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Ostmeyer J, Park JY, von Itzstein MS, Hsiehchen D, Fattah F, Gwin M, Catalan R, Khan S, Raj P, Wakeland EK, Xie Y, Gerber DE. T-cell tolerant fraction as a predictor of immune-related adverse events. J Immunother Cancer 2023; 11:e006437. [PMID: 37580069 PMCID: PMC10432621 DOI: 10.1136/jitc-2022-006437] [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] [Accepted: 06/28/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND Immune checkpoint inhibitor (ICI) therapies may cause unpredictable and potentially severe autoimmune toxicities termed immune-related adverse events (irAEs). Because T cells mediate ICI effects, T cell profiling may provide insight into the risk of irAEs. Here we evaluate a novel metric-the T-cell tolerant fraction-as a predictor of future irAEs. METHODS We examined T-cell receptor beta (TRB) locus sequencing from baseline pretreatment samples from an institutional registry and previously published studies. For each patient, we used TRB sequences to calculate the T-cell tolerant fraction, which was then assessed as a predictor of future irAEs (classified as Common Terminology Criteria for Adverse Event grade 0-1 vs grade ≥2). We then compared the tolerant fraction to TRB clonality and diversity. Finally, the tolerant fraction was assessed on (1) T cells enriched against napsin A, a potential autoantigen of irAEs; (2) thymic versus peripheral blood T cells; and (3) TRBs specific for various infections and autoimmune diseases. RESULTS A total of 77 patients with cancer (22 from an institutional registry and 55 from published studies) receiving ICI therapy (43 CTLA4, 19 PD1/PDL1, 15 combination CTLA4+PD1/PDL1) were included in the study. The tolerant fraction was significantly lower in cases with clinically significant irAEs (p<0.001) and had an area under the receiver operating curve (AUC) of 0.79. The tolerant fraction was lower for each ICI treatment category, reaching statistical significance for CTLA4 (p<0.001) and demonstrating non-significant trends for PD1/PDL1 (p=0.21) and combination ICI (p=0.18). The tolerant fraction for T cells enriched against napsin A was lower than other samples. The tolerant fraction was also lower in thymic versus peripheral blood samples, and lower in some (multiple sclerosis) but not other (type 1 diabetes) autoimmune diseases. In our study cohort, TRB clonality had an AUC of 0.62, and TRB diversity had an AUC of 0.60 for predicting irAEs. CONCLUSIONS Among patients receiving ICI, the baseline T-cell tolerant fraction may serve as a predictor of clinically significant irAEs.
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Affiliation(s)
- Jared Ostmeyer
- Peter O'Donnell School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jason Y Park
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Mitchell S von Itzstein
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - David Hsiehchen
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Harold C Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Farjana Fattah
- Harold C Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Mary Gwin
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Rodrigo Catalan
- Harold C Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Shaheen Khan
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Prithvi Raj
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Edward K Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Yang Xie
- Peter O'Donnell School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Harold C Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - David E Gerber
- Peter O'Donnell School of Public Health, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Harold C Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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2
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Fang M, Su Z, Abolhassani H, Zhang W, Jiang C, Cheng B, Luo L, Wu J, Wang S, Lin L, Wang X, Wang L, Aghamohammadi A, Li T, Zhang X, Hammarström L, Liu X. T Cell Repertoire Abnormality in Immunodeficiency Patients with DNA Repair and Methylation Defects. J Clin Immunol 2022; 42:375-393. [PMID: 34825286 PMCID: PMC8821531 DOI: 10.1007/s10875-021-01178-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/01/2021] [Indexed: 12/25/2022]
Abstract
Both DNA damage response and methylation play a crucial role in antigen receptor recombination by creating a diverse repertoire in developing lymphocytes, but how their defects relate to T cell repertoire and phenotypic heterogeneity of immunodeficiency remains obscure. We studied the TCR repertoire in patients with the mutation in different genes (ATM, DNMT3B, ZBTB24, RAG1, DCLRE1C, and JAK3) and uncovered distinct characteristics of repertoire diversity. We propose that early aberrancies in thymus T cell development predispose to the heterogeneous phenotypes of the immunodeficiency spectrum. Shorter CDR3 lengths in ATM-deficient patients, resulting from a decreased number of nucleotide insertions during VDJ recombination in the pre-selected TCR repertoire, as well as the increment of CDR3 tyrosine residues, lead to the enrichment of pathology-associated TCRs, which may contribute to the phenotypes of ATM deficiency. Furthermore, patients with DNMT3B and ZBTB24 mutations who exhibit discrepant phenotypes present longer CDR3 lengths and reduced number of known pathology-associated TCRs.
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Affiliation(s)
- Mingyan Fang
- BGI-Shenzhen, Shenzhen, 518083, China
- Division of Clinical Immunology at the Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, 141 86, Stockholm, Sweden
| | - Zheng Su
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, The University of New South Wales, Sydney, NSW, Australia
| | - Hassan Abolhassani
- Division of Clinical Immunology at the Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, 141 86, Stockholm, Sweden
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Wei Zhang
- BGI-Shenzhen, Shenzhen, 518083, China
- Department of Computer Science, City University of Hong Kong, Hong Kong, 999077, China
| | | | | | - Lihua Luo
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | | | - Liya Lin
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xie Wang
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Asghar Aghamohammadi
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Tao Li
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Lennart Hammarström
- BGI-Shenzhen, Shenzhen, 518083, China.
- Division of Clinical Immunology at the Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, 141 86, Stockholm, Sweden.
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.
| | - Xiao Liu
- BGI-Shenzhen, Shenzhen, 518083, China.
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China.
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3
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Fu J, Khosravi-Maharlooei M, Sykes M. High Throughput Human T Cell Receptor Sequencing: A New Window Into Repertoire Establishment and Alloreactivity. Front Immunol 2021; 12:777756. [PMID: 34804070 PMCID: PMC8604183 DOI: 10.3389/fimmu.2021.777756] [Citation(s) in RCA: 6] [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: 09/15/2021] [Accepted: 10/20/2021] [Indexed: 12/25/2022] Open
Abstract
Recent advances in high throughput sequencing (HTS) of T cell receptors (TCRs) and in transcriptomic analysis, particularly at the single cell level, have opened the door to a new level of understanding of human immunology and immune-related diseases. In this article, we discuss the use of HTS of TCRs to discern the factors controlling human T cell repertoire development and how this approach can be used in combination with human immune system (HIS) mouse models to understand human repertoire selection in an unprecedented manner. An exceptionally high proportion of human T cells has alloreactive potential, which can best be understood as a consequence of the processes governing thymic selection. High throughput TCR sequencing has allowed assessment of the development, magnitude and nature of the human alloresponse at a new level and has provided a tool for tracking the fate of pre-transplant-defined donor- and host-reactive TCRs following transplantation. New insights into human allograft rejection and tolerance obtained with this method in combination with single cell transcriptional analyses are reviewed here.
