101
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Lin Z, Qian S, Gong Y, Ren J, Zhao L, Wang D, Wang X, Zhang Y, Wang Z, Zhang Q. Deep sequencing of the T cell receptor β repertoire reveals signature patterns and clonal drift in atherosclerotic plaques and patients. Oncotarget 2017; 8:99312-99322. [PMID: 29245903 PMCID: PMC5725094 DOI: 10.18632/oncotarget.19892] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 06/18/2017] [Indexed: 02/06/2023] Open
Abstract
The T cell receptor (TCR) β repertoire directly reflects the status of T cell function. Meanwhile, the immune/inflammatory responses regulated by T cells are the critical determinants of atherosclerosis development. However, due to technical limitations, the composition and molecular characteristics of the TCR repertoire in atherosclerotic patients have not been fully elucidated. In the present study, we use powerful immune repertoire sequencing technology to study this issue. Results show that the utilization of V and/or J genes and the diversity of TCRβ repertoire in atherosclerotic plaques are significantly reduced compared to those in the peripheral blood of normal subjects and atherosclerotic patients. The frequencies of the common T cell clones with certain lengths of the complement determining region 3 regions are notably different among all groups. The high-frequency common clones are also increased in the atherosclerotic plaques compared to that in the other two groups. The expansion of several T cell clonotypes (V29-1J2-1, V20-1J1-6, V6-3J2-7 and V11-2J2-2) is validated in atherosclerotic patients. In short, this study reveals that the diversity of TCR β repertoire significantly decreases in atherosclerotic plaques, probably because of the reduced utilization of VJ genes and marked expansion of some T cell subclones. It provides the basis for understanding the roles of T lymphocytes in the pathogenesis of atherosclerosis.
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Affiliation(s)
- Zongwei Lin
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, and The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Shao Qian
- Department of Women Health Care, Jinan Maternity and Child Care Hospital, Jinan, China
| | - Yan Gong
- Division of Endocrinology and Metabolism, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Jianwei Ren
- Health Division of Guard Bureau, General Staff Department of Chinese PLA, Beijing, China
| | - Lixia Zhao
- Pharmacy Department of Shandong Medical College, Jinan, China
| | - Dongxiao Wang
- Department of Pharmacy, Chinese PLA General Hospital, Beijing, China
| | - Xiaowei Wang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, and The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Yun Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, and The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Zhe Wang
- Division of Endocrinology and Metabolism, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Qunye Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Health, and The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Qilu Hospital of Shandong University, Jinan, China
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102
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Yokota R, Kaminaga Y, Kobayashi TJ. Quantification of Inter-Sample Differences in T-Cell Receptor Repertoires Using Sequence-Based Information. Front Immunol 2017; 8:1500. [PMID: 29187849 PMCID: PMC5694755 DOI: 10.3389/fimmu.2017.01500] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 10/24/2017] [Indexed: 11/13/2022] Open
Abstract
Inter-sample comparisons of T-cell receptor (TCR) repertoires are crucial for gaining a better understanding of the immunological states determined by different collections of T cells from different donor sites, cell types, and genetic and pathological backgrounds. For quantitative comparison, most previous studies utilized conventional methods in ecology, which focus on TCR sequences that overlap between pairwise samples. Some recent studies attempted another approach that is categorized into Poisson abundance models using the abundance distribution of observed TCR sequences. However, these methods ignore the details of the measured sequences and are consequently unable to identify sub-repertoires that might have important contributions to the observed inter-sample differences. Moreover, the sparsity of sequence data due to the huge diversity of repertoires hampers the performance of these methods, especially when few overlapping sequences exist. In this paper, we propose a new approach for REpertoire COmparison in Low Dimensions (RECOLD) based on TCR sequence information, which can estimate the low-dimensional structure by embedding the pairwise sequence dissimilarities in high-dimensional sequence space. The inter-sample differences between repertoires are then quantified by information-theoretic measures among the distributions of data estimated in the embedded space. Using datasets of mouse and human TCR repertoires, we demonstrate that RECOLD can accurately identify the inter-sample hierarchical structures, which have a good correspondence with our intuitive understanding about sample conditions. Moreover, for the dataset of transgenic mice that have strong restrictions on the diversity of their repertoires, our estimated inter-sample structure was consistent with the structure estimated by previous methods based on abundance or overlapping sequence information. For the dataset of human healthy donors and Sézary syndrome patients, our method also showed robust estimation performance even under the condition of high sparsity in TCR sequences, while previous studies failed to estimate the structure. In addition, we identified the sequences that contribute to the pairwise-sample differences between the repertoires with the different genetic backgrounds of mice. Such identification of the sequences contributing to variation in immune cell repertoires may provide substantial insight for the development of new immunotherapies and vaccines.
