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Luque Duque D, Gaevert JA, Thomas PG, López-García M, Lythe G, Molina-París C. Multi-variate model of T cell clonotype competition and homeostasis. Sci Rep 2023; 13:21995. [PMID: 38081863 PMCID: PMC10713556 DOI: 10.1038/s41598-023-46637-4] [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: 07/06/2022] [Accepted: 11/03/2023] [Indexed: 12/18/2023] Open
Abstract
Diversity of the naive T cell repertoire is maintained by competition for stimuli provided by self-peptides bound to major histocompatibility complexes (self-pMHCs). We extend an existing bi-variate competition model to a multi-variate model of the dynamics of multiple T cell clonotypes which share stimuli. In order to understand the late-time behaviour of the system, we analyse: (i) the dynamics until the extinction of the first clonotype, (ii) the time to the first extinction event, (iii) the probability of extinction of each clonotype, and (iv) the size of the surviving clonotypes when the first extinction event takes place. We also find the probability distribution of the number of cell divisions per clonotype before its extinction. The mean size of a new clonotype at quasi-steady state is an increasing function of the stimulus available to it, and a decreasing function of the fraction of stimuli it shares with other clonotypes. Thus, the probability of, and time to, extinction of a new clonotype entering the pool of T cell clonotypes is determined by the extent of competition for stimuli it experiences and by its initial number of cells.
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Affiliation(s)
- Daniel Luque Duque
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, LS2 9JT, UK
| | - Jessica A Gaevert
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN, 38105, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN, 38105, USA
| | - Martín López-García
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, LS2 9JT, UK
| | - Grant Lythe
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, LS2 9JT, UK
| | - Carmen Molina-París
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, LS2 9JT, UK.
- T-6, Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
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2
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Kalinina AA, Khromykh LM, Kazansky DB. T Cell Receptor Chain Centricity: The Phenomenon and Potential Applications in Cancer Immunotherapy. Int J Mol Sci 2023; 24:15211. [PMID: 37894892 PMCID: PMC10607890 DOI: 10.3390/ijms242015211] [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: 08/31/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
T cells are crucial players in adaptive anti-cancer immunity. The gene modification of T cells with tumor antigen-specific T cell receptors (TCRs) was a milestone in personalized cancer immunotherapy. TCR is a heterodimer (either α/β or γ/δ) able to recognize a peptide antigen in a complex with self-MHC molecules. Although traditional concepts assume that an α- and β-chain contribute equally to antigen recognition, mounting data reveal that certain receptors possess chain centricity, i.e., one hemi-chain TCR dominates antigen recognition and dictates its specificity. Chain-centric TCRs are currently poorly understood in terms of their origin and the functional T cell subsets that express them. In addition, the ratio of α- and β-chain-centric TCRs, as well as the exact proportion of chain-centric TCRs in the native repertoire, is generally still unknown today. In this review, we provide a retrospective analysis of studies that evidence chain-centric TCRs, propose patterns of their generation, and discuss the potential applications of such receptors in T cell gene modification for adoptive cancer immunotherapy.
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Affiliation(s)
| | | | - Dmitry B. Kazansky
- N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of the Russian Federation, 115478 Moscow, Russia
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3
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Shen Y, Voigt A, Leng X, Rodriguez AA, Nguyen CQ. A current and future perspective on T cell receptor repertoire profiling. Front Genet 2023; 14:1159109. [PMID: 37408774 PMCID: PMC10319011 DOI: 10.3389/fgene.2023.1159109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 06/12/2023] [Indexed: 07/07/2023] Open
Abstract
T cell receptors (TCR) play a vital role in the immune system's ability to recognize and respond to foreign antigens, relying on the highly polymorphic rearrangement of TCR genes. The recognition of autologous peptides by adaptive immunity may lead to the development and progression of autoimmune diseases. Understanding the specific TCR involved in this process can provide insights into the autoimmune process. RNA-seq (RNA sequencing) is a valuable tool for studying TCR repertoires by providing a comprehensive and quantitative analysis of the RNA transcripts. With the development of RNA technology, transcriptomic data must provide valuable information to model and predict TCR and antigen interaction and, more importantly, identify or predict neoantigens. This review provides an overview of the application and development of bulk RNA-seq and single-cell (SC) RNA-seq to examine the TCR repertoires. Furthermore, discussed here are bioinformatic tools that can be applied to study the structural biology of peptide/TCR/MHC (major histocompatibility complex) and predict antigenic epitopes using advanced artificial intelligence tools.
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Affiliation(s)
- Yiran Shen
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Alexandria Voigt
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Xuebing Leng
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Amy A. Rodriguez
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Cuong Q. Nguyen
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, United States
- Center of Orphaned Autoimmune Diseases, University of Florida, Gainesville, FL, United States
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4
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Zhuo Y, Yang X, Shuai P, Yang L, Wen X, Zhong X, Yang S, Xu S, Liu Y, Zhang Z. Evaluation and comparison of adaptive immunity through analyzing the diversities and clonalities of T-cell receptor repertoires in the peripheral blood. Front Immunol 2022; 13:916430. [PMID: 36159829 PMCID: PMC9493076 DOI: 10.3389/fimmu.2022.916430] [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: 04/20/2022] [Accepted: 07/26/2022] [Indexed: 11/17/2022] Open
Abstract
The adaptive immune system plays an important role in defending against different kinds of diseases, including infection and cancer. There has been a longtime need for a simple method to quantitatively evaluate the potency of adaptive immunity in our bodies. The tremendously diversified T-cell receptor (TCR) repertoires are the foundation of the adaptive immune system. In this study, we analyzed the expressed TCRβ repertoires in the peripheral blood of 582 healthy donors and 60 cancer patients. The TCR repertoire in each individual is different, with different usages of TCR Vβ and Jβ genes. Importantly, the TCR diversity and clonality change along with age and disease situation. Most elder individuals and cancer patients have elevated numbers of large TCRβ clones and reduced numbers of shared common clones, and thus, they have very low TCR diversity index (D50) values. These results reveal the alteration of the expressed TCRβ repertoire with aging and oncogenesis, and thus, we hypothesize that the TCR diversity and clonality in the peripheral blood might be used to evaluate and compare the adaptive immunities among different individuals in clinical practice.
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Affiliation(s)
- Yue Zhuo
- Department of Health Management & Institute of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Xin Yang
- Department of Health Management & Institute of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Ping Shuai
- Department of Health Management & Institute of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Liangliang Yang
- Department of Health Management & Institute of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Xueping Wen
- Department of Technology, Chengdu ExAb Biotechnology, LTD, Chengdu, China
| | - Xuemei Zhong
- Department of Technology, Chengdu ExAb Biotechnology, LTD, Chengdu, China
| | - Shihan Yang
- Department of Technology, Chengdu ExAb Biotechnology, LTD, Chengdu, China
| | - Shaoxian Xu
- Department of Health Management & Institute of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Yuping Liu
- Department of Health Management & Institute of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- *Correspondence: Zhixin Zhang, ; Yuping Liu,
| | - Zhixin Zhang
- Department of Health Management & Institute of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- *Correspondence: Zhixin Zhang, ; Yuping Liu,
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5
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Tian G, Li M, Lv G. Analysis of T-Cell Receptor Repertoire in Transplantation: Fingerprint of T Cell-mediated Alloresponse. Front Immunol 2022; 12:778559. [PMID: 35095851 PMCID: PMC8790170 DOI: 10.3389/fimmu.2021.778559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022] Open
Abstract
T cells play a key role in determining allograft function by mediating allogeneic immune responses to cause rejection, and recent work pointed their role in mediating tolerance in transplantation. The unique T-cell receptor (TCR) expressed on the surface of each T cell determines the antigen specificity of the cell and can be the specific fingerprint for identifying and monitoring. Next-generation sequencing (NGS) techniques provide powerful tools for deep and high-throughput TCR profiling, and facilitate to depict the entire T cell repertoire profile and trace antigen-specific T cells in circulation and local tissues. Tailing T cell transcriptomes and TCR sequences at the single cell level provides a full landscape of alloreactive T-cell clones development and biofunction in alloresponse. Here, we review the recent advances in TCR sequencing techniques and computational tools, as well as the recent discovery in overall TCR profile and antigen-specific T cells tracking in transplantation. We further discuss the challenges and potential of using TCR sequencing-based assays to profile alloreactive TCR repertoire as the fingerprint for immune monitoring and prediction of rejection and tolerance.
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Affiliation(s)
| | - Mingqian Li
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
| | - Guoyue Lv
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
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6
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Lee MY, Jeon JW, Sievers C, Allen CT. Antigen processing and presentation in cancer immunotherapy. J Immunother Cancer 2021; 8:jitc-2020-001111. [PMID: 32859742 PMCID: PMC7454179 DOI: 10.1136/jitc-2020-001111] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2020] [Indexed: 12/25/2022] Open
Abstract
Background Knowledge about and identification of T cell tumor antigens may inform the development of T cell receptor-engineered adoptive cell transfer or personalized cancer vaccine immunotherapy. Here, we review antigen processing and presentation and discuss limitations in tumor antigen prediction approaches. Methods Original articles covering antigen processing and presentation, epitope discovery, and in silico T cell epitope prediction were reviewed. Results Natural processing and presentation of antigens is a complex process that involves proteasomal proteolysis of parental proteins, transportation of digested peptides into the endoplasmic reticulum, loading of peptides onto major histocompatibility complex (MHC) class I molecules, and shuttling of peptide:MHC complexes to the cell surface. A number of T cell tumor antigens have been experimentally validated in patients with cancer. Assessment of predicted MHC class I binding and total score for these validated T cell antigens demonstrated a wide range of values, with nearly one-third of validated antigens carrying an IC50 of greater than 500 nM. Conclusions Antigen processing and presentation is a complex, multistep process. In silico epitope prediction techniques can be a useful tool, but comprehensive experimental testing and validation on a patient-by-patient basis may be required to reliably identify T cell tumor antigens.
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Affiliation(s)
- Maxwell Y Lee
- NIDCD, National Institutes of Health, Bethesda, Maryland, USA
| | - Jun W Jeon
- NIDCD, National Institutes of Health, Bethesda, Maryland, USA
| | - Cem Sievers
- NIDCD, National Institutes of Health, Bethesda, Maryland, USA
| | - Clint T Allen
- NIDCD, National Institutes of Health, Bethesda, Maryland, USA
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7
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Zhang J, Wang Y, Yu H, Chen G, Wang L, Liu F, Yuan J, Ni Q, Xia X, Wan Y. Mapping the spatial distribution of T cells in repertoire dimension. Mol Immunol 2021; 138:161-171. [PMID: 34428621 DOI: 10.1016/j.molimm.2021.08.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 08/01/2021] [Accepted: 08/15/2021] [Indexed: 01/13/2023]
Abstract
T cells mediate adaptive immunity in diverse anatomic compartments through recognition of specific antigens via unique T cell receptor (TCR) structures. However, little is known about the spatial distribution of an organism's TCR repertoire. Here, using high-throughput TCR sequencing (TCRseq), we investigated the TCR repertoires of sixteen tissues in healthy C57B/L6 mice. We found that TCR repertoires generally classified into three categories (lymph nodes, non-lymph node tissues and small intestine) based on sequence similarity. Clonal distribution and diversity analyses showed that small intestine compartment had a more skewed repertoire as compared to lymph nodes and non-lymph node tissues. However, analysis of TRBV and TRBJ gene usage across tissue compartments, as well as comparison of CDR3 length distributions, showed no significant tissue-dependent differences. Interestingly, analysis of clonotype sharing between mice showed that although non-redundant public clonotypes were found more easily in lymph nodes, small intestinal CD4 + T cells harbored more abundant public clonotypes. These findings under healthy physiological conditions offer an important reference dataset, which may contribute to our ability to better manipulate T cell responses against infection and vaccination.
