newly diagnosed CD patients upon enrollment. The potential risk factors were compared between the 2 groups. A 30-week follow-up was performed, and the efficiency of the CD8 cell balance at predicting active CD was analyzed using receiver-operating characteristic curves. The cumulative remission lasting rates (CRLRs) were analyzed using the Kaplan-Meier method.Compared with the control CD group, patients with complicated CD were predominantly male and younger in age; they also had lower body mass indices (BMIs), higher Crohn disease activity indices (CDAIs), higher immunosuppressant and steroid prescription rates, and significantly higher surgical rates. The CD8CD28/CD8CD28 balance was associated with BMI, CDAI, steroids, and surgery. The CD8CD28/CD8CD28 ratios were significantly lower at week 0 and on the 6th, 22nd, and 30th week during follow-up with a shorter lasting time of remission for the complicated CD patients. The CD8CD28/CD8CD28 ratio could accurately predict the active stage for the patients with complicated CD, and the highest sensitivity (89.2%) and specificity (85.3%) were found when the ratio was 1.03. Treatment with steroids and surgery, along with a significantly lower CD8CD28/CD8CD28 ratio and lower CRLRs, was closely related to a worse outcome for the patients with complicated CD.Patients requiring steroids and surgery experience more severe disease activity and thus a disequilibrated immunological balance, which could be the main reason for a decreased CD8CD28/CD8CD28 ratio. This ratio can sensitively predict the active stage for patients with complicated CD, and more care should be taken when this ratio is <1.03.
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Affiliation(s)
- Shi-xue Dai
- Department of Gastroenterology, Guangdong General Hospital and Guangdong Academy of Medical Sciences, South China University of Technology
| | | | - Qian-yi Lin
- The First Clinical Medical School (Nanfang Hospital), Southern Medical University, Guangzhou, Guangdong
| | - Yan-kun Wu
- Department of Clinical Medicine, Zhongshan School of Medicine, Sun Yat-sen University
| | - Xiao-yan Wang
- Department of Clinical Medicine, Zhongshan School of Medicine, Sun Yat-sen University
| | - Shao-zhuo Huang
- The First Clinical Medical School (Nanfang Hospital), Southern Medical University, Guangzhou, Guangdong
| | - Tiao-si Xing
- Department of Anatomy & Cell Biology, Brody School of Medicine, East Carolina University, Greenville, NC, USA
| | - Min-hua Chen
- School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Qing-fang Zhang
- Department of Gastroenterology, Guangdong General Hospital and Guangdong Academy of Medical Sciences, South China University of Technology
| | - Zhong-wen Zheng
- Department of Gastroenterology, Guangdong General Hospital and Guangdong Academy of Medical Sciences, South China University of Technology
| | - Wei-hong Sha
- Department of Gastroenterology, Guangdong General Hospital and Guangdong Academy of Medical Sciences, South China University of Technology
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32
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Kato T, Iwasaki T, Uemura M, Nagahara A, Higashihara H, Osuga K, Ikeda Y, Kiyotani K, Park JH, Nonomura N, Nakamura Y. Characterization of the cryoablation-induced immune response in kidney cancer patients. Oncoimmunology 2017; 6:e1326441. [PMID: 28811963 DOI: 10.1080/2162402x.2017.1326441] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 04/26/2017] [Accepted: 04/29/2017] [Indexed: 10/19/2022] Open
Abstract
Cryoablation is one of treatment modalities for kidney cancer and is expected to induce strong local immune responses as well as systemic T-cell-mediated immune reactions that may lead to the regression of distant metastatic lesions. Thus, the characterization of T cell repertoire and immune environment in tumors before and after treatment should contribute to the better understanding of the cryoablation-induced anticancer immune responses. In this study, we collected tumor tissues from 22 kidney cancer patients, before cryoablation and at 3 mo after cryoablation. In addition, blood samples were collected from 14 patients at the same time points. We applied a next generation sequencing approach to characterize T cell receptor β (TCRB) repertoires using RNAs isolated from tumor tissues and peripheral blood mononuclear cells. TCRB repertoire analysis revealed the expansion of certain T cell clones in tumor tissues by cryoablation. We also found that proportions of abundant TCRB clonotypes (defined as clonotypes with ≥ 1% frequency among total TCRB reads) were significantly increased in the post-cryoablation tissue samples than those of pre-cryoablation tumor samples. Some of these TCRB clonotypes were found to be increased in peripheral blood. Expression analysis of immune-related genes in the tissues of pre- and post-cryoablation showed significantly elevated transcriptional levels of CD8+ , CD4+ , Granzyme A (GZMA), and CD11c along with a high CD8/FOXP3 ratio in the post-cryoablation tissue samples. Our findings revealed that cryoablation could induce strong immune reactions in tumors with oligoclonal expansion of antitumor T cells, which circulate systemically.