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Affiliation(s)
- Ryo Yokota
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
| | - Yuki Kaminaga
- Department of Electrical Engineering and Information Systems, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Tetsuya J Kobayashi
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan.,Department of Electrical Engineering and Information Systems, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.,PRESTO, Japan Science and Technology Agency (JST), Saitama, Japan
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103
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Tolstykh EI, Degteva MO, Vozilova AV, Anspaugh LR. Local bone-marrow exposure: how to interpret the data on stable chromosome aberrations in circulating lymphocytes? (some comments on the use of FISH method for dose reconstruction for Techa riverside Residents). RADIATION AND ENVIRONMENTAL BIOPHYSICS 2017; 56:389-403. [PMID: 28889186 DOI: 10.1007/s00411-017-0712-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 08/30/2017] [Indexed: 06/07/2023]
Abstract
The method of fluorescence in situ hybridization (FISH) applied to peripheral blood T lymphocytes is used for retrospective dose estimation, and the results obtained from the analysis of stable chromosomal aberrations are usually interpreted as a dose accumulated in the red bone marrow (RBM). However, after local internal exposure of the RBM, doses derived from FISH were found to be lower than those derived from direct measurements of radionuclides accumulated in the bodies of exposed persons. These results were obtained for people residing near the Techa River contaminated by 89,90Sr (beta-emitters) in 1949-1956 (Chelyabinsk Oblast, Russia). A new analysis has been performed of the combined results of FISH studies (n = 178) undertaken during 1994-2012 for persons living on the Techa Riverside. Analysis confirms the lower slope of the translocation yield per Gy (8.0 ± 0.7 × 10-3) for Techa residents in comparison with FISH data for donors with external exposures (11.6 ± 1.6 × 10-3, Tawn et al., Radiat Res 184(3):296-303, 2015). It was suggested that some portion of T cells remained unexposed, because they represented the descendants of T cell progenitors, which had migrated to the thymus before the start of 89,90Sr intakes. To clarify this problem, the dynamics of T-cell Genera (TG), combining all descendants of specific T-cell progenitor reaching the thymus, was considered. Rates of TGs produced by RBM over different age periods of human life were estimated with the use of the mathematic model of T-cell homeostasis (Bains, Mathematical modeling of T-cell homeostasis. A thesis submitted for the degree of Doctor of Philosophy of the University College London. http://discovery.ucl.ac.uk/20159/1/20159.pdf , 2010). The rate of TG loss during the lifetime was assumed to be very small in comparison with production rate. The recirculation of mature T lymphocytes in contaminated RBM was taken into account. According to our model estimates, at the time of blood sampling, the fraction of exposed T lymphocytes (whose progenitors were irradiated) ranged from 20 to 80% depending on the donors' age at the start of exposure to 89,90Sr. Dose to T lymphocytes, estimated from FISH studies, should be about 0.6-0.9 of RBM dose for residents of the upper Techa region and about 0.4-0.8 in the middle Techa region. Our results could explain the lower value of translocation yield per Gy obtained for Techa residents. The approaches for further model improvement and validation are discussed in this paper.
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Affiliation(s)
- Evgenia I Tolstykh
- Urals Research Center for Radiation Medicine, 68-A, Vorovsky Street, Chelyabinsk, 454076, Russia.
| | - Marina O Degteva
- Urals Research Center for Radiation Medicine, 68-A, Vorovsky Street, Chelyabinsk, 454076, Russia
| | - Alexandra V Vozilova
- Urals Research Center for Radiation Medicine, 68-A, Vorovsky Street, Chelyabinsk, 454076, Russia
| | - Lynn R Anspaugh
- Emeritus, Radiobiology Division, Department of Radiology, University of Utah, Salt Lake City, USA
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104
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Oakes T, Heather JM, Best K, Byng-Maddick R, Husovsky C, Ismail M, Joshi K, Maxwell G, Noursadeghi M, Riddell N, Ruehl T, Turner CT, Uddin I, Chain B. Quantitative Characterization of the T Cell Receptor Repertoire of Naïve and Memory Subsets Using an Integrated Experimental and Computational Pipeline Which Is Robust, Economical, and Versatile. Front Immunol 2017; 8:1267. [PMID: 29075258 PMCID: PMC5643411 DOI: 10.3389/fimmu.2017.01267] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 09/22/2017] [Indexed: 11/13/2022] Open
Abstract
The T cell receptor (TCR) repertoire can provide a personalized biomarker for infectious and non-infectious diseases. We describe a protocol for amplifying, sequencing, and analyzing TCRs which is robust, sensitive, and versatile. The key experimental step is ligation of a single-stranded oligonucleotide to the 3' end of the TCR cDNA. This allows amplification of all possible rearrangements using a single set of primers per locus. It also introduces a unique molecular identifier to label each starting cDNA molecule. This molecular identifier is used to correct for sequence errors and for effects of differential PCR amplification efficiency, thus producing more accurate measures of the true TCR frequency within the sample. This integrated experimental and computational pipeline is applied to the analysis of human memory and naive subpopulations, and results in consistent measures of diversity and inequality. After error correction, the distribution of TCR sequence abundance in all subpopulations followed a power law over a wide range of values. The power law exponent differed between naïve and memory populations, but was consistent between individuals. The integrated experimental and analysis pipeline we describe is appropriate to studies of T cell responses in a broad range of physiological and pathological contexts.