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Affiliation(s)
- Junying Zhang
- School of Pharmaceutical Sciences and Innovative Drug Research Center, Chongqing University, Chongqing, 401331, China
| | - Yu Wang
- Zunyi Medical University, Zunyi, 563003, China
| | - Haili Yu
- Biomedical Analysis Center, Army Medical University, Chongqing, 400038, China; Chongqing Key Laboratory of Cytomics, Chongqing, 400038, China
| | - Gang Chen
- Biomedical Analysis Center, Army Medical University, Chongqing, 400038, China; Chongqing Key Laboratory of Cytomics, Chongqing, 400038, China
| | - Liting Wang
- Biomedical Analysis Center, Army Medical University, Chongqing, 400038, China; Chongqing Key Laboratory of Cytomics, Chongqing, 400038, China
| | - Fang Liu
- Biomedical Analysis Center, Army Medical University, Chongqing, 400038, China; Chongqing Key Laboratory of Cytomics, Chongqing, 400038, China
| | - Jiangbei Yuan
- Hepato-Pancreato-Biliary Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Guangdong Province, 518036, China
| | - Qingshan Ni
- Biomedical Analysis Center, Army Medical University, Chongqing, 400038, China; Chongqing Key Laboratory of Cytomics, Chongqing, 400038, China.
| | - Xuefeng Xia
- School of Pharmaceutical Sciences and Innovative Drug Research Center, Chongqing University, Chongqing, 401331, China.
| | - Ying Wan
- Biomedical Analysis Center, Army Medical University, Chongqing, 400038, China; Chongqing Key Laboratory of Cytomics, Chongqing, 400038, China; School of Big Data & Software Engineering, Chongqing University, Chongqing, 401331, China.
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8
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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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9
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Yiu HH, Schoettle LN, Garcia-Neuer M, Blattman JN, Johnson PLF. Selection influences naive CD8+ TCR-β repertoire sharing. Immunology 2021; 162:464-475. [PMID: 33345304 DOI: 10.1111/imm.13299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 11/22/2020] [Accepted: 11/29/2020] [Indexed: 11/28/2022] Open
Abstract
Within each individual, the adaptive immune system generates a repertoire of cells expressing receptors capable of recognizing diverse potential pathogens. The theoretical diversity of the T-cell receptor (TCR) repertoire exceeds the actual size of the T-cell population in an individual by several orders of magnitude - making the observation of identical TCRs in different individuals extremely improbable if all receptors were equally likely. Despite this disparity between the theoretical and the realized diversity of the repertoire, these 'public' receptor sequences have been identified in autoimmune, cancer and pathogen interaction contexts. Biased generation processes explain the presence of public TCRs in the naive repertoire, but do not adequately explain the different abundances of these public TCRs. We investigate and characterize the distribution of genomic TCR-β sequences of naive CD8+ T cells from three genetically identical mice, comparing non-productive (non-functional sequences) and productive sequences. We find public TCR-β sequences at higher abundances compared with unshared sequences in the productive, but not in the non-productive, repertoire. We show that neutral processes such as recombination biases, codon degeneracy and generation probability do not fully account for these differences, and conclude that thymic or peripheral selection plays an important role in increasing the abundances of public TCR-β sequences.
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Affiliation(s)
- Hao H Yiu
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Louis N Schoettle
- School of Life Sciences, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Marlene Garcia-Neuer
- School of Life Sciences, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Joseph N Blattman
- School of Life Sciences, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
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10
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Abstract
T cells are an integral component of the adaptive immune response via the recognition of peptides by the cell surface-expressed T cell receptor (TCR). Rearrangement of the TCR genes results in a highly polymorphic repertoire on the T cells within a given individual. Although the diverse repertoire is beneficial for immune responses to foreign pathogens, recognition of self-peptides by T cells can contribute to the development of autoimmune disorders. Increasing evidence supports a pathogenic role for T cells in autoimmune pathology, and it is of interest to determine the TCR repertoires involved in autoimmune disease development. In this review, we summarize methodologies and advancements in the TCR sequencing field and discuss recent studies focused on TCR sequencing in a variety of autoimmune conditions. The rapidly evolving methodology of TCR sequencing has the potential to allow for a better understanding of autoimmune disease pathogenesis, identify disease-specific biomarkers, and aid in developing therapies to prevent and treat a number of these disorders.
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Affiliation(s)
- Angela M Mitchell
- Barbara Davis Center for Diabetes, University of Colorado, Aurora, CO, USA, 80045
| | - Aaron W Michels
- Barbara Davis Center for Diabetes, University of Colorado, Aurora, CO, USA, 80045
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11
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Manfredi F, Cianciotti BC, Potenza A, Tassi E, Noviello M, Biondi A, Ciceri F, Bonini C, Ruggiero E. TCR Redirected T Cells for Cancer Treatment: Achievements, Hurdles, and Goals. Front Immunol 2020; 11:1689. [PMID: 33013822 PMCID: PMC7494743 DOI: 10.3389/fimmu.2020.01689] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/24/2020] [Indexed: 12/11/2022] Open
Abstract
Adoptive T cell therapy (ACT) is a rapidly evolving therapeutic approach designed to harness T cell specificity and function to fight diseases. Based on the evidence that T lymphocytes can mediate a potent anti-tumor response, initially ACT solely relied on the isolation, in vitro expansion, and infusion of tumor-infiltrating or circulating tumor-specific T cells. Although effective in a subset of cases, in the first ACT clinical trials several patients experienced disease progression, in some cases after temporary disease control. This evidence prompted researchers to improve ACT products by taking advantage of the continuously evolving gene engineering field and by improving manufacturing protocols, to enable the generation of effective and long-term persisting tumor-specific T cell products. Despite recent advances, several challenges, including prioritization of antigen targets, identification, and optimization of tumor-specific T cell receptors, in the development of tools enabling T cells to counteract the immunosuppressive tumor microenvironment, still need to be faced. This review aims at summarizing the major achievements, hurdles and possible solutions designed to improve the ACT efficacy and safety profile in the context of liquid and solid tumors.
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Affiliation(s)
- Francesco Manfredi
- Vita-Salute San Raffaele University, Milan, Italy.,Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Beatrice Claudia Cianciotti
- Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Fondazione Centro San Raffaele, Milan, Italy
| | - Alessia Potenza
- Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy.,School of Medicine and Surgery, University of Milano - Bicocca, Milan, Italy
| | - Elena Tassi
- Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maddalena Noviello
- Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Biondi
- Clinica Pediatrica Università degli Studi di Milano Bicocca, Fondazione MBBM, Monza, Italy
| | - Fabio Ciceri
- Vita-Salute San Raffaele University, Milan, Italy.,Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Bonini
- Vita-Salute San Raffaele University, Milan, Italy.,Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Eliana Ruggiero
- Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
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12
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Lee M, Lee E, Han SK, Choi YH, Kwon DI, Choi H, Lee K, Park ES, Rha MS, Joo DJ, Shin EC, Kim S, Kim JK, Lee YJ. Single-cell RNA sequencing identifies shared differentiation paths of mouse thymic innate T cells. Nat Commun 2020; 11:4367. [PMID: 32868763 PMCID: PMC7459300 DOI: 10.1038/s41467-020-18155-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 08/09/2020] [Indexed: 12/19/2022] Open
Abstract
Invariant natural killer T (iNKT), mucosal-associated invariant T (MAIT), and γδ T cells are innate T cells that acquire memory phenotype in the thymus and share similar biological characteristics. However, how their effector differentiation is developmentally regulated is still unclear. Here, we identify analogous effector subsets of these three innate T cell types in the thymus that share transcriptional profiles. Using single-cell RNA sequencing, we show that iNKT, MAIT and γδ T cells mature via shared, branched differentiation rather than linear maturation or TCR-mediated instruction. Simultaneous TCR clonotyping analysis reveals that thymic maturation of all three types is accompanied by clonal selection and expansion. Analyses of mice deficient of TBET, GATA3 or RORγt and additional in vivo experiments corroborate the predicted differentiation paths, while human innate T cells from liver samples display similar features. Collectively, our data indicate that innate T cells share effector differentiation processes in the thymus. Innate T cells such as iNKT, MAIT and γδ T cells all develop in the thymus, but their differentiation paths are still unclear. Here, the authors show, using single-cell RNA sequencing, that all three cell types develop via shared and branched differentiation paths that are corroborated by additional results from gene-deficient mice and human liver T cells.
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Affiliation(s)
- Minji Lee
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Eunmin Lee
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea
| | - Seong Kyu Han
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Yoon Ha Choi
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea
| | - Dong-Il Kwon
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Hyobeen Choi
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Kwanghwan Lee
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Eun Seo Park
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea
| | - Min-Seok Rha
- Laboratory of Immunology and Infectious Diseases, Graduate School of Medical Science and Engineering, KAIST, Daejeon, Korea
| | - Dong Jin Joo
- Department of Surgery, Yonsei University, College of Medicine, Seoul, Republic of Korea.,The Research Institute for Transplantation, Yonsei University, College of Medicine, Seoul, Republic of Korea
| | - Eui-Cheol Shin
- Laboratory of Immunology and Infectious Diseases, Graduate School of Medical Science and Engineering, KAIST, Daejeon, Korea
| | - Sanguk Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
| | - Jong Kyoung Kim
- Department of New Biology, DGIST, Daegu, 42988, Republic of Korea.
| | - You Jeong Lee
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
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13
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Li N, Yuan J, Tian W, Meng L, Liu Y. T-cell receptor repertoire analysis for the diagnosis and treatment of solid tumor: A methodology and clinical applications. Cancer Commun (Lond) 2020; 40:473-483. [PMID: 32677768 PMCID: PMC7571402 DOI: 10.1002/cac2.12074] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022] Open
Abstract
T cells, which are involved in adaptive immunity, are essential in the elimination of tumor cells. Mature T cells can specifically recognize the antigen on the major histocompatibility complex (MHC) molecule through T‐cell receptors (TCR). The unique rearrangement mechanisms during T‐cell maturation provide great diversity to TCR, ensuring specific recognition between T cells and antigens. Thus, TCR repertoire analysis occupied an important position in T‐cell regarding research. Nowadays, next‐generation sequencing technology allows the simultaneous detection of TCR sequences with high throughput, and several evaluation indexes facilitate the measure of TCR repertoire. Based on this new methodology, discoveries are made across a range of tumor types. Results have shed light on the TCR repertoire differences between cancer patients and healthy control as well as between individual's lesions, paracancer, and peripheral blood samples. The potential of TCR repertoire as a biomarker for immunotherapy efficacy is also widely studied as TCR repertoire represents different baseline within individuals and shows dynamic change during treatment. Accurate delineation of the T‐cell repertoire can further the understanding of the immune system response to tumorigenesis. Still, existing researches are insufficient to clarify the specific clinical implications of TCR dynamic change and the definite role of TCR repertoire diversity during the treatment process. The results of some studies are even contrary. In this article, we reviewed TCR rearrangement mechanisms and analysis methods. Recent progress of TCR sequencing technology in tumor research is also discussed. In conclusion, intensive studies over an extended range of cancer types and a broadened group of subjects should be carried to solidify the TCR repertoire's position as an immunotherapy biomarker.
