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Wang Y, Hong Q, Xia Y, Zhang Z, Wen B. The Lysine Demethylase KDM7A Regulates Immediate Early Genes in Neurons. Adv Sci (Weinh) 2023; 10:e2301367. [PMID: 37565374 PMCID: PMC10558696 DOI: 10.1002/advs.202301367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 07/11/2023] [Indexed: 08/12/2023]
Abstract
Lysine demethylase KDM7A removes histone modifications H3K9me1/2 and H3K27me1/2. KDM7A plays critical roles in gene expression and contribute to biological processes including tumorigenesis, metabolism, and embryonic development. However, the functions of KDM7A in mammalian nervous system are still poorly explored. In this study, functional roles of KDM7A are comprehensively investigated in neuronal cells by applying CUT&Tag-seq, RNA-seq and mice models. Knockdown of Kdm7a in N2A cells result in the alteration of histone modifications near transcription start sites (TSSs) and the expression changes of a large number of genes. In particular, the expression of immediate early genes (IEGs), a series of genes maintaining the function of the nervous system and associating with neurological disorders, are significantly decreased upon Kdm7a knockdown. Furthermore, in vivo knockdown of Kdm7a in dentate gyrus (DG) neuron of mice hippocampus, via Adeno-associated virus (AAV)-based stereotaxic microinjection, led to a significant decrease of the expression of c-Fos, a marker of neuron activity. Behavior assays in mice further revealed that Kdm7a knockdown in hippocampus repress neuron activity, which leading to impairment of emotion and memory. Collectively, the study reveals that KDM7A affects neuron functions by regulating IEGs, which may provide new clues for understanding epigenetic mechanisms in neurological disorders.
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Affiliation(s)
- Yifan Wang
- Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan University200032130 Dong An RoadShanghaiChina
| | - Qin Hong
- Shengli Clinical Medical College of Fujian Medical University, Center for Experimental Research in Clinical MedicineFujian Provincial Hospital134 East StreetFuzhou350001China
| | - Yueyue Xia
- Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan University200032130 Dong An RoadShanghaiChina
| | - Zhao Zhang
- Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan University200032130 Dong An RoadShanghaiChina
| | - Bo Wen
- Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan University200032130 Dong An RoadShanghaiChina
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2
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Jaber Sathik Rifayee SB, Chaturvedi SS, Warner C, Wildey J, White W, Thompson M, Schofield CJ, Christov CZ. Catalysis by KDM6 Histone Demethylases - A Synergy between the Non-Heme Iron(II) Center, Second Coordination Sphere, and Long-Range Interactions. Chemistry 2023; 29:e202301305. [PMID: 37258457 PMCID: PMC10526731 DOI: 10.1002/chem.202301305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/02/2023]
Abstract
KDM6A (UTX) and KDM6B (JMJD3) are human non-heme Fe(II) and 2-oxoglutarate (2OG) dependent JmjC oxygenases that catalyze the demethylation of trimethylated lysine 27 in the N-terminal tail of histone H3, a post-translational modification that regulates transcription. A Combined Quantum Mechanics/ Molecular Mechanics (QM/MM) and Molecular Dynamics (MD) study on the catalytic mechanism of KDM6A/B reveals that the transition state for the rate-limiting hydrogen atom transfer (HAT) reaction in KDM6A catalysis is stabilized by polar (Asn217) and aromatic (Trp369)/non-polar (Pro274) residues in contrast to KDM4, KDM6B and KDM7 demethylases where charged residues (Glu, Arg, Asp) are involved. KDM6A employs both σ- and π-electron transfer pathways for HAT, whereas KDM6B employs the σ-electron pathway. Differences in hydrogen bonding of the Fe-chelating Glu252(KDM6B) contribute to the lower energy barriers in KDM6B vs. KDM6A. The study reveals a dependence of the activation barrier of the rebound hydroxylation on the Fe-O-C angle in the transition state of KDM6A. Anti-correlation of the Zn-binding domain with the active site residues is a key factor distinguishing KDM6A/B from KDM7/4s. The results reveal the importance of communication between the Fe center, second coordination sphere, and long-range interactions in catalysis by KDMs and, by implication, other 2OG oxygenases.