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Affiliation(s)
- Theres Oakes
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - James M. Heather
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Katharine Best
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Rachel Byng-Maddick
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Connor Husovsky
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Mazlina Ismail
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Kroopa Joshi
- UCL Cancer Institute, University College London, London, United Kingdom
| | - Gavin Maxwell
- Unilever Safety and Environmental Assurance Centre, Unilever, Sharnbrook, United Kingdom
| | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Natalie Riddell
- School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Tabea Ruehl
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Carolin T. Turner
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Imran Uddin
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, United Kingdom
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105
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Goronzy JJ, Weyand CM. Successful and Maladaptive T Cell Aging. Immunity 2017; 46:364-378. [PMID: 28329703 DOI: 10.1016/j.immuni.2017.03.010] [Citation(s) in RCA: 210] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 02/27/2017] [Accepted: 03/07/2017] [Indexed: 12/21/2022]
Abstract
Throughout life, the T cell system adapts to shifting resources and demands, resulting in a fundamentally restructured immune system in older individuals. Here we review the cellular and molecular features of an aged immune system and discuss the trade-offs inherent to these adaptive mechanisms. Processes include homeostatic proliferation that maintains compartment size at the expense of partial loss in stemness and incomplete differentiation and the activation of negative regulatory programs, which constrain effector T cell expansion and prevent increasing oligoclonality but also interfere with memory cell generation. We propose that immune failure occurs when adaptive strategies developed by the aging T cell system fail and also discuss how, in some settings, the programs associated with T cell aging culminates in a maladaptive response that directly contributes to chronic inflammatory disease.
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Affiliation(s)
- Jörg J Goronzy
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Palo Alto Veterans Administration Health Care System, Palo Alto, CA 94304, USA.
| | - Cornelia M Weyand
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Palo Alto Veterans Administration Health Care System, Palo Alto, CA 94304, USA.
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106
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Cook L, Melamed A, Yaguchi H, Bangham CR. The impact of HTLV-1 on the cellular genome. Curr Opin Virol 2017; 26:125-131. [PMID: 28822906 DOI: 10.1016/j.coviro.2017.07.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/12/2017] [Accepted: 07/18/2017] [Indexed: 10/19/2022]
Abstract
Human T-lymphotropic virus type-1 (HTLV-1) is the causative agent of adult T-cell leukaemia/lymphoma (ATL), an aggressive CD4+ T-cell malignancy. The mechanisms of leukaemogenesis in ATL are incompletely understood. Insertional mutagenesis has not previously been thought to contribute to the pathogenesis of ATL. However, the recent discovery that HTLV-1 binds the key chromatin architectural protein CTCF raises the hypothesis that HTLV-1 deregulates host gene expression by causing abnormal chromatin looping, bringing the strong HTLV-1 promoter-enhancer near to host genes that lie up to 2Mb from the integrated provirus. Here we review current opinion on the mechanisms of oncogenesis in ATL, with particular emphasis on the local and distant impact of HTLV-1 on the structure and expression of the host genome.
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Affiliation(s)
- Lucy Cook
- Section of Virology, Imperial College London, Norfolk Place, London W2 1PG, United Kingdom; National Centre for Human Retrovirology, Imperial College Healthcare NHS Trust, London, United Kingdom; Department of Haematology, Imperial College Healthcare NHS Trust, United Kingdom
| | - Anat Melamed
- Section of Virology, Imperial College London, Norfolk Place, London W2 1PG, United Kingdom
| | - Hiroko Yaguchi
- Section of Virology, Imperial College London, Norfolk Place, London W2 1PG, United Kingdom
| | - Charles Rm Bangham
- Section of Virology, Imperial College London, Norfolk Place, London W2 1PG, United Kingdom.
