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Zou J, Li B, Li D, Bao HF, She CH, Ye JF, Cai JF, Guan JL. Comprehensive analysis of T-cell receptor repertoires reveals antigen-driven T-cell clusters in patients with Behçet's syndrome. Eur J Immunol 2023; 53:e2250181. [PMID: 36747316 DOI: 10.1002/eji.202250181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/23/2023] [Accepted: 01/31/2023] [Indexed: 02/08/2023]
Abstract
T lymphocytes are the major components of adaptive immunity in Behçet's syndrome (BS) pathology. However, the precise mechanism of T-cell-induced inflammatory condition remains to be determined. We applied bulk sequencing of the T-cell receptor (TCR) β chain in peripheral blood samples from 45 patients with BS and 10 healthy donors as controls. TCR repertoires in BS patients displayed more clonality and less diversity than in healthy donors. Male patients exhibited lower diversity metrics of TCR and had a larger proportion in the top 10 clones than females (p = 0.016). There were no TCR clonality differences in other clinical features, such as age, disease duration, organ involvement, disease severity, and activity. By "Grouping of Lymphocyte Interactions by Paratope Hotspots" (GLIPH2) for antigen prediction, we found distinct 2477 clusters of TCR-β sequences that potentially recognize similar antigens shared between BS patients. We observed clonal T-cell expansion in BS patients. Sexual differences in TCR clonal expansion and public TCR groups deserve further study to reveal the underline T-cell-mediated immunity in BS.
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Affiliation(s)
- Jun Zou
- Division of Rheumatology and Immunology, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Bin Li
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University, Shanghai, China
| | - Dan Li
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University, Shanghai, China
| | - Hua-Fang Bao
- Division of Rheumatology and Immunology, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Chun-Hui She
- Division of Rheumatology and Immunology, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Jing-Fen Ye
- Division of Rheumatology and Immunology, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Jian-Fei Cai
- Division of Rheumatology and Immunology, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Jian-Long Guan
- Division of Rheumatology and Immunology, Huadong Hospital Affiliated to Fudan University, Shanghai, China
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2
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Servaas NH, Zaaraoui-Boutahar F, Wichers CGK, Ottria A, Chouri E, Affandi AJ, Silva-Cardoso S, van der Kroef M, Carvalheiro T, van Wijk F, Radstake TRDJ, Andeweg AC, Pandit A. Longitudinal analysis of T-cell receptor repertoires reveals persistence of antigen-driven CD4 + and CD8 + T-cell clusters in systemic sclerosis. J Autoimmun 2020; 117:102574. [PMID: 33307312 DOI: 10.1016/j.jaut.2020.102574] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/10/2020] [Accepted: 11/13/2020] [Indexed: 12/11/2022]
Abstract
The T-cell receptor (TCR) is a highly polymorphic surface receptor that allows T-cells to recognize antigenic peptides presented on the major histocompatibility complex (MHC). Changes in the TCR repertoire have been observed in several autoimmune conditions, and these changes are suggested to predispose autoimmunity. Multiple lines of evidence have implied an important role for T-cells in the pathogenesis of Systemic Sclerosis (SSc), a complex autoimmune disease. One of the major questions regarding the roles of T-cells is whether expansion and activation of T-cells observed in the diseases pathogenesis is antigen driven. To investigate the temporal TCR repertoire dynamics in SSc, we performed high-throughput sequencing of CD4+ and CD8+ TCRβ chains on longitudinal samples obtained from four SSc patients collected over a minimum of two years. Repertoire overlap analysis revealed that samples taken from the same individual over time shared a high number of TCRβ sequences, indicating a clear temporal persistence of the TCRβ repertoire in CD4+ as well as CD8+ T-cells. Moreover, the TCRβs that were found with a high frequency at one time point were also found with a high frequency at the other time points (even after almost four years), showing that frequencies of dominant TCRβs are largely consistent over time. We also show that TCRβ generation probability and observed TCR frequency are not related in SSc samples, showing that clonal expansion and persistence of TCRβs is caused by antigenic selection rather than convergent recombination. Moreover, we demonstrate that TCRβ diversity is lower in CD4+ and CD8+ T-cells from SSc patients compared with memory T-cells from healthy individuals, as SSc TCRβ repertoires are largely dominated by clonally expanded persistent TCRβ sequences. Lastly, using "Grouping of Lymphocyte Interactions by Paratope Hotspots" (GLIPH2), we identify clusters of TCRβ sequences with homologous sequences that potentially recognize the same antigens and contain TCRβs that are persist in SSc patients. In conclusion, our results show that CD4+ and CD8+ T-cells are highly persistent in SSc patients over time, and this persistence is likely a result from antigenic selection. Moreover, persistent TCRs form high similarity clusters with other (non-)persistent sequences that potentially recognize the same epitopes. These data provide evidence for an antigen driven expansion of CD4+/CD8+ T-cells in SSc.