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Affiliation(s)
| | | | - Cait Warner
- Department of Biological Sciences, Michigan Technological University, Houghton, MI-49931, USA
| | - Jon Wildey
- Department of Chemical Engineering, Michigan Technological University, Houghton, MI-49931, USA
| | - Walter White
- Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
| | - Martin Thompson
- Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
| | - Christopher J. Schofield
- Chemistry Research laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, OX1 3TA, United Kingdom
| | - Christo Z. Christov
- Department of Chemistry, Michigan Technological University, Houghton, MI-49931, USA
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3
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Srivastava R, Singh R, Jauhari S, Lodhi N, Srivastava R. Histone Demethylase Modulation: Epigenetic Strategy to Combat Cancer Progression. Epigenomes 2023; 7:epigenomes7020010. [PMID: 37218871 DOI: 10.3390/epigenomes7020010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/24/2023] Open
Abstract
Epigenetic modifications are heritable, reversible changes in histones or the DNA that control gene functions, being exogenous to the genomic sequence itself. Human diseases, particularly cancer, are frequently connected to epigenetic dysregulations. One of them is histone methylation, which is a dynamically reversible and synchronously regulated process that orchestrates the three-dimensional epigenome, nuclear processes of transcription, DNA repair, cell cycle, and epigenetic functions, by adding or removing methylation groups to histones. Over the past few years, reversible histone methylation has become recognized as a crucial regulatory mechanism for the epigenome. With the development of numerous medications that target epigenetic regulators, epigenome-targeted therapy has been used in the treatment of malignancies and has shown meaningful therapeutic potential in preclinical and clinical trials. The present review focuses on the recent advances in our knowledge on the role of histone demethylases in tumor development and modulation, in emphasizing molecular mechanisms that control cancer cell progression. Finally, we emphasize current developments in the advent of new molecular inhibitors that target histone demethylases to regulate cancer progression.
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Affiliation(s)
- Rashmi Srivastava
- Department of Zoology, Babasaheb Bhimrao Ambedkar University, Lucknow 226025, Uttar Pradesh, India
| | - Rubi Singh
- Department of Hematology, Bioreference Laboratories, Elmwood Park, NJ 07407, USA
| | - Shaurya Jauhari
- Division of Education, Training, and Assessment, Global Education Center, Infosys Limited, Mysuru 570027, Karnataka, India
| | - Niraj Lodhi
- Clinical Research (Research and Development Division) Mirna Analytics LLC, Harlem Bio-Space, New York, NY 10027, USA
| | - Rakesh Srivastava
- Molecular Biology and Microbiology, GenTox Research and Development, Lucknow 226001, Uttar Pradesh, India
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Noce B, Di Bello E, Fioravanti R, Mai A. LSD1 inhibitors for cancer treatment: Focus on multi-target agents and compounds in clinical trials. Front Pharmacol 2023; 14:1120911. [PMID: 36817147 PMCID: PMC9932783 DOI: 10.3389/fphar.2023.1120911] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 01/20/2023] [Indexed: 02/05/2023] Open
Abstract
Histone lysine-specific demethylase 1 (LSD1/KDM1A) was first identified in 2004 as an epigenetic enzyme able to demethylate specific lysine residues of histone H3, namely H3K4me1/2 and H3K9me1/2, using FAD as the cofactor. It is ubiquitously overexpressed in many types of cancers (breast, gastric, prostate, hepatocellular, and esophageal cancer, acute myeloid leukemia, and others) leading to block of differentiation and increase of proliferation, migration and invasiveness at cellular level. LSD1 inhibitors can be grouped in covalent and non-covalent agents. Each group includes some hybrid compounds, able to inhibit LSD1 in addition to other target(s) at the same time (dual or multitargeting compounds). To date, 9 LSD1 inhibitors have entered clinical trials, for hematological and/or solid cancers. Seven of them (tranylcypromine, iadademstat (ORY-1001), bomedemstat (IMG-7289), GSK-2879552, INCB059872, JBI-802, and Phenelzine) covalently bind the FAD cofactor, and two are non-covalent LSD1 inhibitors [pulrodemstat (CC-90011) and seclidemstat (SP-2577)]. Another TCP-based LSD1/MAO-B dual inhibitor, vafidemstat (ORY-2001), is in clinical trial for Alzheimer's diseases and personality disorders. The present review summarizes the structure and functions of LSD1, its pathological implications in cancer and non-cancer diseases, and the identification of LSD1 covalent and non-covalent inhibitors with different chemical scaffolds, including those involved in clinical trials, highlighting their potential as potent and selective anticancer agents.
