1
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Anderson G, Cosway EJ, James KD, Ohigashi I, Takahama Y. Generation and repair of thymic epithelial cells. J Exp Med 2024; 221:e20230894. [PMID: 38980292 PMCID: PMC11232892 DOI: 10.1084/jem.20230894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/20/2024] [Accepted: 06/10/2024] [Indexed: 07/10/2024] Open
Abstract
In the vertebrate immune system, thymus stromal microenvironments support the generation of αβT cells from immature thymocytes. Thymic epithelial cells are of particular importance, and the generation of cortical and medullary epithelial lineages from progenitor stages controls the initiation and maintenance of thymus function. Here, we discuss the developmental pathways that regulate thymic epithelial cell diversity during both the embryonic and postnatal periods. We also examine how thymus microenvironments respond to injury, with particular focus on mechanisms that ensure regeneration of thymic epithelial cells for the restoration of thymus function.
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Affiliation(s)
- Graham Anderson
- Institute for Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Emilie J. Cosway
- Institute for Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Kieran D. James
- Institute for Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Izumi Ohigashi
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, Tokushima, Japan
| | - Yousuke Takahama
- Thymus Biology Section, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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2
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Pardini E, Barachini S, Alì G, Infirri GS, Burzi IS, Montali M, Petrini I. Single-cell sequencing has revealed a more complex array of thymic epithelial cells. Immunol Lett 2024; 269:106904. [PMID: 39117004 DOI: 10.1016/j.imlet.2024.106904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/23/2024] [Accepted: 07/29/2024] [Indexed: 08/10/2024]
Abstract
Thymic epithelial cells participate in the maturation and selection of T lymphocytes. This review explores recent insights from single-cell sequencing regarding classifying thymic epithelial cells in both normal and neoplastic thymus. Cortical thymic epithelial cells facilitate thymocyte differentiation and contribute to positive selection. Medullary epithelial cells are distinguished by their expression of AIRE. Cells progress from a pre-AIRE state, containing precursors with cortical and medullary characteristics, termed junctional cells. Mature medullary epithelial cells exhibit promiscuous gene expression and after that downregulate AIRE mRNA. Post-AIRE cells can adopt a Hassall corpuscle-like phenotype or exhibit distinctive differentiation characteristics including tuft cells, ionocytes, neuroendocrine cells, and myoid cells.
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Affiliation(s)
- Eleonora Pardini
- Department of Translational Research and New Surgical and Medical Technologies, University of Pisa, Pisa, Italy
| | - Serena Barachini
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.
| | - Greta Alì
- Department of Surgical, Medical and Molecular Pathology and Critical Care Medicine, Pisa, Italy
| | - Gisella Sardo Infirri
- Department of Translational Research and New Surgical and Medical Technologies, University of Pisa, Pisa, Italy
| | - Irene Sofia Burzi
- Department of Translational Research and New Surgical and Medical Technologies, University of Pisa, Pisa, Italy
| | - Marina Montali
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Iacopo Petrini
- Department of Translational Research and New Surgical and Medical Technologies, University of Pisa, Pisa, Italy
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3
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Huoh YS, Zhang Q, Törner R, Baca SC, Arthanari H, Hur S. Mechanism for controlled assembly of transcriptional condensates by Aire. Nat Immunol 2024; 25:1580-1592. [PMID: 39169234 PMCID: PMC11362013 DOI: 10.1038/s41590-024-01922-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 07/10/2024] [Indexed: 08/23/2024]
Abstract
Transcriptional condensates play a crucial role in gene expression and regulation, yet their assembly mechanisms remain poorly understood. Here, we report a multi-layered mechanism for condensate assembly by autoimmune regulator (Aire), an essential transcriptional regulator that orchestrates gene expression reprogramming for central T cell tolerance. Aire condensates assemble on enhancers, stimulating local transcriptional activities and connecting disparate inter-chromosomal loci. This functional condensate formation hinges upon the coordination between three Aire domains: polymerization domain caspase activation recruitment domain (CARD), histone-binding domain (first plant homeodomain (PHD1)), and C-terminal tail (CTT). Specifically, CTT binds coactivators CBP/p300, recruiting Aire to CBP/p300-rich enhancers and promoting CARD-mediated condensate assembly. Conversely, PHD1 binds to the ubiquitous histone mark H3K4me0, keeping Aire dispersed throughout the genome until Aire nucleates on enhancers. Our findings showed that the balance between PHD1-mediated suppression and CTT-mediated stimulation of Aire polymerization is crucial to form transcriptionally active condensates at target sites, providing new insights into controlled polymerization of transcriptional regulators.
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Affiliation(s)
- Yu-San Huoh
- Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Qianxia Zhang
- Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ricarda Törner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sylvan C Baca
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sun Hur
- Howard Hughes Medical Institute and Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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4
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Goldfarb Y, Abramson J. Z-DNA marks the spot for AIRE. Cell Res 2024; 34:537-538. [PMID: 38684778 PMCID: PMC11291692 DOI: 10.1038/s41422-024-00964-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024] Open
Affiliation(s)
- Yael Goldfarb
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Jakub Abramson
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
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5
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Groegler J, Callebaut A, James EA, Delong T. The insulin secretory granule is a hotspot for autoantigen formation in type 1 diabetes. Diabetologia 2024; 67:1507-1516. [PMID: 38811417 DOI: 10.1007/s00125-024-06164-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/11/2024] [Indexed: 05/31/2024]
Abstract
In type 1 diabetes, the insulin-producing beta cells of the pancreas are destroyed through the activity of autoreactive T cells. In addition to strong and well-documented HLA class II risk haplotypes, type 1 diabetes is associated with noncoding polymorphisms within the insulin gene locus. Furthermore, autoantibody prevalence data and murine studies implicate insulin as a crucial autoantigen for the disease. Studies identify secretory granules, where proinsulin is processed into mature insulin, stored and released in response to glucose stimulation, as a source of antigenic epitopes and neoepitopes. In this review, we integrate established concepts, including the role that susceptible HLA and thymic selection of the T cell repertoire play in setting the stage for autoimmunity, with emerging insights about beta cell and insulin secretory granule biology. In particular, the acidic, peptide-rich environment of secretory granules combined with its array of enzymes generates a distinct proteome that is unique to functional beta cells. These factors converge to generate non-templated peptide sequences that are recognised by autoreactive T cells. Although unanswered questions remain, formation and presentation of these epitopes and the resulting immune responses appear to be key aspects of disease initiation. In addition, these pathways may represent important opportunities for therapeutic intervention.
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Affiliation(s)
- Jason Groegler
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Aïsha Callebaut
- Center for Translational Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Eddie A James
- Center for Translational Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Thomas Delong
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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Chiu H, Weinstein KN, Spath S, Hu A, Varela S, Obata-Ninomiya K, Ziegler SF. SKI Regulates Medullary Thymic Epithelial Cell Differentiation to Control Peripheral T Cell Responses in Mice. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:52-62. [PMID: 38767415 PMCID: PMC11182718 DOI: 10.4049/jimmunol.2300262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 04/15/2024] [Indexed: 05/22/2024]
Abstract
The thymus is an important site for the establishment of an appropriate immune response through positive and negative selection of developing T cells. During selection, developing T cells interact with cortical and medullary thymic epithelial cells (TECs), termed cTECs and mTECs, respectively. Using a Foxn1Cre+/-SKIfl/fl mouse model, we found that TEC-specific deletion of SKI reduced the mTEC compartment in the thymus and that tissue-restricted Ag expression in mTECs was altered. This decrease in the medullary area led to a decrease in CD4 thymocyte cellularity; however, mature CD4 cellularity in the spleen remained normal. Interestingly, naive CD4 T cells purified from SKI-deleted mice showed a defect in proliferation in vitro after global TCR stimulation, and these mice were significantly protected from developing experimental autoimmune encephalomyelitis compared with the control mice. Overall, our findings suggest that SKI signaling in the thymus regulates mTEC differentiation and function as well as downstream peripheral T cell responses and provide evidence for targeting SKI in T cell-driven autoimmune diseases such as multiple sclerosis.
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Kologrivova IV, Naryzhnaya NV, Suslova TE. Thymus in Cardiometabolic Impairments and Atherosclerosis: Not a Silent Player? Biomedicines 2024; 12:1408. [PMID: 39061983 PMCID: PMC11273826 DOI: 10.3390/biomedicines12071408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/11/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
The thymus represents a primary organ of the immune system, harboring the generation and maturation of T lymphocytes. Starting from childhood, the thymus undergoes involution, being replaced with adipose tissue, and by an advanced age nearly all the thymus parenchyma is represented by adipocytes. This decline of thymic function is associated with compromised maturation and selection of T lymphocytes, which may directly impact the development of inflammation and induce various autoinflammatory disorders, including atherosclerosis. For a long time, thymus health in adults has been ignored. The process of adipogenesis in thymus and impact of thymic fat on cardiometabolism remains a mysterious process, with many issues being still unresolved. Meanwhile, thymus functional activity has a potential to be regulated, since islets of thymopoeisis remain in adults even at an advanced age. The present review describes the intricate process of thymic adipose involution, focusing on the issues of the thymus' role in the development of atherosclerosis and metabolic health, tightly interconnected with the state of vessels. We also review the recent information on the key molecular pathways and biologically active substances that may be targeted to manipulate both thymic function and atherosclerosis.
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Affiliation(s)
- Irina V. Kologrivova
- Cardiology Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 111A Kievskaya, Tomsk 634012, Russia; (N.V.N.); (T.E.S.)
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Gootjes C, Zwaginga JJ, Roep BO, Nikolic T. Defining Human Regulatory T Cells beyond FOXP3: The Need to Combine Phenotype with Function. Cells 2024; 13:941. [PMID: 38891073 PMCID: PMC11172350 DOI: 10.3390/cells13110941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/18/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Regulatory T cells (Tregs) are essential to maintain immune homeostasis by promoting self-tolerance. Reduced Treg numbers or functionality can lead to a loss of tolerance, increasing the risk of developing autoimmune diseases. An overwhelming variety of human Tregs has been described, based on either specific phenotype, tissue compartment, or pathological condition, yet the bulk of the literature only addresses CD25-positive and CD127-negative cells, coined by naturally occurring Tregs (nTregs), most of which express the transcription factor Forkhead box protein 3 (FOXP3). While the discovery of FOXP3 was seminal to understanding the origin and biology of nTregs, there is evidence in humans that not all T cells expressing FOXP3 are regulatory, and that not all Tregs express FOXP3. Namely, the activation of human T cells induces the transient expression of FOXP3, irrespective of whether they are regulatory or inflammatory effectors, while some induced T cells that may be broadly defined as Tregs (e.g., Tr1 cells) typically lack demethylation and do not express FOXP3. Furthermore, it is unknown whether and how many nTregs exist without FOXP3 expression. Several other candidate regulatory molecules, such as GITR, Lag-3, GARP, GPA33, Helios, and Neuropilin, have been identified but subsequently discarded as Treg-specific markers. Multiparametric analyses have uncovered a plethora of Treg phenotypes, and neither single markers nor combinations thereof can define all and only Tregs. To date, only the functional capacity to inhibit immune responses defines a Treg and distinguishes Tregs from inflammatory T cells (Teffs) in humans. This review revisits current knowledge of the Treg universe with respect to their heterogeneity in phenotype and function. We propose that it is unavoidable to characterize human Tregs by their phenotype in combination with their function, since phenotype alone does not unambiguously define Tregs. There is an unmet need to align the expression of specific markers or combinations thereof with a particular suppressive function to coin functional Treg entities and categorize Treg diversity.
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Affiliation(s)
- Chelsea Gootjes
- Laboratory of Immunomodulation and Regenerative Cell Therapy, Department of Internal Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (J.J.Z.); (T.N.)
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Ribeiro C, Ferreirinha P, Landry JJM, Macedo F, Sousa LG, Pinto R, Benes V, Alves NL. Foxo3 regulates cortical and medullary thymic epithelial cell homeostasis with implications in T cell development. Cell Death Dis 2024; 15:352. [PMID: 38773063 PMCID: PMC11109193 DOI: 10.1038/s41419-024-06728-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/23/2024]
Abstract
Within the thymus, thymic epithelial cells (TECs) create dedicated microenvironments for T cell development and selection. Considering that TECs are sensitive to distinct pathophysiological conditions, uncovering the molecular elements that coordinate their thymopoietic role has important fundamental and clinical implications. Particularly, medullary thymic epithelial cells (mTECs) play a crucial role in central tolerance. Our previous studies, along with others, suggest that mTECs depend on molecular factors linked to genome-protecting pathways, but the precise mechanisms underlying their function remain unknown. These observations led us to examine the role of Foxo3, as it is expressed in TECs and involved in DNA damage response. Our findings show that mice with TEC-specific deletion of Foxo3 (Foxo3cKO) displayed a disrupted mTEC compartment, with a more profound impact on the numbers of CCL21+ and thymic tuft mTEClo subsets. At the molecular level, Foxo3 controls distinct functional modules in the transcriptome of cTECs and mTECs under normal conditions, which includes the regulation of ribosomal biogenesis and DNA damage response, respectively. These changes in the TEC compartment resulted in a reduced total thymocyte cellularity and specific changes in regulatory T cell and iNKT cell development in the Foxo3cKO thymus. Lastly, the thymic defects observed in adulthood correlated with mild signs of altered peripheral immunotolerance in aged Foxo3cKO mice. Moreover, the deficiency in Foxo3 moderately aggravated the autoimmune predisposition observed in Aire-deficient mice. Our findings highlight the importance of Foxo3 in preserving the homeostasis of TECs and in supporting their role in T cell development and tolerance.
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Affiliation(s)
- Camila Ribeiro
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Pedro Ferreirinha
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Jonathan J M Landry
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Fátima Macedo
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- Departamento de Ciências Médicas, Universidade de Aveiro, Aveiro, Portugal
| | - Laura G Sousa
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Rute Pinto
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Nuno L Alves
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
- IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.
