101
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Liu B, Yang L, Zhu X, Li H, Zhu P, Wu J, Lu T, He L, Liu N, Meng S, Zhou L, Ye B, Tian Y, Fan Z. Yeats4 drives ILC lineage commitment via activation of Lmo4 transcription. J Exp Med 2019; 216:2653-2668. [PMID: 31434684 PMCID: PMC6829595 DOI: 10.1084/jem.20182363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 06/04/2019] [Accepted: 07/22/2019] [Indexed: 12/20/2022] Open
Abstract
Liu et al. show that Yeats4 recruits the Dot1l–RNA Pol II complex onto the Lmo4 promoter by recognizing H3K27ac modification to initiate Lmo4 transcription in α4β7+ CLPs, leading to ILC lineage commitment. Innate lymphoid cells (ILCs) play critical roles in defending infections and maintaining mucosal homeostasis. All ILCs arise from common lymphoid progenitors (CLPs) in bone marrow. However, how CLPs stratify and differentiate into ILC lineages remains elusive. Here, we showed that Yeats4 is highly expressed in ILCs and their progenitors. Yeats4 conditional KO in the hematopoietic system causes decreased numbers of ILCs and impairs their effector functions. Moreover, Yeats4 regulates α4β7+ CLP differentiation toward common helper ILC progenitors (CHILPs). Mechanistically, Yeats4 recruits the Dot1l–RNA Pol II complex onto Lmo4 promoter through recognizing H3K27ac modification to initiate Lmo4 transcription in α4β7+ CLPs. Additionally, Lmo4 deficiency also impairs ILC lineage differentiation and their effector functions. Collectively, the Yeats4–Lmo4 axis is required for ILC lineage commitment.
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Affiliation(s)
- Benyu Liu
- Key Laboratory of Infection and Immunity of the Chinese Academy of Sciences, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Liuliu Yang
- Key Laboratory of Infection and Immunity of the Chinese Academy of Sciences, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoxiao Zhu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Huimu Li
- Key Laboratory of Infection and Immunity of the Chinese Academy of Sciences, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Pingping Zhu
- Key Laboratory of Infection and Immunity of the Chinese Academy of Sciences, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jiayi Wu
- Key Laboratory of Infection and Immunity of the Chinese Academy of Sciences, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Tiankun Lu
- Key Laboratory of Infection and Immunity of the Chinese Academy of Sciences, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Luyun He
- Key Laboratory of Infection and Immunity of the Chinese Academy of Sciences, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Nian Liu
- Key Laboratory of Infection and Immunity of the Chinese Academy of Sciences, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shu Meng
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Liang Zhou
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL
| | - Buqing Ye
- Key Laboratory of Infection and Immunity of the Chinese Academy of Sciences, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yong Tian
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China .,University of Chinese Academy of Sciences, Beijing, China
| | - Zusen Fan
- Key Laboratory of Infection and Immunity of the Chinese Academy of Sciences, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China .,University of Chinese Academy of Sciences, Beijing, China
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102
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Jang S, Song JJ. The big picture of chromatin biology by cryo-EM. Curr Opin Struct Biol 2019; 58:76-87. [PMID: 31233978 DOI: 10.1016/j.sbi.2019.05.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/10/2019] [Accepted: 05/20/2019] [Indexed: 01/07/2023]
Abstract
Modifications of chromatin structure are one of the key mechanisms regulating epigenetic gene expression. Proteins involved in chromatin modification mainly function as large multi-subunit complexes, and each component in the complex contributes to the function and activity of the complex. However, little is known about the structures of whole complexes and the mechanisms by which the chromatin-modifying complexes function, the functional roles of each component in the complexes, and how the complexes recognize the central unit of chromatin, the nucleosome. This lack of information is partially due to the lack of structural information for whole complexes. Recent advances in cryo-EM have begun to reveal the structures of whole chromatin-modifying complexes that enable us to understand the big picture of chromatin biology. In this review, we discuss the recent discoveries related to the mechanisms of chromatin-modifying complexes.
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Affiliation(s)
- Seongmin Jang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Ji-Joon Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
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103
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Worden EJ, Wolberger C. Activation and regulation of H2B-Ubiquitin-dependent histone methyltransferases. Curr Opin Struct Biol 2019; 59:98-106. [PMID: 31229920 DOI: 10.1016/j.sbi.2019.05.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/06/2019] [Accepted: 05/09/2019] [Indexed: 12/22/2022]
Abstract
Covalent modifications of histone proteins regulate a wide variety of cellular processes. Methylation of histone H3K79 and H3K4 is associated with active transcription and is catalyzed by Dot1L and Set1, respectively. Both Dot1L and Set1 are activated by prior ubiquitination of histone H2B on K120 in a process termed 'histone crosstalk'. Recent structures of Dot1L bound to a ubiquitinated nucleosome revealed how Dot1L is activated by ubiquitin and how Dot1L distorts the nucleosome to access its substrate. Structures of Dot1L-interacting proteins have provided insight into how Dot1L is recruited to sites of active transcription. Cryo-EM and crystallographic studies of the complex of proteins associated with Set1 (COMPASS), uncovered the architecture of COMPASS and how Set1 is activated upon complex assembly.
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Affiliation(s)
- Evan J Worden
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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104
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Chan AKN, Chen CW. Rewiring the Epigenetic Networks in MLL-Rearranged Leukemias: Epigenetic Dysregulation and Pharmacological Interventions. Front Cell Dev Biol 2019; 7:81. [PMID: 31157223 PMCID: PMC6529847 DOI: 10.3389/fcell.2019.00081] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 04/30/2019] [Indexed: 12/26/2022] Open
Abstract
Leukemias driven by chromosomal translocation of the mixed-lineage leukemia gene (MLL or KMT2A) are highly prevalent in pediatric oncology. The poor survival rate and lack of an effective targeted therapy for patients with MLL-rearranged (MLL-r) leukemias emphasize an urgent need for improved knowledge and novel therapeutic approaches for these malignancies. The resulting chimeric products of MLL gene rearrangements, i.e., MLL-fusion proteins (MLL-FPs), are capable of transforming hematopoietic stem/progenitor cells (HSPCs) into leukemic blasts. The ability of MLL-FPs to reprogram HSPCs toward leukemia requires the involvement of multiple chromatin effectors, including the histone 3 lysine 79 methyltransferase DOT1L, the chromatin epigenetic reader BRD4, and the super elongation complex. These epigenetic regulators constitute a complicated network that dictates maintenance of the leukemia program, and therefore represent an important cluster of therapeutic opportunities. In this review, we will discuss the role of MLL and its fusion partners in normal HSPCs and hematopoiesis, including the links between chromatin effectors, epigenetic landscapes, and leukemia development, and summarize current approaches to therapeutic targeting of MLL-r leukemias.
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Affiliation(s)
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA, United States
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105
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Structural Basis of Dot1L Stimulation by Histone H2B Lysine 120 Ubiquitination. Mol Cell 2019; 74:1010-1019.e6. [PMID: 30981630 DOI: 10.1016/j.molcel.2019.03.029] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/01/2019] [Accepted: 03/22/2019] [Indexed: 12/31/2022]
Abstract
The essential histone H3 lysine 79 methyltransferase Dot1L regulates transcription and genomic stability and is deregulated in leukemia. The activity of Dot1L is stimulated by mono-ubiquitination of histone H2B on lysine 120 (H2BK120Ub); however, the detailed mechanism is not understood. We report cryo-EM structures of human Dot1L bound to (1) H2BK120Ub and (2) unmodified nucleosome substrates at 3.5 Å and 4.9 Å, respectively. Comparison of both structures, complemented with biochemical experiments, provides critical insights into the mechanism of Dot1L stimulation by H2BK120Ub. Both structures show Dot1L binding to the same extended surface of the histone octamer. In yeast, this surface is used by silencing proteins involved in heterochromatin formation, explaining the mechanism of their competition with Dot1. These results provide a strong foundation for understanding conserved crosstalk between histone modifications found at actively transcribed genes and offer a general model of how ubiquitin might regulate the activity of chromatin enzymes.
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106
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Yao T, Jing W, Hu Z, Tan M, Cao M, Wang Q, Li Y, Yuan G, Lei M, Huang J. Structural basis of the crosstalk between histone H2B monoubiquitination and H3 lysine 79 methylation on nucleosome. Cell Res 2019; 29:330-333. [PMID: 30770869 PMCID: PMC6461977 DOI: 10.1038/s41422-019-0146-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 01/24/2019] [Indexed: 01/07/2023] Open
Affiliation(s)
- Tonghui Yao
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Wei Jing
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Zhiguo Hu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Ming Tan
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Mi Cao
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Qianmin Wang
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yan Li
- National Facility for Protein Sciences in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Guiyong Yuan
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ming Lei
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jing Huang
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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107
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Chistiakov DA, Chekhonin VP. Early-life adversity-induced long-term epigenetic programming associated with early onset of chronic physical aggression: Studies in humans and animals. World J Biol Psychiatry 2019; 20:258-277. [PMID: 28441915 DOI: 10.1080/15622975.2017.1322714] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Objectives: To examine whether chronic physical aggression (CPA) in adulthood can be epigenetically programmed early in life due to exposure to early-life adversity. Methods: Literature search of public databases such as PubMed/MEDLINE and Scopus. Results: Children/adolescents susceptible for CPA and exposed to early-life abuse fail to efficiently cope with stress that in turn results in the development of CPA later in life. This phenomenon was observed in humans and animal models of aggression. The susceptibility to aggression is a complex trait that is regulated by the interaction between environmental and genetic factors. Epigenetic mechanisms mediate this interaction. Subjects exposed to stress early in life exhibited long-term epigenetic programming that can influence their behaviour in adulthood. This programming affects expression of many genes not only in the brain but also in other systems such as neuroendocrine and immune. Conclusions: The propensity to adult CPA behaviour in subjects experienced to early-life adversity is mediated by epigenetic programming that involves long-term systemic epigenetic alterations in a whole genome.