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Affiliation(s)
- Beatrice Noce
- Department of Chemistry and Technology of Drugs, Sapienza University of Rome, Rome, Italy
| | - Elisabetta Di Bello
- Department of Chemistry and Technology of Drugs, Sapienza University of Rome, Rome, Italy
| | - Rossella Fioravanti
- Department of Chemistry and Technology of Drugs, Sapienza University of Rome, Rome, Italy,*Correspondence: Rossella Fioravanti,
| | - Antonello Mai
- Department of Chemistry and Technology of Drugs, Sapienza University of Rome, Rome, Italy,Pasteur Institute, Cenci-Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
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Ojaimi MA, Banimortada BJ, Othman A, Riedhammer KM, Almannai M, El-Hattab AW. Disorders of histone methylation: molecular basis and clinical syndromes. Clin Genet 2022; 102:169-181. [PMID: 35713103 DOI: 10.1111/cge.14181] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 12/01/2022]
Abstract
Epigenetic modifications of DNA and histone tails are essential for gene expression regulation. They play an essential role in neurodevelopment as nervous system development is a complex process requiring a dynamic pattern of gene expression. Histone methylation is one of the vital epigenetic regulators and mostly occurs on lysine residues of histones H3 and H4. Histone methylation is catalyzed by two sets of enzymes: histone lysine methyltransferases (KMTs) and histone lysine demethylases (KDMs). KMT2 enzymes form a distinct multi-subunit complex known as COMPASS to enhance their catalytic activity and diversify their biologic functions. Several neurodevelopmental syndromes result from defects of histone methylation which can be caused by deficiencies in histone methyltransferases and demethylases, loss of the histone methyltransferase activator TASP1, or derangements in COMPASS formation. In this review article, the molecular mechanism of histone methylation is discussed followed by summarizing clinical syndromes caused by monogenic defects in histone methylation.
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Affiliation(s)
- Mode Al Ojaimi
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | | | - Amna Othman
- Genetics and Genomic Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Korbinian M Riedhammer
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Nephrology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Mohammed Almannai
- Genetics and Precision Medicine Department, King Abdullah Specialized Children's Hospital, Riyadh, Saudi Arabia
| | - Ayman W El-Hattab
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates.,Pediatrics Department, University Hospital Sharjah, Sharjah, United Arab Emirates.,Genetics and Metabolic Department, KidsHeart Medical Center, Abu Dhabi, United Arab Emirates
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6
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Yang J, Hu Y, Zhang B, Liang X, Li X. The JMJD Family Histone Demethylases in Crosstalk Between Inflammation and Cancer. Front Immunol 2022; 13:881396. [PMID: 35558079 PMCID: PMC9090529 DOI: 10.3389/fimmu.2022.881396] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/23/2022] [Indexed: 02/05/2023] Open
Abstract
Inflammation has emerged as a key player in regulating cancer initiation, progression, and therapeutics, acting as a double edged sword either facilitating cancer progression and therapeutic resistance or inducing anti-tumor immune responses. Accumulating evidence has linked the epigenetic modifications of histones to inflammation and cancer, and histone modifications-based strategies have shown promising therapeutic potentials against cancer. The jumonji C domain-containing (JMJD) family histone demethylases have exhibited multiple regulator functions in inflammatory processes and cancer development, and a number of therapeutic strategies targeting JMJD histone demethylases to modulate inflammatory cells and their products have been successfully evaluated in clinical or preclinical tumor models. This review summarizes current understanding of the functional roles and mechanisms of JMJD histone demethylases in crosstalk between inflammation and cancer, and highlights recent clinical and preclinical progress on harnessing the JMJD histone demethylases to regulate cancer-related inflammation for future cancer therapeutics.