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Smith JA, Yuen BTK, Purtha W, Balolong JM, Phipps JD, Crawford F, Bluestone JA, Kappler JW, Anderson MS. Aire mediates tolerance to insulin through thymic trimming of high-affinity T cell clones. Proc Natl Acad Sci U S A 2024; 121:e2320268121. [PMID: 38709934 PMCID: PMC11098115 DOI: 10.1073/pnas.2320268121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/16/2024] [Indexed: 05/08/2024] Open
Abstract
Insulin is a central autoantigen in the pathogenesis of T1D, and thymic epithelial cell expression of insulin under the control of the Autoimmune Regulator (Aire) is thought to be a key component of maintaining tolerance to insulin. In spite of this general working model, direct detection of this thymic selection on insulin-specific T cells has been somewhat elusive. Here, we used a combination of highly sensitive T cell receptor transgenic models for detecting thymic selection and sorting and sequencing of Insulin-specific CD4+ T cells from Aire-deficient mice as a strategy to further define their selection. This analysis revealed a number of unique t cell receptor (TCR) clones in Aire-deficient hosts with high affinity for insulin/major histocompatibility complex (MHC) ligands. We then modeled the thymic selection of one of these clones in Aire-deficient versus wild-type hosts and found that this model clone could escape thymic negative selection in the absence of thymic Aire. Together, these results suggest that thymic expression of insulin plays a key role in trimming and removing high-affinity insulin-specific T cells from the repertoire to help promote tolerance.
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Affiliation(s)
- Jennifer A. Smith
- Diabetes Center, University of California San Francisco, San Francisco, CA94143
| | - Benjamin T. K. Yuen
- Diabetes Center, University of California San Francisco, San Francisco, CA94143
| | - Whitney Purtha
- Diabetes Center, University of California San Francisco, San Francisco, CA94143
| | - Jared M. Balolong
- Diabetes Center, University of California San Francisco, San Francisco, CA94143
| | - Jonah D. Phipps
- Diabetes Center, University of California San Francisco, San Francisco, CA94143
| | - Frances Crawford
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO80206
| | - Jeffrey A. Bluestone
- Sean N. Parker Autoimmune Research Laboratory, Diabetes Center, University of California, San Francisco, CA94143
| | - John W. Kappler
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO80206
- Barbara Davis Center for Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO80045
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO80045
| | - Mark S. Anderson
- Diabetes Center, University of California San Francisco, San Francisco, CA94143
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Ushio A, Matsuda-Lennikov M, Kalle-Youngoue F, Shimizu A, Abdelmaksoud A, Kelly MC, Ishimaru N, Takahama Y. Functionally diverse thymic medullary epithelial cells interplay to direct central tolerance. Cell Rep 2024; 43:114072. [PMID: 38581680 PMCID: PMC11079940 DOI: 10.1016/j.celrep.2024.114072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/24/2024] [Accepted: 03/21/2024] [Indexed: 04/08/2024] Open
Abstract
Medullary thymic epithelial cells (mTECs) are essential for the establishment of self-tolerance in T cells. Promiscuous gene expression by a subpopulation of mTECs regulated by the nuclear protein Aire contributes to the display of self-genomic products to newly generated T cells. Recent reports have highlighted additional self-antigen-displaying mTEC subpopulations, namely Fezf2-expressing mTECs and a mosaic of self-mimetic mTECs including thymic tuft cells. In addition, a functionally different subset of mTECs produces chemokine CCL21, which attracts developing thymocytes to the medullary region. Here, we report that CCL21+ mTECs and Aire+ mTECs non-redundantly cooperate to direct self-tolerance to prevent autoimmune pathology by optimizing the deletion of self-reactive T cells and the generation of regulatory T cells. We also detect cooperation for self-tolerance between Aire and Fezf2, the latter of which unexpectedly regulates thymic tuft cells. Our results indicate an indispensable interplay among functionally diverse mTECs for the establishment of central self-tolerance.
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Affiliation(s)
- Aya Ushio
- Thymus Biology Section, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Department of Oral Molecular Pathology, Graduate School of Biomedical Sciences, Tokushima University, Kuramoto, Tokushima 770-8504, Japan
| | - Mami Matsuda-Lennikov
- Thymus Biology Section, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Felix Kalle-Youngoue
- Thymus Biology Section, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21701, USA
| | - Akihide Shimizu
- Thymus Biology Section, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Abdalla Abdelmaksoud
- Center for Cancer Research Collaborative Bioinformatics Resource, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael C Kelly
- Single Cell Analysis Facility, Cancer Research Technology Program, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Naozumi Ishimaru
- Department of Oral Molecular Pathology, Graduate School of Biomedical Sciences, Tokushima University, Kuramoto, Tokushima 770-8504, Japan
| | - Yousuke Takahama
- Thymus Biology Section, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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12
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Larouche JD, Laumont CM, Trofimov A, Vincent K, Hesnard L, Brochu S, Côté C, Humeau JF, Bonneil É, Lanoix J, Durette C, Gendron P, Laverdure JP, Richie ER, Lemieux S, Thibault P, Perreault C. Transposable elements regulate thymus development and function. eLife 2024; 12:RP91037. [PMID: 38635416 PMCID: PMC11026094 DOI: 10.7554/elife.91037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
Transposable elements (TEs) are repetitive sequences representing ~45% of the human and mouse genomes and are highly expressed by medullary thymic epithelial cells (mTECs). In this study, we investigated the role of TEs on T-cell development in the thymus. We performed multiomic analyses of TEs in human and mouse thymic cells to elucidate their role in T-cell development. We report that TE expression in the human thymus is high and shows extensive age- and cell lineage-related variations. TE expression correlates with multiple transcription factors in all cell types of the human thymus. Two cell types express particularly broad TE repertoires: mTECs and plasmacytoid dendritic cells (pDCs). In mTECs, transcriptomic data suggest that TEs interact with transcription factors essential for mTEC development and function (e.g., PAX1 and REL), and immunopeptidomic data showed that TEs generate MHC-I-associated peptides implicated in thymocyte education. Notably, AIRE, FEZF2, and CHD4 regulate small yet non-redundant sets of TEs in murine mTECs. Human thymic pDCs homogenously express large numbers of TEs that likely form dsRNA, which can activate innate immune receptors, potentially explaining why thymic pDCs constitutively secrete IFN ɑ/β. This study highlights the diversity of interactions between TEs and the adaptive immune system. TEs are genetic parasites, and the two thymic cell types most affected by TEs (mTEcs and pDCs) are essential to establishing central T-cell tolerance. Therefore, we propose that orchestrating TE expression in thymic cells is critical to prevent autoimmunity in vertebrates.
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Affiliation(s)
- Jean-David Larouche
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Medicine, Université de MontréalMontréalCanada
| | - Céline M Laumont
- Deeley Research Centre, BC CancerVictoriaCanada
- Department of Medical Genetics, University of British ColumbiaVancouverCanada
| | - Assya Trofimov
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Computer Science and Operations Research, Université de MontréalMontréalCanada
- Fred Hutchinson Cancer CenterSeattleUnited States
- Department of Physics, University of WashingtonSeattleUnited States
| | - Krystel Vincent
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Leslie Hesnard
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Sylvie Brochu
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Caroline Côté
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Juliette F Humeau
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Éric Bonneil
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Joel Lanoix
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Chantal Durette
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | - Patrick Gendron
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
| | | | - Ellen R Richie
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas M.D. Anderson Cancer CenterHoustonUnited States
| | - Sébastien Lemieux
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Biochemistry and Molecular Medicine, Université de MontréalMontrealCanada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Chemistry, Université de MontréalMontréalCanada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de MontréalMontrealCanada
- Department of Medicine, Université de MontréalMontréalCanada
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13
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Perrino M, Voulaz E, Balin S, Cazzato G, Fontana E, Franzese S, Defendi M, De Vincenzo F, Cordua N, Tamma R, Borea F, Aliprandi M, Airoldi M, Cecchi LG, Fazio R, Alloisio M, Marulli G, Santoro A, Di Tommaso L, Ingravallo G, Russo L, Da Rin G, Villa A, Della Bella S, Zucali PA, Mavilio D. Autoimmunity in thymic epithelial tumors: a not yet clarified pathologic paradigm associated with several unmet clinical needs. Front Immunol 2024; 15:1288045. [PMID: 38629065 PMCID: PMC11018877 DOI: 10.3389/fimmu.2024.1288045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 01/29/2024] [Indexed: 04/19/2024] Open
Abstract
Thymic epithelial tumors (TETs) are rare mediastinal cancers originating from the thymus, classified in two main histotypes: thymoma and thymic carcinoma (TC). TETs affect a primary lymphoid organ playing a critical role in keeping T-cell homeostasis and ensuring an adequate immunological tolerance against "self". In particular, thymomas and not TC are frequently associated with autoimmune diseases (ADs), with Myasthenia Gravis being the most common AD present in 30% of patients with thymoma. This comorbidity, in addition to negatively affecting the quality and duration of patients' life, reduces the spectrum of the available therapeutic options. Indeed, the presence of autoimmunity represents an exclusion criteria for the administration of the newest immunotherapeutic treatments with checkpoint inhibitors. The pathophysiological correlation between TETs and autoimmunity remains a mystery. Several studies have demonstrated the presence of a residual and active thymopoiesis in adult patients affected by thymomas, especially in mixed and lymphocytic-rich thymomas, currently known as type AB and B thymomas. The aim of this review is to provide the state of art in regard to the histological features of the different TET histotype, to the role of the different immune cells infiltrating tumor microenvironments and their impact in the break of central immunologic thymic tolerance in thymomas. We discuss here both cellular and molecular immunologic mechanisms inducing the onset of autoimmunity in TETs, limiting the portfolio of therapeutic strategies against TETs and greatly impacting the prognosis of associated autoimmune diseases.
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Affiliation(s)
- Matteo Perrino
- Department of Medical Oncology and Hematology, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Emanuele Voulaz
- Division of Thoracic Surgery, IRCCS Humanitas Research Hospital, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Simone Balin
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy
| | - Gerardo Cazzato
- Section of Pathology, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, Bari, Italy
| | - Elena Fontana
- Istituto di Ricerca Genetica e Biomedica (IRGB), National Research Council (CNR), Milan, Italy
- Human Genome and Biomedical Technologies Unit, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Sara Franzese
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy
- Unit of Clinical and Experimental Immunology, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Martina Defendi
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy
- Unit of Clinical and Experimental Immunology, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Fabio De Vincenzo
- Department of Medical Oncology and Hematology, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Nadia Cordua
- Department of Medical Oncology and Hematology, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Roberto Tamma
- Section of Human Anatomy and Histology, Department of Translational Biomedicine and Neurosciences (DiBraiN), University of Bari “Aldo Moro”, Bari, Italy
| | - Federica Borea
- Department of Medical Oncology and Hematology, IRCCS Humanitas Research Hospital, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Marta Aliprandi
- Department of Medical Oncology and Hematology, IRCCS Humanitas Research Hospital, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Marco Airoldi
- Department of Medical Oncology and Hematology, IRCCS Humanitas Research Hospital, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Luigi Giovanni Cecchi
- Department of Medical Oncology and Hematology, IRCCS Humanitas Research Hospital, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Roberta Fazio
- Department of Medical Oncology and Hematology, IRCCS Humanitas Research Hospital, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Marco Alloisio
- Division of Thoracic Surgery, IRCCS Humanitas Research Hospital, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Giuseppe Marulli
- Division of Thoracic Surgery, IRCCS Humanitas Research Hospital, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Armando Santoro
- Department of Medical Oncology and Hematology, IRCCS Humanitas Research Hospital, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Luca Di Tommaso
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- Department of Pathology, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Giuseppe Ingravallo
- Section of Pathology, Department of Precision and Regenerative Medicine and Ionian Area (DiMePRe-J), University of Bari “Aldo Moro”, Bari, Italy
| | - Laura Russo
- Clinical Laboratory, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Giorgio Da Rin
- Clinical Laboratory, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Anna Villa
- Istituto di Ricerca Genetica e Biomedica (IRGB), National Research Council (CNR), Milan, Italy
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Della Bella
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy
- Unit of Clinical and Experimental Immunology, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Paolo Andrea Zucali
- Department of Medical Oncology and Hematology, IRCCS Humanitas Research Hospital, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Domenico Mavilio
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy
- Unit of Clinical and Experimental Immunology, IRCCS Humanitas Research Hospital, Milan, Italy
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14
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Fang Y, Bansal K, Mostafavi S, Benoist C, Mathis D. AIRE relies on Z-DNA to flag gene targets for thymic T cell tolerization. Nature 2024; 628:400-407. [PMID: 38480882 PMCID: PMC11091860 DOI: 10.1038/s41586-024-07169-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 02/06/2024] [Indexed: 03/18/2024]
Abstract
AIRE is an unconventional transcription factor that enhances the expression of thousands of genes in medullary thymic epithelial cells and promotes clonal deletion or phenotypic diversion of self-reactive T cells1-4. The biological logic of AIRE's target specificity remains largely unclear as, in contrast to many transcription factors, it does not bind to a particular DNA sequence motif. Here we implemented two orthogonal approaches to investigate AIRE's cis-regulatory mechanisms: construction of a convolutional neural network and leveraging natural genetic variation through analysis of F1 hybrid mice5. Both approaches nominated Z-DNA and NFE2-MAF as putative positive influences on AIRE's target choices. Genome-wide mapping studies revealed that Z-DNA-forming and NFE2L2-binding motifs were positively associated with the inherent ability of a gene's promoter to generate DNA double-stranded breaks, and promoters showing strong double-stranded break generation were more likely to enter a poised state with accessible chromatin and already-assembled transcriptional machinery. Consequently, AIRE preferentially targets genes with poised promoters. We propose a model in which Z-DNA anchors the AIRE-mediated transcriptional program by enhancing double-stranded break generation and promoter poising. Beyond resolving a long-standing mechanistic conundrum, these findings suggest routes for manipulating T cell tolerance.
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Affiliation(s)
- Yuan Fang
- Department of Immunology, Harvard Medical School, Boston, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Kushagra Bansal
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Sara Mostafavi
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
- Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | | | - Diane Mathis
- Department of Immunology, Harvard Medical School, Boston, MA, USA.