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Affiliation(s)
- Jianing Fu
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, United States
| | - Mohsen Khosravi-Maharlooei
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, United States
| | - Megan Sykes
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, United States
- Department of Surgery, Columbia University, New York, NY, United States
- Department of Microbiology & Immunology, Columbia University, New York, NY, United States
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4
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Zhao L, Ren L, Gao S, Wang J, Li X, Zhang L, Zhu Y, Li H. Tumor immunology in the age of single-cell genomics. J Leukoc Biol 2021; 110:1069-1079. [PMID: 34184318 DOI: 10.1002/jlb.5mr0321-170r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/11/2021] [Accepted: 06/13/2021] [Indexed: 11/09/2022] Open
Abstract
Immunotherapies that were developed based on our understandings of tumor immunology have revolutionized cancer treatment. However, the success of immunotherapy is eclipsed by several grand challenges, including low response rate, intrinsic/acquired resistance and adverse effects. While a deeper understanding of the interaction between tumor and our immune system, especially the tumor immune niche, is essential to overcome those challenges, we are limited by the fact that most of our knowledge about tumor immunology is based on studies analyzing bulk populations of cells, which are often unable to fully characterize the various cell types and states engaged in immune cell functions. The advent of cutting single-cell genomic technologies empowers us to dissect the tumor immune niche in a genome-wide and spatially resolved manner in single cells, trace their clonal histories, and unveil their regulatory circuits. Future studies on tumor immunology in the age of single-cell genomics, therefore, hold the promise to develop more effective and precise immunotherapies for human cancers. In this perspective, we will discuss how advanced single-cell genomics approaches will revolutionize tumor immunology research and immunotherapies by catering the demand in the field of tumor immunology.
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Affiliation(s)
- Lingyu Zhao
- Department of Pathology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Lili Ren
- Department of Pathology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Shuangshu Gao
- Department of Pathology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Jun Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiaobo Li
- Department of Pathology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Lei Zhang
- Shenzhen Bay Laboratory, Institute of Cancer Research, Shenzhen, China
| | - Yuanyuan Zhu
- Department of Pathology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Hanjie Li
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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5
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Ostmeyer J, Cowell L, Greenberg B, Christley S. Reconstituting T cell receptor selection in-silico. Genes Immun 2021; 22:187-193. [PMID: 34127826 DOI: 10.1038/s41435-021-00141-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/13/2021] [Accepted: 05/26/2021] [Indexed: 11/09/2022]
Abstract
Each T cell receptor (TCR) gene is created without regard for which substances (antigens) the receptor can recognize. T cell selection culls developing T cells when their TCRs (i) fail to recognize major histocompatibility complexes (MHCs) that act as antigen presenting platforms or (ii) recognize with high affinity self-antigens derived from healthy cells and tissue. While T cell selection has been thoroughly studied, little is known about which TCRs are retained or removed by this process. Therefore, we develop an approach using TCR gene sequencing and machine learning to identify patterns in TCR protein sequences influencing the outcome of T cell receptor selection. We verify the trained models classify TCRs from developing T cells as being before selection and TCRs from mature T cells as being after selection. Our approach may provide future avenues for studying the relationship between T cell selection and conditions like autoimmune diseases.
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Affiliation(s)
- Jared Ostmeyer
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA.
| | - Lindsay Cowell
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA
| | - Benjamin Greenberg
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Scott Christley
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, USA
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6
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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 PMCID: PMC7968400 DOI: 10.1111/imm.13299] [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: 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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MESH Headings
- Animals
- CD8-Positive T-Lymphocytes/physiology
- Cells, Cultured
- Clonal Selection, Antigen-Mediated
- Codon Usage
- Genes, T-Cell Receptor beta/genetics
- Humans
- Mice
- Mice, Inbred C57BL
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Recombination, Genetic
- Thymus Gland/immunology
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Affiliation(s)
- Hao H. Yiu
- Department of BiologyUniversity of MarylandCollege ParkMDUSA
| | - Louis N. Schoettle
- School of Life SciencesThe Biodesign InstituteArizona State UniversityTempeAZUSA
| | - Marlene Garcia‐Neuer
- School of Life SciencesThe Biodesign InstituteArizona State UniversityTempeAZUSA
| | - Joseph N. Blattman
- School of Life SciencesThe Biodesign InstituteArizona State UniversityTempeAZUSA
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7
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Giorgetti OB, Shingate P, O'Meara CP, Ravi V, Pillai NE, Tay BH, Prasad A, Iwanami N, Tan HH, Schorpp M, Venkatesh B, Boehm T. Antigen receptor repertoires of one of the smallest known vertebrates. SCIENCE ADVANCES 2021; 7:7/1/eabd8180. [PMID: 33523858 PMCID: PMC7775753 DOI: 10.1126/sciadv.abd8180] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/04/2020] [Indexed: 05/06/2023]
Abstract
The rules underlying the structure of antigen receptor repertoires are not yet fully defined, despite their enormous importance for the understanding of adaptive immunity. With current technology, the large antigen receptor repertoires of mice and humans cannot be comprehensively studied. To circumvent the problems associated with incomplete sampling, we have studied the immunogenetic features of one of the smallest known vertebrates, the cyprinid fish Paedocypris sp. "Singkep" ("minifish"). Despite its small size, minifish has the key genetic facilities characterizing the principal vertebrate lymphocyte lineages. As described for mammals, the frequency distributions of immunoglobulin and T cell receptor clonotypes exhibit the features of fractal systems, demonstrating that self-similarity is a fundamental property of antigen receptor repertoires of vertebrates, irrespective of body size. Hence, minifish achieve immunocompetence via a few thousand lymphocytes organized in robust scale-free networks, thereby ensuring immune reactivity even when cells are lost or clone sizes fluctuate during immune responses.
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Affiliation(s)
- Orlando B Giorgetti
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Prashant Shingate
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore
| | - Connor P O'Meara
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Vydianathan Ravi
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore
| | - Nisha E Pillai
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore
| | - Boon-Hui Tay
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore
| | - Aravind Prasad
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore
| | - Norimasa Iwanami
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Heok Hui Tan
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore 117377, Singapore
| | - Michael Schorpp
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore.
| | - Thomas Boehm
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany.
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8
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Venturi V, Thomas PG. The expanding role of systems immunology in decoding the T cell receptor repertoire. ACTA ACUST UNITED AC 2018; 12:37-45. [PMID: 31106281 DOI: 10.1016/j.coisb.2018.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
T cells play a crucial role in the immune system's defense against many infectious diseases, including persistent infections for which no effective vaccines currently exist. The T cell component of the adaptive immune system is highly complex involving a constantly evolving landscape of various inter-related T cell populations. These T cell populations are characterized by their phenotypic and functional properties as well as the collection, or repertoire, of T cell receptors (TCR) that mediate T cell recognition of antigenic peptides derived from pathogens. Understanding the various processes and factors that impact the development and evolution of the broader T cell repertoire available to recognize and respond to pathogens and the characteristics of antigen-experienced T cell repertoires associated with effective immune control of pathogens is critical to the rational design of T cell-based vaccines and therapies. In this article we discuss, using examples of recent research, the promise that systems immunology approaches, involving quantitative analysis and mathematical and computational modeling of immunological data, hold for decoding the complex TCR repertoire system in the current era of advancing technologies.