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Affiliation(s)
- Na Li
- Department of Central Laboratory, Shenyang Tenth People's Hospital, Shenyang Chest Hospital, Shenyang, Liaoning, 110044, P. R. China
| | - Jiani Yuan
- Novogene Corporation Limited, Beijing, 100083, P. R. China
| | - Wenjia Tian
- Novogene Corporation Limited, Beijing, 100083, P. R. China
| | - Lin Meng
- Novogene Corporation Limited, Beijing, 100083, P. R. China
| | - Yongyu Liu
- Department of Thoracic Surgery, Shenyang Tenth People's Hospital, Shenyang Chest Hospital, Shenyang, Liaoning, 110044, P. R. China
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14
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The Identity Card of T Cells-Clinical Utility of T-cell Receptor Repertoire Analysis in Transplantation. Transplantation 2020; 103:1544-1555. [PMID: 31033649 DOI: 10.1097/tp.0000000000002776] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
There is a clear medical need to change the current strategy of "one-size-fits-all" immunosuppression for controlling transplant rejection to precision medicine and targeted immune intervention. As T cells play a key role in both undesired graft rejection and protection, a better understanding of the fate and function of both alloreactive graft-deteriorating T cells and those protecting to infections is required. The T-cell receptor (TCR) is the individual identity card of each T cell clone and can help to follow single specificities. In this context, tracking of lymphocytes with certain specificity in blood and tissue in clinical follow up is of especial importance. After overcoming technical limitations of the past, novel molecular technologies opened new avenues of diagnostics. Using advantages of next generation sequencing, a method was established for T-cell tracing by detection of variable TCR region as identifiers of individual lymphocyte clones. The current review describes principles of laboratory and computational methods of TCR repertoire analysis, and gives an overview on applications for the basic understanding of transplant biology and immune monitoring. The review also delineates methodological pitfalls and challenges. With the outlook on prediction of antigens in immune-mediated processes including those of unknown causative pathogens, monitoring the fate and function of individual T cell clones, and the adoptive transfer of protective effector or regulatory T cells, this review highlights the current and future capability of TCR repertoire analysis.
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15
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Gupta S, Witas R, Voigt A, Semenova T, Nguyen CQ. Single-Cell Sequencing of T cell Receptors: A Perspective on the Technological Development and Translational Application. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:29-50. [PMID: 32949388 DOI: 10.1007/978-981-15-4494-1_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
T cells recognize peptides bound to major histocompatibility complex (MHC) class I and class II molecules at the cell surface. This recognition is accomplished by the expression of T cell receptors (TCR) which are required to be diverse and adaptable in order to accommodate the various and vast number of antigens presented on the MHCs. Thus, determining TCR repertoires of effector T cells is necessary to understand the immunological process in responding to cancer progression, infection, and autoimmune development. Furthermore, understanding the TCR repertoires will provide a solid framework to predict and test the antigen which is more critical in autoimmunity. However, it has been a technical challenge to sequence the TCRs and provide a conceptual context in correlation to the vast number of TCR repertoires in the immunological system. The exploding field of single-cell sequencing has changed how the repertoires are being investigated and analyzed. In this review, we focus on the biology of TCRs, TCR signaling and its implication in autoimmunity. We discuss important methods in bulk sequencing of many cells. Lastly, we explore the most pertinent platforms in single-cell sequencing and its application in autoimmunity.
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Affiliation(s)
- Shivai Gupta
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Richard Witas
- Department of Oral Biology, College of Dentistry, Gainesville, FL, USA
| | - Alexandria Voigt
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Touyana Semenova
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA
| | - Cuong Q Nguyen
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, Gainesville, FL, USA. .,Department of Oral Biology, College of Dentistry, Gainesville, FL, USA. .,Center of Orphaned Autoimmune Diseases, University of Florida, Gainesville, FL, USA.
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16
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Jimeno R, Lebrusant-Fernandez M, Margreitter C, Lucas B, Veerapen N, Kelly G, Besra GS, Fraternali F, Spencer J, Anderson G, Barral P. Tissue-specific shaping of the TCR repertoire and antigen specificity of iNKT cells. eLife 2019; 8:51663. [PMID: 31841113 PMCID: PMC6930077 DOI: 10.7554/elife.51663] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/15/2019] [Indexed: 12/19/2022] Open
Abstract
Tissue homeostasis is critically dependent on the function of tissue-resident lymphocytes, including lipid-reactive invariant natural killer T (iNKT) cells. Yet, if and how the tissue environment shapes the antigen specificity of iNKT cells remains unknown. By analysing iNKT cells from lymphoid tissues of mice and humans we demonstrate that their T cell receptor (TCR) repertoire is highly diverse and is distinct for cells from various tissues resulting in differential lipid-antigen recognition. Within peripheral tissues iNKT cell recent thymic emigrants exhibit a different TCR repertoire than mature cells, suggesting that the iNKT population is shaped after arrival to the periphery. Consistent with this, iNKT cells from different organs show distinct basal activation, proliferation and clonal expansion. Moreover, the iNKT cell TCR repertoire changes following immunisation and is shaped by age and environmental changes. Thus, post-thymic modification of the TCR-repertoire underpins the distinct antigen specificity for iNKT cells in peripheral tissues
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Affiliation(s)
- Rebeca Jimeno
- The Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom.,The Francis Crick Institute, London, United Kingdom
| | - Marta Lebrusant-Fernandez
- The Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom.,The Francis Crick Institute, London, United Kingdom
| | - Christian Margreitter
- Randall Centre for Cell & Molecular Biophysics, King's College London, London, United Kingdom
| | - Beth Lucas
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Natacha Veerapen
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Gavin Kelly
- Bioinformatics and Biostatistics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Franca Fraternali
- Randall Centre for Cell & Molecular Biophysics, King's College London, London, United Kingdom
| | - Jo Spencer
- The Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom
| | - Graham Anderson
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Patricia Barral
- The Peter Gorer Department of Immunobiology, King's College London, London, United Kingdom.,The Francis Crick Institute, London, United Kingdom
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17
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Georgieva M, Buckee CO, Lipsitch M. Models of immune selection for multi-locus antigenic diversity of pathogens. Nat Rev Immunol 2019; 19:55-62. [PMID: 30479379 DOI: 10.1038/s41577-018-0092-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
It is well accepted that pathogens can evade recognition and elimination by the host immune system by varying their antigenic targets. Thus, it has become a truism that host immunity is a major driver and determinant of the antigenic diversity of pathogens. However, it remains puzzling how host immunity selects for antigenic diversity at the level of the pathogen population, given that hosts have acquired immune responses to multiple antigens of most pathogens - sometimes through multiple effectors of both humoral and cellular immunity. In this Opinion article, we address this puzzle and the related question of why pathogens often have diversity at multiple antigenic loci. Here, we describe five hypotheses to explain the polymorphism of multiple antigens in a single pathogen species and highlight research relevant to our current models of thinking about multi-locus antigenic diversity.
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Affiliation(s)
- Maria Georgieva
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA. .,Department of Physiology, University of Lausanne, Lausanne, Switzerland.
| | - Caroline O Buckee
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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18
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Miyauchi E, Matsuda T, Kiyotani K, Low SK, Hsu YW, Tsukita Y, Ichinose M, Sakurada A, Okada Y, Saito R, Nakamura Y. Significant differences in T cell receptor repertoires in lung adenocarcinomas with and without epidermal growth factor receptor mutations. Cancer Sci 2019; 110:867-874. [PMID: 30582659 PMCID: PMC6398877 DOI: 10.1111/cas.13919] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Recent clinical trials of non‐small cell lung cancer with immune checkpoint inhibitors revealed that patients with epidermal growth factor receptor (EGFR) mutations had more unfavorable outcomes compared with those with wild‐type EGFR. However, the underlying mechanism for the link between EGFR mutations and immune resistance remains unclear. We performed T cell receptor (TCR) repertoire analysis of resected lung adenocarcinoma tissues with and without EGFR mutations to investigate the characteristics of TCR repertoires. We collected a total of 39 paired (normal and tumor) lung tissue samples (20 had EGFR mutations) and conducted TCR repertoire analysis as well as whole‐exome sequencing (WES) and transcriptome analysis. The TCR diversity index in EGFR‐mutant tumors was significantly higher than that in EGFR‐wild‐type tumors (median [range] 552 [162‐1,135] vs 230 [30‐764]; P < .01), suggesting higher T cell clonal expansion in EGFR‐wild‐type tumors than in EGFR‐mutant tumors. In WES, EGFR‐mutant tumors showed lower numbers of non‐synonymous mutations and predicted neoantigens than EGFR‐wild‐type tumors (P < .01, P = .03, respectively). The number of non‐synonymous mutations revealed a positive correlation with the sum of frequencies of the TCRβ clonotypes of 1% or higher in tumors (r = .52, P = .04). The present study demonstrates significant differences in TCR repertoires and the number of predicted neoantigens between EGFR‐mutant and wild‐type lung tumors. Our findings provide important information for understanding the molecular mechanism behind EGFR‐mutant patients showing unfavorable responses to immune checkpoint inhibitors.
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Affiliation(s)
- Eisaku Miyauchi
- Department of Medicine, The University of Chicago, Chicago, Illinois.,Department of Respiratory Medicine, Tohoku University, Sendai, Japan
| | - Tatsuo Matsuda
- Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Kazuma Kiyotani
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Siew-Kee Low
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yu-Wen Hsu
- Department of Medicine, The University of Chicago, Chicago, Illinois.,The Ph.D. Program for Translational Medicine, Taipei Medical University and Academia Sinica, Taipei, Taiwan
| | - Yoko Tsukita
- Department of Respiratory Medicine, Tohoku University, Sendai, Japan
| | - Masakazu Ichinose
- Department of Respiratory Medicine, Tohoku University, Sendai, Japan
| | - Akira Sakurada
- Department of Thoracic Surgery, Tohoku University, Sendai, Japan
| | - Yoshinori Okada
- Department of Thoracic Surgery, Tohoku University, Sendai, Japan
| | - Ryoko Saito
- Department of Pathology, Tohoku University Hospital, Sendai, Japan
| | - Yusuke Nakamura
- Department of Medicine, The University of Chicago, Chicago, Illinois.,Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Surgery, The University of Chicago, Chicago, Illinois
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19
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Wanjalla CN, McDonnell WJ, Koethe JR. Adipose Tissue T Cells in HIV/SIV Infection. Front Immunol 2018; 9:2730. [PMID: 30559739 PMCID: PMC6286992 DOI: 10.3389/fimmu.2018.02730] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 11/05/2018] [Indexed: 12/12/2022] Open
Abstract
Adipose tissue comprises one of the largest organs in the body and performs diverse functions including energy storage and release, regulation of appetite and other neuroendocrine signaling, and modulation of immuity, among others. Adipocytes reside in a complex compartment where antigen, antigen presenting cells, innate immune cells, and adaptive immune cells interact locally and exert systemic effects on inflammation, circulating immune cell profiles, and metabolic homeostasis. T lymphocytes are a major component of the adipose tissue milieu which are altered in disease states such as obesity and human immunodeficiency virus (HIV) infection. While obesity, HIV infection, and simian immunodeficiency virus (SIV; a non-human primate virus similar to HIV) infection are accompanied by enrichment of CD8+ T cells in the adipose tissue, major phenotypic differences in CD4+ T cells and other immune cell populations distinguish HIV/SIV infection from obesity. Furthermore, DNA and RNA species of HIV and SIV can be detected in the stromal vascular fraction of visceral and subcutaneous adipose tissue, and replication-competent HIV resides in local CD4+ T cells. Here, we review studies of adipose tissue CD4+ and CD8+ T cell populations in HIV and SIV, and contrast the findings with those reported in obesity.
