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de Boer RJ, Tesselaar K, Borghans JAM. Better safe than sorry: Naive T-cell dynamics in healthy ageing. Semin Immunol 2023; 70:101839. [PMID: 37716048 DOI: 10.1016/j.smim.2023.101839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/01/2023] [Accepted: 09/02/2023] [Indexed: 09/18/2023]
Abstract
It is well-known that the functioning of the immune system gradually deteriorates with age, and we are increasingly confronted with its consequences as the life expectancy of the human population increases. Changes in the T-cell pool are among the most prominent features of the changing immune system during healthy ageing, and changes in the naive T-cell pool in particular are generally held responsible for its gradual deterioration. These changes in the naive T-cell pool are thought to be due to involution of the thymus. It is commonly believed that the gradual loss of thymic output induces compensatory mechanisms to maintain the number of naive T cells at a relatively constant level, and induces a loss of diversity in the T-cell repertoire. Here we review the studies that support or challenge this widely-held view of immune ageing and discuss the implications for vaccination strategies.
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Affiliation(s)
- Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, the Netherlands
| | - Kiki Tesselaar
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - José A M Borghans
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, the Netherlands.
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2
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Fang M, Su Z, Abolhassani H, Zhang W, Jiang C, Cheng B, Luo L, Wu J, Wang S, Lin L, Wang X, Wang L, Aghamohammadi A, Li T, Zhang X, Hammarström L, Liu X. T Cell Repertoire Abnormality in Immunodeficiency Patients with DNA Repair and Methylation Defects. J Clin Immunol 2021; 42:375-393. [PMID: 34825286 PMCID: PMC8821531 DOI: 10.1007/s10875-021-01178-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/01/2021] [Indexed: 12/25/2022]
Abstract
Both DNA damage response and methylation play a crucial role in antigen receptor recombination by creating a diverse repertoire in developing lymphocytes, but how their defects relate to T cell repertoire and phenotypic heterogeneity of immunodeficiency remains obscure. We studied the TCR repertoire in patients with the mutation in different genes (ATM, DNMT3B, ZBTB24, RAG1, DCLRE1C, and JAK3) and uncovered distinct characteristics of repertoire diversity. We propose that early aberrancies in thymus T cell development predispose to the heterogeneous phenotypes of the immunodeficiency spectrum. Shorter CDR3 lengths in ATM-deficient patients, resulting from a decreased number of nucleotide insertions during VDJ recombination in the pre-selected TCR repertoire, as well as the increment of CDR3 tyrosine residues, lead to the enrichment of pathology-associated TCRs, which may contribute to the phenotypes of ATM deficiency. Furthermore, patients with DNMT3B and ZBTB24 mutations who exhibit discrepant phenotypes present longer CDR3 lengths and reduced number of known pathology-associated TCRs.
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Affiliation(s)
- Mingyan Fang
- BGI-Shenzhen, Shenzhen, 518083, China.,Division of Clinical Immunology at the Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, 141 86, Stockholm, Sweden
| | - Zheng Su
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, The University of New South Wales, Sydney, NSW, Australia
| | - Hassan Abolhassani
- Division of Clinical Immunology at the Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, 141 86, Stockholm, Sweden.,Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Wei Zhang
- BGI-Shenzhen, Shenzhen, 518083, China.,Department of Computer Science, City University of Hong Kong, Hong Kong, 999077, China
| | | | | | - Lihua Luo
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | | | - Liya Lin
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xie Wang
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Asghar Aghamohammadi
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Tao Li
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Lennart Hammarström
- BGI-Shenzhen, Shenzhen, 518083, China. .,Division of Clinical Immunology at the Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, 141 86, Stockholm, Sweden. .,Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.
| | - Xiao Liu
- BGI-Shenzhen, Shenzhen, 518083, China. .,Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China.
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3
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Baran-Gale J, Morgan MD, Maio S, Dhalla F, Calvo-Asensio I, Deadman ME, Handel AE, Maynard A, Chen S, Green F, Sit RV, Neff NF, Darmanis S, Tan W, May AP, Marioni JC, Ponting CP, Holländer GA. Ageing compromises mouse thymus function and remodels epithelial cell differentiation. eLife 2020; 9:e56221. [PMID: 32840480 PMCID: PMC7490013 DOI: 10.7554/elife.56221] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 08/22/2020] [Indexed: 12/13/2022] Open
Abstract
Ageing is characterised by cellular senescence, leading to imbalanced tissue maintenance, cell death and compromised organ function. This is first observed in the thymus, the primary lymphoid organ that generates and selects T cells. However, the molecular and cellular mechanisms underpinning these ageing processes remain unclear. Here, we show that mouse ageing leads to less efficient T cell selection, decreased self-antigen representation and increased T cell receptor repertoire diversity. Using a combination of single-cell RNA-seq and lineage-tracing, we find that progenitor cells are the principal targets of ageing, whereas the function of individual mature thymic epithelial cells is compromised only modestly. Specifically, an early-life precursor cell population, retained in the mouse cortex postnatally, is virtually extinguished at puberty. Concomitantly, a medullary precursor cell quiesces, thereby impairing maintenance of the medullary epithelium. Thus, ageing disrupts thymic progenitor differentiation and impairs the core immunological functions of the thymus.
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Affiliation(s)
| | - Michael D Morgan
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- Cancer Research United Kingdom - Cambridge Institute, Li Ka Shing Centre, University of CambridgeCambridgeUnited Kingdom
| | - Stefano Maio
- Weatherall Institute of Molecular Medicine, University of OxfordOxfordUnited Kingdom
- Department of Paediatrics, University of Oxford, Cancer ResearchOxfordUnited Kingdom
| | - Fatima Dhalla
- Weatherall Institute of Molecular Medicine, University of OxfordOxfordUnited Kingdom
- Department of Paediatrics, University of Oxford, Cancer ResearchOxfordUnited Kingdom
| | - Irene Calvo-Asensio
- Department of Biomedicine, University of Basel, and University Children’s HospitalBaselSwitzerland
| | - Mary E Deadman
- Weatherall Institute of Molecular Medicine, University of OxfordOxfordUnited Kingdom
- Department of Paediatrics, University of Oxford, Cancer ResearchOxfordUnited Kingdom
| | - Adam E Handel
- Weatherall Institute of Molecular Medicine, University of OxfordOxfordUnited Kingdom
| | | | - Steven Chen
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Foad Green
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Rene V Sit
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Norma F Neff
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | | | - Weilun Tan
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Andy P May
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - John C Marioni
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
- Cancer Research United Kingdom - Cambridge Institute, Li Ka Shing Centre, University of CambridgeCambridgeUnited Kingdom
- EMBL-EBI, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Chris P Ponting
- MRC Human Genetics Unit, University of EdinburghEdinburghUnited Kingdom
| | - Georg A Holländer
- Weatherall Institute of Molecular Medicine, University of OxfordOxfordUnited Kingdom
- Department of Paediatrics, University of Oxford, Cancer ResearchOxfordUnited Kingdom
- Department of Biomedicine, University of Basel, and University Children’s HospitalBaselSwitzerland
- Department of Biosystems Science and Engineering, ETH ZurichBaselSwitzerland
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4
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Egorov ES, Kasatskaya SA, Zubov VN, Izraelson M, Nakonechnaya TO, Staroverov DB, Angius A, Cucca F, Mamedov IZ, Rosati E, Franke A, Shugay M, Pogorelyy MV, Chudakov DM, Britanova OV. The Changing Landscape of Naive T Cell Receptor Repertoire With Human Aging. Front Immunol 2018; 9:1618. [PMID: 30087674 PMCID: PMC6066563 DOI: 10.3389/fimmu.2018.01618] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/29/2018] [Indexed: 12/22/2022] Open
Abstract
Human aging is associated with a profound loss of thymus productivity, yet naïve T lymphocytes still maintain their numbers by division in the periphery for many years. The extent of such proliferation may depend on the cytokine environment, including IL-7 and T-cell receptor (TCR) “tonic” signaling mediated by self pMHCs recognition. Additionally, intrinsic properties of distinct subpopulations of naïve T cells could influence the overall dynamics of aging-related changes within the naïve T cell compartment. Here, we investigated the differences in the architecture of TCR beta repertoires for naïve CD4, naïve CD8, naïve CD4+CD25−CD31+ (enriched with recent thymic emigrants, RTE), and mature naïve CD4+CD25−CD31− peripheral blood subsets between young and middle-age/old healthy individuals. In addition to observing the accumulation of clonal expansions (as was shown previously), we reveal several notable changes in the characteristics of T cell repertoire. We observed significant decrease of CDR3 length, NDN insert, and number of non-template added N nucleotides within TCR beta CDR3 with aging, together with a prominent change of physicochemical properties of the central part of CDR3 loop. These changes were similar across CD4, CD8, RTE-enriched, and mature CD4 subsets of naïve T cells, with minimal or no difference observed between the latter two subsets for individuals of the same age group. We also observed an increase in “publicity” (fraction of shared clonotypes) of CD4, but not CD8 naïve T cell repertoires. We propose several explanations for these phenomena built upon previous studies of naïve T-cell homeostasis, and call for further studies of the mechanisms causing the observed changes and of consequences of these changes in respect of the possible holes formed in the landscape of naïve T cell TCR repertoire.
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Affiliation(s)
- Evgeny S Egorov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Sofya A Kasatskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Vasiliy N Zubov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Mark Izraelson
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | | | - Andrea Angius
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Italy
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Italy
| | - Ilgar Z Mamedov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Elisa Rosati
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Mikhail Shugay
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | - Dmitriy M Chudakov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Olga V Britanova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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5
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Britanova OV, Shugay M, Merzlyak EM, Staroverov DB, Putintseva EV, Turchaninova MA, Mamedov IZ, Pogorelyy MV, Bolotin DA, Izraelson M, Davydov AN, Egorov ES, Kasatskaya SA, Rebrikov DV, Lukyanov S, Chudakov DM. Dynamics of Individual T Cell Repertoires: From Cord Blood to Centenarians. THE JOURNAL OF IMMUNOLOGY 2016; 196:5005-13. [PMID: 27183615 DOI: 10.4049/jimmunol.1600005] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/16/2016] [Indexed: 01/29/2023]
Abstract
The diversity, architecture, and dynamics of the TCR repertoire largely determine our ability to effectively withstand infections and malignancies with minimal mistargeting of immune responses. In this study, we have employed deep TCRβ repertoire sequencing with normalization based on unique molecular identifiers to explore the long-term dynamics of T cell immunity. We demonstrate remarkable stability of repertoire, where approximately half of all T cells in peripheral blood are represented by clones that persist and generally preserve their frequencies for 3 y. We further characterize the extremes of lifelong TCR repertoire evolution, analyzing samples ranging from umbilical cord blood to centenarian peripheral blood. We show that the fetal TCR repertoire, albeit structurally maintained within regulated borders due to the lower numbers of randomly added nucleotides, is not limited with respect to observed functional diversity. We reveal decreased efficiency of nonsense-mediated mRNA decay in umbilical cord blood, which may reflect specific regulatory mechanisms in development. Furthermore, we demonstrate that human TCR repertoires are functionally more similar at birth but diverge during life, and we track the lifelong behavior of CMV- and EBV-specific T cell clonotypes. Finally, we reveal gender differences in dynamics of TCR diversity constriction, which come to naught in the oldest age. Based on our data, we propose a more general explanation for the previous observations on the relationships between longevity and immunity.
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Affiliation(s)
- Olga V Britanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Mikhail Shugay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Ekaterina M Merzlyak
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Dmitriy B Staroverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Ekaterina V Putintseva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Maria A Turchaninova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Ilgar Z Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Mikhail V Pogorelyy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Dmitriy A Bolotin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Mark Izraelson
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Alexey N Davydov
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Evgeny S Egorov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
| | - Sofya A Kasatskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Denis V Rebrikov
- Pirogov Russian National Research Medical University, Moscow 117997, Russia; Vavilov Institute of General Genetics of the Russian Academy of Sciences, Moscow 119991, Russia
| | - Sergey Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia; Pirogov Russian National Research Medical University, Moscow 117997, Russia; Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic; and
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6
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Ghislin S, Ouzren-Zarhloul N, Kaminski S, Frippiat JP. Hypergravity exposure during gestation modifies the TCRβ repertoire of newborn mice. Sci Rep 2015; 5:9318. [PMID: 25792033 PMCID: PMC5380131 DOI: 10.1038/srep09318] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 03/02/2015] [Indexed: 01/03/2023] Open
Abstract
During spaceflight, organisms are subjected to mechanical force changes (gravity (G) changes) that affect the immune system. However, gravitational effects on lymphopoiesis have rarely been studied. Consequently, we investigated whether the TCRβ repertoire, created by V(D)J recombination during T lymphopoiesis, is affected by hypergravity exposure during murine development. To address this question, C57BL/6j mice were mated in a centrifuge so that embryonic development, birth and TCRβ rearrangements occurred at 2G. Pups were sacrificed at birth, and their thymus used to quantify transcripts coding for factors required for V(D)J recombination and T lymphopoiesis. We also created cDNA mini-libraries of TCRβ transcripts to study the impact of hypergravity on TCRβ diversity. Our data show that hypergravity exposure increases the transcription of TCRβ chains, and of genes whose products are involved in TCR signaling, and affects the V(D)J recombination process. We also observed that ~85% of the TCRβ repertoire is different between hypergravity and control pups. These data indicate that changing a mechanical force (the gravity) during ontogeny will likely affect host immunity because properties of loops constituting TCR antigen-binding sites are modified in hypergravity newborns. The spectrum of peptides recognized by TCR will therefore likely be different.
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Affiliation(s)
- Stéphanie Ghislin
- EA7300, Stress Immunity Pathogens Laboratory, Faculty of Medicine, Lorraine University, F-54500 Vandœuvre-lès-Nancy, France
| | - Nassima Ouzren-Zarhloul
- EA7300, Stress Immunity Pathogens Laboratory, Faculty of Medicine, Lorraine University, F-54500 Vandœuvre-lès-Nancy, France
| | - Sandra Kaminski
- EA7300, Stress Immunity Pathogens Laboratory, Faculty of Medicine, Lorraine University, F-54500 Vandœuvre-lès-Nancy, France
| | - Jean-Pol Frippiat
- EA7300, Stress Immunity Pathogens Laboratory, Faculty of Medicine, Lorraine University, F-54500 Vandœuvre-lès-Nancy, France
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7
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Petrovic Berglund J, Petrovc Berglund J, Mariotti-Ferrandiz E, Rosmaraki E, Hall H, Cazenave PA, Six A, Höglund P. TCR repertoire dynamics in the pancreatic lymph nodes of non-obese diabetic (NOD) mice at the time of disease initiation. Mol Immunol 2008; 45:3059-64. [PMID: 18471883 DOI: 10.1016/j.molimm.2008.03.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2008] [Revised: 03/17/2008] [Accepted: 03/19/2008] [Indexed: 11/17/2022]
Abstract
Mouse T-cell development is unfinished at birth and continues during the first month of life, when T cells exit from the thymus and colonize secondary hematopoietic organs to build up a peripheral T-cell repertoire. T-cell responses against beta-cell-derived autoantigens are initiated in the pancreatic lymph nodes (PLN) of non-obese diabetic (NOD) mice during the same time period. We hypothesized that the combined effect of T-cell development and T-cell activation against tissue-specific antigens would create unique TCR repertoires in two different lymph node stations in NOD mice. To test this hypothesis, we determined the length distribution of the third complementarity-determining region (CDR3) of the TCR in the PLN and the inguinal lymph nodes (ILN) of 10, 14, 18 and 22-day-old NOD females. The analysis of all the BV genes revealed significant perturbations of the repertoire between days 10 and 22 but with no statistical differences between the PLN and ILN repertoires. In contrast, when a set of BV chains were amplified using BJ-specific primers, several unique TCR perturbations were observed in the PLN compared to the ILN. We propose that the TCR repertoire in peripheral lymph nodes of NOD mice develops dynamically between 10 and 22 days of age as a result of a developmental process. On top of that development, the local environment may fine-tune that repertoire, possibly by means of stimulation of T cells by tissue-specific antigens presented by local APC.
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Affiliation(s)
- Jelena Petrovic Berglund
- Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, Box 280, S-171 77 Stockholm, Sweden
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8
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Cherrier M, D'Andon MF, Rougeon F, Doyen N. Identification of a new cis-regulatory element of the terminal deoxynucleotidyl transferase gene in the 5' region of the murine locus. Mol Immunol 2007; 45:1009-17. [PMID: 17854898 DOI: 10.1016/j.molimm.2007.07.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2007] [Revised: 07/26/2007] [Accepted: 07/27/2007] [Indexed: 10/22/2022]
Abstract
Terminal deoxynucleotidyl transferase (TdT) expression is controlled at the transcriptional level, however, the TdT core promoter combining D, D', an initiator (Inr) and downstream basal elements (DBE) does not recapitulate the whole complex regulation of TdT expression. We hypothesized that important cis-regulatory elements of the gene are located outside of the TdT promoter. In an attempt to identify these elements, we performed DNase I hypersensitivity assays over 24kb including a 10kb region located upstream of the transcription start site (+1) and a 14kb region spanning exons and introns I to VI. Hypersensitive sites (HS) HS1 and HS2 were localized 8.5 and 8kb upstream of the transcription start site, respectively, and were exclusively detected in TdT+ cell types. HS3, HS4 and HS5 were mapped at positions -7, -3.4 and -3kb, respectively, and detected in both TdT negative and positive cells. HS6, HS7 and HS8 were detected immediately upstream of the TdT promoter. HS10 and HS11 were localized in the first and third intron of the gene. Luciferase reporter assays revealed that HS1, HS2 and HS3 synergize with the TdT promoter to activate transcription in a TdT+ pre-T cell line but not in a TdT+ pro-B cell line. In summary novel cis-regulatory elements have been identified in the 5' region of the TdT locus that synergize with the promoter to activate gene expression and our results suggest these elements may be more active in T cells.
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Affiliation(s)
- Marie Cherrier
- Développement des tissus lymphoïdes, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France.
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9
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Bartl S, Miracle AL, Rumfelt LL, Kepler TB, Mochon E, Litman GW, Flajnik MF. Terminal deoxynucleotidyl transferases from elasmobranchs reveal structural conservation within vertebrates. Immunogenetics 2003; 55:594-604. [PMID: 14579105 DOI: 10.1007/s00251-003-0608-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2003] [Revised: 08/25/2003] [Indexed: 01/21/2023]
Abstract
The DNA polymerase (pol) X family is an ancient group of enzymes that function in DNA replication and repair (pol beta), translesion synthesis (pol lambda and pol micro) and terminal addition of non-templated nucleotides. This latter terminal deoxynucleotidyl transferase (TdT) activity performs the unique function of providing diversity at coding joins of immunoglobulin and T-cell receptor genes. The first isolated full-length TdT genes from shark and skate are reported here. Comparisons with the three-dimensional structure of mouse TdT indicate structural similarity with elasmobranch orthologues that supports both a template-independent mode of replication and a lack of strong nucleotide bias. The vertebrate TdTs appear more closely related to pol micro and fungal polymerases than to pol lambda and pol beta. Thus, unlike other molecules of adaptive immunity, TdT is a member of an ancient gene family with a clear gene phylogeny and a high degree of similarity, which implies the existence of TdT ancestors in jawless fishes and invertebrates.
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Affiliation(s)
- Simona Bartl
- Moss Landing Marine Laboratories, 8272 Moss Landing Road, CA 95039, Moss Landing, USA.
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