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Mowery CT, Freimer JW, Chen Z, Casaní-Galdón S, Umhoefer JM, Arce MM, Gjoni K, Daniel B, Sandor K, Gowen BG, Nguyen V, Simeonov DR, Garrido CM, Curie GL, Schmidt R, Steinhart Z, Satpathy AT, Pollard KS, Corn JE, Bernstein BE, Ye CJ, Marson A. Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells. Nat Genet 2024; 56:1156-1167. [PMID: 38811842 PMCID: PMC11176074 DOI: 10.1038/s41588-024-01743-5] [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: 12/20/2022] [Accepted: 04/04/2024] [Indexed: 05/31/2024]
Abstract
Cis-regulatory elements (CREs) interact with trans regulators to orchestrate gene expression, but how transcriptional regulation is coordinated in multi-gene loci has not been experimentally defined. We sought to characterize the CREs controlling dynamic expression of the adjacent costimulatory genes CD28, CTLA4 and ICOS, encoding regulators of T cell-mediated immunity. Tiling CRISPR interference (CRISPRi) screens in primary human T cells, both conventional and regulatory subsets, uncovered gene-, cell subset- and stimulation-specific CREs. Integration with CRISPR knockout screens and assay for transposase-accessible chromatin with sequencing (ATAC-seq) profiling identified trans regulators influencing chromatin states at specific CRISPRi-responsive elements to control costimulatory gene expression. We then discovered a critical CCCTC-binding factor (CTCF) boundary that reinforces CRE interaction with CTLA4 while also preventing promiscuous activation of CD28. By systematically mapping CREs and associated trans regulators directly in primary human T cell subsets, this work overcomes longstanding experimental limitations to decode context-dependent gene regulatory programs in a complex, multi-gene locus critical to immune homeostasis.
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Grants
- NIH grants 1R01DK129364-01A1, P01AI138962, and R01HG008140; the Larry L. Hillblom Foundation (grant no. 2020-D-002-NET); and Northern California JDRF Center of Excellence. A.M. is a member of the Parker Institute for Cancer Immunotherapy (PICI), and has received funding from the Arc Institute, Chan Zuckerberg Biohub, Innovative Genomics Institute (IGI), Cancer Research Institute (CRI) Lloyd J. Old STAR award, a gift from the Jordan Family, a gift from the Byers family and a gift from B. Bakar.
- UCSF ImmunoX Computational Immunology Fellow, is supported by NIH grant F30AI157167, and has received support from NIH grants T32DK007418 and T32GM007618
- NIH grant R01HG008140
- Career Award for Medical Scientists from the Burroughs Wellcome Fund, a Lloyd J. Old STAR Award from the Cancer Research Institute, and the Parker Institute for Cancer Immunotherapy
- NIH grant U01HL157989
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Affiliation(s)
- Cody T Mowery
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Jacob W Freimer
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Zeyu Chen
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
| | - Salvador Casaní-Galdón
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
| | - Jennifer M Umhoefer
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Maya M Arce
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ketrin Gjoni
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Bence Daniel
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, South San Francisco, CA, USA
| | - Katalin Sandor
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Benjamin G Gowen
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Vinh Nguyen
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, 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
- UCSF CoLabs, University of California, San Francisco, San Francisco, CA, USA
| | - Dimitre R Simeonov
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Christian M Garrido
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Gemma L Curie
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Ralf Schmidt
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Zachary Steinhart
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Ansuman T Satpathy
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Program in Immunology, Stanford University, Stanford, CA, USA
| | - Katherine S Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub SF, San Francisco, CA, USA
| | - Jacob E Corn
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Bradley E Bernstein
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA, USA
| | - Chun Jimmie Ye
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
- Chan Zuckerberg Biohub SF, San Francisco, CA, USA.
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, CA, USA.
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
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2
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Alvarez F, Liu Z, Bay A, Piccirillo CA. Deciphering the developmental trajectory of tissue-resident Foxp3 + regulatory T cells. Front Immunol 2024; 15:1331846. [PMID: 38605970 PMCID: PMC11007185 DOI: 10.3389/fimmu.2024.1331846] [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: 11/01/2023] [Accepted: 02/14/2024] [Indexed: 04/13/2024] Open
Abstract
Foxp3+ TREG cells have been at the focus of intense investigation for their recognized roles in preventing autoimmunity, facilitating tissue recuperation following injury, and orchestrating a tolerance to innocuous non-self-antigens. To perform these critical tasks, TREG cells undergo deep epigenetic, transcriptional, and post-transcriptional changes that allow them to adapt to conditions found in tissues both at steady-state and during inflammation. The path leading TREG cells to express these tissue-specialized phenotypes begins during thymic development, and is further driven by epigenetic and transcriptional modifications following TCR engagement and polarizing signals in the periphery. However, this process is highly regulated and requires TREG cells to adopt strategies to avoid losing their regulatory program altogether. Here, we review the origins of tissue-resident TREG cells, from their thymic and peripheral development to the transcriptional regulators involved in their tissue residency program. In addition, we discuss the distinct signalling pathways that engage the inflammatory adaptation of tissue-resident TREG cells, and how they relate to their ability to recognize tissue and pathogen-derived danger signals.
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Affiliation(s)
- Fernando Alvarez
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- Infectious Diseases and Immunology in Global Health Program, The Research Institute of the McGill University Health Centre (RI-MUHC), Montréal, QC, Canada
- Centre of Excellence in Translational Immunology (CETI), Montréal, QC, Canada
| | - Zhiyang Liu
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- Infectious Diseases and Immunology in Global Health Program, The Research Institute of the McGill University Health Centre (RI-MUHC), Montréal, QC, Canada
- Centre of Excellence in Translational Immunology (CETI), Montréal, QC, Canada
| | - Alexandre Bay
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- Infectious Diseases and Immunology in Global Health Program, The Research Institute of the McGill University Health Centre (RI-MUHC), Montréal, QC, Canada
- Centre of Excellence in Translational Immunology (CETI), Montréal, QC, Canada
| | - Ciriaco A. Piccirillo
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- Infectious Diseases and Immunology in Global Health Program, The Research Institute of the McGill University Health Centre (RI-MUHC), Montréal, QC, Canada
- Centre of Excellence in Translational Immunology (CETI), Montréal, QC, Canada
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3
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Sumida TS, Cheru NT, Hafler DA. The regulation and differentiation of regulatory T cells and their dysfunction in autoimmune diseases. Nat Rev Immunol 2024:10.1038/s41577-024-00994-x. [PMID: 38374298 DOI: 10.1038/s41577-024-00994-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2024] [Indexed: 02/21/2024]
Abstract
The discovery of FOXP3+ regulatory T (Treg) cells as a distinct cell lineage with a central role in regulating immune responses provided a deeper understanding of self-tolerance. The transcription factor FOXP3 serves a key role in Treg cell lineage determination and maintenance, but is not sufficient to enable the full potential of Treg cell suppression, indicating that other factors orchestrate the fine-tuning of Treg cell function. Moreover, FOXP3-independent mechanisms have recently been shown to contribute to Treg cell dysfunction. FOXP3 mutations in humans cause lethal fulminant systemic autoinflammation (IPEX syndrome). However, it remains unclear to what degree Treg cell dysfunction is contributing to the pathophysiology of common autoimmune diseases. In this Review, we discuss the origins of Treg cells in the periphery and the multilayered mechanisms by which Treg cells are induced, as well as the FOXP3-dependent and FOXP3-independent cellular programmes that maintain the suppressive function of Treg cells in humans and mice. Further, we examine evidence for Treg cell dysfunction in the context of common autoimmune diseases such as multiple sclerosis, inflammatory bowel disease, systemic lupus erythematosus and rheumatoid arthritis.
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Affiliation(s)
- Tomokazu S Sumida
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA.
| | - Nardos T Cheru
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - David A Hafler
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA.
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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4
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Johnson M, Lazarus SK, Bennett AE, Tovar-Salazar A, Robertson CE, Kofonow JM, Li S, McCollister B, Nunes MC, Madhi SA, Frank DN, Weinberg A. Gut Microbiota and Other Factors Associated With Increased Regulatory T Cells in Hiv-exposed Uninfected Infants. RESEARCH SQUARE 2024:rs.3.rs-3909424. [PMID: 38352510 PMCID: PMC10862973 DOI: 10.21203/rs.3.rs-3909424/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
HIV-exposed uninfected infants (HEU) have higher infectious morbidity than HIV-unexposed infants (HUU). HEU have multiple immune defects of unknown origin. We hypothesized that HEU have higher regulatory T cells (Treg) than HUU, which may dampen their immune defenses against pathogens. We compared 25 Treg subsets between HEU and HUU and sought the factors that may affect Treg frequencies. At birth, 3 Treg subsets, including CD4 + FOXP3 + and CD4 + FOXP3 + CD25+, had higher frequencies in 123 HEU than 117 HUU and 3 subsets were higher in HUU. At 28 and 62 weeks of life, 5 Treg subsets were higher in HEU, and none were higher in HUU. The frequencies of the discrepant Treg subsets correlated at birth with differential abundances of bacterial taxas in maternal gut microbiome and at subsequent visits in infant gut microbiomes. In vitro, bacterial taxa most abundant in HEU expanded Treg subsets with higher frequencies in HEU, recapitulating the in vivo observations. Other factors that correlated with increased Treg were low maternal CD4 + T cells in HEU at birth and male sex in HUU at 28 weeks. We conclude that maternal and infant gut dysbiosis are central to the Treg increase in HEU and may be targeted by mitigating interventions.
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5
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Rodolfi S, Davidson C, Vecellio M. Regulatory T cells in spondyloarthropathies: genetic evidence, functional role, and therapeutic possibilities. Front Immunol 2024; 14:1303640. [PMID: 38288110 PMCID: PMC10822883 DOI: 10.3389/fimmu.2023.1303640] [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: 09/28/2023] [Accepted: 12/28/2023] [Indexed: 01/31/2024] Open
Abstract
Regulatory T cells (Tregs) are a very specialized subset of T lymphocytes: their main function is controlling immune responses during inflammation. T-regs involvement in autoimmune and immune-mediated rheumatic diseases is well-described. Here, we critically review the up-to-date literature findings on the role of Tregs in spondyloarthropathies, particularly in ankylosing spondylitis (AS), a polygenic inflammatory rheumatic disease that preferentially affects the spine and the sacroiliac joints. Genetics discoveries helped in elucidating pathogenic T-regs gene modules and functional involvement. We highlight T-regs tissue specificity as crucial point, as T-regs might have a distinct epigenomic and molecular profiling depending on the different site of tissue inflammation. Furthermore, we speculate about possible therapeutic interventions targeting, or enhancing, Treg cells in spondyloarthropathies.
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Affiliation(s)
- Stefano Rodolfi
- Department of Rheumatology and Clinical Immunology, IRCCS Humanitas Research Hospital, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Connor Davidson
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Matteo Vecellio
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Centro Ricerche Fondazione Italiana Ricerca Sull’Artrite (FIRA), Fondazione Pisana per la Scienza ONLUS, San Giuliano Terme, Italy
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6
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Inhibition of FOXP3 by stapled alpha-helical peptides dampens regulatory T cell function. Proc Natl Acad Sci U S A 2022; 119:e2209044119. [PMID: 36227917 PMCID: PMC9586281 DOI: 10.1073/pnas.2209044119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Therapies and preclinical probes designed to drug and better understand the specific functions of intracellular protein–protein interactions (PPIs) remain an area of unmet need. This study describes the development of prototype therapeutics against the FOXP3 homodimer, a PPI essential for regulatory T cell suppressive capacity. We demonstrate that hydrocarbon stapled peptides designed to block this interaction can dampen regulatory T cell (Treg cell) suppressive function and lead to genetic signatures of immune reactivation. This work provides strong scientific justification for continued development of FOXP3-specific peptide-based inhibitors and provides mechanistic insights into the design and delivery of specific inhibitors of the coiled-coil region of FOXP3. These studies ultimately could lead to new immunotherapeutic strategies to amplify immune responsiveness in a number of settings. Despite continuing advances in the development of novel cellular-, antibody-, and chemotherapeutic-based strategies to enhance immune reactivity, the presence of regulatory T cells (Treg cells) remains a complicating factor for their clinical efficacy. To overcome dosing limitations and off-target effects from antibody-based Treg cell deletional strategies or small molecule drugging, we investigated the ability of hydrocarbon stapled alpha-helical (SAH) peptides to target FOXP3, the master transcription factor regulator of Treg cell development, maintenance, and suppressive function. Using the crystal structure of the FOXP3 homodimer as a guide, we developed SAHs in the likeness of a portion of the native FOXP3 antiparallel coiled-coil homodimerization domain (SAH-FOXP3) to block this key FOXP3 protein-protein interaction (PPI) through molecular mimicry. We describe the design, synthesis, and biochemical evaluation of single- and double-stapled SAHs covering the entire coiled-coil expanse. We show that lead SAH-FOXP3s bind FOXP3, are cell permeable and nontoxic to T cells, induce dose-dependent transcript and protein level alterations of FOXP3 target genes, impede Treg cell function, and lead to Treg cell gene expression changes in vivo consistent with FOXP3 dysfunction. These results demonstrate a proof of concept for rationally designed FOXP3-directed peptide therapeutics that could be used as approaches to amplify endogenous immune responsiveness.