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Affiliation(s)
- Vanessa Venturi
- Infection Analytics Program, Kirby Institute for Infection and Immunity, UNSW Australia, Sydney, NSW, Australia
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
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9
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Migalska M, Sebastian A, Radwan J. Profiling of the TCRβ repertoire in non-model species using high-throughput sequencing. Sci Rep 2018; 8:11613. [PMID: 30072736 PMCID: PMC6072738 DOI: 10.1038/s41598-018-30037-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 07/19/2018] [Indexed: 02/06/2023] Open
Abstract
In recent years, immune repertoire profiling with high-throughput sequencing (HTS) has advanced our understanding of adaptive immunity. However, fast progress in the field applied mostly to human and mouse research, with only few studies devoted to other model vertebrates. We present the first in-depth characterization of the T-cell receptor (TCR) repertoire in a non-model mammal (bank vole, Myodes glareolus), widely used in ecological and evolutionary research. We used RNA from spleens, 5′RACE and HTS to describe V and J segments of TCRβ, qualitatively characterize preferential V–J segment usage and CDR3 length distribution. Overall orthology to murine genes was preserved, with 11 J and 37 V genes found in voles (although 3 V genes lacked a close orthologue). Further, we implemented unique molecular identifiers for quantitative analysis of CDR3 repertoire with stringent error correction. A conservative, lower bound estimation of the TCRβ repertoire was similar to that found for mice (1.7–2.3 × 105 clonotypes). We hope that by providing an easy-to-follow molecular protocol and on-line bioinformatics tools that do not require reference sequences (AmpliTCR and AmpliCDR3), we will encourage HTS immune repertoire profiling in other non-model vertebrates, thus opening new research avenues in e.g. comparative immunology, ecology and evolutionary biology.
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Affiliation(s)
- Magdalena Migalska
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland.
| | - Alvaro Sebastian
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland.,Instituto Aragonés de Empleo (INAEM), c/Royo Villanova 1, 50007, Zaragoza, Spain
| | - Jacek Radwan
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland
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10
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Textor J, Fähnrich A, Meinhardt M, Tune C, Klein S, Pagel R, König P, Kalies K, Westermann J. Deep Sequencing Reveals Transient Segregation of T Cell Repertoires in Splenic T Cell Zones during an Immune Response. THE JOURNAL OF IMMUNOLOGY 2018; 201:350-358. [PMID: 29884700 DOI: 10.4049/jimmunol.1800091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/19/2018] [Indexed: 11/19/2022]
Abstract
Immunological differences between hosts, such as diverse TCR repertoires, are widely credited for reducing the risk of pathogen spread and adaptation in a population. Within-host immunological diversity might likewise be important for robust pathogen control, but to what extent naive TCR repertoires differ across different locations in the same host is unclear. T cell zones (TCZs) in secondary lymphoid organs provide secluded microenvironmental niches. By harboring distinct TCRs, such niches could enhance within-host immunological diversity. In contrast, rapid T cell migration is expected to dilute such diversity. In this study, we combined tissue microdissection and deep sequencing of the TCR β-chain to examine the extent to which TCR repertoires differ between TCZs in murine spleens. In the absence of Ag, we found little evidence for differences between TCZs of the same spleen. Yet, 3 d after immunization with sheep RBCs, we observed a >10-fold rise in the number of clones that appeared to localize to individual zones. Remarkably, these differences largely disappeared at 4 d after immunization, when hallmarks of an ongoing immune response were still observed. These data suggest that in the absence of Ag, any repertoire differences observed between TCZs of the same host can largely be attributed to random clone distribution. Upon Ag challenge, TCR repertoires in TCZs first segregate and then homogenize within days. Such "transient mosaic" dynamics could be an important barrier for pathogen adaptation and spread during an immune response.
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Affiliation(s)
- Johannes Textor
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands; and
| | - Anke Fähnrich
- Center for Structural and Cell Biology in Medicine, Institute of Anatomy, University of Lübeck, 23538 Lübeck, Germany
| | - Martin Meinhardt
- Center for Structural and Cell Biology in Medicine, Institute of Anatomy, University of Lübeck, 23538 Lübeck, Germany
| | - Cornelia Tune
- Center for Structural and Cell Biology in Medicine, Institute of Anatomy, University of Lübeck, 23538 Lübeck, Germany
| | - Sebastian Klein
- Center for Structural and Cell Biology in Medicine, Institute of Anatomy, University of Lübeck, 23538 Lübeck, Germany
| | - Rene Pagel
- Center for Structural and Cell Biology in Medicine, Institute of Anatomy, University of Lübeck, 23538 Lübeck, Germany
| | - Peter König
- Center for Structural and Cell Biology in Medicine, Institute of Anatomy, University of Lübeck, 23538 Lübeck, Germany
| | - Kathrin Kalies
- Center for Structural and Cell Biology in Medicine, Institute of Anatomy, University of Lübeck, 23538 Lübeck, Germany
| | - Jürgen Westermann
- Center for Structural and Cell Biology in Medicine, Institute of Anatomy, University of Lübeck, 23538 Lübeck, Germany
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11
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Ichinohe T, Miyama T, Kawase T, Honjo Y, Kitaura K, Sato H, Shin-I T, Suzuki R. Next-Generation Immune Repertoire Sequencing as a Clue to Elucidate the Landscape of Immune Modulation by Host-Gut Microbiome Interactions. Front Immunol 2018; 9:668. [PMID: 29666626 PMCID: PMC5891584 DOI: 10.3389/fimmu.2018.00668] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 03/19/2018] [Indexed: 12/23/2022] Open
Abstract
The human immune system is a fine network consisted of the innumerable numbers of functional cells that balance the immunity and tolerance against various endogenous and environmental challenges. Although advances in modern immunology have revealed a role of many unique immune cell subsets, technologies that enable us to capture the whole landscape of immune responses against specific antigens have been not available to date. Acquired immunity against various microorganisms including host microbiome is principally founded on T cell and B cell populations, each of which expresses antigen-specific receptors that define a unique clonotype. Over the past several years, high-throughput next-generation sequencing has been developed as a powerful tool to profile T- and B-cell receptor repertoires in a given individual at the single-cell level. Sophisticated immuno-bioinformatic analyses by use of this innovative methodology have been already implemented in clinical development of antibody engineering, vaccine design, and cellular immunotherapy. In this article, we aim to discuss the possible application of high-throughput immune receptor sequencing in the field of nutritional and intestinal immunology. Although there are still unsolved caveats, this emerging technology combined with single-cell transcriptomics/proteomics provides a critical tool to unveil the previously unrecognized principle of host–microbiome immune homeostasis. Accumulation of such knowledge will lead to the development of effective ways for personalized immune modulation through deeper understanding of the mechanisms by which the intestinal environment affects our immune ecosystem.