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Affiliation(s)
- Taigo Kato
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Tomoyuki Iwasaki
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Motohide Uemura
- Department of Urology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Akira Nagahara
- Department of Urology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Hiroki Higashihara
- Department of Diagnostic and Interventional Radiology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Keigo Osuga
- Department of Diagnostic and Interventional Radiology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yuji Ikeda
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Kazuma Kiyotani
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Jae-Hyun Park
- Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Norio Nonomura
- Department of Urology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yusuke Nakamura
- Department of Medicine, The University of Chicago, Chicago, IL, USA.,Department of Surgery, The University of Chicago, Chicago, IL, USA
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33
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Wong GK, Heather JM, Barmettler S, Cobbold M. Immune dysregulation in immunodeficiency disorders: The role of T-cell receptor sequencing. J Autoimmun 2017; 80:1-9. [PMID: 28400082 DOI: 10.1016/j.jaut.2017.04.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/01/2017] [Accepted: 04/03/2017] [Indexed: 11/28/2022]
Abstract
Immune dysregulation is a prominent feature of primary immunodeficiency disorders, which commonly manifested as autoimmunity, cytopenias and inflammatory bowel disease. In partial T-cell immunodeficiency disorders, it has been proposed that the imbalance between effector and regulatory T-cells drives the breakdown of peripheral tolerance. While there is no robust test for immune dysregulation, the T-cell receptor repertoire is used as a surrogate marker, and has been shown to be perturbed in a number of immunodeficiency disorders featuring immune dysregulation including Omenn's Syndrome, Wiskott-Aldrich Syndrome, and common variable immunodeficiency. This review discusses how recent advances in TCR next-generation sequencing and bioinformatics have led to the in-depth characterization of CDR3 sequences and an exponential growth in examinable parameters. Specifically, we highlight the use of junctional diversity as a means to differentiate intrinsic T-cell defects from secondary causes of repertoire perturbation in primary immunodeficiency disorders. However, key questions, such as the identity of antigenic targets for large, expanded T-cell clonotypes, remain unanswered despite the fact that such clones are likely to play a pathogenic role in driving immune dysregulation and autoimmunity. Finally, we discuss a number of emerging technologies such as in silico reconstruction, high-throughput pairwise αβ sequencing and single-cell RNAseq that offer the potential to define the antigenic epitope and function of a given T-cell, thereby enhancing our understanding in this field.
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Affiliation(s)
- Gabriel K Wong
- Institute of Immunology and Immunontherapy, Medical School, University of Birmingham, Edgbaston, B15 2TT, UK; UCB Pharma, Slough, Berkshire, SL1 3WE, UK
| | - James M Heather
- Massachusetts General Hospital Cancer Center and Department of Medicine Harvard Medical School, 13th Street, Charlestown, MA, 02129, USA
| | - Sara Barmettler
- Massachusetts General Hospital Cancer Center and Department of Medicine Harvard Medical School, 13th Street, Charlestown, MA, 02129, USA
| | - Mark Cobbold
- Massachusetts General Hospital Cancer Center and Department of Medicine Harvard Medical School, 13th Street, Charlestown, MA, 02129, USA.
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