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7
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Raugh A, Allard D, Bettini M. Nature vs. nurture: FOXP3, genetics, and tissue environment shape Treg function. Front Immunol 2022; 13:911151. [PMID: 36032083 PMCID: PMC9411801 DOI: 10.3389/fimmu.2022.911151] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 07/11/2022] [Indexed: 12/11/2022] Open
Abstract
The importance of regulatory T cells (Tregs) in preventing autoimmunity has been well established; however, the precise alterations in Treg function in autoimmune individuals and how underlying genetic associations impact the development and function of Tregs is still not well understood. Polygenetic susceptibly is a key driving factor in the development of autoimmunity, and many of the pathways implicated in genetic association studies point to a potential alteration or defect in regulatory T cell function. In this review transcriptomic control of Treg development and function is highlighted with a focus on how these pathways are altered during autoimmunity. In combination, observations from autoimmune mouse models and human patients now provide insights into epigenetic control of Treg function and stability. How tissue microenvironment influences Treg function, lineage stability, and functional plasticity is also explored. In conclusion, the current efficacy and future direction of Treg-based therapies for Type 1 Diabetes and other autoimmune diseases is discussed. In total, this review examines Treg function with focuses on genetic, epigenetic, and environmental mechanisms and how Treg functions are altered within the context of autoimmunity.
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Affiliation(s)
- Arielle Raugh
- Department of Pathology, Microbiology and Immunology, University of Utah, Salt Lake City, UT, United States
- Translational Biology and Molecular Medicine Graduate Program, Baylor College of Medicine, Houston, TX, United States
| | - Denise Allard
- Department of Pathology, Microbiology and Immunology, University of Utah, Salt Lake City, UT, United States
| | - Maria Bettini
- Department of Pathology, Microbiology and Immunology, University of Utah, Salt Lake City, UT, United States
- *Correspondence: Maria Bettini,
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8
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Okamura T, Hamaguchi M, Tominaga H, Kitagawa N, Hashimoto Y, Majima S, Senmaru T, Okada H, Ushigome E, Nakanishi N, Shichino S, Fukui M. Characterization of Peripheral Blood TCR in Patients with Type 1 Diabetes Mellitus by BD RhapsodyTM VDJ CDR3 Assay. Cells 2022; 11:cells11101623. [PMID: 35626661 PMCID: PMC9139223 DOI: 10.3390/cells11101623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/04/2022] [Accepted: 05/10/2022] [Indexed: 02/05/2023] Open
Abstract
The sequence of complementarity-determining region 3 of the T-cell receptor (TCR) varies widely due to the insertion of random bases during V-(D)-J recombination. In this study, we used single-cell VDJ sequencing using the latest technology, BD Rhapsody, to identify the TCR sequences of autoreactive T-cells characteristic of Japanese type 1 diabetes mellitus (T1DM) and to clarify the pairing of TCR of peripheral blood mononuclear cells from four patients with T1DM at the single-cell level. The expression levels of the TCR alpha variable (TRAV) 17 and TRAV21 in T1DM patients were higher than those in healthy Japanese subjects. Furthermore, the Shannon index of CD8+ T cells and FOXP3+ cells in T1DM patients was lower than that of healthy subjects. The gene expression of PRF1, GZMH, ITGB2, NKG7, CTSW, and CST7 was increased, while the expression of CD4, CD7, CD5, HLA-A, CD27, and IL-32 was decreased in the CD8+ T cells of T1DM patients. The upregulated gene expression was IL4R and TNFRSF4 in FOXP3+ cells of T1DM patients. Overall, these findings demonstrate that TCR diversity and gene expression of CD8+ and FOXP3+ cells are different in patients with T1DM and healthy subjects.
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Affiliation(s)
- Takuro Okamura
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (T.O.); (M.H.); (H.T.); (N.K.); (Y.H.); (S.M.); (T.S.); (H.O.); (E.U.); (N.N.)
| | - Masahide Hamaguchi
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (T.O.); (M.H.); (H.T.); (N.K.); (Y.H.); (S.M.); (T.S.); (H.O.); (E.U.); (N.N.)
| | - Hiroyuki Tominaga
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (T.O.); (M.H.); (H.T.); (N.K.); (Y.H.); (S.M.); (T.S.); (H.O.); (E.U.); (N.N.)
| | - Noriyuki Kitagawa
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (T.O.); (M.H.); (H.T.); (N.K.); (Y.H.); (S.M.); (T.S.); (H.O.); (E.U.); (N.N.)
| | - Yoshitaka Hashimoto
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (T.O.); (M.H.); (H.T.); (N.K.); (Y.H.); (S.M.); (T.S.); (H.O.); (E.U.); (N.N.)
| | - Saori Majima
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (T.O.); (M.H.); (H.T.); (N.K.); (Y.H.); (S.M.); (T.S.); (H.O.); (E.U.); (N.N.)
| | - Takafumi Senmaru
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (T.O.); (M.H.); (H.T.); (N.K.); (Y.H.); (S.M.); (T.S.); (H.O.); (E.U.); (N.N.)
| | - Hiroshi Okada
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (T.O.); (M.H.); (H.T.); (N.K.); (Y.H.); (S.M.); (T.S.); (H.O.); (E.U.); (N.N.)
| | - Emi Ushigome
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (T.O.); (M.H.); (H.T.); (N.K.); (Y.H.); (S.M.); (T.S.); (H.O.); (E.U.); (N.N.)
| | - Naoko Nakanishi
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (T.O.); (M.H.); (H.T.); (N.K.); (Y.H.); (S.M.); (T.S.); (H.O.); (E.U.); (N.N.)
| | - Shigeyuki Shichino
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Chiba 278-0022, Japan;
| | - Michiaki Fukui
- Department of Endocrinology and Metabolism, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan; (T.O.); (M.H.); (H.T.); (N.K.); (Y.H.); (S.M.); (T.S.); (H.O.); (E.U.); (N.N.)
- Correspondence: ; Tel.: +81-75-251-5505
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9
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Qu G, Chen J, Li Y, Yuan Y, Liang R, Li B. Current status and perspectives of regulatory T cell-based therapy. J Genet Genomics 2022; 49:599-611. [DOI: 10.1016/j.jgg.2022.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/08/2022] [Accepted: 05/18/2022] [Indexed: 02/08/2023]
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10
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Lamarthée B, Marchal A, Charbonnier S, Blein T, Leon J, Martin E, Rabaux L, Vogt K, Titeux M, Delville M, Vinçon H, Six E, Pallet N, Michonneau D, Anglicheau D, Legendre C, Taupin JL, Nemazanyy I, Sawitzki B, Latour S, Cavazzana M, André I, Zuber J. Transient mTOR inhibition rescues 4-1BB CAR-Tregs from tonic signal-induced dysfunction. Nat Commun 2021; 12:6446. [PMID: 34750385 PMCID: PMC8575891 DOI: 10.1038/s41467-021-26844-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 10/25/2021] [Indexed: 12/30/2022] Open
Abstract
The use of chimeric antigen receptor (CAR)-engineered regulatory T cells (Tregs) has emerged as a promising strategy to promote immune tolerance. However, in conventional T cells (Tconvs), CAR expression is often associated with tonic signaling, which can induce CAR-T cell dysfunction. The extent and effects of CAR tonic signaling vary greatly according to the expression intensity and intrinsic properties of the CAR. Here, we show that the 4-1BB CSD-associated tonic signal yields a more dramatic effect in CAR-Tregs than in CAR-Tconvs with respect to activation and proliferation. Compared to CD28 CAR-Tregs, 4-1BB CAR-Tregs exhibit decreased lineage stability and reduced in vivo suppressive capacities. Transient exposure of 4-1BB CAR-Tregs to a Treg stabilizing cocktail, including an mTOR inhibitor and vitamin C, during ex vivo expansion sharply improves their in vivo function and expansion after adoptive transfer. This study demonstrates that the negative effects of 4-1BB tonic signaling in Tregs can be mitigated by transient mTOR inhibition.
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MESH Headings
- Animals
- CD28 Antigens/immunology
- CD28 Antigens/metabolism
- Graft vs Host Disease/immunology
- Graft vs Host Disease/therapy
- HLA-A2 Antigen/immunology
- HLA-A2 Antigen/metabolism
- Humans
- Immunosuppressive Agents/pharmacology
- Immunotherapy, Adoptive/methods
- Jurkat Cells
- Male
- Mice, Inbred NOD
- Mice, Knockout
- Mice, SCID
- Receptors, Chimeric Antigen/immunology
- Receptors, Chimeric Antigen/metabolism
- Signal Transduction/drug effects
- Signal Transduction/immunology
- Sirolimus/pharmacology
- T-Lymphocytes, Regulatory/cytology
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
- TOR Serine-Threonine Kinases/antagonists & inhibitors
- TOR Serine-Threonine Kinases/immunology
- TOR Serine-Threonine Kinases/metabolism
- Transplantation, Heterologous
- Tumor Necrosis Factor Receptor Superfamily, Member 9/immunology
- Tumor Necrosis Factor Receptor Superfamily, Member 9/metabolism
- Mice
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Affiliation(s)
- Baptiste Lamarthée
- Laboratoire de lymphohématopoïèse humaine, INSERM UMR 1163, IHU IMAGINE, Paris, France
| | - Armance Marchal
- Laboratoire de lymphohématopoïèse humaine, INSERM UMR 1163, IHU IMAGINE, Paris, France
| | - Soëli Charbonnier
- Laboratoire de lymphohématopoïèse humaine, INSERM UMR 1163, IHU IMAGINE, Paris, France
| | - Tifanie Blein
- Laboratoire de lymphohématopoïèse humaine, INSERM UMR 1163, IHU IMAGINE, Paris, France
| | - Juliette Leon
- Department of Immunology, Harvard Medical School, Boston, MA, 02115, USA
| | - Emmanuel Martin
- Lymphocyte activation and susceptibility to EBV, INSERM UMR 1163, IHU IMAGINE, Paris, France
| | - Lucas Rabaux
- Laboratoire de lymphohématopoïèse humaine, INSERM UMR 1163, IHU IMAGINE, Paris, France
| | - Katrin Vogt
- Department of Immunology, Charité University Hospital, Berlin, Germany
| | - Matthias Titeux
- Maladie génétique cutanée, INSERM UMR 1163, IHU IMAGINE, Paris, France
| | - Marianne Delville
- Laboratoire de lymphohématopoïèse humaine, INSERM UMR 1163, IHU IMAGINE, Paris, France
- Université de Paris, Paris, France
- Service de Biothérapie et Thérapie Génique Clinique, Assistance Publique-Hôpitaux de Paris, Hôpital Necker, Paris, France
| | - Hélène Vinçon
- Laboratoire de lymphohématopoïèse humaine, INSERM UMR 1163, IHU IMAGINE, Paris, France
| | - Emmanuelle Six
- Laboratoire de lymphohématopoïèse humaine, INSERM UMR 1163, IHU IMAGINE, Paris, France
| | - Nicolas Pallet
- Université de Paris, INSERM U1138, Centre de Recherche des Cordeliers, 75006, Paris, France
| | | | - Dany Anglicheau
- Université de Paris, Paris, France
- Service de Transplantation rénale adulte, Assistance Publique-Hôpitaux de Paris, Hôpital Necker, Paris, France
- INSERM U1151, Institut Necker Enfants Malades, Paris, France
| | - Christophe Legendre
- Université de Paris, Paris, France
- Service de Transplantation rénale adulte, Assistance Publique-Hôpitaux de Paris, Hôpital Necker, Paris, France
| | - Jean-Luc Taupin
- Université de Paris, Paris, France
- Laboratoire d'immunologie et histocompatibilité, Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Louis, Paris, France
| | - Ivan Nemazanyy
- Plateforme de Métabolique, Structure Fédérative de Recherche, Necker, INSERM US24/CNRS UMS, 3633, Paris, France
| | - Birgit Sawitzki
- Department of Immunology, Charité University Hospital, Berlin, Germany
| | - Sylvain Latour
- Lymphocyte activation and susceptibility to EBV, INSERM UMR 1163, IHU IMAGINE, Paris, France
| | - Marina Cavazzana
- Laboratoire de lymphohématopoïèse humaine, INSERM UMR 1163, IHU IMAGINE, Paris, France
- Université de Paris, Paris, France
- Service de Biothérapie et Thérapie Génique Clinique, Assistance Publique-Hôpitaux de Paris, Hôpital Necker, Paris, France
| | - Isabelle André
- Laboratoire de lymphohématopoïèse humaine, INSERM UMR 1163, IHU IMAGINE, Paris, France
| | - Julien Zuber
- Laboratoire de lymphohématopoïèse humaine, INSERM UMR 1163, IHU IMAGINE, Paris, France.
- Université de Paris, Paris, France.
- Service de Transplantation rénale adulte, Assistance Publique-Hôpitaux de Paris, Hôpital Necker, Paris, France.