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Affiliation(s)
- Celestine N Wanjalla
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States.,Center for Translational Immunology and Infectious Disease, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Wyatt J McDonnell
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States.,Center for Translational Immunology and Infectious Disease, Vanderbilt University Medical Center, Nashville, TN, United States.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN, United States
| | - John R Koethe
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States.,Center for Translational Immunology and Infectious Disease, Vanderbilt University Medical Center, Nashville, TN, United States
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20
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McDonnell WJ, Koethe JR, Mallal SA, Pilkinton MA, Kirabo A, Ameka MK, Cottam MA, Hasty AH, Kennedy AJ. High CD8 T-Cell Receptor Clonality and Altered CDR3 Properties Are Associated With Elevated Isolevuglandins in Adipose Tissue During Diet-Induced Obesity. Diabetes 2018; 67:2361-2376. [PMID: 30181158 PMCID: PMC6198339 DOI: 10.2337/db18-0040] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 08/20/2018] [Indexed: 12/29/2022]
Abstract
Adipose tissue (AT) CD4+ and CD8+ T cells contribute to obesity-associated insulin resistance. Prior studies identified conserved T-cell receptor (TCR) chain families in obese AT, but the presence and clonal expansion of specific TCR sequences in obesity has not been assessed. We characterized AT and liver CD8+ and CD4+ TCR repertoires of mice fed a low-fat diet (LFD) and high-fat diet (HFD) using deep sequencing of the TCRβ chain to quantify clonal expansion, gene usage, and CDR3 sequence. In AT CD8+ T cells, HFD reduced TCR diversity, increased the prevalence of public TCR clonotypes, and selected for TCR CDR3 regions enriched in positively charged and less polarized amino acids. Although TCR repertoire alone could distinguish between LFD- and HFD-fed mice, these properties of the CDR3 region of AT CD8+ T cells from HFD-fed mice led us to examine the role of negatively charged and nonpolar isolevuglandin (isoLG) adduct-containing antigen-presenting cells within AT. IsoLG-adducted protein species were significantly higher in AT macrophages of HFD-fed mice; isoLGs were elevated in M2-polarized macrophages, promoting CD8+ T-cell activation. Our findings demonstrate that clonal TCR expansion that favors positively charged CDR3s accompanies HFD-induced obesity, which may be an antigen-driven response to isoLG accumulation in macrophages.
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Affiliation(s)
- Wyatt J McDonnell
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN
- Center for Translational Immunology and Infectious Disease, Vanderbilt University Medical Center, Nashville, TN
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN
| | - John R Koethe
- Center for Translational Immunology and Infectious Disease, Vanderbilt University Medical Center, Nashville, TN
- Department of Medicine, Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN
- Veterans Administration Tennessee Valley Healthcare System, Nashville, TN
| | - Simon A Mallal
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN
- Center for Translational Immunology and Infectious Disease, Vanderbilt University Medical Center, Nashville, TN
- Department of Medicine, Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia
| | - Mark A Pilkinton
- Center for Translational Immunology and Infectious Disease, Vanderbilt University Medical Center, Nashville, TN
- Department of Medicine, Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN
- Veterans Administration Tennessee Valley Healthcare System, Nashville, TN
| | - Annet Kirabo
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Magdalene K Ameka
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
| | - Matthew A Cottam
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
| | - Alyssa H Hasty
- Veterans Administration Tennessee Valley Healthcare System, Nashville, TN
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
| | - Arion J Kennedy
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN
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21
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De Simone M, Rossetti G, Pagani M. Single Cell T Cell Receptor Sequencing: Techniques and Future Challenges. Front Immunol 2018; 9:1638. [PMID: 30072991 PMCID: PMC6058020 DOI: 10.3389/fimmu.2018.01638] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 07/03/2018] [Indexed: 12/19/2022] Open
Abstract
The peculiarity of T cell is their ability to recognize an infinite range of self and foreign antigens. This ability is achieved during thymic development through a complex molecular mechanism based on somatic recombination that leads to the expression of a very heterogeneous population of surface antigen receptors, the T Cell Receptors (TCRs). TCRs are cell specific and represent a sort of “molecular tag” of T cells and have been widely studied to monitor the dynamics of T cells in terms of clonality and diversity in several contexts including lymphoid malignancies, infectious diseases, autoimmune diseases, and tumor immunology. In this review, we provide an overview of the strategies used to investigate the TCR repertoire from the pioneering techniques based on the V segments identification to the revolution introduced by Next-Generation Sequencing that allows for high-throughput sequencing of alpha and beta chains. Single cell based approaches brought the analysis to a higher level of complexity and now provide the opportunity to sequence paired alpha and beta chains. We also discuss novel approaches that through the integration of TCR tracking and mRNA single cell sequencing offer a valuable tool to associate antigen specificity to transcriptional dynamics and to understand the molecular mechanisms of T cell plasticity.
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Affiliation(s)
- Marco De Simone
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Grazisa Rossetti
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Massimiliano Pagani
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
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22
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Sharma A, Rudra D. Emerging Functions of Regulatory T Cells in Tissue Homeostasis. Front Immunol 2018; 9:883. [PMID: 29887862 PMCID: PMC5989423 DOI: 10.3389/fimmu.2018.00883] [Citation(s) in RCA: 171] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/10/2018] [Indexed: 01/12/2023] Open
Abstract
CD4+Foxp3+ regulatory T-cells (Tregs) are a unique subset of helper T-cells, which regulate immune response and establish peripheral tolerance. Tregs not only maintain the tone and tenor of an immune response by dominant tolerance but, in recent years, have also been identified as key players in resolving tissue inflammation and as mediators of tissue healing. Apart from being diverse in their origin (thymic and peripheral) and location (lymphoid and tissue resident), Tregs are also phenotypically heterogeneous as per the orientation of ongoing immune response. In this review, we discuss the recent advances in the field of Treg biology in general, and non-lymphoid and tissue-resident Tregs in particular. We elaborate upon well-known visceral adipose tissue, colon, skin, and tumor-infiltrating Tregs and newly identified tissue Treg populations as in lungs, skeletal muscle, placenta, and other tissues. Our attempt is to differentiate Tregs based on distinctive properties of their location, origin, ligand specificity, chemotaxis, and specific suppressive mechanisms. Despite ever expanding roles in maintaining systemic homeostasis, Tregs are employed by large varieties of tumors to dampen antitumor immunity. Thus, a comprehensive understanding of Treg biology in the context of inflammation can be instrumental in effectively managing tissue transplantation, autoimmunity, and antitumor immune responses.
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Affiliation(s)
- Amit Sharma
- Academy of Immunology and Microbiology, Institute for Basic Science (IBS), Pohang, South Korea.,Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, South Korea
| | - Dipayan Rudra
- Academy of Immunology and Microbiology, Institute for Basic Science (IBS), Pohang, South Korea.,Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, South Korea
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23
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Cerqueira-Rodrigues B, Mendes A, Correia-Neves M, Nobrega C. Ag85-focused T-cell immune response controls Mycobacterium avium chronic infection. PLoS One 2018; 13:e0193596. [PMID: 29499041 PMCID: PMC5834192 DOI: 10.1371/journal.pone.0193596] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 02/14/2018] [Indexed: 01/09/2023] Open
Abstract
CD4+ T cells are essential players for the control of mycobacterial infections. Several mycobacterial antigens have been identified for eliciting a relevant CD4+ T cell mediated-immune response, and numerous studies explored this issue in the context of Mycobacterium tuberculosis infection. Antigen 85 (Ag85), a highly conserved protein across Mycobacterium species, is secreted at the early phase of M. tuberculosis infection leading to the proliferation of Ag85-specific CD4+ T cells. However, in the context of Mycobacterium avium infection, little is known about the expression of this antigen and the elicited immune response. In the current work, we investigated if a T cell receptor (TCR) repertoire mostly, but not exclusively, directed at Ag85 is sufficient to mount a protective immune response against M. avium. We show that P25 mice, whose majority of T cells express a transgenic TCR specific for Ag85, control M. avium infection at the same level as wild type (WT) mice up to 20 weeks post-infection (wpi). During M. avium infection, Ag85 antigen is easily detected in the liver of 20 wpi mice by immunohistochemistry. In spite of the propensity of P25 CD4+ T cells to produce higher amounts of interferon-gamma (IFNγ) upon ex vivo stimulation, no differences in serum IFNγ levels are detected in P25 compared to WT mice, nor enhanced immunopathology is detected in P25 mice. These results indicate that a T cell response dominated by Ag85-specific T cells is appropriate to control M. avium infection with no signs of immunopathology.
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Affiliation(s)
- Bruno Cerqueira-Rodrigues
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal
- ICVS/3B’s, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Ana Mendes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal
- ICVS/3B’s, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Margarida Correia-Neves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal
- ICVS/3B’s, PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Claudia Nobrega
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal
- ICVS/3B’s, PT Government Associate Laboratory, Braga/Guimarães, Portugal
- * E-mail:
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24
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Marrack P, Krovi SH, Silberman D, White J, Kushnir E, Nakayama M, Crooks J, Danhorn T, Leach S, Anselment R, Scott-Browne J, Gapin L, Kappler J. The somatically generated portion of T cell receptor CDR3α contributes to the MHC allele specificity of the T cell receptor. eLife 2017; 6:30918. [PMID: 29148973 PMCID: PMC5701794 DOI: 10.7554/elife.30918] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 11/16/2017] [Indexed: 01/24/2023] Open
Abstract
Mature T cells bearing αβ T cell receptors react with foreign antigens bound to alleles of major histocompatibility complex proteins (MHC) that they were exposed to during their development in the thymus, a phenomenon known as positive selection. The structural basis for positive selection has long been debated. Here, using mice expressing one of two different T cell receptor β chains and various MHC alleles, we show that positive selection-induced MHC bias of T cell receptors is affected both by the germline encoded elements of the T cell receptor α and β chain and, surprisingly, dramatically affected by the non germ line encoded portions of CDR3 of the T cell receptor α chain. Thus, in addition to determining specificity for antigen, the non germline encoded elements of T cell receptors may help the proteins cope with the extremely polymorphic nature of major histocompatibility complex products within the species.
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Affiliation(s)
- Philippa Marrack
- Howard Hughes Medical Institute, Denver, United States.,Department of Biomedical Research, National Jewish Health, Denver, United States.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States
| | - Sai Harsha Krovi
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States
| | - Daniel Silberman
- Department of Biomedical Research, National Jewish Health, Denver, United States.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States
| | - Janice White
- Department of Biomedical Research, National Jewish Health, Denver, United States
| | - Eleanor Kushnir
- Department of Biomedical Research, National Jewish Health, Denver, United States
| | - Maki Nakayama
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States.,Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, United States
| | - James Crooks
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, United States
| | - Thomas Danhorn
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, United States
| | - Sonia Leach
- Department of Biomedical Research, National Jewish Health, Denver, United States.,Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, United States
| | - Randy Anselment
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, United States
| | | | - Laurent Gapin
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States
| | - John Kappler
- Howard Hughes Medical Institute, Denver, United States.,Department of Biomedical Research, National Jewish Health, Denver, United States.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, United States
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25
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Artalejo JR, Gómez-Corral A, López-García M, Molina-París C. Stochastic descriptors to study the fate and potential of naive T cell clonotypes in the periphery. J Math Biol 2017; 74:673-708. [PMID: 27350044 PMCID: PMC5258823 DOI: 10.1007/s00285-016-1020-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 04/20/2016] [Indexed: 12/11/2022]
Abstract
The population of naive T cells in the periphery is best described by determining both its T cell receptor diversity, or number of clonotypes, and the sizes of its clonal subsets. In this paper, we make use of a previously introduced mathematical model of naive T cell homeostasis, to study the fate and potential of naive T cell clonotypes in the periphery. This is achieved by the introduction of several new stochastic descriptors for a given naive T cell clonotype, such as its maximum clonal size, the time to reach this maximum, the number of proliferation events required to reach this maximum, the rate of contraction of the clonotype during its way to extinction, as well as the time to a given number of proliferation events. Our results show that two fates can be identified for the dynamics of the clonotype: extinction in the short-term if the clonotype experiences too hostile a peripheral environment, or establishment in the periphery in the long-term. In this second case the probability mass function for the maximum clonal size is bimodal, with one mode near one and the other mode far away from it. Our model also indicates that the fate of a recent thymic emigrant (RTE) during its journey in the periphery has a clear stochastic component, where the probability of extinction cannot be neglected, even in a friendly but competitive environment. On the other hand, a greater deterministic behaviour can be expected in the potential size of the clonotype seeded by the RTE in the long-term, once it escapes extinction.