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Affiliation(s)
- Dimitry A Chistiakov
- a Department of Fundamental and Applied Neurobiology , Serbsky Federal Medical Research Center of Psychiatry and Narcology , Moscow , Russia
| | - Vladimir P Chekhonin
- a Department of Fundamental and Applied Neurobiology , Serbsky Federal Medical Research Center of Psychiatry and Narcology , Moscow , Russia.,b Department of Medical Nanobiotechnology , Pirogov Russian State Medical University (RSMU) , Moscow , Russia
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108
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Jang S, Kang C, Yang HS, Jung T, Hebert H, Chung KY, Kim SJ, Hohng S, Song JJ. Structural basis of recognition and destabilization of the histone H2B ubiquitinated nucleosome by the DOT1L histone H3 Lys79 methyltransferase. Genes Dev 2019; 33:620-625. [PMID: 30923167 PMCID: PMC6546062 DOI: 10.1101/gad.323790.118] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 03/08/2019] [Indexed: 01/01/2023]
Abstract
In this study, Jang et al. present cryo-EM structures of DOT1L complexes with unmodified or H2B ubiquitinated nucleosomes, showing that DOT1L recognizes H2B ubiquitin and the H2A/H2B acidic patch through a C-terminal hydrophobic helix and an arginine anchor in DOT1L, respectively. Their results establish the molecular basis of the cross-talk between H2B ubiquitination and H3 Lys79 methylation as well as nucleosome destabilization by DOT1L. DOT1L is a histone H3 Lys79 methyltransferase whose activity is stimulated by histone H2B Lys120 ubiquitination, suggesting cross-talk between histone H3 methylation and H2B ubiquitination. Here, we present cryo-EM structures of DOT1L complexes with unmodified or H2B ubiquitinated nucleosomes, showing that DOT1L recognizes H2B ubiquitin and the H2A/H2B acidic patch through a C-terminal hydrophobic helix and an arginine anchor in DOT1L, respectively. Furthermore, the structures combined with single-molecule FRET experiments show that H2B ubiquitination enhances a noncatalytic function of the DOT1L-destabilizing nucleosome. These results establish the molecular basis of the cross-talk between H2B ubiquitination and H3 Lys79 methylation as well as nucleosome destabilization by DOT1L.
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Affiliation(s)
- Seongmin Jang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Chanshin Kang
- Department of Physics and Astronomy, Seoul National University, Seoul 08826, Korea
| | - Han-Sol Yang
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Taeyang Jung
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, Department of Biomedical Engineering and Health Systems, KTH Royal Institute of Technology, S-141 52 Huddinge, Sweden.,Department of Biosciences and Nutrition, Karolinska Institutet, S-141 52 Huddinge, Sweden
| | - Hans Hebert
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, Department of Biomedical Engineering and Health Systems, KTH Royal Institute of Technology, S-141 52 Huddinge, Sweden.,Department of Biosciences and Nutrition, Karolinska Institutet, S-141 52 Huddinge, Sweden
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Seung Joong Kim
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Sungchul Hohng
- Department of Physics and Astronomy, Seoul National University, Seoul 08826, Korea
| | - Ji-Joon Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
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109
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Worden EJ, Hoffmann NA, Hicks CW, Wolberger C. Mechanism of Cross-talk between H2B Ubiquitination and H3 Methylation by Dot1L. Cell 2019; 176:1490-1501.e12. [PMID: 30765112 PMCID: PMC6498860 DOI: 10.1016/j.cell.2019.02.002] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/22/2019] [Accepted: 02/01/2019] [Indexed: 12/21/2022]
Abstract
Methylation of histone H3 K79 by Dot1L is a hallmark of actively transcribed genes that depends on monoubiquitination of H2B K120 (H2B-Ub) and is an example of histone modification cross-talk that is conserved from yeast to humans. We report here cryo-EM structures of Dot1L bound to ubiquitinated nucleosome that show how H2B-Ub stimulates Dot1L activity and reveal a role for the histone H4 tail in positioning Dot1L. We find that contacts mediated by Dot1L and the H4 tail induce a conformational change in the globular core of histone H3 that reorients K79 from an inaccessible position, thus enabling this side chain to insert into the active site in a position primed for catalysis. Our study provides a comprehensive mechanism of cross-talk between histone ubiquitination and methylation and reveals structural plasticity in histones that makes it possible for histone-modifying enzymes to access residues within the nucleosome core.
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Affiliation(s)
- Evan J Worden
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Niklas A Hoffmann
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Chad W Hicks
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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110
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Fellous A, Earley RL, Silvestre F. The Kdm/Kmt gene families in the self-fertilizing mangrove rivulus fish, Kryptolebias marmoratus, suggest involvement of histone methylation machinery in development and reproduction. Gene 2019; 687:173-187. [DOI: 10.1016/j.gene.2018.11.046] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 11/06/2018] [Accepted: 11/15/2018] [Indexed: 12/16/2022]
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111
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Guo Q, Liao S, Kwiatkowski S, Tomaka W, Yu H, Wu G, Tu X, Min J, Drozak J, Xu C. Structural insights into SETD3-mediated histidine methylation on β-actin. eLife 2019; 8:43676. [PMID: 30785395 PMCID: PMC6400499 DOI: 10.7554/elife.43676] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/19/2019] [Indexed: 01/01/2023] Open
Abstract
SETD3 is a member of the SET (Su(var)3–9, Enhancer of zeste, and Trithorax) domain protein superfamily and plays important roles in hypoxic pulmonary hypertension, muscle differentiation, and carcinogenesis. Previously, we identified SETD3 as the actin-specific methyltransferase that methylates the N3 of His73 on β-actin (Kwiatkowski et al., 2018). Here, we present two structures of S-adenosyl-L-homocysteine-bound SETD3 in complex with either an unmodified β-actin peptide or its His-methylated variant. Structural analyses, supported by biochemical experiments and enzyme activity assays, indicate that the recognition and methylation of β-actin by SETD3 are highly sequence specific, and that both SETD3 and β-actin adopt pronounced conformational changes upon binding to each other. In conclusion, this study is the first to show a catalytic mechanism of SETD3-mediated histidine methylation on β-actin, which not only throws light on the protein histidine methylation phenomenon but also facilitates the design of small molecule inhibitors of SETD3.
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Affiliation(s)
- Qiong Guo
- Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Shanhui Liao
- Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Sebastian Kwiatkowski
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Weronika Tomaka
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Huijuan Yu
- Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Gao Wu
- Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Xiaoming Tu
- Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, Toronto, Canada.,Department of Physiology, University of Toronto, Toronto, Canada
| | - Jakub Drozak
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Chao Xu
- Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
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112
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Zhou Z, Chen H, Xie R, Wang H, Li S, Xu Q, Xu N, Cheng Q, Qian Y, Huang R, Shao Z, Xiang M. Epigenetically modulated FOXM1 suppresses dendritic cell maturation in pancreatic cancer and colon cancer. Mol Oncol 2019; 13:873-893. [PMID: 30628173 PMCID: PMC6441919 DOI: 10.1002/1878-0261.12443] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 12/10/2018] [Accepted: 12/21/2018] [Indexed: 01/01/2023] Open
Abstract
Forkhead box transcription factor M1 (FOXM1) is a proliferation‐associated transcription factor involved in tumorigenesis through transcriptional regulation of its target genes in various cells, including dendritic cells (DCs). Although previous work has shown that FOXM1 enhances DC maturation in response to house dust mite allergens, it is not known whether FOXM1 affects DC maturation in the context of tumor‐specific immunity. In this study, we examined the central role of FOXM1 in regulating bone marrow‐derived dendritic cell (BMDC) maturation phenotypes and function in pancreatic cancer and colon cancer. FOXM1 retarded maturation phenotypes of BMDCs, inhibited promotion of T‐cell proliferation, and decreased interleukin‐12 (IL‐12) p70 in tumor‐bearing mice (TBM). Notably, FOXM1 expression was epigenetically regulated by dimethylation on H3 lysine 79 (H3K79me2), a modification present in both tumor cells and BMDCs. Increased H3K79me2 enrichment was observed at the FOXM1 promoter in both BMDCs from TBM, and in BMDCs from wild‐type mice cultured with tumor‐conditioned medium that mimics the tumor microenvironment (TME). Furthermore, inhibition of the H3K79 methyltransferase DOT1L not only decreased enrichment of H3K79me2, but also downregulated expression of FOXM1 and partially reversed its immunosuppressive effects on BMDCs. Furthermore, we found that FOXM1 upregulated transcription of Wnt family number 5A (Wnt5a) in BMDCs in vitro; we also observed that exogenous Wnt5a expression abrogated BMDC maturation phenotypes by inhibiting FOXM1 and H3K79me2 modification. Therefore, our results reveal that upregulation of FOXM1 by H3K79me2 in pancreatic cancer and colon cancer significantly inhibits maturation phenotypes and function of BMDCs through the Wnt5a signaling pathway, and thus provide novel insights into FOXM1‐based antitumor immunotherapy.
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Affiliation(s)
- Zhongshi Zhou
- Department of Pharmacology, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Hongdan Chen
- Department of Pharmacology, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Rui Xie
- Department of Pharmacology, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Hongjie Wang
- Section of Neurobiology, Torrey Pines Institute for Molecular Studies, Port St Lucie, FL, USA
| | - Senlin Li
- Department of Pharmacology, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Qianqian Xu
- Department of Pharmacology, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Na Xu
- Department of Pharmacology, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Qi Cheng
- Department of Pharmacology, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Ying Qian
- Department of Pharmacology, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Rongrong Huang
- Department of Pharmacology, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Zekun Shao
- Department of Pharmacology, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Ming Xiang
- Department of Pharmacology, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
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113
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Ciafrè S, Carito V, Ferraguti G, Greco A, Chaldakov GN, Fiore M, Ceccanti M. How alcohol drinking affects our genes: an epigenetic point of view. Biochem Cell Biol 2018; 97:345-356. [PMID: 30412425 DOI: 10.1139/bcb-2018-0248] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
This work highlights recent studies in epigenetic mechanisms that play a role in alcoholism, which is a complex multifactorial disorder. There is a large body of evidence showing that alcohol can modify gene expression through epigenetic processes, namely DNA methylation and nucleosomal remodeling via histone modifications. In that regard, chronic exposure to ethanol modifies DNA and histone methylation, histone acetylation, and microRNA expression. The alcohol-mediated chromatin remodeling in the brain promotes the transition from use to abuse and addiction. Unravelling the multiplex pattern of molecular modifications induced by ethanol could support the development of new therapies for alcoholism and drug addiction targeting epigenetic processes.
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Affiliation(s)
- Stefania Ciafrè
- a Institute of Translational Pharmacology, IFT-CNR, 100 via del Fosso del Cavaliere, Rome 00133, Italy
| | - Valentina Carito
- b Institute of Cell Biology and Neurobiology, IBCN-CNR, c/o Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico, 155 (00161), Rome, Italy
| | - Giampiero Ferraguti
- c Department of Experimental Medicine, Sapienza University of Rome, Viale del Policlinico, 155 (00161), Rome, Italy
| | - Antonio Greco
- d Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico, 155 (00161), Rome, Italy
| | - George N Chaldakov
- e Laboratory of Cell Biology, Department of Anatomy and Histology, Medical University, BG-9002 Varna, Bulgaria
| | - Marco Fiore
- b Institute of Cell Biology and Neurobiology, IBCN-CNR, c/o Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico, 155 (00161), Rome, Italy
| | - Mauro Ceccanti
- f Centro Riferimento Alcologico Regione Lazio, Sapienza University of Rome, Viale del Policlinico, 155 (00161), Rome, Italy
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114
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Zhang L, Chen Y, Liu N, Li L, Xiao S, Li X, Chen K, Luo C, Chen S, Chen H. Design, synthesis and anti leukemia cells proliferation activities of pyrimidylaminoquinoline derivatives as DOT1L inhibitors. Bioorg Chem 2018; 80:649-654. [DOI: 10.1016/j.bioorg.2018.07.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/11/2018] [Accepted: 07/18/2018] [Indexed: 11/30/2022]
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115
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Lillico R, Lawrence CK, Lakowski TM. Selective DOT1L, LSD1, and HDAC Class I Inhibitors Reduce HOXA9 Expression in MLL-AF9 Rearranged Leukemia Cells, But Dysregulate the Expression of Many Histone-Modifying Enzymes. J Proteome Res 2018; 17:2657-2667. [PMID: 29972300 DOI: 10.1021/acs.jproteome.8b00118] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mixed lineage leukemia results from chromosomal rearrangements of the gene mixed lineage leukemia (MLL). MLL-AF9 is one such rearrangement that recruits the lysine methyltransferase, human disruptor of telomere silencing 1-like (DOT1L) and lysine specific demethylase 1 (LSD1), resulting in elevated expression of the Homeobox protein A9 (HOXA9), and leukemia. Inhibitors of LSD1 or DOT1L reduce HOXA9 expression, kill MLL-rearranged cells, and may treat leukemia. To quantify their effects on histone modifying enzyme activity and expression in MLL-rearranged leukemia, we tested inhibitors of DOT1L (EPZ-5676), LSD1 (GSK2879552), and HDAC (mocetinostat), in the MLL-AF9 cell line MOLM-13. All inhibitors reduced MOLM-13 viability but only mocetinostat induced apoptosis. EPZ-5676 increased total histone lysine dimethylation, which was attributed to a reduction in LSD1 expression, and was indistinguishable from direct LSD1 inhibition by GSK2879552. All compounds directly inhibit, or reduce the expression of, HOXA9, DOT1L and LSD1 by qPCR, increase total histone lysine methylation and acetylation by LC-MS/MS, and specifically reduce H3K79Me2 and increase H3K14Ac. Each inhibitor altered the expression of many histone modifying enzymes which may precipitate additional changes in expression. To the extent that this decreases HOXA9 expression it benefits mixed lineage leukemia treatment, all other expression changes are off-target effects.
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Affiliation(s)
- Ryan Lillico
- Rady Faculty of Health Science, College of Pharmacy, Pharmaceutical Analysis Laboratory , University of Manitoba , 750 McDermot Avenue , Winnipeg , Manitoba Canada , R3E 0T5
| | - Courtney K Lawrence
- Rady Faculty of Health Science, College of Pharmacy, Pharmaceutical Analysis Laboratory , University of Manitoba , 750 McDermot Avenue , Winnipeg , Manitoba Canada , R3E 0T5
| | - Ted M Lakowski
- Rady Faculty of Health Science, College of Pharmacy, Pharmaceutical Analysis Laboratory , University of Manitoba , 750 McDermot Avenue , Winnipeg , Manitoba Canada , R3E 0T5
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116
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Abstract
Protein lysine methylation is a distinct posttranslational modification that causes minimal changes in the size and electrostatic status of lysine residues. Lysine methylation plays essential roles in regulating fates and functions of target proteins in an epigenetic manner. As a result, substrates and degrees (free versus mono/di/tri) of protein lysine methylation are orchestrated within cells by balanced activities of protein lysine methyltransferases (PKMTs) and demethylases (KDMs). Their dysregulation is often associated with neurological disorders, developmental abnormalities, or cancer. Methyllysine-containing proteins can be recognized by downstream effector proteins, which contain methyllysine reader domains, to relay their biological functions. While numerous efforts have been made to annotate biological roles of protein lysine methylation, limited work has been done to uncover mechanisms associated with this modification at a molecular or atomic level. Given distinct biophysical and biochemical properties of methyllysine, this review will focus on chemical and biochemical aspects in addition, recognition, and removal of this posttranslational mark. Chemical and biophysical methods to profile PKMT substrates will be discussed along with classification of PKMT inhibitors for accurate perturbation of methyltransferase activities. Semisynthesis of methyllysine-containing proteins will also be covered given the critical need for these reagents to unambiguously define functional roles of protein lysine methylation.
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Affiliation(s)
- Minkui Luo
- Chemical Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States.,Program of Pharmacology, Weill Graduate School of Medical Science , Cornell University , New York , New York 10021 , United States
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117
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Chen Y, Liu X, Li Y, Quan C, Zheng L, Huang K. Lung Cancer Therapy Targeting Histone Methylation: Opportunities and Challenges. Comput Struct Biotechnol J 2018; 16:211-223. [PMID: 30002791 PMCID: PMC6039709 DOI: 10.1016/j.csbj.2018.06.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 06/10/2018] [Accepted: 06/11/2018] [Indexed: 12/18/2022] Open
Abstract
Lung cancer is one of the most common malignancies. In spite of the progress made in past decades, further studies to improve current therapy for lung cancer are required. Dynamically controlled by methyltransferases and demethylases, methylation of lysine and arginine residues on histone proteins regulates chromatin organization and thereby gene transcription. Aberrant alterations of histone methylation have been demonstrated to be associated with the progress of multiple cancers including lung cancer. Inhibitors of methyltransferases and demethylases have exhibited anti-tumor activities in lung cancer, and multiple lead candidates are under clinical trials. Here, we summarize how histone methylation functions in lung cancer, highlighting most recent progresses in small molecular inhibitors for lung cancer treatment.
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Key Words
- ALK, anaplastic lymphoma kinase
- DUSP3, dual-specificity phosphatase 3
- EMT, epithelial-to-mesenchymal transition
- Elk1, ETS-domain containing protein
- HDAC, histone deacetylase
- Histone demethylase
- Histone demethylation
- Histone methylation
- Histone methyltransferase
- IHC, immunohistochemistry
- Inhibitors
- KDMs, lysine demethylases
- KLF2, Kruppel-like factor 2
- KMTs, lysine methyltransferases
- LSDs, lysine specific demethylases
- Lung cancer
- MEP50, methylosome protein 50
- NSCLC, non-small cell lung cancer
- PAD4, peptidylarginine deiminase 4
- PCNA, proliferating cell nuclear antigen
- PDX, patient-derived xenografts
- PRC2, polycomb repressive complex 2
- PRMTs, protein arginine methyltrasferases
- PTMs, posttranslational modifications
- SAH, S-adenosyl-L-homocysteine
- SAM, S-adenosyl-L-methionine
- SCLC, small cell lung cancer
- TIMP3, tissue inhibitor of metalloproteinase 3
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Affiliation(s)
- Yuchen Chen
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430030, China
| | - Xinran Liu
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430030, China
| | - Yangkai Li
- Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430030, China
| | - Chuntao Quan
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430030, China
| | - Ling Zheng
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Kun Huang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430030, China
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118
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Hauser AT, Robaa D, Jung M. Epigenetic small molecule modulators of histone and DNA methylation. Curr Opin Chem Biol 2018; 45:73-85. [PMID: 29579619 DOI: 10.1016/j.cbpa.2018.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/05/2018] [Accepted: 03/07/2018] [Indexed: 12/14/2022]
Abstract
DNA and histone methylation belong to the key regulatory components in the epigenetic machinery, and dysregulations of these processes have been associated with various human diseases. Small molecule modulators of these epigenetic targets are highly valuable both as chemical probes to study the biological roles of the target proteins, and as potential therapeutics. Indeed, recent years have seen the discovery of chemical modulators of several epigenetic targets, some of which are already marketed drugs or undergoing clinical trials. In this review, we will focus on small molecule modulators of DNA and histone methylation.
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Affiliation(s)
- Alexander-Thomas Hauser
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, 79104 Freiburg im Breisgau, Germany
| | - Dina Robaa
- Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Wolfgang-Langenbeck-Straße 4, 06120 Halle (Saale), Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, 79104 Freiburg im Breisgau, Germany.
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119
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Wood K, Tellier M, Murphy S. DOT1L and H3K79 Methylation in Transcription and Genomic Stability. Biomolecules 2018; 8:E11. [PMID: 29495487 PMCID: PMC5871980 DOI: 10.3390/biom8010011] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/20/2018] [Accepted: 02/21/2018] [Indexed: 01/08/2023] Open
Abstract
The organization of eukaryotic genomes into chromatin provides challenges for the cell to accomplish basic cellular functions, such as transcription, DNA replication and repair of DNA damage. Accordingly, a range of proteins modify and/or read chromatin states to regulate access to chromosomal DNA. Yeast Dot1 and the mammalian homologue DOT1L are methyltransferases that can add up to three methyl groups to histone H3 lysine 79 (H3K79). H3K79 methylation is implicated in several processes, including transcription elongation by RNA polymerase II, the DNA damage response and cell cycle checkpoint activation. DOT1L is also an important drug target for treatment of mixed lineage leukemia (MLL)-rearranged leukemia where aberrant transcriptional activation is promoted by DOT1L mislocalisation. This review summarizes what is currently known about the role of Dot1/DOT1L and H3K79 methylation in transcription and genomic stability.
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Affiliation(s)
- Katherine Wood
- Department of Biochemistry, University of Oxford, Oxford OX1 3RE, UK.
- School of Biological Sciences, University of Manchester, Manchester M13 9PL, UK.
| | - Michael Tellier
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK.
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120
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Duan Y, Wu X, Zhao Q, Gao J, Huo D, Liu X, Ye Z, Dong X, Fu Z, Shang Y, Xuan C. DOT1L promotes angiogenesis through cooperative regulation of VEGFR2 with ETS-1. Oncotarget 2018; 7:69674-69687. [PMID: 27626484 PMCID: PMC5342507 DOI: 10.18632/oncotarget.11939] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 09/02/2016] [Indexed: 01/16/2023] Open
Abstract
Histone methyltransferase DOT1L is implicated in various biological processes including cell proliferation, differentiation and embryogenesis. Gene ablation of Dot1l results in embryonic lethality and cardiovascular defects including decreased vasculature. However, how DOT1L might contribute to the development of vasculature is not clear. Here, we report that DOT1L is required for angiogenesis. We demonstrated that silencing of DOT1L in human umbilical vein endothelial cells (HUVECs) leads to decreased cell viability, migration, tube formation, and capillary sprout formation in vitro, as well as reduced formation of functional vascular networks in matrigel plugs in vivo. Genome-wide analysis of DOT1L targets via H3K79me2 ChIP-seq annotation in HUVECs identified a number of genes including VEGFR2 that are critically involved in angiogenesis. We showed that DOT1L cooperates with transcription factor ETS-1 to stimulate the expression of VEGFR2, thereby activating ERK1/2 and AKT signaling pathways and promoting angiogenesis. Our study revealed a mechanistic role for DOT1L in the promotion of angiogenesis, adding to the understanding of the biological function of this histone methyltransferase.
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Affiliation(s)
- Yang Duan
- Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Xue Wu
- Geneseeq Technology Inc., Toronto, M5G1L7, Canada
| | - Qiang Zhao
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jie Gao
- Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Dawei Huo
- Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Xinhua Liu
- Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Zheng Ye
- Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Xu Dong
- Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Zheng Fu
- Department of Immunology, Tianjin Medical University, Tianjin 300070, China
| | - Yongfeng Shang
- Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Chenghao Xuan
- Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
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121
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Zhu B, Chen S, Wang H, Yin C, Han C, Peng C, Liu Z, Wan L, Zhang X, Zhang J, Lian CG, Ma P, Xu ZX, Prince S, Wang T, Gao X, Shi Y, Liu D, Liu M, Wei W, Wei Z, Pan J, Wang Y, Xuan Z, Hess J, Hayward NK, Goding CR, Chen X, Zhou J, Cui R. The protective role of DOT1L in UV-induced melanomagenesis. Nat Commun 2018; 9:259. [PMID: 29343685 PMCID: PMC5772495 DOI: 10.1038/s41467-017-02687-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 12/13/2017] [Indexed: 11/09/2022] Open
Abstract
The DOT1L histone H3 lysine 79 (H3K79) methyltransferase plays an oncogenic role in MLL-rearranged leukemogenesis. Here, we demonstrate that, in contrast to MLL-rearranged leukemia, DOT1L plays a protective role in ultraviolet radiation (UVR)-induced melanoma development. Specifically, the DOT1L gene is located in a frequently deleted region and undergoes somatic mutation in human melanoma. Specific mutations functionally compromise DOT1L methyltransferase enzyme activity leading to reduced H3K79 methylation. Importantly, in the absence of DOT1L, UVR-induced DNA damage is inefficiently repaired, so that DOT1L loss promotes melanoma development in mice after exposure to UVR. Mechanistically, DOT1L facilitates DNA damage repair, with DOT1L-methylated H3K79 involvement in binding and recruiting XPC to the DNA damage site for nucleotide excision repair (NER). This study indicates that DOT1L plays a protective role in UVR-induced melanomagenesis.
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Affiliation(s)
- Bo Zhu
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, 02118, USA.,Shandong Provincial Key Laboratory of Animal Resistance Biology, Institute of Biomedical Sciences, College of Life Sciences, Shandong Normal University, 250014, Jinan, China
| | - Shuyang Chen
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, 02118, USA.,Department of Dermatology & China Hunan key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, 410008, Changsha, China
| | - Hongshen Wang
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, 02118, USA.,Shanghai University of Traditional Chinese Medicine, 201203, Shanghai, China
| | - Chengqian Yin
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, 02118, USA.,Institute of Life Science, Jiangsu University, 212013, Zhenjiang, China
| | - Changpeng Han
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, 02118, USA.,Shanghai University of Traditional Chinese Medicine, 201203, Shanghai, China
| | - Cong Peng
- Department of Dermatology & China Hunan key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, 410008, Changsha, China
| | - Zhaoqian Liu
- Department of Dermatology & China Hunan key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, 410008, Changsha, China
| | - Lixin Wan
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Xiaoyang Zhang
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Jie Zhang
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Christine G Lian
- Department of Pathology, The Brigham and Women's Hospital, Harvard Medical School, 221 Longwood Ave, Boston, MA, 02115, USA
| | - Peilin Ma
- Department of Pathology, Indiana University School of Medicine, 340 West 10th Street, Fairbanks 6200, Indianapolis, IN, 46202, USA
| | - Zhi-Xiang Xu
- Division of Hematology/Oncology, Department of Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, AL, 35233, USA
| | - Sharon Prince
- Department of Human Biology, University of Cape Town, Rondebosch, Cape Town, 7700, South Africa
| | - Tao Wang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 300193, Tianjin, China
| | - Xiumei Gao
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 300193, Tianjin, China
| | - Yujiang Shi
- Department of Medicine, Endocrinology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Min Liu
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Institute of Biomedical Sciences, College of Life Sciences, Shandong Normal University, 250014, Jinan, China
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02115, USA
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Jingxuan Pan
- Cancer Pharmacology Research Institute, Jinan University, 510632, Guangzhou, China
| | - Yongjun Wang
- Shanghai University of Traditional Chinese Medicine, 201203, Shanghai, China
| | - Zhenyu Xuan
- Department of Biological Sciences, Center for Systems Biology, University of Texas at Dallas, Richardson, TX, 75080, USA
| | - Jay Hess
- Department of Pathology, Indiana University School of Medicine, 340 West 10th Street, Fairbanks 6200, Indianapolis, IN, 46202, USA
| | - Nicholas K Hayward
- QIMR Berghofer Medical Research Institute, Brisbane City, QLD, 4006, Australia
| | - Colin R Goding
- Ludwig Institute for Cancer Research, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Xiang Chen
- Department of Dermatology & China Hunan key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, 410008, Changsha, China.
| | - Jun Zhou
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Institute of Biomedical Sciences, College of Life Sciences, Shandong Normal University, 250014, Jinan, China.
| | - Rutao Cui
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, 02118, USA.
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122
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Disruptor of telomeric silencing 1-like (DOT1L): disclosing a new class of non-nucleoside inhibitors by means of ligand-based and structure-based approaches. J Comput Aided Mol Des 2018; 32:435-458. [PMID: 29335872 DOI: 10.1007/s10822-018-0096-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 01/06/2018] [Indexed: 01/25/2023]
Abstract
Chemical inhibition of chromatin-mediated signaling involved proteins is an established strategy to drive expression networks and alter disease progression. Protein methyltransferases are among the most studied proteins in epigenetics and, in particular, disruptor of telomeric silencing 1-like (DOT1L) lysine methyltransferase plays a key role in MLL-rearranged acute leukemia Selective inhibition of DOT1L is an established attractive strategy to breakdown aberrant H3K79 methylation and thus overexpression of leukemia genes, and leukemogenesis. Although numerous DOT1L inhibitors have been several structural data published no pronounced computational efforts have been yet reported. In these studies a first tentative of multi-stage and LB/SB combined approach is reported in order to maximize the use of available data. Using co-crystallized ligand/DOT1L complexes, predictive 3-D QSAR and COMBINE models were built through a python implementation of previously reported methodologies. The models, validated by either modeled or experimental external test sets, proved to have good predictive abilities. The application of these models to an internal library led to the selection of two unreported compounds that were found able to inhibit DOT1L at micromolar level. To the best of our knowledge this is the first report of quantitative LB and SB DOT1L inhibitors models and their application to disclose new potential epigenetic modulators.
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123
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Pan MR, Hsu MC, Chen LT, Hung WC. Orchestration of H3K27 methylation: mechanisms and therapeutic implication. Cell Mol Life Sci 2018; 75:209-223. [PMID: 28717873 PMCID: PMC5756243 DOI: 10.1007/s00018-017-2596-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/06/2017] [Accepted: 07/13/2017] [Indexed: 01/08/2023]
Abstract
Histone proteins constitute the core component of the nucleosome, the basic unit of chromatin. Chemical modifications of histone proteins affect their interaction with genomic DNA, the accessibility of recognized proteins, and the recruitment of enzymatic complexes to activate or diminish specific transcriptional programs to modulate cellular response to extracellular stimuli or insults. Methylation of histone proteins was demonstrated 50 years ago; however, the biological significance of each methylated residue and the integration between these histone markers are still under intensive investigation. Methylation of histone H3 on lysine 27 (H3K27) is frequently found in the heterochromatin and conceives a repressive marker that is linked with gene silencing. The identification of enzymes that add or erase the methyl group of H3K27 provides novel insights as to how this histone marker is dynamically controlled under different circumstances. Here we summarize the methyltransferases and demethylases involved in the methylation of H3K27 and show the new evidence by which the H3K27 methylation can be established via an alternative mechanism. Finally, the progress of drug development targeting H3K27 methylation-modifying enzymes and their potential application in cancer therapy are discussed.
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Affiliation(s)
- Mei-Ren Pan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Ming-Chuan Hsu
- National Institute of Cancer Research, National Health Research Institutes, Tainan, 704, Taiwan
| | - Li-Tzong Chen
- National Institute of Cancer Research, National Health Research Institutes, Tainan, 704, Taiwan
- Division of Hematology/Oncology, Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, 704, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 804, Taiwan
| | - Wen-Chun Hung
- National Institute of Cancer Research, National Health Research Institutes, Tainan, 704, Taiwan.
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 804, Taiwan.
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124
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Castelli G, Pelosi E, Testa U. Targeting histone methyltransferase and demethylase in acute myeloid leukemia therapy. Onco Targets Ther 2017; 11:131-155. [PMID: 29343972 PMCID: PMC5749389 DOI: 10.2147/ott.s145971] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Acute myeloid leukemia (AML) is a clonal disorder of myeloid progenitors characterized by the acquisition of chromosomal abnormalities, somatic mutations, and epigenetic changes that determine a consistent degree of biological and clinical heterogeneity. Advances in genomic technologies have increasingly shown the complexity and heterogeneity of genetic and epigenetic alterations in AML. Among the genetic alterations occurring in AML, frequent are the genetic alterations at the level of various genes involved in the epigenetic control of the DNA methylome and histone methylome. In fact, genes involved in DNA demethylation (such as DNMT3A, TET2, IDH1, and IDH2) or histone methylation and demethylation (EZH2, MLL, DOT1L) are frequently mutated in primary and secondary AML. Furthermore, some histone demethylases, such as LSD1, are frequently overexpressed in AML. These observations have strongly supported a major role of dysregulated epigenetic regulatory processes in leukemia onset and development. This conclusion was further supported by the observation that mutations in genes encoding epigenetic modifiers, such as DMT3A, ASXL1, TET2, IDH1, and IDH2, are usually acquired early and are present in the founding leukemic clone. These observations have contributed to development of the idea that targeting epigenetic abnormalities could represent a potentially promising strategy for the development of innovative treatments of AML. In this review, we analyze those proteins and their inhibitors that have already reached the first stages of clinical trials in AML, namely the histone methyltransferase DOT1L, the demethylase LSD1, and the MLL-interacting protein menin.
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Affiliation(s)
- Germana Castelli
- Department of Oncology, Istituto Superiore di Sanità, Rome, Italy
| | - Elvira Pelosi
- Department of Oncology, Istituto Superiore di Sanità, Rome, Italy
| | - Ugo Testa
- Department of Oncology, Istituto Superiore di Sanità, Rome, Italy
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125
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He D, Liu J, Hai Y, Zhu Q, Shen Y, Guo S, Zhang W, Zhou X. Increased DOT1L in synovial biopsies of patients with OA and RA. Clin Rheumatol 2017; 37:1327-1332. [PMID: 29234911 DOI: 10.1007/s10067-017-3941-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 11/20/2017] [Accepted: 11/29/2017] [Indexed: 01/15/2023]
Abstract
The studies aimed to determine the changes of histone methylation in synovial tissues of patients with osteoarthritis (OA) and rheumatoid arthritis (RA). Synovial tissues were obtained from 30 patients including 12 OA, 16 RA, and 2 trauma that were used as control. A histone methyltransferase DOT1L of the tissues was examined for transcript level with quantitative RT-PCR and protein expression with western blot. Methylation status of DOT1L substrate, H3K79, was examined with immunohistochemistry and western blot. Two-tailed non-pair T test and chi-square test were applied for age/disease duration and gender distribution, respectively. Kruskal-Wallis test and Post hoc Dunn's test were used for examine the difference between control, OA and RA. Both transcript and protein levels of DOT1L appeared the highest in synovial tissues of RA patients and increased in that of OA patients compared to the controls with ratios of 13.8/4.7/1 and 15.5/11.2/1.0 for RA/OA/control, respectively. The changes between RA and control, and RA and OA patients were statistically significant. Both immunohistochemistry study and western blot showed an increased methylation of H3K79 in synovial tissues of OA and RA patients. Gene and protein expression of DOT1L was increased in synovial tissues of both OA and RA patients. A high level of di-methylated H3K79 was also observed in the patients. Considering the important functions of DOT1L and H3K79 contributing to the initiation and maintenance of active transcription in the genome, these unprecedented findings, although still unclear how to impact diseases, may provide novel insights to further explore pathological mechanism of OA and RA.
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Affiliation(s)
- Dongyi He
- Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai, China
| | - Jia Liu
- Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai, China
| | - Yamei Hai
- University of Shanghai Traditional Chinese Medicine, Shanghai, China
| | - Qi Zhu
- Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai, China
| | - Yu Shen
- Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai, China
| | - Shicheng Guo
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, WI, USA
| | - Wenzheng Zhang
- Department of Regenerative and Cancer Cell Biology, Albany Medical College, Albany, NY, USA
| | - Xiaodong Zhou
- Division of Rheumatology and Clinical Immunogenetics, The University of Texas Medical School at Houston, Houston, TX, USA.
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Ljungman M, Parks L, Hulbatte R, Bedi K. The role of H3K79 methylation in transcription and the DNA damage response. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 780:48-54. [PMID: 31395348 DOI: 10.1016/j.mrrev.2017.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 10/19/2017] [Accepted: 11/15/2017] [Indexed: 12/16/2022]
Abstract
Chromatin plays a critical role in organizing and protecting DNA. However, chromatin acts as an impediment for transcription and DNA repair. Histone modifications, such as H3K79 methylation, promote transcription and genomic stability by enhancing transcription elongation and by serving as landing sites for proteins involved in the DNA damage response. This review summarizes the current understanding of the role of H3K79 methylation in transcription, how it affects genome stability and opportunities to develop impactful therapeutic interventions for cancer.
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Affiliation(s)
- Mats Ljungman
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, United States; Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, United States.
| | - Luke Parks
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, United States; Department of Cell and Molecular Biology, Uppsala University, Box 256, 75105 Uppsala, Sweden
| | - Radhika Hulbatte
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, United States
| | - Karan Bedi
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, United States
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Jakobsson ME, Malecki J, Nilges BS, Moen A, Leidel SA, Falnes PØ. Methylation of human eukaryotic elongation factor alpha (eEF1A) by a member of a novel protein lysine methyltransferase family modulates mRNA translation. Nucleic Acids Res 2017; 45:8239-8254. [PMID: 28520920 PMCID: PMC5737405 DOI: 10.1093/nar/gkx432] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/03/2017] [Indexed: 02/04/2023] Open
Abstract
Many cellular proteins are methylated on lysine residues and this has been most intensively studied for histone proteins. Lysine methylations on non-histone proteins are also frequent, but in most cases the functional significance of the methylation event, as well as the identity of the responsible lysine (K) specific methyltransferase (KMT), remain unknown. Several recently discovered KMTs belong to the so-called seven-β-strand (7BS) class of MTases and we have here investigated an uncharacterized human 7BS MTase currently annotated as part of the endothelin converting enzyme 2, but which should be considered a separate enzyme. Combining in vitro enzymology and analyzes of knockout cells, we demonstrate that this MTase efficiently methylates K36 in eukaryotic translation elongation factor 1 alpha (eEF1A) in vitro and in vivo. We suggest that this novel KMT is named eEF1A-KMT4 (gene name EEF1AKMT4), in agreement with the recently established nomenclature. Furthermore, by ribosome profiling we show that the absence of K36 methylation affects translation dynamics and changes translation speed of distinct codons. Finally, we show that eEF1A-KMT4 is part of a novel family of human KMTs, defined by a shared sequence motif in the active site and we demonstrate the importance of this motif for catalytic activity.
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Affiliation(s)
- Magnus E Jakobsson
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0316, Norway
| | - Jedrzej Malecki
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0316, Norway
| | - Benedikt S Nilges
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany.,Cells-in-Motion Cluster of Excellence, University of Muenster, 48149 Muenster, Germany
| | - Anders Moen
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0316, Norway
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany.,Cells-in-Motion Cluster of Excellence, University of Muenster, 48149 Muenster, Germany
| | - Pål Ø Falnes
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo 0316, Norway
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129
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Protein lysine methylation by seven-β-strand methyltransferases. Biochem J 2017; 473:1995-2009. [PMID: 27407169 DOI: 10.1042/bcj20160117] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/24/2016] [Indexed: 11/17/2022]
Abstract
Methylation of biomolecules is a frequent biochemical reaction within the cell, and a plethora of highly specific methyltransferases (MTases) catalyse the transfer of a methyl group from S-adenosylmethionine (AdoMet) to various substrates. The posttranslational methylation of lysine residues, catalysed by numerous lysine (K)-specific protein MTases (KMTs), is a very common and important protein modification, which recently has been subject to intense studies, particularly in the case of histone proteins. The majority of KMTs belong to a class of MTases that share a defining 'SET domain', and these enzymes mostly target lysines in the flexible tails of histones. However, the so-called seven-β-strand (7BS) MTases, characterized by a twisted beta-sheet structure and certain conserved sequence motifs, represent the largest MTase class, and these enzymes methylate a wide range of substrates, including small metabolites, lipids, nucleic acids and proteins. Until recently, the histone-specific Dot1/DOT1L was the only identified eukaryotic 7BS KMT. However, a number of novel 7BS KMTs have now been discovered, and, in particular, several recently characterized human and yeast members of MTase family 16 (MTF16) have been found to methylate lysines in non-histone proteins. Here, we review the status and recent progress on the 7BS KMTs, and discuss these enzymes at the levels of sequence/structure, catalytic mechanism, substrate recognition and biological significance.
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130
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Hyun K, Jeon J, Park K, Kim J. Writing, erasing and reading histone lysine methylations. Exp Mol Med 2017; 49:e324. [PMID: 28450737 PMCID: PMC6130214 DOI: 10.1038/emm.2017.11] [Citation(s) in RCA: 676] [Impact Index Per Article: 96.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 02/08/2023] Open
Abstract
Histone modifications are key epigenetic regulatory features that have important roles in many cellular events. Lysine methylations mark various sites on the tail and globular domains of histones and their levels are precisely balanced by the action of methyltransferases ('writers') and demethylases ('erasers'). In addition, distinct effector proteins ('readers') recognize specific methyl-lysines in a manner that depends on the neighboring amino-acid sequence and methylation state. Misregulation of histone lysine methylation has been implicated in several cancers and developmental defects. Therefore, histone lysine methylation has been considered a potential therapeutic target, and clinical trials of several inhibitors of this process have shown promising results. A more detailed understanding of histone lysine methylation is necessary for elucidating complex biological processes and, ultimately, for developing and improving disease treatments. This review summarizes enzymes responsible for histone lysine methylation and demethylation and how histone lysine methylation contributes to various biological processes.
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Affiliation(s)
- Kwangbeom Hyun
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jongcheol Jeon
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Kihyun Park
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jaehoon Kim
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
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131
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Kudithipudi S, Schuhmacher MK, Kebede AF, Jeltsch A. The SUV39H1 Protein Lysine Methyltransferase Methylates Chromatin Proteins Involved in Heterochromatin Formation and VDJ Recombination. ACS Chem Biol 2017; 12:958-968. [PMID: 28169523 DOI: 10.1021/acschembio.6b01076] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
SUV39H1 is an H3K9 methyltransferase involved in the formation of heterochromatin. We investigated its substrate specificity profile and show recognition of H3 residues between K4 and G12 with highly specific readout of R8. The specificity profile of SUV39H1 is distinct from its paralog SUV39H2, indicating that they can have different additional substrates. Using the specificity profile, several novel SUV39H1 candidate substrates were identified. We observed methylation of 19 novel substrates at the peptide level and for six of them at the protein level. Methylation of RAG2, SET8, and DOT1L was confirmed in cells, which all have important roles in chromatin regulation. Methylation of SET8 allosterically stimulates its H4K20 monomethylation activity connecting SUV39H1 to the generation of increased H4K20me3 levels, another heterochromatic modification. Methylation of RAG2 alters its subnuclear localization, indicating that SUV39H1 might regulate VDJ recombination. Taken together, our results indicate that beyond the generation of H3K9me3, SUV39H1 has additional roles in chromatin biology by direct stimulation of the establishment of H4K20me3 and the regulation of chromatin binding of RAG2.
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Affiliation(s)
- Srikanth Kudithipudi
- Institute
of Biochemistry, Stuttgart University, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | | | - Adam Fiseha Kebede
- School
of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Albert Jeltsch
- Institute
of Biochemistry, Stuttgart University, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
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Abstract
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Post-translational
modifications of histones by protein methyltransferases
(PMTs) and histone demethylases (KDMs) play an important role in the
regulation of gene expression and transcription and are implicated
in cancer and many other diseases. Many of these enzymes also target
various nonhistone proteins impacting numerous crucial biological
pathways. Given their key biological functions and implications in
human diseases, there has been a growing interest in assessing these
enzymes as potential therapeutic targets. Consequently, discovering
and developing inhibitors of these enzymes has become a very active
and fast-growing research area over the past decade. In this review,
we cover the discovery, characterization, and biological application
of inhibitors of PMTs and KDMs with emphasis on key advancements in
the field. We also discuss challenges, opportunities, and future directions
in this emerging, exciting research field.
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Affiliation(s)
- H Ümit Kaniskan
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Michael L Martini
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Jian Jin
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
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Abstract
Cancer cell hallmarks are underpinned by transcriptional programmes operating in the context of a dynamic and complicit epigenomic environment. Somatic alterations of chromatin modifiers are among the most prevalent cancer perturbations. There is a pressing need for targeted chemical probes to dissect these complex, interconnected gene regulatory circuits. Validated chemical probes empower mechanistic research while providing the pharmacological proof of concept that is required to translate drug-like derivatives into therapy for cancer patients. In this Review, we describe chemical probe development for epigenomic effector proteins that are linked to cancer pathogenesis. By annotating these reagents, we aim to share our perspectives on an informative 'epigenomic toolbox' of broad utility to the research community.
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Affiliation(s)
- Jake Shortt
- Gene Regulation Laboratory, Research Division, Peter MacCallum Cancer Centre, Melbourne 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville 3052, Australia
- School of Clinical Sciences at Monash Health, Monash University, Clayton 3168, Australia
| | - Christopher J Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215, USA
- Center for the Science of Therapeutics, Broad Institute, Cambridge, Massachusetts 02142, USA
| | - Ricky W Johnstone
- Gene Regulation Laboratory, Research Division, Peter MacCallum Cancer Centre, Melbourne 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville 3052, Australia
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215, USA
- Center for the Science of Therapeutics, Broad Institute, Cambridge, Massachusetts 02142, USA
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134
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Discovery of Novel Disruptor of Silencing Telomeric 1-Like (DOT1L) Inhibitors using a Target-Specific Scoring Function for the (S)-Adenosyl-l-methionine (SAM)-Dependent Methyltransferase Family. J Med Chem 2017; 60:2026-2036. [DOI: 10.1021/acs.jmedchem.6b01785] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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135
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Wong M, Tee AEL, Milazzo G, Bell JL, Poulos RC, Atmadibrata B, Sun Y, Jing D, Ho N, Ling D, Liu PY, Zhang XD, Hüttelmaier S, Wong JWH, Wang J, Polly P, Perini G, Scarlett CJ, Liu T. The Histone Methyltransferase DOT1L Promotes Neuroblastoma by Regulating Gene Transcription. Cancer Res 2017; 77:2522-2533. [PMID: 28209620 DOI: 10.1158/0008-5472.can-16-1663] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/08/2016] [Accepted: 01/17/2017] [Indexed: 11/16/2022]
Abstract
Myc oncoproteins exert tumorigenic effects by regulating expression of target oncogenes. Histone H3 lysine 79 (H3K79) methylation at Myc-responsive elements of target gene promoters is a strict prerequisite for Myc-induced transcriptional activation, and DOT1L is the only known histone methyltransferase that catalyzes H3K79 methylation. Here, we show that N-Myc upregulates DOT1L mRNA and protein expression by binding to the DOT1L gene promoter. shRNA-mediated depletion of DOT1L reduced mRNA and protein expression of N-Myc target genes ODC1 and E2F2 DOT1L bound to the Myc Box II domain of N-Myc protein, and knockdown of DOT1L reduced histone H3K79 methylation and N-Myc protein binding at the ODC1 and E2F2 gene promoters and reduced neuroblastoma cell proliferation. Treatment with the small-molecule DOT1L inhibitor SGC0946 reduced H3K79 methylation and proliferation of MYCN gene-amplified neuroblastoma cells. In mice xenografts of neuroblastoma cells stably expressing doxycycline-inducible DOT1L shRNA, ablating DOT1L expression with doxycycline significantly reduced ODC1 and E2F2 expression, reduced tumor progression, and improved overall survival. In addition, high levels of DOT1L gene expression in human neuroblastoma tissues correlated with high levels of MYCN, ODC1, and E2F2 gene expression and independently correlated with poor patient survival. Taken together, our results identify DOT1L as a novel cofactor in N-Myc-mediated transcriptional activation of target genes and neuroblastoma oncogenesis. Furthermore, they characterize DOT1L inhibitors as novel anticancer agents against MYCN-amplified neuroblastoma. Cancer Res; 77(9); 2522-33. ©2017 AACR.
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Affiliation(s)
| | - Andrew E L Tee
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia
| | - Giorgio Milazzo
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Jessica L Bell
- Institute of Molecular Medicine, Martin Luther University, ZAMED, Halle, Germany
| | - Rebecca C Poulos
- Prince of Wales Clinical School and Lowy Cancer Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Bernard Atmadibrata
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia
| | - Yuting Sun
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia
| | - Duohui Jing
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia
| | - Nicholas Ho
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia
| | - Dora Ling
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia
| | - Pei Yan Liu
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia
| | - Xu Dong Zhang
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Martin Luther University, ZAMED, Halle, Germany
| | - Jason W H Wong
- Prince of Wales Clinical School and Lowy Cancer Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Jenny Wang
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia.,Centre for Childhood Cancer Research, UNSW Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Patsie Polly
- Department of Pathology and Mechanisms of Disease and Translational Research, University of New South Wales, Sydney, New South Wales, Australia
| | - Giovanni Perini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Christopher J Scarlett
- School of Environmental & Life Sciences, University of Newcastle, Ourimbah, New South Wales, Australia
| | - Tao Liu
- Children's Cancer Institute Australia for Medical Research, University of New South Wales, Sydney, Australia. .,Centre for Childhood Cancer Research, UNSW Medicine, University of New South Wales, Sydney, New South Wales, Australia
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136
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The Relationship Between DOT1L, Histone H3 Methylation, and Genome Stability in Cancer. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s40610-017-0051-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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137
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Zhang X, Liu D, Li M, Cao C, Wan D, Xi B, Li W, Tan J, Wang J, Wu Z, Ma D, Gao Q. Prognostic and therapeutic value of disruptor of telomeric silencing-1-like (DOT1L) expression in patients with ovarian cancer. J Hematol Oncol 2017; 10:29. [PMID: 28114995 PMCID: PMC5259947 DOI: 10.1186/s13045-017-0400-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/13/2017] [Indexed: 01/07/2023] Open
Abstract
Background Epigenetics has been known to play a critical role in regulating the malignant phenotype. This study was designed to examine the expression of DOT1L (histone 3 lysine 79 methyltransferase) and H3K79 methylation in normal ovarian tissues and ovarian tumors and to explore the function of DOT1L and its underline mechanisms in ovarian cancer. Methods The expression of DOT1L and H3K79 methylation in 250 ovarian tumor samples and 24 normal ovarian samples was assessed by immunohistochemistry. The effects of DOT1L on cell proliferation in vitro were evaluated using CCK8, colony formation and flow cytometry. The DOT1L-targeted genes were determined using chromatin immune-precipitation coupled with high-throughput sequencing (ChIP-seq) and ChIP-PCR. Gene expression levels were measured by real-time PCR and immunoblotting. The effects of DOT1L on tumor growth in vivo were evaluated using an orthotopic ovarian tumor model. Results DOT1L expression and H3K79 methylation was significantly increased in malignant ovarian tumors. High DOT1L expression was associated with International Federation of Gynecology and Obstetrics (FIGO) stage, histologic grade, and lymphatic metastasis. DOT1L was an independent prognostic factor for the overall survival (OS) and progression-free survival (PFS) of ovarian cancer, and higher DOT1L expression was associated with poorer OS and PFS. Furthermore, DOT1L regulates the transcription of G1 phase genes CDK6 and CCND3 through H3K79 dimethylation; therefore, blocking DOT1L could result in G1 arrest and thereby impede the cell proliferation in vitro and tumor growth in vivo. Conclusions Our findings first demonstrate that DOT1L over-expression has important clinical significance in ovarian cancer and also clarify that it drives cell cycle progression through transcriptional regulation of CDK6 and CCND3 through H3K79 methylation, suggesting that DOT1L might be potential target for prognostic assessment and therapeutic intervention in ovarian cancer. Electronic supplementary material The online version of this article (doi:10.1186/s13045-017-0400-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaoxue Zhang
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Dan Liu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Mengchen Li
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Canhui Cao
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Dongyi Wan
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Bixin Xi
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Wenqian Li
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Jiahong Tan
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Ji Wang
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Zhongcai Wu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Ding Ma
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Qinglei Gao
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China.
