1
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Amable L, Ferreira Martins LA, Pierre R, Do Cruseiro M, Chabab G, Sergé A, Kergaravat C, Delord M, Viret C, Jaubert J, Liu C, Karray S, Marie JC, Irla M, Georgiev H, Clave E, Toubert A, Lucas B, Klibi J, Benlagha K. Intrinsic factors and CD1d1 but not CD1d2 expression levels control invariant natural killer T cell subset differentiation. Nat Commun 2023; 14:7922. [PMID: 38040679 PMCID: PMC10692182 DOI: 10.1038/s41467-023-43424-7] [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: 02/14/2023] [Accepted: 11/08/2023] [Indexed: 12/03/2023] Open
Abstract
Invariant natural killer T (NKT) cell subsets are defined based on their cytokine-production profiles and transcription factors. Their distribution is different in C57BL/6 (B6) and BALB/c mice, with a bias for NKT1 and NKT2/NKT17 subsets, respectively. Here, we show that the non-classical class I-like major histocompatibility complex CD1 molecules CD1d2, expressed in BALB/c and not in B6 mice, could not account for this difference. We find however that NKT cell subset distribution is intrinsic to bone marrow derived NKT cells, regardless of syngeneic CD1d-ligand recognition, and that multiple intrinsic factors are likely involved. Finally, we find that CD1d expression levels in combination with T cell antigen receptor signal strength could also influence NKT cell distribution and function. Overall, this study indicates that CD1d-mediated TCR signals and other intrinsic signals integrate to influence strain-specific NKT cell differentiation programs and subset distributions.
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Affiliation(s)
- Ludivine Amable
- Université Paris Cité, Institut de Recherche Saint-Louis (IRSL), EMiLy, Paris, France
| | | | - Remi Pierre
- Plateforme de recombinaison homologue et de cryoconservation (PRHTEC), Institut Cochin, Université Paris Descartes, Paris, France
| | - Marcio Do Cruseiro
- Plateforme de recombinaison homologue et de cryoconservation (PRHTEC), Institut Cochin, Université Paris Descartes, Paris, France
| | - Ghita Chabab
- Tumor Escape Resistance and Immunity department, Cancer Research Center of Lyon INSERM U1052, CNRS UMR 5286, Centre Léon Bérard, Lyon, France
| | - Arnauld Sergé
- Laboratoire Adhésion Inflammation (LAI), CNRS, INSERM, Aix-Marseille Université, Marseille, France
| | - Camille Kergaravat
- Université Paris Cité, Institut de Recherche Saint-Louis (IRSL), EMiLy, Paris, France
| | | | - Christophe Viret
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, INSERM U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Jean Jaubert
- Mouse Genetics Unit, Institut Pasteur, Paris, France
| | - Chaohong Liu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science Technology, Wuhan, China
| | - Saoussen Karray
- Université Paris Cité, INSERM U976, Institut de Recherche Saint-Louis (IRSL), Hôpital Saint-Louis, Paris, France
| | - Julien C Marie
- Tumor Escape Resistance and Immunity department, Cancer Research Center of Lyon INSERM U1052, CNRS UMR 5286, Centre Léon Bérard, Lyon, France
| | - Magali Irla
- Centre d'Immunologie de Marseille-Luminy (CIML), CNRS, INSERM, Aix-Marseille Université, Marseille, France
| | - Hristo Georgiev
- Institute of immunology, Hannover Medical School, Hannover, Germany
| | - Emmanuel Clave
- Université Paris Cité, Institut de Recherche Saint-Louis (IRSL), EMiLy, Paris, France
| | - Antoine Toubert
- Université Paris Cité, Institut de Recherche Saint-Louis (IRSL), EMiLy, Paris, France
| | - Bruno Lucas
- Institut Cochin, Centre National de la Recherche Scientifique UMR8104, INSERM U1016, Université Paris Descartes, Paris, France
| | - Jihene Klibi
- Université Paris Cité, Institut de Recherche Saint-Louis (IRSL), EMiLy, Paris, France
| | - Kamel Benlagha
- Université Paris Cité, Institut de Recherche Saint-Louis (IRSL), EMiLy, Paris, France.
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2
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Qu L, Yin T, Zhao Y, Lv W, Liu Z, Chen C, Liu K, Shan S, Zhou R, Li X, Dong H. Histone demethylases in the regulation of immunity and inflammation. Cell Death Discov 2023; 9:188. [PMID: 37353521 DOI: 10.1038/s41420-023-01489-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/22/2023] [Accepted: 06/15/2023] [Indexed: 06/25/2023] Open
Abstract
Pathogens or danger signals trigger the immune response. Moderate immune response activation removes pathogens and avoids excessive inflammation and tissue damage. Histone demethylases (KDMs) regulate gene expression and play essential roles in numerous physiological processes by removing methyl groups from lysine residues on target proteins. Abnormal expression of KDMs is closely associated with the pathogenesis of various inflammatory diseases such as liver fibrosis, lung injury, and autoimmune diseases. Despite becoming exciting targets for diagnosing and treating these diseases, the role of these enzymes in the regulation of immune and inflammatory response is still unclear. Here, we review the underlying mechanisms through which KDMs regulate immune-related pathways and inflammatory responses. In addition, we also discuss the future applications of KDMs inhibitors in immune and inflammatory diseases.
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Affiliation(s)
- Lihua Qu
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, China
| | - Tong Yin
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Yijin Zhao
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Wenting Lv
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Ziqi Liu
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Chao Chen
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Kejun Liu
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Shigang Shan
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, China
| | - Rui Zhou
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Xiaoqing Li
- Biological Targeted Therapy Key Laboratory in Hubei, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Center for Stem Cell Research and Application, Union Hospital, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Huifen Dong
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China.
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China.
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3
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Tayari MM, Fang C, Ntziachristos P. Context-Dependent Functions of KDM6 Lysine Demethylases in Physiology and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1433:139-165. [PMID: 37751139 DOI: 10.1007/978-3-031-38176-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Histone lysine methylation is a major epigenetic modification that participates in several cellular processes including gene regulation and chromatin structure. This mark can go awry in disease contexts such as cancer. Two decades ago, the discovery of histone demethylase enzymes thirteen years ago sheds light on the complexity of the regulation of this mark. Here we address the roles of lysine demethylases JMJD3 and UTX in physiological and disease contexts. The two demethylases play pivotal roles in many developmental and disease contexts via regulation of di- and trimethylation of lysine 27 on histone H3 (H3K27me2/3) in repressing gene expression programs. JMJD3 and UTX participate in several biochemical settings including methyltransferase and chromatin remodeling complexes. They have histone demethylase-dependent and -independent activities and a variety of context-specific interacting factors. The structure, amounts, and function of the demethylases can be altered in disease due to genetic alterations or aberrant gene regulation. Therefore, academic and industrial initiatives have targeted these enzymes using a number of small molecule compounds in therapeutic approaches. In this chapter, we will touch upon inhibitor formulations, their properties, and current efforts to test them in preclinical contexts to optimize their therapeutic outcomes. Demethylase inhibitors are currently used in targeted therapeutic approaches that might be particularly effective when used in conjunction with systemic approaches such as chemotherapy.