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Affiliation(s)
- Tatsuo Ichinohe
- Department of Hematology and Oncology, Research Institute for Radiation Biology and Medicine (RIRBM), Hiroshima University, Hiroshima, Japan
| | - Takahiko Miyama
- Department of Hematology and Oncology, Research Institute for Radiation Biology and Medicine (RIRBM), Hiroshima University, Hiroshima, Japan
| | - Takakazu Kawase
- Department of Hematology and Oncology, Research Institute for Radiation Biology and Medicine (RIRBM), Hiroshima University, Hiroshima, Japan
| | - Yasuko Honjo
- Department of Hematology and Oncology, Research Institute for Radiation Biology and Medicine (RIRBM), Hiroshima University, Hiroshima, Japan
| | | | | | | | - Ryuji Suzuki
- Repertoire Genesis Incorporation, Ibaraki, Japan.,Department of Rheumatology and Clinical Immunology, Clinical Research Center for Rheumatology and Allergy, National Hospital Organization Sagamihara Hospital, Sagamihara, Japan
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12
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Fu X, Sun J, Tan E, Shimizu K, Reza MS, Watabe S, Asakawa S. High-Throughput Sequencing of the Expressed Torafugu ( Takifugu rubripes) Antibody Sequences Distinguishes IgM and IgT Repertoires and Reveals Evidence of Convergent Evolution. Front Immunol 2018. [PMID: 29515575 PMCID: PMC5826340 DOI: 10.3389/fimmu.2018.00251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
B-cell antigen receptor (BCR) or antibody diversity arises from somatic recombination of immunoglobulin (Ig) gene segments and is concentrated within the Ig heavy (H) chain complementarity-determining region 3 (CDR-H3). We performed high-throughput sequencing of the expressed antibody heavy-chain repertoire from adult torafugu. We found that torafugu use between 70 and 82% of all possible V (variable), D (diversity), and J (joining) gene segment combinations and that they share a similar frequency distribution of these VDJ combinations. The CDR-H3 sequence repertoire observed in individuals is biased with the preferential use of a small number of VDJ, dominated by sequences containing inserted nucleotides. We uncovered the common CDR-H3 amino-acid (aa) sequences shared by individuals. Common CDR-H3 sequences feature highly convergent nucleic-acid recombination compared with private ones. Finally, we observed differences in repertoires between IgM and IgT, including the unequal usage frequencies of V gene segment and the biased number of nucleotide insertion/deletion at VDJ junction regions that leads to distinct distributions of CDR-H3 lengths.
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Affiliation(s)
- Xi Fu
- State Key Laboratory of Biotherapy, West China Hospital, Collaborative Innovation Center and Sichuan University, Chengdu, China.,Laboratory of Aquatic Molecular Biology and Biotechnology, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Jianqiang Sun
- Bioinformational Engineering Laboratory, Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Engkong Tan
- Laboratory of Aquatic Molecular Biology and Biotechnology, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kentaro Shimizu
- Bioinformational Engineering Laboratory, Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Md Shaheed Reza
- School of Marine Biosciences, Kitasato University, Kanagawa, Japan.,Department of Fisheries Technology, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Shugo Watabe
- School of Marine Biosciences, Kitasato University, Kanagawa, Japan
| | - Shuichi Asakawa
- Laboratory of Aquatic Molecular Biology and Biotechnology, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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13
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Izraelson M, Nakonechnaya TO, Moltedo B, Egorov ES, Kasatskaya SA, Putintseva EV, Mamedov IZ, Staroverov DB, Shemiakina II, Zakharova MY, Davydov AN, Bolotin DA, Shugay M, Chudakov DM, Rudensky AY, Britanova OV. Comparative analysis of murine T-cell receptor repertoires. Immunology 2017; 153:133-144. [PMID: 29080364 DOI: 10.1111/imm.12857] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/06/2017] [Accepted: 10/06/2017] [Indexed: 12/21/2022] Open
Abstract
For understanding the rules and laws of adaptive immunity, high-throughput profiling of T-cell receptor (TCR) repertoires becomes a powerful tool. The structure of TCR repertoires is instructive even before the antigen specificity of each particular receptor becomes available. It embodies information about the thymic and peripheral selection of T cells; the readiness of an adaptive immunity to withstand new challenges; the character, magnitude and memory of immune responses; and the aetiological and functional proximity of T-cell subsets. Here, we describe our current analytical approaches for the comparative analysis of murine TCR repertoires, and show several examples of how these approaches can be applied for particular experimental settings. We analyse the efficiency of different metrics used for estimation of repertoire diversity, repertoire overlap, V-gene and J-gene segments usage similarity, and amino acid composition of CDR3. We discuss basic differences of these metrics and their advantages and limitations in different experimental models, and we provide guidelines for choosing an efficient way to lead a comparative analysis of TCR repertoires. Applied to the various known and newly developed mouse models, such analysis should allow us to disentangle multiple sophisticated puzzles in adaptive immunity.
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Affiliation(s)
- Mark Izraelson
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Tatiana O Nakonechnaya
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Bruno Moltedo
- Howard Hughes Medical Institute and Immunology Program, Ludwig Center at Memorial Sloan Kettering Cancer Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Evgeniy S Egorov
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Sofya A Kasatskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Ilgar Z Mamedov
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitriy B Staroverov
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Irina I Shemiakina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Maria Y Zakharova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Dmitriy A Bolotin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia.,MiLaboratory LLC, Skolkovo Innovation Centre, Moscow, Russia
| | - Mikhail Shugay
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia.,Central European Institute of Technology, Brno, Czech Republic.,Centre for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Dmitriy M Chudakov
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia.,Central European Institute of Technology, Brno, Czech Republic.,Centre for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Alexander Y Rudensky
- Howard Hughes Medical Institute and Immunology Program, Ludwig Center at Memorial Sloan Kettering Cancer Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Olga V Britanova
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
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14
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Castro R, Navelsaker S, Krasnov A, Du Pasquier L, Boudinot P. Describing the diversity of Ag specific receptors in vertebrates: Contribution of repertoire deep sequencing. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 75:28-37. [PMID: 28259700 DOI: 10.1016/j.dci.2017.02.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 02/16/2017] [Accepted: 02/22/2017] [Indexed: 06/06/2023]
Abstract
During the last decades, gene and cDNA cloning identified TCR and Ig genes across vertebrates; genome sequencing of TCR and Ig loci in many species revealed the different organizations selected during evolution under the pressure of generating diverse repertoires of Ag receptors. By detecting clonotypes over a wide range of frequency, deep sequencing of Ig and TCR transcripts provides a new way to compare the structure of expressed repertoires in species of various sizes, at different stages of development, with different physiologies, and displaying multiple adaptations to the environment. In this review, we provide a short overview of the technologies currently used to produce global description of immune repertoires, describe how they have already been used in comparative immunology, and we discuss the future potential of such approaches. The development of these methodologies in new species holds promise for new discoveries concerning particular adaptations. As an example, understanding the development of adaptive immunity across metamorphosis in frogs has been made possible by such approaches. Repertoire sequencing is now widely used, not only in basic research but also in the context of immunotherapy and vaccination. Analysis of fish responses to pathogens and vaccines has already benefited from these methods. Finally, we also discuss potential advances based on repertoire sequencing of multigene families of immune sensors and effectors in invertebrates.