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Qu Y, Liu L, Wang J, Xi W, Xia Y, Bai Q, Xiong Y, Long Q, Xu J, Guo J. Dot1l expression predicts adverse postoperative prognosis of patients with clear-cell renal cell carcinoma. Oncotarget 2016; 7:84775-84784. [PMID: 27713173 PMCID: PMC5356697 DOI: 10.18632/oncotarget.12476] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 09/22/2016] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Disruptor of telomeric silencing 1-like (Dot1l), a histone methyltransferase that targets the histone H3 lysine 79 (H3K79), has been reported that its high expression is associated with various cancers, while the association between Dot1l expression and clear-cell renal cell carcinoma (ccRCC) is still unknown. PATIENTS AND METHODS We retrospectively enrolled 282 patients with ccRCC undergoing nephrectomy from a single institution between 2005 and 2007, with a median follow-up of 99 months. Dot1l expression was evaluated by immunohistochemistry in clinical specimens. We compared the clinical outcomes by Kaplan-Meier survival analyses and assessed the prognostic value of Dot1l expression. Harrell's concordance index (C-index) was used to assess the predictive accuracy of different prognostic models. RESULTS Higher Dot1l expression indicated poorer OS (P<0.001) and RFS (P<0.001) in patients with ccRCC. Moreover, Dot1l expression could stratify ccRCC patients in pT stage, Fuhrman grade and SSIGN/ Leibovich subgroups, which might redefine individual risk stratification. Multivariate analyses further indicated that Dot1l expression was an independent prognostic factor for OS (P=0.007) and RFS (P=0.001). The prognostic accuracy of conventional prognostic models was notably improved with Dot1l integration. Two nomograms and calibration plots were built to predict OS and RFS for patients with ccRCC and performed better based on C-index value. CONCLUSION Dot1l expression is a promising independent prognostic indicator for postoperative recurrence and survival of patients with ccRCC.
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Affiliation(s)
- Yang Qu
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Li Liu
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jiajun Wang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Wei Xi
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yu Xia
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Qi Bai
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Ying Xiong
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Qilai Long
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jiejie Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jianming Guo
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
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Pruitt K. Molecular and Cellular Changes During Cancer Progression Resulting From Genetic and Epigenetic Alterations. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2016; 144:3-47. [PMID: 27865461 DOI: 10.1016/bs.pmbts.2016.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Tumorigenesis is a complex process that involves a persistent dismantling of cellular safeguards and checkpoints. These molecular and cellular changes that accumulate over months or decades lead to a change in the fundamental identity of a cell as it transitions from normal to malignant. In this chapter, we will examine some of the molecular changes in the evolving relationship between the genome and epigenome and highlight some of the key changes that occur as normal cells progress to tumor cells. For many years tumorigenesis was almost exclusively attributed to mutations in protein-coding genes. This notion that mutations in protein-coding genes were a fundamental driver of tumorigenesis enabled the development of several novel therapeutics that targeted the mutant protein or overactive pathway responsible for driving a significant portion of the tumor growth. However, because many therapeutic challenges remained in the face of these advances, it was clear that other pieces to the puzzle had yet to be discovered. Advances in molecular and genomics techniques continued and the study of epigenetics began to expand and helped reshape the view that drivers of tumorigenesis extended beyond mutations in protein-coding genes. Studies in the field of epigenetics began to identify aberrant epigenetic marks which created altered chromatin structures and enabled protein expression in tissues that defied rules governing tissue-specificity. Not only were epigenetic alterations found to enable overexpression of proto-oncogenes, they also led to the silencing of tumor suppressor genes. With these discoveries, it became clear that tumor growth could be stimulated by much more than mutations in protein-coding genes. In fact, it became increasingly clear that much of the human genome, while transcribed, did not lead to proteins. This discovery further led to studies that began to uncover the role of noncoding RNAs in regulating chromatin structure, gene transcription, and tumor biology. In this chapter, some of the key alterations in the genome and epigenome will be explored, and some of the cancer therapies that were developed as a result of these discoveries will be discussed.
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Affiliation(s)
- K Pruitt
- Texas Tech University Health Sciences Center, Lubbock, TX, United States.
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141
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Liu Q, Wang MW. Histone lysine methyltransferases as anti-cancer targets for drug discovery. Acta Pharmacol Sin 2016; 37:1273-1280. [PMID: 27397541 DOI: 10.1038/aps.2016.64] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 05/03/2016] [Indexed: 12/22/2022] Open
Abstract
Post-translational epigenetic modification of histones is controlled by a number of histone-modifying enzymes. Such modification regulates the accessibility of DNA and the subsequent expression or silencing of a gene. Human histone methyltransferases (HMTs)constitute a large family that includes histone lysine methyltransferases (HKMTs) and histone/protein arginine methyltransferases (PRMTs). There is increasing evidence showing a correlation between HKMTs and cancer pathogenesis. Here, we present an overview of representative HKMTs, including their biological and biochemical properties as well as the profiles of small molecule inhibitors for a comprehensive understanding of HKMTs in drug discovery.
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142
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Schapira M. Chemical Inhibition of Protein Methyltransferases. Cell Chem Biol 2016; 23:1067-1076. [PMID: 27569753 DOI: 10.1016/j.chembiol.2016.07.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/08/2016] [Accepted: 07/15/2016] [Indexed: 01/16/2023]
Abstract
Protein methyltransferases (PMTs) participate in the epigenetic control of cell fate and other signaling pathways that are deregulated in disease, and the first PMT inhibitors have entered clinical trials in oncology. This review discusses structural studies that recently uncovered the mode of action of compounds in the clinic, as well as challenges and opportunities in the development of PMT inhibitors. It examines inhibitors that compete with the highly polar cofactor but preserve cell penetrance, and allosteric modes of inhibition. Vectors of optimization at the substrate-binding site and the potential of fragment screening approaches are discussed. Finally, the review presents strategies focused on targeting non-catalytic domains of PMTs or scaffolding subunits of chromatin complexes. Overall, although targeting PMTs remains a challenge, recent successes in the field are diverse and encouraging.
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Affiliation(s)
- Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada.
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143
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Chen C, Zhu H, Stauffer F, Caravatti G, Vollmer S, Machauer R, Holzer P, Möbitz H, Scheufler C, Klumpp M, Tiedt R, Beyer KS, Calkins K, Guthy D, Kiffe M, Zhang J, Gaul C. Discovery of Novel Dot1L Inhibitors through a Structure-Based Fragmentation Approach. ACS Med Chem Lett 2016; 7:735-40. [PMID: 27563395 DOI: 10.1021/acsmedchemlett.6b00167] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 06/01/2016] [Indexed: 11/30/2022] Open
Abstract
Oncogenic MLL fusion proteins aberrantly recruit Dot1L, a histone methyltransferase, to ectopic loci, leading to local hypermethylation of H3K79 and misexpression of HoxA genes driving MLL-rearranged leukemias. Inhibition of the methyltransferase activity of Dot1L in this setting is predicted to reverse aberrant H3K79 methylation, leading to repression of leukemogenic genes and tumor growth inhibition. In the context of our Dot1L drug discovery program, high-throughput screening led to the identification of 2, a weak Dot1L inhibitor with an unprecedented, induced pocket binding mode. A medicinal chemistry campaign, strongly guided by structure-based consideration and ligand-based morphing, enabled the discovery of 12 and 13, potent, selective, and structurally completely novel Dot1L inhibitors.
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Affiliation(s)
- Chao Chen
- Novartis Institutes for Biomedical Research, Shanghai 201203, China
| | - Hugh Zhu
- Novartis Institutes for Biomedical Research, Shanghai 201203, China
| | - Frédéric Stauffer
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Giorgio Caravatti
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Susanne Vollmer
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Rainer Machauer
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Philipp Holzer
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Henrik Möbitz
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Clemens Scheufler
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Martin Klumpp
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Ralph Tiedt
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Kim S. Beyer
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Keith Calkins
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Daniel Guthy
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Michael Kiffe
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Jeff Zhang
- Novartis Institutes for Biomedical Research, Shanghai 201203, China
| | - Christoph Gaul
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
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144
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Scheufler C, Möbitz H, Gaul C, Ragot C, Be C, Fernández C, Beyer KS, Tiedt R, Stauffer F. Optimization of a Fragment-Based Screening Hit toward Potent DOT1L Inhibitors Interacting in an Induced Binding Pocket. ACS Med Chem Lett 2016; 7:730-4. [PMID: 27563394 DOI: 10.1021/acsmedchemlett.6b00168] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 06/01/2016] [Indexed: 12/15/2022] Open
Abstract
Mixed lineage leukemia (MLL) gene rearrangement induces leukemic transformation by ectopic recruitment of disruptor of telomeric silencing 1-like protein (DOT1L), a lysine histone methyltransferase, leading to local hypermethylation of H3K79 and misexpression of genes (including HoxA), which drive the leukemic phenotype. A weak fragment-based screening hit identified by SPR was cocrystallized with DOT1L and optimized using structure-based ligand optimization to yield compound 8 (IC50 = 14 nM). This series of inhibitors is structurally not related to cofactor SAM and is not interacting within the SAM binding pocket but induces a pocket adjacent to the SAM binding site.