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Affiliation(s)
- Mina Masoumeh Tayari
- Department of Human Genetics, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Celestia Fang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Panagiotis Ntziachristos
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Center for Medical Genetics, Ghent University, Medical Research Building 2 (MRB2), Entrance 38, Corneel Heymanslaan 10, 9000, Ghent, Belgium.
- Center for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
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4
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Xu WD, Huang Q, Huang AF. Emerging role of EZH2 in rheumatic diseases: A comprehensive review. Int J Rheum Dis 2022; 25:1230-1238. [PMID: 35933601 DOI: 10.1111/1756-185x.14416] [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: 04/17/2022] [Revised: 07/03/2022] [Accepted: 07/23/2022] [Indexed: 11/29/2022]
Abstract
Enhancer of zeste homolog 2 (EZH2) is a histone methylated enzyme. It trimethylates histone 3 lysine 27 (H3K27) to regulate epigenetic processes. Recently, studies showed excessive expression of EZH2 in rheumatic diseases, such as systemic lupus erythematosus, rheumatoid arthritis, osteoarthritis, and systemic sclerosis. Moreover, epigenetic modification of EZH2 regulates differentiation and proliferation of different immune cells. Therefore, in this review, we comprehensively discuss the role of EZH2 in rheumatic diseases. Collection of the evidence may provide a basis for further understanding the role of EZH2 and give potential for targeting these diseases.
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Affiliation(s)
- Wang-Dong Xu
- Department of Evidence-Based Medicine, Southwest Medical University, Luzhou, China
| | - Qi Huang
- Department of Evidence-Based Medicine, Southwest Medical University, Luzhou, China
| | - An-Fang Huang
- Department of Rheumatology and Immunology, Affiliated Hospital of Southwest Medical University, Luzhou, China
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5
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Morgan RC, Kee BL. Genomic and Transcriptional Mechanisms Governing Innate-like T Lymphocyte Development. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:208-216. [PMID: 35821098 DOI: 10.4049/jimmunol.2200141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/18/2022] [Indexed: 12/16/2022]
Abstract
Innate-like lymphocytes are a subset of lymphoid cells that function as a first line of defense against microbial infection. These cells are activated by proinflammatory cytokines or broadly expressed receptors and are able to rapidly perform their effector functions owing to a uniquely primed chromatin state that is acquired as a part of their developmental program. These cells function in many organs to protect against disease, but they release cytokines and cytotoxic mediators that can also lead to severe tissue pathologies. Therefore, harnessing the capabilities of these cells for therapeutic interventions will require a deep understanding of how these cells develop and regulate their effector functions. In this review we discuss recent advances in the identification of the transcription factors and the genomic regions that guide the development and function of invariant NKT cells and we highlight related mechanisms in other innate-like lymphocytes.
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Affiliation(s)
- Roxroy C Morgan
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL; and
| | - Barbara L Kee
- Cancer Biology and Immunology, Department of Pathology, University of Chicago, Chicago, IL
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6
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Dutta A, Venkataganesh H, Love PE. New Insights into Epigenetic Regulation of T Cell Differentiation. Cells 2021; 10:3459. [PMID: 34943965 PMCID: PMC8700096 DOI: 10.3390/cells10123459] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 12/13/2022] Open
Abstract
Immature CD4- CD8- thymocytes progress through several developmental steps in the thymus, ultimately emerging as mature CD4+ (helper) or CD8+ (cytotoxic) T cells. Activation of naïve CD4+ and CD8+ T cells in the presence of specific cytokines results in the induction of transcriptional programs that result in their differentiation into effector or memory cells and in the case of CD4+ T cells, the adoption of distinct T-helper fates. Previous studies have shown that histone modification and DNA methylation play important roles in each of these events. More recently, the roles of specific epigenetic regulators in T cell differentiation have been clarified. The identification of the epigenetic modifications and modifiers that control mature T cell differentiation and specification has also provided further insights into how dysregulation of these processes can lead to cancer or autoimmune diseases. In this review, we summarize recent findings that have provided new insights into epigenetic regulation of T cell differentiation in both mice and humans.
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Affiliation(s)
- Avik Dutta
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (A.D.); (H.V.)
| | - Harini Venkataganesh
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (A.D.); (H.V.)
- Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Paul E. Love
- Section on Hematopoiesis and Lymphocyte Biology, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA; (A.D.); (H.V.)
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7
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Huang J, Zhang J, Guo Z, Li C, Tan Z, Wang J, Yang J, Xue L. Easy or Not-The Advances of EZH2 in Regulating T Cell Development, Differentiation, and Activation in Antitumor Immunity. Front Immunol 2021; 12:741302. [PMID: 34737746 PMCID: PMC8560704 DOI: 10.3389/fimmu.2021.741302] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/28/2021] [Indexed: 01/10/2023] Open
Abstract
Enhancer of zeste homolog 2 (EZH2) is the catalytic subunit of polycomb repressive complex 2 (PRC2), which regulates downstream gene expression by trimethylation of lysine 27 in histone H3 (H3K27me3). EZH2 mutations or overexpressions are associated with many types of cancer. As inhibition of EZH2 activity could upregulate the expression of tumor suppressor genes, EZH2 has recently become an interesting therapeutic target for cancer therapy. Moreover, accumulating evidence has shown that EZH2 may contribute to the regulation of immune cells, especially T cells. EZH2 regulates T cell development, differentiation, and function, suggesting that EZH2 also regulates immune homeostasis in addition to tumor suppressor genes. Moreover, EZH2 can regulate T cell fate by targeting non-T cell factors such as metabolism, cytokines, and myeloid-derived suppressor cells. The role of EZH2 in this process has not been fully addressed. This review discusses up-to-date research on EZH2-mediated regulation of immunological function and the progress of immunological therapeutic strategies based on this regulation.
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Affiliation(s)
- Jiaqi Huang
- Department of Radiation Oncology, Peking University Third Hospital, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
| | - Jie Zhang
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
| | - Zhengyang Guo
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
| | - Chen Li
- Department of Radiation Oncology, Peking University Third Hospital, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
| | - Zhen Tan
- Department of Bone and Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Junjie Wang
- Department of Radiation Oncology, Peking University Third Hospital, Beijing, China
| | - Jianling Yang
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
| | - Lixiang Xue
- Department of Radiation Oncology, Peking University Third Hospital, Beijing, China.,Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
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8
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Kwesi-Maliepaard EM, Jacobs H, van Leeuwen F. Signals for antigen-independent differentiation of memory CD8 + T cells. Cell Mol Life Sci 2021; 78:6395-6408. [PMID: 34398252 PMCID: PMC8558200 DOI: 10.1007/s00018-021-03912-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/23/2021] [Accepted: 08/03/2021] [Indexed: 12/18/2022]
Abstract
Conventional CD8+ memory T cells develop upon stimulation with foreign antigen and provide increased protection upon re-challenge. Over the past two decades, new subsets of CD8+ T cells have been identified that acquire memory features independently of antigen exposure. These antigen-inexperienced memory T cells (TAIM) are described under several names including innate memory, virtual memory, and memory phenotype. TAIM cells exhibit characteristics of conventional or true memory cells, including antigen-specific responses. In addition, they show responsiveness to innate stimuli and have been suggested to provide additional levels of protection toward infections and cancer. Here, we discuss the current understanding of TAIM cells, focusing on extrinsic and intrinsic molecular conditions that favor their development, their molecular definitions and immunological properties, as well as their transcriptional and epigenetic regulation.