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Affiliation(s)
- N H Servaas
- Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - F Zaaraoui-Boutahar
- Department of Viroscience, Erasmus Medical Center Rotterdam, Rotterdam, the Netherlands
| | - C G K Wichers
- Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - A Ottria
- Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - E Chouri
- Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - A J Affandi
- Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - S Silva-Cardoso
- Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - M van der Kroef
- Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - T Carvalheiro
- Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - F van Wijk
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - T R D J Radstake
- Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - A C Andeweg
- Department of Viroscience, Erasmus Medical Center Rotterdam, Rotterdam, the Netherlands
| | - A Pandit
- Department of Rheumatology & Clinical Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands; Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
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3
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Chu ND, Bi HS, Emerson RO, Sherwood AM, Birnbaum ME, Robins HS, Alm EJ. Longitudinal immunosequencing in healthy people reveals persistent T cell receptors rich in highly public receptors. BMC Immunol 2019; 20:19. [PMID: 31226930 PMCID: PMC6588944 DOI: 10.1186/s12865-019-0300-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 06/06/2019] [Indexed: 11/18/2022] Open
Abstract
Background The adaptive immune system maintains a diversity of T cells capable of recognizing a broad array of antigens. Each T cell’s specificity for antigens is determined by its T cell receptors (TCRs), which together across all T cells form a repertoire of millions of unique receptors in each individual. Although many studies have examined how TCR repertoires change in response to disease or drugs, few have explored the temporal dynamics of the TCR repertoire in healthy individuals. Results Here we report immunosequencing of TCR β chains (TCRβ) from the blood of three healthy individuals at eight time points over one year. TCRβ repertoires of all peripheral-blood T cells and sorted memory T cells clustered clearly by individual, systematically demonstrating that TCRβ repertoires are specific to individuals across time. This individuality was absent from TCRβs from naive T cells, suggesting that the differences resulted from an individual’s antigen exposure history, not genetic background. Many characteristics of the TCRβ repertoire (e.g., diversity, clonality) were stable across time, although we found evidence of T cell expansion dynamics even within healthy individuals. We further identified a subset of “persistent” TCRβs present across all time points. These receptors were rich in clonal and highly public receptors and may play a key role in immune system maintenance. Conclusions Our results highlight the importance of longitudinal sampling of the immune system, providing a much-needed baseline for TCRβ dynamics in healthy individuals. Such a baseline will improve interpretation of changes in the TCRβ repertoire during disease or treatment. Electronic supplementary material The online version of this article (10.1186/s12865-019-0300-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nathaniel D Chu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Haixin Sarah Bi
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.,Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | - Michael E Birnbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Harlan S Robins
- Adaptive Biotechnologies, Seattle, WA, USA.,Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Eric J Alm
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Broad Institute, Cambridge, MA, 02139, USA.
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Bolen CR, Rubelt F, Vander Heiden JA, Davis MM. The Repertoire Dissimilarity Index as a method to compare lymphocyte receptor repertoires. BMC Bioinformatics 2017; 18:155. [PMID: 28264647 PMCID: PMC5340033 DOI: 10.1186/s12859-017-1556-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 02/21/2017] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The B and T cells of the human adaptive immune system leverage a highly diverse repertoire of antigen-specific receptors to protect the human body from pathogens. The sequencing and analysis of immune repertoires is emerging as an important tool to understand immune responses, whether beneficial or harmful (in the case of autoimmunity). However, methods for studying these repertoires, and for directly comparing different immune repertoires, are lacking. RESULTS In this paper, we present a non-parametric method for directly comparing sequencing repertoires, with the goal of rigorously quantifying differences in V, D, and J gene segment utilization. This method, referred to as the Repertoire Dissimilarity Index (RDI), uses a bootstrapped subsampling approach to account for variance in sequencing depth, and, coupled with a data simulation approach, allows for direct quantification of the average variation between repertoires. We use the RDI method to recapitulate known differences in the formation of the CD4+ and CD8+ T cell repertoires, and further show that antigen-driven activation of naïve CD8+ T cells is more selective than in the CD4+ repertoire, resulting in a more specialized CD8+ memory repertoire. CONCLUSIONS We prove that the RDI method is an accurate and versatile method for comparisons of immune repertoires. The RDI method has been implemented as an R package, and is available for download through Bitbucket.