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Affiliation(s)
- J R Artalejo
- Department of Statistics and Operations Research, Faculty of Mathematics, Complutense University of Madrid, 28040, Madrid, Spain
| | - A Gómez-Corral
- Department of Statistics and Operations Research, Faculty of Mathematics, Complutense University of Madrid, 28040, Madrid, Spain
- Instituto de Ciencias Matemáticas, CSIC-UAM-UC3M-UCM, Calle Nicolás Cabrera 13-15, Campus de Cantoblanco UAM, 28049, Madrid, Spain
| | - M López-García
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, LS2 9JT, UK
| | - C Molina-París
- Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds, LS2 9JT, UK.
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26
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Structural interplay between germline interactions and adaptive recognition determines the bandwidth of TCR-peptide-MHC cross-reactivity. Nat Immunol 2016; 17:87-94. [PMID: 26523866 PMCID: PMC4684756 DOI: 10.1038/ni.3310] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 09/29/2015] [Indexed: 01/07/2023]
Abstract
The T cell antigen receptor (TCR)-peptide-major histocompatibility complex (MHC) interface is composed of conserved and diverse regions, yet the relative contribution of each in shaping recognition by T cells remains unclear. Here we isolated cross-reactive peptides with limited homology, which allowed us to compare the structural properties of nine peptides for a single TCR-MHC pair. The TCR's cross-reactivity was rooted in highly similar recognition of an apical 'hot-spot' position in the peptide with tolerance of sequence variation at ancillary positions. Furthermore, we found a striking structural convergence onto a germline-mediated interaction between the TCR CDR1α region and the MHC α2 helix in twelve TCR-peptide-MHC complexes. Our studies suggest that TCR-MHC germline-mediated constraints, together with a focus on a small peptide hot spot, might place limits on peptide antigen cross-reactivity.
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27
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Vincent B, Buntzman A, Hopson B, McEwen C, Cowell L, Akoglu A, Zhang H, Frelinger J. iWAS--A novel approach to analyzing Next Generation Sequence data for immunology. Cell Immunol 2015; 299:6-13. [PMID: 26547365 DOI: 10.1016/j.cellimm.2015.10.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 10/28/2015] [Accepted: 10/28/2015] [Indexed: 01/12/2023]
Abstract
In this communication we describe a novel way to use Next Generation Sequence from the receptors expressed on T and B cells. This informatics methodology is named iWAS, for immunonome Wide Association Study, where we use the immune receptor sequences derived from T and B cells and the features of those receptors (sequences themselves, V/J gene usage, length and character each of the CDR3 sub-regions) to define biomarkers of health and disease, as well as responses to therapies. Unlike GWAS, which do not provide immediate access to mechanism, the associations with immune receptors immediately suggest possible and plausible entrée's into disease pathogenesis and treatment.
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Affiliation(s)
- Benjamin Vincent
- Department of Medicine, University of North Carolina, Chapel Hill, NC 2714, United States.
| | - Adam Buntzman
- Department of Immunobiology, University of Arizona, Tucson, AZ 85724, United States.
| | - Benjamin Hopson
- School of Engineering, The University of Edinburgh, Edinburgh EH9 3JL, UK; Cambridge Consultants, Science Park, Milton Rd, Cambridge CB4 0DW, UK.
| | - Chris McEwen
- Cambridge Consultants, Science Park, Milton Rd, Cambridge CB4 0DW, UK.
| | - Lindsay Cowell
- Division of Biomedical Informatics, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States.
| | - Ali Akoglu
- Department of Electrical and Computer Engineering, University of Arizona, Tucson, AZ 85721, United States.
| | - Helen Zhang
- Department of Mathematics, University of Arizona, Tucson, AZ 85721, United States.
| | - Jeffrey Frelinger
- Department of Immunobiology, University of Arizona, Tucson, AZ 85724, United States.
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28
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Requirement of full TCR repertoire for regulatory T cells to maintain intestinal homeostasis. Proc Natl Acad Sci U S A 2015; 112:12770-5. [PMID: 26420876 DOI: 10.1073/pnas.1516617112] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The regulation of intestinal homeostasis by the immune system involves the dynamic interplay between gut commensal microbiota and resident immune cells. It is well known that a large and diverse lymphocyte antigen receptor repertoire enables the immune system to recognize and respond to a wide range of invading pathogens. There is also an emerging appreciation for a critical role the T-cell receptor (TCR) repertoire serves in the maintenance of peripheral tolerance by regulatory T cells (Tregs). Nevertheless, how the diversity of the TCR repertoire in Tregs affects intestinal homeostasis remains unknown. To address this question, we studied mice whose T cells express a restricted TCR repertoire. We observed the development of spontaneous colitis, accompanied by the induction of T-helper type 17 cells in the colon that is driven by gut commensal microbiota. We provide further evidence that a restricted TCR repertoire causes a loss of tolerogenicity to microbiota, accompanied by a paucity of peripherally derived, Helios(-) Tregs and hyperactivation of migratory dendritic cells. These results thus reveal a new facet of the TCR repertoire in which Tregs require a diverse TCR repitoire for intestinal homeostasis, suggesting an additional driving force in the evolutional significance of the TCR repertoire.
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29
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Nunes-Alves C, Booty MG, Carpenter SM, Rothchild AC, Martin CJ, Desjardins D, Steblenko K, Kløverpris HN, Madansein R, Ramsuran D, Leslie A, Correia-Neves M, Behar SM. Human and Murine Clonal CD8+ T Cell Expansions Arise during Tuberculosis Because of TCR Selection. PLoS Pathog 2015; 11:e1004849. [PMID: 25945999 PMCID: PMC4422591 DOI: 10.1371/journal.ppat.1004849] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 04/01/2015] [Indexed: 12/17/2022] Open
Abstract
The immune system can recognize virtually any antigen, yet T cell responses against several pathogens, including Mycobacterium tuberculosis, are restricted to a limited number of immunodominant epitopes. The host factors that affect immunodominance are incompletely understood. Whether immunodominant epitopes elicit protective CD8+ T cell responses or instead act as decoys to subvert immunity and allow pathogens to establish chronic infection is unknown. Here we show that anatomically distinct human granulomas contain clonally expanded CD8+ T cells with overlapping T cell receptor (TCR) repertoires. Similarly, the murine CD8+ T cell response against M. tuberculosis is dominated by TB10.44-11-specific T cells with extreme TCRβ bias. Using a retrogenic model of TB10.44-11-specific CD8+ T cells, we show that TCR dominance can arise because of competition between clonotypes driven by differences in affinity. Finally, we demonstrate that TB10.4-specific CD8+ T cells mediate protection against tuberculosis, which requires interferon-γ production and TAP1-dependent antigen presentation in vivo. Our study of how immunodominance, biased TCR repertoires, and protection are inter-related, provides a new way to measure the quality of T cell immunity, which if applied to vaccine evaluation, could enhance our understanding of how to elicit protective T cell immunity. While T cells are required for protection against Mycobacterium tuberculosis infection, attempts to prevent tuberculosis by vaccines designed to elicit memory T cells have only been partially successful. Several vaccine candidates are in clinical trials, but progress has been slow because their ability to prevent disease must be empirically tested. There is little understanding of why certain antigens are targets of protective immunity. We have characterized an immunodominant CD8+ T cell response to the M. tuberculosis antigen TB10.4 (EsxH). CD8+ T cells specific for the TB10.44–11 epitope are primed early during infection and account for 30–50% of lung CD8+ T cells during chronic infection. Now we have used deep sequencing to characterize the TCR repertoire of TB10.44-11-specific CD8+ T cells in the lungs of infected mice. Interestingly, TB10.44-11-specific CD8+ T cells exhibit extreme clonal expansion of certain TCRβ with common structural features, most likely because of affinity selection. Affinity selection of T cells is more important when antigen presentation is limiting. Although the lung contains numerous bacteria during infection, antigen-presentation by infected APC may be limiting, mimicking a “low antigen” state. Thus, even T cells that have the potential to mediate protection may function inefficiently because of suboptimal T cell activation.
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Affiliation(s)
- Cláudio Nunes-Alves
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Matthew G. Booty
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Program in Immunology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Stephen M. Carpenter
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Division of Infectious Disease, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Division of Infectious Disease, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Alissa C. Rothchild
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Program in Immunology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Constance J. Martin
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Danielle Desjardins
- Division of Infectious Disease, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Katherine Steblenko
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Henrik N. Kløverpris
- KwaZulu-Natal Research Institute for TB and HIV, Durban, South Africa
- Nelson Mandela School of Medicine, University of Kwa-Zulu-Natal, Durban, South Africa
- Department of International Health, Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Rajhmun Madansein
- Nelson Mandela School of Medicine, University of Kwa-Zulu-Natal, Durban, South Africa
| | - Duran Ramsuran
- KwaZulu-Natal Research Institute for TB and HIV, Durban, South Africa
| | - Alasdair Leslie
- KwaZulu-Natal Research Institute for TB and HIV, Durban, South Africa
- Nelson Mandela School of Medicine, University of Kwa-Zulu-Natal, Durban, South Africa
| | - Margarida Correia-Neves
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Samuel M. Behar
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail:
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30
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Analyses of the TCR repertoire of MHC class II-restricted innate CD4⁺ T cells. Exp Mol Med 2015; 47:e154. [PMID: 25813222 PMCID: PMC4351420 DOI: 10.1038/emm.2015.7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 11/05/2014] [Accepted: 12/04/2014] [Indexed: 11/08/2022] Open
Abstract
Analysis of the T-cell receptor (TCR) repertoire of innate CD4(+) T cells selected by major histocompatibility complex (MHC) class II-dependent thymocyte-thymocyte (T-T) interaction (T-T CD4(+) T cells) is essential for predicting the characteristics of the antigens that bind to these T cells and for distinguishing T-T CD4(+) T cells from other types of innate T cells. Using the TCR(mini) Tg mouse model, we show that the repertoire of TCRα chains in T-T CD4(+) T cells was extremely diverse, in contrast to the repertoires previously described for other types of innate T cells. The TCRα chain sequences significantly overlapped between T-T CD4(+) T cells and conventional CD4(+) T cells in the thymus and spleen. However, the diversity of the TCRα repertoire of T-T CD4(+) T cells seemed to be restricted compared with that of conventional CD4(+) T cells. Interestingly, the frequency of the parental OT-II TCRα chains was significantly reduced in the process of T-T interaction. This diverse and shifted repertoire in T-T CD4(+) T cells has biological relevance in terms of defense against diverse pathogens and a possible regulatory role during peripheral T-T interaction.
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31
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Clemens EB, Doherty PC, La Gruta NL, Turner SJ. Fixed expression of single influenza virus-specific TCR chains demonstrates the capacity for TCR α- and β-chain diversity in the face of peptide-MHC class I specificity. THE JOURNAL OF IMMUNOLOGY 2014; 194:898-910. [PMID: 25535284 DOI: 10.4049/jimmunol.1401792] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The characteristics of the TCR repertoire expressed by epitope-specific CD8(+) T cells can be an important determinant of the quality of immune protection against virus infection. Most studies of epitope-specific TCR repertoires focus solely on an analysis of TCR β-chains, rather than the combined TCRαβ heterodimers that confer specificity. Hence, the importance of complementary α- and β-chain pairing in determining TCR specificity and T cell function is not well understood. Our earlier study of influenza-specific TCR repertoires in a C57BL/6J mouse model described a structural basis for preferred TCRαβ pairing that determined exquisite specificity for the D(b)PA224 epitope from influenza A virus. We have now extended this analysis using retrogenic mice engineered to express single TCR α- or β-chains specific for the D(b)NP366 or D(b)PA224 epitopes derived from influenza A virus. We found that particular TCRαβ combinations were selected for recognition of these epitopes following infection, indicating that pairing of certain α- and β-chain sequences is key for determining TCR specificity. Furthermore, we demonstrated that some TCRαβ heterodimers were preferentially expanded from the naive repertoire in response to virus infection, suggesting that appropriate αβ pairing confers optimal T cell responsiveness to Ag.
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Affiliation(s)
- E Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia; and
| | - Peter C Doherty
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia; and Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105
| | - Nicole L La Gruta
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia; and
| | - Stephen J Turner
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia; and
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32
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Rybakin V, Westernberg L, Fu G, Kim HO, Ampudia J, Sauer K, Gascoigne NRJ. Allelic exclusion of TCR α-chains upon severe restriction of Vα repertoire. PLoS One 2014; 9:e114320. [PMID: 25500569 PMCID: PMC4264757 DOI: 10.1371/journal.pone.0114320] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 11/07/2014] [Indexed: 11/18/2022] Open
Abstract
Development of thymocytes through the positive selection checkpoint requires the rearrangement and expression of a suitable T cell receptor (TCR) α-chain that can pair with the already-expressed β-chain to make a TCR that is selectable. That is, it must have sufficient affinity for self MHC-peptide to induce the signals required for differentiation, but not too strong so as to induce cell death. Because both alleles of the α-chain continue to rearrange until a positively-selectable heterodimer is formed, thymocytes and T cells can in principle express dual α-chains. However, cell-surface expression of two TCRs is comparatively rare in mature T cells because of post-transcriptional regulatory mechanisms termed “phenotypic allelic exclusion”. We produced mice transgenic for a rearranged β-chain and for two unrearranged α-chains on a genetic background where endogenous α-chains could not be rearranged. Both Vα3.2 and Vα2 containing α-chains were efficiently positively selected, to the extent that a population of dual α-chain-bearing cells was not distinguishable from single α-chain-expressors. Surprisingly, Vα3.2-expressing cells were much more frequent than the Vα2 transgene-expressing cells, even though this Vα3.2-Vβ5 combination can reconstitute a known selectable TCR. In accord with previous work on the Vα3 repertoire, T cells bearing Vα3.2 expressed from the rearranged minilocus were predominantly selected into the CD8+ T cell subpopulation. Because of the dominance of Vα3.2 expression over Vα2 expressed from the miniloci, the peripheral T cell population was predominantly CD8+ cells.
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Affiliation(s)
- Vasily Rybakin
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore
- Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States of America
| | - Luise Westernberg
- Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States of America
| | - Guo Fu
- Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States of America
| | - Hee-Ok Kim
- Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States of America
| | - Jeanette Ampudia
- Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States of America
| | - Karsten Sauer
- Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States of America
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States of America
| | - Nicholas R. J. Gascoigne
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore
- Department of Immunology and Microbial Science, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States of America
- * E-mail:
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33
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Smith SN, Wang Y, Baylon JL, Singh NK, Baker BM, Tajkhorshid E, Kranz DM. Changing the peptide specificity of a human T-cell receptor by directed evolution. Nat Commun 2014; 5:5223. [PMID: 25376839 PMCID: PMC4225554 DOI: 10.1038/ncomms6223] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 09/10/2014] [Indexed: 11/09/2022] Open
Abstract
Binding of a T-cell receptor (TCR) to a peptide/major histocompatibility complex is the key interaction involved in antigen specificity of T cells. The recognition involves up to six complementarity determining regions (CDR) of the TCR. Efforts to examine the structural basis of these interactions and to exploit them in adoptive T-cell therapies has required the isolation of specific T-cell clones and their clonotypic TCRs. Here we describe a strategy using in vitro-directed evolution of a single TCR to change its peptide specificity, thereby avoiding the need to isolate T-cell clones. The human TCR A6, which recognizes the viral peptide Tax/HLA-A2, was converted to TCR variants that recognized the cancer peptide MART1/HLA-A2. Mutational studies and molecular dynamics simulations identified CDR residues that were predicted to be important in the specificity switch. Thus, in vitro engineering strategies alone can be used to discover TCRs with desired specificities.
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Affiliation(s)
- Sheena N. Smith
- Department of Biochemistry, University of Illinois, 600 S. Matthews Ave., Urbana, IL 61801, USA
| | - Yuhang Wang
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61802, USA
| | - Javier L. Baylon
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61802, USA
| | - Nishant K. Singh
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 1234 Notre Dame Avenue, South Bend, IN 46557, USA
| | - Brian M. Baker
- Department of Chemistry and Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, 1234 Notre Dame Avenue, South Bend, IN 46557, USA
| | - Emad Tajkhorshid
- Department of Biochemistry, University of Illinois, 600 S. Matthews Ave., Urbana, IL 61801, USA
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61802, USA
| | - David M. Kranz
- Department of Biochemistry, University of Illinois, 600 S. Matthews Ave., Urbana, IL 61801, USA
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34
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Cipolletta D. Adipose tissue-resident regulatory T cells: phenotypic specialization, functions and therapeutic potential. Immunology 2014; 142:517-25. [PMID: 24484282 DOI: 10.1111/imm.12262] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 01/21/2014] [Accepted: 01/27/2014] [Indexed: 12/12/2022] Open
Abstract
Foxp3(+) CD4(+) regulatory T (Treg) cells, recognized to be one of the most important defences of the human body against an inappropriate immune response, have recently gained attention from those outside immunology thanks to the compelling evidence for their capability to exert non-canonical immune functions in a variety of tissues in health and disease. The recent discovery of the differences between tissue-resident Treg cells and those derived from lymphoid organs is affecting the mindset of many investigators now questioning the broad applicability of observations originally based on peripheral blood/lymphoid organ cells. So far, the best characterized 'Treg flavour' comes from studies focused on their role in suppressing adipose tissue inflammation and obesity-driven insulin resistance. Adipose tissue derived Treg cells are distinct from their counterparts in lymphoid organs based on their transcriptional profile, T-cell receptor repertoire, and cytokine and chemokine receptor expression pattern. These cells are abundant in visceral adipose tissue of lean mice but their number is greatly reduced in insulin-resistant animal models of obesity. Interestingly, peroxisome-proliferator-activated receptor γ expression by visceral adipose tissue Treg cells is crucial for their accumulation, phenotype and function in the fat and surprisingly necessary for complete restoration of insulin sensitivity in obese mice by the anti-diabetic drug Pioglitazone. This review surveys recent findings relating to the unique phenotype and function of adipose tissue-resident Treg cells, speculates on the nature of their dynamics in lean and obese mouse models, and analyses their potential therapeutic application in the treatment of type 2 diabetes.
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35
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Stadinski BD, Trenh P, Duke B, Huseby PG, Li G, Stern LJ, Huseby ES. Effect of CDR3 sequences and distal V gene residues in regulating TCR-MHC contacts and ligand specificity. THE JOURNAL OF IMMUNOLOGY 2014; 192:6071-82. [PMID: 24813203 DOI: 10.4049/jimmunol.1303209] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The mature T cell repertoire has the ability to orchestrate immunity to a wide range of potential pathogen challenges. This ability stems from thymic development producing individual T cell clonotypes that express TCRs with unique patterns of Ag reactivity. The Ag specificity of TCRs is created from the combinatorial pairing of one of a set of germline encoded TCR Vα and Vβ gene segments with randomly created CDR3 sequences. How the amalgamation of germline encoded and randomly created TCR sequences results in Ag receptors with unique patterns of ligand specificity is not fully understood. Using cellular, biophysical, and structural analyses, we show that CDR3α residues can modulate the geometry in which TCRs bind peptide-MHC (pMHC), governing whether and how germline encoded TCR Vα and Vβ residues interact with MHC. In addition, a CDR1α residue that is positioned distal to the TCR-pMHC binding interface is shown to contribute to the peptide specificity of T cells. These findings demonstrate that the specificity of individual T cell clonotypes arises not only from TCR residues that create direct contacts with the pMHC, but also from a collection of indirect effects that modulate how TCR residues are used to bind pMHC.
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Affiliation(s)
- Brian D Stadinski
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Peter Trenh
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Brian Duke
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Priya G Huseby
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Guoqi Li
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Lawrence J Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655
| | - Eric S Huseby
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655; and
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36
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Six A, Mariotti-Ferrandiz ME, Chaara W, Magadan S, Pham HP, Lefranc MP, Mora T, Thomas-Vaslin V, Walczak AM, Boudinot P. The past, present, and future of immune repertoire biology - the rise of next-generation repertoire analysis. Front Immunol 2013; 4:413. [PMID: 24348479 PMCID: PMC3841818 DOI: 10.3389/fimmu.2013.00413] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 11/12/2013] [Indexed: 01/09/2023] Open
Abstract
T and B cell repertoires are collections of lymphocytes, each characterized by its antigen-specific receptor. We review here classical technologies and analysis strategies developed to assess immunoglobulin (IG) and T cell receptor (TR) repertoire diversity, and describe recent advances in the field. First, we describe the broad range of available methodological tools developed in the past decades, each of which answering different questions and showing complementarity for progressive identification of the level of repertoire alterations: global overview of the diversity by flow cytometry, IG repertoire descriptions at the protein level for the identification of IG reactivities, IG/TR CDR3 spectratyping strategies, and related molecular quantification or dynamics of T/B cell differentiation. Additionally, we introduce the recent technological advances in molecular biology tools allowing deeper analysis of IG/TR diversity by next-generation sequencing (NGS), offering systematic and comprehensive sequencing of IG/TR transcripts in a short amount of time. NGS provides several angles of analysis such as clonotype frequency, CDR3 diversity, CDR3 sequence analysis, V allele identification with a quantitative dimension, therefore requiring high-throughput analysis tools development. In this line, we discuss the recent efforts made for nomenclature standardization and ontology development. We then present the variety of available statistical analysis and modeling approaches developed with regards to the various levels of diversity analysis, and reveal the increasing sophistication of those modeling approaches. To conclude, we provide some examples of recent mathematical modeling strategies and perspectives that illustrate the active rise of a "next-generation" of repertoire analysis.
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Affiliation(s)
- Adrien Six
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, CIC-BTi Biotherapy , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, Département Hospitalo-Universitaire (DHU), Inflammation-Immunopathology-Biotherapy (i2B) , Paris , France
| | - Maria Encarnita Mariotti-Ferrandiz
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, Département Hospitalo-Universitaire (DHU), Inflammation-Immunopathology-Biotherapy (i2B) , Paris , France
| | - Wahiba Chaara
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, CIC-BTi Biotherapy , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, Département Hospitalo-Universitaire (DHU), Inflammation-Immunopathology-Biotherapy (i2B) , Paris , France
| | - Susana Magadan
- Institut National de la Recherche Agronomique, Unité de Virologie et Immunologie Moléculaires , Jouy-en-Josas , France
| | - Hang-Phuong Pham
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France
| | - Marie-Paule Lefranc
- IMGT®, The International ImMunoGeneTics Information System®, Institut de Génétique Humaine, UPR CNRS 1142, Université Montpellier 2 , Montpellier , France
| | - Thierry Mora
- Laboratoire de Physique Statistique, UMR8550, CNRS and Ecole Normale Supérieure , Paris , France
| | - Véronique Thomas-Vaslin
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, Département Hospitalo-Universitaire (DHU), Inflammation-Immunopathology-Biotherapy (i2B) , Paris , France
| | - Aleksandra M Walczak
- Laboratoire de Physique Théorique, UMR8549, CNRS and Ecole Normale Supérieure , Paris , France
| | - Pierre Boudinot
- Institut National de la Recherche Agronomique, Unité de Virologie et Immunologie Moléculaires , Jouy-en-Josas , France
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Greene J, Birtwistle MR, Ignatowicz L, Rempala GA. Bayesian multivariate Poisson abundance models for T-cell receptor data. J Theor Biol 2013; 326:1-10. [PMID: 23467198 DOI: 10.1016/j.jtbi.2013.02.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 11/02/2012] [Accepted: 02/14/2013] [Indexed: 11/19/2022]
Abstract
A major feature of an adaptive immune system is its ability to generate B- and T-cell clones capable of recognizing and neutralizing specific antigens. These clones recognize antigens with the help of the surface molecules, called antigen receptors, acquired individually during the clonal development process. In order to ensure a response to a broad range of antigens, the number of different receptor molecules is extremely large, resulting in a huge clonal diversity of both B- and T-cell receptor populations and making their experimental comparisons statistically challenging. To facilitate such comparisons, we propose a flexible parametric model of multivariate count data and illustrate its use in a simultaneous analysis of multiple antigen receptor populations derived from mammalian T-cells. The model relies on a representation of the observed receptor counts as a multivariate Poisson abundance mixture (m PAM). A Bayesian parameter fitting procedure is proposed, based on the complete posterior likelihood, rather than the conditional one used typically in similar settings. The new procedure is shown to be considerably more efficient than its conditional counterpart (as measured by the Fisher information) in the regions of m PAM parameter space relevant to model T-cell data.
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Affiliation(s)
- Joshua Greene
- Department of Biostatistics, Georgia Health Sciences University, Augusta, GA 30912, USA
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38
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Ndifon W, Gal H, Shifrut E, Aharoni R, Yissachar N, Waysbort N, Reich-Zeliger S, Arnon R, Friedman N. Chromatin conformation governs T-cell receptor Jβ gene segment usage. Proc Natl Acad Sci U S A 2012; 109:15865-70. [PMID: 22984176 PMCID: PMC3465372 DOI: 10.1073/pnas.1203916109] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
T cells play fundamental roles in adaptive immunity, relying on a diverse repertoire of T-cell receptor (TCR) α and β chains. Diversity of the TCR β chain is generated in part by a random yet intrinsically biased combinatorial rearrangement of variable (Vβ), diversity (Dβ), and joining (Jβ) gene segments. The mechanisms that determine biases in gene segment use remain unclear. Here we show, using a high-throughput TCR sequencing approach, that a physical model of chromatin conformation at the DJβ genomic locus explains more than 80% of the biases in Jβ use that we measured in murine T cells. This model also predicts correctly how differences in intersegment genomic distances between humans and mice translate into differences in Jβ bias between TCR repertoires of these two species. As a consequence of these structural and other biases, TCR sequences are produced with different a priori frequencies, thus affecting their probability of becoming public TCRs that are shared among individuals. Surprisingly, we find that many more TCR sequences are shared among all five mice we studied than among only subgroups of three or four mice. We derive a necessary mathematical condition explaining this finding, which indicates that the TCR repertoire contains a core set of receptor sequences that are highly abundant among individuals, if their a priori probability of being produced by the recombination process is higher than a defined threshold. Our results provide evidence for an expanded role of chromatin conformation in VDJ rearrangement, from control of gene accessibility to precise determination of gene segment use.
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Affiliation(s)
| | | | - Eric Shifrut
- Department of Immunology, Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Rina Aharoni
- Department of Immunology, Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Nissan Yissachar
- Department of Immunology, Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Nir Waysbort
- Department of Immunology, Weizmann Institute of Science, Rehovot, 76100 Israel
| | | | - Ruth Arnon
- Department of Immunology, Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Nir Friedman
- Department of Immunology, Weizmann Institute of Science, Rehovot, 76100 Israel
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Abstract
In this work, the authors introduce a stochastic model of lymphoma. Two clonotypes of T cells of the immune system compete with each other and with other clonotypes for survival stimuli. One of the clonotypes is normal and the other is tumourous. To model the tumourous clonotype the authors include a rate of influx of new naive T cells (descendants of mutated precursor cells) from the thymus. The authors obtain a deterministic approximation to the stochastic model and analyse eight cases of competition between the two clonotypes of T cells. The authors obtain two possible scenarios, depending on the values of parameters: either both clonotypes survive in the repertoire or the clonotype of the normal T cells becomes extinct, meanwhile the clonotype of the tumourous T cells is maintained, after achieving some maximum level of growth. The authors show that if the income of the new tumourous T cells from the thymus is augmented, then the tumourous clonotype, would never be removed from the repertoire; meanwhile the normal clonotype could become extinct if it was not specialised enough to compete effectively for survival stimuli provided by professional cells.
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Affiliation(s)
- J M Chrobak
- Departamento de Matemáticas, Facultad de Ciencias Químicas, Universidad de Castilla-La Mancha, 13071 Ciudad Real, Spain
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Galleu A, Fozza C, Simula MP, Contini S, Virdis P, Corda G, Pardini S, Cottoni F, Pruneddu S, Angeloni A, Ceccarelli S, Longinotti M. CD4+ and CD8+ T-cell skewness in classic Kaposi sarcoma. Neoplasia 2012; 14:487-94. [PMID: 22787430 PMCID: PMC3394191 DOI: 10.1596/neo.11646] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2011] [Revised: 04/23/2012] [Accepted: 04/24/2012] [Indexed: 11/17/2022]
Abstract
It is widely accepted that a deranged immune system plays a key role in the onset and evolution of classic Kaposi sarcoma (CKS). Nevertheless, the usage of the T-cell receptor (TCR) β-variable (BV) chain repertoire expressed by peripheral blood lymphocytes in patients with CKS is still unknown. With the aim of providing some further insights into the complex role of the immune system in CKS pathogenesis, we performed an extensive analysis of the TCR BV repertoire in both CD4(+) and CD8(+) T cells in 30 human herpesvirus 8-positive Sardinian patients with CKS and an equal number of age-matched healthy controls. We used a panel of monoclonal antibodies covering approximately 70% of human BV subfamilies and third complementarity determining region (CDR3) spectratyping. Patients with CKS showed an increased frequency of BV expansions in both CD4(+) and CD8(+) lymphocytes, with no prevalent clones. On spectratyping analysis, most of the 720 BV CDR3 profiles obtained from both CD4(+) and CD8(+) T cells in patients with CKS were skewed. In particular, the surprising increase of BV skewing observed in CD4(+) lymphocytes mimics the pattern of progressive TCR BV narrowing described in responses to persistent viral antigen stimulations. Our findings support the hypothesis that CKS evolution is associated with inadequate activation rather than impairment of the immune system.
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Affiliation(s)
- Antonio Galleu
- Haematology Section, Department of Biomedical Sciences, University of Sassari, Sassari, Italy.
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41
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T cell populations in the pancreatic lymph node naturally and consistently expand and contract in NOD mice as disease progresses. Mol Immunol 2012; 52:9-18. [PMID: 22580347 DOI: 10.1016/j.molimm.2012.04.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Revised: 04/10/2012] [Accepted: 04/16/2012] [Indexed: 11/21/2022]
Abstract
Nonobese diabetic (NOD) mice develop spontaneous autoimmune Type 1 diabetes (T1D) that results from the destruction of insulin secreting β cells by diabetogenic T cells. The activation of autoreactive T cells occurs in the pancreatic lymph nodes (PLN) from where effector T cells migrate to the pancreas. This study was designed to explore whether T cell populations in the NOD PLN expand in a predictable and reproducible way during disease progression. Complementary determining region (CDR) 3 length spectratype analysis of 19 TCR Vβ families was used to identify the relative frequency of T populations in PLN of 4 and 10 week old NOD mice and mice at T1D onset. Significant and highly reproducible changes in specific T cell populations were detected in 14 of Vβ families tested at all stages of disease. However, of these, the CDR3 spectratype of only four Vβ families was significantly more perturbed at T1D onset than in 10 week old mice. Intriguingly, when diabetes was induced in 10 week old mice with cyclophosphamide (CYP) the same four Vβ families, Vβ5.1, Vβ9, Vβ10, and Vβ15, were again significantly more perturbed than in the untreated non-diabetic age matched mice. Taken together the data show that while T cell responses in PLN of NOD mice are heterogeneous, they are ordered and consistent throughout disease development. The finding that within this heterogeneous response four Vβ families are significantly more perturbed in diabetic mice, whether spontaneous or induced, strongly suggests their selection as part of the disease process.
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42
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Weiss VL, Lee TH, Song H, Kouo TS, Black CM, Sgouros G, Jaffee EM, Armstrong TD. Trafficking of high avidity HER-2/neu-specific T cells into HER-2/neu-expressing tumors after depletion of effector/memory-like regulatory T cells. PLoS One 2012; 7:e31962. [PMID: 22359647 PMCID: PMC3281086 DOI: 10.1371/journal.pone.0031962] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 01/16/2012] [Indexed: 02/02/2023] Open
Abstract
Background Cancer vaccines are designed to activate and enhance cancer-antigen-targeted T cells that are suppressed through multiple mechanisms of immune tolerance in cancer-bearing hosts. T regulatory cell (Treg) suppression of tumor-specific T cells is one barrier to effective immunization. A second mechanism is the deletion of high avidity tumor-specific T cells, which leaves a less effective low avidity tumor specific T cell repertoire available for activation by vaccines. Treg depleting agents including low dose cyclophosphamide (Cy) and antibodies that deplete CD25-expressing Tregs have been used with limited success to enhance the potency of tumor-specific vaccines. In addition, few studies have evaluated mechanisms that activate low avidity cancer antigen-specific T cells. Therefore, we developed high and low avidity HER-2/neu-specific TCR transgenic mouse colonies specific for the same HER-2/neu epitope to define the tolerance mechanisms that specifically affect high versus low avidity tumor-specific T cells. Methodology/Principal Findings High and low avidity CD8+ T cell receptor (TCR) transgenic mice specific for the breast cancer antigen HER-2/neu (neu) were developed to provide a purified source of naïve, tumor-specific T cells that can be used to study tolerance mechanisms. Adoptive transfer studies into tolerant FVB/N-derived HER-2/neu transgenic (neu-N) mice demonstrated that high avidity, but not low avidity, neu-specific T cells are inhibited by Tregs as the dominant tolerizing mechanism. High avidity T cells persisted, produced IFNγ, trafficked into tumors, and lysed tumors after adoptive transfer into mice treated with a neu-specific vaccine and low dose Cy to deplete Tregs. Analysis of Treg subsets revealed a Cy-sensitive CD4+Foxp3+CD25low tumor-seeking migratory phenotype, characteristic of effector/memory Tregs, and capable of high avidity T cell suppression. Conclusion/Significance Depletion of CD25low Tregs allows activation of tumor-clearing high avidity T cells. Thus, the development of agents that specifically deplete Treg subsets should translate into more effective immunotherapies while avoiding autoimmunity.