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Affiliation(s)
- Rosario Castro
- Department of Animal Health, Faculty of Veterinary Sciences, Complutense University, Madrid, Spain
| | - Sofie Navelsaker
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Department of Basic Sciences and Aquatic Medicine, Adamstuen Campus, Oslo 0454, Norway; Virologie et Immunologie Moléculaires, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | | | | | - Pierre Boudinot
- Virologie et Immunologie Moléculaires, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
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15
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Greiff V, Weber CR, Palme J, Bodenhofer U, Miho E, Menzel U, Reddy ST. Learning the High-Dimensional Immunogenomic Features That Predict Public and Private Antibody Repertoires. THE JOURNAL OF IMMUNOLOGY 2017; 199:2985-2997. [DOI: 10.4049/jimmunol.1700594] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 08/16/2017] [Indexed: 11/19/2022]
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16
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Dash P, Fiore-Gartland AJ, Hertz T, Wang GC, Sharma S, Souquette A, Crawford JC, Clemens EB, Nguyen THO, Kedzierska K, La Gruta NL, Bradley P, Thomas PG. Quantifiable predictive features define epitope-specific T cell receptor repertoires. Nature 2017. [PMID: 28636592 DOI: 10.1038/nature22383] [Citation(s) in RCA: 519] [Impact Index Per Article: 74.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
T cells are defined by a heterodimeric surface receptor, the T cell receptor (TCR), that mediates recognition of pathogen-associated epitopes through interactions with peptide and major histocompatibility complexes (pMHCs). TCRs are generated by genomic rearrangement of the germline TCR locus, a process termed V(D)J recombination, that has the potential to generate marked diversity of TCRs (estimated to range from 1015 (ref. 1) to as high as 1061 (ref. 2) possible receptors). Despite this potential diversity, TCRs from T cells that recognize the same pMHC epitope often share conserved sequence features, suggesting that it may be possible to predictively model epitope specificity. Here we report the in-depth characterization of ten epitope-specific TCR repertoires of CD8+ T cells from mice and humans, representing over 4,600 in-frame single-cell-derived TCRαβ sequence pairs from 110 subjects. We developed analytical tools to characterize these epitope-specific repertoires: a distance measure on the space of TCRs that permits clustering and visualization, a robust repertoire diversity metric that accommodates the low number of paired public receptors observed when compared to single-chain analyses, and a distance-based classifier that can assign previously unobserved TCRs to characterized repertoires with robust sensitivity and specificity. Our analyses demonstrate that each epitope-specific repertoire contains a clustered group of receptors that share core sequence similarities, together with a dispersed set of diverse 'outlier' sequences. By identifying shared motifs in core sequences, we were able to highlight key conserved residues driving essential elements of TCR recognition. These analyses provide insights into the generalizable, underlying features of epitope-specific repertoires and adaptive immune recognition.
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Affiliation(s)
- Pradyot Dash
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Andrew J Fiore-Gartland
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Tomer Hertz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - George C Wang
- Division of Geriatric Medicine and Gerontology, Biology of Healthy Aging Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21224, USA
| | - Shalini Sharma
- Department of Veterinary Physiology and Biochemistry, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, Haryana 125004, India
| | - Aisha Souquette
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - Jeremy Chase Crawford
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
| | - E Bridie Clemens
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia
| | - Thi H O Nguyen
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia
| | - Katherine Kedzierska
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia
| | - Nicole L La Gruta
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Philip Bradley
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.,Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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17
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Britanova OV, Shugay M, Merzlyak EM, Staroverov DB, Putintseva EV, Turchaninova MA, Mamedov IZ, Pogorelyy MV, Bolotin DA, Izraelson M, Davydov AN, Egorov ES, Kasatskaya SA, Rebrikov DV, Lukyanov S, Chudakov DM. Dynamics of Individual T Cell Repertoires: From Cord Blood to Centenarians. THE JOURNAL OF IMMUNOLOGY 2016; 196:5005-13. [PMID: 27183615 DOI: 10.4049/jimmunol.1600005] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/16/2016] [Indexed: 01/29/2023]
Abstract
The diversity, architecture, and dynamics of the TCR repertoire largely determine our ability to effectively withstand infections and malignancies with minimal mistargeting of immune responses. In this study, we have employed deep TCRβ repertoire sequencing with normalization based on unique molecular identifiers to explore the long-term dynamics of T cell immunity. We demonstrate remarkable stability of repertoire, where approximately half of all T cells in peripheral blood are represented by clones that persist and generally preserve their frequencies for 3 y. We further characterize the extremes of lifelong TCR repertoire evolution, analyzing samples ranging from umbilical cord blood to centenarian peripheral blood. We show that the fetal TCR repertoire, albeit structurally maintained within regulated borders due to the lower numbers of randomly added nucleotides, is not limited with respect to observed functional diversity. We reveal decreased efficiency of nonsense-mediated mRNA decay in umbilical cord blood, which may reflect specific regulatory mechanisms in development. Furthermore, we demonstrate that human TCR repertoires are functionally more similar at birth but diverge during life, and we track the lifelong behavior of CMV- and EBV-specific T cell clonotypes. Finally, we reveal gender differences in dynamics of TCR diversity constriction, which come to naught in the oldest age. Based on our data, we propose a more general explanation for the previous observations on the relationships between longevity and immunity.