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Affiliation(s)
- Jia Yang
- Department of Gynecology and Obstetrics and Pediatric Nephrology Nursing, Development and Related Disease of Women and Children Key Laboratory of Sichuan Province, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second Hospital, Sichuan University, Chengdu, China
| | - Yuan Hu
- Department of Gynecology and Obstetrics and Pediatric Nephrology Nursing, Development and Related Disease of Women and Children Key Laboratory of Sichuan Province, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second Hospital, Sichuan University, Chengdu, China
| | - Binjing Zhang
- State Key Laboratory of Oral Disease, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xiao Liang
- Department of Gynecology and Obstetrics and Pediatric Nephrology Nursing, Development and Related Disease of Women and Children Key Laboratory of Sichuan Province, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second Hospital, Sichuan University, Chengdu, China
| | - Xin Li
- State Key Laboratory of Oral Disease, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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Yang Y, Luan Y, Feng Q, Chen X, Qin B, Ren KD, Luan Y. Epigenetics and Beyond: Targeting Histone Methylation to Treat Type 2 Diabetes Mellitus. Front Pharmacol 2022; 12:807413. [PMID: 35087408 PMCID: PMC8788853 DOI: 10.3389/fphar.2021.807413] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/24/2021] [Indexed: 12/30/2022] Open
Abstract
Diabetes mellitus is a global public health challenge with high morbidity. Type 2 diabetes mellitus (T2DM) accounts for 90% of the global prevalence of diabetes. T2DM is featured by a combination of defective insulin secretion by pancreatic β-cells and the inability of insulin-sensitive tissues to respond appropriately to insulin. However, the pathogenesis of this disease is complicated by genetic and environmental factors, which needs further study. Numerous studies have demonstrated an epigenetic influence on the course of this disease via altering the expression of downstream diabetes-related proteins. Further studies in the field of epigenetics can help to elucidate the mechanisms and identify appropriate treatments. Histone methylation is defined as a common histone mark by adding a methyl group (-CH3) onto a lysine or arginine residue, which can alter the expression of downstream proteins and affect cellular processes. Thus, in tthis study will discuss types and functions of histone methylation and its role in T2DM wilsed. We will review the involvement of histone methyltransferases and histone demethylases in the progression of T2DM and analyze epigenetic-based therapies. We will also discuss the potential application of histone methylation modification as targets for the treatment of T2DM.
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Affiliation(s)
- Yang Yang
- Department of Translational Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Luan
- Department of Physiology and Neurobiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Qi Feng
- Research Institute of Nephrology, Zhengzhou University, Zhengzhou, China
| | - Xing Chen
- Department of Translational Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Bo Qin
- Department of Translational Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Kai-Di Ren
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, China
| | - Yi Luan
- Department of Translational Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Fang H, Shao Y, Wu G. Reprogramming of Histone H3 Lysine Methylation During Plant Sexual Reproduction. Front Plant Sci 2021; 12:782450. [PMID: 34917115 PMCID: PMC8669150 DOI: 10.3389/fpls.2021.782450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/08/2021] [Indexed: 06/14/2023]
Abstract
Plants undergo extensive reprogramming of chromatin status during sexual reproduction, a process vital to cell specification and pluri- or totipotency establishment. As a crucial way to regulate chromatin organization and transcriptional activity, histone modification can be reprogrammed during sporogenesis, gametogenesis, and embryogenesis in flowering plants. In this review, we first introduce enzymes required for writing, recognizing, and removing methylation marks on lysine residues in histone H3 tails, and describe their differential expression patterns in reproductive tissues, then we summarize their functions in the reprogramming of H3 lysine methylation and the corresponding chromatin re-organization during sexual reproduction in Arabidopsis, and finally we discuss the molecular significance of histone reprogramming in maintaining the pluri- or totipotency of gametes and the zygote, and in establishing novel cell fates throughout the plant life cycle. Despite rapid achievements in understanding the molecular mechanism and function of the reprogramming of chromatin status in plant development, the research in this area still remains a challenge. Technological breakthroughs in cell-specific epigenomic profiling in the future will ultimately provide a solution for this challenge.