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107
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Rosati E, Dowds CM, Liaskou E, Henriksen EKK, Karlsen TH, Franke A. Overview of methodologies for T-cell receptor repertoire analysis. BMC Biotechnol 2017; 17:61. [PMID: 28693542 PMCID: PMC5504616 DOI: 10.1186/s12896-017-0379-9] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/26/2017] [Indexed: 12/13/2022] Open
Abstract
Background The T-cell receptor (TCR), located on the surface of T cells, is responsible for the recognition of the antigen-major histocompatibility complex, leading to the initiation of an inflammatory response. Analysing the TCR repertoire may help to gain a better understanding of the immune system features and of the aetiology and progression of diseases, in particular those with unknown antigenic triggers. The extreme diversity of the TCR repertoire represents a major analytical challenge; this has led to the development of specialized methods which aim to characterize the TCR repertoire in-depth. Currently, next generation sequencing based technologies are most widely employed for the high-throughput analysis of the immune cell repertoire. Results Here, we report on the latest methodological advancements in the field by describing and comparing the available tools; from the choice of the starting material and library preparation method, to the sequencing technologies and data analysis. Finally, we provide a practical example and our own experience by reporting some exemplary results from a small internal benchmark study, where current approaches from the literature and the market are employed and compared. Conclusions Several valid methods for clonotype identification and TCR repertoire analysis exist, however, a gold standard method for the field has not yet been identified. Depending on the purpose of the scientific study, some approaches may be more suitable than others. Finally, due to possible method specific biases, scientists must be careful when comparing results obtained using different methods. Electronic supplementary material The online version of this article (doi:10.1186/s12896-017-0379-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elisa Rosati
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Str. 12, 24105, Kiel, Germany
| | - C Marie Dowds
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Str. 12, 24105, Kiel, Germany
| | - Evaggelia Liaskou
- Centre for Liver Research and NIHR Birmingham Liver Biomedical Research Unit, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Eva Kristine Klemsdal Henriksen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Research Institute of Internal Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.,K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Tom H Karlsen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Str. 12, 24105, Kiel, Germany.
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108
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Eftimie R, Perez M, Buono PL. Pattern formation in a nonlocal mathematical model for the multiple roles of the TGF-β pathway in tumour dynamics. Math Biosci 2017; 289:96-115. [PMID: 28511959 DOI: 10.1016/j.mbs.2017.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 05/01/2017] [Accepted: 05/12/2017] [Indexed: 02/06/2023]
Abstract
The growth and invasion of cancer cells are very complex processes, which can be regulated by the cross-talk between various signalling pathways, or by single signalling pathways that can control multiple aspects of cell behaviour. TGF-β is one of the most investigated signalling pathways in oncology, since it can regulate multiple aspects of cell behaviour: cell proliferation and apoptosis, cell-cell adhesion and epithelial-to-mesenchimal transition via loss of cell adhesion. In this study, we use a mathematical modelling approach to investigate the complex roles of TGF-β signalling pathways on the inhibition and growth of tumours, as well as on the epithelial-to-mesenchimal transition involved in the metastasis of tumour cells. We show that the nonlocal mathematical model derived here to describe repulsive and adhesive cell-cell interactions can explain the formation of new tumour cell aggregations at positions in space that are further away from the main aggregation. Moreover, we show that the increase in cell-cell adhesion leads to fewer but larger aggregations, and the increase in TGF-β molecules - whose late-stage effect is to decrease cell adhesion - leads to many small cellular aggregations. Finally, we perform a sensitivity analysis on some parameters associated with TGF-β dynamics, and use it to investigate the relation between the tumour size and its metastatic spread.
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Affiliation(s)
- Raluca Eftimie
- Division of Mathematics, University of Dundee, Dundee, DD1 4HN, United Kingdom.
| | - Matthieu Perez
- Institut National Des Sciences Appliquees de Rouen, 76801 Saint Etienne du Rouvray Cedex, France
| | - Pietro-Luciano Buono
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, L1H 7K4, Canada
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109
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Chen G, Yang X, Ko A, Sun X, Gao M, Zhang Y, Shi A, Mariuzza RA, Weng NP. Sequence and Structural Analyses Reveal Distinct and Highly Diverse Human CD8 + TCR Repertoires to Immunodominant Viral Antigens. Cell Rep 2017; 19:569-583. [PMID: 28423320 DOI: 10.1016/j.celrep.2017.03.072] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Revised: 02/02/2017] [Accepted: 03/24/2017] [Indexed: 01/07/2023] Open
Abstract
A diverse T cell receptor (TCR) repertoire is essential for controlling viral infections. However, information about TCR repertoires to defined viral antigens is limited. We performed a comprehensive analysis of CD8+ TCR repertoires for two dominant viral epitopes: pp65495-503 (NLV) of cytomegalovirus and M158-66 (GIL) of influenza A virus. The highly individualized repertoires (87-5,533 α or β clonotypes per subject) comprised thousands of unique TCRα and TCRβ sequences and dozens of distinct complementary determining region (CDR)3α and CDR3β motifs. However, diversity is effectively restricted by preferential V-J combinations, CDR3 lengths, and CDR3α/CDR3β pairings. Structures of two GIL-specific TCRs bound to GIL-HLA-A2 provided a potential explanation for the lower diversity of GIL-specific versus NLV-specific repertoires. These anti-viral TCRs occupied up to 3.4% of the CD8+ TCRβ repertoire, ensuring broad T cell responses to single epitopes. Our portrait of two anti-viral TCR repertoires may inform the development of predictors of immune protection.