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11
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Regulatory T cells function in established systemic inflammation and reverse fatal autoimmunity. Nat Immunol 2021; 22:1163-1174. [PMID: 34426690 PMCID: PMC9341271 DOI: 10.1038/s41590-021-01001-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 07/14/2021] [Indexed: 12/22/2022]
Abstract
The immunosuppressive function of regulatory T (Treg) cells is dependent on continuous expression of the transcription factor Foxp3. Foxp3 loss-of-function or induced ablation of Treg cells results in a fatal autoimmune disease featuring all known types of inflammatory responses with every manifestation stemming from Treg cell paucity, highlighting a vital function of Treg cells in preventing fatal autoimmune inflammation. However, a major question remains whether Treg cells can persist and effectively exert their function in a disease state, where a broad spectrum of inflammatory mediators can either inactivate Treg cells or render innate and adaptive pro-inflammatory effector cells insensitive to suppression. By reinstating Foxp3 protein expression and suppressor function in cells expressing a reversible Foxp3 null allele in severely diseased mice, we found that the resulting single pool of “redeemed” Treg cells normalized immune activation, quelled severe tissue inflammation, reversed fatal autoimmune disease, and provided long-term protection against them. Thus, Treg cells are functional in settings of established broad spectrum systemic inflammation and are capable of affording sustained reset of immune homeostasis.
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12
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Lu J, Liang Y, Meng H, Zhang A, Zhao J, Zhang C. Metabolic Controls on Epigenetic Reprogramming in Regulatory T Cells. Front Immunol 2021; 12:728783. [PMID: 34421930 PMCID: PMC8374078 DOI: 10.3389/fimmu.2021.728783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 07/23/2021] [Indexed: 01/20/2023] Open
Abstract
Forkhead box protein 3 (Foxp3+)-expressing regulatory T (Treg) cells are a unique CD4+T cell subset that suppresses excessive immune responses. The epigenetic plasticity and metabolic traits of Treg cells are crucial for the acquisition of their phenotypic and functional characteristics. Therefore, alterations to the epigenetics and metabolism affect Treg cell development and function. Recent evidence reveals that altering the metabolic pathways and generation of metabolites can regulate the epigenetics of Treg cells. Specifically, some intermediates of cell metabolism can directly act as substrates or cofactors of epigenetic-modifying enzymes. Here, we describe the metabolic and epigenetic features during Treg cell development, and discuss how metabolites can contribute to epigenetic alterations of Treg cells, which affects Treg cell activation, differentiation, and function.
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Affiliation(s)
- Jingli Lu
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou, China.,Zhengzhou Key Laboratory of Clinical Mass Spectrometry, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yan Liang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou, China.,Zhengzhou Key Laboratory of Clinical Mass Spectrometry, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Haiyang Meng
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou, China.,Zhengzhou Key Laboratory of Clinical Mass Spectrometry, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ailing Zhang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou, China.,Zhengzhou Key Laboratory of Clinical Mass Spectrometry, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Junjie Zhao
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou, China.,Zhengzhou Key Laboratory of Clinical Mass Spectrometry, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chengliang Zhang
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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13
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Shimojima Y, Ichikawa T, Kishida D, Takamatsu R, Sekijima Y. Circulating regulatory T cells in adult-onset Still's disease: Focusing on their plasticity and stability. Clin Exp Immunol 2021; 206:184-195. [PMID: 34319596 DOI: 10.1111/cei.13648] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/23/2021] [Accepted: 07/21/2021] [Indexed: 11/28/2022] Open
Abstract
We investigated the characteristics of regulatory T cells in adult-onset Still's disease (AOSD) with a focus on their plasticity, stability and relationship to disease severity. The proportion of circulating CD4+ CD25+ forkhead box protein 3 (FoxP3+ ) cells (Tregs ) and intracellular expression of effector cytokines, including interferon (IFN)-γ, interleukin (IL)-17 and IL-4, was analysed in 27 untreated patients with AOSD (acute AOSD), 11 of the 27 patients after remission and 16 healthy controls (HC) using flow cytometry. The suppressive ability of Tregs was also evaluated. Regression analyses of the results were performed. The proportion of Tregs was significantly lower in patients with acute AOSD than in the HC. The expression levels of IFN-γ, IL-17 and IL-4 in Tregs were significantly increased in patients with acute AOSD. IFN-γ and IL-4 expression levels were inversely correlated with the proportion of Tregs and positively correlated with serum ferritin levels. Decreased expression of FoxP3 in CD4+ CD25+ cells, which was correlated with increased expression of IL-17, and impaired suppressive function were observed in Tregs in acute AOSD. However, these aberrant findings in Tregs , including the reduced circulating proportion and functional ability and altered intracellular expression levels of cytokines and FoxP3, were significantly improved after remission. In acute AOSD, Tregs show plastic changes, including effector cytokine production and reductions in their proportion and functional activity. IFN-γ and IL-4 expression levels in Tregs may be associated with disease severity. Also, down-regulation of FoxP3 may be related to IL-17 expression in Tregs . Importantly, the stability of Tregs can be restored in remission.
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Affiliation(s)
- Yasuhiro Shimojima
- Department of Medicine (Neurology and Rheumatology), Shinshu University School of Medicine, Matsumoto, Japan
| | - Takanori Ichikawa
- Department of Medicine (Neurology and Rheumatology), Shinshu University School of Medicine, Matsumoto, Japan
| | - Dai Kishida
- Department of Medicine (Neurology and Rheumatology), Shinshu University School of Medicine, Matsumoto, Japan
| | - Ryota Takamatsu
- Department of Medicine (Neurology and Rheumatology), Shinshu University School of Medicine, Matsumoto, Japan
| | - Yoshiki Sekijima
- Department of Medicine (Neurology and Rheumatology), Shinshu University School of Medicine, Matsumoto, Japan
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14
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Mijnheer G, Lutter L, Mokry M, van der Wal M, Scholman R, Fleskens V, Pandit A, Tao W, Wekking M, Vervoort S, Roberts C, Petrelli A, Peeters JGC, Knijff M, de Roock S, Vastert S, Taams LS, van Loosdregt J, van Wijk F. Conserved human effector Treg cell transcriptomic and epigenetic signature in arthritic joint inflammation. Nat Commun 2021; 12:2710. [PMID: 33976194 PMCID: PMC8113485 DOI: 10.1038/s41467-021-22975-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 04/08/2021] [Indexed: 02/07/2023] Open
Abstract
Treg cells are critical regulators of immune homeostasis, and environment-driven Treg cell differentiation into effector (e)Treg cells is crucial for optimal functioning. However, human Treg cell programming in inflammation is unclear. Here, we combine transcriptional and epigenetic profiling to identify a human eTreg cell signature. Inflammation-derived functional Treg cells have a transcriptional profile characterized by upregulation of both a core Treg cell (FOXP3, CTLA4, TIGIT) and effector program (GITR, BLIMP-1, BATF). We identify a specific human eTreg cell signature that includes the vitamin D receptor (VDR) as a predicted regulator in eTreg cell differentiation. H3K27ac/H3K4me1 occupancy indicates an altered (super-)enhancer landscape, including enrichment of the VDR and BATF binding motifs. The Treg cell profile has striking overlap with tumor-infiltrating Treg cells. Our data demonstrate that human inflammation-derived Treg cells acquire a conserved and specific eTreg cell profile guided by epigenetic changes, and fine-tuned by environment-specific adaptations.
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MESH Headings
- Adolescent
- Arthritis, Juvenile/genetics
- Arthritis, Juvenile/immunology
- Arthritis, Juvenile/pathology
- Base Sequence
- Basic-Leucine Zipper Transcription Factors/genetics
- Basic-Leucine Zipper Transcription Factors/immunology
- CTLA-4 Antigen/genetics
- CTLA-4 Antigen/immunology
- Case-Control Studies
- Cell Differentiation
- Child
- Child, Preschool
- Epigenesis, Genetic
- Female
- Forkhead Transcription Factors/genetics
- Forkhead Transcription Factors/immunology
- Gene Expression Profiling
- Gene Regulatory Networks
- Glucocorticoid-Induced TNFR-Related Protein/genetics
- Glucocorticoid-Induced TNFR-Related Protein/immunology
- Histones/genetics
- Histones/immunology
- Humans
- Joints/immunology
- Joints/pathology
- Male
- Metabolic Networks and Pathways/genetics
- Metabolic Networks and Pathways/immunology
- Positive Regulatory Domain I-Binding Factor 1/genetics
- Positive Regulatory Domain I-Binding Factor 1/immunology
- Primary Cell Culture
- Receptors, Calcitriol/genetics
- Receptors, Calcitriol/immunology
- Receptors, Immunologic/genetics
- Receptors, Immunologic/immunology
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/pathology
- Transcriptome
- Young Adult
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Affiliation(s)
- Gerdien Mijnheer
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Lisanne Lutter
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Michal Mokry
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Regenerative Medicine Center Utrecht, Department of Pediatrics, University Medical Center Utrecht, Utrecht, The Netherlands
- Epigenomics facility, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marlot van der Wal
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Rianne Scholman
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Veerle Fleskens
- Centre for Inflammation Biology and Cancer Immunology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Aridaman Pandit
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Weiyang Tao
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Mark Wekking
- Epigenomics facility, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Stephin Vervoort
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Regenerative Medicine Center Utrecht, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ceri Roberts
- Centre for Inflammation Biology and Cancer Immunology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Alessandra Petrelli
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Janneke G C Peeters
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marthe Knijff
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Sytze de Roock
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Sebastiaan Vastert
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Leonie S Taams
- Centre for Inflammation Biology and Cancer Immunology, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Jorg van Loosdregt
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Regenerative Medicine Center Utrecht, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Femke van Wijk
- Center for Translational Immunology, Pediatric Immunology & Rheumatology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
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15
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Inoue M, Yamashita K, Tsuji Y, Miki M, Amano S, Okumura T, Kuge K, Tone T, Enomoto S, Yoshimine C, Morita Y, Ando D, Kamada H, Mikami N, Tsutsumi Y, Tsunoda SI. Characterization of a TNFR2-Selective Agonistic TNF-α Mutant and Its Derivatives as an Optimal Regulatory T Cell Expander. THE JOURNAL OF IMMUNOLOGY 2021; 206:1740-1751. [PMID: 33782090 DOI: 10.4049/jimmunol.2000871] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 02/02/2021] [Indexed: 12/26/2022]
Abstract
Regulatory T cells (Tregs) are a subpopulation of lymphocytes that play a role in suppressing and regulating immune responses. Recently, it was suggested that controlling the functions and activities of Tregs might be applicable to the treatment of human diseases such as autoimmune diseases, organ transplant rejection, and graft-versus-host disease. TNF receptor type 2 (TNFR2) is a target molecule that modulates Treg functions. In this study, we investigated the role of TNFR2 signaling in the differentiation and activation of mouse Tregs. We previously reported the generation of a TNFR2-selective agonist TNF mutant, termed R2agoTNF, by using our unique cytokine modification method based on phage display. R2agoTNF activates cell signaling via mouse TNFR2. In this study, we evaluated the efficacy of R2agoTNF for the proliferation and activation of Tregs in mice. R2agoTNF expanded and activated mouse CD4+CD25+ Tregs ex vivo. The structural optimization of R2agoTNF by internal cross-linking or IgG-Fc fusion selectively and effectively enhanced Treg expansion in vivo. Furthermore, the IgG-Fc fusion protein suppressed skin-contact hypersensitivity reactions in mice. TNFR2 agonists are expected to be new Treg expanders.