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Zaghet N, Madsen K, Rossi F, Perez DF, Amendola PG, Demharter S, Pfisterer U, Khodosevich K, Pasini D, Salcini AE. Coordinated maintenance of H3K36/K27 methylation by histone demethylases preserves germ cell identity and immortality. Cell Rep 2021; 37:110050. [PMID: 34818537 PMCID: PMC8640224 DOI: 10.1016/j.celrep.2021.110050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 09/18/2021] [Accepted: 11/02/2021] [Indexed: 12/01/2022] Open
Abstract
Germ cells have evolved unique mechanisms to ensure the transmission of genetically and nongenetically encoded information, whose alteration compromises germ cell immortality. Chromatin factors play fundamental roles in these mechanisms. H3K36 and H3K27 methyltransferases shape and propagate a pattern of histone methylation essential for C. elegans germ cell maintenance, but the role of respective histone demethylases remains unexplored. Here, we show that jmjd-5 regulates H3K36me2 and H3K27me3 levels, preserves germline immortality, and protects germ cell identity by controlling gene expression. The transcriptional and biological effects of jmjd-5 loss can be hindered by the removal of H3K27demethylases, indicating that H3K36/K27 demethylases act in a transcriptional framework and promote the balance between H3K36 and H3K27 methylation required for germ cell immortality. Furthermore, we find that in wild-type, but not in jmjd-5 mutants, alterations of H3K36 methylation and transcription occur at high temperature, suggesting a role for jmjd-5 in adaptation to environmental changes. jmjd-5 is required for germ cell immortality at high temperature jmjd-5 sustains the expression of germline genes and represses somatic fate Mutations in jmjd-5 result in a global increase of H3K36me2 and H3K27me3 Ablation of H3K27 demethylases counteracts the effects of jmjd-5 mutations
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Affiliation(s)
- Nico Zaghet
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Katrine Madsen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Federico Rossi
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Daniel Fernandez Perez
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Pier Giorgio Amendola
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Samuel Demharter
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Ulrich Pfisterer
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Konstantin Khodosevich
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Diego Pasini
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy; Department of Health Sciences, University of Milan, Via A. di Rudini 8, 20142 Milan, Italy
| | - Anna Elisabetta Salcini
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark.
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Jamshidi S, Catchpole S, Chen J, So CWE, Burchell J, Rahman KM, Taylor-Papadimitriou J. KDM5B protein expressed in viable and fertile ΔARID mice exhibit no demethylase activity. Int J Oncol 2021; 59:96. [PMID: 34713299 PMCID: PMC8562390 DOI: 10.3892/ijo.2021.5276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 08/09/2021] [Indexed: 12/18/2022] Open
Abstract
Post‑translational modification of histones serve a crucial role in the control of gene transcription. Trimethylation of lysine 4 on histone 3 is associated with transcription activation. There are currently six known methylases and six known demethylases that can control the methylation status of this site. Lysine demethylase 5B (KDM5B) is one such demethylase, which can repress gene expression. In particular KDM5B has been found to be overexpressed in a number of cancer types, and small‑molecular weight inhibitors of its demethylase activity have been identified. Previous characterisation of Kdm5b knock‑out mice has revealed that this genotype leads to either embryonic or neonatal lethality. However, the ΔA‑T rich interaction domain (ΔARID)‑KDM5B strain of mice, which have the ARID domain and five amino acids within the Jumonji (Jmj)N domain spliced out from KDM5B, remain viable and fertile. In the present study, ΔARID‑KDM5B was found to have no demethylase activity as determined by in vitro demethylase assays and by immunofluorescence in transfected Cos‑1 cells. Furthermore, molecular dynamic simulations revealed conformational changes within the ΔARID‑KDM5B structure compared with that in WT‑KDM5B, particularly in the JmjC domain, which is responsible for the catalytic activity of WT‑KDM5B. This supports the experimental data that shows the loss of demethylase activity. Since Kdm5b knock‑out mice show varying degrees of lethality, these data suggest that KDM5B serves a crucial function in development in a manner that is independent of its demethylase activity.