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Affiliation(s)
- Christopher R. Bolen
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, 94305 CA USA
- Genentech, Inc., 1 DNA Way, MS 93, South San Francisco, 94080 CA USA
| | - Florian Rubelt
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, 94305 CA USA
| | - Jason A. Vander Heiden
- Interdepartmental Program in Computational Biology and Bioinformatics, Department of Computational Biology & Bioinformatics, Yale University, New Haven, 06520 CT USA
| | - Mark M. Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, 94305 CA USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, 94305 CA USA
- Institute of Immunity, Department of Microbiology and Immunology, Transplantation and Infection, Stanford University School of Medicine, Stanford, 94305 CA USA
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5
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Salson M, Giraud M, Caillault A, Grardel N, Duployez N, Ferret Y, Duez M, Herbert R, Rocher T, Sebda S, Quief S, Villenet C, Figeac M, Preudhomme C. High-throughput sequencing in acute lymphoblastic leukemia: Follow-up of minimal residual disease and emergence of new clones. Leuk Res 2016; 53:1-7. [PMID: 27930944 DOI: 10.1016/j.leukres.2016.11.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 10/28/2016] [Accepted: 11/11/2016] [Indexed: 01/22/2023]
Abstract
Minimal residual disease (MRD) is known to be an independent prognostic factor in patients with acute lymphoblastic leukemia (ALL). High-throughput sequencing (HTS) is currently used in routine practice for the diagnosis and follow-up of patients with hematological neoplasms. In this retrospective study, we examined the role of immunoglobulin/T-cell receptor-based MRD in patients with ALL by HTS analysis of immunoglobulin H and/or T-cell receptor gamma chain loci in bone marrow samples from 11 patients with ALL, at diagnosis and during follow-up. We assessed the clinical feasibility of using combined HTS and bioinformatics analysis with interactive visualization using Vidjil software. We discuss the advantages and drawbacks of HTS for monitoring MRD. HTS gives a more complete insight of the leukemic population than conventional real-time quantitative PCR (qPCR), and allows identification of new emerging clones at each time point of the monitoring. Thus, HTS monitoring of Ig/TR based MRD is expected to improve the management of patients with ALL.
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Affiliation(s)
- Mikaël Salson
- Univ. Lille, CNRS, Centrale Lille, Inria, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000 Lille, France.
| | - Mathieu Giraud
- Univ. Lille, CNRS, Centrale Lille, Inria, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000 Lille, France.
| | - Aurélie Caillault
- Univ. Lille, CHU Lille, Department of Hematology, F-59000 Lille, France.
| | - Nathalie Grardel
- Univ. Lille, CHU Lille, Department of Hematology, F-59000 Lille, France.
| | - Nicolas Duployez
- Univ. Lille, CHU Lille, Department of Hematology, F-59000 Lille, France
| | - Yann Ferret
- Univ. Lille, CHU Lille, Department of Hematology, F-59000 Lille, France
| | - Marc Duez
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Ryan Herbert
- Univ. Lille, CNRS, Centrale Lille, Inria, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000 Lille, France
| | - Tatiana Rocher
- Univ. Lille, CNRS, Centrale Lille, Inria, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, F-59000 Lille, France
| | - Shéhérazade Sebda
- Univ. Lille, Plate-forme de génomique fonctionnelle et structurale, F-59000 Lille, France
| | - Sabine Quief
- Univ. Lille, Plate-forme de génomique fonctionnelle et structurale, F-59000 Lille, France
| | - Céline Villenet
- Univ. Lille, Plate-forme de génomique fonctionnelle et structurale, F-59000 Lille, France
| | - Martin Figeac
- Univ. Lille, Plate-forme de génomique fonctionnelle et structurale, F-59000 Lille, France; Univ. Lille, CHU Lille, Cellule bioinformatique, plateau commun de séquençage, F-59000 Lille, France
| | - Claude Preudhomme
- Univ. Lille, CHU Lille, Department of Hematology, F-59000 Lille, France.
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Bagaev DV, Zvyagin IV, Putintseva EV, Izraelson M, Britanova OV, Chudakov DM, Shugay M. VDJviz: a versatile browser for immunogenomics data. BMC Genomics 2016; 17:453. [PMID: 27297497 PMCID: PMC4907000 DOI: 10.1186/s12864-016-2799-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 05/25/2016] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The repertoire of T- and B-cell receptor sequences encodes the antigen specificity of adaptive immunity system, determines its present state and guides its ability to mount effective response against encountered antigens in future. High throughput sequencing of immune repertoires (Rep-Seq) is a promising technique that allows to profile millions of antigen receptors of an individual in a single experiment. While a substantial number of tools for mapping and assembling Rep-Seq data were published recently, the field still lacks an intuitive and flexible tool that can be used by researchers with little or no computational background for in-depth analysis of immune repertoire profiles. RESULTS Here we report VDJviz, a web tool that can be used to browse, analyze and perform quality control of Rep-Seq results generated by various pre-processing software. On a set of real data examples we show that VDJviz can be used to explore key repertoire characteristics such as spectratype, repertoire clonality, V-(D)-J recombination patterns and to identify shared clonotypes. We also demonstrate the utility of VDJviz in detection of critical Rep-Seq biases such as artificial repertoire diversity and cross-sample contamination. CONCLUSIONS VDJviz is a versatile and lightweight tool that can be easily employed by biologists, immunologists and immunogeneticists for routine analysis and quality control of Rep-Seq data. The software is freely available for non-commercial purposes, and can be downloaded from: https://github.com/antigenomics/vdjviz .
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Affiliation(s)
- Dmitriy V. Bagaev
- />Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Ivan V. Zvyagin
- />Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- />Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
- />Central European Institute of Technology, Masaryk University, Brno, Czech republic
| | - Ekaterina V. Putintseva
- />Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- />Central European Institute of Technology, Masaryk University, Brno, Czech republic
| | - Mark Izraelson
- />Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- />Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
- />Central European Institute of Technology, Masaryk University, Brno, Czech republic
| | - Olga V. Britanova
- />Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- />Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
- />Central European Institute of Technology, Masaryk University, Brno, Czech republic
| | - Dmitriy M. Chudakov
- />Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- />Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
- />Central European Institute of Technology, Masaryk University, Brno, Czech republic
| | - Mikhail Shugay
- />Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- />Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
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Zhang Q, Jia Q, Deng T, Song B, Li L. Heterogeneous expansion of CD4+ tumor-infiltrating T-lymphocytes in clear cell renal cell carcinomas. Biochem Biophys Res Commun 2015; 458:70-6. [PMID: 25637538 DOI: 10.1016/j.bbrc.2015.01.069] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Accepted: 01/16/2015] [Indexed: 11/18/2022]
Abstract
Aberrant expression of tumor-associated antigens (TAAs) mediates the effective mounting of adaptive immunity in human solid tumors. The foundations of this tumor-host interaction strongly depend on specific recognition via TAA-cognate-receptors in T-cell repertoires. Previous studies focused on the phenotypic and functional properties of CD4+/CD8+ tumor-infiltrating T-lymphocytes (TILs), but the detailed composition of T-cell repertoires of these fundamental subsets remains largely unknown. This study recruited 10 clear cell renal cell carcinoma (ccRCC) patients and obtained samples from various tissues, including tumors, adjacent healthy renal tissue and peripheral blood. We utilized deep sequencing of T-cell receptor beta chains (TCRB), which serve as a unique identifier for each T clonotype, to characterize the CD4+/CD8+ TIL repertoire in ccRCC patients, assess the diversity and clonality of infiltrated T-cells in distinct tissues from patients and depict the clonal expansion events that occur in anti-tumor immune responses. We found that the CD4+ TIL repertoire exhibited signatures of heterogeneous T-cell expansion, which were characterized by divergent TRBV/J usage and an enrichment of expanded dominant clones. Taken together, our findings provide additional evidence of CD4+ T-cell-mediated anti-tumor immunity. The identification of the underlying molecular mechanisms of this process may provide novel avenues for targeted immunotherapeutic interventions.
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MESH Headings
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/pathology
- CD4-Positive T-Lymphocytes/physiology
- CD8-Positive T-Lymphocytes/pathology
- Carcinoma, Renal Cell/immunology
- Carcinoma, Renal Cell/pathology
- Humans
- Kidney Neoplasms/immunology
- Kidney Neoplasms/pathology
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/pathology
- Lymphocytes, Tumor-Infiltrating/physiology
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Tumor Microenvironment/genetics
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Affiliation(s)
- Qian Zhang
- Department of Urology, XinQiao Hospital, Third Military Medical University, Chongqing, China; Department of Urology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Qingzhu Jia
- Biomedical Analysis Center, Third Military Medical University, Chongqing, China
| | - Tianxing Deng
- Department of Urology, XinQiao Hospital, Third Military Medical University, Chongqing, China
| | - Bo Song
- Department of Urology, Southwest Hospital, Third Military Medical University, Chongqing, China.
| | - Longkun Li
- Department of Urology, XinQiao Hospital, Third Military Medical University, Chongqing, China.
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