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Michelson DA, Mathis D. Thymic Mimetic Cells: Ontogeny as Immunology. Annu Rev Cell Dev Biol 2024. [PMID: 38608315 DOI: 10.1146/annurev-cellbio-112122-023316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024]
Abstract
Medullary thymic epithelial cells (mTECs) generate immunological self-tolerance by ectopically expressing peripheral-tissue antigens (PTAs) within the thymus to preview the peripheral self to maturing T cells. Recent work, drawing inspiration from old histological observations, has shown that subtypes of mTECs, collectively termed mimetic cells, co-opt developmental programs from throughout the organism to express biologically coherent groups of PTAs. Here, we review key aspects of mimetic cells, especially as they relate to the larger contexts of molecular, cellular, developmental, and evolutionary biology. We highlight lineage-defining transcription factors as key regulators of mimetic cells and speculate as to what other factors, including Aire and the chromatin potential of mTECs, permit mimetic cell differentiation and function. Last, we consider what mimetic cells can teach us about not only the thymus but also other tissues.
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Affiliation(s)
- Daniel A Michelson
- 1Harvard-MIT Program in Health Sciences and Technology, Harvard Medical School, Boston, Massachusetts, USA;
| | - Diane Mathis
- 2Department of Immunology, Harvard Medical School, Boston, Massachusetts, USA;
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Yaghi OK, Hanna BS, Langston PK, Michelson DA, Jayewickreme T, Marin-Rodero M, Benoist C, Mathis D. A discrete 'early-responder' stromal-cell subtype orchestrates immunocyte recruitment to injured tissue. Nat Immunol 2023; 24:2053-2067. [PMID: 37932455 PMCID: PMC10792729 DOI: 10.1038/s41590-023-01669-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 10/05/2023] [Indexed: 11/08/2023]
Abstract
Following acute injury, stromal cells promote tissue regeneration by a diversity of mechanisms. Time-resolved single-cell RNA sequencing of muscle mesenchymal stromal cells (MmSCs) responding to acute injury identified an 'early-responder' subtype that spiked on day 1 and expressed a notable array of transcripts encoding immunomodulators. IL-1β, TNF-α and oncostatin M each strongly and rapidly induced MmSCs transcribing this immunomodulatory program. Macrophages amplified the program but were not strictly required for its induction. Transfer of the inflammatory MmSC subtype, tagged with a unique surface marker, into healthy hindlimb muscle induced inflammation primarily driven by neutrophils and macrophages. Among the abundant inflammatory transcripts produced by this subtype, Cxcl5 was stroma-specific and highly upregulated with injury. Depletion of this chemokine early after injury revealed a substantial impact on recruitment of neutrophils, a prolongation of inflammation to later times and an effect on tissue regeneration. Mesenchymal stromal cell subtypes expressing a comparable inflammatory program were found in a mouse model of muscular dystrophy and in several other tissues and pathologies in both mice and humans. These 'early-responder' mesenchymal stromal cells, already in place, permit rapid and coordinated mobilization and amplification of critical cell collaborators in response to injury.
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Affiliation(s)
- Omar K Yaghi
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Bola S Hanna
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - P Kent Langston
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Daniel A Michelson
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Teshika Jayewickreme
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Miguel Marin-Rodero
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Christophe Benoist
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Diane Mathis
- Department of Immunology, Harvard Medical School, Boston, MA, USA.
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.