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Affiliation(s)
- Masaki Inoue
- Laboratory of Cellular and Molecular Physiology, The Faculty of Pharmaceutical Sciences, Kobe Gakuin University, Chuo-ku, Kobe 650-8586, Japan.,Laboratory of Biopharmaceutical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan.,Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Kanako Yamashita
- Laboratory of Cellular and Molecular Physiology, The Faculty of Pharmaceutical Sciences, Kobe Gakuin University, Chuo-ku, Kobe 650-8586, Japan
| | - Yuta Tsuji
- Laboratory of Cellular and Molecular Physiology, The Faculty of Pharmaceutical Sciences, Kobe Gakuin University, Chuo-ku, Kobe 650-8586, Japan
| | - Midori Miki
- Laboratory of Cellular and Molecular Physiology, The Faculty of Pharmaceutical Sciences, Kobe Gakuin University, Chuo-ku, Kobe 650-8586, Japan
| | - Shota Amano
- Laboratory of Cellular and Molecular Physiology, The Faculty of Pharmaceutical Sciences, Kobe Gakuin University, Chuo-ku, Kobe 650-8586, Japan
| | - Taichi Okumura
- Laboratory of Cellular and Molecular Physiology, The Faculty of Pharmaceutical Sciences, Kobe Gakuin University, Chuo-ku, Kobe 650-8586, Japan
| | - Koki Kuge
- Laboratory of Cellular and Molecular Physiology, The Faculty of Pharmaceutical Sciences, Kobe Gakuin University, Chuo-ku, Kobe 650-8586, Japan
| | - Takao Tone
- Laboratory of Cellular and Molecular Physiology, The Faculty of Pharmaceutical Sciences, Kobe Gakuin University, Chuo-ku, Kobe 650-8586, Japan
| | - Shota Enomoto
- Laboratory of Cellular and Molecular Physiology, The Faculty of Pharmaceutical Sciences, Kobe Gakuin University, Chuo-ku, Kobe 650-8586, Japan
| | - Chinatsu Yoshimine
- Laboratory of Cellular and Molecular Physiology, The Faculty of Pharmaceutical Sciences, Kobe Gakuin University, Chuo-ku, Kobe 650-8586, Japan
| | - Yuki Morita
- Laboratory of Cellular and Molecular Physiology, The Faculty of Pharmaceutical Sciences, Kobe Gakuin University, Chuo-ku, Kobe 650-8586, Japan
| | - Daisuke Ando
- Laboratory of Biopharmaceutical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan.,National Institutes of Health Sciences, Kawasaki-ku, Kawasaki 210-9501, Japan
| | - Haruhiko Kamada
- Laboratory of Biopharmaceutical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan.,Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan.,Global Center for Medical Engineering and Informatics, Osaka University, Suita, Osaka 565-0871, Japan
| | - Norihisa Mikami
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Suita, Osaka 65-0871, Japan; and
| | - Yasuo Tsutsumi
- Global Center for Medical Engineering and Informatics, Osaka University, Suita, Osaka 565-0871, Japan.,Laboratory of Toxicology and Safety Science, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shin-Ichi Tsunoda
- Laboratory of Cellular and Molecular Physiology, The Faculty of Pharmaceutical Sciences, Kobe Gakuin University, Chuo-ku, Kobe 650-8586, Japan; .,Laboratory of Biopharmaceutical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan.,Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan.,Global Center for Medical Engineering and Informatics, Osaka University, Suita, Osaka 565-0871, Japan
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16
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Kasatskaya SA, Ladell K, Egorov ES, Miners KL, Davydov AN, Metsger M, Staroverov DB, Matveyshina EK, Shagina IA, Mamedov IZ, Izraelson M, Shelyakin PV, Britanova OV, Price DA, Chudakov DM. Functionally specialized human CD4 + T-cell subsets express physicochemically distinct TCRs. eLife 2020; 9:57063. [PMID: 33289628 PMCID: PMC7773335 DOI: 10.7554/elife.57063] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 12/04/2020] [Indexed: 12/26/2022] Open
Abstract
The organizational integrity of the adaptive immune system is determined by functionally discrete subsets of CD4+ T cells, but it has remained unclear to what extent lineage choice is influenced by clonotypically expressed T-cell receptors (TCRs). To address this issue, we used a high-throughput approach to profile the αβ TCR repertoires of human naive and effector/memory CD4+ T-cell subsets, irrespective of antigen specificity. Highly conserved physicochemical and recombinatorial features were encoded on a subset-specific basis in the effector/memory compartment. Clonal tracking further identified forbidden and permitted transition pathways, mapping effector/memory subsets related by interconversion or ontogeny. Public sequences were largely confined to particular effector/memory subsets, including regulatory T cells (Tregs), which also displayed hardwired repertoire features in the naive compartment. Accordingly, these cumulative repertoire portraits establish a link between clonotype fate decisions in the complex world of CD4+ T cells and the intrinsic properties of somatically rearranged TCRs.
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Affiliation(s)
- Sofya A Kasatskaya
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russian Federation.,Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Evgeniy S Egorov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Kelly L Miners
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Alexey N Davydov
- Adaptive Immunity Group, Central European Institute of Technology, Brno, Czech Republic
| | - Maria Metsger
- Adaptive Immunity Group, Central European Institute of Technology, Brno, Czech Republic
| | - Dmitry B Staroverov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.,Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Elena K Matveyshina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Irina A Shagina
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.,Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Ilgar Z Mamedov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.,Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Mark Izraelson
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.,Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - Pavel V Shelyakin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russian Federation.,Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Olga V Britanova
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.,Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom.,Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Dmitriy M Chudakov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russian Federation.,Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation.,Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russian Federation
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17
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van der Veeken J, Glasner A, Zhong Y, Hu W, Wang ZM, Bou-Puerto R, Charbonnier LM, Chatila TA, Leslie CS, Rudensky AY. The Transcription Factor Foxp3 Shapes Regulatory T Cell Identity by Tuning the Activity of trans-Acting Intermediaries. Immunity 2020; 53:971-984.e5. [PMID: 33176163 DOI: 10.1016/j.immuni.2020.10.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/06/2020] [Accepted: 10/14/2020] [Indexed: 12/16/2022]
Abstract
Regulatory T (Treg) cell identity is defined by the lineage-specifying transcription factor (TF) Foxp3. Here we examined mechanisms of Foxp3 function by leveraging naturally occurring genetic variation in wild-derived inbred mice, which enables the identification of DNA sequence motifs driving epigenetic features. Chromatin accessibility, TF binding, and gene expression patterns in resting and activated subsets of Treg cells, conventional CD4 T cells, and cells expressing a Foxp3 reporter null allele revealed that the majority of Foxp3-dependent changes occurred at sites not bound by Foxp3. Chromatin accessibility of these indirect Foxp3 targets depended on the presence of DNA binding motifs for other TFs, including TCF1. Foxp3 expression correlated with decreased TCF1 and reduced accessibility of TCF1-bound chromatin regions. Deleting one copy of the Tcf7 gene recapitulated Foxp3-dependent negative regulation of chromatin accessibility. Thus, Foxp3 defines Treg cell identity in a largely indirect manner by fine-tuning the activity of other major chromatin remodeling TFs such as TCF1.
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Affiliation(s)
- Joris van der Veeken
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Ariella Glasner
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yi Zhong
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA; Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wei Hu
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhong-Min Wang
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA; Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Regina Bou-Puerto
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Louis-Marie Charbonnier
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Talal A Chatila
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Christina S Leslie
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander Y Rudensky
- Howard Hughes Medical Institute and Immunology Program, Sloan Kettering Institute, and Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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18
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Brown CY, Sadlon T, Hope CM, Wong YY, Wong S, Liu N, Withers H, Brown K, Bandara V, Gundsambuu B, Pederson S, Breen J, Robertson SA, Forrest A, Beyer M, Barry SC. Molecular Insights Into Regulatory T-Cell Adaptation to Self, Environment, and Host Tissues: Plasticity or Loss of Function in Autoimmune Disease. Front Immunol 2020; 11:1269. [PMID: 33072063 PMCID: PMC7533603 DOI: 10.3389/fimmu.2020.01269] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 05/19/2020] [Indexed: 12/19/2022] Open
Abstract
There has been much interest in the ability of regulatory T cells (Treg) to switch function in vivo, either as a result of genetic risk of disease or in response to environmental and metabolic cues. The relationship between levels of FOXP3 and functional fitness plays a significant part in this plasticity. There is an emerging role for Treg in tissue repair that may be less dependent on FOXP3, and the molecular mechanisms underpinning this are not fully understood. As a result of detailed, high-resolution functional genomics, the gene regulatory networks and key functional mediators of Treg phenotype downstream of FOXP3 have been mapped, enabling a mechanistic insight into Treg function. This transcription factor-driven programming of T-cell function to generate Treg requires the switching on and off of key genes that form part of the Treg gene regulatory network and raises the possibility that this is reversible. It is plausible that subtle shifts in expression levels of specific genes, including transcription factors and non-coding RNAs, change the regulation of the Treg gene network. The subtle skewing of gene expression initiates changes in function, with the potential to promote chronic disease and/or to license appropriate inflammatory responses. In the case of autoimmunity, there is an underlying genetic risk, and the interplay of genetic and environmental cues is complex and impacts gene regulation networks frequently involving promoters and enhancers, the regulatory elements that control gene expression levels and responsiveness. These promoter–enhancer interactions can operate over long distances and are highly cell type specific. In autoimmunity, the genetic risk can result in changes in these enhancer/promoter interactions, and this mainly impacts genes which are expressed in T cells and hence impacts Treg/conventional T-cell (Tconv) function. Genetic risk may cause the subtle alterations to the responsiveness of gene regulatory networks which are controlled by or control FOXP3 and its target genes, and the application of assays of the 3D organization of chromatin, enabling the connection of non-coding regulatory regions to the genes they control, is revealing the direct impact of environmental/metabolic/genetic risk on T-cell function and is providing mechanistic insight into susceptibility to inflammatory and autoimmune conditions.
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Affiliation(s)
- Cheryl Y Brown
- Molecular Immunology, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Timothy Sadlon
- Molecular Immunology, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia.,Women's and Children's Health Network, North Adelaide, SA, Australia
| | | | - Ying Y Wong
- Molecular Immunology, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Soon Wong
- Molecular Immunology, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Ning Liu
- Bioinformatics Hub, University of Adelaide, Adelaide, SA, Australia
| | - Holly Withers
- Molecular Immunology, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Katherine Brown
- Molecular Immunology, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Veronika Bandara
- Molecular Immunology, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Batjargal Gundsambuu
- Molecular Immunology, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Stephen Pederson
- Bioinformatics Hub, University of Adelaide, Adelaide, SA, Australia
| | - James Breen
- Bioinformatics Hub, University of Adelaide, Adelaide, SA, Australia
| | - Sarah Anne Robertson
- Molecular Immunology, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Alistair Forrest
- QEII Medical Centre and Centre for Medical Research, Harry Perkins Institute of Medical Research, Murdoch, WA, Australia
| | - Marc Beyer
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Simon Charles Barry
- Molecular Immunology, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia.,Women's and Children's Health Network, North Adelaide, SA, Australia
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19
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Ng MSF, Roth TL, Mendoza VF, Marson A, Burt TD. Helios enhances the preferential differentiation of human fetal CD4 + naïve T cells into regulatory T cells. Sci Immunol 2020; 4:4/41/eaav5947. [PMID: 31757834 DOI: 10.1126/sciimmunol.aav5947] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 10/24/2019] [Indexed: 12/14/2022]
Abstract
T cell receptor (TCR) stimulation and cytokine cues drive the differentiation of CD4+ naïve T cells into effector T cell populations with distinct proinflammatory or regulatory functions. Unlike adult naïve T cells, human fetal naïve CD4+ T cells preferentially differentiate into FOXP3+ regulatory T (Treg) cells upon TCR activation independent of exogenous cytokine signaling. This cell-intrinsic predisposition for Treg differentiation is implicated in the generation of tolerance in utero; however, the underlying mechanisms remain largely unknown. Here, we identify epigenetic and transcriptional programs shared between fetal naïve T and committed Treg cells that are inactive in adult naïve T cells and show that fetal-derived induced Treg (iTreg) cells retain this transcriptional program. We show that a subset of Treg-specific enhancers is accessible in fetal naïve T cells, including two active superenhancers at Helios Helios is expressed in fetal naïve T cells but not in adult naïve T cells, and fetal iTreg cells maintain Helios expression. CRISPR-Cas9 ablation of Helios in fetal naïve T cells impaired their differentiation into iTreg cells upon TCR stimulation, reduced expression of immunosuppressive genes in fetal iTreg cells such as IL10, and increased expression of proinflammatory genes including IFNG Consequently, Helios knockout fetal iTreg cells had reduced IL-10 and increased IFN-γ cytokine production. Together, our results reveal important roles for Helios in enhancing preferential fetal Treg differentiation and fine-tuning eventual Treg function. The Treg-biased programs identified within fetal naïve T cells could potentially be used to engineer enhanced iTreg populations for adoptive cellular therapies.
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Affiliation(s)
- Melissa S F Ng
- Biomedical Sciences Graduate Program, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA.,Singapore Immunology Network, Agency for Science, Technology and Research, Biopolis, Singapore 138648, Singapore
| | - Theodore L Roth
- Biomedical Sciences Graduate Program, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA.,Department of Microbiology and Immunology, UCSF, San Francisco, CA 94143, USA.,Diabetes Center, UCSF, San Francisco, CA 94143, USA
| | - Ventura F Mendoza
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA 94143, USA
| | - Alexander Marson
- Department of Microbiology and Immunology, UCSF, San Francisco, CA 94143, USA.,Diabetes Center, UCSF, San Francisco, CA 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.,Department of Medicine, UCSF, San Francisco, CA 94143, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.,UCSF Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, CA 94158, USA.,Parker Institute for Cancer Immunotherapy, San Francisco, CA 94129, USA
| | - Trevor D Burt
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA 94143, USA. .,Department of Pediatrics, Division of Neonatology, UCSF, San Francisco, CA 94110, USA
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20
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Nasrallah R, Imianowski CJ, Bossini-Castillo L, Grant FM, Dogan M, Placek L, Kozhaya L, Kuo P, Sadiyah F, Whiteside SK, Mumbach MR, Glinos D, Vardaka P, Whyte CE, Lozano T, Fujita T, Fujii H, Liston A, Andrews S, Cozzani A, Yang J, Mitra S, Lugli E, Chang HY, Unutmaz D, Trynka G, Roychoudhuri R. A distal enhancer at risk locus 11q13.5 promotes suppression of colitis by T reg cells. Nature 2020; 583:447-452. [PMID: 32499651 PMCID: PMC7116706 DOI: 10.1038/s41586-020-2296-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 03/10/2020] [Indexed: 02/02/2023]
Abstract
Genetic variations underlying susceptibility to complex autoimmune and allergic diseases are concentrated within noncoding regulatory elements termed enhancers1. The functions of a large majority of disease-associated enhancers are unknown, in part owing to their distance from the genes they regulate, a lack of understanding of the cell types in which they operate, and our inability to recapitulate the biology of immune diseases in vitro. Here, using shared synteny to guide loss-of-function analysis of homologues of human enhancers in mice, we show that the prominent autoimmune and allergic disease risk locus at chromosome 11q13.52-7 contains a distal enhancer that is functional in CD4+ regulatory T (Treg) cells and required for Treg-mediated suppression of colitis. The enhancer recruits the transcription factors STAT5 and NF-κB to mediate signal-driven expression of Lrrc32, which encodes the protein glycoprotein A repetitions predominant (GARP). Whereas disruption of the Lrrc32 gene results in early lethality, mice lacking the enhancer are viable but lack GARP expression in Foxp3+ Treg cells, which are unable to control colitis in a cell-transfer model of the disease. In human Treg cells, the enhancer forms conformational interactions with the promoter of LRRC32 and enhancer risk variants are associated with reduced histone acetylation and GARP expression. Finally, functional fine-mapping of 11q13.5 using CRISPR-activation (CRISPRa) identifies a CRISPRa-responsive element in the vicinity of risk variant rs11236797 capable of driving GARP expression. These findings provide a mechanistic basis for association of the 11q13.5 risk locus with immune-mediated diseases and identify GARP as a potential target in their therapy.