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Affiliation(s)
- Shirin Jamshidi
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 9NN, UK
| | - Steven Catchpole
- Breast Cancer Biology, Innovation Hub, School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Cancer Centre, Guy's Hospital, London SE1 9RT, UK
| | - Jie Chen
- Leukaemia and Stem Cell Biology Group, School of Cancer and Pharmaceutical Sciences, Denmark Hill Campus, King's College London, London SE5 9RJ, UK
| | - Chi Wai Eric So
- Leukaemia and Stem Cell Biology Group, School of Cancer and Pharmaceutical Sciences, Denmark Hill Campus, King's College London, London SE5 9RJ, UK
| | - Joy Burchell
- Breast Cancer Biology, Innovation Hub, School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Cancer Centre, Guy's Hospital, London SE1 9RT, UK
| | - Khondaker Miraz Rahman
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 9NN, UK
| | - Joyce Taylor-Papadimitriou
- Breast Cancer Biology, Innovation Hub, School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Cancer Centre, Guy's Hospital, London SE1 9RT, UK
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11
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Teresa Borrello M, Benelkebir H, Lee A, Hin Tam C, Shafat M, Rushworth SA, Bowles KM, Douglas L, Duriez PJ, Bailey S, Crabb SJ, Packham G, Ganesan A. Synthesis of Carboxamide-Containing Tranylcypromine Analogues as LSD1 (KDM1A) Inhibitors Targeting Acute Myeloid Leukemia. ChemMedChem 2021; 16:1316-1324. [PMID: 33533576 DOI: 10.1002/cmdc.202000754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/18/2020] [Indexed: 01/14/2023]
Abstract
Lysine-specific demethylase 1 (LSD1/KDM1A) oxidatively removes methyl groups from histone proteins, and its aberrant activity has been correlated with cancers including acute myeloid leukemia (AML). We report a novel series of tranylcypromine analogues with a carboxamide at the 4-position of the aryl ring. These compounds, such as 5 a and 5 b with benzyl and phenethylamide substituents, respectively, had potent sub-micromolar IC50 values for the inhibition of LSD1 as well as cell proliferation in a panel of AML cell lines. The dose-dependent increase in cellular expression levels of H3K4me2, CD86, CD11b and CD14 supported a mechanism involving LSD1 inhibition. The tert-butyl and ethyl carbamate derivatives of these tranylcypromines, although inactive in LSD1 inhibition, were of similar potency in cell-based assays with a more rapid onset of action. This suggests that carbamates can act as metabolically labile tranylcypromine prodrugs with superior pharmacokinetics.