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Michelson DA, Zuo C, Verzi M, Benoist C, Mathis D. Hnf4 activates mimetic-cell enhancers to recapitulate gut and liver development within the thymus. J Exp Med 2023; 220:e20230461. [PMID: 37399024 PMCID: PMC10318407 DOI: 10.1084/jem.20230461] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/16/2023] [Accepted: 06/16/2023] [Indexed: 07/04/2023] Open
Abstract
Mimetic cells are medullary thymic epithelial cells (mTECs) that mimic extra-thymic cell types to tolerize T cells to self-antigens. Here, we dissected the biology of entero-hepato mTECs, mimetic cells expressing gut- and liver-associated transcripts. Entero-hepato mTECs conserved their thymic identity yet accessed wide swaths of enterocyte chromatin and transcriptional programs via the transcription factors Hnf4α and Hnf4γ. Deletion of Hnf4α and Hnf4γ in TECs ablated entero-hepato mTECs and downregulated numerous gut- and liver-associated transcripts, with a primary contribution from Hnf4γ. Loss of Hnf4 impaired enhancer activation and CTCF redistribution in mTECs but did not impact Polycomb-mediated repression or promoter-proximal histone marks. By single-cell RNA sequencing, Hnf4 loss produced three distinct effects on mimetic cell state, fate, and accumulation. Serendipitously, a requirement for Hnf4 in microfold mTECs was discovered, which exposed a requirement for Hnf4γ in gut microfold cells and the IgA response. Study of Hnf4 in entero-hepato mTECs thus revealed mechanisms of gene control in the thymus and periphery alike.
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Affiliation(s)
| | - Chong Zuo
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | - Michael Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | | | - Diane Mathis
- Department of Immunology, Harvard Medical School, Boston, MA, USA
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Abstract
Medullary thymic epithelial cells (mTECs) clonally delete or divert autoreactive T cells by ectopically expressing a diverse array of peripheral-tissue antigens (PTAs) within the thymus. Although thymic stromal cells with histological features of extra-thymic cell types, like myocytes or neurons, have been observed by light microscopy since the mid-1800s, most modern work on PTA expression has focused on the transcription factor Aire. Here, we highlight recent work that has refocused attention on such 'misplaced' thymic cells, referred to collectively as thymic mimetic cells. We review the molecular underpinnings of mimetic cells and their roles in establishing T cell tolerance, and we propose that mimetic cells play important roles in autoimmunity. Finally, we suggest future directions for this emerging area.
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Affiliation(s)
| | - Diane Mathis
- Department of Immunology, Harvard Medical School, Boston, MA 02115, USA.
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Bansal K, Michelson DA, Ramirez RN, Viny AD, Levine RL, Benoist C, Mathis D. Aire regulates chromatin looping by evicting CTCF from domain boundaries and favoring accumulation of cohesin on superenhancers. Proc Natl Acad Sci U S A 2021; 118:e2110991118. [PMID: 34518235 PMCID: PMC8463806 DOI: 10.1073/pnas.2110991118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2021] [Indexed: 11/18/2022] Open
Abstract
Aire controls immunological tolerance by driving promiscuous expression of a large swath of the genome in medullary thymic epithelial cells (mTECs). Its molecular mechanism remains enigmatic. High-resolution chromosome-conformation capture (Hi-C) experiments on ex vivo mTECs revealed Aire to have a widespread impact on higher-order chromatin structure, disfavoring architectural loops while favoring transcriptional loops. In the presence of Aire, cohesin complexes concentrated on superenhancers together with mediator complexes, while the CCCTC-binding factor (CTCF) was relatively depleted from structural domain boundaries. In particular, Aire associated with the cohesin loader, NIPBL, strengthening this factor's affiliation with cohesin's enzymatic subunits. mTEC transcripts up-regulated in the presence of Aire corresponded closely to those down-regulated in the absence of one of the cohesin subunits, SA-2. A mechanistic model incorporating these findings explains many of the unusual features of Aire's impact on mTEC transcription, providing molecular insight into tolerance induction.