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15
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James KD, Cosway EJ, Parnell SM, White AJ, Jenkinson WE, Anderson G. Assembling the thymus medulla: Development and function of epithelial cell heterogeneity. Bioessays 2024; 46:e2300165. [PMID: 38161233 DOI: 10.1002/bies.202300165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024]
Abstract
The thymus is a unique primary lymphoid organ that supports the production of self-tolerant T-cells essential for adaptive immunity. Intrathymic microenvironments are microanatomically compartmentalised, forming defined cortical, and medullary regions each differentially supporting critical aspects of thymus-dependent T-cell maturation. Importantly, the specific functional properties of thymic cortical and medullary compartments are defined by highly specialised thymic epithelial cells (TEC). For example, in the medulla heterogenous medullary TEC (mTEC) contribute to the enforcement of central tolerance by supporting deletion of autoreactive T-cell clones, thereby counterbalancing the potential for random T-cell receptor generation to contribute to autoimmune disease. Recent advances have further shed light on the pathways and mechanisms that control heterogeneous mTEC development and how differential mTEC functionality contributes to control self-tolerant T-cell development. Here we discuss recent findings in relation to mTEC development and highlight examples of how mTEC diversity contribute to thymus medulla function.
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Affiliation(s)
- Kieran D James
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Emilie J Cosway
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Sonia M Parnell
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Andrea J White
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - William E Jenkinson
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Graham Anderson
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
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16
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Lammers S, Barrera V, Brennecke P, Miller C, Yoon J, Balolong J, Anderson MS, Ho Sui S, Steinmetz LM, von Andrian UH, Rattay K. Ehf and Fezf2 regulate late medullary thymic epithelial cell and thymic tuft cell development. Front Immunol 2024; 14:1277365. [PMID: 38420512 PMCID: PMC10901246 DOI: 10.3389/fimmu.2023.1277365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/29/2023] [Indexed: 03/02/2024] Open
Abstract
Thymic epithelial cells are indispensable for T cell maturation and selection and the induction of central immune tolerance. The self-peptide repertoire expressed by medullary thymic epithelial cells is in part regulated by the transcriptional regulator Aire (Autoimmune regulator) and the transcription factor Fezf2. Due to the high complexity of mTEC maturation stages (i.e., post-Aire, Krt10+ mTECs, and Dclk1+ Tuft mTECs) and the heterogeneity in their gene expression profiles (i.e., mosaic expression patterns), it has been challenging to identify the additional factors complementing the transcriptional regulation. We aimed to identify the transcriptional regulators involved in the regulation of mTEC development and self-peptide expression in an unbiased and genome-wide manner. We used ATAC footprinting analysis as an indirect approach to identify transcription factors involved in the gene expression regulation in mTECs, which we validated by ChIP sequencing. This study identifies Fezf2 as a regulator of the recently described thymic Tuft cells (i.e., Tuft mTECs). Furthermore, we identify that transcriptional regulators of the ELF, ESE, ERF, and PEA3 subfamily of the ETS transcription factor family and members of the Krüppel-like family of transcription factors play a role in the transcriptional regulation of genes involved in late mTEC development and promiscuous gene expression.
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Affiliation(s)
- Sören Lammers
- Institute for Theoretical Physics, Heidelberg University, Heidelberg, Germany
| | - Victor Barrera
- Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Philip Brennecke
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, United States
- Stanford Genome Technology Center, Stanford University, Stanford, CA, United States
| | - Corey Miller
- Diabetes Center, University of California, San Francisco (UCSF), San Francisco, CA, United States
| | - Joon Yoon
- Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Jared Balolong
- Diabetes Center, University of California, San Francisco (UCSF), San Francisco, CA, United States
| | - Mark S. Anderson
- Diabetes Center, University of California, San Francisco (UCSF), San Francisco, CA, United States
| | - Shannan Ho Sui
- Bioinformatics Core, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Lars M. Steinmetz
- Department of Genetics, Stanford University, School of Medicine, Stanford, CA, United States
- Stanford Genome Technology Center, Stanford University, Stanford, CA, United States
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Ulrich H. von Andrian
- Department of Immunology & HMS Center for Immune Imaging, Harvard Medical School, Boston, MA, United States
- The Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, United States
| | - Kristin Rattay
- Department of Immunology & HMS Center for Immune Imaging, Harvard Medical School, Boston, MA, United States
- Pharmacological Institute, Biochemical Pharmacological Center, University of Marburg, Marburg, Germany
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17
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Miccoli A, Pianese V, Bidoli C, Fausto AM, Scapigliati G, Picchietti S. Transcriptome profiling of microdissected cortex and medulla unravels functional regionalization in the European sea bass Dicentrarchus labrax thymus. FISH & SHELLFISH IMMUNOLOGY 2024; 145:109319. [PMID: 38145782 DOI: 10.1016/j.fsi.2023.109319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 12/27/2023]
Abstract
The thymus is a sophisticated primary lymphoid organ in jawed vertebrates, but knowledge on teleost thymus remains scarce. In this study, for the first time in the European sea bass, laser capture microdissection was leveraged to collect two thymic regions based on histological features, namely the cortex and the medulla. The two regions were then processed by RNAseq and in-depth functional transcriptome analyses with the aim of revealing differential gene expression patterns and gene sets enrichments, ultimately unraveling unique microenvironments imperative for the development of functional T cells. The sea bass cortex emerged as a hub of T cell commitment, somatic recombination, chromatin remodeling, cell cycle regulation, and presentation of self antigens from autophagy-, proteasome- or proteases-processed proteins. The cortex therefore accommodated extensive thymocyte proliferation and differentiation up to the checkpoint of positive selection. The medulla instead appeared as the center stage in autoimmune regulation by negative selection and deletion of autoreactive T cells, central tolerance mechanisms and extracellular matrix organization. Region-specific canonical markers of T and non-T lineage cells as well as signals for migration to/from, and trafficking within, the thymus were identified, shedding light on the highly coordinated and exquisitely complex bi-directional interactions among thymocytes and stromal components. Markers ascribable to thymic nurse cells and poorly characterized post-aire mTEC populations were found in the cortex and medulla, respectively. An in-depth data mining also exposed previously un-annotated genomic resources with differential signatures. Overall, our findings contribute to a broader understanding of the relationship between regional organization and function in the European sea bass thymus, and provide essential insights into the molecular mechanisms underlying T-cell mediated adaptive immune responses in teleosts.
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Affiliation(s)
- A Miccoli
- National Research Council, Institute for Marine Biological Resources and Biotechnology (IRBIM), 60125, Ancona, Italy
| | - V Pianese
- Dept. for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, Largo Dell'Università Snc, 01100, Viterbo, Italy
| | - C Bidoli
- Dept. of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - A M Fausto
- Dept. for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, Largo Dell'Università Snc, 01100, Viterbo, Italy
| | - G Scapigliati
- Dept. for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, Largo Dell'Università Snc, 01100, Viterbo, Italy
| | - S Picchietti
- Dept. for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, Largo Dell'Università Snc, 01100, Viterbo, Italy.
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18
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Nevo S, Frenkel N, Kadouri N, Gome T, Rosenthal N, Givony T, Avin A, Peligero Cruz C, Kedmi M, Lindzen M, Ben Dor S, Damari G, Porat Z, Haffner-Krausz R, Keren-Shaul H, Yarden Y, Munitz A, Leshkowitz D, Goldfarb Y, Abramson J. Tuft cells and fibroblasts promote thymus regeneration through ILC2-mediated type 2 immune response. Sci Immunol 2024; 9:eabq6930. [PMID: 38215193 DOI: 10.1126/sciimmunol.abq6930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 11/15/2023] [Indexed: 01/14/2024]
Abstract
The thymus is a primary lymphoid organ that is essential for the establishment of adaptive immunity through generation of immunocompetent T cells. In response to various stress signals, the thymus undergoes acute but reversible involution. However, the mechanisms governing its recovery are incompletely understood. Here, we used a dexamethasone-induced acute thymic involution mouse model to investigate how thymic hematopoietic cells (excluding T cells) contribute to thymic regeneration. scRNA-seq analysis revealed marked transcriptional and cellular changes in various thymic populations and highlighted thymus-resident innate lymphoid cells type 2 (ILC2) as a key cell type involved in the response to damage. We identified that ILC2 are activated by the alarmins IL-25 and IL-33 produced in response to tissue damage by thymic tuft cells and fibroblasts, respectively. Moreover, using mouse models deficient in either tuft cells and/or IL-33, we found that these alarmins are required for effective thymus regeneration after dexamethasone-induced damage. We also demonstrate that upon their damage-dependent activation, thymic ILC2 produce several effector molecules linked to tissue regeneration, such as amphiregulin and IL-13, which in turn promote thymic epithelial cell differentiation. Collectively, our study elucidates a previously undescribed role for thymic tuft cells and fibroblasts in thymus regeneration through activation of the type 2 immune response.
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Affiliation(s)
- Shir Nevo
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Noga Frenkel
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Noam Kadouri
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tom Gome
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Rosenthal
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Givony
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ayelet Avin
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Cristina Peligero Cruz
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Merav Kedmi
- Genomics Unit, Life Science Core Facility, Weizmann Institute of Science, Rehovot, Israel
| | - Moshit Lindzen
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shifra Ben Dor
- Bioinformatics Unit, Life Science Core Facility, Weizmann Institute of Science, Rehovot, Israel
| | - Golda Damari
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Ziv Porat
- Flow Cytometry Unit, Life Science Core Facility, Weizmann Institute of Science, Rehovot, Israel
| | | | - Hadas Keren-Shaul
- Genomics Unit, Life Science Core Facility, Weizmann Institute of Science, Rehovot, Israel
| | - Yosef Yarden
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ariel Munitz
- Department of Microbiology and Clinical Immunology, Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Dena Leshkowitz
- Bioinformatics Unit, Life Science Core Facility, Weizmann Institute of Science, Rehovot, Israel
| | - Yael Goldfarb
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jakub Abramson
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
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19
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Kina E, Laverdure JP, Durette C, Lanoix J, Courcelles M, Zhao Q, Apavaloaei A, Larouche JD, Hardy MP, Vincent K, Gendron P, Hesnard L, Thériault C, Ruiz Cuevas MV, Ehx G, Thibault P, Perreault C. Breast cancer immunopeptidomes contain numerous shared tumor antigens. J Clin Invest 2024; 134:e166740. [PMID: 37906288 PMCID: PMC10760959 DOI: 10.1172/jci166740] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 10/23/2023] [Indexed: 11/02/2023] Open
Abstract
Hormone receptor-positive breast cancer (HR+) is immunologically cold and has not benefited from advances in immunotherapy. In contrast, subsets of triple-negative breast cancer (TNBC) display high leukocytic infiltration and respond to checkpoint blockade. CD8+ T cells, the main effectors of anticancer responses, recognize MHC I-associated peptides (MAPs). Our work aimed to characterize the repertoire of MAPs presented by HR+ and TNBC tumors. Using mass spectrometry, we identified 57,094 unique MAPs in 26 primary breast cancer samples. MAP source genes highly overlapped between both subtypes. We identified 25 tumor-specific antigens (TSAs) mainly deriving from aberrantly expressed regions. TSAs were most frequently identified in TNBC samples and were more shared among The Cancer Genome Atlas (TCGA) database TNBC than HR+ samples. In the TNBC cohort, the predicted number of TSAs positively correlated with leukocytic infiltration and overall survival, supporting their immunogenicity in vivo. We detected 49 tumor-associated antigens (TAAs), some of which derived from cancer-associated fibroblasts. Functional expansion of specific T cell assays confirmed the in vitro immunogenicity of several TSAs and TAAs. Our study identified attractive targets for cancer immunotherapy in both breast cancer subtypes. The higher prevalence of TSAs in TNBC tumors provides a rationale for their responsiveness to checkpoint blockade.
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Affiliation(s)
- Eralda Kina
- Institute for Research in Immunology and Cancer (IRIC), and
- Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | | | | | - Joël Lanoix
- Institute for Research in Immunology and Cancer (IRIC), and
| | | | - Qingchuan Zhao
- Institute for Research in Immunology and Cancer (IRIC), and
- Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Anca Apavaloaei
- Institute for Research in Immunology and Cancer (IRIC), and
- Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Jean-David Larouche
- Institute for Research in Immunology and Cancer (IRIC), and
- Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | | | | | | | - Leslie Hesnard
- Institute for Research in Immunology and Cancer (IRIC), and
| | | | - Maria Virginia Ruiz Cuevas
- Institute for Research in Immunology and Cancer (IRIC), and
- Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Grégory Ehx
- Laboratory of Hematology, GIGA-I3, University of Liege and CHU of Liège, Liege, Belgium
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer (IRIC), and
- Department of Chemistry, University of Montreal, Montreal, Quebec, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer (IRIC), and
- Department of Medicine, University of Montreal, Montreal, Quebec, Canada
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20
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Filipp D, Manning J, Petrusová J. Extrathymic AIRE-Expressing Cells: A Historical Perspective. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1444:33-49. [PMID: 38467971 DOI: 10.1007/978-981-99-9781-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Since its discovery, Aire has been the topic of numerous studies in its role as a transcriptional regulator in the thymus where it promotes the "promiscuous" expression of a large repertoire of tissue-restricted antigens (TRAs) that are normally expressed only in the immune periphery. This process occurs in specialized medullary thymic epithelial cells (mTECs) and mediates the elimination of self-reactive T cells or promotes their conversion to the Foxp3+ regulatory T cell lineage, both of which are required for the prevention of autoimmunity. In recent years, there has been increasing interest in the role of extrathymic Aire expression in peripheral organs. The focus has primarily been on the identification of the cellular source(s) and mechanism(s) by which extrathymic AIRE affects tolerance-related or other physiological processes. A cadre of OMICs tools including single cell RNA sequencing and novel transgenic models to trace Aire expression to perform lineage tracing experiments have shed light on a phenomenon that is more complex than previously thought. In this chapter, we provide a deeper analysis of how extrathymic Aire research has developed and progressed, how cellular sources were identified, and how the function of AIRE was determined. Current data suggests that extrathymic AIRE fulfills a function that differs from what has been observed in the thymus and strongly argues that its main purpose is to regulate transcriptional programs in a cell content-dependent manner. Surprisingly, there is data that also suggests a non-transcriptional role of extrathymic AIRE in the cytoplasm. We have arrived at a potential turning point that will take the field from the classical understanding of AIRE as a transcription factor in control of TRA expression to its role in immunological and non-immunological processes in the periphery.