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Affiliation(s)
- Guobing Chen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Xinbo Yang
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Annette Ko
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Xiaoping Sun
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Mingming Gao
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Yongqing Zhang
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Alvin Shi
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Roy A Mariuzza
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Nan-Ping Weng
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD 21224, USA.
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110
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Tickotsky N, Sagiv T, Prilusky J, Shifrut E, Friedman N. McPAS-TCR: a manually curated catalogue of pathology-associated T cell receptor sequences. Bioinformatics 2017; 33:2924-2929. [DOI: 10.1093/bioinformatics/btx286] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 05/02/2017] [Indexed: 11/14/2022] Open
Affiliation(s)
- Nili Tickotsky
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Sagiv
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Jaime Prilusky
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Eric Shifrut
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Nir Friedman
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
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111
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Modelling and investigation of theCD4+T cells – Macrophages paradox in melanoma immunotherapies. J Theor Biol 2017; 420:82-104. [DOI: 10.1016/j.jtbi.2017.02.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 02/12/2017] [Accepted: 02/16/2017] [Indexed: 12/18/2022]
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112
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Nakamura S, Ohmura R, Nakanishi I. An Interaction-based Approach for Affinity Prediction between Antigen Peptide and Human Leukocyte Antigen Using COMBINE Analysis. CHEM-BIO INFORMATICS JOURNAL 2017. [DOI: 10.1273/cbij.17.93] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | - Rie Ohmura
- Department of Pharmaceutical Sciences, Kindai University
| | - Isao Nakanishi
- Department of Pharmaceutical Sciences, Kindai University
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113
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Xu L, You X, Zheng P, Zhang BM, Gupta PK, Lavori P, Meyer E, Zehnder JL. Methodologic Considerations in the Application of Next-Generation Sequencing of Human TRB Repertoires for Clinical Use. J Mol Diagn 2016; 19:72-83. [PMID: 27815002 DOI: 10.1016/j.jmoldx.2016.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/24/2016] [Accepted: 07/28/2016] [Indexed: 01/08/2023] Open
Abstract
Next-generation sequencing (NGS) of immune receptors has become a standard tool to assess minimal residual disease (MRD) in patients treated for lymphoid malignancy, and it is being used to study the T-cell repertoire in many clinical settings. To better understanding the potential clinical utility and limitations of this application outside of MRD, we developed a BIOMED-2 primer-based NGS method and characterized its performance in controls and patients with graft-versus-host disease (GVHD) after allogeneic hematopoietic transplant. For controls and patients with GVHD, replicate sequencing of the same T-cell receptor β (TRB) libraries was highly reproducible. Higher variability was observed in sequencing of different TRB libraries made from the same DNA stock. Variability was increased in patients with GVHD compared with controls; patients with GVHD also had lower diversity than controls. In the T-cell repertoire of a healthy person, approximately 99.6% of the CDR3 clones were in low abundance, with frequency <10-3. A single library could identify >93% of the clones with frequency ≥10-3 in the repertoire. Sequencing in duplicate increased the average detection rate to >97%. This work demonstrates that NGS reliably and robustly characterizes TRB populations in healthy individuals and patients with GVHD with frequency ≥10-3 and provides a methodologic framework for applying NGS immune repertoire methods to clinical testing applications beyond MRD.
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Affiliation(s)
- Liwen Xu
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, California
| | - Xiaoqing You
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, California
| | - PingPing Zheng
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford School of Medicine, Stanford University, Stanford, California
| | - Bing M Zhang
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, California
| | - Puja K Gupta
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford School of Medicine, Stanford University, Stanford, California
| | - Philip Lavori
- Department of Biomedical Data Science, Stanford School of Medicine, Stanford University, Stanford, California
| | - Everett Meyer
- Division of Blood and Marrow Transplantation, Department of Medicine, Stanford School of Medicine, Stanford University, Stanford, California
| | - James L Zehnder
- Department of Pathology, Stanford School of Medicine, Stanford University, Stanford, California.