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Affiliation(s)
| | - Hanae Benelkebir
- School of Pharmacy, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Adam Lee
- School of Pharmacy, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Chak Hin Tam
- School of Pharmacy, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Manar Shafat
- Norwich Medical School, University of East Anglia, Norwich, NR4 7TJ, UK
| | | | - Kristian M Bowles
- Norwich Medical School, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Leon Douglas
- Protein Core Facility and Cancer Sciences, Cancer Research UK Centre and Experimental Cancer Medicines Centre University of Southampton Southampton General Hospital, Southampton, SO16 6YD, UK
| | - Patrick J Duriez
- Protein Core Facility and Cancer Sciences, Cancer Research UK Centre and Experimental Cancer Medicines Centre University of Southampton Southampton General Hospital, Southampton, SO16 6YD, UK
| | - Sarah Bailey
- Protein Core Facility and Cancer Sciences, Cancer Research UK Centre and Experimental Cancer Medicines Centre University of Southampton Southampton General Hospital, Southampton, SO16 6YD, UK
| | - Simon J Crabb
- Protein Core Facility and Cancer Sciences, Cancer Research UK Centre and Experimental Cancer Medicines Centre University of Southampton Southampton General Hospital, Southampton, SO16 6YD, UK
| | - Graham Packham
- Protein Core Facility and Cancer Sciences, Cancer Research UK Centre and Experimental Cancer Medicines Centre University of Southampton Southampton General Hospital, Southampton, SO16 6YD, UK
| | - A Ganesan
- School of Pharmacy, University of East Anglia, Norwich, NR4 7TJ, UK
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12
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Walters ZS, Aladowicz E, Villarejo-Balcells B, Nugent G, Selfe JL, Eve P, Blagg J, Rossanese O, Shipley J. Role for the Histone Demethylase KDM4B in Rhabdomyosarcoma via CDK6 and CCNA2: Compensation by KDM4A and Apoptotic Response of Targeting Both KDM4B and KDM4A. Cancers (Basel) 2021; 13:1734. [PMID: 33917420 PMCID: PMC8038694 DOI: 10.3390/cancers13071734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/02/2021] [Accepted: 04/04/2021] [Indexed: 01/10/2023] Open
Abstract
Histone demethylases are epigenetic modulators that play key roles in regulating gene expression related to many critical cellular functions and are emerging as promising therapeutic targets in a number of tumor types. We previously identified histone demethylase family members as overexpressed in the pediatric sarcoma, rhabdomyosarcoma. Here we show high sensitivity of rhabdomyosarcoma cells to a pan-histone demethylase inhibitor, JIB-04 and identify a key role for the histone demethylase KDM4B in rhabdomyosarcoma cell growth through an RNAi-screening approach. Decreasing KDM4B levels affected cell cycle progression and transcription of G1/S and G2/M checkpoint genes including CDK6 and CCNA2, which are bound by KDM4B in their promoter regions. However, after sustained knockdown of KDM4B, rhabdomyosarcoma cell growth recovered. We show that this can be attributed to acquired molecular compensation via recruitment of KDM4A to the promoter regions of CDK6 and CCNA2 that are otherwise bound by KDM4B. Furthermore, upfront silencing of both KDM4B and KDM4A led to RMS cell apoptosis, not seen by reducing either alone. To circumvent compensation and elicit stronger therapeutic responses, our study supports targeting histone demethylase sub-family proteins through selective poly-pharmacology as a therapeutic approach.
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Affiliation(s)
- Zoë S. Walters
- Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, Sutton, London SM2 5NG, UK; (Z.S.W.); (E.A.); (B.V.-B.); (J.L.S.)
- Cancer Sciences, Faculty of Medicine, Southampton General Hospital, Southampton SO16 6YD, UK
| | - Ewa Aladowicz
- Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, Sutton, London SM2 5NG, UK; (Z.S.W.); (E.A.); (B.V.-B.); (J.L.S.)
| | - Barbara Villarejo-Balcells
- Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, Sutton, London SM2 5NG, UK; (Z.S.W.); (E.A.); (B.V.-B.); (J.L.S.)
| | - Gary Nugent
- Division of Cancer Therapeutics, The Institute of Cancer Research, Sutton, London SM2 5NG, UK; (G.N.); (P.E.); (J.B.); (O.R.)
| | - Joanna L. Selfe
- Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, Sutton, London SM2 5NG, UK; (Z.S.W.); (E.A.); (B.V.-B.); (J.L.S.)
| | - Paul Eve
- Division of Cancer Therapeutics, The Institute of Cancer Research, Sutton, London SM2 5NG, UK; (G.N.); (P.E.); (J.B.); (O.R.)
| | - Julian Blagg
- Division of Cancer Therapeutics, The Institute of Cancer Research, Sutton, London SM2 5NG, UK; (G.N.); (P.E.); (J.B.); (O.R.)
| | - Olivia Rossanese
- Division of Cancer Therapeutics, The Institute of Cancer Research, Sutton, London SM2 5NG, UK; (G.N.); (P.E.); (J.B.); (O.R.)
| | - Janet Shipley
- Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, Sutton, London SM2 5NG, UK; (Z.S.W.); (E.A.); (B.V.-B.); (J.L.S.)