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Affiliation(s)
| | - Heinz Jacobs
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands.
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, 1105AZ, Amsterdam, The Netherlands.
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9
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Sun H, Wang Y, Wang Y, Ji F, Wang A, Yang M, He X, Li L. Bivalent Regulation and Related Mechanisms of H3K4/27/9me3 in Stem Cells. Stem Cell Rev Rep 2021; 18:165-178. [PMID: 34417934 DOI: 10.1007/s12015-021-10234-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2021] [Indexed: 12/24/2022]
Abstract
The "bivalent domain" is a unique histone modification region consisting of two histone tri-methylation modifications. Over the years, it has been revealed that the maintenance and dynamic changes of the bivalent domains play a vital regulatory role in the differentiation of various stem cell systems, as well as in other cells, such as immunomodulation. Tri-methylation modifications involved in the formation of the bivalent domains are interrelated and mutually regulated, thus regulating many life processes of cells. Tri-methylation of histone H3 at lysine 4 (H3K4me3), tri-methylation of histone H3 at lysine 9 (H3K9me3) and tri-methylation of histone H3 at lysine 27 (H3K27me3) are the main tri-methylation modifications involved in the formation of bivalent domains. The three form different bivalent domains in pairs. Furthermore, it is equally clear that H3K4me3 is a positive regulator of transcription and that H3K9me3/H3K27me3 are negative regulators. Enzymes related to the regulation of histone methylation play a significant role in the "homeostasis" and "breaking homeostasis" of the bivalent domains. Bivalent domains regulate target genes, upstream transcription, downstream targeting regulation and related cytokines during the establishment and breakdown of homeostasis, and exert the specific regulation of stem cells. Indeed, a unified mechanism to explain the bivalent modification in all stem cells has been difficult to define, and whether the bivalent modification is antagonistic in inducing the differentiation of homologous stem cells is controversial. In this review, we focus on the different bivalent modifications in several key stem cells and explore the main mechanisms and effects of these modifications involved. Finally, we discussed the close relationship between bivalent domains and immune cells, and put forward the prospect of the application of bivalent domains in the field of stem cells.
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Affiliation(s)
- Han Sun
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Yin Wang
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Ying Wang
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Feng Ji
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - An Wang
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Ming Yang
- Department of Molecular Biology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China.
| | - Xu He
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China.
| | - Lisha Li
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China.
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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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Rosenberg M, Blum R, Kesner B, Aeby E, Garant JM, Szanto A, Lee JT. Motif-driven interactions between RNA and PRC2 are rheostats that regulate transcription elongation. Nat Struct Mol Biol 2021; 28:103-117. [PMID: 33398172 PMCID: PMC8050941 DOI: 10.1038/s41594-020-00535-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 10/20/2020] [Indexed: 01/30/2023]
Abstract
Although Polycomb repressive complex 2 (PRC2) is now recognized as an RNA-binding complex, the full range of binding motifs and why PRC2-RNA complexes often associate with active genes have not been elucidated. Here we identify high-affinity RNA motifs whose mutations weaken PRC2 binding and attenuate its repressive function in mouse embryonic stem cells. Interactions occur at promoter-proximal regions and frequently coincide with pausing of RNA Polymerase II (POL-II). Surprisingly, while PRC2-associated nascent transcripts are highly expressed, ablating PRC2 further upregulates expression via loss of pausing and enhanced transcription elongation. Thus, PRC2-nascent RNA complexes operate as rheostats to fine-tune transcription by regulating transitions between pausing and elongation, explaining why PRC2-RNA complexes frequently occur within active genes. Nascent RNA also targets PRC2 in cis and downregulates neighboring genes. We propose a unifying model in which RNA specifically recruits PRC2 to repress genes through POL-II pausing and, more classically, H3K27-trimethylation.
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Affiliation(s)
- Michael Rosenberg
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Roy Blum
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Barry Kesner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Eric Aeby
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jean-Michel Garant
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada.,RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine et des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Attila Szanto
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, USA.
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12
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Reduction of Global H3K27me 3 Enhances HER2/ErbB2 Targeted Therapy. Cell Rep 2020; 29:249-257.e8. [PMID: 31597089 DOI: 10.1016/j.celrep.2019.08.105] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 07/12/2019] [Accepted: 08/29/2019] [Indexed: 02/08/2023] Open
Abstract
Monoclonal antibodies (mAbs) targeting the oncogenic receptor tyrosine kinase ERBB2/HER2, such as Trastuzumab, are the standard of care therapy for breast cancers driven by ERBB2 overexpression and activation. However, a substantial proportion of patients exhibit de novo resistance. Here, by comparing matched Trastuzumab-naive and post-treatment patient samples from a neoadjuvant trial, we link resistance with elevation of H3K27me3, a repressive histone modification catalyzed by polycomb repressor complex 2 (PRC2). In ErbB2+ breast cancer models, PRC2 silences endogenous retroviruses (ERVs) to suppress anti-tumor type-I interferon (IFN) responses. In patients, elevated H3K27me3 in tumor cells following Trastuzumab treatment correlates with suppression of interferon-driven viral defense gene expression signatures and poor response. Using an immunocompetent model, we provide evidence that EZH2 inhibitors promote interferon-driven immune responses that enhance the efficacy of anti-ErbB2 mAbs, suggesting the potential clinical benefit of epigenomic reprogramming by H3K27me3 depletion in Trastuzumab-resistant disease.
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13
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Kwesi-Maliepaard EM, Aslam MA, Alemdehy MF, van den Brand T, McLean C, Vlaming H, van Welsem T, Korthout T, Lancini C, Hendriks S, Ahrends T, van Dinther D, den Haan JMM, Borst J, de Wit E, van Leeuwen F, Jacobs H. The histone methyltransferase DOT1L prevents antigen-independent differentiation and safeguards epigenetic identity of CD8 + T cells. Proc Natl Acad Sci U S A 2020; 117:20706-20716. [PMID: 32764145 PMCID: PMC7456197 DOI: 10.1073/pnas.1920372117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Cytotoxic T cell differentiation is guided by epigenome adaptations, but how epigenetic mechanisms control lymphocyte development has not been well defined. Here we show that the histone methyltransferase DOT1L, which marks the nucleosome core on active genes, safeguards normal differentiation of CD8+ T cells. T cell-specific ablation of Dot1L resulted in loss of naïve CD8+ T cells and premature differentiation toward a memory-like state, independent of antigen exposure and in a cell-intrinsic manner. Mechanistically, DOT1L controlled CD8+ T cell differentiation by ensuring normal T cell receptor density and signaling. DOT1L also maintained epigenetic identity, in part by indirectly supporting the repression of developmentally regulated genes. Finally, deletion of Dot1L in T cells resulted in an impaired immune response. Through our study, DOT1L is emerging as a central player in physiology of CD8+ T cells, acting as a barrier to prevent premature differentiation and controlling epigenetic integrity.
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Affiliation(s)
| | - Muhammad Assad Aslam
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, 60800 Multan, Pakistan
| | - Mir Farshid Alemdehy
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Teun van den Brand
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Chelsea McLean
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Hanneke Vlaming
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Tibor van Welsem
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Tessy Korthout
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Cesare Lancini
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Sjoerd Hendriks
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Tomasz Ahrends
- Division of Tumor Biology and Immunology, Oncode Institute, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Dieke van Dinther
- Department of Molecular Cell Biology and Immunology, Amsterdam University Medical Center (UMC), Vrije Universiteit Amsterdam, 1081HV Amsterdam, The Netherlands
| | - Joke M M den Haan
- Department of Molecular Cell Biology and Immunology, Amsterdam University Medical Center (UMC), Vrije Universiteit Amsterdam, 1081HV Amsterdam, The Netherlands
| | - Jannie Borst
- Division of Tumor Biology and Immunology, Oncode Institute, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Elzo de Wit
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands;
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, 1105AZ Amsterdam, The Netherlands
| | - Heinz Jacobs
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands;
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14
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Nutt SL, Keenan C, Chopin M, Allan RS. EZH2 function in immune cell development. Biol Chem 2020; 401:933-943. [DOI: 10.1515/hsz-2019-0436] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 01/31/2020] [Indexed: 12/17/2022]
Abstract
AbstractThe polycomb repressive complex 2 (PRC2) consists of three core components EZH2, SUZ12 and EED. EZH2 catalyzes the methylation of lysine 27 of histone H3, a modification associated with gene silencing. Through gene duplication higher vertebrate genomes also encode a second partially redundant methyltransferase, EZH1. Within the mammalian immune system most research has concentrated on EZH2 which is expressed predominantly in proliferating cells. EZH2 and other PRC2 components are required for hematopoietic stem cell function and lymphocyte development, at least in part by repressing cell cycle inhibitors. At later stages of immune cell differentiation, EZH2 plays essential roles in humoral and cell-mediated adaptive immunity, as well as the maintenance of immune homeostasis. EZH2 is often overactive in cancers, through both gain-of-function mutations and over-expression, an observation that has led to the development and clinical testing of specific EZH2 inhibitors. Such inhibitors may also be of use in inflammatory and autoimmune settings, as EZH2 inhibition dampens the immune response. Here, we will review the current state of understanding of the roles for EZH2, and PRC2 more generally, in the development and function of the immune system.
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Affiliation(s)
- Stephen L. Nutt
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Christine Keenan
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Michaël Chopin
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Rhys S. Allan
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
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15
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Li B, Chng WJ. EZH2 abnormalities in lymphoid malignancies: underlying mechanisms and therapeutic implications. J Hematol Oncol 2019; 12:118. [PMID: 31752930 PMCID: PMC6868783 DOI: 10.1186/s13045-019-0814-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 10/27/2019] [Indexed: 02/08/2023] Open
Abstract
EZH2 is the catalytic subunit of the polycomb repressive complex 2 (PRC2), which along with other PRC2 components mediates gene expression suppression via the methylation of Histone H3 at lysine 27. Recent studies have revealed a dichotomous role of EZH2 in physiology and in the pathogenesis of cancer. While it plays an essential role in the development of the lymphoid system, its deregulation, whether due to genetic or non-genetic causes, promotes B cell- and T cell-related lymphoma or leukemia. These findings triggered a boom in the development of therapeutic EZH2 inhibitors in recent years. Here, we discuss physiologic and pathogenic function of EZH2 in lymphoid context, various internal causes of EZH2 aberrance and how EZH2 modulates lymphomagenesis through epigenetic silencing, post-translational modifications (PTMs), orchestrating with surrounding tumor micro-environment and associating with RNA or viral partners. We also summarize different strategies to directly inhibit PRC2-EZH2 or to intervene EZH2 upstream signaling.
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Affiliation(s)
- Boheng Li
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Wee-Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore. .,Department of Haematology-Oncology, National University Cancer Institute of Singapore, Singapore, Singapore. .,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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16
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Fujii SI, Shimizu K. Immune Networks and Therapeutic Targeting of iNKT Cells in Cancer. Trends Immunol 2019; 40:984-997. [PMID: 31676264 DOI: 10.1016/j.it.2019.09.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 01/08/2023]
Abstract
One of the primary goals in tumor immunotherapy is to reset the immune system from tolerogenic to immunogenic - a process in which invariant natural killer T (iNKT) cells are implicated. iNKT cells develop in the thymus and perform immunosurveillance against tumor cells peripherally. When optimally stimulated, iNKT cells differentiate and display more efficient immune functions. Some cells survive and act as effector memory cells. We discuss the putative roles of iNKT cells in antitumor immunity, and posit that it may be possible to develop novel therapeutic strategies to treat cancers using iNKT cells. In particular, we highlight the challenge of uniquely energizing iNKT cell-licensed dendritic cells to serve as effective immunoadjuvants for both arms of the immune system, thus coupling immunological networks.
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Affiliation(s)
- Shin-Ichiro Fujii
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan.
| | - Kanako Shimizu
- Laboratory for Immunotherapy, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, Japan
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17
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Bosselut R. Control of Intra-Thymic αβ T Cell Selection and Maturation by H3K27 Methylation and Demethylation. Front Immunol 2019; 10:688. [PMID: 31001282 PMCID: PMC6456692 DOI: 10.3389/fimmu.2019.00688] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/13/2019] [Indexed: 12/25/2022] Open
Abstract
In addition to transcription factor binding, the dynamics of DNA modifications (methylation) and chromatin structure are essential contributors to the control of transcription in eukaryotes. Research in the past few years has emphasized the importance of histone H3 methylation at lysine 27 for lineage specific gene repression, demonstrated that deposition of this mark at specific genes is subject to differentiation-induced changes during development, and identified enzymatic activities, methyl transferases and demethylases, that control these changes. The present review discusses the importance of these mechanisms during intrathymic αβ T cell selection and late differentiation.
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Affiliation(s)
- Rémy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
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18
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Ezh2 controls development of natural killer T cells, which cause spontaneous asthma-like pathology. J Allergy Clin Immunol 2019; 144:549-560.e10. [PMID: 30851295 DOI: 10.1016/j.jaci.2019.02.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 01/10/2019] [Accepted: 02/08/2019] [Indexed: 11/21/2022]
Abstract
BACKGROUND Natural killer T (NKT) cells express a T-cell receptor that recognizes endogenous and environmental glycolipid antigens. Several subsets of NKT cells have been identified, including IFN-γ-producing NKT1 cells, IL-4-producing NKT2 cells, and IL-17-producing NKT17 cells. However, little is known about the factors that regulate their differentiation and respective functions within the immune system. OBJECTIVE We sought to determine whether the polycomb repressive complex 2 protein enhancer of zeste homolog 2 (Ezh2) restrains pathogenicity of NKT cells in the context of asthma-like lung disease. METHODS Numbers of invariant natural killer T (iNKT) 1, iNKT2, and iNKT17 cells and tissue distribution, cytokine production, lymphoid tissue localization, and transcriptional profiles of iNKT cells from wild-type and Ezh2 knockout (KO) iNKT mice were determined. The contribution of NKT cells to development of spontaneous and house dust mite-induced airways pathology, including airways hyperreactivity (AHR) to methacholine, was also assessed in wild-type, Ezh2 KO, and Ezh2 KO mice lacking NKT cells. RESULTS Ezh2 restrains development of pathogenic NKT cells, which induce spontaneous asthma-like disease in mice. Deletion of Ezh2 increased production of IL-4 and IL-13 and induced spontaneous AHR, lung inflammation, mucus production, and IgE. Increased IL-4 and IL-13 levels, AHR, lung inflammation, and IgE levels were all dependent on iNKT cells. In house dust mite-exposed animals Ezh2 KO resulted in enhanced AHR that was also dependent on iNKT cells. CONCLUSION Ezh2 is a central regulator of iNKT pathogenicity and suppresses the ability of iNKT cells to induce asthma-like pathology.
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19
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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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20
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Krovi SH, Gapin L. Invariant Natural Killer T Cell Subsets-More Than Just Developmental Intermediates. Front Immunol 2018; 9:1393. [PMID: 29973936 PMCID: PMC6019445 DOI: 10.3389/fimmu.2018.01393] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 06/05/2018] [Indexed: 01/01/2023] Open
Abstract
Invariant natural killer T (iNKT) cells are a CD1d-restricted T cell population that can respond to lipid antigenic stimulation within minutes by secreting a wide variety of cytokines. This broad functional scope has placed iNKT cells at the frontlines of many kinds of immune responses. Although the diverse functional capacities of iNKT cells have long been acknowledged, only recently have distinct iNKT cell subsets, each with a marked functional predisposition, been appreciated. Furthermore, the subsets can frequently occupy distinct niches in different tissues and sometimes establish long-term tissue residency where they can impact homeostasis and respond quickly when they sense perturbations. In this review, we discuss the developmental origins of the iNKT cell subsets, their localization patterns, and detail what is known about how different subsets specifically influence their surroundings in conditions of steady and diseased states.
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Affiliation(s)
- S. Harsha Krovi
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Laurent Gapin
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Biomedical Research, National Jewish Health, Denver, CO, United States
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21
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Kasler HG, Lee IS, Lim HW, Verdin E. Histone Deacetylase 7 mediates tissue-specific autoimmunity via control of innate effector function in invariant Natural Killer T Cells. eLife 2018; 7:e32109. [PMID: 29664401 PMCID: PMC5943034 DOI: 10.7554/elife.32109] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 04/05/2018] [Indexed: 12/13/2022] Open
Abstract
We report that Histone Deacetylase 7 (HDAC7) controls the thymic effector programming of Natural Killer T (NKT) cells, and that interference with this function contributes to tissue-specific autoimmunity. Gain of HDAC7 function in thymocytes blocks both negative selection and NKT development, and diverts Vα14/Jα18 TCR transgenic thymocytes into a Tconv-like lineage. Conversely, HDAC7 deletion promotes thymocyte apoptosis and causes expansion of innate-effector cells. Investigating the mechanisms involved, we found that HDAC7 binds PLZF and modulates PLZF-dependent transcription. Moreover, HDAC7 and many of its transcriptional targets are human risk loci for IBD and PSC, autoimmune diseases that strikingly resemble the disease we observe in HDAC7 gain-of-function in mice. Importantly, reconstitution of iNKT cells in these mice mitigated their disease, suggesting that the combined defects in negative selection and iNKT cells due to altered HDAC7 function can cause tissue-restricted autoimmunity, a finding that may explain the association between HDAC7 and hepatobiliary autoimmunity.
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Affiliation(s)
- Herbert G Kasler
- Gladstone Institute of Virology and ImmunologySan FranciscoUnited States
- Department of MedicineUniversity of California, San FranciscoSan FranciscoUnited States
- Buck Institute for Research on AgingNovatoUnited States
| | - Intelly S Lee
- Gladstone Institute of Virology and ImmunologySan FranciscoUnited States
- Department of MedicineUniversity of California, San FranciscoSan FranciscoUnited States
| | - Hyung W Lim
- Gladstone Institute of Virology and ImmunologySan FranciscoUnited States
- Department of MedicineUniversity of California, San FranciscoSan FranciscoUnited States
| | - Eric Verdin
- Gladstone Institute of Virology and ImmunologySan FranciscoUnited States
- Department of MedicineUniversity of California, San FranciscoSan FranciscoUnited States
- Buck Institute for Research on AgingNovatoUnited States
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22
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Dobenecker MW, Park JS, Marcello J, McCabe MT, Gregory R, Knight SD, Rioja I, Bassil AK, Prinjha RK, Tarakhovsky A. Signaling function of PRC2 is essential for TCR-driven T cell responses. J Exp Med 2018. [PMID: 29523590 PMCID: PMC5881460 DOI: 10.1084/jem.20170084] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
PRC2 is a known chromatin regulator. Here the authors show novel cytosolic components of PRC2 and that PRC2 inactivation results in attenuation of MAPK/Erk signaling and impaired T cell activation. Systemic PRC2 inhibition in vivo cures the autoimmune syndrome caused by regulatory T cell depletion. Differentiation and activation of T cells require the activity of numerous histone lysine methyltransferases (HMT) that control the transcriptional T cell output. One of the most potent regulators of T cell differentiation is the HMT Ezh2. Ezh2 is a key enzymatic component of polycomb repressive complex 2 (PRC2), which silences gene expression by histone H3 di/tri-methylation at lysine 27. Surprisingly, in many cell types, including T cells, Ezh2 is localized in both the nucleus and the cytosol. Here we show the presence of a nuclear-like PRC2 complex in T cell cytosol and demonstrate a role of cytosolic PRC2 in T cell antigen receptor (TCR)–mediated signaling. We show that short-term suppression of PRC2 precludes TCR-driven T cell activation in vitro. We also demonstrate that pharmacological inhibition of PRC2 in vivo greatly attenuates the severe T cell–driven autoimmunity caused by regulatory T cell depletion. Our data reveal cytoplasmic PRC2 is one of the most potent regulators of T cell activation and point toward the therapeutic potential of PRC2 inhibitors for the treatment of T cell–driven autoimmune diseases.
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Affiliation(s)
- Marc-Werner Dobenecker
- Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, NY
| | - Joon Seok Park
- Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, NY
| | - Jonas Marcello
- Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, NY.,Now, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Michael T McCabe
- Epigenetics Discovery Performance Unit, Oncology R&D, GlaxoSmithKline, Collegeville, PA
| | - Richard Gregory
- Epigenetics Discovery Performance Unit, Immuno-Inflammation TA, Medicines Research Centre, GlaxoSmithKline Research and Development, Stevenage, England, UK
| | - Steven D Knight
- Epigenetics Discovery Performance Unit, Oncology R&D, GlaxoSmithKline, Collegeville, PA
| | - Inmaculada Rioja
- Epigenetics Discovery Performance Unit, Immuno-Inflammation TA, Medicines Research Centre, GlaxoSmithKline Research and Development, Stevenage, England, UK
| | - Anna K Bassil
- Epigenetics Discovery Performance Unit, Immuno-Inflammation TA, Medicines Research Centre, GlaxoSmithKline Research and Development, Stevenage, England, UK
| | - Rabinder K Prinjha
- Epigenetics Discovery Performance Unit, Immuno-Inflammation TA, Medicines Research Centre, GlaxoSmithKline Research and Development, Stevenage, England, UK
| | - Alexander Tarakhovsky
- Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, NY
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23
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Transcriptional and epigenetic regulation of innate-like T lymphocyte development. Curr Opin Immunol 2018; 51:39-45. [PMID: 29452898 DOI: 10.1016/j.coi.2018.01.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/29/2018] [Indexed: 01/19/2023]
Abstract
Invariant Natural Killer T (iNKT) cells are a heterogeneous innate T cell population that recognizes lipid antigens. Despite the monospecific nature of their T cell receptor, iNKT cells differentiate into stable sublineages during thymic development, before foreign antigen encounter. How iNKT cell subsets acquire and maintain their functional programs is a central question in innate lymphocyte biology. Global transcriptional and epigenetic profiling of iNKT subsets has provided insights into the internal wiring of these subsets that defines their identity. Comparison of the iNKT transcriptional programs with those of other adaptive and innate lymphocyte lineages revealed common core regulatory circuits that may dictate effector functions. In this review, we summarize recent advances on the molecular mechanisms involved in iNKT cell development.
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24
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Naito T, Muroi S, Taniuchi I, Kondo M. Loss of Eed leads to lineage instability and increased CD8 expression of mouse CD4+ T cells upon TGFβ signaling. Mol Immunol 2018; 94:140-152. [DOI: 10.1016/j.molimm.2017.12.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 12/18/2017] [Accepted: 12/22/2017] [Indexed: 12/21/2022]
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25
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Kwon DI, Lee YJ. Lineage Differentiation Program of Invariant Natural Killer T Cells. Immune Netw 2017; 17:365-377. [PMID: 29302250 PMCID: PMC5746607 DOI: 10.4110/in.2017.17.6.365] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 10/27/2017] [Accepted: 11/02/2017] [Indexed: 02/07/2023] Open
Abstract
Invariant natural killer T (iNKT) cells are innate T cells restricted by CD1d molecules. They are positively selected in the thymic cortex and migrate to the medullary area, in which they differentiate into 3 different lineages. Promyelocytic leukemia zinc finger (PLZF) modulates this process, and PLZFhigh, PLZFintermediate, and PLZFlow iNKT cells are designated as NKT2, NKT17, and NKT1 cells, respectively. Analogous to conventional helper CD4 T cells, each subset expresses distinct combinations of transcription factors and produces different cytokines. In lymphoid organs, iNKT subsets have unique localizations, which determine their cytokine responses upon antigenic challenge. The lineage differentiation programs of iNKT cells are differentially regulated in various mice strains in a cell-intrinsic manner, and BALB/c mice contain a high frequency of NKT2 cells. In the thymic medulla, steady state IL-4 from NKT2 cells directly conditions CD8 T cells to become memory-like cells expressing Eomesodermin, which function as premade memory effectors. The genetic signature of iNKT cells is more similar to that of γδ T cells and innate lymphoid cells (ILCs) than of conventional helper T cells, suggesting that ILCs and innate T cells share common developmental programs.
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Affiliation(s)
- Dong-Il Kwon
- Academy of Immunology and Microbiology, Institute for Basic Science, Pohang 37673, Korea.,Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 37673, Korea
| | - You Jeong Lee
- Academy of Immunology and Microbiology, Institute for Basic Science, Pohang 37673, Korea.,Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 37673, Korea
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26
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Legoux F, Salou M, Lantz O. Unconventional or Preset αβ T Cells: Evolutionarily Conserved Tissue-Resident T Cells Recognizing Nonpeptidic Ligands. Annu Rev Cell Dev Biol 2017; 33:511-535. [PMID: 28661722 DOI: 10.1146/annurev-cellbio-100616-060725] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A majority of T cells bearing the αβ T cell receptor (TCR) are specific for peptides bound to polymorphic classical major histocompatibility complex (MHC) molecules. Smaller subsets of T cells are reactive toward various nonpeptidic ligands associated with nonpolymorphic MHC class-Ib (MHC-Ib) molecules. These cells have been termed unconventional for decades, even though only the composite antigen is different from the one seen by classical T cells. Herein, we discuss the identity of these particular T cells in light of the coevolution of their TCR and MHC-Ib restricting elements. We examine their original thymic development: selection on hematopoietic cells leading to the acquisition of an original differentiation program. Most of these cells acquire memory cell features during thymic maturation and exhibit unique patterns of migration into peripheral nonlymphoid tissues to become tissue resident. Thus, these cells are termed preset T cells, as they also display a variety of effector functions. They may act as microbial or danger sentinels, fight microbes, or regulate tissue homeostasis.
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Affiliation(s)
- Francois Legoux
- Institut Curie, PSL Research University, INSERM, U 932, 75005 Paris, France; , ,
| | - Marion Salou
- Institut Curie, PSL Research University, INSERM, U 932, 75005 Paris, France; , ,
| | - Olivier Lantz
- Institut Curie, PSL Research University, INSERM, U 932, 75005 Paris, France; , , .,Center of Clinical Investigations, CIC-1428 IGR/Curie, 75005 Paris, France.,Laboratoire d'immunologie clinique, Institut Curie, 75005 Paris, France
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27
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The Role of Epigenetic Mechanisms in the Regulation of Gene Expression in the Nervous System. J Neurosci 2017; 36:11427-11434. [PMID: 27911745 DOI: 10.1523/jneurosci.2492-16.2016] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 08/29/2016] [Accepted: 08/31/2016] [Indexed: 11/21/2022] Open
Abstract
Neuroepigenetics is a newly emerging field in neurobiology that addresses the epigenetic mechanism of gene expression regulation in various postmitotic neurons, both over time and in response to environmental stimuli. In addition to its fundamental contribution to our understanding of basic neuronal physiology, alterations in these neuroepigenetic mechanisms have been recently linked to numerous neurodevelopmental, psychiatric, and neurodegenerative disorders. This article provides a selective review of the role of DNA and histone modifications in neuronal signal-induced gene expression regulation, plasticity, and survival and how targeting these mechanisms could advance the development of future therapies. In addition, we discuss a recent discovery on how double-strand breaks of genomic DNA mediate the rapid induction of activity-dependent gene expression in neurons.
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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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29
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Vasanthakumar A, Xu D, Lun AT, Kueh AJ, van Gisbergen KP, Iannarella N, Li X, Yu L, Wang D, Williams BR, Lee SC, Majewski IJ, Godfrey DI, Smyth GK, Alexander WS, Herold MJ, Kallies A, Nutt SL, Allan RS. A non-canonical function of Ezh2 preserves immune homeostasis. EMBO Rep 2017; 18:619-631. [PMID: 28223321 DOI: 10.15252/embr.201643237] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 01/18/2017] [Accepted: 01/22/2017] [Indexed: 12/22/2022] Open
Abstract
Enhancer of zeste 2 (Ezh2) mainly methylates lysine 27 of histone-H3 (H3K27me3) as part of the polycomb repressive complex 2 (PRC2) together with Suz12 and Eed. However, Ezh2 can also modify non-histone substrates, although it is unclear whether this mechanism has a role during development. Here, we present evidence for a chromatin-independent role of Ezh2 during T-cell development and immune homeostasis. T-cell-specific depletion of Ezh2 induces a pronounced expansion of natural killer T (NKT) cells, although Ezh2-deficient T cells maintain normal levels of H3K27me3. In contrast, removal of Suz12 or Eed destabilizes canonical PRC2 function and ablates NKT cell development completely. We further show that Ezh2 directly methylates the NKT cell lineage defining transcription factor PLZF, leading to its ubiquitination and subsequent degradation. Sustained PLZF expression in Ezh2-deficient mice is associated with the expansion of a subset of NKT cells that cause immune perturbation. Taken together, we have identified a chromatin-independent function of Ezh2 that impacts on the development of the immune system.
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Affiliation(s)
- Ajithkumar Vasanthakumar
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Vic., Australia
| | - Dakang Xu
- Institute of Ageing Research, Hangzhou Normal University School of Medicine, Hangzhou, China.,Hudson Institute of Medical Research, Monash University, Clayton, Vic., Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Vic., Australia
| | - Aaron Tl Lun
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Vic., Australia
| | - Andrew J Kueh
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Vic., Australia
| | - Klaas Pjm van Gisbergen
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Vic., Australia
| | - Nadia Iannarella
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia
| | - Xiaofang Li
- Institute of Ageing Research, Hangzhou Normal University School of Medicine, Hangzhou, China.,Hudson Institute of Medical Research, Monash University, Clayton, Vic., Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Vic., Australia
| | - Liang Yu
- Hudson Institute of Medical Research, Monash University, Clayton, Vic., Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Vic., Australia
| | - Die Wang
- Hudson Institute of Medical Research, Monash University, Clayton, Vic., Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Vic., Australia
| | - Bryan Rg Williams
- Hudson Institute of Medical Research, Monash University, Clayton, Vic., Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Vic., Australia
| | - Stanley Cw Lee
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Vic., Australia
| | - Ian J Majewski
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Vic., Australia
| | - Dale I Godfrey
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Vic., Australia.,ARC Centre of Excellence for Advanced Molecular Imaging, The University of Melbourne, Parkville, Vic., Australia
| | - Gordon K Smyth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Mathematics and Statistics, The University of Melbourne, Parkville, Vic., Australia
| | - Warren S Alexander
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Vic., Australia
| | - Marco J Herold
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Vic., Australia
| | - Axel Kallies
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Vic., Australia
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia .,Department of Medical Biology, The University of Melbourne, Parkville, Vic., Australia
| | - Rhys S Allan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Vic., Australia .,Department of Medical Biology, The University of Melbourne, Parkville, Vic., Australia
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30
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Beyaz S, Kim JH, Pinello L, Xifaras ME, Hu Y, Huang J, Kerenyi MA, Das PP, Barnitz RA, Herault A, Dogum R, Haining WN, Yilmaz ÖH, Passegue E, Yuan GC, Orkin SH, Winau F. The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells. Nat Immunol 2017; 18:184-195. [PMID: 27992400 PMCID: PMC5247321 DOI: 10.1038/ni.3644] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/23/2016] [Indexed: 12/13/2022]
Abstract
Invariant natural killer T cells (iNKT cells) are innate-like lymphocytes that protect against infection, autoimmune disease and cancer. However, little is known about the epigenetic regulation of iNKT cell development. Here we found that the H3K27me3 histone demethylase UTX was an essential cell-intrinsic factor that controlled an iNKT-cell lineage-specific gene-expression program and epigenetic landscape in a demethylase-activity-dependent manner. UTX-deficient iNKT cells exhibited impaired expression of iNKT cell signature genes due to a decrease in activation-associated H3K4me3 marks and an increase in repressive H3K27me3 marks within the promoters occupied by UTX. We found that JunB regulated iNKT cell development and that the expression of genes that were targets of both JunB and the iNKT cell master transcription factor PLZF was UTX dependent. We identified iNKT cell super-enhancers and demonstrated that UTX-mediated regulation of super-enhancer accessibility was a key mechanism for commitment to the iNKT cell lineage. Our findings reveal how UTX regulates the development of iNKT cells through multiple epigenetic mechanisms.
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Affiliation(s)
- Semir Beyaz
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Ji Hyung Kim
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA, and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Luca Pinello
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA, and Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Michael E Xifaras
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA, and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Yu Hu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA, and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Jialiang Huang
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA, and Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Marc A Kerenyi
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pharmacology and Translational Research, Boehringer Ingelheim, Vienna, Austria
| | - Partha P Das
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - R Anthony Barnitz
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Broad Institute of MIT and Harvard, Cambridge, USA
| | - Aurelie Herault
- The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California San Francisco, San Francisco, California, USA, and Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, California, USA
| | - Rizkullah Dogum
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA, and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - W Nicholas Haining
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Broad Institute of MIT and Harvard, Cambridge, USA
| | - Ömer H Yilmaz
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA, and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Emmanuelle Passegue
- The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California San Francisco, San Francisco, California, USA, and Department of Medicine, Division of Hematology/Oncology, University of California San Francisco, San Francisco, California, USA
| | - Guo-Cheng Yuan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA, and Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Florian Winau
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA, and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
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31
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32
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Histone Post-Translational Modifications and Nucleosome Organisation in Transcriptional Regulation: Some Open Questions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017. [PMID: 28639249 DOI: 10.1007/5584_2017_58] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The organisation of chromatin is first discussed to conclude that nucleosomes play both structural and transcription-regulatory roles. The presence of nucleosomes makes difficult the access of transcriptional factors to their target sequences and the action of RNA polymerases. The histone post-translational modifications and nucleosome remodelling are first discussed, from a historical point of view, as mechanisms to remove the obstacles imposed by chromatin structure to transcription. Instead of reviewing the state of the art of the whole field, this review is centred on some open questions. First, some "non-classical" histone modifications, such as short-chain acylations other than acetylation, are considered to conclude that their relationship with the concentration of metabolic intermediaries might make of them a sensor of the physiological state of the cells. Then attention is paid to the interest of studying chromatin organisation and epigenetic marks at a single nucleosome level as a complement to genome-wide approaches. Finally, as a consequence of the above questions, the review focuses on the presence of multiple histone post-translational modifications on a single nucleosome. The methods to detect them and their meaning, with special emphasis on bivalent marks, are discussed.
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33
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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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34
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von Schimmelmann M, Feinberg PA, Sullivan JM, Ku SM, Badimon A, Duff MK, Wang Z, Lachmann A, Dewell S, Ma'ayan A, Han MH, Tarakhovsky A, Schaefer A. Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration. Nat Neurosci 2016; 19:1321-30. [PMID: 27526204 PMCID: PMC5088783 DOI: 10.1038/nn.4360] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/14/2016] [Indexed: 12/13/2022]
Abstract
Normal brain function depends on the interaction between highly specialized neurons that operate within anatomically and functionally distinct brain regions. Neuronal specification is driven by transcriptional programs that are established during early neuronal development and remain in place in the adult brain. The fidelity of neuronal specification depends on the robustness of the transcriptional program that supports the neuron type-specific gene expression patterns. Here we show that polycomb repressive complex 2 (PRC2), which supports neuron specification during differentiation, contributes to the suppression of a transcriptional program that is detrimental to adult neuron function and survival. We show that PRC2 deficiency in striatal neurons leads to the de-repression of selected, predominantly bivalent PRC2 target genes that are dominated by self-regulating transcription factors normally suppressed in these neurons. The transcriptional changes in PRC2-deficient neurons lead to progressive and fatal neurodegeneration in mice. Our results point to a key role of PRC2 in protecting neurons against degeneration.