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114
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Bondar AV, Gumovskaya YP, Polevshchikov AV. Modeling of T-lymphocyte extravasation into a lymph node: The connection between the morphological basis of the process and the clonal selection theory. Biophysics (Nagoya-shi) 2016. [DOI: 10.1134/s000635091605002x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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115
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Toor AA, Toor AA, Rahmani M, Manjili MH. On the organization of human T-cell receptor loci: log-periodic distribution of T-cell receptor gene segments. J R Soc Interface 2016; 13:20150911. [PMID: 26763333 DOI: 10.1098/rsif.2015.0911] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The human T-cell repertoire is complex and is generated by the rearrangement of variable (V), diversity (D) and joining (J) segments on the T-cell receptor (TCR) loci. The T-cell repertoire demonstrates self-similarity in terms clonal frequencies when defined by V, D and J gene segment usage; therefore to determine whether the structural ordering of these gene segments on the TCR loci contributes to the observed clonal frequencies, the TCR loci were examined for self-similarity and periodicity in terms of gene segment organization. Logarithmic transformation of numeric sequence order demonstrated that the V and J gene segments for both T-cell receptor α (TRA) and β (TRB) loci are arranged in a self-similar manner when the spacing between the adjacent segments was considered as a function of the size of the neighbouring gene segment, with an average fractal dimension of approximately 1.5. Accounting for the gene segments occurring on helical DNA molecules with a logarithmic distribution, sine and cosine functions of the log-transformed angular coordinates of the start and stop nucleotides of successive TCR gene segments showed an ordered progression from the 5' to the 3' end of the locus, supporting a log-periodic organization. T-cell clonal frequency estimates, based on V and J segment usage, from normal stem cell donors were plotted against the V and J segment on TRB locus and demonstrated a periodic distribution. We hypothesize that this quasi-periodic variation in gene-segment representation in the T-cell clonal repertoire may be influenced by the location of the gene segments on the periodic-logarithmically scaled TCR loci. Interactions between the two strands of DNA in the double helix may influence the probability of gene segment usage by means of either constructive or destructive interference resulting from the superposition of the two helices.
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Affiliation(s)
- Amir A Toor
- Bone Marrow Transplant Program, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Abdullah A Toor
- School of Engineering, Virginia Commonwealth University, Richmond, VA, USA
| | - Mohamed Rahmani
- Hematology and Oncology, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Masoud H Manjili
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
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116
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Mathematical Models for Immunology: Current State of the Art and Future Research Directions. Bull Math Biol 2016; 78:2091-2134. [PMID: 27714570 PMCID: PMC5069344 DOI: 10.1007/s11538-016-0214-9] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 09/26/2016] [Indexed: 01/01/2023]
Abstract
The advances in genetics and biochemistry that have taken place over the last 10 years led to significant advances in experimental and clinical immunology. In turn, this has led to the development of new mathematical models to investigate qualitatively and quantitatively various open questions in immunology. In this study we present a review of some research areas in mathematical immunology that evolved over the last 10 years. To this end, we take a step-by-step approach in discussing a range of models derived to study the dynamics of both the innate and immune responses at the molecular, cellular and tissue scales. To emphasise the use of mathematics in modelling in this area, we also review some of the mathematical tools used to investigate these models. Finally, we discuss some future trends in both experimental immunology and mathematical immunology for the upcoming years.
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117
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T cell receptor diversity in the human thymus. Mol Immunol 2016; 76:116-22. [DOI: 10.1016/j.molimm.2016.07.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 07/01/2016] [Accepted: 07/04/2016] [Indexed: 01/21/2023]
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118
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Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq. Genome Med 2016; 8:80. [PMID: 27460926 PMCID: PMC4962388 DOI: 10.1186/s13073-016-0335-7] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 07/11/2016] [Indexed: 11/24/2022] Open
Abstract
Accurate characterization of the repertoire of the T-cell receptor (TCR) alpha and beta chains is critical to understanding adaptive immunity. Such characterization has many applications across such fields as vaccine development and response, clone-tracking in cancer, and immunotherapy. Here we present a new methodology called single-cell TCRseq (scTCRseq) for the identification and assembly of full-length rearranged V(D)J T-cell receptor sequences from paired-end single-cell RNA sequencing reads. The method allows accurate identification of the V(D)J rearrangements for each individual T-cell and has the novel ability to recover paired alpha and beta segments. Source code is available at https://github.com/ElementoLab/scTCRseq.
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119
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Abstract
Human immune system aging results in impaired responses to pathogens or vaccines. In the innate immune system, which mediates the earliest pro-inflammatory responses to immunologic challenge, processes ranging from Toll-like Receptor function to Neutrophil Extracellular Trap formation are generally diminished in older adults. Dysregulated, enhanced basal inflammation with age reflecting activation by endogenous damage-associated ligands contributes to impaired innate immune responses. In the adaptive immune system, T and B cell subsets and function alter with age. The control of cytomegalovirus infection, particularly in the T lineage, plays a dominant role in the differentiation and diversity of the T cell compartment.
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Affiliation(s)
- Thilinie Bandaranayake
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Albert C Shaw
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA.
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120
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Restif O, Graham AL. Within-host dynamics of infection: from ecological insights to evolutionary predictions. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0304. [PMID: 26150670 PMCID: PMC4528502 DOI: 10.1098/rstb.2014.0304] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- Olivier Restif
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Andrea L Graham
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
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121
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Robinson MW, Hughes J, Wilkie GS, Swann R, Barclay ST, Mills PR, Patel AH, Thomson EC, McLauchlan J. Tracking TCRβ Sequence Clonotype Expansions during Antiviral Therapy Using High-Throughput Sequencing of the Hypervariable Region. Front Immunol 2016; 7:131. [PMID: 27092143 PMCID: PMC4820669 DOI: 10.3389/fimmu.2016.00131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 03/21/2016] [Indexed: 01/01/2023] Open
Abstract
To maintain a persistent infection viruses such as hepatitis C virus (HCV) employ a range of mechanisms that subvert protective T cell responses. The suppression of antigen-specific T cell responses by HCV hinders efforts to profile T cell responses during chronic infection and antiviral therapy. Conventional methods of detecting antigen-specific T cells utilize either antigen stimulation (e.g., ELISpot, proliferation assays, cytokine production) or antigen-loaded tetramer staining. This limits the ability to profile T cell responses during chronic infection due to suppressed effector function and the requirement for prior knowledge of antigenic viral peptide sequences. Recently, high-throughput sequencing (HTS) technologies have been developed for the analysis of T cell repertoires. In the present study, we have assessed the feasibility of HTS of the TCRβ complementarity determining region (CDR)3 to track T cell expansions in an antigen-independent manner. Using sequential blood samples from HCV-infected individuals undergoing antiviral therapy, we were able to measure the population frequencies of >35,000 TCRβ sequence clonotypes in each individual over the course of 12 weeks. TRBV/TRBJ gene segment usage varied markedly between individuals but remained relatively constant within individuals across the course of therapy. Despite this stable TRBV/TRBJ gene segment usage, a number of TCRβ sequence clonotypes showed dramatic changes in read frequency. These changes could not be linked to therapy outcomes in the present study; however, the TCRβ CDR3 sequences with the largest fold changes did include sequences with identical TRBV/TRBJ gene segment usage and high junction region homology to previously published CDR3 sequences from HCV-specific T cells targeting the HLA-B*0801-restricted 1395HSKKKCDEL1403 and HLA-A*0101-restricted 1435ATDALMTGY1443 epitopes. The pipeline developed in this proof of concept study provides a platform for the design of future experiments to accurately address the question of whether T cell responses contribute to SVR upon antiviral therapy. This pipeline represents a novel technique to analyze T cell dynamics in situations where conventional antigen-dependent methods are limited due to suppression of T cell functions and highly diverse antigenic sequences.
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Affiliation(s)
- Mark W Robinson
- MRC - University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK; School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Joseph Hughes
- MRC - University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, University of Glasgow , Glasgow , UK
| | - Gavin S Wilkie
- MRC - University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, University of Glasgow , Glasgow , UK
| | - Rachael Swann
- MRC - University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK; Gartnavel General Hospital, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - Stephen T Barclay
- Glasgow Royal Infirmary, NHS Greater Glasgow and Clyde , Glasgow , UK
| | - Peter R Mills
- Gartnavel General Hospital, NHS Greater Glasgow and Clyde , Glasgow , UK
| | - Arvind H Patel
- MRC - University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, University of Glasgow , Glasgow , UK
| | - Emma C Thomson
- MRC - University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, University of Glasgow , Glasgow , UK
| | - John McLauchlan
- MRC - University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, University of Glasgow , Glasgow , UK
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122
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Lossius A, Johansen JN, Vartdal F, Holmøy T. High-throughput sequencing of immune repertoires in multiple sclerosis. Ann Clin Transl Neurol 2016; 3:295-306. [PMID: 27081660 PMCID: PMC4818741 DOI: 10.1002/acn3.295] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/21/2015] [Accepted: 01/18/2016] [Indexed: 12/24/2022] Open
Abstract
T cells and B cells are crucial in the initiation and maintenance of multiple sclerosis (MS), and the activation of these cells is believed to be mediated through specific recognition of antigens by the T‐ and B‐cell receptors. The antigen receptors are highly polymorphic due to recombination (T‐ and B‐cell receptors) and mutation (B‐cell receptors) of the encoding genes, which can therefore be used as fingerprints to track individual T‐ and B‐cell clones. Such studies can shed light on mechanisms driving the immune responses and provide new insights into the pathogenesis. Here, we summarize studies that have explored the T‐ and B‐cell receptor repertoires using earlier methodological approaches, and we focus on how high‐throughput sequencing has provided new knowledge by surveying the immune repertoires in MS in even greater detail and with unprecedented depth.