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Affiliation(s)
- Olga V Britanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Mikhail Shugay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Ekaterina M Merzlyak
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Dmitriy B Staroverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Ekaterina V Putintseva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Maria A Turchaninova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Ilgar Z Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Mikhail V Pogorelyy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Dmitriy A Bolotin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Mark Izraelson
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Alexey N Davydov
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Evgeny S Egorov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Sofya A Kasatskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Denis V Rebrikov
- Pirogov Russian National Research Medical University, Moscow 117997, Russia; Vavilov Institute of General Genetics of the Russian Academy of Sciences, Moscow 119991, Russia
| | - Sergey Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
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18
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Covacu R, Philip H, Jaronen M, Almeida J, Kenison JE, Darko S, Chao CC, Yaari G, Louzoun Y, Carmel L, Douek DC, Efroni S, Quintana FJ. System-wide Analysis of the T Cell Response. Cell Rep 2016; 14:2733-44. [PMID: 26972015 PMCID: PMC4805488 DOI: 10.1016/j.celrep.2016.02.056] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 01/12/2016] [Accepted: 02/02/2016] [Indexed: 01/01/2023] Open
Abstract
The T cell receptor (TCR) controls the cellular adaptive immune response to antigens, but our understanding of TCR repertoire diversity and response to challenge is still incomplete. For example, TCR clones shared by different individuals with minimal alteration to germline gene sequences (public clones) are detectable in all vertebrates, but their significance is unknown. Although small in size, the zebrafish TCR repertoire is controlled by processes similar to those operating in mammals. Thus, we studied the zebrafish TCR repertoire and its response to stimulation with self and foreign antigens. We found that cross-reactive public TCRs dominate the T cell response, endowing a limited TCR repertoire with the ability to cope with diverse antigenic challenges. These features of vertebrate public TCRs might provide a mechanism for the rapid generation of protective T cell immunity, allowing a short temporal window for the development of more specific private T cell responses.
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Affiliation(s)
- Ruxandra Covacu
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Hagit Philip
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Merja Jaronen
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Jorge Almeida
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, MD 20892, USA
| | - Jessica E Kenison
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Samuel Darko
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, MD 20892, USA
| | - Chun-Cheih Chao
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Gur Yaari
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan 52900, Israel; Gonda Brain Research Center, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Liran Carmel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, MD 20892, USA.
| | - Sol Efroni
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel.
| | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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19
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Hou XL, Wang L, Ding YL, Xie Q, Diao HY. Current status and recent advances of next generation sequencing techniques in immunological repertoire. Genes Immun 2016; 17:153-64. [PMID: 26963138 DOI: 10.1038/gene.2016.9] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 01/20/2016] [Accepted: 01/20/2016] [Indexed: 01/26/2023]
Abstract
To ward off a wide variety of pathogens, the human adaptive immune system harbors a vast array of T-cell receptors (TCRs) and B-cell receptors (BCRs), collectively referred to as the immune repertoire. High-throughput sequencing (HTS) of TCR/BCR genes allows in-depth molecular analysis of T/B-cell clones, providing an unprecedented level of detail when examining the T/B-cell repertoire of individuals. It can evaluate TCR/BCR complementarity-determining region 3 (CDR3) diversity and assess the clonal composition, including the size of the repertoire; similarities between repertoires; V(D)J segment use; nucleotide insertions and deletions; CDR3 lengths; and amino acid distributions along the CDR3s at sequence-level resolution. Deep sequencing of B-cell and T-cell repertoires offers the potential for a quantitative understanding of the adaptive immune system in healthy and disease states. Recently, paired sequencing strategies have also been developed, which can provide information about the identity of immune receptor pairs encoded by individual T or B lymphocytes. HTS technology provides a previously unimaginable amount of sequence data, accompanied, however, by numerous challenges associated with error correction and interpretation that remain to be solved. The review details some of the technologies and some of the recent achievements in this field.
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Affiliation(s)
- X-L Hou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - L Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Y-L Ding
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Q Xie
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - H-Y Diao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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20
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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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21
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Attaf M, Huseby E, Sewell AK. αβ T cell receptors as predictors of health and disease. Cell Mol Immunol 2015; 12:391-9. [PMID: 25619506 PMCID: PMC4496535 DOI: 10.1038/cmi.2014.134] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 12/17/2014] [Indexed: 02/08/2023] Open
Abstract
The diversity of antigen receptors and the specificity it underlies are the hallmarks of the cellular arm of the adaptive immune system. T and B lymphocytes are indeed truly unique in their ability to generate receptors capable of recognizing virtually any pathogen. It has been known for several decades that T lymphocytes recognize short peptides derived from degraded proteins presented by major histocompatibility complex (MHC) molecules at the cell surface. Interaction between peptide-MHC (pMHC) and the T cell receptor (TCR) is central to both thymic selection and peripheral antigen recognition. It is widely assumed that TCR diversity is required, or at least highly desirable, to provide sufficient immune coverage. However, a number of immune responses are associated with the selection of predictable, narrow, or skewed repertoires and public TCR chains. Here, we summarize the current knowledge on the formation of the TCR repertoire and its maintenance in health and disease. We also outline the various molecular mechanisms that govern the composition of the pre-selection, naive and antigen-specific TCR repertoires. Finally, we suggest that with the development of high-throughput sequencing, common TCR 'signatures' raised against specific antigens could provide important diagnostic biomarkers and surrogate predictors of disease onset, progression and outcome.
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Affiliation(s)
- Meriem Attaf
- Cardiff University School of Medicine, Cardiff, UK
| | - Eric Huseby
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
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22
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Egorov ES, Merzlyak EM, Shelenkov AA, Britanova OV, Sharonov GV, Staroverov DB, Bolotin DA, Davydov AN, Barsova E, Lebedev YB, Shugay M, Chudakov DM. Quantitative Profiling of Immune Repertoires for Minor Lymphocyte Counts Using Unique Molecular Identifiers. THE JOURNAL OF IMMUNOLOGY 2015; 194:6155-63. [DOI: 10.4049/jimmunol.1500215] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/08/2015] [Indexed: 12/11/2022]
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23
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van Schaik B, Klarenbeek P, Doorenspleet M, van Kampen A, Moody DB, de Vries N, Van Rhijn I. Discovery of invariant T cells by next-generation sequencing of the human TCR α-chain repertoire. THE JOURNAL OF IMMUNOLOGY 2014; 193:5338-44. [PMID: 25339678 DOI: 10.4049/jimmunol.1401380] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
During infection and autoimmune disease, activation and expansion of T cells take place. Consequently, the TCR repertoire contains information about ongoing and past diseases. Analysis and interpretation of the human TCR repertoire are hampered by its size and stochastic variation and by the diversity of Ags and Ag-presenting molecules encoded by the MHC, but are highly desirable and would greatly impact fundamental and clinical immunology. A subset of the TCR repertoire is formed by invariant T cells. Invariant T cells express interdonor-conserved TCRs and recognize a limited set of Ags, presented by nonpolymorphic Ag-presenting molecules. Discovery of the three known invariant T cell populations has been a tedious and slow process, identifying them one by one. Because conservation of the TCR α-chain of invariant T cells is much higher than the β-chain, and because the TCR α-chain V gene segment TRAV1-2 is used by two of the three known invariant TCRs, we employed next-generation sequencing of TCR α-chains that contain the TRAV1-2 gene segment to identify 16 invariant TCRs shared among many blood donors. Frequency analysis of individual clones indicates these T cells are expanded in many donors, implying an important role in human immunity. This approach extends the number of known interdonor-conserved TCRs and suggests that many more exist and that these TCR patterns can be used to systematically evaluate human Ag exposure.