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Affiliation(s)
- Rabab Nasrallah
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
| | - Charlotte J Imianowski
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
| | | | - Francis M Grant
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
| | | | | | | | - Paula Kuo
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Firas Sadiyah
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Sarah K Whiteside
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Maxwell R Mumbach
- Howard Hughes Medical Institute and Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Dafni Glinos
- Immune Genomics Group, Wellcome Sanger Institute, Cambridge, UK
| | - Panagiota Vardaka
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Carly E Whyte
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
| | - Teresa Lozano
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
| | - Toshitsugu Fujita
- Chromatin Biochemistry Research Group, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Hodaka Fujii
- Chromatin Biochemistry Research Group, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Adrian Liston
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge, UK
| | - Adeline Cozzani
- Inserm UMR1277/CNRS9020, Institut pour la Recherche sur le Cancer de Lille, Lille, France
| | - Jie Yang
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Suman Mitra
- Inserm UMR1277/CNRS9020, Institut pour la Recherche sur le Cancer de Lille, Lille, France
| | - Enrico Lugli
- Humanitas Clinical and Research Center, Milan, Italy
| | - Howard Y Chang
- Howard Hughes Medical Institute and Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Gosia Trynka
- Immune Genomics Group, Wellcome Sanger Institute, Cambridge, UK.
- Open Targets, Wellcome Genome Campus, Cambridge, UK.
| | - Rahul Roychoudhuri
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
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21
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Ayroldi E, Grohmann U. Exemplifying complexity of immune suppression by a "canonical" speech: A glimpse into TNFRSF-activated signaling pathways in Treg cells. Eur J Immunol 2020; 50:944-948. [PMID: 32428262 DOI: 10.1002/eji.202048711] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Indexed: 01/03/2023]
Abstract
Regulatory T (Treg) cells are crucial mediators of immune tolerance suppressing self-reactive T cells and preventing autoimmune diseases. Besides activation of the T cell receptor (TCR), empowerment of Treg cell functions requires co-accessory signals, such as those released by the TNF receptor superfamily (TNFRSF) that, however, can also promote immunostimulatory responses when engaged by effector T cells. In this issue of European Journal of Immunology, Lubrano di Ricco et al. [Eur. J. Immunol. 2020. 50: 972-985] have taken a closer look at the important question of the functional meaning of TNFRSF-activated signaling pathways in Treg cells. They have demonstrated that costimulation by TNFR2, 4-1BB, GITR, DR3, but not OX40 in mouse Foxp3+ Treg cells activates the same and unique signaling pathway, i.e., canonical NF-κB, which in turn leads to Foxp3 gene upregulation, cell expansion in vitro and in vivo, and suppressive activity in an experimental model of colitis. Moreover, induction of markers of T helper 2 (Th2) and Th17 as well as of genes encoding proteins involved in noncanonical NF-κΒ was also observed. We here discussed how these findings further highlight the emerging concept of Treg cell plasticity in immune tolerance.
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Affiliation(s)
- Emira Ayroldi
- Department of Medicine, University of Perugia, Perugia, Italy
| | - Ursula Grohmann
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
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22
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Ohkura N, Yasumizu Y, Kitagawa Y, Tanaka A, Nakamura Y, Motooka D, Nakamura S, Okada Y, Sakaguchi S. Regulatory T Cell-Specific Epigenomic Region Variants Are a Key Determinant of Susceptibility to Common Autoimmune Diseases. Immunity 2020; 52:1119-1132.e4. [DOI: 10.1016/j.immuni.2020.04.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 02/19/2020] [Accepted: 04/15/2020] [Indexed: 12/11/2022]
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23
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Transcriptional and epigenetic basis of Treg cell development and function: its genetic anomalies or variations in autoimmune diseases. Cell Res 2020; 30:465-474. [PMID: 32367041 PMCID: PMC7264322 DOI: 10.1038/s41422-020-0324-7] [Citation(s) in RCA: 141] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 04/08/2020] [Indexed: 01/01/2023] Open
Abstract
Naturally arising regulatory CD4+ T (Treg) cells, which specifically express the transcription factor FoxP3 in the nucleus and CD25 and CTLA-4 on the cell surface, are a T-cell subpopulation specialized for immune suppression, playing a key role in maintaining immunological self-tolerance and homeostasis. FoxP3 is required for Treg function, especially for its suppressive activity. However, FoxP3 expression per se is not necessary for Treg cell lineage commitment in the thymus and insufficient for full Treg-type gene expression in mature Treg cells. It is Treg-specific epigenetic changes such as CpG demethylation and histone modification that can confer a stable and heritable pattern of Treg type gene expression on developing Treg cells in a FoxP3-independent manner. Anomalies in the formation of Treg-specific epigenome, in particular, Treg-specific super-enhancers, which largely include Treg-specific DNA demethylated regions, are indeed able to cause autoimmune diseases in rodents. Furthermore, in humans, single nucleotide polymorphisms in Treg-specific DNA demethylated regions associated with Treg signature genes, such as IL2RA (CD25) and CTLA4, can affect the development and function of naïve Treg cells rather than effector T cells. Such genetic variations are therefore causative of polygenic common autoimmune diseases including type 1 diabetes and rheumatoid arthritis via affecting endogenous natural Treg cells. These findings on the transcription factor network with FoxP3 at a key position as well as Treg-specific epigenetic landscape facilitate our understanding of Treg cell development and function, and can be exploited to prepare functionally stable FoxP3-expressing Treg cells from antigen-specific conventional T cells to treat autoimmune diseases.
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24
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Raffin C, Vo LT, Bluestone JA. T reg cell-based therapies: challenges and perspectives. Nat Rev Immunol 2020; 20:158-172. [PMID: 31811270 PMCID: PMC7814338 DOI: 10.1038/s41577-019-0232-6] [Citation(s) in RCA: 365] [Impact Index Per Article: 91.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2019] [Indexed: 12/25/2022]
Abstract
Cellular therapies using regulatory T (Treg) cells are currently undergoing clinical trials for the treatment of autoimmune diseases, transplant rejection and graft-versus-host disease. In this Review, we discuss the biology of Treg cells and describe new efforts in Treg cell engineering to enhance specificity, stability, functional activity and delivery. Finally, we envision that the success of Treg cell therapy in autoimmunity and transplantation will encourage the clinical use of adoptive Treg cell therapy for non-immune diseases, such as neurological disorders and tissue repair.
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Affiliation(s)
- Caroline Raffin
- Sean N. Parker Autoimmune Research Laboratory, Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Linda T Vo
- Sean N. Parker Autoimmune Research Laboratory, Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey A Bluestone
- Sean N. Parker Autoimmune Research Laboratory, Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.
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25
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Lubrano di Ricco M, Ronin E, Collares D, Divoux J, Grégoire S, Wajant H, Gomes T, Grinberg-Bleyer Y, Baud V, Marodon G, Salomon BL. Tumor necrosis factor receptor family costimulation increases regulatory T-cell activation and function via NF-κB. Eur J Immunol 2020; 50:972-985. [PMID: 32012260 PMCID: PMC7383872 DOI: 10.1002/eji.201948393] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 12/10/2019] [Accepted: 01/30/2020] [Indexed: 01/06/2023]
Abstract
Several drugs targeting members of the TNF superfamily or TNF receptor superfamily (TNFRSF) are widely used in medicine or are currently being tested in therapeutic trials. However, their mechanism of action remains poorly understood. Here, we explored the effects of TNFRSF co-stimulation on murine Foxp3+ regulatory T cell (Treg) biology, as they are pivotal modulators of immune responses. We show that engagement of TNFR2, 4-1BB, GITR, and DR3, but not OX40, increases Treg proliferation and survival. Triggering these TNFRSF in Tregs induces similar changes in gene expression patterns, suggesting that they engage common signal transduction pathways. Among them, we identified a major role of canonical NF-κB. Importantly, TNFRSF co-stimulation improves the ability of Tregs to suppress colitis. Our data demonstrate that stimulation of discrete TNFRSF members enhances Treg activation and function through a shared mechanism. Consequently, therapeutic effects of drugs targeting TNFRSF or their ligands may be mediated by their effect on Tregs.
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Affiliation(s)
- Martina Lubrano di Ricco
- Sorbonne Université, INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Emilie Ronin
- Sorbonne Université, INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Davi Collares
- Université Paris Descartes, Sorbonne Paris Cité, Laboratoire NF-κB, Différenciation et Cancer, Paris, France
| | - Jordane Divoux
- Sorbonne Université, INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Sylvie Grégoire
- Sorbonne Université, INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Harald Wajant
- Division Molecular Internal Medicine, Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Tomás Gomes
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Yenkel Grinberg-Bleyer
- Centre de Recherche en Cancérologie de Lyon, UMR INSERM 1052, CNRS 5286, Université Claude Bernard Lyon 1, Labex DEVweCAN, Centre Léon Bérard, Lyon, France
| | - Véronique Baud
- Université Paris Descartes, Sorbonne Paris Cité, Laboratoire NF-κB, Différenciation et Cancer, Paris, France
| | - Gilles Marodon
- Sorbonne Université, INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Benoît L Salomon
- Sorbonne Université, INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
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26
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Sakaguchi S, Mikami N, Wing JB, Tanaka A, Ichiyama K, Ohkura N. Regulatory T Cells and Human Disease. Annu Rev Immunol 2020; 38:541-566. [PMID: 32017635 DOI: 10.1146/annurev-immunol-042718-041717] [Citation(s) in RCA: 514] [Impact Index Per Article: 128.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Naturally occurring CD4+ regulatory T cells (Tregs), which specifically express the transcription factor FoxP3 in the nucleus and CD25 and CTLA-4 on the cell surface, are a functionally distinct T cell subpopulation actively engaged in the maintenance of immunological self-tolerance and homeostasis. Recent studies have facilitated our understanding of the cellular and molecular basis of their generation, function, phenotypic and functional stability, and adaptability. It is under investigation in humans how functional or numerical Treg anomalies, whether genetically determined or environmentally induced, contribute to immunological diseases such as autoimmune diseases. Also being addressed is how Tregs can be targeted to control physiological and pathological immune responses, for example, by depleting them to enhance tumor immunity or by expanding them to treat immunological diseases. This review discusses our current understanding of Treg immunobiology in normal and disease states, with a perspective on the realization of Treg-targeting therapies in the clinic.
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Affiliation(s)
- Shimon Sakaguchi
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan; .,Laboratory of Experimental Immunology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Norihisa Mikami
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan;
| | - James B Wing
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan;
| | - Atsushi Tanaka
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan;
| | - Kenji Ichiyama
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan;
| | - Naganari Ohkura
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan;
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27
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Lin Y, Li Y, Zhu X, Huang Y, Li Y, Li M. Genetic Contexts Characterize Dynamic Histone Modification Patterns Among Cell Types. Interdiscip Sci 2019; 11:698-710. [PMID: 31165438 DOI: 10.1007/s12539-019-00338-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/18/2019] [Accepted: 05/27/2019] [Indexed: 11/29/2022]
Abstract
Histone modifications play critical roles in mammalian development, regulating chromatin structure and gene expression. Dynamic histone modifications among cell types have been shown to associate with changes in mammalian development. However, how to quantitatively measure the histone modification alterations and how histone modifications vary across cell types under different genetic contexts remain largely unexplored and whether these changes are related to the primary DNA sequence remains limited. Here, we employed an entropy-based method to measure histone modification alterations in six definite genomic regions across five cell types and identified lineage-specific histone modification genes. We observed that histone modification alterations prefer to enrich in 5'-UTR exons, and also in 3'-UTR exons and its downstream. Then we built a model to predict the histone modification patterns from the primary DNA sequence. We found that the frequencies of k-mer sequence compositions are predictive of histone modification patterns, suggesting that the primary DNA sequence correlated with the histone modification alterations among cell types. Additionally, the lineage-specific histone modification genes display a higher conservation and lower GC-content. Together, we performed a systematic analysis for histone modification alterations and demonstrated how to identify genomic region-specific elements of epigenetic and genetic regulation and histone modification patterns across different cell types.
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Affiliation(s)
- Yanmei Lin
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Yan Li
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Xingyong Zhu
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Yuyao Huang
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Yizhou Li
- College of Chemistry, Sichuan University, Chengdu, 610064, China. .,College of Cybersecurity, Sichuan University, Chengdu, 610064, Sichuan, China.
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, 610064, China.
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28
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Abstract
Functional interpretation of noncoding genetic variants identified by genome-wide association studies is a major challenge in human genetics and gene regulation. We generated epigenomics data using primary cells from type 1 diabetes patients. Using these data, we identified and validated multiple novel risk variants for this disease. In addition, our ranked list of candidate risk SNPs represents the most comprehensive annotation based on T1D-specific T-cell data. Because many autoimmune diseases share some genetic underpinnings, our dataset may be used to understand causal noncoding mutations in related autoimmune diseases. Genome-wide association studies (GWASs) have revealed 59 genomic loci associated with type 1 diabetes (T1D). Functional interpretation of the SNPs located in the noncoding region of these loci remains challenging. We perform epigenomic profiling of two enhancer marks, H3K4me1 and H3K27ac, using primary TH1 and TREG cells isolated from healthy and T1D subjects. We uncover a large number of deregulated enhancers and altered transcriptional circuitries in both cell types of T1D patients. We identify four SNPs (rs10772119, rs10772120, rs3176792, rs883868) in linkage disequilibrium (LD) with T1D-associated GWAS lead SNPs that alter enhancer activity and expression of immune genes. Among them, rs10772119 and rs883868 disrupt the binding of retinoic acid receptor α (RARA) and Yin and Yang 1 (YY1), respectively. Loss of binding by YY1 also results in the loss of long-range enhancer–promoter interaction. These findings provide insights into how noncoding variants affect the transcriptomes of two T-cell subtypes that play critical roles in T1D pathogenesis.
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29
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Johanson TM, Lun ATL, Coughlan HD, Tan T, Smyth GK, Nutt SL, Allan RS. Transcription-factor-mediated supervision of global genome architecture maintains B cell identity. Nat Immunol 2018; 19:1257-1264. [PMID: 30323344 DOI: 10.1038/s41590-018-0234-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/04/2018] [Indexed: 01/09/2023]
Abstract
Recent studies have elucidated cell-lineage-specific three-dimensional genome organization; however, how such specific architecture is established or maintained is unclear. We hypothesized that lineage-defining transcription factors maintain cell identity via global control of genome organization. These factors bind many genomic sites outside of the genes that they directly regulate and thus are potentially implicated in three-dimensional genome organization. Using chromosome-conformation-capture techniques, we show that the transcription factor Paired box 5 (Pax5) is critical for the establishment and maintenance of the global lineage-specific architecture of B cells. Pax5 was found to supervise genome architecture throughout B cell differentiation, until the plasmablast stage, in which Pax5 is naturally silenced and B cell-specific genome structure is lost. Crucially, Pax5 did not rely on ongoing transcription to organize the genome. These results implicate sequence-specific DNA-binding proteins in global genome organization to establish and maintain lineage fidelity.
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Affiliation(s)
- Timothy M Johanson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Aaron T L Lun
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Hannah D Coughlan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Tania Tan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Gordon K Smyth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,School of Mathematics and Statistics, University of Melbourne, Melbourne, Victoria, Australia
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. .,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia.
| | - Rhys S Allan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. .,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia.
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30
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Salomon BL, Leclerc M, Tosello J, Ronin E, Piaggio E, Cohen JL. Tumor Necrosis Factor α and Regulatory T Cells in Oncoimmunology. Front Immunol 2018; 9:444. [PMID: 29593717 PMCID: PMC5857565 DOI: 10.3389/fimmu.2018.00444] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 02/19/2018] [Indexed: 12/13/2022] Open
Abstract
Tumor necrosis factor α (TNF) is a potent pro-inflammatory cytokine that has deleterious effect in some autoimmune diseases, which led to the use of anti-TNF drugs in some of these diseases. However, some rare patients treated with these drugs paradoxically develop an aggravation of their disease or new onset autoimmunity, revealing an immunosuppressive facet of TNF. A possible mechanism of this observation is the direct and positive effect of TNF on regulatory T cells (Tregs) through its binding to the TNF receptor type 2 (TNFR2). Indeed, TNF is able to increase expansion, stability, and possibly function of Tregs via TNFR2. In this review, we discuss the role of TNF in graft-versus-host disease as an example of the ambivalence of this cytokine in the pathophysiology of an immunopathology, highlighting the therapeutic potential of triggering TNFR2 to boost Treg expansion. We also describe new targets in immunotherapy of cancer, emphasizing on the putative suppressive effect of TNF in antitumor immunity and of the interest of blocking TNFR2 to regulate the Treg compartment.
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Affiliation(s)
- Benoît L Salomon
- Sorbonne Université, INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Mathieu Leclerc
- Université Paris-Est and INSERM U955, Créteil, France.,Service d'Hématologie Clinique et de Thérapie Cellulaire, Assistance Publique Hôpitaux de Paris (APHP), Hôpital H. Mondor, Créteil, France
| | - Jimena Tosello
- Center of Cancer Immunotherapy and Centre d'Investigation Clinique Biothérapie 1428, Institut Curie, PSL Research University, INSERM U932, Paris, France
| | - Emilie Ronin
- Sorbonne Université, INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Eliane Piaggio
- Center of Cancer Immunotherapy and Centre d'Investigation Clinique Biothérapie 1428, Institut Curie, PSL Research University, INSERM U932, Paris, France
| | - José L Cohen
- Université Paris-Est and INSERM U955, Créteil, France.,Centre d'Investigation Clinique Biothérapie, Assistance Publique Hôpitaux de Paris (APHP), Hôpital H. Mondor, Créteil, France
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31
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Sadlon T, Brown CY, Bandara V, Hope CM, Schjenken JE, Pederson SM, Breen J, Forrest A, Beyer M, Robertson S, Barry SC. Unravelling the molecular basis for regulatory T-cell plasticity and loss of function in disease. Clin Transl Immunology 2018; 7:e1011. [PMID: 29497530 PMCID: PMC5827651 DOI: 10.1002/cti2.1011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/28/2018] [Accepted: 01/29/2018] [Indexed: 12/14/2022] Open
Abstract
Regulatory T cells (Treg) are critical for preventing autoimmunity and curtailing responses of conventional effector T cells (Tconv). The reprogramming of T‐cell fate and function to generate Treg requires switching on and off of key gene regulatory networks, which may be initiated by a subtle shift in expression levels of specific genes. This can be achieved by intermediary regulatory processes that include microRNA and long noncoding RNA‐based regulation of gene expression. There are well‐documented microRNA profiles in Treg and Tconv, and these can operate to either reinforce or reduce expression of a specific set of target genes, including FOXP3 itself. This type of feedforward/feedback regulatory loop is normally stable in the steady state, but can alter in response to local cues or genetic risk. This may go some way to explaining T‐cell plasticity. In addition, in chronic inflammation or autoimmunity, altered Treg/Tconv function may be influenced by changes in enhancer–promoter interactions, which are highly cell type‐specific. These interactions are impacted by genetic risk based on genome‐wide association studies and may cause subtle alterations to the gene regulatory networks controlled by or controlling FOXP3 and its target genes. Recent insights into the 3D organisation of chromatin and the mapping of noncoding regulatory regions to the genes they control are shedding new light on the direct impact of genetic risk on T‐cell function and susceptibility to inflammatory and autoimmune conditions.
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Affiliation(s)
- Timothy Sadlon
- Women's and Children's Health Network North Adelaide SA Australia.,Molecular immunology Robinson Research Institute University of Adelaide Adelaide SA Australia
| | - Cheryl Y Brown
- Molecular immunology Robinson Research Institute University of Adelaide Adelaide SA Australia
| | - Veronika Bandara
- Molecular immunology Robinson Research Institute University of Adelaide Adelaide SA Australia
| | | | - John E Schjenken
- Reproductive Immunology Robinson Research Institute University of Adelaide Adelaide SA Australia
| | - Stephen M Pederson
- Molecular immunology Robinson Research Institute University of Adelaide Adelaide SA Australia.,University of Adelaide Bioinformatics Hub University of Adelaide Adelaide SA Australia
| | - James Breen
- Molecular immunology Robinson Research Institute University of Adelaide Adelaide SA Australia.,University of Adelaide Bioinformatics Hub University of Adelaide Adelaide SA Australia
| | - Alistair Forrest
- Harry Perkins Institute of Medical Research University of Western Australia Perth, WA Australia
| | - Marc Beyer
- Deutsches Zentrum fur Neurodegenerative Erkrankungen Bonn Germany
| | - Sarah Robertson
- Reproductive Immunology Robinson Research Institute University of Adelaide Adelaide SA Australia
| | - Simon C Barry
- Molecular immunology Robinson Research Institute University of Adelaide Adelaide SA Australia
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32
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Nowak A, Lock D, Bacher P, Hohnstein T, Vogt K, Gottfreund J, Giehr P, Polansky JK, Sawitzki B, Kaiser A, Walter J, Scheffold A. CD137+CD154- Expression As a Regulatory T Cell (Treg)-Specific Activation Signature for Identification and Sorting of Stable Human Tregs from In Vitro Expansion Cultures. Front Immunol 2018; 9:199. [PMID: 29467769 PMCID: PMC5808295 DOI: 10.3389/fimmu.2018.00199] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 01/23/2018] [Indexed: 01/30/2023] Open
Abstract
Regulatory T cells (Tregs) are an attractive therapeutic tool for several different immune pathologies. Therapeutic Treg application often requires prolonged in vitro culture to generate sufficient Treg numbers or to optimize their functionality, e.g., via genetic engineering of their antigen receptors. However, purity of clinical Treg expansion cultures is highly variable, and currently, it is impossible to identify and separate stable Tregs from contaminating effector T cells, either ex vivo or after prior expansion. This represents a major obstacle for quality assurance of expanded Tregs and raises significant safety concerns. Here, we describe a Treg activation signature that allows identification and sorting of epigenetically imprinted Tregs even after prolonged in vitro culture. We show that short-term reactivation resulted in expression of CD137 but not CD154 on stable FoxP3+ Tregs that displayed a demethylated Treg-specific demethylated region, high suppressive potential, and lack of inflammatory cytokine expression. We also applied this Treg activation signature for rapid testing of chimeric antigen receptor functionality in human Tregs and identified major differences in the signaling requirements regarding CD137 versus CD28 costimulation. Taken together, CD137+CD154- expression emerges as a universal Treg activation signature ex vivo and upon in vitro expansion allowing the identification and isolation of epigenetically stable antigen-activated Tregs and providing a means for their rapid functional testing in vitro.
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Affiliation(s)
- Anna Nowak
- German Rheumatism Research Centre (DRFZ) Berlin, Leibniz Association, Berlin, Germany
| | - Dominik Lock
- Miltenyi Biotec GmbH, Bergisch Gladbach, Germany
| | - Petra Bacher
- Department of Cellular Immunology, Clinic for Rheumatology and Clinical Immunology, Charité - University Medicine, Berlin, Germany
| | - Thordis Hohnstein
- Department of Cellular Immunology, Clinic for Rheumatology and Clinical Immunology, Charité - University Medicine, Berlin, Germany
| | - Katrin Vogt
- Institute for Medical Immunology, Charité - University Medicine, Berlin, Germany
| | - Judith Gottfreund
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Pascal Giehr
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Julia K Polansky
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité - University Medicine, Berlin, Germany
| | - Birgit Sawitzki
- Institute for Medical Immunology, Charité - University Medicine, Berlin, Germany
| | | | - Jörn Walter
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Alexander Scheffold
- German Rheumatism Research Centre (DRFZ) Berlin, Leibniz Association, Berlin, Germany.,Department of Cellular Immunology, Clinic for Rheumatology and Clinical Immunology, Charité - University Medicine, Berlin, Germany
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33
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Weinberg A, Lindsey J, Bosch R, Persaud D, Sato P, Ogwu A, Asmelash A, Bwakura-Dangarambezi M, Chi BH, Canniff J, Lockman S, Gaseitsiwe S, Moyo S, Smith CE, Moraka NO, Levin MJ. B and T Cell Phenotypic Profiles of African HIV-Infected and HIV-Exposed Uninfected Infants: Associations with Antibody Responses to the Pentavalent Rotavirus Vaccine. Front Immunol 2018; 8:2002. [PMID: 29403482 PMCID: PMC5780413 DOI: 10.3389/fimmu.2017.02002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 12/26/2017] [Indexed: 12/23/2022] Open
Abstract
We examined associations between B and T cell phenotypic profiles and antibody responses to the pentavalent rotavirus vaccine (RV5) in perinatally HIV-infected (PHIV) infants on antiretroviral therapy and in HIV-exposed uninfected (PHEU) infants enrolled in International Maternal Pediatric Adolescent AIDS Clinical Trials P1072 study (NCT00880698). Of 17 B and T cell subsets analyzed, PHIV and PHEU differed only in the number of CD4+ T cells and frequency of naive B cells, which were higher in PHEU than in PHIV. In contrast, the B and T cell phenotypic profiles of PHIV and PHEU markedly differed from those of geographically matched contemporary HIV-unexposed infants. The frequency of regulatory T and B cells (Treg, Breg) of PHIV and PHEU displayed two patterns of associations: FOXP3+ CD25+ Treg positively correlated with CD4+ T cell numbers; while TGFβ+ Treg and IL10+ Treg and Breg positively correlated with the frequencies of inflammatory and activated T cells. Moreover, the frequencies of activated and inflammatory T cells of PHIV and PHEU positively correlated with the frequency of immature B cells. Correlations were not affected by HIV status and persisted over time. PHIV and PHEU antibody responses to RV5 positively correlated with CD4+ T cell counts and negatively with the proportion of immature B cells, similarly to what has been previously described in chronic HIV infection. Unique to PHIV and PHEU, anti-RV5 antibodies positively correlated with CD4+/CD8+FOXP3+CD25+% and negatively with CD4+IL10+% Tregs. In conclusion, PHEU shared with PHIV abnormal B and T cell phenotypic profiles. PHIV and PHEU antibody responses to RV5 were modulated by typical HIV-associated immune response modifiers except for the association between CD4+/CD8+FOXP3+CD25+Treg and increased antibody production.
