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Theofilatos D, Ho T, Waitt G, Äijö T, Schiapparelli LM, Soderblom EJ, Tsagaratou A. Deciphering the TET3 interactome in primary thymic developing T cells. iScience 2024; 27:109782. [PMID: 38711449 PMCID: PMC11070343 DOI: 10.1016/j.isci.2024.109782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 03/04/2024] [Accepted: 04/15/2024] [Indexed: 05/08/2024] Open
Abstract
Ten-eleven translocation (TET) proteins are DNA dioxygenases that mediate active DNA demethylation. TET3 is the most highly expressed TET protein in thymic developing T cells. TET3, either independently or in cooperation with TET1 or TET2, has been implicated in T cell lineage specification by regulating DNA demethylation. However, TET-deficient mice exhibit complex phenotypes, suggesting that TET3 exerts multifaceted roles, potentially by interacting with other proteins. We performed liquid chromatography with tandem mass spectrometry in primary developing T cells to identify TET3 interacting partners in endogenous, in vivo conditions. We discover TET3 interacting partners. Our data establish that TET3 participates in a plethora of fundamental biological processes, such as transcriptional regulation, RNA polymerase elongation, splicing, DNA repair, and DNA replication. This resource brings in the spotlight emerging functions of TET3 and sets the stage for systematic studies to dissect the precise mechanistic contributions of TET3 in shaping T cell biology.
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Affiliation(s)
- Dimitris Theofilatos
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tricia Ho
- Duke Proteomics and Metabolomics Core Facility, Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Greg Waitt
- Duke Proteomics and Metabolomics Core Facility, Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Tarmo Äijö
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Erik J. Soderblom
- Duke Proteomics and Metabolomics Core Facility, Duke Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
- Department of Cell Biology, Duke University, Durham, NC, USA
| | - Ageliki Tsagaratou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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2
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Jin M, Ji J, Chen X, Zhou Y, Wang D, Liu A. The emerging role of TET enzymes in the immune microenvironment at the maternal-fetal interface during decidualization and early pregnancy. Front Immunol 2023; 13:1066599. [PMID: 36685517 PMCID: PMC9850229 DOI: 10.3389/fimmu.2022.1066599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/28/2022] [Indexed: 01/07/2023] Open
Abstract
A dysregulated immune microenvironment at the maternal-fetal interface in early pregnancy may lead to early pregnancy loss, fetal growth restriction, and preeclampsia. However, major questions about how epigenetic modifications regulate the immune microenvironment during the decidualization process and embryo implantation remain unanswered. DNA methylation, the main epigenetic mechanism involved in the endometrial cycle, is crucial for specific transcriptional networks associated with endometrial stromal cell (ESC) proliferation, hormone response, decidualization, and embryo implantation. Ten-eleven translocation (TET) enzymes, responsible for catalyzing the conversion of 5-methylcytosine to 5-hydroxymethylcyosine, 5-formylytosine, and 5-carboxylcyosine to achieve the DNA demethylation process, appear to play a critical role in decidualization and embryo implantation. Here, we provide a comprehensive view of their structural similarities and the common mechanism of regulation in the microenvironment at the maternal-fetal interface during decidualization and early pregnancy. We also discuss their physiological role in the decidual immune microenvironment. Finally, we propose a key hypothesis regarding TET enzymes at the maternal-fetal interface between decidual immune cells and ESCs. Future work is needed to elucidate their functional role and examine therapeutic strategies targeting these enzymes in pregnancy-related disease preclinical models, which would be of great value for future implications in disease diagnosis or treatment.
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Affiliation(s)
- Mengmeng Jin
- Department of Reproductive Endocrinology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China,Key Laboratory of Reproductive Genetics (Ministry of Education), Zhejiang University, Hangzhou, China
| | - Jianxiong Ji
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xi Chen
- Department of Reproductive Endocrinology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China,Key Laboratory of Reproductive Genetics (Ministry of Education), Zhejiang University, Hangzhou, China
| | - Ying Zhou
- Department of Reproductive Endocrinology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China,Key Laboratory of Reproductive Genetics (Ministry of Education), Zhejiang University, Hangzhou, China
| | - Dimin Wang
- Department of Reproductive Endocrinology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China,Key Laboratory of Reproductive Genetics (Ministry of Education), Zhejiang University, Hangzhou, China,*Correspondence: Aixia Liu, ; Dimin Wang,
| | - Aixia Liu
- Department of Reproductive Endocrinology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China,Key Laboratory of Reproductive Genetics (Ministry of Education), Zhejiang University, Hangzhou, China,Department of Reproductive Medicine, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, China,*Correspondence: Aixia Liu, ; Dimin Wang,
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3
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Äijö T, Theofilatos D, Cheng M, Smith MD, Xiong Y, Baldwin AS, Tsagaratou A. TET proteins regulate T cell and iNKT cell lineage specification in a TET2 catalytic dependent manner. Front Immunol 2022; 13:940995. [PMID: 35990681 PMCID: PMC9389146 DOI: 10.3389/fimmu.2022.940995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/07/2022] [Indexed: 12/13/2022] Open
Abstract
TET proteins mediate DNA demethylation by oxidizing 5-methylcytosine to 5-hydroxymethylcytosine (5hmC) and other oxidative derivatives. We have previously demonstrated a dynamic enrichment of 5hmC during T and invariant natural killer T cell lineage specification. Here, we investigate shared signatures in gene expression of Tet2/3 DKO CD4 single positive (SP) and iNKT cells in the thymus. We discover that TET proteins exert a fundamental role in regulating the expression of the lineage specifying factor Th-POK, which is encoded by Zbtb7b. We demonstrate that TET proteins mediate DNA demethylation - surrounding a proximal enhancer, critical for the intensity of Th-POK expression. In addition, TET proteins drive the DNA demethylation of site A at the Zbtb7b locus to facilitate GATA3 binding. GATA3 induces Th-POK expression in CD4 SP cells. Finally, by introducing a novel mouse model that lacks TET3 and expresses full length, catalytically inactive TET2, we establish a causal link between TET2 catalytic activity and lineage specification of both conventional and unconventional T cells.