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13
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Keyzor C, Mermaz B, Trigazis E, Jo S, Song J. Histone Demethylases ELF6 and JMJ13 Antagonistically Regulate Self-Fertility in Arabidopsis. Front Plant Sci 2021; 12:640135. [PMID: 33643367 PMCID: PMC7907638 DOI: 10.3389/fpls.2021.640135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 01/21/2021] [Indexed: 05/17/2023]
Abstract
The chromatin modification H3K27me3 is involved in almost every developmental stage in Arabidopsis. Much remains unknown about the dynamic regulation of this histone modification in flower development and control of self-fertility. Here we demonstrate that the H3K27me3-specific demethylases ELF6 and JMJ13 antagonistically regulate carpel and stamen growth and thus modulate self-fertility. Transcriptome and epigenome data are used to identify potential targets of ELF6 and JMJ13 responsible for these physiological functions. We find that ELF6 relieves expansin genes of epigenetic silencing to promote cell elongation in the carpel, enhancing carpel growth and therefore encouraging out-crossing. On the other hand, JMJ13 activates genes of the jasmonic acid regulatory network alongside the auxin responsive SAUR26, to inhibit carpel growth, enhance stamen growth, and overall promote self-pollination. Our evidence provides novel mechanisms of self-fertility regulation in A. thaliana demonstrating how chromatin modifying enzymes govern the equilibrium between flower self-pollination and out-crossing.
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14
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Yang Y, Zhang X, Zhang X, Wang Y, Wang X, Hu L, Zhao Y, Wang H, Wang Z, Wang H, Wang L, Dirks WG, Drexler HG, Xu X, Hu Z. Modulators of histone demethylase JMJD1C selectively target leukemic stem cells. FEBS Open Bio 2020; 11:265-277. [PMID: 33289299 PMCID: PMC7780120 DOI: 10.1002/2211-5463.13054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/19/2020] [Accepted: 11/30/2020] [Indexed: 12/24/2022] Open
Abstract
Leukemic stem cells (LSCs) comprise a very rare cell population that results in the development of acute myeloid leukemia. The selective targeting of drivers in LSCs with small molecule inhibitors holds promise for treatment of acute myeloid leukemia. Recently, we reported the identification of inhibitors of the histone lysine demethylase JMJD1C that preferentially kill MLL rearranged acute leukemia cells. Here, we report the identification of jumonji domain modulator #7 (JDM‐7). Surface plasmon resonance analysis showed that JDM‐7 binds to JMJD1C and its family homolog JMJD1B. JDM‐7 did not significantly suppress cell proliferation in liquid cell culture at higher doses, although it led to a significant decrease in semi‐solid colony formation experiments at lower concentrations. Moreover, low doses of JDM‐7 did not suppress the proliferation of erythroid progenitor cells. We identified that JDM‐7 downregulates the LSC self‐renewal gene HOXA9 in leukemia cells. We further found that the structure of JDM‐7 is similar to that of tadalafil, a drug approved by the US Food and Drug Administration. Molecular docking and surface plasmon resonance analysis showed that tadalafil binds to JMJD1C. Moreover, similar to JDM‐7, tadalafil suppressed colony formation of leukemia cells in semi‐solid cell culture at a concentration that did not affect primary umbilical cord blood cells. In summary, we have identified JDM‐7 and tadalafil as potential JMJD1C modulators that selectively inhibit the growth of LSCs.
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Affiliation(s)
- Yong Yang
- Laboratory for Stem Cell and Regenerative Medicine & Clinical Research Center, The Affiliated Hospital of Weifang Medical University, China
| | - Xinjing Zhang
- Department of Anesthesiology, Zibo Central Hospital, China
| | - Xiaoyan Zhang
- The Department of Obstetrics and Gynecology, The Affiliated Hospital of Weifang Medical University, China
| | - Yishu Wang
- Laboratory for Stem Cell and Regenerative Medicine & Clinical Research Center, The Affiliated Hospital of Weifang Medical University, China
| | - Xintong Wang
- Beijing Beike Deyuan Bio-Pharm Technology Co. