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Lagattuta KA, Kang JB, Nathan A, Pauken KE, Jonsson AH, Rao DA, Sharpe AH, Ishigaki K, Raychaudhuri S. Repertoire analyses reveal T cell antigen receptor sequence features that influence T cell fate. Nat Immunol 2022; 23:446-457. [PMID: 35177831 PMCID: PMC8904286 DOI: 10.1038/s41590-022-01129-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 01/05/2022] [Indexed: 01/02/2023]
Abstract
T cells acquire a regulatory phenotype when their T cell receptors (TCRs) experience an intermediate-to-high affinity interaction with a self-peptide presented via the major histocompatibility complex (MHC). Using TCRβ sequences from flow-sorted human cells, we identified TCR features that promote regulatory T cell (Treg) fate. From these results, we developed a scoring system to quantify TCR-intrinsic regulatory potential (TiRP). When applied to the tumor microenvironment, TiRP scoring helped to explain why only some T cell clones maintained the Tconv phenotype through expansion. To elucidate drivers of these predictive TCR features, we then examined the two elements of the Treg TCR ligand separately: the self-peptide, and the human MHC II molecule. These analyses revealed that hydrophobicity in the third complementarity determining region (CDR3β) of the TCR promotes reactivity to self-peptides, while TCR variable gene (TRBV gene) usage shapes the TCR’s general propensity for human MHC II-restricted activation.
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Affiliation(s)
- Kaitlyn A Lagattuta
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joyce B Kang
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aparna Nathan
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kristen E Pauken
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Anna Helena Jonsson
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Deepak A Rao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Arlene H Sharpe
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Kazuyoshi Ishigaki
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA. .,Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA. .,Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA. .,Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA. .,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Centre for Genetics and Genomics Versus Arthritis, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
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Balcells F, Martínez Monteros MJ, Gómez AL, Cazorla SI, Perdigón G, Maldonado-Galdeano C. Probiotic Consumption Boosts Thymus in Obesity and Senescence Mouse Models. Nutrients 2022; 14:nu14030616. [PMID: 35276973 PMCID: PMC8838891 DOI: 10.3390/nu14030616] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/21/2022] [Accepted: 01/23/2022] [Indexed: 02/01/2023] Open
Abstract
The ability of the immune system to respond to different pathogens throughout life requires the constant production and selection of T cells in the thymus. This immune organ is very sensitive to age, infectious processes and nutrition disorders (obesity and malnutrition). Several studies have shown that the incorporation of some probiotic bacteria or probiotic fermented milk in the diet has beneficial effects, not only at the intestinal level but also on distant mucosal tissues, improving the architecture of the thymus in a malnutrition model. The aim of the present study was to determine whether supplementation with the probiotic strain Lactobacillus casei CRL 431 and/or its cell wall could improve body weight, intestinal microbiota and thymus structure and function in both obese and aging mice. We evaluated probiotic administration to BALB/c mice in 2 experimental mouse models: obesity and senescence, including mice of different ages (21, 28, 45, 90 and 180 days). Changes in thymus size and histology were recorded. T-lymphocyte population and cytokine production were also determined. The consumption of probiotics improved the cortical/medullary ratio, the production and regulation of cytokines and the recovery of mature T-lymphocyte populations of the thymus in obese and old mice. Probiotic incorporation into the diet could not only modulate the immune system but also lead to thymus function recovery, thus improving quality of life.
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Affiliation(s)
- Florencia Balcells
- Laboratorio de Inmunología, Centro de Referencia para Lactobacilos (CERELA-CONICET), San Miguel de Tucumán 4000, Argentina; (F.B.); (M.J.M.M.); (S.I.C.); (G.P.)
| | - María José Martínez Monteros
- Laboratorio de Inmunología, Centro de Referencia para Lactobacilos (CERELA-CONICET), San Miguel de Tucumán 4000, Argentina; (F.B.); (M.J.M.M.); (S.I.C.); (G.P.)
| | - Alba Lorena Gómez
- PatLab Laboratorio de Anatomía Patológica Citopatología e Inmunohistoquímica, San Miguel de Tucumán 4000, Argentina;
| | - Silvia Inés Cazorla
- Laboratorio de Inmunología, Centro de Referencia para Lactobacilos (CERELA-CONICET), San Miguel de Tucumán 4000, Argentina; (F.B.); (M.J.M.M.); (S.I.C.); (G.P.)
- Cátedra de Inmunología, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, San Miguel de Tucumán 4000, Argentina
| | - Gabriela Perdigón
- Laboratorio de Inmunología, Centro de Referencia para Lactobacilos (CERELA-CONICET), San Miguel de Tucumán 4000, Argentina; (F.B.); (M.J.M.M.); (S.I.C.); (G.P.)
| | - Carolina Maldonado-Galdeano
- Laboratorio de Inmunología, Centro de Referencia para Lactobacilos (CERELA-CONICET), San Miguel de Tucumán 4000, Argentina; (F.B.); (M.J.M.M.); (S.I.C.); (G.P.)
- Cátedra de Inmunología, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, San Miguel de Tucumán 4000, Argentina
- Correspondence:
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Galindo-Albarrán A, Castan S, Santamaria JC, Joffre OP, Haegeman B, Romagnoli P, van Meerwijk JPM. The Repertoire of Newly Developing Regulatory T Cells in the Type 1 Diabetes-Prone NOD Mouse Is Very Diverse. Diabetes 2021; 70:1729-1737. [PMID: 34035042 DOI: 10.2337/db20-1072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 05/17/2021] [Indexed: 11/13/2022]
Abstract
Regulatory T lymphocytes expressing the forkhead/winged helix transcription factor Foxp3 (Treg) play a vital role in the protection of the organism from autoimmune disease and other immunopathologies. The antigen specificity of Treg plays an important role in their in vivo activity. We therefore assessed the diversity of the T-cell receptors (TCRs) for antigen expressed by Treg newly developed in the thymus of autoimmune type 1 diabetes-prone NOD mice and compared it to the control mouse strain C57BL/6. Our results demonstrate that use of the TCRα and TCRβ variable (V) and joining (J) segments, length of the complementarity determining region (CDR) 3, and the diversity of the TCRα and TCRβ chains are comparable between NOD and C57BL/6 mice. Genetic defects affecting the diversity of the TCR expressed by newly developed Treg therefore do not appear to be involved in the etiology of type 1 diabetes in the NOD mouse.
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MESH Headings
- Animals
- Diabetes Mellitus, Type 1/genetics
- Diabetes Mellitus, Type 1/immunology
- Diabetes Mellitus, Type 1/pathology
- Mice
- Mice, Inbred C57BL
- Mice, Inbred NOD
- Mice, Transgenic
- Receptors, Antigen, T-Cell/genetics
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/pathology
- Thymus Gland/immunology
- Thymus Gland/pathology
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Affiliation(s)
- Ariel Galindo-Albarrán
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291-CNRS UMR5051-Université Paul Sabatier (UPS), Toulouse, France
- Station d'Écologie Théorique et Expérimentale, CNRS-Université Paul Sabatier (UPS), Moulis, France
| | - Sarah Castan
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291-CNRS UMR5051-Université Paul Sabatier (UPS), Toulouse, France
| | - Jérémy C Santamaria
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291-CNRS UMR5051-Université Paul Sabatier (UPS), Toulouse, France
| | - Olivier P Joffre
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291-CNRS UMR5051-Université Paul Sabatier (UPS), Toulouse, France
| | - Bart Haegeman
- Station d'Écologie Théorique et Expérimentale, CNRS-Université Paul Sabatier (UPS), Moulis, France
| | - Paola Romagnoli
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291-CNRS UMR5051-Université Paul Sabatier (UPS), Toulouse, France
| | - Joost P M van Meerwijk
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), INSERM UMR1291-CNRS UMR5051-Université Paul Sabatier (UPS), Toulouse, France
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Darrigues J, Santamaria JC, Galindo-Albarrán A, Robey EA, Joffre OP, van Meerwijk JPM, Romagnoli P. Robust intrathymic development of regulatory T cells in young NOD mice is rapidly restrained by recirculating cells. Eur J Immunol 2020; 51:580-593. [PMID: 32730634 DOI: 10.1002/eji.202048743] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/03/2020] [Accepted: 07/28/2020] [Indexed: 12/11/2022]
Abstract
Regulatory T lymphocytes (Treg) play a vital role in the protection of the organism against autoimmune pathology. It is therefore paradoxical that comparatively large numbers of Treg were found in the thymus of type I diabetes-prone NOD mice. The Treg population in the thymus is composed of newly developing cells and cells that had recirculated from the periphery back to the thymus. We here demonstrate that exceptionally large numbers of Treg develop in the thymus of young, but not adult, NOD mice. Once emigrated from the thymus, an unusually large proportion of these Treg is activated in the periphery, which causes a particularly abundant accumulation of recirculating Treg in the thymus. These cells then rapidly inhibit de novo development of Treg. The proportions of developing Treg thus reach levels similar to or lower than those found in most other, type 1 diabetes-resistant, inbred mouse strains. Thus, in adult NOD mice the particularly large Treg-niche is actually composed of mostly recirculating cells and only few newly developing Treg.