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Affiliation(s)
- Adriana Weinberg
- Department of Pediatrics, Section of Pediatric Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Medicine, Section of Pediatric Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Pathology, Section of Pediatric Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Jane Lindsey
- Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, MA, United States
| | - Ronald Bosch
- Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston, MA, United States
| | - Deborah Persaud
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Paul Sato
- Maternal Adolescent and Pediatric Research Branch, NIAID, NIH, Bethesda, MD, United States
| | | | | | - Mutsa Bwakura-Dangarambezi
- Department of Paediatrics and Child Health, University of Zimbabwe College of Health Sciences, Harare, Zimbabwe
| | - Benjamin H Chi
- Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jennifer Canniff
- Department of Pediatrics, Section of Pediatric Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Shahin Lockman
- Department of Pediatrics, Section of Pediatric Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Simani Gaseitsiwe
- Department of Pediatrics, Section of Pediatric Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Christiana Elizabeth Smith
- Department of Pediatrics, Section of Pediatric Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | | | - Myron J Levin
- Department of Pediatrics, Section of Pediatric Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.,Department of Medicine, Section of Pediatric Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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34
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FoxP3 scanning mutagenesis reveals functional variegation and mild mutations with atypical autoimmune phenotypes. Proc Natl Acad Sci U S A 2017; 115:E253-E262. [PMID: 29269391 DOI: 10.1073/pnas.1718599115] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
FoxP3+ regulatory T cells (Tregs) are a central element of immunological tolerance. FoxP3 is the key determining transcription factor of the Treg lineage, interacting with numerous cofactors and transcriptional targets to determine the many facets of Treg function. Its absence leads to devastating lymphoproliferation and autoimmunity in scurfy mutant mice and immunodysregulation polyendocrinopathy enteropathy X-linked (IPEX) patients. To finely map transcriptionally active regions of the protein, with respect to disease-causing variation, we performed a systematic alanine-scan mutagenesis of FoxP3, assessing mutational impacts on DNA binding and transcriptional activation or repression. The mutations affected transcriptional activation and repression in a variegated manner involving multiple regions of the protein and varying between different transcriptional targets of FoxP3. There appeared to be different modalities for target genes related to classic immunosuppressive function vs. those related to atypical or tissue-Treg functions. Relevance to in vivo Treg biology was established by introducing some of the subtle Foxp3 mutations into the mouse germline by CRISPR-based genome editing. The resulting mice showed Treg populations in normal numbers and exhibited no overt autoimmune manifestations. However, Treg functional defects were revealed upon competition or by system stress, manifest as a strikingly heightened susceptibility to provoked colitis, and conversely by greater resistance to tumors. These observations suggest that some of the missense mutations that segregate in human populations, but do not induce IPEX manifestations, may have unappreciated consequences in other diseases.
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35
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Bocian K, Kiernozek E, Domagała-Kulawik J, Korczak-Kowalska G, Stelmaszczyk-Emmel A, Drela N. Expanding Diversity and Common Goal of Regulatory T and B Cells. I: Origin, Phenotype, Mechanisms. Arch Immunol Ther Exp (Warsz) 2017; 65:501-520. [PMID: 28477096 PMCID: PMC5688216 DOI: 10.1007/s00005-017-0469-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 03/14/2017] [Indexed: 12/21/2022]
Abstract
Immunosuppressive activity of regulatory T and B cells is critical to limit autoimmunity, excessive inflammation, and pathological immune response to conventional antigens or allergens. Both types of regulatory cells are intensively investigated, however, their development and mechanisms of action are still not completely understood. Both T and B regulatory cells represent highly differentiated populations in terms of phenotypes and origin, however, they use similar mechanisms of action. The most investigated CD4+CD25+ regulatory T cells are characterized by the expression of Foxp3+ transcription factor, which is not sufficient to maintain their lineage stability and suppressive function. Currently, it is considered that specific epigenetic changes are critical for defining regulatory T cell stability in the context of their suppressive function. It is not yet known if similar epigenetic regulation determines development, lineage stability, and function of regulatory B cells. Phenotype diversity, confirmed or hypothetical developmental pathways, multiple mechanisms of action, and role of epigenetic changes in these processes are the subject of this review.
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Affiliation(s)
- Katarzyna Bocian
- Department of Immunology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Ewelina Kiernozek
- Department of Immunology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | | | - Grażyna Korczak-Kowalska
- Department of Immunology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- Department of Clinical Immunology, Transplantation Institute, Medical University of Warsaw, Warsaw, Poland
| | - Anna Stelmaszczyk-Emmel
- Department of Laboratory Diagnostics and Clinical Immunology of Developmental Age, Medical University of Warsaw, Warsaw, Poland
| | - Nadzieja Drela
- Department of Immunology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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36
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Kwon HK, Chen HM, Mathis D, Benoist C. Different molecular complexes that mediate transcriptional induction and repression by FoxP3. Nat Immunol 2017; 18:1238-1248. [PMID: 28892470 PMCID: PMC5679728 DOI: 10.1038/ni.3835] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/15/2017] [Indexed: 12/13/2022]
Abstract
FoxP3 conditions the transcriptional signature and functional facets of regulatory T cells (Treg cells). Its mechanism of action, whether as an activator or a repressor, has remained unclear. Here, chromatin analysis showed that FoxP3 bound active enhancer elements, not repressed chromatin, around loci over- or under-expressed in Treg cells. We evaluated the impact of a panel of FoxP3 mutants on its transcriptional activity and interactions with DNA, transcriptional cofactors and chromatin. Computational integration, confirmed by biochemical interaction and size analyses, showed that FoxP3 existed in distinct multimolecular complexes. It was active and primarily an activator when complexed with the transcriptional factors RELA, IKZF2 and KAT5. In contrast, FoxP3 was inactive when complexed with the histone methyltransferase EZH2 and transcription factors YY1 and IKZF3. The latter complex partitioned to a peripheral region of the nucleus, as shown by super-resolution microscopy. Thus, FoxP3 acts in multimodal fashion to directly activate or repress transcription, in a context- and partner-dependent manner, to govern Treg cell phenotypes.
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Affiliation(s)
- Ho-Keun Kwon
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, and Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston MA 02115, USA
| | - Hui-Min Chen
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, and Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston MA 02115, USA
| | - Diane Mathis
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, and Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston MA 02115, USA
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, and Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston MA 02115, USA
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37
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Zuber J, Sykes M. Mechanisms of Mixed Chimerism-Based Transplant Tolerance. Trends Immunol 2017; 38:829-843. [PMID: 28826941 PMCID: PMC5669809 DOI: 10.1016/j.it.2017.07.008] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 06/24/2017] [Accepted: 07/19/2017] [Indexed: 02/06/2023]
Abstract
Immune responses to allografts represent a major barrier in organ transplantation. Immune tolerance to avoid chronic immunosuppression is a critical goal in the field, recently achieved in the clinic by combining bone marrow transplantation (BMT) with kidney transplantation following non-myeloablative conditioning. At high levels of chimerism such protocols can permit central deletional tolerance, but with a significant risk of graft-versus-host (GVH) disease (GVHD). By contrast, transient chimerism-based tolerance is devoid of GVHD risk and appears to initially depend on regulatory T cells (Tregs) followed by gradual, presumably peripheral, clonal deletion of donor-reactive T cells. Here we review recent mechanistic insights into tolerance and the development of more robust and safer protocols for tolerance induction that will be guided by innovative immune monitoring tools.
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Affiliation(s)
- Julien Zuber
- Service de Transplantation Rénale, Hôpital Necker, Université Paris Descartes, Paris, France; INSERM UMRS_1163, IHU Imagine, Paris, France.
| | - Megan Sykes
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY 10032, USA; Department of Surgery, Columbia University, New York, NY 10032, USA; Department of Microbiology and Immunology, Columbia University Center, New York, NY 10032, USA.
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38
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Molecular control of regulatory T cell development and function. Curr Opin Immunol 2017; 49:64-70. [PMID: 29065384 DOI: 10.1016/j.coi.2017.10.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 10/04/2017] [Accepted: 10/05/2017] [Indexed: 01/01/2023]
Abstract
Treg cells expressing the transcription factor Foxp3 are essential for immunological tolerance and homeostasis. Recent genome-wide studies have revealed that Foxp3+ natural Treg cells possess a number of unique transcriptional and epigenetic features, which appear to be acquired along the course of Treg cell development and maintained throughout their lifespan. These studies also provide novel insights into how genomic variations contribute to genetic susceptibility to human autoimmune diseases by affecting Treg cell development and function.
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39
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Mumbach MR, Satpathy AT, Boyle EA, Dai C, Gowen BG, Cho SW, Nguyen ML, Rubin AJ, Granja JM, Kazane KR, Wei Y, Nguyen T, Greenside PG, Corces MR, Tycko J, Simeonov DR, Suliman N, Li R, Xu J, Flynn RA, Kundaje A, Khavari PA, Marson A, Corn JE, Quertermous T, Greenleaf WJ, Chang HY. Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements. Nat Genet 2017; 49:1602-1612. [PMID: 28945252 DOI: 10.1038/ng.3963] [Citation(s) in RCA: 312] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 09/01/2017] [Indexed: 12/14/2022]
Abstract
The challenge of linking intergenic mutations to target genes has limited molecular understanding of human diseases. Here we show that H3K27ac HiChIP generates high-resolution contact maps of active enhancers and target genes in rare primary human T cell subtypes and coronary artery smooth muscle cells. Differentiation of naive T cells into T helper 17 cells or regulatory T cells creates subtype-specific enhancer-promoter interactions, specifically at regions of shared DNA accessibility. These data provide a principled means of assigning molecular functions to autoimmune and cardiovascular disease risk variants, linking hundreds of noncoding variants to putative gene targets. Target genes identified with HiChIP are further supported by CRISPR interference and activation at linked enhancers, by the presence of expression quantitative trait loci, and by allele-specific enhancer loops in patient-derived primary cells. The majority of disease-associated enhancers contact genes beyond the nearest gene in the linear genome, leading to a fourfold increase in the number of potential target genes for autoimmune and cardiovascular diseases.
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Affiliation(s)
- Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Evan A Boyle
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Chao Dai
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Benjamin G Gowen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Seung Woo Cho
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Michelle L Nguyen
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Adam J Rubin
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Katelynn R Kazane
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Yuning Wei
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Trieu Nguyen
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Peyton G Greenside
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Josh Tycko
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Dimitre R Simeonov
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA.,Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, California, USA
| | - Nabeela Suliman
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Jin Xu
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Ryan A Flynn
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Alexander Marson
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA.,Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA.,Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Jacob E Corn
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Thomas Quertermous
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.,Chan Zuckerberg Biohub, San Francisco, California, USA.,Department of Applied Physics, Stanford University, Stanford, California, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
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40
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Hayatsu N, Miyao T, Tachibana M, Murakami R, Kimura A, Kato T, Kawakami E, Endo TA, Setoguchi R, Watarai H, Nishikawa T, Yasuda T, Yoshida H, Hori S. Analyses of a Mutant Foxp3 Allele Reveal BATF as a Critical Transcription Factor in the Differentiation and Accumulation of Tissue Regulatory T Cells. Immunity 2017; 47:268-283.e9. [PMID: 28778586 DOI: 10.1016/j.immuni.2017.07.008] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 05/02/2017] [Accepted: 07/10/2017] [Indexed: 12/25/2022]
Abstract
Foxp3 controls the development and function of regulatory T (Treg) cells, but it remains elusive how Foxp3 functions in vivo. Here, we established mouse models harboring three unique missense Foxp3 mutations that were identified in patients with the autoimmune disease IPEX. The I363V and R397W mutations were loss-of-function mutations, causing multi-organ inflammation by globally compromising Treg cell physiology. By contrast, the A384T mutation induced a distinctive tissue-restricted inflammation by specifically impairing the ability of Treg cells to compete with pathogenic T cells in certain non-lymphoid tissues. Mechanistically, repressed BATF expression contributed to these A384T effects. At the molecular level, the A384T mutation altered Foxp3 interactions with its specific target genes including Batf by broadening its DNA-binding specificity. Our findings identify BATF as a critical regulator of tissue Treg cells and suggest that sequence-specific perturbations of Foxp3-DNA interactions can influence specific facets of Treg cell physiology and the immunopathologies they regulate.
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Affiliation(s)
- Norihito Hayatsu
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
| | - Takahisa Miyao
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
| | - Masashi Tachibana
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
| | - Ryuichi Murakami
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan; Laboratory of Immunology and Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Akihiko Kimura
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
| | - Takako Kato
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
| | - Eiryo Kawakami
- Laboratory for Disease Systems Modeling, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan; Disease Biology Group, RIKEN Medical Sciences Innovation Hub Program, Kanagawa 230-0045, Japan
| | - Takaho A Endo
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
| | - Ruka Setoguchi
- Laboratory for Immunogenetics, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
| | - Hiroshi Watarai
- Division of Stem Cell Cellomics, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Sciences, The University of Tokyo, Tokyo 108-8639, Japan
| | - Takeshi Nishikawa
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
| | - Takuwa Yasuda
- Laboratory for Immunogenetics, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
| | - Hisahiro Yoshida
- Laboratory for Immunogenetics, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
| | - Shohei Hori
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan; Laboratory of Immunology and Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan.
