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A high-throughput real-time PCR tissue-of-origin test to distinguish blood from lymphoblastoid cell line DNA for (epi)genomic studies. Sci Rep 2022; 12:4684. [PMID: 35304543 PMCID: PMC8933453 DOI: 10.1038/s41598-022-08663-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/09/2022] [Indexed: 12/13/2022] Open
Abstract
Lymphoblastoid cell lines (LCLs) derive from blood infected in vitro by Epstein–Barr virus and were used in several genetic, transcriptomic and epigenomic studies. Although few changes were shown between LCL and blood genotypes (SNPs) validating their use in genetics, more were highlighted for other genomic features and/or in their transcriptome and epigenome. This could render them less appropriate for these studies, notably when blood DNA could still be available. Here we developed a simple, high-throughput and cost-effective real-time PCR approach allowing to distinguish blood from LCL DNA samples based on the presence of EBV relative load and rearranged T-cell receptors γ and β. Our approach was able to achieve 98.5% sensitivity and 100% specificity on DNA of known origin (458 blood and 316 LCL DNA). It was further applied to 1957 DNA samples from the CEPH Aging cohort comprising DNA of uncertain origin, identifying 784 blood and 1016 LCL DNA. A subset of these DNA was further analyzed with an epigenetic clock indicating that DNA extracted from blood should be preferred to LCL for DNA methylation-based age prediction analysis. Our approach could thereby be a powerful tool to ascertain the origin of DNA in old collections prior to (epi)genomic studies.
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2
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Link CS, Hölig K, Rücker-Braun E, Lang K, Kuhn M, Eugster A, Klesse C, Schmiedgen M, Heidenreich F, Oelschlägel U, Dahl A, Bornhäuser M, Bonifacio E, Schetelig J. Assessment of the T cell receptor repertoire in long-term platelet donors by next generation sequencing. Br J Haematol 2017; 181:389-391. [PMID: 28272738 DOI: 10.1111/bjh.14576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Cornelia S Link
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany.,DFG Research Centre for Regenerative Therapies Dresden, TU Dresden, Dresden, Germany
| | - Kristina Hölig
- Fachbereich Transfusionsmedizin, Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Elke Rücker-Braun
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | | | - Matthias Kuhn
- Institut für medizinische Informatik und Biometrie (IMB), Medizinische Fakultät der TU Dresden, Dresden, Germany
| | - Anne Eugster
- DFG Research Centre for Regenerative Therapies Dresden, TU Dresden, Dresden, Germany
| | | | - Maria Schmiedgen
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Falk Heidenreich
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Uta Oelschlägel
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Andreas Dahl
- DFG Research Centre for Regenerative Therapies Dresden, TU Dresden, Dresden, Germany.,BIOTEChnology Centre, TU Dresden, Dresden, Germany
| | - Martin Bornhäuser
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany.,DFG Research Centre for Regenerative Therapies Dresden, TU Dresden, Dresden, Germany
| | - Ezio Bonifacio
- DFG Research Centre for Regenerative Therapies Dresden, TU Dresden, Dresden, Germany
| | - Johannes Schetelig
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany.,DKMS Clinical Trials Unit, Dresden, Germany
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3
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Machnes-Maayan D, Lev A, Katz U, Mishali D, Vardi A, Simon AJ, Somech R. Insight into normal thymic activity by assessment of peripheral blood samples. Immunol Res 2015; 61:198-205. [PMID: 25294167 DOI: 10.1007/s12026-014-8558-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The thymus is a highly specialized organ for T cell receptor (TCR) rearrangement and selection mechanisms that ensure the formation of functional and self-tolerant cells. Little is known about how peripheral blood assessment of thymic function reflects thymus activity during infancy. We compared thymic function-related markers in the thymus with those in peripheral blood in order to check their correlations. We concomitantly blood samples from immunocompetent infants who underwent cardiac surgery that involved thymectomy. The studied thymic markers included TCR excision circles (TRECs), four different TCRD (TCR delta chain) gene rearrangements, the TCR repertoire, regulatory T cells (Tregs, defined as the CD4+CD25+FOXP3+ cell population) and real-time quantitative polymerase chain reaction (RQ-PCR) mRNA expression of forkhead box P3 (FOXP3). Twenty patients were enrolled in this study. Their mean age at the time of the surgery was 3 months/5 days ± 3 months/18 days. There was a significant correlation between thymic and peripheral blood levels of TREC, all four TCRD gene rearrangements and the amount of Tregs. The levels of these parameters were significantly higher in the thymus than those detected in the peripheral blood. The TCR repertoire distribution in both samples was similar. FOXP3 mRNA levels in the thymus and peripheral blood correlated well. Our findings demonstrated a strong and significant correlation between peripheral blood and intra-thymic activity parameters during infancy. Assessment of these parameters in peripheral blood can be used to accurately estimate different intra-thymic capacities for assessing T cell function in health and disease.
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Affiliation(s)
- Diti Machnes-Maayan
- Pediatric Department B, Pediatric Immunology Service, Jeffrey Modell Foundation (JMF) Center, Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, 52621, Tel Hashomer, Israel
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Gold MC, Napier RJ, Lewinsohn DM. MR1-restricted mucosal associated invariant T (MAIT) cells in the immune response to Mycobacterium tuberculosis. Immunol Rev 2015; 264:154-66. [PMID: 25703558 DOI: 10.1111/imr.12271] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The intracellular pathogen Mycobacterium tuberculosis (Mtb) and its human host have long co-evolved. Although the host cellular immune response is critical to the control of the bacterium information on the specific contribution of different immune cell subsets in humans is incomplete. Mucosal associated invariant T (MAIT) cells are a prevalent and unique T-cell population in humans with the capacity to detect intracellular infection with bacteria including Mtb. MAIT cells detect bacterially derived metabolites presented by the evolutionarily conserved major histocompatibility complex-like molecule MR1. Here, we review recent advances in our understanding of this T-cell subset and address the potential roles for MR1-restricted T cells in the control, diagnosis, and therapy of tuberculosis.
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Affiliation(s)
- Marielle C Gold
- Pulmonary and Critical Care Medicine, Oregon Health and Science University, Portland, OR, USA; VA Portland Health Care System (VAPORHCS), Portland, OR, USA; Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA
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5
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Napier RJ, Adams EJ, Gold MC, Lewinsohn DM. The Role of Mucosal Associated Invariant T Cells in Antimicrobial Immunity. Front Immunol 2015. [PMID: 26217338 PMCID: PMC4492155 DOI: 10.3389/fimmu.2015.00344] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mucosal associated invariant T (MAIT) cells are an innate-like T cell subset prevalent in humans and distributed throughout the blood and mucosal sites. Human MAIT cells are defined by the expression of the semi-invariant TCRα chain TRAV1-2/TRAJ12/20/33 and are restricted by the non-polymorphic major histocompatibility complex (MHC) class I-like molecule, MHC-related protein 1, MR1. MAIT cells are activated by small organic molecules, derived from the riboflavin biosynthesis pathway of bacteria and fungi, presented by MR1. Traditionally, MAIT cells were thought to recognize a limited number of antigens due to usage of an invariant TCRα chain and restriction by a non-polymorphic MHC molecule. However, recent studies demonstrate that the TCR repertoire of MAIT cells is more heterogeneous, suggesting there is a more diverse array of MR1 antigens that MAIT cells can recognize. In response to infected cells, MAIT cells produce the pro-inflammatory cytokines, IFN-γ and TNF, and are cytolytic. Studies performed in MR1-deficient mice suggest that MAIT cells can provide anti-bacterial control within the first few days post-infection, as well as contribute to enhanced adaptive immunity in murine models of respiratory infections. In humans, the role of MAIT cells is unclear; however, evidence points to interplay between MAIT cells and microbial infections, including Mycobacterium tuberculosis. Given that MAIT cells are pro-inflammatory, serve in early control of bacterial infections, and appear enriched at tissue sites where microbes interface and gain access to the body, we postulate that they play an important role in antimicrobial immune responses. In this review, we discuss the most recent studies on the function and phenotype of MAIT cells, including their TCR diversity and antigenic repertoire, with a focus on the contribution of human MAIT cells in the immune response to microbial infection.
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Affiliation(s)
- Ruth J Napier
- Pulmonary and Critical Care Medicine, Oregon Health & Science University , Portland, OR , USA
| | | | - Marielle C Gold
- Pulmonary and Critical Care Medicine, Oregon Health & Science University , Portland, OR , USA ; VA Portland Health Care System (VAPORHCS) , Portland, OR , USA ; Molecular Microbiology and Immunology, Oregon Health & Science University , Portland, OR , USA
| | - David M Lewinsohn
- Pulmonary and Critical Care Medicine, Oregon Health & Science University , Portland, OR , USA ; VA Portland Health Care System (VAPORHCS) , Portland, OR , USA ; Molecular Microbiology and Immunology, Oregon Health & Science University , Portland, OR , USA
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6
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Carico Z, Krangel MS. Chromatin Dynamics and the Development of the TCRα and TCRδ Repertoires. Adv Immunol 2015; 128:307-61. [DOI: 10.1016/bs.ai.2015.07.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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7
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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: 22] [Impact Index Per Article: 2.2] [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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8
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Muraille E. Generation of individual diversity: a too neglected fundamental property of adaptive immune system. Front Immunol 2014; 5:208. [PMID: 24860570 PMCID: PMC4026687 DOI: 10.3389/fimmu.2014.00208] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 04/27/2014] [Indexed: 12/25/2022] Open
Abstract
The fitness gains resulting from development of the adaptive immune system (AIS) during evolution are still the subject of hot debate. A large random repertoire of antigenic receptors is costly to develop and could be the source of autoimmune reactions. And yet, despite their drawbacks, AIS-like systems seem to have been independently acquired in several phyla of metazoans with very different anatomies, longevities, and lifestyles. This article is a speculative attempt to explore the selective pressures, which favored this striking convergent evolution. It is well known that the AIS enables an organism to produce a specific immune response against all natural or artificial antigenic structures. However, it is frequently neglected that this response is highly variable among individuals. In practice, each individual possesses a "private" adaptive immune repertoire. This individualization of immune defenses implies that invasion and escape immune mechanisms developed by pathogens will certainly not always be successful as the specific targets and organization of the immune response are somewhat unpredictable. In a population, where individuals display heterogeneous immune responses to infection, the probability that a pathogen is able to infect all individuals could be reduced compared to a homogeneous population. This suggests that the individual diversity of the immune repertoire is not a by-product of the AIS but of its fundamental properties and could be in part responsible for repeated selection and conservation of the AIS during metazoan evolution. The capacity of the AIS to improve the management of cooperative or parasitic symbiotic relationships at the individual level could be a secondary development due to its progressive integration into the innate immune system. This hypothesis constitutes a new scenario for AIS emergence and explains the selection of MHC restriction and MHC diversification.
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Affiliation(s)
- Eric Muraille
- Laboratoire de Parasitologie, Faculté de Médecine, Université Libre de Bruxelles, Brussels, Belgium
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9
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Calis JJA, Maybeno M, Greenbaum JA, Weiskopf D, De Silva AD, Sette A, Keşmir C, Peters B. Properties of MHC class I presented peptides that enhance immunogenicity. PLoS Comput Biol 2013; 9:e1003266. [PMID: 24204222 PMCID: PMC3808449 DOI: 10.1371/journal.pcbi.1003266] [Citation(s) in RCA: 509] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 08/23/2013] [Indexed: 12/14/2022] Open
Abstract
T-cells have to recognize peptides presented on MHC molecules to be activated and elicit their effector functions. Several studies demonstrate that some peptides are more immunogenic than others and therefore more likely to be T-cell epitopes. We set out to determine which properties cause such differences in immunogenicity. To this end, we collected and analyzed a large set of data describing the immunogenicity of peptides presented on various MHC-I molecules. Two main conclusions could be drawn from this analysis: First, in line with previous observations, we showed that positions P4–6 of a presented peptide are more important for immunogenicity. Second, some amino acids, especially those with large and aromatic side chains, are associated with immunogenicity. This information was combined into a simple model that was used to demonstrate that immunogenicity is, to a certain extent, predictable. This model (made available at http://tools.iedb.org/immunogenicity/) was validated with data from two independent epitope discovery studies. Interestingly, with this model we could show that T-cells are equipped to better recognize viral than human (self) peptides. After the past successful elucidation of different steps in the MHC-I presentation pathway, the identification of variables that influence immunogenicity will be an important next step in the investigation of T-cell epitopes and our understanding of cellular immune responses. T-cells have to recognize peptides presented on MHC molecules to be activated and elicit their effector functions. Some peptide-MHC-I complexes (pMHCs) are better recognized by T-cells; we call such pMHCs more immunogenic. For other pMHCs, no recognizing T-cells seem to exist; we call such pMHCs non-immunogenic. We set out to determine which properties of pMHCs cause such differences in immunogenicity, by carefully collecting a large set of immunogenic and non-immunogenic pMHCs, and analysing the difference between these sets. Two important observations were made: First, in line with previous observations, we showed that positions P4–6 of a presented peptide are more important for immunogenicity. Second, some amino acids, especially those with large and aromatic side chains, seem to be better recognized by T-cells as they associate with immunogenicity. Next, this information was combined into a simple model to predict the immunogenicity of new pMHCs (this model is made available at http://tools.iedb.org/immunogenicity/). Interestingly, with this model we could show that T-cells are equipped to strongly recognize viral peptides. After the past successful elucidation of different steps in the MHC-I presentation pathway, the identification of variables that influence immunogenicity will be an important next step in the investigation of T-cell epitopes and our understanding of cellular immune responses.
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Affiliation(s)
- Jorg J. A. Calis
- Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, The Netherlands
- * E-mail:
| | - Matt Maybeno
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Jason A. Greenbaum
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Aruna D. De Silva
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
- Genetech Research Institute, Colombo, Sri Lanka
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
| | - Can Keşmir
- Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, United States of America
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Tuulasvaara A, Baussand J, Laine P, Paulin L, Salminen J, Auvinen P, Gorochov G, Arstila TP. High-sequence diversity and structural conservation in the human T-cell receptor β junctional region during thymic development. Eur J Immunol 2013; 43:2185-93. [DOI: 10.1002/eji.201343360] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Revised: 03/28/2013] [Accepted: 05/08/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Anni Tuulasvaara
- Department of Bacteriology and Immunology; Haartman Institute; University of Helsinki; Helsinki; Finland
| | | | - Pia Laine
- Institute of Biotechnology; University of Helsinki; Helsinki; Finland
| | - Lars Paulin
- Institute of Biotechnology; University of Helsinki; Helsinki; Finland
| | - Jukka Salminen
- Department of Surgery; Hospital for Children and Adolescents; Helsinki University Hospital; Helsinki; Finland
| | - Petri Auvinen
- Institute of Biotechnology; University of Helsinki; Helsinki; Finland
| | | | - T. Petteri Arstila
- Department of Bacteriology and Immunology; Haartman Institute; University of Helsinki; Helsinki; Finland
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12
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Highly diverse TCRα chain repertoire of pre-immune CD8⁺ T cells reveals new insights in gene recombination. EMBO J 2012; 31:1666-78. [PMID: 22373576 DOI: 10.1038/emboj.2012.48] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 02/02/2012] [Indexed: 01/13/2023] Open
Abstract
Although the T-cell receptor αδ (TCRαδ) locus harbours large libraries of variable (TRAV) and junctional (TRAJ) gene segments, according to previous studies the TCRα chain repertoire is of limited diversity due to restrictions imposed by sequential coordinate TRAV-TRAJ recombinations. By sequencing tens of millions of TCRα chain transcripts from naive mouse CD8(+) T cells, we observed a hugely diverse repertoire, comprising nearly all possible TRAV-TRAJ combinations. Our findings are not compatible with sequential coordinate gene recombination, but rather with a model in which contraction and DNA looping in the TCRαδ locus provide equal access to TRAV and TRAJ gene segments, similarly to that demonstrated for IgH gene recombination. Generation of the observed highly diverse TCRα chain repertoire necessitates deletion of failed attempts by thymic-positive selection and is essential for the formation of highly diverse TCRαβ repertoires, capable of providing good protective immunity.
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Abstract
Historically, sharing T cell receptors (TCRs) between individuals has been speculated to be impossible, considering the dramatic discrepancy between the potential enormity of the TCR repertoire and the limited number of T cells generated in each individual. However, public T cell response, in which multiple individuals share identical TCRs in responding to a same antigenic epitope, has been extensively observed in a variety of immune responses across many species. Public T cell responses enable individuals within a population to generate similar antigen-specific TCRs against certain ubiquitous pathogens, leading to favorable biological outcomes. However, the relatively concentrated feature of TCR repertoire may limit T cell response in a population to some other pathogens. It could be a great benefit for human health if public T cell responses can be manipulated. Therefore, the mechanistic insight of public TCR generation is important to know. Recently, high-throughput DNA sequencing has revolutionized the study of immune receptor repertoires, which allows a much better understanding of the factors that determine the overlap of TCR repertoire among individuals. Here, we summarize the current knowledge on public T-cell response and discuss future challenges in this field.
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Affiliation(s)
- Hanjie Li
- State Key Laboratory of Cellular Stress Biology and School of Life Sciences, Xiamen University, Xiamen, Fujian, China
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Scandurra M, Mian M, Greiner TC, Rancoita PMV, De Campos CP, Chan WC, Vose JM, Chigrinova E, Inghirami G, Chiappella A, Baldini L, Ponzoni M, Ferreri AJ, Franceschetti S, Gaidano G, Montes-Moreno S, Piris MA, Facchetti F, Tucci A, Nomdedeu JF, Lazure T, Lambotte O, Uccella S, Pinotti G, Pruneri G, Martinelli G, Young KH, Tibiletti MG, Rinaldi A, Zucca E, Kwee I, Bertoni F. Genomic lesions associated with a different clinical outcome in diffuse large B-Cell lymphoma treated with R-CHOP-21. Br J Haematol 2010; 151:221-31. [DOI: 10.1111/j.1365-2141.2010.08326.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Schwienbacher C, De Grandi A, Fuchsberger C, Facheris MF, Svaldi M, Wjst M, Pramstaller PP, Hicks AA. Copy number variation and association over T-cell receptor genes--influence of DNA source. Immunogenetics 2010; 62:561-7. [PMID: 20582410 DOI: 10.1007/s00251-010-0459-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Accepted: 06/04/2010] [Indexed: 11/30/2022]
Abstract
Genomic copy number variants (CNVs) are a common, heritable source of inter-individual differences in genomic sequence. Their influence on phenotypic variability and their involvement in the pathogenesis of several common diseases is well established and the object of many current studies. In the course of examining CNV association to various quantitative traits in a general population, we have detected a strong association of CNVs over the four TCR genes to lymphocyte and neutrophil numbers in blood. In a small replication series, we have further characterized the nature of these CNVs and found them not to be germline, but dependent on the origin of analysed DNA. Germline deletion and rearrangement around the T-cell receptor (TCR) genes naturally occurs in white blood cells. Blood DNA derived from persons with high lymphocyte counts generates variable intensity signals which behave like germline CNVs over these genes. As DNA containing a relative high proportion of these CNV-like events involving the TCR genes has the ability to influence genotype counts of SNPs in the regions of these genes, care should be taken in interpreting and replicating association signals on variants within these genes when blood-derived DNA is the only source of data.
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Numerical modelling of the V-J combinations of the T cell receptor TRA/TRD locus. PLoS Comput Biol 2010; 6:e1000682. [PMID: 20174554 PMCID: PMC2824756 DOI: 10.1371/journal.pcbi.1000682] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Accepted: 01/21/2010] [Indexed: 01/07/2023] Open
Abstract
T-Cell antigen Receptor (TR) repertoire is generated through rearrangements of V and J genes encoding α and β chains. The quantification and frequency for every V-J combination during ontogeny and development of the immune system remain to be precisely established. We have addressed this issue by building a model able to account for Vα-Jα gene rearrangements during thymus development of mice. So we developed a numerical model on the whole TRA/TRD locus, based on experimental data, to estimate how Vα and Jα genes become accessible to rearrangements. The progressive opening of the locus to V-J gene recombinations is modeled through windows of accessibility of different sizes and with different speeds of progression. Furthermore, the possibility of successive secondary V-J rearrangements was included in the modelling. The model points out some unbalanced V-J associations resulting from a preferential access to gene rearrangements and from a non-uniform partition of the accessibility of the J genes, depending on their location in the locus. The model shows that 3 to 4 successive rearrangements are sufficient to explain the use of all the V and J genes of the locus. Finally, the model provides information on both the kinetics of rearrangements and frequencies of each V-J associations. The model accounts for the essential features of the observed rearrangements on the TRA/TRD locus and may provide a reference for the repertoire of the V-J combinatorial diversity. Lymphocytes of the immune system ensure the body defense by the expression of receptors which are specific of targets, termed antigens. Each lymphocyte, deriving from the same original clone, expresses the same unique receptor. To achieve the production of receptors covering the wide variety of antigens, lymphocytes use a specialized genetic mechanism consisting of gene rearrangements. For instance, the genes encoding the receptor of the alpha chain of the T lymphocyte receptor (TRA) spread over a 1500 Kb genetic region which includes around 100 V genes, 60 J genes, and a single C gene. To constitute a functional alpha chain, one of the V and one of the J genes rearrange together to form a single exon. The precise definition of these V-J combinations is essential to understand the repertoire of TRA. We have developed a numerical model simulating all of the V-J combinations of TRA, fitting the available experimental observations obtained from the analysis of TRA in T lymphocytes of the thymus and the blood. Our model gives new insights on the rules controlling the use of V and J genes in providing a dynamic estimation of the total V-J combinations.
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Salameire D, Le Bris Y, Fabre B, Fauconnier J, Solly F, Pernollet M, Bonnefoix T, Leroux D, Plumas J, Jacob MC. Efficient characterization of the TCR repertoire in lymph nodes by flow cytometry. Cytometry A 2009; 75:743-51. [PMID: 19582873 DOI: 10.1002/cyto.a.20767] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Analysis of the T-cell receptor (TCR) repertoire by flow cytometry proved to be relevant for investigating T-cell diversity and detecting reactive cells in blood samples. We used this approach to characterize non-malignant T-lymphocytes in lymph nodes and give insights into their origin. The TCR repertoire of CD4+ and CD8+ T-cells from 81 lymph nodes was analyzed with a four-color flow cytometer using a wide panel of 25 anti-Vbeta monoclonal antibodies. Flow cytometry proved to be a useful and informative technique. We demonstrated a diversified TCR-Vbeta repertoire, and only low level expansions, in 53% of the samples. They involved nearly all Vbeta families, were more frequent in the CD8+ subset of older patients, but were not related to pathology. No evidence could be demonstrated in favor of stimulation by common antigens. Interestingly, the TCR-Vbeta repertoire proved to be very similar in lymph nodes and blood samples. Our results argue that in the cases studied, lymph node enlargement is mainly due to an increased homing of circulating T-cells. They also provide reference values for expression of 25 TCR-Vbeta in lymph nodes, which could serve as a basis for further applications in diagnosis of T-cell lymphoproliferative disorders.
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Affiliation(s)
- D Salameire
- Université Joseph Fourier Grenoble 1, F-38000, France
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Freeman JD, Warren RL, Webb JR, Nelson BH, Holt RA. Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing. Genome Res 2009; 19:1817-24. [PMID: 19541912 DOI: 10.1101/gr.092924.109] [Citation(s) in RCA: 287] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
T-cell receptor (TCR) genomic loci undergo somatic V(D)J recombination, plus the addition/subtraction of nontemplated bases at recombination junctions, in order to generate the repertoire of structurally diverse T cells necessary for antigen recognition. TCR beta subunits can be unambiguously identified by their hypervariable CDR3 (Complement Determining Region 3) sequence. This is the site of V(D)J recombination encoding the principal site of antigen contact. The complexity and dynamics of the T-cell repertoire remain unknown because the potential repertoire size has made conventional sequence analysis intractable. Here, we use 5'-RACE, Illumina sequencing, and a novel short read assembly strategy to sample CDR3(beta) diversity in human T lymphocytes from peripheral blood. Assembly of 40.5 million short reads identified 33,664 distinct TCR(beta) clonotypes and provides precise measurements of CDR3(beta) length diversity, usage of nontemplated bases, sequence convergence, and preferences for TRBV (T-cell receptor beta variable gene) and TRBJ (T-cell receptor beta joining gene) gene usage and pairing. CDR3 length between conserved residues of TRBV and TRBJ ranged from 21 to 81 nucleotides (nt). TRBV gene usage ranged from 0.01% for TRBV17 to 24.6% for TRBV20-1. TRBJ gene usage ranged from 1.6% for TRBJ2-6 to 17.2% for TRBJ2-1. We identified 1573 examples of convergence where the same amino acid translation was specified by distinct CDR3(beta) nucleotide sequences. Direct sequence-based immunoprofiling will likely prove to be a useful tool for understanding repertoire dynamics in response to immune challenge, without a priori knowledge of antigen.
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Affiliation(s)
- J Douglas Freeman
- Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
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19
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Narcolepsy is strongly associated with the T-cell receptor alpha locus. Nat Genet 2009; 41:708-11. [PMID: 19412176 PMCID: PMC2803042 DOI: 10.1038/ng.372] [Citation(s) in RCA: 333] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2008] [Accepted: 03/05/2009] [Indexed: 11/09/2022]
Abstract
Narcolepsy with cataplexy, characterized by sleepiness and rapid onset into REM sleep, affects 1 in 2,000 individuals. Narcolepsy was first shown to be tightly associated with HLA-DR2 (ref. 3) and later sublocalized to DQB1*0602 (ref. 4). Following studies in dogs and mice, a 95% loss of hypocretin-producing cells in postmortem hypothalami from narcoleptic individuals was reported. Using genome-wide association (GWA) in Caucasians with replication in three ethnic groups, we found association between narcolepsy and polymorphisms in the TRA@ (T-cell receptor alpha) locus, with highest significance at rs1154155 (average allelic odds ratio 1.69, genotypic odds ratios 1.94 and 2.55, P < 10(-21), 1,830 cases, 2,164 controls). This is the first documented genetic involvement of the TRA@ locus, encoding the major receptor for HLA-peptide presentation, in any disease. It is still unclear how specific HLA alleles confer susceptibility to over 100 HLA-associated disorders; thus, narcolepsy will provide new insights on how HLA-TCR interactions contribute to organ-specific autoimmune targeting and may serve as a model for over 100 other HLA-associated disorders.
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Jouvin-Marche E, Fuschiotti P, Marche PN. Dynamic Aspects of TCRα Gene Recombination: Qualitative and Quantitative Assessments of the TCRα Chain Repertoire in Man and Mouse. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2009; 650:82-92. [DOI: 10.1007/978-1-4419-0296-2_7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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21
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Venturi V, Price DA, Douek DC, Davenport MP. The molecular basis for public T-cell responses? Nat Rev Immunol 2008; 8:231-8. [PMID: 18301425 DOI: 10.1038/nri2260] [Citation(s) in RCA: 257] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Public T-cell responses, in which T cells bearing identical T-cell receptors (TCRs) are observed to dominate the response to the same antigenic epitope in multiple individuals, have long been a focus of immune T-cell repertoire studies. However, the mechanism that enables the survival of a specific TCR from the diverse repertoire produced in the thymus through to its involvement in a public immune response remains unclear. In this Opinion article, we propose that the frequency of production of T cells bearing different TCRs during recombination has an important role in the sharing of TCRs in an immune response, with variable levels of 'convergent recombination' driving production frequencies.
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Affiliation(s)
- Vanessa Venturi
- Complex Systems Biology Group, Centre for Vascular Research, University of New South Wales, Kensington New South Wales 2052, Australia
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