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Affiliation(s)
- Melanie von Schimmelmann
- Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Philip A Feinberg
- Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Josefa M Sullivan
- Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Stacy M Ku
- Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ana Badimon
- Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mary Kaye Duff
- Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Zichen Wang
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Alexander Lachmann
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Scott Dewell
- Genomics Resource Center, The Rockefeller University, New York, New York, USA
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,BD2K-LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ming-Hu Han
- Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Alexander Tarakhovsky
- Laboratory of Immune Cell Epigenetics and Signaling, The Rockefeller University, New York, New York, USA
| | - Anne Schaefer
- Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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35
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Histone Demethylase KDM6A Controls the Mammary Luminal Lineage through Enzyme-Independent Mechanisms. Mol Cell Biol 2016; 36:2108-20. [PMID: 27215382 DOI: 10.1128/mcb.00089-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/08/2016] [Indexed: 02/06/2023] Open
Abstract
Establishment of the mammary luminal cell lineage is controlled primarily by hormones and through specific transcription factors (TFs). Previous studies have linked histone methyltransferases to the differentiation of mammary epithelium, thus opening the possibility of biological significance of counteracting demethylases. We have now demonstrated an essential role for the H3K27me3 demethylase KDM6A in generating a balanced alveolar compartment. Deletion of Kdm6a in the mammary luminal cell lineage led to a paucity of luminal cells and an excessive expansion of basal cells, both in vivo and in vitro The inability to form structurally normal ducts and alveoli during pregnancy resulted in lactation failure. Mutant luminal cells did not exhibit their distinctive transcription factor pattern and displayed basal characteristics. The genomic H3K27me3 landscape was unaltered in mutant tissue, and support for a demethylase-independent mechanism came from mice expressing a catalytically inactive KDM6A. Mammary tissue developed normally in these mice. Chromatin immunoprecipitation sequencing (ChIP-seq) experiments demonstrated KDM6A binding to putative enhancers enriched for key mammary TFs and H3K27ac. This study demonstrated for the first time that the mammary luminal lineage relies on KDM6A to ensure a transcription program leading to differentiated alveoli. Failure to fully implement this program results in structurally and functionally impaired mammary tissue.
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36
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Arcipowski KM, Martinez CA, Ntziachristos P. Histone demethylases in physiology and cancer: a tale of two enzymes, JMJD3 and UTX. Curr Opin Genet Dev 2016; 36:59-67. [PMID: 27151432 DOI: 10.1016/j.gde.2016.03.010] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/24/2016] [Indexed: 01/17/2023]
Abstract
Gene regulation is fine-tuned by a dynamic balance between transcriptionally activating and repressive modifications of histone tails. It has been well-established that lysine and arginine methylation can be reversed by two groups of evolutionarily conserved enzymes known as histone demethylases, which have been shown to play critical roles in development, differentiation and diseases like cancer. Recent work has demonstrated demethylase-independent functions of these proteins, highlighting the complex mechanisms by which these proteins exert their effects on gene expression. Here, we discuss the roles of lysine 27 demethylases, JMJD3 and UTX, in cancer and potential therapeutic avenues targeting these enzymes. Despite a high degree of sequence similarity in the catalytic domain between JMJD3 and UTX, numerous studies revealed surprisingly contrasting roles in cellular reprogramming and cancer, particularly leukemia. Understanding the demethylase-dependent and demethylase-independent functions of the enzymes affecting histone methylation, their post-translational modifications and participation in different complexes, as well as in vivo modeling of the mutations affecting those enzymes in cancer, can shed light on their unique physiological roles. This information cumulated in the future will aid in the development of improved inhibitors to treat cancers affected by demethylase mutations and aberrant gene activation.
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Affiliation(s)
- Kelly Marie Arcipowski
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Carlos Alberto Martinez
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA
| | - Panagiotis Ntziachristos
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, 320 E. Superior Street, Chicago, IL 60611, USA.
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37
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Gapin L. Development of invariant natural killer T cells. Curr Opin Immunol 2016; 39:68-74. [PMID: 26802287 DOI: 10.1016/j.coi.2016.01.001] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 12/16/2015] [Accepted: 01/02/2016] [Indexed: 01/09/2023]
Abstract
Invariant natural killer T (iNKT) cells develop into functionally distinct subsets. Each subset expresses a unique combination of transcription factors that regulate cytokine gene transcription upon activation. The tissue distribution and localization within tissues also varies between subsets. Importantly, the relative abundance of the various subsets is directly responsible for altering several immunological parameters, which subsequently affect the immune response. Here, I review recent advances in our understanding of the molecular regulation of iNKT cell subset development.
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Affiliation(s)
- Laurent Gapin
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical campus and National Jewish Health, Aurora, CO 80045, USA.
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38
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Bosselut R. Pleiotropic Functions of H3K27Me3 Demethylases in Immune Cell Differentiation. Trends Immunol 2016; 37:102-113. [PMID: 26796037 DOI: 10.1016/j.it.2015.12.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 12/12/2015] [Accepted: 12/13/2015] [Indexed: 02/06/2023]
Abstract
The trimethylation of histone H3 lysine 27 (H3K27Me3) contributes to gene repression, notably through recruitment of Polycomb complexes, and has long been considered essential to maintain cell identity. Whereas H3K27Me3 was thought to be stable and not catalytically reversible, the discovery of the Utx and Jmjd3 demethylases changed this notion, raising new questions on the role of these enzymes in gene expression and cell differentiation. Recent studies have demonstrated critical roles for Utx and Jmjd3 in the development and function of immune cells, and revealed both demethylase and demethylase-independent activities of these enzymes. I review these finding here, and discuss the current understanding of the mechanisms that underlie the broad, yet highly cell- and gene-specific, impact of these enzymes in vivo.
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Affiliation(s)
- Rémy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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39
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Manna S, Kim JK, Baugé C, Cam M, Zhao Y, Shetty J, Vacchio MS, Castro E, Tran B, Tessarollo L, Bosselut R. Histone H3 Lysine 27 demethylases Jmjd3 and Utx are required for T-cell differentiation. Nat Commun 2015; 6:8152. [PMID: 26328764 PMCID: PMC4569738 DOI: 10.1038/ncomms9152] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/23/2015] [Indexed: 12/22/2022] Open
Abstract
Although histone H3 lysine 27 trimethylation (H3K27Me3) is associated with gene silencing, whether H3K27Me3 demethylation affects transcription and cell differentiation in vivo has remained elusive. To investigate this, we conditionally inactivated the two H3K27Me3 demethylases, Jmjd3 and Utx, in non-dividing intrathymic CD4(+) T-cell precursors. Here we show that both enzymes redundantly promote H3K27Me3 removal at, and expression of, a specific subset of genes involved in terminal thymocyte differentiation, especially S1pr1, encoding a sphingosine-phosphate receptor required for thymocyte egress. Thymocyte expression of S1pr1 was not rescued in Jmjd3- and Utx-deficient male mice, which carry the catalytically inactive Utx homolog Uty, supporting the conclusion that it requires H3K27Me3 demethylase activity. These findings demonstrate that Jmjd3 and Utx are required for T-cell development, and point to a requirement for their H3K27Me3 demethylase activity in cell differentiation.
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Affiliation(s)
- Sugata Manna
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jong Kyong Kim
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Catherine Baugé
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Margaret Cam
- Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Yongmei Zhao
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Jyoti Shetty
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Melanie S Vacchio
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Ehydel Castro
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Bao Tran
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, USA
| | - Lino Tessarollo
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Rémy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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