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Affiliation(s)
- Dominik Filipp
- Laboratory of Immunobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.
| | - Jasper Manning
- Laboratory of Immunobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jana Petrusová
- Laboratory of Immunobiology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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21
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Peterson P. Novel Insights into the Autoimmunity from the Genetic Approach of the Human Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1444:3-18. [PMID: 38467969 DOI: 10.1007/978-981-99-9781-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Autoimmune-polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) is a monogenic inborn error of autoimmunity that is caused by damaging germline variants in the AIRE gene and clinically manifests with multiple autoimmune diseases in patients. Studies on the function of the AIRE gene, discovered in 1997, have contributed to fundamental aspects of human immunology as they have been important in understanding the basic mechanism of immune balance between self and non-self. This chapter looks back to the discovery of the AIRE gene, reviews its main properties, and discusses the key findings of its function in the thymus. However, more recent autoantibody profilings in APECED patients have highlighted a gap in our knowledge of the disease pathology and point to the need to revisit the current paradigm of AIRE function. The chapter reviews these new findings in APECED patients, which potentially trigger new thoughts on the mechanism of immune tolerance.
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Affiliation(s)
- Pärt Peterson
- Institute of Biomedical and Translational Medicine, University of Tartu, Tartu, Estonia.
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22
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Rackaityte E, Proekt I, Miller HS, Ramesh A, Brooks JF, Kung AF, Mandel-Brehm C, Yu D, Zamecnik CR, Bair R, Vazquez SE, Sunshine S, Abram CL, Lowell CA, Rizzuto G, Wilson MR, Zikherman J, Anderson MS, DeRisi JL. Validation of a murine proteome-wide phage display library for identification of autoantibody specificities. JCI Insight 2023; 8:e174976. [PMID: 37934865 PMCID: PMC10795829 DOI: 10.1172/jci.insight.174976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/25/2023] [Indexed: 11/09/2023] Open
Abstract
Autoimmunity is characterized by loss of tolerance to tissue-specific as well as systemic antigens, resulting in complex autoantibody landscapes. Here, we introduce and extensively validate the performance characteristics of a murine proteome-wide library for phage display immunoprecipitation and sequencing (PhIP-seq) in profiling mouse autoantibodies. This library was validated using 7 genetically distinct mouse lines across a spectrum of autoreactivity. Mice deficient in antibody production (Rag2-/- and μMT) were used to model nonspecific peptide enrichments, while cross-reactivity was evaluated using anti-ovalbumin B cell receptor-restricted OB1 mice as a proof of principle. The PhIP-seq approach was then utilized to interrogate 3 distinct autoimmune disease models. First, serum from Lyn-/- IgD+/- mice with lupus-like disease was used to identify nuclear and apoptotic bleb reactivities. Second, serum from nonobese diabetic (NOD) mice, a polygenic model of pancreas-specific autoimmunity, was enriched in peptides derived from both insulin and predicted pancreatic proteins. Lastly, Aire-/- mouse sera were used to identify numerous autoantigens, many of which were also observed in previous studies of humans with autoimmune polyendocrinopathy syndrome type 1 carrying recessive mutations in AIRE. These experiments support the use of murine proteome-wide PhIP-seq for antigenic profiling and autoantibody discovery, which may be employed to study a range of immune perturbations in mouse models of autoimmunity profiling.
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Affiliation(s)
| | | | - Haleigh S. Miller
- Department of Biochemistry and Biophysics
- Biological and Medical Informatics Program
| | - Akshaya Ramesh
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine
| | - Jeremy F. Brooks
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, and
| | - Andrew F. Kung
- Department of Biochemistry and Biophysics
- Biological and Medical Informatics Program
| | | | - David Yu
- Diabetes Center, School of Medicine
| | - Colin R. Zamecnik
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine
| | - Rebecca Bair
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine
| | - Sara E. Vazquez
- Department of Biochemistry and Biophysics
- Diabetes Center, School of Medicine
| | | | - Clare L. Abram
- Department of Laboratory Medicine, UCSF, San Francisco, California, USA
| | | | - Gabrielle Rizzuto
- Human Oncology & Pathogenesis Program and Department of Pathology & Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Michael R. Wilson
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine
| | - Julie Zikherman
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, and
| | | | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics
- Chan Zuckerberg Biohub, San Francisco, California, USA
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23
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Gruper Y, Wolff ASB, Glanz L, Spoutil F, Marthinussen MC, Osickova A, Herzig Y, Goldfarb Y, Aranaz-Novaliches G, Dobeš J, Kadouri N, Ben-Nun O, Binyamin A, Lavi B, Givony T, Khalaila R, Gome T, Wald T, Mrazkova B, Sochen C, Besnard M, Ben-Dor S, Feldmesser E, Orlova EM, Hegedűs C, Lampé I, Papp T, Felszeghy S, Sedlacek R, Davidovich E, Tal N, Shouval DS, Shamir R, Guillonneau C, Szondy Z, Lundin KEA, Osicka R, Prochazka J, Husebye ES, Abramson J. Autoimmune amelogenesis imperfecta in patients with APS-1 and coeliac disease. Nature 2023; 624:653-662. [PMID: 37993717 DOI: 10.1038/s41586-023-06776-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/23/2023] [Indexed: 11/24/2023]
Abstract
Ameloblasts are specialized epithelial cells in the jaw that have an indispensable role in tooth enamel formation-amelogenesis1. Amelogenesis depends on multiple ameloblast-derived proteins that function as a scaffold for hydroxyapatite crystals. The loss of function of ameloblast-derived proteins results in a group of rare congenital disorders called amelogenesis imperfecta2. Defects in enamel formation are also found in patients with autoimmune polyglandular syndrome type-1 (APS-1), caused by AIRE deficiency3,4, and in patients diagnosed with coeliac disease5-7. However, the underlying mechanisms remain unclear. Here we show that the vast majority of patients with APS-1 and coeliac disease develop autoantibodies (mostly of the IgA isotype) against ameloblast-specific proteins, the expression of which is induced by AIRE in the thymus. This in turn results in a breakdown of central tolerance, and subsequent generation of corresponding autoantibodies that interfere with enamel formation. However, in coeliac disease, the generation of such autoantibodies seems to be driven by a breakdown of peripheral tolerance to intestinal antigens that are also expressed in enamel tissue. Both conditions are examples of a previously unidentified type of IgA-dependent autoimmune disorder that we collectively name autoimmune amelogenesis imperfecta.
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Affiliation(s)
- Yael Gruper
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Anette S B Wolff
- Department of Clinical Science and K.G. Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway.
- Department of Medicine, Haukeland University Hospital, Bergen, Norway.
| | - Liad Glanz
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Frantisek Spoutil
- Czech Centre for Phenogenomics & Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences v.v.i 252 50, Vestec, Czech Republic
| | - Mihaela Cuida Marthinussen
- Department of Clinical Dentistry, Faculty of Medicine, University of Bergen, Bergen, Norway
- Oral Health Centre of Expertise in Western Norway/Vestland, Bergen, Norway
| | - Adriana Osickova
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Yonatan Herzig
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yael Goldfarb
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Goretti Aranaz-Novaliches
- Czech Centre for Phenogenomics & Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences v.v.i 252 50, Vestec, Czech Republic
| | - Jan Dobeš
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Noam Kadouri
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Osher Ben-Nun
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Amit Binyamin
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Bar Lavi
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Givony
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Razi Khalaila
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tom Gome
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tomáš Wald
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Blanka Mrazkova
- Czech Centre for Phenogenomics & Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences v.v.i 252 50, Vestec, Czech Republic
| | - Carmel Sochen
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Marine Besnard
- Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes, France
| | - Shifra Ben-Dor
- Bioinformatics Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ester Feldmesser
- Bioinformatics Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Elisaveta M Orlova
- Endocrinological Research Center, Institute of Pediatric Endocrinology, Moscow, Russian Federation
| | - Csaba Hegedűs
- Department of Biomaterials and Prosthetic Dentistry, Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
| | - István Lampé
- Department of Biomaterials and Prosthetic Dentistry, Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
| | - Tamás Papp
- Division of Dental Anatomy, Department of Basic Medical Sciences, Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
| | - Szabolcs Felszeghy
- Division of Dental Anatomy, Department of Basic Medical Sciences, Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
- Institute of Dentistry, University of Eastern Finland, Kuopio, Finland
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics & Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences v.v.i 252 50, Vestec, Czech Republic
| | - Esti Davidovich
- Department of Pediatric Dentistry, The Hebrew University-Hadassah School of Dental Medicine, Jerusalem, Israel
| | - Noa Tal
- The Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center of Israel, Petach Tikvah, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Dror S Shouval
- The Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center of Israel, Petach Tikvah, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Raanan Shamir
- The Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children's Medical Center of Israel, Petach Tikvah, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Carole Guillonneau
- Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, Nantes, France
| | - Zsuzsa Szondy
- Division of Dental Biochemistry, Department of Basic Medical Sciences, Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Knut E A Lundin
- K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
- Department of Gastroenterology, Oslo University Hospital, Oslo, Norway
| | - Radim Osicka
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Prochazka
- Czech Centre for Phenogenomics & Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences v.v.i 252 50, Vestec, Czech Republic
| | - Eystein S Husebye
- Department of Clinical Science and K.G. Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Jakub Abramson
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
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24
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Malin J, Martinez-Ruiz GU, Zhao Y, Shissler SC, Cowan JE, Ding Y, Morales-Sanchez A, Ishikawa M, Lavaert M, Das A, Butcher D, Warner AC, Kallarakal M, Chen J, Kedei N, Kelly M, Brinster LR, Allman D, Bhandoola A. Expression of the transcription factor Klf6 by thymic epithelial cells is required for thymus development. SCIENCE ADVANCES 2023; 9:eadg8126. [PMID: 37967174 PMCID: PMC10651122 DOI: 10.1126/sciadv.adg8126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 10/16/2023] [Indexed: 11/17/2023]
Abstract
Thymic epithelial cells (TEC) control T cell development and play essential roles in establishing self-tolerance. By using Foxn1-Cre-driven ablation of Klf6 gene in TEC, we identified Klf6 as a critical factor in TEC development. Klf6 deficiency resulted in a hypoplastic thymus-evident from fetal stages into adulthood-in which a dramatic increase in the frequency of apoptotic TEC was observed. Among cortical TEC (cTEC), a previously unreported cTEC population expressing the transcription factor Sox10 was relatively expanded. Within medullary TEC (mTEC), mTEC I and Tuft-like mTEC IV were disproportionately decreased. Klf6 deficiency altered chromatin accessibility and affected TEC chromatin configuration. Consistent with these defects, naïve conventional T cells and invariant natural killer T cells were reduced in the spleen. Late stages of T cell receptor-dependent selection of thymocytes were affected, and mice exhibited autoimmunity. Thus, Klf6 has a prosurvival role and affects the development of specific TEC subsets contributing to thymic function.
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Affiliation(s)
- Justin Malin
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gustavo Ulises Martinez-Ruiz
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Research Division, Faculty of Medicine, National Autonomous University of Mexico, Mexico City, Mexico
- Children’s Hospital Federico Gomez, Mexico City, Mexico
| | - Yongge Zhao
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Susannah C. Shissler
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer E. Cowan
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Institute of Immunity and Transplantation, University College London, London, UK
| | - Yi Ding
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Abigail Morales-Sanchez
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Children’s Hospital Federico Gomez, Mexico City, Mexico
| | - Masaki Ishikawa
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Marieke Lavaert
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Arundhoti Das
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Donna Butcher
- Molecular Histopathology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Andrew C. Warner
- Molecular Histopathology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Melissa Kallarakal
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jingqiu Chen
- Office of Science and Technology Resources, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- ACROBiosystems, Newark, DE, USA
| | - Noemi Kedei
- Office of Science and Technology Resources, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael Kelly
- Single Cell Analysis Facility, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lauren R. Brinster
- Division of Veterinary Resources, Office of Research Services, National Institutes of Health, Bethesda, MD, USA
| | - David Allman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Avinash Bhandoola
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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25
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Borelli A, Zamit C, Irla M. Medullary Thymic Epithelial Cell Antigen-presentation Assays. Bio Protoc 2023; 13:e4865. [PMID: 37969750 PMCID: PMC10632154 DOI: 10.21769/bioprotoc.4865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 11/17/2023] Open
Abstract
Medullary thymic epithelial cells (mTEC) are bona fide antigen-presenting cells that play a crucial role in the induction of T-cell tolerance. By their unique ability to express a broad range of tissue-restricted self-antigens, mTEC control the clonal deletion (also known as negative selection) of potentially hazardous autoreactive T cells and the generation of Foxp3+ regulatory T cells. Here, we describe a protocol to assess major histocompatibility complex (MHC) class II antigen-presentation capacity of mTEC to CD4+ T cells. We detail the different steps of thymus enzymatic digestion, immunostaining, cell sorting of mTEC and CD4+ T cells, peptide-loading of mTEC, and the co-culture between these two cell types. Finally, we describe the flow cytometry protocol and the subsequent analysis to assess the activation of CD4+ T cells. This rapid co-culture assay enables the evaluation of the ability of mTEC to present antigens to CD4+ T cells in an antigen-specific context. Key features • This protocol builds upon the method used by Lopes et al. (2018 and 2022) and Charaix et al. (2022). • This protocol requires transgenic mice, such as OTIIxRag2-/- mice and the cognate peptide OVA323-339, to assess mTEC antigen presentation to CD4+ T cells. • This requires specific equipment such as a Miltenyi Biotec AutoMACS® Pro Separator, a BD FACSAriaTM III cell sorter, and a BD® LSR II flow cytometer.