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Affiliation(s)
- Tarmo Äijö
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Dimitris Theofilatos
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Meng Cheng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Matthew D. Smith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Yue Xiong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Albert S. Baldwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ageliki Tsagaratou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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4
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Stolz P, Mantero AS, Tvardovskiy A, Ugur E, Wange LE, Mulholland CB, Cheng Y, Wierer M, Enard W, Schneider R, Bartke T, Leonhardt H, Elsässer SJ, Bultmann S. TET1 regulates gene expression and repression of endogenous retroviruses independent of DNA demethylation. Nucleic Acids Res 2022; 50:8491-8511. [PMID: 35904814 PMCID: PMC9410877 DOI: 10.1093/nar/gkac642] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 04/25/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
DNA methylation (5-methylcytosine (5mC)) is critical for genome stability and transcriptional regulation in mammals. The discovery that ten-eleven translocation (TET) proteins catalyze the oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) revolutionized our perspective on the complexity and regulation of DNA modifications. However, to what extent the regulatory functions of TET1 can be attributed to its catalytic activity remains unclear. Here, we use genome engineering and quantitative multi-omics approaches to dissect the precise catalytic vs. non-catalytic functions of TET1 in murine embryonic stem cells (mESCs). Our study identifies TET1 as an essential interaction hub for multiple chromatin modifying complexes and a global regulator of histone modifications. Strikingly, we find that the majority of transcriptional regulation depends on non-catalytic functions of TET1. In particular, we show that TET1 is critical for the establishment of H3K9me3 and H4K20me3 at endogenous retroviral elements (ERVs) and their silencing that is independent of its canonical role in DNA demethylation. Furthermore, we provide evidence that this repression of ERVs depends on the interaction between TET1 and SIN3A. In summary, we demonstrate that the non-catalytic functions of TET1 are critical for regulation of gene expression and the silencing of endogenous retroviruses in mESCs.
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Affiliation(s)
- Paul Stolz
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Angelo Salazar Mantero
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet 17165 Stockholm, Sweden, Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet 17177 Stockholm, Sweden
| | - Andrey Tvardovskiy
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Enes Ugur
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany.,Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Lucas E Wange
- Faculty of Biology, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München 82152, Planegg-Martinsried, Germany
| | - Christopher B Mulholland
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Yuying Cheng
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet 17165 Stockholm, Sweden, Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet 17177 Stockholm, Sweden
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Wolfgang Enard
- Faculty of Biology, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München 82152, Planegg-Martinsried, Germany
| | - Robert Schneider
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Till Bartke
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Heinrich Leonhardt
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Simon J Elsässer
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet 17165 Stockholm, Sweden, Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet 17177 Stockholm, Sweden
| | - Sebastian Bultmann
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
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5
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Gerecke C, Egea Rodrigues C, Homann T, Kleuser B. The Role of Ten-Eleven Translocation Proteins in Inflammation. Front Immunol 2022; 13:861351. [PMID: 35386689 PMCID: PMC8977485 DOI: 10.3389/fimmu.2022.861351] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/28/2022] [Indexed: 12/11/2022] Open
Abstract
Ten-eleven translocation proteins (TET1-3) are dioxygenases that oxidize 5-methyldeoxycytosine, thus taking part in passive and active demethylation. TETs have shown to be involved in immune cell development, affecting from self-renewal of stem cells and lineage commitment to terminal differentiation. In fact, dysfunction of TET proteins have been vastly associated with both myeloid and lymphoid leukemias. Recently, there has been accumulating evidence suggesting that TETs regulate immune cell function during innate and adaptive immune responses, thereby modulating inflammation. In this work, we pursue to review the current and recent evidence on the mechanistic aspects by which TETs regulate immune cell maturation and function. We will also discuss the complex interplay of TET expression and activity by several factors to modulate a multitude of inflammatory processes. Thus, modulating TET enzymes could be a novel pharmacological approach to target inflammation-related diseases and myeloid and lymphoid leukemias, when their activity is dysregulated.
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Affiliation(s)
- Christian Gerecke
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Freie Universität Berlin, Germany
| | - Caue Egea Rodrigues
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Freie Universität Berlin, Germany
| | - Thomas Homann
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Freie Universität Berlin, Germany
| | - Burkhard Kleuser
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Freie Universität Berlin, Germany
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6
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Tan L, Fu L, Zheng L, Fan W, Tan H, Tao Z, Xu Y. TET2 Regulates 5-Hydroxymethylcytosine Signature and CD4 + T-Cell Balance in Allergic Rhinitis. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2022; 14:254-272. [PMID: 35255541 PMCID: PMC8914607 DOI: 10.4168/aair.2022.14.2.254] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/03/2022] [Accepted: 01/16/2022] [Indexed: 11/23/2022]
Abstract
Purpose Previous studies have shown the role of ten-eleven translocation 2 (TET2) in CD4+ T cells. However, its function in CD4+ T cells under allergic inflammation is unclear. We aimed to investigate the epigenomic distribution of DNA 5-hydroxymethylcytosine (5hmC) and the role of TET2 in CD4+ T cells of allergic rhinitis (AR). Methods The hMeDIP-seq was performed to identify sequences with 5hmC deposition in CD4+ T cells of AR patients. Tet2-deficient or wild type mice were stimulated with ovalbumin (OVA) to develop an AR mouse model. The histopathology in nasal mucosae, Th1/Th2/Treg/Th17 cell percentage, concentrations of Th-related cytokines, expression of Tet and differential hydroxymethylated genes (DhMG), and the global deposition of 5hmC in sorted CD4+ T cells were detected. Results Epigenome-wide 5hmC landscape and DhMG in the CD4+ T cells of AR patients were identified. Tet2 depletion did not led to spontaneous inflammation. However, under the stimulation of allergen, OVA, loss of Tet2 resulted in the exacerbation of allergic inflammation, which was characterized by severer allergic symptoms, more inflammatory cells infiltrating the nasal lamina propria, sharper imbalances between Th1/Th2 and Treg/Th17 cells, and excessive secretion of OVA-specific IgE and Th2-related cytokines. Moreover, altered mRNA production of several DhMG and sharp decrease in 5hmC deposition were also observed in Tet2-deficient OVA-exposed mice. Conclusions TET2 may regulate DNA 5hmC, DhMG expressions, and CD4+ T cell balance in AR.