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Affiliation(s)
- Barbera van Schaik
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Academic Medical Center, University of Amsterdam, 1100 DD Amsterdam, the Netherlands
| | - Paul Klarenbeek
- Department of Clinical Immunology and Rheumatology, Academic Medical Center, University of Amsterdam, 1100 DD Amsterdam, the Netherlands; Laboratory for Genome Analysis, Academic Medical Center, University of Amsterdam, 1100 DD Amsterdam, the Netherlands
| | - Marieke Doorenspleet
- Department of Clinical Immunology and Rheumatology, Academic Medical Center, University of Amsterdam, 1100 DD Amsterdam, the Netherlands; Laboratory for Genome Analysis, Academic Medical Center, University of Amsterdam, 1100 DD Amsterdam, the Netherlands
| | - Antoine van Kampen
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Academic Medical Center, University of Amsterdam, 1100 DD Amsterdam, the Netherlands
| | - D Branch Moody
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115; and
| | - Niek de Vries
- Department of Clinical Immunology and Rheumatology, Academic Medical Center, University of Amsterdam, 1100 DD Amsterdam, the Netherlands; Laboratory for Genome Analysis, Academic Medical Center, University of Amsterdam, 1100 DD Amsterdam, the Netherlands
| | - Ildiko Van Rhijn
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115; and Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584CL Utrecht, the Netherlands
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24
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Madi A, Shifrut E, Reich-Zeliger S, Gal H, Best K, Ndifon W, Chain B, Cohen IR, Friedman N. T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity. Genome Res 2014; 24:1603-12. [PMID: 25024161 PMCID: PMC4199372 DOI: 10.1101/gr.170753.113] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The T-cell receptor (TCR) repertoire is formed by random recombinations of genomic precursor elements; the resulting combinatorial diversity renders unlikely extensive TCR sharing between individuals. Here, we studied CDR3β amino acid sequence sharing in a repertoire-wide manner, using high-throughput TCR-seq in 28 healthy mice. We uncovered hundreds of public sequences shared by most mice. Public CDR3 sequences, relative to private sequences, are two orders of magnitude more abundant on average, express restricted V/J segments, and feature high convergent nucleic acid recombination. Functionally, public sequences are enriched for MHC-diverse CDR3 sequences that were previously associated with autoimmune, allograft, and tumor-related reactions, but not with anti-pathogen-related reactions. Public CDR3 sequences are shared between mice of different MHC haplotypes, but are associated with different, MHC-dependent, V genes. Thus, despite their random generation process, TCR repertoires express a degree of uniformity in their post-genomic organization. These results, together with numerical simulations of TCR genomic rearrangements, suggest that biases and convergence in TCR recombination combine with ongoing selection to generate a restricted subset of self-associated, public CDR3 TCR sequences, and invite reexamination of the basic mechanisms of T-cell repertoire formation.
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Affiliation(s)
- Asaf Madi
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eric Shifrut
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Hilah Gal
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Katharine Best
- Division of Infection and Immunity, The Cruciform Building, UCL, London WC1 6BT, United Kingdom
| | - Wilfred Ndifon
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Benjamin Chain
- Division of Infection and Immunity, The Cruciform Building, UCL, London WC1 6BT, United Kingdom
| | - Irun R Cohen
- 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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25
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Liu P, Liu D, Yang X, Gao J, Chen Y, Xiao X, Liu F, Zou J, Wu J, Ma J, Zhao F, Zhou X, Gao GF, Zhu B. Characterization of human αβTCR repertoire and discovery of D-D fusion in TCRβ chains. Protein Cell 2014; 5:603-15. [PMID: 24866699 PMCID: PMC4130922 DOI: 10.1007/s13238-014-0060-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Accepted: 04/01/2014] [Indexed: 11/28/2022] Open
Abstract
The characterization of the human T-cell receptor (TCR) repertoire has made remarkable progress, with most of the work focusing on the TCRβ chains. Here, we analyzed the diversity and complexity of both the TCRα and TCRβ repertoires of three healthy donors. We found that the diversity of the TCRα repertoire is higher than that of the TCRβ repertoire, whereas the usages of the V and J genes tended to be preferential with similar TRAV and TRAJ patterns in all three donors. The V-J pairings, like the V and J gene usages, were slightly preferential. We also found that the TRDV1 gene rearranges with the majority of TRAJ genes, suggesting that TRDV1 is a shared TRAV/DV gene (TRAV42/DV1). Moreover, we uncovered the presence of tandem TRBD (TRB D gene) usage in ~2% of the productive human TCRβ CDR3 sequences.
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Affiliation(s)
- Peipei Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China,
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26
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Distinctive properties of identical twins' TCR repertoires revealed by high-throughput sequencing. Proc Natl Acad Sci U S A 2014; 111:5980-5. [PMID: 24711416 DOI: 10.1073/pnas.1319389111] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Adaptive immunity in humans is provided by hypervariable Ig-like molecules on the surface of B and T cells. The final set of these molecules in each organism is formed under the influence of two forces: individual genetic traits and the environment, which includes the diverse spectra of alien and self-antigens. Here we assess the impact of individual genetic factors on the formation of the adaptive immunity by analyzing the T-cell receptor (TCR) repertoires of three pairs of monozygous twins by next-generation sequencing. Surprisingly, we found that an overlap between the TCR repertoires of monozygous twins is similar to an overlap between the TCR repertoires of nonrelated individuals. However, the number of identical complementary determining region 3 sequences in two individuals is significantly increased for twin pairs in the fraction of highly abundant TCR molecules, which is enriched by the antigen-experienced T cells. We found that the initial recruitment of particular TCR V genes for recombination and subsequent selection in the thymus is strictly determined by individual genetic factors. J genes of TCRs are selected randomly for recombination; however, the subsequent selection in the thymus gives preference to some α but not β J segments. These findings provide a deeper insight into the mechanism of TCR repertoire generation.
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27
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Britanova OV, Putintseva EV, Shugay M, Merzlyak EM, Turchaninova MA, Staroverov DB, Bolotin DA, Lukyanov S, Bogdanova EA, Mamedov IZ, Lebedev YB, Chudakov DM. Age-related decrease in TCR repertoire diversity measured with deep and normalized sequence profiling. THE JOURNAL OF IMMUNOLOGY 2014; 192:2689-98. [PMID: 24510963 DOI: 10.4049/jimmunol.1302064] [Citation(s) in RCA: 303] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The decrease of TCR diversity with aging has never been studied by direct methods. In this study, we combined high-throughput Illumina sequencing with unique cDNA molecular identifier technology to achieve deep and precisely normalized profiling of TCR β repertoires in 39 healthy donors aged 6-90 y. We demonstrate that TCR β diversity per 10(6) T cells decreases roughly linearly with age, with significant reduction already apparent by age 40. The percentage of naive T cells showed a strong correlation with measured TCR diversity and decreased linearly up to age 70. Remarkably, the oldest group (average age 82 y) was characterized by a higher percentage of naive CD4(+) T cells, lower abundance of expanded clones, and increased TCR diversity compared with the previous age group (average age 62 y), suggesting the influence of age selection and association of these three related parameters with longevity. Interestingly, cross-analysis of individual TCR β repertoires revealed a set >10,000 of the most representative public TCR β clonotypes, whose abundance among the top 100,000 clones correlated with TCR diversity and decreased with aging.