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Affiliation(s)
- Alexia Borelli
- Aix-Marseille University, CNRS, INSERM, CIML, Centre d’Immunologie de Marseille-Luminy, Marseille, France
| | - Cloé Zamit
- Aix-Marseille University, CNRS, INSERM, CIML, Centre d’Immunologie de Marseille-Luminy, Marseille, France
| | - Magali Irla
- Aix-Marseille University, CNRS, INSERM, CIML, Centre d’Immunologie de Marseille-Luminy, Marseille, France
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26
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Horie K, Namiki K, Kinoshita K, Miyauchi M, Ishikawa T, Hayama M, Maruyama Y, Hagiwara N, Miyao T, Murata S, Kobayashi TJ, Akiyama N, Akiyama T. Acute irradiation causes a long-term disturbance in the heterogeneity and gene expression profile of medullary thymic epithelial cells. Front Immunol 2023; 14:1186154. [PMID: 38022666 PMCID: PMC10652284 DOI: 10.3389/fimmu.2023.1186154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
The thymus has the ability to regenerate from acute injury caused by radiation, infection, and stressors. In addition to thymocytes, thymic epithelial cells in the medulla (mTECs), which are crucial for T cell self-tolerance by ectopically expressing and presenting thousands of tissue-specific antigens (TSAs), are damaged by these insults and recover thereafter. However, given recent discoveries on the high heterogeneity of mTECs, it remains to be determined whether the frequency and properties of mTEC subsets are restored during thymic recovery from radiation damage. Here we demonstrate that acute total body irradiation with a sublethal dose induces aftereffects on heterogeneity and gene expression of mTECs. Single-cell RNA-sequencing (scRNA-seq) analysis showed that irradiation reduces the frequency of mTECs expressing AIRE, which is a critical regulator of TSA expression, 15 days after irradiation. In contrast, transit-amplifying mTECs (TA-mTECs), which are progenitors of AIRE-expressing mTECs, and Ccl21a-expressing mTECs, were less affected. Interestingly, a detailed analysis of scRNA-seq data suggested that the proportion of a unique mTEC cluster expressing Ccl25 and a high level of TSAs was severely decreased by irradiation. In sum, we propose that the effects of acute irradiation disrupt the heterogeneity and properties of mTECs over an extended period, which potentially leads to an impairment of thymic T cell selection.
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Affiliation(s)
- Kenta Horie
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Kano Namiki
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Kyouhei Kinoshita
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Maki Miyauchi
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
| | - Tatsuya Ishikawa
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Mio Hayama
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Yuya Maruyama
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Naho Hagiwara
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
| | - Takahisa Miyao
- YCI Laboratory for Immunological Transcriptomics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Shigeo Murata
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | | | - Nobuko Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Taishin Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center of Integrative Medical Sciences, Yokohama, Japan
- Immunobiology, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
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27
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Ni D, Tan J, Robert R, Taitz J, Ge A, Potier-Villette C, Reyes JGA, Spiteri A, Wishart C, Mackay C, Piccio L, King NJC, Macia L. GPR109A expressed on medullary thymic epithelial cells affects thymic Treg development. Eur J Immunol 2023; 53:e2350521. [PMID: 37595951 DOI: 10.1002/eji.202350521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/31/2023] [Accepted: 08/17/2023] [Indexed: 08/20/2023]
Abstract
Regulatory T cells (Treg) maintain immune homeostasis due to their anti-inflammatory functions. They can be generated either centrally in the thymus or in peripheral organs. Metabolites such as short-chain fatty acids produced by intestinal microbiota can induce peripheral Treg differentiation, by activating G-protein-coupled-receptors like GPR109A. In this study, we identified a novel role for GPR109A in thymic Treg development. We found that Gpr109a-/- mice had increased Treg under basal conditions in multiple organs compared with WT mice. GPR109A was not expressed on T cells but on medullary thymic epithelial cells (mTECs), as revealed by single-cell RNA sequencing in both mice and humans and confirmed by flow cytometry in mice. mTECs isolated from Gpr109a-/- mice had higher expression of autoimmune regulator (AIRE), the key regulator of Treg development, while the subset of mTECs that did not express Gpr109a in the WT displayed increased Aire expression and also enhanced signaling related to mTEC functionality. Increased thymic Treg in Gpr109a-/- mice was associated with protection from experimental autoimmune encephalomyelitis, with ameliorated clinical signs and reduced inflammation. This work identifies a novel role for GPR109A and possibly the gut microbiota, on thymic Treg development via its regulation of mTECs.
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Affiliation(s)
- Duan Ni
- Charles Perkins Centre, The University of Sydney, The University of Sydney, New South Wales, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Jian Tan
- Charles Perkins Centre, The University of Sydney, The University of Sydney, New South Wales, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Remy Robert
- Department of Physiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jemma Taitz
- Charles Perkins Centre, The University of Sydney, The University of Sydney, New South Wales, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Anjie Ge
- Charles Perkins Centre, The University of Sydney, The University of Sydney, New South Wales, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Camille Potier-Villette
- Charles Perkins Centre, The University of Sydney, The University of Sydney, New South Wales, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Julen Gabirel Araneta Reyes
- Charles Perkins Centre, The University of Sydney, The University of Sydney, New South Wales, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Alanna Spiteri
- Charles Perkins Centre, The University of Sydney, The University of Sydney, New South Wales, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Viral Immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, The School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Claire Wishart
- Charles Perkins Centre, The University of Sydney, The University of Sydney, New South Wales, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Viral Immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, The School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Charles Mackay
- Department of Physiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Laura Piccio
- Charles Perkins Centre, The University of Sydney, The University of Sydney, New South Wales, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Brain and Mind Centre, The University of Sydney, Sydney, New South Wales, Australia
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Nicholas Jonathan Cole King
- Charles Perkins Centre, The University of Sydney, The University of Sydney, New South Wales, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Viral Immunopathology Laboratory, Infection, Immunity and Inflammation Research Theme, The School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Laurence Macia
- Charles Perkins Centre, The University of Sydney, The University of Sydney, New South Wales, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Sydney Cytometry, The University of Sydney and Centenary Institute, Sydney, New South Wales, Australia
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28
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Sin JH, Sucharov J, Kashyap S, Wang Y, Proekt I, Liu X, Parent AV, Gupta A, Kastner P, Chan S, Gardner JM, Ntranos V, Miller CN, Anderson MS, Schjerven H, Waterfield MR. Ikaros is a principal regulator of Aire + mTEC homeostasis, thymic mimetic cell diversity, and central tolerance. Sci Immunol 2023; 8:eabq3109. [PMID: 37889983 DOI: 10.1126/sciimmunol.abq3109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/04/2023] [Indexed: 10/29/2023]
Abstract
Mutations in the gene encoding the zinc-finger transcription factor Ikaros (IKZF1) are found in patients with immunodeficiency, leukemia, and autoimmunity. Although Ikaros has a well-established function in modulating gene expression programs important for hematopoietic development, its role in other cell types is less well defined. Here, we uncover functions for Ikaros in thymic epithelial lineage development in mice and show that Ikzf1 expression in medullary thymic epithelial cells (mTECs) is required for both autoimmune regulator-positive (Aire+) mTEC development and tissue-specific antigen (TSA) gene expression. Accordingly, TEC-specific deletion of Ikzf1 in mice results in a profound decrease in Aire+ mTECs, a global loss of TSA gene expression, and the development of autoimmunity. Moreover, Ikaros shapes thymic mimetic cell diversity, and its deletion results in a marked expansion of thymic tuft cells and muscle-like mTECs and a loss of other Aire-dependent mimetic populations. Single-cell analysis reveals that Ikaros modulates core transcriptional programs in TECs that correlate with the observed cellular changes. Our findings highlight a previously undescribed role for Ikaros in regulating epithelial lineage development and function and suggest that failed thymic central tolerance could contribute to the autoimmunity seen in humans with IKZF1 mutations.
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Affiliation(s)
- Jun Hyung Sin
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Juliana Sucharov
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Sujit Kashyap
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Yi Wang
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
- 10x Genomics, Pleasanton, CA, USA
| | - Irina Proekt
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Xian Liu
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Audrey V Parent
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Alexander Gupta
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Philippe Kastner
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, Université de Strasbourg, 67404 Illkirch, France
| | - Susan Chan
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, Université de Strasbourg, 67404 Illkirch, France
| | - James M Gardner
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Vasilis Ntranos
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Corey N Miller
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Mark S Anderson
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Hilde Schjerven
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Michael R Waterfield
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
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29
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Givony T, Leshkowitz D, Del Castillo D, Nevo S, Kadouri N, Dassa B, Gruper Y, Khalaila R, Ben-Nun O, Gome T, Dobeš J, Ben-Dor S, Kedmi M, Keren-Shaul H, Heffner-Krausz R, Porat Z, Golani O, Addadi Y, Brenner O, Lo DD, Goldfarb Y, Abramson J. Thymic mimetic cells function beyond self-tolerance. Nature 2023; 622:164-172. [PMID: 37674082 DOI: 10.1038/s41586-023-06512-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/03/2023] [Indexed: 09/08/2023]
Abstract
Development of immunocompetent T cells in the thymus is required for effective defence against all types of pathogens, including viruses, bacteria and fungi. To this end, T cells undergo a very strict educational program in the thymus, during which both non-functional and self-reactive T cell clones are eliminated by means of positive and negative selection1.Thymic epithelial cells (TECs) have an indispensable role in these processes, and previous studies have shown the notable heterogeneity of these cells2-7. Here, using multiomic analysis, we provide further insights into the functional and developmental diversity of TECs in mice, and reveal a detailed atlas of the TEC compartment according to cell transcriptional states and chromatin landscapes. Our analysis highlights unconventional TEC subsets that are similar to functionally well-defined parenchymal populations, including endocrine cells, microfold cells and myocytes. By focusing on the endocrine and microfold TEC populations, we show that endocrine TECs require Insm1 for their development and are crucial to maintaining thymus cellularity in a ghrelin-dependent manner; by contrast, microfold TECs require Spib for their development and are essential for the generation of thymic IgA+ plasma cells. Collectively, our study reveals that medullary TECs have the potential to differentiate into various types of molecularly distinct and functionally defined cells, which not only contribute to the induction of central tolerance, but also regulate the homeostasis of other thymus-resident populations.
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Affiliation(s)
- Tal Givony
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Dena Leshkowitz
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Diana Del Castillo
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Shir Nevo
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Noam Kadouri
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Bareket Dassa
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Yael Gruper
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Razi Khalaila
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Osher Ben-Nun
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tom Gome
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jan Dobeš
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Shifra Ben-Dor
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Merav Kedmi
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, Rehovot, Israel
| | - Hadas Keren-Shaul
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, Rehovot, Israel
| | | | - Ziv Porat
- Flow Cytometry Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ofra Golani
- MICC Cell Observatory, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Yoseph Addadi
- MICC Cell Observatory, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ori Brenner
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - David D Lo
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Yael Goldfarb
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
| | - Jakub Abramson
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel.
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30
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Taves MD, Donahue KM, Bian J, Cam MC, Ashwell JD. Aire drives steroid hormone biosynthesis by medullary thymic epithelial cells. Sci Immunol 2023; 8:eabo7975. [PMID: 37595021 PMCID: PMC10732315 DOI: 10.1126/sciimmunol.abo7975] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 07/25/2023] [Indexed: 08/20/2023]
Abstract
Thymic epithelial cells (TECs) produce glucocorticoids, which antagonize negative selection of autoreactive thymocytes and promote a competent T cell antigen-specific repertoire. To characterize their source, we generated a knock-in reporter mouse in which endogenous Cyp11b1, the final enzyme in de novo production of active glucocorticoids, was fluorescently tagged with mScarlet. Here, we find that Cyp11b1 is expressed in medullary TECs (mTECs) but not cortical TECs or other cells in the thymus. A distinct characteristic of mTECs is the presence of Aire, a transcription factor that drives expression of tissue-restricted antigens (TRAs) important for establishing immune tolerance. Cyp11b1 expression was highest in Aire+ mTECs, lower in post-Aire mTECs, and absent in mTECs of Aire-deficient mice. Transcriptomic analyses found that multiple enzymatic biosynthetic pathways are expressed specifically in mTECs and are also Aire dependent. In particular, we found that the thymus expresses messenger RNA for enzymes that catalyze production of many bioactive steroids and that glucocorticoids and sex steroids were secreted by cultured thymi. Expression of the transcripts for these genes and production of their final steroid products were markedly reduced in the absence of Aire. Thus, in addition to its well-established role in inducing TRAs that promote negative selection, Aire has an additional and contrary function of inducing glucocorticoids that antagonize negative selection, which together may expand and enhance the TCR repertoire. Furthermore, because Aire drives expression of multiple enzymes responsible for production of other non-gene-encoded bioactive molecules, it might have yet other roles in thymus development and function.
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Affiliation(s)
- Matthew D. Taves
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Kaitlynn M. Donahue
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jing Bian
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, Bethesda, MD 20892, USA
| | - Margaret C. Cam
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, Bethesda, MD 20892, USA
| | - Jonathan D. Ashwell
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
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31
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Lagou MK, Karagiannis GS. Obesity-induced thymic involution and cancer risk. Semin Cancer Biol 2023; 93:3-19. [PMID: 37088128 DOI: 10.1016/j.semcancer.2023.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 04/25/2023]
Abstract
Declining thymic functions associated either with old age (i.e., age-related thymic involution), or with acute involution as a result of stress, infectious disease, or cytoreductive therapies (e.g., chemotherapy/radiotherapy), have been associated with cancer development. A key mechanism underlying such increased cancer risk is the thymus-dependent debilitation of adaptive immunity, which is responsible for orchestrating immunoediting mechanisms and tumor immune surveillance. In the past few years, a blooming set of evidence has intriguingly linked obesity with cancer development and progression. The majority of such studies has focused on obesity-driven chronic inflammation, steroid/sex hormone and adipokine production, and hyperinsulinemia, as principal factors affecting the tumor microenvironment and driving the development of primary malignancy. However, experimental observations about the negative impact of obesity on T cell development and maturation have existed for more than half a century. Here, we critically discuss the molecular and cellular mechanisms of obesity-driven thymic involution as a previously underrepresented intermediary pathology leading to cancer development and progression. This knowledge could be especially relevant in the context of childhood obesity, because impaired thymic function in young individuals leads to immune system abnormalities, and predisposes to various pediatric cancers. A thorough understanding behind the molecular and cellular circuitries governing obesity-induced thymic involution could therefore help towards the rationalized development of targeted thymic regeneration strategies for obese individuals at high risk of cancer development.