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Affiliation(s)
- Kushagra Bansal
- Department of Immunology, Harvard Medical School, Boston, MA 02115
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560 064, India
| | - Daniel A Michelson
- Department of Immunology, Harvard Medical School, Boston, MA 02115
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Ricardo N Ramirez
- Department of Immunology, Harvard Medical School, Boston, MA 02115
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Aaron D Viny
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Christophe Benoist
- Department of Immunology, Harvard Medical School, Boston, MA 02115;
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
| | - Diane Mathis
- Department of Immunology, Harvard Medical School, Boston, MA 02115;
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115
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Galvan-Pena S, Leon J, Chowdhary K, Michelson DA, Vijaykumar B, Yang L, Magnuson A, Manickas-Hill Z, Piechocka-Trocha A, Worrall DP, Hall KE, Ghebremichael M, Walker BD, Li JZ, Yu XG, Mathis D, Benoist C. Profound Treg perturbations correlate with COVID-19 severity. bioRxiv 2020. [PMID: 33330871 DOI: 10.1101/2020.12.11.416180] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The hallmark of severe COVID-19 disease has been an uncontrolled inflammatory response, resulting from poorly understood immunological dysfunction. We explored the hypothesis that perturbations in FoxP3+ T regulatory cells (Treg), key enforcers of immune homeostasis, contribute to COVID-19 pathology. Cytometric and transcriptomic profiling revealed a distinct Treg phenotype in severe COVID-19 patients, with an increase in both Treg proportions and intracellular levels of the lineage-defining transcription factor FoxP3, which correlated with poor outcomes. Accordingly, these Tregs over-expressed a range of suppressive effectors, but also pro-inflammatory molecules like IL32. Most strikingly, they acquired similarity to tumor-infiltrating Tregs, known to suppress local anti-tumor responses. These traits were most marked in acute patients with severe disease, but persisted somewhat in convalescent patients. These results suggest that Tregs may play nefarious roles in COVID-19, via suppressing anti-viral T cell responses during the severe phase of the disease, and/or via a direct pro-inflammatory role.
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Dinesh RK, Barnhill B, Ilanges A, Wu L, Michelson DA, Senigl F, Alinikula J, Shabanowitz J, Hunt DF, Schatz DG. Transcription factor binding at Ig enhancers is linked to somatic hypermutation targeting. Eur J Immunol 2019; 50:380-395. [PMID: 31821534 DOI: 10.1002/eji.201948357] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/05/2019] [Accepted: 12/02/2019] [Indexed: 01/15/2023]
Abstract
Secondary diversification of the Ig repertoire occurs through somatic hypermutation (SHM), gene conversion (GCV), and class switch recombination (CSR)-three processes that are initiated by activation-induced cytidine deaminase (AID). AID targets Ig genes at orders of magnitude higher than the rest of the genome, but the basis for this specificity is poorly understood. We have previously demonstrated that enhancers and enhancer-like sequences from Ig genes are capable of stimulating SHM of neighboring genes in a capacity distinct from their roles in increasing transcription. Here, we use an in vitro proteomics approach to identify E-box, MEF2, Ets, and Ikaros transcription factor family members as potential binders of these enhancers. ChIP assays in the hypermutating Ramos B cell line confirmed that many of these factors bound the endogenous Igλ enhancer and/or the IgH intronic enhancer (Eμ) in vivo. Further investigation using SHM reporter assays identified binding sites for E2A and MEF2B in Eμ and demonstrated an association between loss of factor binding and decreases in the SHM stimulating activity of Eμ mutants. Our results provide novel insights into trans-acting factors that dictate SHM targeting and link their activity to specific DNA binding sites within Ig enhancers.
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Affiliation(s)
- Ravi K Dinesh
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Benjamin Barnhill
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Anoj Ilanges
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Lizhen Wu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Daniel A Michelson
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Filip Senigl
- Institute of Molecular Genetics, Czech Academy of Sciences, Videnska 1083, CZ-14220, Prague 4, Czech Republic
| | - Jukka Alinikula
- Institute of Biomedicine, University of Turku, Turku, Finland
| | | | - Donald F Hunt
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.,Department of Pathology, University of Virginia, Charlottesville, VA, USA
| | - David G Schatz
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
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