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41
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Liu Q, Jiang C, Xu J, Zhao MT, Van Bortle K, Cheng X, Wang G, Chang HY, Wu JC, Snyder MP. Genome-Wide Temporal Profiling of Transcriptome and Open Chromatin of Early Cardiomyocyte Differentiation Derived From hiPSCs and hESCs. Circ Res 2017; 121:376-391. [PMID: 28663367 DOI: 10.1161/circresaha.116.310456] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 06/21/2017] [Accepted: 06/28/2017] [Indexed: 01/13/2023]
Abstract
RATIONALE Recent advances have improved our ability to generate cardiomyocytes from human induced pluripotent stem cells (hiPSCs) and human embryonic stem cells (hESCs). However, our understanding of the transcriptional regulatory networks underlying early stages (ie, from mesoderm to cardiac mesoderm) of cardiomyocyte differentiation remains limited. OBJECTIVE To characterize transcriptome and chromatin accessibility during early cardiomyocyte differentiation from hiPSCs and hESCs. METHODS AND RESULTS We profiled the temporal changes in transcriptome and chromatin accessibility at genome-wide levels during cardiomyocyte differentiation derived from 2 hiPSC lines and 2 hESC lines at 4 stages: pluripotent stem cells, mesoderm, cardiac mesoderm, and differentiated cardiomyocytes. Overall, RNA sequencing analysis revealed that transcriptomes during early cardiomyocyte differentiation were highly concordant between hiPSCs and hESCs, and clustering of 4 cell lines within each time point demonstrated that changes in genome-wide chromatin accessibility were similar across hiPSC and hESC cell lines. Weighted gene co-expression network analysis (WGCNA) identified several modules that were strongly correlated with different stages of cardiomyocyte differentiation. Several novel genes were identified with high weighted connectivity within modules and exhibited coexpression patterns with other genes, including noncoding RNA LINC01124 and uncharacterized RNA AK127400 in the module related to the mesoderm stage; E-box-binding homeobox 1 (ZEB1) in the module correlated with postcardiac mesoderm. We further demonstrated that ZEB1 is required for early cardiomyocyte differentiation. In addition, based on integrative analysis of both WGCNA and transcription factor motif enrichment analysis, we determined numerous transcription factors likely to play important roles at different stages during cardiomyocyte differentiation, such as T and eomesodermin (EOMES; mesoderm), lymphoid enhancer-binding factor 1 (LEF1) and mesoderm posterior BHLH transcription factor 1 (MESP1; from mesoderm to cardiac mesoderm), meis homeobox 1 (MEIS1) and GATA-binding protein 4 (GATA4) (postcardiac mesoderm), JUN and FOS families, and MEIS2 (cardiomyocyte). CONCLUSIONS Both hiPSCs and hESCs share similar transcriptional regulatory mechanisms underlying early cardiac differentiation, and our results have revealed transcriptional regulatory networks and new factors (eg, ZEB1) controlling early stages of cardiomyocyte differentiation.
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Affiliation(s)
- Qing Liu
- From the Department of Genetics (Q.L., C.J., K.V.B., M.P.S.), Center for Personal Dynamic Regulomes (J.X., H.Y.C.), Stanford Cardiovascular Institute (M.T.Z., J.C.W.), and Stem Cell Core Facility, Department of Genetics (X.C., G.W.), Stanford University School of Medicine, CA
| | - Chao Jiang
- From the Department of Genetics (Q.L., C.J., K.V.B., M.P.S.), Center for Personal Dynamic Regulomes (J.X., H.Y.C.), Stanford Cardiovascular Institute (M.T.Z., J.C.W.), and Stem Cell Core Facility, Department of Genetics (X.C., G.W.), Stanford University School of Medicine, CA
| | - Jin Xu
- From the Department of Genetics (Q.L., C.J., K.V.B., M.P.S.), Center for Personal Dynamic Regulomes (J.X., H.Y.C.), Stanford Cardiovascular Institute (M.T.Z., J.C.W.), and Stem Cell Core Facility, Department of Genetics (X.C., G.W.), Stanford University School of Medicine, CA
| | - Ming-Tao Zhao
- From the Department of Genetics (Q.L., C.J., K.V.B., M.P.S.), Center for Personal Dynamic Regulomes (J.X., H.Y.C.), Stanford Cardiovascular Institute (M.T.Z., J.C.W.), and Stem Cell Core Facility, Department of Genetics (X.C., G.W.), Stanford University School of Medicine, CA
| | - Kevin Van Bortle
- From the Department of Genetics (Q.L., C.J., K.V.B., M.P.S.), Center for Personal Dynamic Regulomes (J.X., H.Y.C.), Stanford Cardiovascular Institute (M.T.Z., J.C.W.), and Stem Cell Core Facility, Department of Genetics (X.C., G.W.), Stanford University School of Medicine, CA
| | - Xun Cheng
- From the Department of Genetics (Q.L., C.J., K.V.B., M.P.S.), Center for Personal Dynamic Regulomes (J.X., H.Y.C.), Stanford Cardiovascular Institute (M.T.Z., J.C.W.), and Stem Cell Core Facility, Department of Genetics (X.C., G.W.), Stanford University School of Medicine, CA
| | - Guangwen Wang
- From the Department of Genetics (Q.L., C.J., K.V.B., M.P.S.), Center for Personal Dynamic Regulomes (J.X., H.Y.C.), Stanford Cardiovascular Institute (M.T.Z., J.C.W.), and Stem Cell Core Facility, Department of Genetics (X.C., G.W.), Stanford University School of Medicine, CA
| | - Howard Y Chang
- From the Department of Genetics (Q.L., C.J., K.V.B., M.P.S.), Center for Personal Dynamic Regulomes (J.X., H.Y.C.), Stanford Cardiovascular Institute (M.T.Z., J.C.W.), and Stem Cell Core Facility, Department of Genetics (X.C., G.W.), Stanford University School of Medicine, CA
| | - Joseph C Wu
- From the Department of Genetics (Q.L., C.J., K.V.B., M.P.S.), Center for Personal Dynamic Regulomes (J.X., H.Y.C.), Stanford Cardiovascular Institute (M.T.Z., J.C.W.), and Stem Cell Core Facility, Department of Genetics (X.C., G.W.), Stanford University School of Medicine, CA
| | - Michael P Snyder
- From the Department of Genetics (Q.L., C.J., K.V.B., M.P.S.), Center for Personal Dynamic Regulomes (J.X., H.Y.C.), Stanford Cardiovascular Institute (M.T.Z., J.C.W.), and Stem Cell Core Facility, Department of Genetics (X.C., G.W.), Stanford University School of Medicine, CA.
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42
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Scaling single-cell genomics from phenomenology to mechanism. Nature 2017; 541:331-338. [PMID: 28102262 DOI: 10.1038/nature21350] [Citation(s) in RCA: 463] [Impact Index Per Article: 66.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 11/14/2016] [Indexed: 02/08/2023]
Abstract
Three of the most fundamental questions in biology are how individual cells differentiate to form tissues, how tissues function in a coordinated and flexible fashion and which gene regulatory mechanisms support these processes. Single-cell genomics is opening up new ways to tackle these questions by combining the comprehensive nature of genomics with the microscopic resolution that is required to describe complex multicellular systems. Initial single-cell genomic studies provided a remarkably rich phenomenology of heterogeneous cellular states, but transforming observational studies into models of dynamics and causal mechanisms in tissues poses fresh challenges and requires stronger integration of theoretical, computational and experimental frameworks.
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43
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Flicr, a long noncoding RNA, modulates Foxp3 expression and autoimmunity. Proc Natl Acad Sci U S A 2017; 114:E3472-E3480. [PMID: 28396406 DOI: 10.1073/pnas.1700946114] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A combination of transcription factors, enhancers, and epigenetic marks determines the expression of the key transcription factor FoxP3 in regulatory T cells (Tregs). Adding an additional layer of complexity, the long noncoding RNA (lncRNA) Flicr (Foxp3 long intergenic noncoding RNA) is a negative regulator that tunes Foxp3 expression, resulting in a subset of Tregs with twofold- to fivefold-lower levels of FoxP3 protein. The impact of Flicr is particularly marked in conditions of IL-2 deficiency, and, conversely, IL-2 represses Flicr expression. Flicr neighbors Foxp3 in mouse and human genomes, is specifically expressed in mature Tregs, and acts only in cis It does not affect DNA methylation, but modifies chromatin accessibility in the conserved noncoding sequence 3 (CNS3)/Accessible region 5 (AR5) region of Foxp3 Like many lncRNAs, Flicr's molecular effects are subtle, but by curtailing Treg activity, Flicr markedly promotes autoimmune diabetes and, conversely, restrains antiviral responses. This mechanism of FoxP3 control may allow escape from dominant Treg control during infection or cancer, at the cost of heightened autoimmunity.
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44
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Khor B. Regulatory T Cells: Central Concepts from Ontogeny to Therapy. Transfus Med Rev 2016; 31:36-44. [PMID: 27523957 DOI: 10.1016/j.tmrv.2016.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 07/06/2016] [Accepted: 07/18/2016] [Indexed: 02/07/2023]
Abstract
The balanced differentiation of naive CD4+ T cells into either pro- or anti-inflammatory fates is a central regulator of immune homeostasis, dysregulation of which can lead to inflammatory disease or cancer. Accordingly, the development of diagnostics and therapeutics to measure and modulate this balance is of great interest. In this review, we focus on the predominant anti-inflammatory subset, regulatory T cells, discussing key concepts including development, function, antigen specificity, and lineage stability. In particular, we highlight how these notions are shaping the evolution of therapeutics, especially in the context of the transfusion medicine specialist, and identify several key areas that urgently need to be addressed.
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Affiliation(s)
- Bernard Khor
- Department of Pathology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA.
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45
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Arvey A, van der Veeken J, Plitas G, Rich SS, Concannon P, Rudensky AY. Genetic and epigenetic variation in the lineage specification of regulatory T cells. eLife 2015; 4:e07571. [PMID: 26510014 PMCID: PMC4623597 DOI: 10.7554/elife.07571] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 09/15/2015] [Indexed: 01/12/2023] Open
Abstract
Regulatory T (Treg) cells, which suppress autoimmunity and other inflammatory states, are characterized by a distinct set of genetic elements controlling their gene expression. However, the extent of genetic and associated epigenetic variation in the Treg cell lineage and its possible relation to disease states in humans remain unknown. We explored evolutionary conservation of regulatory elements and natural human inter-individual epigenetic variation in Treg cells to identify the core transcriptional control program of lineage specification. Analysis of single nucleotide polymorphisms in core lineage-specific enhancers revealed disease associations, which were further corroborated by high-resolution genotyping to fine map causal polymorphisms in lineage-specific enhancers. Our findings suggest that a small set of regulatory elements specify the Treg lineage and that genetic variation in Treg cell-specific enhancers may alter Treg cell function contributing to polygenic disease. DOI:http://dx.doi.org/10.7554/eLife.07571.001 The immune system protects the body from infection. Key to this protection is the ability to mount an immune response that is sufficient to deal with the threat, but is not so large that the damage it causes to the body exceeds its immediate benefit. Immune cells called regulatory T cells (or Treg cells for short) help to shut down the immune response after a threat has been successfully destroyed. They also prevent the immune system from attacking the body's own cells, a phenomenon known as autoimmunity. All cells in the body carry the same set of genes, but the activity of these genes varies between cell types to enable the cells to perform their different jobs. This is possible because our DNA contains regions called regulatory elements that can control the expression of particular genes. These regions can be activated in specific types of cells, which results in specific chemical modifications to DNA that only affect gene activity in those cells. The DNA sequences of these regulatory elements vary between individuals. This ‘genetic variation’ can lead to differences in the chemical modifications that occur to DNA, which is known as epigenetic variation. This means that Treg cells in one person may work in a different way to those in another individual, which could make some individuals more susceptible to autoimmune diseases than others. However, it was not clear how much genetic and epigenetic variation exists in Treg cells. Here, Arvey et al. examined Treg and other immune cells from human and mouse donors. The experiments show that some of the epigenetic modifications present in many individuals only in Treg cells, which indicates that they may be important for the activity of the Treg cells. Unexpectedly, most of the epigenetic modifications were specific to either mice or humans, but Arvey et al. identified a core set of genes that had been modified only in Treg cells in both species. In the human cells, Arvey et al. also identified genetic differences in regulatory elements that are associated with autoimmune diseases. Arvey et al.'s findings suggest that a small set of regulatory elements are crucial to the role of Treg cells in the immune system. Furthermore, genetic variation in these elements can lead to epigenetic changes in Treg cells that contribute to autoimmune diseases in humans. Further study may lead to the development of new treatments for these diseases. DOI:http://dx.doi.org/10.7554/eLife.07571.002
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Affiliation(s)
- Aaron Arvey
- Immunology Program, Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Joris van der Veeken
- Immunology Program, Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States
| | - George Plitas
- Ludwig Center for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, United States.,Breast Service, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, Division of Biostatistics and Epidemiology, University of Virginia, Charlottesville, United States
| | - Patrick Concannon
- Genetics Institute, Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Florida, United States
| | - Alexander Y Rudensky
- Immunology Program, Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, United States.,Ludwig Center for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, United States
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