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Affiliation(s)
- Maria K Lagou
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA; Tumor Microenvironment of Metastasis Program, Albert Einstein Cancer Center, Bronx, NY, USA
| | - George S Karagiannis
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA; Tumor Microenvironment of Metastasis Program, Albert Einstein Cancer Center, Bronx, NY, USA; Cancer Dormancy and Tumor Microenvironment Institute, Albert Einstein College of Medicine, Bronx, NY, USA; Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA; Integrated Imaging Program for Cancer Research, Albert Einstein College of Medicine, Bronx, NY, USA.
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32
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Rackaityte E, Proekt I, Miller HS, Ramesh A, Brooks JF, Kung AF, Mandel-Brehm C, Yu D, Zamecnik C, Bair R, Vazquez SE, Sunshine S, Abram CL, Lowell CA, Rizzuto G, Wilson MR, Zikherman J, Anderson MS, DeRisi JL. Validation of a murine proteome-wide phage display library for the identification of autoantibody specificities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.07.535899. [PMID: 37066405 PMCID: PMC10104109 DOI: 10.1101/2023.04.07.535899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Autoimmunity is characterized by loss of tolerance to tissue-specific as well as systemic antigens, resulting in complex autoantibody landscapes. Here, we introduce and extensively validate the performance characteristics of a murine proteome-wide library for phage display immunoprecipitation and sequencing (PhIP-seq), to profile mouse autoantibodies. This system and library were validated using seven genetic mouse models across a spectrum of autoreactivity. Mice deficient in antibody production (Rag2-/- and μMT) were used to model non-specific peptide enrichments, while cross-reactivity was evaluated using anti-ovalbumin B cell receptor (BCR)-restricted OB1 mice as a proof of principle. The PhIP-seq approach was then utilized to interrogate three distinct autoimmune disease models. First, serum from Lyn-/- IgD+/- mice with lupus-like disease was used to identify nuclear and apoptotic bleb reactivities, lending support to the hypothesis that apoptosis is a shared origin of these antigens. Second, serum from non-obese diabetic (NOD) mice, a polygenic model of pancreas-specific autoimmunity, enriched peptides derived from both insulin and predicted pancreatic proteins. Lastly, Aire-/- mouse sera were used to identify numerous auto-antigens, many of which were also observed in previous studies of humans with autoimmune polyendocrinopathy syndrome type 1 (APS1) carrying recessive mutations in AIRE. Among these were peptides derived from Perilipin-1, a validated autoimmune biomarker of generalized acquired lipodystrophy in humans. Autoreactivity to Perilipin-1 correlated with lymphocyte infiltration in adipose tissue and underscores the approach in revealing previously unknown specificities. These experiments support the use of murine proteome-wide PhIP-seq for antigenic profiling and autoantibody discovery, which may be employed to study a range of immune perturbations in mouse models of autoimmunity.
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Affiliation(s)
- Elze Rackaityte
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA USA
| | - Irina Proekt
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Haleigh S. Miller
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA USA
- Biological and Medical Informatics Program, University of California San Francisco, San Francisco, CA USA
| | - Akshaya Ramesh
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Jeremy F. Brooks
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Andrew F. Kung
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA USA
- Biological and Medical Informatics Program, University of California San Francisco, San Francisco, CA USA
| | - Caleigh Mandel-Brehm
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA USA
| | - David Yu
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Colin Zamecnik
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Rebecca Bair
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Sara E. Vazquez
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA USA
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Sara Sunshine
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA USA
| | - Clare L. Abram
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Clifford A. Lowell
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Gabrielle Rizzuto
- Human Oncology & Pathogenesis Program and Department of Pathology & Laboratory Medicine, Memorial Sloan Kettering Cancer Center, NY, NY
| | - Michael R. Wilson
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Julie Zikherman
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Mark S. Anderson
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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33
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Chiu H, Linsley PS, Ziegler SF. Investigating Thymic Epithelial Cell Diversity Using Systems Biology. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:888-894. [PMID: 36947816 PMCID: PMC10037528 DOI: 10.4049/jimmunol.2200610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/12/2022] [Indexed: 03/24/2023]
Abstract
The thymus is an intricate organ consisting of a diverse population of thymic epithelial cells (TECs). Cortical and medullary TECs and their subpopulations have distinct roles in coordinating the development and selection of functionally competent and self-tolerant T cells. Recent advances made in technologies such as single-cell RNA sequencing have made it possible to investigate and resolve the heterogeneity in TECs. These findings have provided further understanding of the molecular mechanisms regulating TEC function and expression of tissue-restricted Ags. In this brief review, we focus on the newly characterized subsets of TECs and their diversity in relation to their functions in supporting T cell development. We also discuss recent discoveries in expression of self-antigens in the context of TEC development as well as the cellular and molecular changes occurring during embryonic development to thymic involution.
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34
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Sundaresan B, Shirafkan F, Ripperger K, Rattay K. The Role of Viral Infections in the Onset of Autoimmune Diseases. Viruses 2023; 15:v15030782. [PMID: 36992490 PMCID: PMC10051805 DOI: 10.3390/v15030782] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 03/31/2023] Open
Abstract
Autoimmune diseases (AIDs) are the consequence of a breach in immune tolerance, leading to the inability to sufficiently differentiate between self and non-self. Immune reactions that are targeted towards self-antigens can ultimately lead to the destruction of the host's cells and the development of autoimmune diseases. Although autoimmune disorders are comparatively rare, the worldwide incidence and prevalence is increasing, and they have major adverse implications for mortality and morbidity. Genetic and environmental factors are thought to be the major factors contributing to the development of autoimmunity. Viral infections are one of the environmental triggers that can lead to autoimmunity. Current research suggests that several mechanisms, such as molecular mimicry, epitope spreading, and bystander activation, can cause viral-induced autoimmunity. Here we describe the latest insights into the pathomechanisms of viral-induced autoimmune diseases and discuss recent findings on COVID-19 infections and the development of AIDs.
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Affiliation(s)
- Bhargavi Sundaresan
- Institute of Pharmacology, Biochemical Pharmacological Center, University of Marburg, 35043 Marburg, Germany
| | - Fatemeh Shirafkan
- Institute of Pharmacology, Biochemical Pharmacological Center, University of Marburg, 35043 Marburg, Germany
| | - Kevin Ripperger
- Institute of Pharmacology, Biochemical Pharmacological Center, University of Marburg, 35043 Marburg, Germany
| | - Kristin Rattay
- Institute of Pharmacology, Biochemical Pharmacological Center, University of Marburg, 35043 Marburg, Germany
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35
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Rosichini M, Bordoni V, Silvestris DA, Mariotti D, Matusali G, Cardinale A, Zambruno G, Condorelli AG, Flamini S, Genah S, Catanoso M, Del Nonno F, Trezzi M, Galletti L, De Stefanis C, Cicolani N, Petrini S, Quintarelli C, Agrati C, Locatelli F, Velardi E. SARS-CoV-2 infection of thymus induces loss of function that correlates with disease severity. J Allergy Clin Immunol 2023; 151:911-921. [PMID: 36758836 PMCID: PMC9907790 DOI: 10.1016/j.jaci.2023.01.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 12/14/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023]
Abstract
BACKGROUND Lymphopenia, particularly when restricted to the T-cell compartment, has been described as one of the major clinical hallmarks in patients with coronavirus disease 2019 (COVID-19) and proposed as an indicator of disease severity. Although several mechanisms fostering COVID-19-related lymphopenia have been described, including cell apoptosis and tissue homing, the underlying causes of the decline in T-cell count and function are still not completely understood. OBJECTIVE Given that viral infections can directly target thymic microenvironment and impair the process of T-cell generation, we sought to investigate the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on thymic function. METHODS We performed molecular quantification of T-cell receptor excision circles and κ-deleting recombination excision circles to assess, respectively, T- and B-cell neogenesis in SARS-CoV-2-infected patients. We developed a system for in vitro culture of primary human thymic epithelial cells (TECs) to mechanistically investigate the impact of SARS-CoV-2 on TEC function. RESULTS We showed that patients with COVID-19 had reduced thymic function that was inversely associated with the severity of the disease. We found that angiotensin-converting enzyme 2, through which SARS-CoV-2 enters the host cells, was expressed by thymic epithelium, and in particular by medullary TECs. We also demonstrated that SARS-CoV-2 can target TECs and downregulate critical genes and pathways associated with epithelial cell adhesion and survival. CONCLUSIONS Our data demonstrate that the human thymus is a target of SARS-CoV-2 and thymic function is altered following infection. These findings expand our current knowledge of the effects of SARS-CoV-2 infection on T-cell homeostasis and suggest that monitoring thymic activity may be a useful marker to predict disease severity and progression.
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Affiliation(s)
- Marco Rosichini
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy,Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Veronica Bordoni
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy,Cellular Immunology Laboratory, INMI L Spallanzani – IRCCS, Rome, Italy
| | - Domenico Alessandro Silvestris
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Davide Mariotti
- Cellular Immunology Laboratory, INMI L Spallanzani – IRCCS, Rome, Italy
| | - Giulia Matusali
- Virology Laboratory, INMI L Spallanzani – IRCCS, Rome, Italy
| | - Antonella Cardinale
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Giovanna Zambruno
- Genodermatosis Unit, Genetics and Rare Diseases Research Division, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Angelo Giuseppe Condorelli
- Genodermatosis Unit, Genetics and Rare Diseases Research Division, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Sara Flamini
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Shirley Genah
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Marialuigia Catanoso
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy,Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | | | - Matteo Trezzi
- Cardiac Surgery Unit, Department of Pediatric Cardiology and Cardiac Surgery, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Lorenzo Galletti
- Cardiac Surgery Unit, Department of Pediatric Cardiology and Cardiac Surgery, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Cristiano De Stefanis
- Pathology Unit, Core Research Laboratories, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Nicolò Cicolani
- Confocal Microscopy Core Facility, Research Center, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Stefania Petrini
- Confocal Microscopy Core Facility, Research Center, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Concetta Quintarelli
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy,Department of Clinical Medicine and Surgery, University of Naples Federico II, Rome, Italy
| | - Chiara Agrati
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy,Cellular Immunology Laboratory, INMI L Spallanzani – IRCCS, Rome, Italy
| | - Franco Locatelli
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy,Catholic University of the Sacred Heart, Rome, Italy
| | - Enrico Velardi
- Department of Pediatric Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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Rodrigues PM, Sousa LG, Perrod C, Maceiras AR, Ferreirinha P, Pombinho R, Romera-Cárdenas G, Gomez-Lazaro M, Senkara M, Pistolic J, Cabanes D, Klein L, Saftig P, Alves NL. LAMP2 regulates autophagy in the thymic epithelium and thymic stroma-dependent CD4 T cell development. Autophagy 2023; 19:426-439. [PMID: 35535798 PMCID: PMC9851248 DOI: 10.1080/15548627.2022.2074105] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Within the thymus, thymic epithelial cells (TECs) provide dedicated thymic stroma microenvironments for T cell development. Because TEC functionality is sensitive to aging and cytoablative therapies, unraveling the molecular elements that coordinate their thymopoietic role has fundamental and clinical implications. Particularly, the selection of CD4 T cells depends on interactions between TCRs expressed on T cell precursors and self-peptides:MHC II complexes presented by cortical TECs (cTECs). Although the macroautophagy/autophagy-lysosomal protein degradation pathway is implicated in CD4 T cell selection, the molecular mechanism that controls the generation of selecting MHC II ligands remains elusive. LAMP2 (lysosomal-associated membrane protein 2) is a well-recognized mediator of autolysosome (AL) maturation. We showed that LAMP2 is highly expressed in cTECs. Notably, genetic inactivation of Lamp2 in thymic stromal cells specifically impaired the development of CD4 T cells that completed positive selection, without misdirecting MHC II-restricted cells into the CD8 lineage. Mechanistically, defects in autophagy in lamp2-deficient cTECs were linked to alterations in MHC II processing, which was associated with a marked reduction in CD4 TCR repertoire diversity selected within the lamp2-deficient thymic stroma. Together, our findings suggest that LAMP2 interconnects the autophagy-lysosomal axis and the processing of selecting self-peptides:MHC II complexes in cTECs, underling its implications for the generation of a broad CD4 TCR repertoire.Abbreviations: AIRE: autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy); AL: autolysosome; AP: autophagosome; Baf-A1: bafilomycin A1; B2M: beta-2 microglobulin; CTSL: cathepsin L; CD74/Ii: CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated); CFSE: carboxyfluorescein succinimidyl ester; CFU: colony-forming unit; CLIP: class II-associated invariant chain peptides; cTECs: cortical TECs dKO: double knockout; DN: double negative; DP: double positive; ENPEP/LY51: glutamyl aminopeptidase; FOXP3: forkhead box; P3 IFNG/IFNγ: interferon gamma; IKZF2/HELIOS: IKAROS family zinc finger 2; IL2RA/CD25: interleukin 2 receptor, alpha chain; KO: knockout; LAMP2: lysosomal-associated membrane protein 2; LIP: lymphopenia-induced proliferation; Lm: Listeria monocytogenes; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MHC: major histocompatibility complex; mTECs: medullary TECs; PRSS16/TSSP: protease, serine 16 (thymus); SELL/CD62L: selectin, lymphocyte; SP: single positive; TCR: T cell receptor; TCRB: T cell receptor beta chain; TECs: thymic epithelial cells; UEA-1: Ulex europaeus agglutinin-1; WT: wild-type.