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Affiliation(s)
- Clemens Scheufler
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Henrik Möbitz
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Christoph Gaul
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Christian Ragot
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Céline Be
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - César Fernández
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Kim S. Beyer
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Ralph Tiedt
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Frédéric Stauffer
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
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145
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Abeykoon AH, Noinaj N, Choi BE, Wise L, He Y, Chao CC, Wang G, Gucek M, Ching WM, Chock PB, Buchanan SK, Yang DCH. Structural Insights into Substrate Recognition and Catalysis in Outer Membrane Protein B (OmpB) by Protein-lysine Methyltransferases from Rickettsia. J Biol Chem 2016; 291:19962-74. [PMID: 27474738 DOI: 10.1074/jbc.m116.723460] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Indexed: 11/06/2022] Open
Abstract
Rickettsia belong to a family of Gram-negative obligate intracellular infectious bacteria that are the causative agents of typhus and spotted fever. Outer membrane protein B (OmpB) occurs in all rickettsial species, serves as a protective envelope, mediates host cell adhesion and invasion, and is a major immunodominant antigen. OmpBs from virulent strains contain multiple trimethylated lysine residues, whereas the avirulent strain contains mainly monomethyllysine. Two protein-lysine methyltransferases (PKMTs) that catalyze methylation of recombinant OmpB at multiple sites with varying sequences have been identified and overexpressed. PKMT1 catalyzes predominantly monomethylation, whereas PKMT2 catalyzes mainly trimethylation. Rickettsial PKMT1 and PKMT2 are unusual in that their primary substrate appears to be limited to OmpB, and both are capable of methylating multiple lysyl residues with broad sequence specificity. Here we report the crystal structures of PKMT1 from Rickettsia prowazekii and PKMT2 from Rickettsia typhi, both the apo form and in complex with its cofactor S-adenosylmethionine or S-adenosylhomocysteine. The structure of PKMT1 in complex with S-adenosylhomocysteine is solved to a resolution of 1.9 Å. Both enzymes are dimeric with each monomer containing an S-adenosylmethionine binding domain with a core Rossmann fold, a dimerization domain, a middle domain, a C-terminal domain, and a centrally located open cavity. Based on the crystal structures, residues involved in catalysis, cofactor binding, and substrate interactions were examined using site-directed mutagenesis followed by steady state kinetic analysis to ascertain their catalytic functions in solution. Together, our data reveal new structural and mechanistic insights into how rickettsial methyltransferases catalyze OmpB methylation.
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Affiliation(s)
- Amila H Abeykoon
- From the Department of Chemistry, Georgetown University, Washington, D. C. 20057
| | - Nicholas Noinaj
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907,
| | - Bok-Eum Choi
- From the Department of Chemistry, Georgetown University, Washington, D. C. 20057
| | - Lindsay Wise
- From the Department of Chemistry, Georgetown University, Washington, D. C. 20057
| | - Yi He
- Laboratory of Biochemistry and
| | - Chien-Chung Chao
- Viral and Rickettsial Diseases Department, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, Maryland 20910
| | | | | | - Wei-Mei Ching
- Viral and Rickettsial Diseases Department, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, Maryland 20910
| | | | - Susan K Buchanan
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, and
| | - David C H Yang
- From the Department of Chemistry, Georgetown University, Washington, D. C. 20057,
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146
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Luo M, Wang H, Zou Y, Zhang S, Xiao J, Jiang G, Zhang Y, Lai Y. Identification of phenoxyacetamide derivatives as novel DOT1L inhibitors via docking screening and molecular dynamics simulation. J Mol Graph Model 2016; 68:128-139. [PMID: 27434826 DOI: 10.1016/j.jmgm.2016.06.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/16/2016] [Accepted: 06/17/2016] [Indexed: 10/21/2022]
Abstract
Dot1-like protein (DOT1L) is a histone methyltransferase that has become a novel and promising target for acute leukemias bearing mixed lineage leukemia (MLL) gene rearrangements. In this study, a hierarchical docking-based virtual screening combined with molecular dynamic (MD) simulation was performed to identify DOT1L inhibitors with novel scaffolds. Consequently, 8 top-ranked hits were eventually identified and were further subjected to MD simulation. It was indicated that all hits could reach equilibrium with DOT1L in the MD simulation and further binding free energy calculations suggested that phenoxyacetamide-derived hits such as L01, L03, L04 and L05 exhibited remarkably higher binding affinity compared to other hits. Among them, L03 showed both the lowest glide score (-12.281) and the most favorable binding free energy (-303.9+/-16.5kJ/mol), thereby making it a promising lead for further optimization.
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Affiliation(s)
- Minghao Luo
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, China
| | - Hui Wang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, China
| | - Yi Zou
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, China
| | - Shengping Zhang
- School of Chemical Sciences, The University of Auckland, 23 Symonds St., Auckland 1142, New Zealand
| | - Jianhu Xiao
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, China
| | - Guangde Jiang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1345 Center Drive, Gainesville, FL 32610, USA
| | - Yihua Zhang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, China
| | - Yisheng Lai
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, China.
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147
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Song Y, Wu F, Wu J. Targeting histone methylation for cancer therapy: enzymes, inhibitors, biological activity and perspectives. J Hematol Oncol 2016; 9:49. [PMID: 27316347 PMCID: PMC4912745 DOI: 10.1186/s13045-016-0279-9] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/07/2016] [Indexed: 12/31/2022] Open
Abstract
Post-translational methylation of histone lysine or arginine residues plays important roles in gene regulation and other physiological processes. Aberrant histone methylation caused by a gene mutation, translocation, or overexpression can often lead to initiation of a disease such as cancer. Small molecule inhibitors of such histone modifying enzymes that correct the abnormal methylation could be used as novel therapeutics for these diseases, or as chemical probes for investigation of epigenetics. Discovery and development of histone methylation modulators are in an early stage and undergo a rapid expansion in the past few years. A number of highly potent and selective compounds have been reported, together with extensive preclinical studies of their biological activity. Several compounds have been in clinical trials for safety, pharmacokinetics, and efficacy, targeting several types of cancer. This review summarizes the biochemistry, structures, and biology of cancer-relevant histone methylation modifying enzymes, small molecule inhibitors and their preclinical and clinical antitumor activities. Perspectives for targeting histone methylation for cancer therapy are also discussed.
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Affiliation(s)
- Yongcheng Song
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA. .,Dan L. Duncan Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
| | - Fangrui Wu
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Jingyu Wu
- Department of Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
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148
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Mechanisms of histone lysine-modifying enzymes: A computational perspective on the role of the protein environment. J Mol Graph Model 2016; 67:69-84. [DOI: 10.1016/j.jmgm.2016.04.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/28/2016] [Accepted: 04/29/2016] [Indexed: 12/13/2022]
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149
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Morera L, Lübbert M, Jung M. Targeting histone methyltransferases and demethylases in clinical trials for cancer therapy. Clin Epigenetics 2016; 8:57. [PMID: 27222667 PMCID: PMC4877953 DOI: 10.1186/s13148-016-0223-4] [Citation(s) in RCA: 279] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/04/2016] [Indexed: 12/13/2022] Open
Abstract
The term epigenetics is defined as heritable changes in gene expression that are not due to alterations of the DNA sequence. In the last years, it has become more and more evident that dysregulated epigenetic regulatory processes have a central role in cancer onset and progression. In contrast to DNA mutations, epigenetic modifications are reversible and, hence, suitable for pharmacological interventions. Reversible histone methylation is an important process within epigenetic regulation, and the investigation of its role in cancer has led to the identification of lysine methyltransferases and demethylases as promising targets for new anticancer drugs. In this review, we describe those enzymes and their inhibitors that have already reached the first stages of clinical trials in cancer therapy, namely the histone methyltransferases DOT1L and EZH2 as well as the demethylase LSD1.
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Affiliation(s)
- Ludovica Morera
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Michael Lübbert
- Department of Hematology and Oncology, University of Freiburg Medical Center, Hugstetter Straße 55, 79106 Freiburg, Germany ; German Cancer Consortium (DKTK), Freiburg, Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, Albertstraße 25, 79104 Freiburg, Germany ; German Cancer Consortium (DKTK), Freiburg, Germany
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150
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Wang X, Chen CW, Armstrong SA. The role of DOT1L in the maintenance of leukemia gene expression. Curr Opin Genet Dev 2016; 36:68-72. [PMID: 27151433 DOI: 10.1016/j.gde.2016.03.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 03/31/2016] [Indexed: 12/15/2022]
Abstract
Chromatin based (Epigenetic) mechanisms have been shown to play important roles in the regulation of gene expression during tumorigenesis and development. Mouse modeling suggests the methyltransferase DOT1L as a potential therapeutic target for MLL-rearranged leukemia. Epigenomic profiling indicates an abnormal H3K79me2 pattern on MLL-fusion targeted genes, but the molecular mechanism underlying this epigenetic dependency is not well understood. In this review, we will discuss recent advances in understanding the epigenetic mechanisms governed by DOT1L in the maintenance of gene expression. We will highlight the structural basis of chromatin targeting of DOT1L through its cofactors and the role of DOT1L in repelling transcription repressive complexes during leukemia development.
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Affiliation(s)
- Xi Wang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Chun-Wei Chen
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott A Armstrong
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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