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Affiliation(s)
- Olga V Britanova
- Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 117997 Moscow, Russia
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28
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Putintseva EV, Britanova OV, Staroverov DB, Merzlyak EM, Turchaninova MA, Shugay M, Bolotin DA, Pogorelyy MV, Mamedov IZ, Bobrynina V, Maschan M, Lebedev YB, Chudakov DM. Mother and child T cell receptor repertoires: deep profiling study. Front Immunol 2013; 4:463. [PMID: 24400004 PMCID: PMC3872299 DOI: 10.3389/fimmu.2013.00463] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 12/03/2013] [Indexed: 12/03/2022] Open
Abstract
The relationship between maternal and child immunity has been actively studied in the context of complications during pregnancy, autoimmune diseases, and haploidentical transplantation of hematopoietic stem cells and solid organs. Here, we have for the first time used high-throughput Illumina HiSeq sequencing to perform deep quantitative profiling of T cell receptor (TCR) repertoires for peripheral blood samples of three mothers and their six children. Advanced technology allowed accurate identification of 5 × 105 to 2 × 106 TCR beta clonotypes per individual. We performed comparative analysis of these TCR repertoires with the aim of revealing characteristic features that distinguish related mother-child pairs, such as relative TCR beta variable segment usage frequency and relative overlap of TCR beta complementarity-determining region 3 (CDR3) repertoires. We show that thymic selection essentially and similarly shapes the initial output of the TCR recombination machinery in both related and unrelated pairs, with minor effect from inherited differences. The achieved depth of TCR profiling also allowed us to test the hypothesis that mature T cells transferred across the placenta during pregnancy can expand and persist as functional microchimeric clones in their new host, using characteristic TCR beta CDR3 variants as clonal identifiers.
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Affiliation(s)
- Ekaterina V Putintseva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Olga V Britanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Dmitriy B Staroverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Ekaterina M Merzlyak
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Maria A Turchaninova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Mikhail Shugay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Dmitriy A Bolotin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Mikhail V Pogorelyy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Ilgar Z Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Vlasta Bobrynina
- Federal Scientific Clinical Center of Pediatric Hematology, Oncology and Immunology , Moscow , Russia
| | - Mikhail Maschan
- Federal Scientific Clinical Center of Pediatric Hematology, Oncology and Immunology , Moscow , Russia
| | - Yuri B Lebedev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia ; Central European Institute of Technology (CEITEC), Masaryk University , Brno , Czech Republic
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29
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Shugay M, Bolotin DA, Putintseva EV, Pogorelyy MV, Mamedov IZ, Chudakov DM. Huge Overlap of Individual TCR Beta Repertoires. Front Immunol 2013; 4:466. [PMID: 24400005 PMCID: PMC3872297 DOI: 10.3389/fimmu.2013.00466] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 09/12/2013] [Indexed: 11/29/2022] Open
Affiliation(s)
- Mikhail Shugay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Dmitriy A Bolotin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Ekaterina V Putintseva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Mikhail V Pogorelyy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia
| | - Ilgar Z Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia ; Central European Institute of Technology (CEITEC), Masaryk University , Brno , Czech Republic
| | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science , Moscow , Russia ; Central European Institute of Technology (CEITEC), Masaryk University , Brno , Czech Republic
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30
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Venturi V, Rudd BD, Davenport MP. Specificity, promiscuity, and precursor frequency in immunoreceptors. Curr Opin Immunol 2013; 25:639-45. [PMID: 23880376 DOI: 10.1016/j.coi.2013.07.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 07/01/2013] [Accepted: 07/01/2013] [Indexed: 10/26/2022]
Abstract
The immune system is comprised of various immune cell populations that utilize a spectrum of immunoreceptors characterized by different levels of specificity, diversity, and prevalence within a host and across a population. These range from the universal receptors employed by both innate cells and innate-like cells, such as NKT and MAIT cells, through to receptors expressed on T cells with sporadic incidence. Here we review recent advances in understanding the molecular mechanisms that drive the observed spectra of T cell receptors in vivo.
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Affiliation(s)
- Vanessa Venturi
- Computational Biology Group, Centre for Vascular Research, University of New South Wales, Kensington, New South Wales 2052, Australia.
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31
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La Gruta NL, Thomas PG. Interrogating the relationship between naïve and immune antiviral T cell repertoires. Curr Opin Virol 2013; 3:447-51. [PMID: 23849601 DOI: 10.1016/j.coviro.2013.06.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 05/22/2013] [Accepted: 06/18/2013] [Indexed: 11/26/2022]
Abstract
Understanding how naïve virus-specific CD8+ T cells influence the type of immune response generated after virus infection is critical for the development of enhanced therapeutic and vaccination strategies to exploit CD8+ T cell-mediated immunity. Recent technological advances in T cell isolation and T receptor sequencing have allowed for greater understanding of the basic structure of immune T cell repertoires, the diversity of responses within and between individuals, and changes in repertoires over time and in response to infection conditions. In this review, we discuss the current understanding of how T cell repertoires contribute to potent antiviral responses. Additionally we compare the state of the art in receptor sequencing, highlighting the advantages and disadvantages of the three most common approaches: next-generation sequencing, template-switch anchored RT-PCR, and multiplex single cell PCR. Finally, we describe how TCR sequencing has delineated the relationship between naïve and immune T cell repertoires.
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Affiliation(s)
- Nicole L La Gruta
- Department of Microbiology & Immunology, University of Melbourne, Parkville, VIC 3010, Australia.
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32
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Baum PD, Venturi V, Price DA. Wrestling with the repertoire: the promise and perils of next generation sequencing for antigen receptors. Eur J Immunol 2013; 42:2834-9. [PMID: 23108932 DOI: 10.1002/eji.201242999] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Next generation sequencing technologies are revolutionizing the study of immune repertoires. These methods provide a previously unimaginable amount of sequence data, unfortunately accompanied by numerous challenges associated with error correction and interpretation that remain to be solved. For antigen receptors, these challenges will require dedicated solutions beyond those developed for genome sequencing, which may differ depending on the sequencing technology used and the purpose of the experiment. Many investigators are developing such methods, based on different sequencing platforms, but critical details of protocol and performance are proprietary. The field will move forward when these methods are shared and standardized, and when the accuracy, sensitivity and reproducibility of various sequencing, and analytic methods are evaluated using standardized samples in comparative experiments.
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Affiliation(s)
- Paul D Baum
- Department of Medicine, University of California, San Francisco, CA 94114, USA.
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