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Affiliation(s)
- Pedro M. Rodrigues
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal,Instituto de Biologia Molecular e Celular, Porto, Portugal
| | - Laura G. Sousa
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal,Instituto de Biologia Molecular e Celular, Porto, Portugal,Doctoral Program in Molecular and Cell Biology, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Chiara Perrod
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal,Instituto de Biologia Molecular e Celular, Porto, Portugal
| | - Ana R. Maceiras
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Pedro Ferreirinha
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal,Instituto de Biologia Molecular e Celular, Porto, Portugal
| | - Rita Pombinho
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal,Instituto de Biologia Molecular e Celular, Porto, Portugal
| | - Gema Romera-Cárdenas
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal,Instituto de Biologia Molecular e Celular, Porto, Portugal
| | - María Gomez-Lazaro
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal,Instituto de Engenharia Biomédica, Porto, Portugal
| | - Meryem Senkara
- Biochemisches Institut, Christian Albrechts-Universität Kiel, Kiel, Germany
| | - Jelena Pistolic
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Didier Cabanes
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal,Instituto de Biologia Molecular e Celular, Porto, Portugal
| | - Ludger Klein
- Faculty of Medicine, LMU Munich, Planegg-Martinsried, Institute for Immunology, Biomedical Center Munich, Munich, Germany
| | - Paul Saftig
- Biochemisches Institut, Christian Albrechts-Universität Kiel, Kiel, Germany
| | - Nuno L. Alves
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal,Instituto de Biologia Molecular e Celular, Porto, Portugal,CONTACT Nuno L. Alves Instituto de Investigação e Inovação em Saúde (i3S), Rua Alfredo Allen, 208, Porto4200-135, Portugal
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Casanova JL, Anderson MS. Unlocking life-threatening COVID-19 through two types of inborn errors of type I IFNs. J Clin Invest 2023; 133:e166283. [PMID: 36719370 PMCID: PMC9888384 DOI: 10.1172/jci166283] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Since 2003, rare inborn errors of human type I IFN immunity have been discovered, each underlying a few severe viral illnesses. Autoantibodies neutralizing type I IFNs due to rare inborn errors of autoimmune regulator (AIRE)-driven T cell tolerance were discovered in 2006, but not initially linked to any viral disease. These two lines of clinical investigation converged in 2020, with the discovery that inherited and/or autoimmune deficiencies of type I IFN immunity accounted for approximately 15%-20% of cases of critical COVID-19 pneumonia in unvaccinated individuals. Thus, insufficient type I IFN immunity at the onset of SARS-CoV-2 infection may be a general determinant of life-threatening COVID-19. These findings illustrate the unpredictable, but considerable, contribution of the study of rare human genetic diseases to basic biology and public health.
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Affiliation(s)
- Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Paris Cité University, Imagine Institute, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, New York, USA
| | - Mark S. Anderson
- Diabetes Center and
- Department of Medicine, UCSF, San Francisco, California, USA
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Wang L, Li X, Yang S, Chen X, Li J, Wang S, Zhang M, Zheng Z, Zhou J, Wang L, Wu Y. Proteomic identification of MHC class I-associated peptidome derived from non-obese diabetic mouse thymus and pancreas. J Proteomics 2023; 270:104746. [PMID: 36210013 DOI: 10.1016/j.jprot.2022.104746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/17/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022]
Abstract
The peptides repertoire presented to CD8+ T cells by major histocompatibility complex (MHC) class I molecules is referred to as the MHC I-associated peptidome (MIP), which regulates thymus development, peripheral survival and function during lifetime of CD8+ T cells. Type 1 diabetes (T1D) is an organ-specific autoimmune disease caused by pancreatic β cells destruction mediated primarily by autoreactive CD8+ T cells. Non-obese diabetic (NOD) mouse is an important animal model of T1D. Here, we deeply analyzed the MIP derived from NOD mice thymus and pancreas, and demonstrated that the thymus MIP source proteins partially shared with the MIP source proteins derived from NOD mice pancreas and β cell line. One H-2Kd restricted peptide SLC35B126-34 which was shared by MIP derived from both NOD mice pancreatic tissues and islet β-cell line, but absent in MIP from NOD thymus tissues, showed ability to stimulate IFN-γ secretion and proliferation of NOD mice splenic CD8+ T cells. The global view of the MHC I-associated self-peptides repertoire in the thymus and pancreas of NOD mice may serve as a biological reference to identify potential autoantigens targeted by autoreactive CD8+ T cells in T1D. Data are available via ProteomeXchange with identifier PXD031966. SIGNIFICANCE: The peptides repertoire presented to CD8+ T cells by major histocompatibility complex (MHC) class I molecules is referred to as the MHC I-associated peptidome (MIP). The MIP presented by thymic antigen presenting cells (APCs) is crucial for shaping CD8+ T cell repertoire and self-tolerance, while the MIP presented by peripheral tissues and organs is not only involved in maintaining periphery CD8+ T cell survival and homeostasis, but also mediates immune surveillance and autoimmune responses of CD8+ T cells under pathological conditions. Type 1 diabetes (T1D) is an organ-specific autoimmune disease caused by the destruction of pancreatic β cells, mediated primarily by autoreactive CD8+ T cells. Non-obese diabetic (NOD) mouse is one of important animal models of spontaneous autoimmune diabetes that shares several key features with human T1D. The global view of the MHC I-associated self-peptides repertoire in the thymus and pancreas of NOD mice may serve as a good biological reference to identify potential autoantigens targeted by autoreactive CD8+ T cells in T1D. It has great significance for further clarifying the immune recognition and effect mechanism of autoreactive CD8+ T cells in the pathogenesis of T1D, and then developing antigen-specific immune intervention strategies.
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Affiliation(s)
- Lina Wang
- Department of Immunology, Medical College of Qingdao University, Qingdao, Shandong 266071, China; Institute of Immunology PLA & Department of Immunology, College of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, China; Department of Immunology, College of Basic Medicine, Weifang Medical University, Weifang 261053, China
| | - Xiangqian Li
- Institute of Immunology PLA & Department of Immunology, College of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Shushu Yang
- Institute of Immunology PLA & Department of Immunology, College of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Xiaoling Chen
- Institute of Immunology PLA & Department of Immunology, College of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Jie Li
- Institute of Immunology PLA & Department of Immunology, College of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Shufeng Wang
- Institute of Immunology PLA & Department of Immunology, College of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Mengjun Zhang
- Department of Pharmaceutical Analysis, College of Pharmacy, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Zhengni Zheng
- Department of Dermatology, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Jie Zhou
- Department of Dermatology, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Li Wang
- Institute of Immunology PLA & Department of Immunology, College of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, China.
| | - Yuzhang Wu
- Department of Immunology, Medical College of Qingdao University, Qingdao, Shandong 266071, China; Institute of Immunology PLA & Department of Immunology, College of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, China.
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39
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Mandel-Brehm C, Vazquez SE, Liverman C, Cheng M, Quandt Z, Kung AF, Parent A, Miao B, Disse E, Cugnet-Anceau C, Dalle S, Orlova E, Frolova E, Alba D, Michels A, Oftedal BE, Lionakis MS, Husebye ES, Agarwal AK, Li X, Zhu C, Li Q, Oral E, Brown R, Anderson MS, Garg A, DeRisi JL. Autoantibodies to Perilipin-1 Define a Subset of Acquired Generalized Lipodystrophy. Diabetes 2023; 72:59-70. [PMID: 35709010 PMCID: PMC9797316 DOI: 10.2337/db21-1172] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 06/06/2022] [Indexed: 02/04/2023]
Abstract
Acquired lipodystrophy is often characterized as an idiopathic subtype of lipodystrophy. Despite suspicion of an immune-mediated pathology, biomarkers such as autoantibodies are generally lacking. Here, we used an unbiased proteome-wide screening approach to identify autoantibodies to the adipocyte-specific lipid droplet protein perilipin 1 (PLIN1) in a murine model of autoimmune polyendocrine syndrome type 1 (APS1). We then tested for PLIN1 autoantibodies in human subjects with acquired lipodystrophy with two independent severe breaks in immune tolerance (including APS1) along with control subjects using a specific radioligand binding assay and indirect immunofluorescence on fat tissue. We identified autoantibodies to PLIN1 in these two cases, including the first reported case of APS1 with acquired lipodystrophy and a second patient who acquired lipodystrophy as an immune-related adverse event following cancer immunotherapy. Lastly, we also found PLIN1 autoantibodies to be specifically enriched in a subset of patients with acquired generalized lipodystrophy (17 of 46 [37%]), particularly those with panniculitis and other features of autoimmunity. These data lend additional support to new literature that suggests that PLIN1 autoantibodies represent a marker of acquired autoimmune lipodystrophies and further link them to a break in immune tolerance.
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Affiliation(s)
- Caleigh Mandel-Brehm
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
| | - Sara E. Vazquez
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
- Diabetes Center, University of California, San Francisco, San Francisco, CA
| | - Christopher Liverman
- Department of Pathology, University of California, San Francisco, San Francisco, CA
| | - Mickie Cheng
- Diabetes Center, University of California, San Francisco, San Francisco, CA
| | - Zoe Quandt
- Diabetes Center, University of California, San Francisco, San Francisco, CA
- Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Andrew F. Kung
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
| | - Audrey Parent
- Diabetes Center, University of California, San Francisco, San Francisco, CA
| | - Brenda Miao
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
- Diabetes Center, University of California, San Francisco, San Francisco, CA
| | - Emmanuel Disse
- Endocrinology Diabetology and Nutrition Department, Lyon Sud Hospital, Hospices Civils de Lyon, Pierre-Bénite, France
- ImmuCare, Cancer Institute of Hospices Civils de Lyon (IC-HCL), Lyon, France
| | - Christine Cugnet-Anceau
- Endocrinology Diabetology and Nutrition Department, Lyon Sud Hospital, Hospices Civils de Lyon, Pierre-Bénite, France
- ImmuCare, Cancer Institute of Hospices Civils de Lyon (IC-HCL), Lyon, France
| | - Stéphane Dalle
- ImmuCare, Cancer Institute of Hospices Civils de Lyon (IC-HCL), Lyon, France
- Dermatology Department, Lyon Sud Hospital, Hospices Civils de Lyon, Pierre-Bénite, France
| | - Elizaveta Orlova
- Endocrinology Research Centre, Institute of Paediatric Endocrinology, Moscow, Russia
| | - Elena Frolova
- National Medical Research Center of Children’s Health, Moscow, Russia
| | - Diana Alba
- Diabetes Center, University of California, San Francisco, San Francisco, CA
- Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Aaron Michels
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO
| | - Bergithe E. Oftedal
- University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Michail S. Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Eystein S. Husebye
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science and K.G. Jebsen Center for Autoimmune Disorders, University of Bergen, Bergen, Norway
| | - Anil K. Agarwal
- Division of Nutrition and Metabolic Diseases, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX
| | - Xilong Li
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX
| | - Chengsong Zhu
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX
| | - Quan Li
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX
| | - Elif Oral
- Division of Metabolism, Endocrinology & Diabetes and Caswell Diabetes Institute, University of Michigan, Ann Arbor, MI
| | - Rebecca Brown
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Mark S. Anderson
- Diabetes Center, University of California, San Francisco, San Francisco, CA
- Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Abhimanyu Garg
- Division of Nutrition and Metabolic Diseases, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA
- Chan Zuckerberg Biohub, San Francisco, CA
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40
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Matsumoto M, Yoshida H, Tsuneyama K, Oya T, Matsumoto M. Revisiting Aire and tissue-restricted antigens at single-cell resolution. Front Immunol 2023; 14:1176450. [PMID: 37207224 PMCID: PMC10191227 DOI: 10.3389/fimmu.2023.1176450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/20/2023] [Indexed: 05/21/2023] Open
Abstract
The thymus is a highly specialized organ that plays an indispensable role in the establishment of self-tolerance, a process characterized by the "education" of developing T-cells. To provide competent T-cells tolerant to self-antigens, medullary thymic epithelial cells (mTECs) orchestrate negative selection by ectopically expressing a wide range of genes, including various tissue-restricted antigens (TRAs). Notably, recent advancements in the high-throughput single-cell analysis have revealed remarkable heterogeneity in mTECs, giving us important clues for dissecting the mechanisms underlying TRA expression. We overview how recent single-cell studies have furthered our understanding of mTECs, with a focus on the role of Aire in inducing mTEC heterogeneity to encompass TRAs.
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Affiliation(s)
- Minoru Matsumoto
- Department of Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima, Japan
- *Correspondence: Minoru Matsumoto,
| | - Hideyuki Yoshida
- YCI Laboratory for Immunological Transcriptomics, RIKEN Center for Integrative Medical Science, Yokohama, Japan
| | - Koichi Tsuneyama
- Department of Pathology and Laboratory Medicine, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Takeshi Oya
- Department of Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima, Japan
| | - Mitsuru Matsumoto
- Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University, Tokushima, Japan
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Morales-Sanchez A, Shissler SC, Cowan JE, Bhandoola A. Revelations in Thymic Epithelial Cell Biology and Heterogeneity from Single-Cell RNA Sequencing and Lineage Tracing Methodologies. Methods Mol Biol 2023; 2580:25-49. [PMID: 36374449 PMCID: PMC10802793 DOI: 10.1007/978-1-0716-2740-2_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Thymic epithelial cells (TECs) make up the thymic microenvironments that support the generation of a functionally competent and self-tolerant T-cell repertoire. Cortical (c)TECs, present in the cortex, are essential for early thymocyte development including selection of thymocytes expressing functional TCRs (positive selection). Medullary (m)TECs, located in the medulla, play a key role in late thymocyte development, including depletion of self-reactive T cells (negative selection) and selection of regulatory T cells. In recent years, transcriptomic analysis by single-cell (sc)RNA sequencing (Seq) has revealed TEC heterogeneity previously masked by population-level RNA-Seq or phenotypic studies. We summarize the discoveries made possible by scRNA-Seq, including the identification of novel mTEC subsets, advances in understanding mTEC promiscuous gene expression, and TEC alterations from embryonic to adult stages. Whereas pseudotime analyses of scRNA-Seq data can suggest relationships between TEC subsets, experimental methods such as lineage tracing and reaggregate thymic organ culture (RTOC) are required to test these hypotheses. Lineage tracing - namely, of β5t or Aire expressing cells - has exposed progenitor and parent-daughter cellular relationships within TEC.