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Affiliation(s)
- Julie Darrigues
- Centre de Physiopathologie Toulouse Purpan (CPTP), Inserm U1043, CNRS UMR 5282, Université de Toulouse III (UPS), Toulouse, France
| | - Jeremy C Santamaria
- Centre de Physiopathologie Toulouse Purpan (CPTP), Inserm U1043, CNRS UMR 5282, Université de Toulouse III (UPS), Toulouse, France
| | - Ariel Galindo-Albarrán
- Centre de Physiopathologie Toulouse Purpan (CPTP), Inserm U1043, CNRS UMR 5282, Université de Toulouse III (UPS), Toulouse, France.,Station d'Ecologie Théorique et Expérimentale, CNRS, Moulis, France, Université Paul Sabatier, Moulis, France
| | - Ellen A Robey
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, CA
| | - Olivier P Joffre
- Centre de Physiopathologie Toulouse Purpan (CPTP), Inserm U1043, CNRS UMR 5282, Université de Toulouse III (UPS), Toulouse, France
| | - Joost P M van Meerwijk
- Centre de Physiopathologie Toulouse Purpan (CPTP), Inserm U1043, CNRS UMR 5282, Université de Toulouse III (UPS), Toulouse, France
| | - Paola Romagnoli
- Centre de Physiopathologie Toulouse Purpan (CPTP), Inserm U1043, CNRS UMR 5282, Université de Toulouse III (UPS), Toulouse, France
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O'Hagan KL, Choi J, Pryshchep O, Chernoff J, Phee H. Pak2 Links TCR Signaling Strength to the Development of Regulatory T Cells and Maintains Peripheral Tolerance. THE JOURNAL OF IMMUNOLOGY 2015; 195:1564-77. [PMID: 26157175 DOI: 10.4049/jimmunol.1500843] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 06/10/2015] [Indexed: 01/01/2023]
Abstract
Although significant effort has been devoted to understanding the thymic development of Foxp3(+) regulatory T cells (Tregs), the precise signaling pathways that govern their lineage commitment still remain enigmatic. Our findings show a novel role for the actin cytoskeletal remodeling protein, p21-activated kinase 2 (Pak2), in Treg development and homeostasis. The absence of Pak2 in T cells resulted in a marked reduction in both thymus- and peripherally derived Tregs, accompanied by the development of spontaneous colitis in Pak2-deficient mice. Additionally, Pak2 was required for the proper differentiation of in vitro-induced Tregs as well as maintenance of Tregs. Interestingly, Pak2 was necessary for generating the high-affinity TCR- and IL-2-mediated signals that are required by developing Tregs for their lineage commitment. These findings provide novel insight into how developing thymocytes translate lineage-specific high-affinity TCR signals to adopt the Treg fate, and they further posit Pak2 as an essential regulator for this process.
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Affiliation(s)
- Kyle Leonard O'Hagan
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611; and
| | - Jinyong Choi
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611; and
| | - Olga Pryshchep
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611; and
| | - Jonathan Chernoff
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA 19111
| | - Hyewon Phee
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611; and
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Bains I, van Santen HM, Seddon B, Yates AJ. Models of self-peptide sampling by developing T cells identify candidate mechanisms of thymic selection. PLoS Comput Biol 2013; 9:e1003102. [PMID: 23935465 PMCID: PMC3723501 DOI: 10.1371/journal.pcbi.1003102] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 05/01/2013] [Indexed: 11/18/2022] Open
Abstract
Conventional and regulatory T cells develop in the thymus where they are exposed to samples of self-peptide MHC (pMHC) ligands. This probabilistic process selects for cells within a range of responsiveness that allows the detection of foreign antigen without excessive responses to self. Regulatory T cells are thought to lie at the higher end of the spectrum of acceptable self-reactivity and play a crucial role in the control of autoimmunity and tolerance to innocuous antigens. While many studies have elucidated key elements influencing lineage commitment, we still lack a full understanding of how thymocytes integrate signals obtained by sampling self-peptides to make fate decisions. To address this problem, we apply stochastic models of signal integration by T cells to data from a study quantifying the development of the two lineages using controllable levels of agonist peptide in the thymus. We find two models are able to explain the observations; one in which T cells continually re-assess fate decisions on the basis of multiple summed proximal signals from TCR-pMHC interactions; and another in which TCR sensitivity is modulated over time, such that contact with the same pMHC ligand may lead to divergent outcomes at different stages of development. Neither model requires that T(conv) and T(reg) are differentially susceptible to deletion or that the two lineages need qualitatively different signals for development, as have been proposed. We find additional support for the variable-sensitivity model, which is able to explain apparently paradoxical observations regarding the effect of partial and strong agonists on T(conv) and T(reg) development.
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Affiliation(s)
- Iren Bains
- Immune Cell Biology, MRC National Institute for Medical Research, Mill Hill, London, United Kingdom
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, New York, New York, United States of America
| | - Hisse M. van Santen
- Centro Biologia Molecular Severo Ochoa, CSIC/Universidad Autonoma de Madrid, Madrid, Spain
| | - Benedict Seddon
- Immune Cell Biology, MRC National Institute for Medical Research, Mill Hill, London, United Kingdom
| | - Andrew J. Yates
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, New York, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York, United States of America
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