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Affiliation(s)
- Vivian L. Weiss
- The Sidney Kimmel Cancer Center at Johns Hopkins, John Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Oncology, John Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Graduate Program in Immunology, John Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Timothy H. Lee
- The Sidney Kimmel Cancer Center at Johns Hopkins, John Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Oncology, John Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Hong Song
- The Sidney Kimmel Cancer Center at Johns Hopkins, John Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Oncology, John Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Radiology and Nuclear Medicine, John Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Theodore S. Kouo
- The Sidney Kimmel Cancer Center at Johns Hopkins, John Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Oncology, John Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Graduate Program in Immunology, John Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Chelsea M. Black
- The Sidney Kimmel Cancer Center at Johns Hopkins, John Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Oncology, John Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Graduate Program in Cellular and Molecular Medicine, John Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - George Sgouros
- The Sidney Kimmel Cancer Center at Johns Hopkins, John Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Oncology, John Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Radiology and Nuclear Medicine, John Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Elizabeth M. Jaffee
- The Sidney Kimmel Cancer Center at Johns Hopkins, John Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Oncology, John Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Graduate Program in Immunology, John Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Graduate Program in Cellular and Molecular Medicine, John Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Graduate Program in Pharmacology, John Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- The Skip Viragh Pancreatic Cancer Center, and Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Todd D. Armstrong
- The Sidney Kimmel Cancer Center at Johns Hopkins, John Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Oncology, John Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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Abstract
Historically, sharing T cell receptors (TCRs) between individuals has been speculated to be impossible, considering the dramatic discrepancy between the potential enormity of the TCR repertoire and the limited number of T cells generated in each individual. However, public T cell response, in which multiple individuals share identical TCRs in responding to a same antigenic epitope, has been extensively observed in a variety of immune responses across many species. Public T cell responses enable individuals within a population to generate similar antigen-specific TCRs against certain ubiquitous pathogens, leading to favorable biological outcomes. However, the relatively concentrated feature of TCR repertoire may limit T cell response in a population to some other pathogens. It could be a great benefit for human health if public T cell responses can be manipulated. Therefore, the mechanistic insight of public TCR generation is important to know. Recently, high-throughput DNA sequencing has revolutionized the study of immune receptor repertoires, which allows a much better understanding of the factors that determine the overlap of TCR repertoire among individuals. Here, we summarize the current knowledge on public T-cell response and discuss future challenges in this field.
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Affiliation(s)
- Hanjie Li
- State Key Laboratory of Cellular Stress Biology and School of Life Sciences, Xiamen University, Xiamen, Fujian, China
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44
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Föhse L, Suffner J, Suhre K, Wahl B, Lindner C, Lee CW, Schmitz S, Haas JD, Lamprecht S, Koenecke C, Bleich A, Hämmerling GJ, Malissen B, Suerbaum S, Förster R, Prinz I. High TCR diversity ensures optimal function and homeostasis of Foxp3+ regulatory T cells. Eur J Immunol 2011; 41:3101-13. [PMID: 21932448 DOI: 10.1002/eji.201141986] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 08/24/2011] [Accepted: 08/31/2011] [Indexed: 01/08/2023]
Abstract
Dominant tolerance to self-antigen requires the presence of sufficient numbers of CD4(+) Foxp3(+) Treg cells with matching antigen specificity. However, the size and role of TCR repertoire diversity for antigen-specific immuno-regulation through Treg cells is not clear. Here, we developed and applied a novel high-throughput (HT) TCR sequencing approach to analyze the TCR repertoire of Treg cells and revealed the importance of high diversity for Treg-cell homeostasis and function. We found that highly polyclonal Treg cells from WT mice vigorously expanded after adoptive transfer into non-lymphopenic TCR-transgenic recipients with low Treg-cell diversity. In that system, we identified specific Treg-cell TCR preferences in distinct anatomic locations such as the mesenteric LN indicating that Treg cells continuously compete for MHC class-II-presented self-, food-, or flora-antigen. Functionally, we showed that high TCR diversity was required for optimal suppressive function of Treg cells in experimental acute graft versus host disease (GvHD). In conclusion, we suggest that efficient immuno-regulation by Treg cells requires high TCR diversity. Thereby, continuous competition of peripheral Treg cells for limited self-antigen shapes an organ-optimized, yet highly diverse, local TCR repertoire.
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Affiliation(s)
- Lisa Föhse
- Institute of Immunology, Hannover Medical School, Hannover, Germany
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45
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Miconnet I, Marrau A, Farina A, Taffé P, Vigano S, Harari A, Pantaleo G. Large TCR Diversity of Virus-Specific CD8 T Cells Provides the Mechanistic Basis for Massive TCR Renewal after Antigen Exposure. THE JOURNAL OF IMMUNOLOGY 2011; 186:7039-49. [DOI: 10.4049/jimmunol.1003309] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Day EB, Charlton KL, La Gruta NL, Doherty PC, Turner SJ. Effect of MHC class I diversification on influenza epitope-specific CD8+ T cell precursor frequency and subsequent effector function. THE JOURNAL OF IMMUNOLOGY 2011; 186:6319-28. [PMID: 21536802 DOI: 10.4049/jimmunol.1000883] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Earlier studies of influenza-specific CD8(+) T cell immunodominance hierarchies indicated that expression of the H2K(k) MHC class I allele greatly diminishes responses to the H2D(b)-restriced D(b)PA(224) epitope (acid polymerase, residues 224-233 complexed with H2D(b)). The results suggested that the presence of H2K(k) during thymic differentiation led to the deletion of a prominent Vβ7(+) subset of D(b)PA(224)-specific TCRs. The more recent definition of D(b)PA(224)-specific TCR CDR3β repertoires in H2(b) mice provides a new baseline for looking again at this possible H2K(k) effect on D(b)PA(224)-specific TCR selection. We found that immune responses to several H2D(b)- and H2K(b)-restricted influenza epitopes were indeed diminished in H2(bxk) F(1) versus homozygous mice. In the case of D(b)PA(224), lower numbers of naive precursors were part of the explanation, though a similar decrease in those specific for the D(b)NP(366) epitope did not affect response magnitude. Changes in precursor frequency were not associated with any major loss of TCR diversity and could not fully account for the diminished D(b)PA(224)-specific response. Further functional and phenotypic characterization of influenza-specific CD8(+) T cells suggested that the expansion and differentiation of the D(b)PA(224)-specific set is impaired in the H2(bxk) F(1) environment. Thus, the D(b)PA(224) response in H2(bxk) F(1) mice is modulated by factors that affect the generation of naive epitope-specific precursors and the expansion and differentiation of these T cells during infection, rather than clonal deletion of a prominent Vβ7(+) subset. Such findings illustrate the difficulties of predicting and defining the effects of MHC class I diversification on epitope-specific responses.
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Affiliation(s)
- E Bridie Day
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
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47
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Abstract
This essay provides an analysis of the inadequacy of the current view of restrictive recognition of peptide by the T-cell antigen receptor. A competing model is developed, and the experimental evidence for the prevailing model is reinterpreted in the new framework. The goal is to contrast the two models with respect to their consistency, coverage of the data, explanatory power, and predictability.
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Affiliation(s)
- Melvin Cohn
- Conceptual Immunology Group, The Salk Institute For Biological Studies, La Jolla, CA 92037, USA.
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48
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Venturi V, Quigley MF, Greenaway HY, Ng PC, Ende ZS, McIntosh T, Asher TE, Almeida JR, Levy S, Price DA, Davenport MP, Douek DC. A mechanism for TCR sharing between T cell subsets and individuals revealed by pyrosequencing. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2011; 186:4285-94. [PMID: 21383244 DOI: 10.4049/jimmunol.1003898] [Citation(s) in RCA: 146] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The human naive T cell repertoire is the repository of a vast array of TCRs. However, the factors that shape their hierarchical distribution and relationship with the memory repertoire remain poorly understood. In this study, we used polychromatic flow cytometry to isolate highly pure memory and naive CD8(+) T cells, stringently defined with multiple phenotypic markers, and used deep sequencing to characterize corresponding portions of their respective TCR repertoires from four individuals. The extent of interindividual TCR sharing and the overlap between the memory and naive compartments within individuals were determined by TCR clonotype frequencies, such that higher-frequency clonotypes were more commonly shared between compartments and individuals. TCR clonotype frequencies were, in turn, predicted by the efficiency of their production during V(D)J recombination. Thus, convergent recombination shapes the TCR repertoire of the memory and naive T cell pools, as well as their interrelationship within and between individuals.
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MESH Headings
- Adult
- Clone Cells
- Gene Rearrangement, beta-Chain T-Cell Antigen Receptor/immunology
- High-Throughput Nucleotide Sequencing/methods
- Humans
- Immunoglobulin Variable Region/biosynthesis
- Immunoglobulin Variable Region/genetics
- Immunoglobulin Variable Region/isolation & purification
- Immunologic Memory/genetics
- Male
- Middle Aged
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/isolation & purification
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Recombination, Genetic/immunology
- Resting Phase, Cell Cycle/genetics
- Resting Phase, Cell Cycle/immunology
- T-Lymphocyte Subsets/cytology
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
- Young Adult
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Affiliation(s)
- Vanessa Venturi
- Computational Biology Group, Centre for Vascular Research, University of New South Wales, Sydney, New South Wales 2052, Australia
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49
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Sun JC, Beilke JN, Bezman NA, Lanier LL. Homeostatic proliferation generates long-lived natural killer cells that respond against viral infection. ACTA ACUST UNITED AC 2011; 208:357-68. [PMID: 21262959 PMCID: PMC3039854 DOI: 10.1084/jem.20100479] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Like memory T cells, natural killer cells that undergo homeostatic expansion in mice self-renew and retain the ability to respond to subsequent viral infection. Cells of the immune system undergo homeostatic proliferation during times of lymphopenia induced by certain viral infections or caused by chemotherapy and radiation treatment. Natural killer (NK) cells are no exception and can rapidly expand in number when placed into an environment devoid of these cells. We explored the lifespan and function of mouse NK cells that have undergone homeostatic proliferation in various settings of immunodeficiency. Adoptive transfer of mature NK cells into lymphopenic mice resulted in the generation of a long-lived population of NK cells. These homeostasis-driven NK cells reside in both lymphoid and nonlymphoid organs for >6 mo and, similar to memory T cells, self-renew and slowly turn over at steady state. Furthermore, homeostatically expanded NK cells retained their functionality many months after initial transfer and responded robustly to viral infection. These findings highlight the ability of mature NK cells to self-renew and possibly persist in the host for months or years and might be of clinical importance during NK cell adoptive immunotherapy for the treatment of certain cancers.
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Affiliation(s)
- Joseph C Sun
- Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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Quigley MF, Greenaway HY, Venturi V, Lindsay R, Quinn KM, Seder RA, Douek DC, Davenport MP, Price DA. Convergent recombination shapes the clonotypic landscape of the naive T-cell repertoire. Proc Natl Acad Sci U S A 2010; 107:19414-9. [PMID: 20974936 PMCID: PMC2984183 DOI: 10.1073/pnas.1010586107] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Adaptive T-cell immunity relies on the recruitment of antigen-specific clonotypes, each defined by the expression of a distinct T-cell receptor (TCR), from an array of naïve T-cell precursors. Despite the enormous clonotypic diversity that resides within the naïve T-cell pool, interindividual sharing of TCR sequences has been observed within mobilized T-cell responses specific for certain peptide-major histocompatibility complex (pMHC) antigens. The mechanisms that underlie this phenomenon have not been fully elucidated, however. A mechanism of convergent recombination has been proposed to account for the occurrence of shared, or "public," TCRs in specific memory T-cell populations. According to this model, TCR sharing between individuals is directly related to TCR production frequency; this, in turn, is determined on a probabilistic basis by the relative generation efficiency of particular nucleotide and amino acid sequences during the recombination process. Here, we tested the key predictions of convergent recombination in a comprehensive evaluation of the naïve CD8(+) TCRβ repertoire in mice. Within defined segments of the naïve CD8(+) T-cell repertoire, TCRβ sequences with convergent features were (i) present at higher copy numbers within individual mice and (ii) shared between individual mice. Thus, the naïve CD8(+) T-cell repertoire is not flat, but comprises a hierarchy of recurrence rates for individual clonotypes that is determined by relative production frequencies. These findings provide a framework for understanding the early mobilization of public CD8(+) T-cell clonotypes, which can exert profound biological effects during acute infectious processes.
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Affiliation(s)
- Máire F Quigley
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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