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Affiliation(s)
- Andreas Lossius
- Department of Immunology and Transfusion Medicine Oslo University Hospital Rikshospitalet Oslo Norway; Department of Neurology Oslo University Hospital Rikshospitalet Oslo Norway; Institute of Clinical Medicine University of Oslo Oslo Norway
| | - Jorunn N Johansen
- Department of Immunology and Transfusion Medicine Oslo University Hospital Rikshospitalet Oslo Norway
| | - Frode Vartdal
- Department of Immunology and Transfusion Medicine Oslo University Hospital Rikshospitalet Oslo Norway; Institute of Clinical Medicine University of Oslo Oslo Norway
| | - Trygve Holmøy
- Institute of Clinical Medicine University of Oslo Oslo Norway; Department of Neurology Akershus University Hospital Lørenskog Norway
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123
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Goronzy JJ, Qi Q, Olshen RA, Weyand CM. High-throughput sequencing insights into T-cell receptor repertoire diversity in aging. Genome Med 2015; 7:117. [PMID: 26582264 PMCID: PMC4652363 DOI: 10.1186/s13073-015-0242-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Decline in T-cell generation leading to T-cell receptor repertoire contraction is a cornerstone of immune system aging, and consequent disorders. High-throughput sequencing enables in-depth immune repertoire characterization, but blood samples are too small to capture its total diversity. New computational models could enable accurate estimation of this diversity.
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Affiliation(s)
- Jörg J Goronzy
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Department of Medicine, VAPAHCS, Palo Alto, CA, 94306, USA.
| | - Qian Qi
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Medicine, VAPAHCS, Palo Alto, CA, 94306, USA
| | - Richard A Olshen
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Cornelia M Weyand
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Medicine, VAPAHCS, Palo Alto, CA, 94306, USA
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124
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Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires. Trends Immunol 2015; 36:738-749. [DOI: 10.1016/j.it.2015.09.006] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 09/15/2015] [Accepted: 09/15/2015] [Indexed: 01/16/2023]
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125
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Galson JD, Trück J, Fowler A, Münz M, Cerundolo V, Pollard AJ, Lunter G, Kelly DF. In-Depth Assessment of Within-Individual and Inter-Individual Variation in the B Cell Receptor Repertoire. Front Immunol 2015; 6:531. [PMID: 26528292 PMCID: PMC4601265 DOI: 10.3389/fimmu.2015.00531] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/28/2015] [Indexed: 11/24/2022] Open
Abstract
High-throughput sequencing of the B cell receptor (BCR) repertoire can provide rapid characterization of the B cell response in a wide variety of applications in health, after vaccination and in infectious, inflammatory and immune-driven disease, and is starting to yield clinical applications. However, the interpretation of repertoire data is compromised by a lack of studies to assess the intra and inter-individual variation in the BCR repertoire over time in healthy individuals. We applied a standardized isotype-specific BCR repertoire deep sequencing protocol to a single highly sampled participant, and then evaluated the method in 9 further participants to comprehensively describe such variation. We assessed total repertoire metrics of mutation, diversity, VJ gene usage and isotype subclass usage as well as tracking specific BCR sequence clusters. There was good assay reproducibility (both in PCR amplification and biological replicates), but we detected striking fluctuations in the repertoire over time that we hypothesize may be due to subclinical immune activation. Repertoire properties were unique for each individual, which could partly be explained by a decrease in IgG2 with age, and genetic differences at the immunoglobulin locus. There was a small repertoire of public clusters (0.5, 0.3, and 1.4% of total IgA, IgG, and IgM clusters, respectively), which was enriched for expanded clusters containing sequences with suspected specificity toward antigens that should have been historically encountered by all participants through prior immunization or infection. We thus provide baseline BCR repertoire information that can be used to inform future study design, and aid in interpretation of results from these studies. Furthermore, our results indicate that BCR repertoire studies could be used to track changes in the public repertoire in and between populations that might relate to population immunity against infectious diseases, and identify the characteristics of inflammatory and immunological diseases.
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Affiliation(s)
- Jacob D. Galson
- Oxford Vaccine Group, Department of Paediatrics, The NIHR Oxford Biomedical Research Center, University of Oxford, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Johannes Trück
- Oxford Vaccine Group, Department of Paediatrics, The NIHR Oxford Biomedical Research Center, University of Oxford, Oxford, UK
- Paediatric Immunology, University Children’s Hospital, Zürich, Switzerland
| | - Anna Fowler
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Márton Münz
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Vincenzo Cerundolo
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Andrew J. Pollard
- Oxford Vaccine Group, Department of Paediatrics, The NIHR Oxford Biomedical Research Center, University of Oxford, Oxford, UK
| | - Gerton Lunter
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Dominic F. Kelly
- Oxford Vaccine Group, Department of Paediatrics, The NIHR Oxford Biomedical Research Center, University of Oxford, Oxford, UK
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