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Affiliation(s)
- Abigail Morales-Sanchez
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
- Children's Hospital of Mexico Federico Gomez, Mexico City, Mexico.
| | - Susannah C Shissler
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer E Cowan
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Avinash Bhandoola
- Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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CTLA-4 on thymic epithelial cells complements Aire for T cell central tolerance. Proc Natl Acad Sci U S A 2022; 119:e2215474119. [PMID: 36409920 PMCID: PMC9860321 DOI: 10.1073/pnas.2215474119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Medullary thymic epithelial cells (mTECs) are essential for the establishment of T cell central tolerance. The transcription factor Aire plays a key role in this process, but other factors remain understudied. We found that a small population of mTECs expressed the coinhibitory receptor cytotoxic T lymphocyte-associated protein 4 (CTLA-4). These CTLA-4+ cells were detectable in perinates, peaked around young adulthood and expanded sixfold in the absence of Aire. Single-cell transcriptomics revealed CTLA-4+ mTECs to express a distinct gene signature encoding molecules associated with antigen presentation and interferon-gamma signaling. Mice conditionally lacking CTLA-4 in thymic epithelial cells had no major immunological deficiencies but displayed a mildly increased inflammatory tone and a partial defect in the generation of Foxp3+CD4+ regulatory T cells. Consequently, these mice developed modest levels of autoantibodies and lymphocytic infiltration of peripheral tissues. Thus, CTLA-4 expression in mTECs complements Aire to establish T cell central tolerance.
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43
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AIRE in Male Fertility: A New Hypothesis. Cells 2022; 11:cells11193168. [PMID: 36231130 PMCID: PMC9563308 DOI: 10.3390/cells11193168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 09/29/2022] [Accepted: 10/08/2022] [Indexed: 11/16/2022] Open
Abstract
Male infertility affects approximately 14% of all European men, of which ~44% are characterized as idiopathic. There is an urgency to identify the factors that affect male fertility. One such factor, Autoimmune Regulator (AIRE), a protein found in the thymus, has been studied in the context of central tolerance functioning as a nuclear transcription modulator, responsible for the expression of tissue-restricted antigens in specialized thymic cells that prevent autoimmunity. While its expression in the testes remains enigmatic, we recently observed that sterility in mice correlates with the absence of Aire in the testes, regardless of the deficient expression in medullary thymic epithelial cells or cells of the hematopoietic system. By assessing the Aire transcript levels, we discovered that Sertoli cells are the exclusive source of Aire in the testes, where it most likely plays a non-immune role, suggesting an unknown mechanism by which testicular Aire regulates fertility. Here, we discuss these results in the context of previous reports which have suggested that infertility observed in Aire deficient mice is of an autoimmune aetiology. We present an alternative point of view for the role of Aire in testes in respect to fertility altering the perspective of how Aire's function in the testes is currently perceived.
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44
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Manjili MH. The adaptation model of immunity: Is the goal of central tolerance to eliminate defective T cells or self-reactive T cells? Scand J Immunol 2022; 96:e13209. [PMID: 36239215 PMCID: PMC9539632 DOI: 10.1111/sji.13209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/09/2022] [Accepted: 08/01/2022] [Indexed: 11/29/2022]
Abstract
The self-non-self model and the danger model are designed to understand how an immune response is induced. These models are not meant to predict if an immune response may succeed or fail in destroying/controlling its target. However, these immunological models rely on either self-antigens or self-dendritic cells for understanding of central tolerance, which have been discussed by Fuchs and Matzinger in response to Al-Yassin. In an attempt to address some questions that these models are facing when it comes to understanding central tolerance, I propose that the goal of negative selection in the thymus is to eliminate defective T cells but not self-reactive T cells. Therefore, any escape from negative selection could increase lymphopenia because of the depletion of defective naïve T cells outside the thymus, as seen in the elderly.
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Affiliation(s)
- Masoud H. Manjili
- Department of Microbiology & Immunology, VCU School of MedicineVCU Massey Cancer CenterRichmondVirginiaUSA
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45
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Michelson DA, Mathis D. Thymic mimetic cells: tolerogenic masqueraders. Trends Immunol 2022; 43:782-791. [PMID: 36008259 PMCID: PMC9509455 DOI: 10.1016/j.it.2022.07.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 10/15/2022]
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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Szwarc MM, Hai L, Maurya VK, Rajapakshe K, Perera D, Ittmann MM, Mo Q, Lin Y, Bettini ML, Coarfa C, Lydon JP. Histopathologic and transcriptomic phenotypes of a conditional RANKL transgenic mouse thymus. Cytokine 2022; 160:156022. [PMID: 36099756 DOI: 10.1016/j.cyto.2022.156022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/16/2022] [Accepted: 08/22/2022] [Indexed: 11/19/2022]
Abstract
Although conventional knockout and transgenic mouse models have significantly advanced our understanding of Receptor Activator of NF-κB Ligand (RANKL) signaling in intra-thymic crosstalk that establishes self-tolerance and later stages of lymphopoiesis, the unique advantages of conditional mouse transgenesis have yet to be explored. A main advantage of conditional transgenesis is the ability to express a transgene in a spatiotemporal restricted manner, enabling the induction (or de-induction) of transgene expression during predetermined stages of embryogenesis or during defined postnatal developmental or physiological states, such as puberty, adulthood, and pregnancy. Here, we describe the K5: RANKL bigenic mouse, in which transgene derived RANKL expression is induced by doxycycline and targeted to cytokeratin 5 positive medullary thymic epithelial cells (mTECs). Short-term doxycycline induction reveals that RANKL transgene expression is significantly induced in the thymic medulla and only in response to doxycycline. Prolonged doxycycline induction in the K5: RANKL bigenic results in a significantly enlarged thymus in which mTECs are hyperproliferative. Flow cytometry showed that there is a marked enrichment of CD4+ and CD8+ single positive thymocytes with a concomitant depletion of CD4+ CD8+ double positives. Furthermore, there is an increase in the number of FOXP3+ T regulatory (Treg) cells and Ulex Europaeus Agglutinin 1+ (UEA1+) mTECs. Transcriptomics revealed that a remarkable array of signals-cytokines, chemokines, growth factors, transcription factors, and morphogens-are governed by RANKL and drive in part the K5: RANKL thymic phenotype. Extended doxycycline administration to 6-weeks results in a K5: RANKL thymus that begins to display distinct histopathological features, such as medullary epithelial hyperplasia, extensive immune cell infiltration, and central tissue necrosis. As there are intense efforts to develop clinical approaches to restore thymic medullary function in the adult to treat immunopathological conditions in which immune cell function is compromised following cancer therapy or toxin exposure, an improved molecular understanding of RANKL's involvement in thymic medulla enlargement will be required. We believe the versatility of the conditional K5: RANKL mouse represents a tractable model system to assist in addressing this requirement as well as many other questions related to RANKL's role in thymic normal physiology and disease processes.
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Affiliation(s)
- Maria M Szwarc
- Department of Molecular & Cellular Biology, United States
| | - Lan Hai
- Department of Molecular & Cellular Biology, United States
| | - Vineet K Maurya
- Department of Molecular & Cellular Biology, United States
| | | | - Dimuthu Perera
- Department of Molecular & Cellular Biology, United States
| | - Michael M Ittmann
- Department of Pathology, Baylor College of Medicine, Houston, TX, United States
| | - Qianxing Mo
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, United States
| | - Yong Lin
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Matthew L Bettini
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Cristian Coarfa
- Department of Molecular & Cellular Biology, United States
| | - John P Lydon
- Department of Molecular & Cellular Biology, United States.
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47
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Benlaribi R, Gou Q, Takaba H. Thymic self-antigen expression for immune tolerance and surveillance. Inflamm Regen 2022; 42:28. [PMID: 36056452 PMCID: PMC9440513 DOI: 10.1186/s41232-022-00211-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 04/27/2022] [Indexed: 11/10/2022] Open
Abstract
T cells are a group of lymphocytes that play a central role in the immune system, notably, eliminating pathogens and attacking cancer while being tolerant of the self. Elucidating how immune tolerance is ensured has become a significant research issue for understanding the pathogenesis of autoimmune diseases as well as cancer immunity. T cell immune tolerance is established mainly in the thymic medulla by the removal of self-responsive T cells and the generation of regulatory T cells, this process depends mainly on the expression of a variety of tissue restricted antigens (TRAs) by medullary thymic epithelial cells (mTECs). The expression of TRAs is known to be regulated by at least two independent factors, Fezf2 and Aire, which play non-redundant and complementary roles by different mechanisms. In this review, we introduce the molecular logic of thymic self-antigen expression that underlies T cell selection for the prevention of autoimmunity and the establishment of immune surveillance.
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Affiliation(s)
- Rayene Benlaribi
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Qiao Gou
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Takaba
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan.
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48
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Taves MD, Ashwell JD. Effects of sex steroids on thymic epithelium and thymocyte development. Front Immunol 2022; 13:975858. [PMID: 36119041 PMCID: PMC9478935 DOI: 10.3389/fimmu.2022.975858] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Sex steroid hormones have major effects on the thymus. Age-related increases in androgens and estrogens and pregnancy-induced increases in progestins all cause dramatic thymic atrophy. Atrophy can also be induced by treatment with exogenous sex steroids and reversed by ablation of endogenous sex steroids. Although these observations are frequently touted as evidence of steroid lymphotoxicity, they are often driven by steroid signaling in thymic epithelial cells (TEC), which are highly steroid responsive. Here, we outline the effects of sex steroids on the thymus and T cell development. We focus on studies that have examined steroid signaling in vivo, aiming to emphasize the actions of endogenous steroids which, via TEC, have remarkable programming effects on the TCR repertoire. Due to the dramatic effects of steroids on TEC, especially thymic involution, the direct effects of sex steroid signaling in thymocytes are less well understood. We outline studies that could be important in addressing these possibilities, and highlight suggestive findings of sex steroid generation within the thymus itself.
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Affiliation(s)
- Matthew D. Taves
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, United States
| | - Jonathan D. Ashwell
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
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49
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Two major genes associated with autoimmune arthritis, Ncf1 and Fcgr2b, additively protect mice by strengthening T cell tolerance. Cell Mol Life Sci 2022; 79:482. [PMID: 35963953 PMCID: PMC9375767 DOI: 10.1007/s00018-022-04501-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/13/2022] [Accepted: 07/22/2022] [Indexed: 11/18/2022]
Abstract
A breach of T cell tolerance is considered as a major step in the pathogenesis of rheumatoid arthritis. In collagen-induced arthritis (CIA) model, immunization with type II collagen (COL2) leads to arthritis in mice through T cells responding to the immunodominant COL2259–273 peptide. T cells could escape from thymus negative selection because endogenous COL2259–273 peptide only weakly binds to the major histocompatibility complex class II (MHCII) molecule Aq. To investigate the regulation of T cell tolerance, we used a new mouse strain BQ.Col2266E with homozygous D266E mutations in the Col2 gene leading to a replacement of the endogenous aspartic acid (D) to glutamic acid (E) at position 266 of the COL2259–273 peptide, resulting in stronger binding to Aq. We also established BQ.Col2264R mice carrying an additional K264R mutation changed the lysine (K) at position 264 to eliminate the major TCR recognition site. The BQ.Col2266E mice were fully resistant to CIA, while the BQ.Col2264R mice developed severe arthritis. Furthermore, we studied two of the most important non-MHCII genes associated with CIA, i.e., Ncf1 and Fcgr2b. Deficiency of either gene induced arthritis in BQ.Col2266E mice, and the downstream effects differ as Ncf1 deficiency reduced Tregs and was likely to decrease expression of autoimmune regulator (AIRE) while Fcgr2b did not. In conclusion, the new human-mimicking mouse model has strong T cell tolerance to COL2, which can be broken by deficiency of Fcgr2b or Ncf1, allowing activation of autoreactive T cells and development of arthritis.
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50
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Carter JA, Strömich L, Peacey M, Chapin SR, Velten L, Steinmetz LM, Brors B, Pinto S, Meyer HV. Transcriptomic diversity in human medullary thymic epithelial cells. Nat Commun 2022; 13:4296. [PMID: 35918316 PMCID: PMC9345899 DOI: 10.1038/s41467-022-31750-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 06/30/2022] [Indexed: 12/03/2022] Open
Abstract
The induction of central T cell tolerance in the thymus depends on the presentation of peripheral self-epitopes by medullary thymic epithelial cells (mTECs). This promiscuous gene expression (pGE) drives mTEC transcriptomic diversity, with non-canonical transcript initiation, alternative splicing, and expression of endogenous retroelements (EREs) representing important but incompletely understood contributors. Here we map the expression of genome-wide transcripts in immature and mature human mTECs using high-throughput 5' cap and RNA sequencing. Both mTEC populations show high splicing entropy, potentially driven by the expression of peripheral splicing factors. During mTEC maturation, rates of global transcript mis-initiation increase and EREs enriched in long terminal repeat retrotransposons are up-regulated, the latter often found in proximity to differentially expressed genes. As a resource, we provide an interactive public interface for exploring mTEC transcriptomic diversity. Our findings therefore help construct a map of transcriptomic diversity in the healthy human thymus and may ultimately facilitate the identification of those epitopes which contribute to autoimmunity and immune recognition of tumor antigens.
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Affiliation(s)
- Jason A. Carter
- grid.225279.90000 0004 0387 3667Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY USA ,grid.36425.360000 0001 2216 9681Medical Scientist Training Program, Stony Brook University, Stony Brook, NY USA ,grid.34477.330000000122986657Department of Surgery, University of Washington, Seattle, WA USA
| | - Léonie Strömich
- grid.7497.d0000 0004 0492 0584German Cancer Research Center, Heidelberg, Germany ,grid.7445.20000 0001 2113 8111Present Address: Imperial College London, London, UK
| | - Matthew Peacey
- grid.225279.90000 0004 0387 3667School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY USA
| | - Sarah R. Chapin
- grid.225279.90000 0004 0387 3667Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY USA
| | - Lars Velten
- grid.473715.30000 0004 6475 7299Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain ,grid.5612.00000 0001 2172 2676Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Lars M. Steinmetz
- grid.4709.a0000 0004 0495 846XEuropean Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany ,grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA USA ,grid.168010.e0000000419368956Stanford Genome Technology Center, Palo Alto, CA USA
| | - Benedikt Brors
- grid.7497.d0000 0004 0492 0584German Cancer Research Center, Heidelberg, Germany
| | - Sheena Pinto
- grid.7497.d0000 0004 0492 0584German Cancer Research Center, Heidelberg, Germany
| | - Hannah V. Meyer
- grid.225279.90000 0004 0387 3667Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY USA
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