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Affiliation(s)
- Lu Tan
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Lisheng Fu
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Li Zheng
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Wenjun Fan
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Hanyu Tan
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zezhang Tao
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yu Xu
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China.,Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan, China.
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7
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Nishikawa K, Seno S, Yoshihara T, Narazaki A, Sugiura Y, Shimizu R, Kikuta J, Sakaguchi R, Suzuki N, Takeda N, Semba H, Yamamoto M, Okuzaki D, Motooka D, Kobayashi Y, Suematsu M, Koseki H, Matsuda H, Yamamoto M, Tobita S, Mori Y, Ishii M. Osteoclasts adapt to physioxia perturbation through DNA demethylation. EMBO Rep 2021; 22:e53035. [PMID: 34661337 PMCID: PMC8647016 DOI: 10.15252/embr.202153035] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 09/03/2021] [Accepted: 09/16/2021] [Indexed: 12/12/2022] Open
Abstract
Oxygen plays an important role in diverse biological processes. However, since quantitation of the partial pressure of cellular oxygen in vivo is challenging, the extent of oxygen perturbation in situ and its cellular response remains underexplored. Using two‐photon phosphorescence lifetime imaging microscopy, we determine the physiological range of oxygen tension in osteoclasts of live mice. We find that oxygen tension ranges from 17.4 to 36.4 mmHg, under hypoxic and normoxic conditions, respectively. Physiological normoxia thus corresponds to 5% and hypoxia to 2% oxygen in osteoclasts. Hypoxia in this range severely limits osteoclastogenesis, independent of energy metabolism and hypoxia‐inducible factor activity. We observe that hypoxia decreases ten‐eleven translocation (TET) activity. Tet2/3 cooperatively induces Prdm1 expression via oxygen‐dependent DNA demethylation, which in turn activates NFATc1 required for osteoclastogenesis. Taken together, our results reveal that TET enzymes, acting as functional oxygen sensors, regulate osteoclastogenesis within the physiological range of oxygen tension, thus opening new avenues for research on in vivo response to oxygen perturbation.
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Affiliation(s)
- Keizo Nishikawa
- Laboratory of Cell Biology and Metabolic Biochemistry, Department of Medical Life Systems, Graduate School of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan.,Department of Immunology and Cell Biology, WPI-Immunology Frontier Research Center, Osaka University, Suita, Japan.,Graduate School of Medicine/Frontier Biosciences, Osaka University, Suita, Japan
| | - Shigeto Seno
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Toshitada Yoshihara
- Department of Chemistry and Chemical Biology, Gunma University, Kiryu, Japan
| | - Ayako Narazaki
- Graduate School of Medicine/Frontier Biosciences, Osaka University, Suita, Japan
| | - Yuki Sugiura
- Department of Biochemistry, Keio University, Tokyo, Japan
| | - Reito Shimizu
- Laboratory of Cell Biology and Metabolic Biochemistry, Department of Medical Life Systems, Graduate School of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Junichi Kikuta
- Department of Immunology and Cell Biology, WPI-Immunology Frontier Research Center, Osaka University, Suita, Japan.,Graduate School of Medicine/Frontier Biosciences, Osaka University, Suita, Japan.,Laboratory of Bioimaging and Drug Discovery, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Japan
| | - Reiko Sakaguchi
- WPI-Research Initiative-Institute for Integrated Cell-Material Science, Kyoto University, Kyoto, Japan.,Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Norio Suzuki
- Division of Oxygen Biology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Norihiko Takeda
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Semba
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Cardiovascular Medicine/Basic Research, The Cardiovascular Institute, Tokyo, Japan
| | - Masamichi Yamamoto
- Department of Artificial Kidneys, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Daisuke Okuzaki
- Single Cell Genomics, Human Immunology, WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Yasuhiro Kobayashi
- Institute for Oral Science, Matsumoto Dental University, Shiojiri, Japan
| | | | - Haruhiko Koseki
- Developmental Genetics Group, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Hideo Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Masayuki Yamamoto
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Seiji Tobita
- Department of Chemistry and Chemical Biology, Gunma University, Kiryu, Japan
| | - Yasuo Mori
- WPI-Research Initiative-Institute for Integrated Cell-Material Science, Kyoto University, Kyoto, Japan.,Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Masaru Ishii
- Department of Immunology and Cell Biology, WPI-Immunology Frontier Research Center, Osaka University, Suita, Japan.,Graduate School of Medicine/Frontier Biosciences, Osaka University, Suita, Japan.,Laboratory of Bioimaging and Drug Discovery, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Japan
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8
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Yue X, Samaniego-Castruita D, González-Avalos E, Li X, Barwick BG, Rao A. Whole-genome analysis of TET dioxygenase function in regulatory T cells. EMBO Rep 2021; 22:e52716. [PMID: 34288360 PMCID: PMC8339674 DOI: 10.15252/embr.202152716] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 12/13/2022] Open
Abstract
TET methylcytosine dioxygenases are essential for the stability and function of regulatory T cells (Treg cells), which maintain immune homeostasis and self‐tolerance and express the lineage‐determining transcription factor Foxp3. Here, we use whole‐genome analyses to show that the transcriptional program and epigenetic features (DNA modification, chromatin accessibility) of Treg cells are attenuated in the absence of Tet2 and Tet3. Conversely, the addition of the TET activator vitamin C during TGFβ‐induced iTreg cell differentiation in vitro potentiates the expression of Treg signature genes and alters the epigenetic landscape to better resemble that of Treg cells generated in vivo. Vitamin C enhances IL‐2 responsiveness in iTreg cells by increasing IL2Rα expression, STAT5 phosphorylation, and STAT5 binding, mimicking the IL‐2/STAT5 dependence of Treg cells generated in vivo. In summary, TET proteins play essential roles in maintaining Treg molecular features and promoting their dependence on IL‐2. TET activity during endogenous Treg development and potentiation of TET activity by vitamin C during iTreg differentiation are necessary to maintain the transcriptional and epigenetic features of Treg cells.
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Affiliation(s)
- Xiaojing Yue
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Daniela Samaniego-Castruita
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA.,Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Edahí González-Avalos
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA.,Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Xiang Li
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - Benjamin G Barwick
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA.,Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
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9
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Tsiouplis NJ, Bailey DW, Chiou LF, Wissink FJ, Tsagaratou A. TET-Mediated Epigenetic Regulation in Immune Cell Development and Disease. Front Cell Dev Biol 2021; 8:623948. [PMID: 33520997 PMCID: PMC7843795 DOI: 10.3389/fcell.2020.623948] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
TET proteins oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and further oxidation products in DNA. The oxidized methylcytosines (oxi-mCs) facilitate DNA demethylation and are also novel epigenetic marks. TET loss-of-function is strongly associated with cancer; TET2 loss-of-function mutations are frequently observed in hematological malignancies that are resistant to conventional therapies. Importantly, TET proteins govern cell fate decisions during development of various cell types by activating a cell-specific gene expression program. In this review, we seek to provide a conceptual framework of the mechanisms that fine tune TET activity. Then, we specifically focus on the multifaceted roles of TET proteins in regulating gene expression in immune cell development, function, and disease.
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Affiliation(s)
- Nikolas James Tsiouplis
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, United States
| | - David Wesley Bailey
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, United States.,University of North Carolina Center of Translational Immunology, Chapel Hill, NC, United States.,University of North Carolina Institute of Inflammatory Disease, Chapel Hill, NC, United States
| | - Lilly Felicia Chiou
- University of North Carolina Curriculum in Genetics and Molecular Biology, Chapel Hill, NC, United States
| | - Fiona Jane Wissink
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, United States
| | - Ageliki Tsagaratou
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, United States.,University of North Carolina Center of Translational Immunology, Chapel Hill, NC, United States.,University of North Carolina Institute of Inflammatory Disease, Chapel Hill, NC, United States.,University of North Carolina Curriculum in Genetics and Molecular Biology, Chapel Hill, NC, United States.,University of North Carolina Department of Genetics, Chapel Hill, NC, United States.,University of North Carolina Department of Microbiology and Immunology, Chapel Hill, NC, United States
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10
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Tsagaratou A. Deciphering the multifaceted roles of TET proteins in T-cell lineage specification and malignant transformation. Immunol Rev 2021; 300:22-36. [PMID: 33410200 DOI: 10.1111/imr.12940] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/23/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022]
Abstract
TET proteins are DNA demethylases that can oxidize 5-methylcytosine (5mC) to generate 5-hydroxymethylcytosine (5hmC) and other oxidized mC bases (oxi-mCs). Importantly, TET proteins govern cell fate decisions during development of various cell types by activating a cell-specific gene expression program. In this review, we focus on the role of TET proteins in T-cell lineage specification. We explore the multifaceted roles of TET proteins in regulating gene expression in the contexts of T-cell development, lineage specification, function, and disease. Finally, we discuss the future directions and experimental strategies required to decipher the precise mechanisms employed by TET proteins to fine-tune gene expression and safeguard cell identity.
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Affiliation(s)
- Ageliki Tsagaratou
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Center of Translational Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Institute of Inflammatory Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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11
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Kharat SS, Ding X, Swaminathan D, Suresh A, Singh M, Sengodan SK, Burkett S, Marks H, Pamala C, He Y, Fox SD, Buehler EC, Muegge K, Martin SE, Sharan SK. Degradation of 5hmC-marked stalled replication forks by APE1 causes genomic instability. Sci Signal 2020; 13:13/645/eaba8091. [PMID: 32817374 DOI: 10.1126/scisignal.aba8091] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Synthetic lethality between poly(ADP-ribose) polymerase (PARP) inhibition and BRCA deficiency is exploited to treat breast and ovarian tumors. However, resistance to PARP inhibitors (PARPis) is common. To identify potential resistance mechanisms, we performed a genome-wide RNAi screen in BRCA2-deficient mouse embryonic stem cells and validation in KB2P1.21 mouse mammary tumor cells. We found that resistance to multiple PARPi emerged with reduced expression of TET2 (ten-eleven translocation), which promotes DNA demethylation by oxidizing 5-methylcytosine (5mC) to 5-hydroxymethycytosine (5hmC) and other products. TET2 knockdown in BRCA2-deficient cells protected stalled replication forks (RFs). Increasing 5hmC abundance induced the degradation of stalled RFs in KB2P1.21 and human cancer cells by recruiting the base excision repair-associated apurinic/apyrimidinic endonuclease APE1, independent of the BRCA2 status. TET2 loss did not affect the recruitment of the repair protein RAD51 to sites of double-strand breaks (DSBs) or the abundance of proteins associated with RF integrity. The loss of TET2, of its product 5hmC, and of APE1 recruitment to stalled RFs promoted resistance to the chemotherapeutic cisplatin. Our findings reveal a previously unknown role for the epigenetic mark 5hmC in maintaining the integrity of stalled RFs and a potential resistance mechanism to PARPi and cisplatin.
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Affiliation(s)
- Suhas S Kharat
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Xia Ding
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Divya Swaminathan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Akshey Suresh
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Manish Singh
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Satheesh K Sengodan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Sandra Burkett
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Hanna Marks
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Chinmayi Pamala
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Yafeng He
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Stephen D Fox
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Eugen C Buehler
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850, USA
| | - Kathrin Muegge
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.,Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Scott E Martin
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850, USA
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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12
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Down-regulation of Tet2 is associated with Foxp3 TSDR hypermethylation in regulatory T cell of allergic rhinitis. Life Sci 2020; 241:117101. [DOI: 10.1016/j.lfs.2019.117101] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/13/2019] [Accepted: 11/22/2019] [Indexed: 12/11/2022]
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13
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DNA (Hydroxy)Methylation in T Helper Lymphocytes. Trends Biochem Sci 2019; 44:589-598. [DOI: 10.1016/j.tibs.2019.01.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/22/2019] [Accepted: 01/25/2019] [Indexed: 12/24/2022]
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14
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Feng Y, Li X, Cassady K, Zou Z, Zhang X. TET2 Function in Hematopoietic Malignancies, Immune Regulation, and DNA Repair. Front Oncol 2019; 9:210. [PMID: 31001476 PMCID: PMC6454012 DOI: 10.3389/fonc.2019.00210] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 03/11/2019] [Indexed: 12/13/2022] Open
Abstract
Over the last decade, investigation of Ten-Eleven Translocation 2 (TET2) gene function and TET2 mutation have become of increasing interest in the field of hematology. This heightened interest was sparked by the seminal discoveries that (1) TET2 mutation is associated with development of hematological malignancies and that (2) the TET family of proteins is critical in promoting DNA demethylation and immune homeostasis. Since then, additional studies have begun to unravel the question “Does TET2 have additional biological functions in the regulation of hematopoiesis?” Here, we present a mini-review focused on the current understanding of TET2 in hematopoiesis, hematological malignancies, and immune regulation. Importantly, we highlight the critical function that TET2 facilitates in maintaining the stability of the genome. Based on our review of the literature, we provide a new hypothesis that loss of TET2 may lead to dysregulation of the DNA repair response, augment genome instability, and subsequently sensitize myeloid leukemia cells to PARP inhibitor treatment.
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Affiliation(s)
- Yimei Feng
- Department of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, China.,State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, China
| | - Xiaoping Li
- Department of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, China.,State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, China
| | - Kaniel Cassady
- Irell and Manella Graduate School of Biological Sciences of City of Hope, Duarte, CA, United States.,Henry E. Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, United States
| | - Zhongmin Zou
- Department of Chemical Defense, School of Preventive Medicine, Army Medical University, Chongqing, China
| | - Xi Zhang
- Department of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, China.,State Key Laboratory of Trauma, Burns and Combined Injury, Army Medical University, Chongqing, China
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15
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Dai R, Edwards MR, Heid B, Ahmed SA. 17β-Estradiol and 17α-Ethinyl Estradiol Exhibit Immunologic and Epigenetic Regulatory Effects in NZB/WF1 Female Mice. Endocrinology 2019; 160:101-118. [PMID: 30418530 PMCID: PMC6305969 DOI: 10.1210/en.2018-00824] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 11/06/2018] [Indexed: 02/07/2023]
Abstract
17α-Ethinyl estradiol (EE), a synthetic analog of natural estrogen 17β-estradiol (E2), is extensively used in hormonal contraceptives and estrogen replacement therapy, and it has also been found in sewage effluents. Given that E2 is a well-known immunomodulator, surprisingly there has been only limited information on the cellular and molecular immunologic consequences of exposure to EE. To address this fundamental gap, we directly compared the effects of EE with E2 on splenic leukocytes of New Zealand Black × New Zealand White F1 progeny (NZB/WF1) mice during the preautoimmune period. We found that EE and E2 have common, as well as distinctive, immunologic effects, with EE exposure resulting in more profound effects. Both EE and E2 increased numbers of splenic neutrophils, enhanced neutrophil serine proteases and myeloperoxidase expression, promoted the production of nitric oxide and monocyte chemoattractant protein-1, and altered adaptive immune T cell subsets. However, activation of splenic leukocytes through the T cell receptor or Toll-like receptor (TLR)4 revealed not only common (IL-10), but also hormone-specific alterations of cytokines (IFNγ, IL-1β, ΤΝFα, IL-2). Furthermore, in EE-exposed mice, TLR9 stimulation suppressed IFNα, in contrast to increased IFNα from E2-exposed mice. EE and E2 regulated common and hormone-specific expression of immune-related genes. Furthermore, EE exposure resulted in more marked alterations in miRNA expression levels than for E2. Only EE was able to reduce global DNA methylation significantly in splenic leukocytes. Taken together, our novel data revealed that EE and E2 exposure confers more similar effects in innate immune system-related cell development and responses, but has more differential regulatory effects in adaptive immune-related cell development and responses.
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Affiliation(s)
- Rujuan Dai
- Department of Biomedical Sciences and Pathobiology, Infectious Disease Research Facility (IDRF), Virginia-Maryland College of Veterinary Medicine, Virginia Tech/Virginia Polytechnic Institute and State University, Blacksburg, Virginia
| | - Michael R Edwards
- Department of Biomedical Sciences and Pathobiology, Infectious Disease Research Facility (IDRF), Virginia-Maryland College of Veterinary Medicine, Virginia Tech/Virginia Polytechnic Institute and State University, Blacksburg, Virginia
| | - Bettina Heid
- Department of Biomedical Sciences and Pathobiology, Infectious Disease Research Facility (IDRF), Virginia-Maryland College of Veterinary Medicine, Virginia Tech/Virginia Polytechnic Institute and State University, Blacksburg, Virginia
| | - S Ansar Ahmed
- Department of Biomedical Sciences and Pathobiology, Infectious Disease Research Facility (IDRF), Virginia-Maryland College of Veterinary Medicine, Virginia Tech/Virginia Polytechnic Institute and State University, Blacksburg, Virginia
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16
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Unveiling the regulation of NKT17 cell differentiation and function. Mol Immunol 2018; 105:55-61. [PMID: 30496977 DOI: 10.1016/j.molimm.2018.11.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/19/2018] [Accepted: 11/20/2018] [Indexed: 12/12/2022]
Abstract
Invariant natural killer T cells (iNKTs) are distinct from conventional T cells. iNKT cells express a semi-invariant T cell receptor (TCR) that can specifically recognize lipid antigens presented by CD1d, an MHC class I-like antigen-presenting molecule. Currently, iNKT cells are distinguished in three functionally distinct subsets. Each subset is defined by lineage-specifying factors: T-bet shapes the fate of NKT1 subset that mainly secretes IFNγ, Gata3 specifies the NKT2 subset that produces robustly IL-4 whereas RORγt seals the differentiation of NKT17 subset that secretes IL-17. In the present review, the focus is placed on the regulation of NKT17 specification and their function.
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17
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Tsagaratou A. TET mediated epigenetic regulation of iNKT cell lineage fate choice and function. Mol Immunol 2018; 101:564-573. [PMID: 30176520 DOI: 10.1016/j.molimm.2018.08.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/19/2018] [Accepted: 08/18/2018] [Indexed: 12/14/2022]
Abstract
During the last years, intensive research has shed light in the transcriptional networks that shape the invariant NKT (iNKT) cell lineage and guide the choices towards functionally distinct iNKT cell subsets (Constantinides and Bendelac, 2013; Engel and Kronenberg, 2014; Gapin, 2016; Kim et al., 2015). However, the epigenetic players that regulate gene expression and orchestrate the iNKT cell lineage choices remain poorly understood. Here, we summarize recent advances in our understanding of epigenetic regulation of iNKT cell development and lineage choice. Particular emphasis is placed on DNA modifications and the Ten Eleven Translocation (TET) family of DNA demethylases.
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Affiliation(s)
- Ageliki Tsagaratou
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, San Diego, CA, 92037, USA.
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18
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Tsagaratou A, Lio CWJ, Yue X, Rao A. TET Methylcytosine Oxidases in T Cell and B Cell Development and Function. Front Immunol 2017; 8:220. [PMID: 28408905 PMCID: PMC5374156 DOI: 10.3389/fimmu.2017.00220] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 02/16/2017] [Indexed: 11/13/2022] Open
Abstract
DNA methylation is established by DNA methyltransferases and is a key epigenetic mark. Ten-eleven translocation (TET) proteins are enzymes that oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and further oxidization products (oxi-mCs), which indirectly promote DNA demethylation. Here, we provide an overview of the effect of TET proteins and altered DNA modification status in T and B cell development and function. We summarize current advances in our understanding of the role of TET proteins and 5hmC in T and B cells in both physiological and pathological contexts. We describe how TET proteins and 5hmC regulate DNA modification, chromatin accessibility, gene expression, and transcriptional networks and discuss potential underlying mechanisms and open questions in the field.
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Affiliation(s)
- Ageliki Tsagaratou
- Department of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Chan-Wang J Lio
- Department of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Xiaojing Yue
- Department of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Anjana Rao
- Department of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.,Department of Pharmacology and Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
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19
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Pollock RA, Abji F, Gladman DD. Epigenetics of psoriatic disease: A systematic review and critical appraisal. J Autoimmun 2017; 78:29-38. [DOI: 10.1016/j.jaut.2016.12.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/22/2016] [Accepted: 12/04/2016] [Indexed: 12/20/2022]
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20
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TET proteins regulate the lineage specification and TCR-mediated expansion of iNKT cells. Nat Immunol 2016; 18:45-53. [PMID: 27869820 DOI: 10.1038/ni.3630] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Accepted: 10/25/2016] [Indexed: 12/12/2022]
Abstract
TET proteins oxidize 5-methylcytosine in DNA to 5-hydroxymethylcytosine and other oxidation products. We found that simultaneous deletion of Tet2 and Tet3 in mouse CD4+CD8+ double-positive thymocytes resulted in dysregulated development and proliferation of invariant natural killer T cells (iNKT cells). Tet2-Tet3 double-knockout (DKO) iNKT cells displayed pronounced skewing toward the NKT17 lineage, with increased DNA methylation and impaired expression of genes encoding the key lineage-specifying factors T-bet and ThPOK. Transfer of purified Tet2-Tet3 DKO iNKT cells into immunocompetent recipient mice resulted in an uncontrolled expansion that was dependent on the nonclassical major histocompatibility complex (MHC) protein CD1d, which presents lipid antigens to iNKT cells. Our data indicate that TET proteins regulate iNKT cell fate by ensuring their proper development and maturation and by suppressing aberrant proliferation mediated by the T cell antigen receptor (TCR).
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21
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Jiang H, Lv X, Lei X, Yang Y, Yang X, Jiao J. Immune Regulator MCPIP1 Modulates TET Expression during Early Neocortical Development. Stem Cell Reports 2016; 7:439-453. [PMID: 27523618 PMCID: PMC5031990 DOI: 10.1016/j.stemcr.2016.07.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 07/10/2016] [Accepted: 07/11/2016] [Indexed: 12/15/2022] Open
Abstract
MCPIP1 is a recently identified immune regulator that plays critical roles in preventing immune disorders, and is also present in the brain. Currently an unresolved question remains as to how MCPIP1 performs its non-immune functions in normal brain development. Here, we report that MCPIP1 is abundant in neural progenitor cells (NPCs) and newborn neurons during the early stages of neurogenesis. The suppression of MCPIP1 expression impairs normal neuronal differentiation, cell-cycle exit, and concomitant NPC proliferation. MCPIP1 is important for maintenance of the NPC pool. Notably, we demonstrate that MCPIP1 reduces TET (TET1/TET2/TET3) levels and then decreases 5-hydroxymethylcytosine levels. Furthermore, the MCPIP1 interaction with TETs is involved in neurogenesis and in establishing the proper number of NPCs in vivo. Collectively, our findings not only demonstrate that MCPIP1 plays an important role in early cortical neurogenesis but also reveal an unexpected link between neocortical development, immune regulators, and epigenetic modification. MCPIP1 is abundant during early neocortical development MCPIP1 suppression impairs normal neocortical neurogenesis MCPIP1 directly targets Tets and regulates TET expression levels
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Affiliation(s)
- Huihui Jiang
- State Key Laboratory of Stem Cells and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaohui Lv
- State Key Laboratory of Stem Cells and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuepei Lei
- State Key Laboratory of Stem Cells and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Yang
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xin Yang
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianwei Jiao
- State Key Laboratory of Stem Cells and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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22
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Hohos NM, Lee K, Ji L, Yu M, Kandasamy MM, Phillips BG, Baile CA, He C, Schmitz RJ, Meagher RB. DNA cytosine hydroxymethylation levels are distinct among non-overlapping classes of peripheral blood leukocytes. J Immunol Methods 2016; 436:1-15. [PMID: 27164004 PMCID: PMC5131182 DOI: 10.1016/j.jim.2016.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 04/19/2016] [Accepted: 05/02/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND Peripheral blood leukocytes are the most commonly used surrogates to study epigenome-induced risk and epigenomic response to disease-related stress. We considered the hypothesis that the various classes of peripheral leukocytes differentially regulate the synthesis of 5-methylcytosine (5mCG) and its removal via Ten-Eleven Translocation (TET) dioxygenase catalyzed hydroxymethylation to 5-hydroxymethylcytosine (5hmCG), reflecting their responsiveness to environment. Although it is known that reductions in TET1 and/or TET2 activity lead to the over-proliferation of various leukocyte precursors in bone marrow and in development of chronic myelomonocytic leukemia and myeloproliferative neoplasms, the role of 5mCG hydroxymethylation in peripheral blood is less well studied. RESULTS We developed simplified protocols to rapidly and reiteratively isolate non-overlapping leukocyte populations from a single small sample of fresh or frozen whole blood. Among peripheral leukocyte types we found extreme variation in the levels of transcripts encoding proteins involved in cytosine methylation (DNMT1, 3A, 3B), the turnover of 5mC by demethylation (TET1, 2, 3), and DNA repair (GADD45A, B, G) and in the global and gene-region-specific levels of DNA 5hmCG (CD4+ T cells≫CD14+ monocytes>CD16+ neutrophils>CD19+ B cells>CD56+ NK cells>Siglec8+ eosinophils>CD8+ T cells). CONCLUSIONS Our data taken together suggest a potential hierarchy of responsiveness among classes of leukocytes with CD4+, CD8+ T cells and CD14+ monocytes being the most distinctly poised for a rapid methylome response to physiological stress and disease.
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Affiliation(s)
- Natalie M Hohos
- Department of Foods and Nutrition, University of Georgia, Athens, GA, USA.
| | - Kevin Lee
- Department of Genetics, University of Georgia, Athens, GA, USA.
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA.
| | - Miao Yu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
| | | | - Bradley G Phillips
- Clinical and Administrative Pharmacy, University of Georgia, Athens, GA, USA.
| | - Clifton A Baile
- Department of Foods and Nutrition, University of Georgia, Athens, GA, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
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23
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Fong KSK, Hufnagel RB, Khadka VS, Corley MJ, Maunakea AK, Fogelgren B, Ahmed ZM, Lozanoff S. A mutation in the tuft mouse disrupts TET1 activity and alters the expression of genes that are crucial for neural tube closure. Dis Model Mech 2016; 9:585-96. [PMID: 26989192 PMCID: PMC4892663 DOI: 10.1242/dmm.024109] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/09/2016] [Indexed: 01/19/2023] Open
Abstract
Genetic variations affecting neural tube closure along the head result in malformations of the face and brain. Neural tube defects (NTDs) are among the most common birth defects in humans. We previously reported a mouse mutant called tuft that arose spontaneously in our wild-type 3H1 colony. Adult tuft mice present midline craniofacial malformations with or without an anterior cephalocele. In addition, affected embryos presented neural tube closure defects resulting in insufficient closure of the anterior neuropore or exencephaly. Here, through whole-genome sequencing, we identified a nonsense mutation in the Tet1 gene, which encodes a methylcytosine dioxygenase (TET1), co-segregating with the tuft phenotype. This mutation resulted in premature termination that disrupts the catalytic domain that is involved in the demethylation of cytosine. We detected a significant loss of TET enzyme activity in the heads of tuft embryos that were homozygous for the mutation and had NTDs. RNA-Seq transcriptome analysis indicated that multiple gene pathways associated with neural tube closure were dysregulated in tuft embryo heads. Among them, the expressions of Cecr2, Epha7 and Grhl2 were significantly reduced in some embryos presenting neural tube closure defects, whereas one or more components of the non-canonical WNT signaling pathway mediating planar cell polarity and convergent extension were affected in others. We further show that the recombinant mutant TET1 protein was capable of entering the nucleus and affected the expression of endogenous Grhl2 in IMCD-3 (inner medullary collecting duct) cells. These results indicate that TET1 is an epigenetic determinant for regulating genes that are crucial to closure of the anterior neural tube and its mutation has implications to craniofacial development, as presented by the tuft mouse. Summary: We propose an epigenetic mechanism establishing the regulation of genes that are crucial for neural tube closure. This mechanism could be a novel target for resolving such birth defects and associated disorders.
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Affiliation(s)
- Keith S K Fong
- Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI 96813, USA
| | - Robert B Hufnagel
- Department of Pediatrics, Division of Human Genetics, Cincinnati Children's Hospital, College of Medicine, University of Cincinnati, 3333 Burnet Ave, ML 7003, Cincinnati, OH 45229, USA Unit on Pediatric, Development & Genetic Ophthalmology, Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vedbar S Khadka
- Office of Biostatistics and Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI 96813, USA
| | - Michael J Corley
- Epigenomics Research Program, Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI 96813, USA
| | - Alika K Maunakea
- Epigenomics Research Program, Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI 96813, USA
| | - Ben Fogelgren
- Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI 96813, USA
| | - Zubair M Ahmed
- Department of Pediatrics, Division of Human Genetics, Cincinnati Children's Hospital, College of Medicine, University of Cincinnati, 3333 Burnet Ave, ML 7003, Cincinnati, OH 45229, USA Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, BioPark Bldg1, 800 West Baltimore Street, Room 404, Baltimore, MD 21201, USA
| | - Scott Lozanoff
- Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI 96813, USA
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24
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Yue X, Trifari S, Äijö T, Tsagaratou A, Pastor WA, Zepeda-Martínez JA, Lio CWJ, Li X, Huang Y, Vijayanand P, Lähdesmäki H, Rao A. Control of Foxp3 stability through modulation of TET activity. J Exp Med 2016; 213:377-97. [PMID: 26903244 PMCID: PMC4813667 DOI: 10.1084/jem.20151438] [Citation(s) in RCA: 242] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 01/01/2016] [Indexed: 12/29/2022] Open
Abstract
TET2 and TET3 redundantly regulate Foxp3 stability, and their activity can be modulated by vitamin C. Ten-eleven translocation (TET) enzymes oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine and other oxidized methylcytosines, intermediates in DNA demethylation. In this study, we examine the role of TET proteins in regulating Foxp3, a transcription factor essential for the development and function of regulatory T cells (T reg cells), a distinct lineage of CD4+ T cells that prevent autoimmunity and maintain immune homeostasis. We show that during T reg cell development in the thymus, TET proteins mediate the loss of 5mC in T reg cell–specific hypomethylated regions, including CNS1 and CNS2, intronic cis-regulatory elements in the Foxp3 locus. Similar to CNS2-deficient T reg cells, the stability of Foxp3 expression is markedly compromised in T reg cells from Tet2/Tet3 double-deficient mice. Vitamin C potentiates TET activity and acts through Tet2/Tet3 to increase the stability of Foxp3 expression in TGF-β–induced T reg cells. Our data suggest that targeting TET enzymes with small molecule activators such as vitamin C might increase induced T reg cell efficacy.
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Affiliation(s)
- Xiaojing Yue
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Sara Trifari
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Tarmo Äijö
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037 Department of Computer Science, Aalto University School of Science, 00076 Aalto, Finland
| | - Ageliki Tsagaratou
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - William A Pastor
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Jorge A Zepeda-Martínez
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Chan-Wang J Lio
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Xiang Li
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037 Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037
| | - Yun Huang
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Pandurangan Vijayanand
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University School of Science, 00076 Aalto, Finland
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037 Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037 Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093 Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093
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Sasidharan Nair V, Song MH, Oh KI. Vitamin C Facilitates Demethylation of the Foxp3 Enhancer in a Tet-Dependent Manner. THE JOURNAL OF IMMUNOLOGY 2016; 196:2119-31. [DOI: 10.4049/jimmunol.1502352] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 12/28/2015] [Indexed: 12/17/2022]
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Differential regulation of genomic imprinting by TET proteins in embryonic stem cells. Stem Cell Res 2015; 15:435-43. [PMID: 26397890 DOI: 10.1016/j.scr.2015.08.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/25/2015] [Accepted: 08/27/2015] [Indexed: 12/13/2022] Open
Abstract
TET proteins have been found to play an important role in active demethylation at CpG sites in mammals. There are some reports implicating their functions in removal of DNA methylation imprint at the imprinted regions in the germline. However, it is not well established whether TET proteins can also be involved in demethylation of DNA methylation imprint in embryonic stem (ES) cells. Here we report that loss of TET proteins caused a significant increase in DNA methylation at the Igf2-H19 imprinted region in ES cells. We also observed a variable increase in DNA methylation at the Peg1 imprinted region in the ES clones devoid of TET proteins, in particular in the differentiated ES cells. By contrast, we did not observe a significant increase of DNA methylation imprint at the Peg3, Snrpn and Dlk1-Dio3 imprinted regions in ES cells lacking TET proteins. Interestingly, loss of TET proteins did not result in a significant increase of DNA methylation imprint at the Igf2-H19 and Peg1 imprinted regions in the embryoid bodies (EB). Therefore, TET proteins seem to be differentially involved in maintaining DNA methylation imprint at a subset of imprinted regions in ES cells and EBs.
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Dynamic switching of active promoter and enhancer domains regulates Tet1 and Tet2 expression during cell state transitions between pluripotency and differentiation. Mol Cell Biol 2015; 35:1026-42. [PMID: 25582196 DOI: 10.1128/mcb.01172-14] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Tet 5-methylcytosine dioxygenases catalyze DNA demethylation by producing 5-hydroxymethylcytosine and further oxidized products. Tet1 and Tet2 are highly expressed in mouse pluripotent cells and downregulated to different extents in somatic cells, but the transcriptional mechanisms are unclear. Here we defined the promoter and enhancer domains in Tet1 and Tet2. Within a 15-kb "superenhancer" of Tet1, there are two transcription start sites (TSSs) with different activation patterns during development. A 6-kb promoter region upstream of the distal TSS is highly active in naive pluripotent cells, autonomously reports Tet1 expression in a transgenic system, and rapidly undergoes DNA methylation and silencing upon differentiation in cultured cells and native epiblast. A second TSS downstream, associated with a constitutively weak CpG-rich promoter, is activated by a neighboring enhancer in naive embryonic stem cells (ESCs) and primed epiblast-like cells (EpiLCs). Tet2 has a CpG island promoter with pluripotency-independent activity and an ESC-specific distal intragenic enhancer; the latter is rapidly downregulated in EpiLCs. Our study reveals distinct modes of transcriptional regulation at Tet1 and Tet2 during cell state transitions of early development. New transgenic reporters using Tet1 and Tet2 cis-regulatory domains may serve to distinguish nuanced changes in pluripotent states and the underlying epigenetic variations.
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Dissecting the dynamic changes of 5-hydroxymethylcytosine in T-cell development and differentiation. Proc Natl Acad Sci U S A 2014; 111:E3306-15. [PMID: 25071199 DOI: 10.1073/pnas.1412327111] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The discovery of Ten Eleven Translocation proteins, enzymes that oxidize 5-methylcytosine (5mC) in DNA, has revealed novel mechanisms for the regulation of DNA methylation. We have mapped 5-hydroxymethylcytosine (5hmC) at different stages of T-cell development in the thymus and T-cell differentiation in the periphery. We show that 5hmC is enriched in the gene body of highly expressed genes at all developmental stages and that its presence correlates positively with gene expression. Further emphasizing the connection with gene expression, we find that 5hmC is enriched in active thymus-specific enhancers and that genes encoding key transcriptional regulators display high intragenic 5hmC levels in precursor cells at those developmental stages where they exert a positive effect. Our data constitute a valuable resource that will facilitate detailed analysis of the role of 5hmC in T-cell development and differentiation.
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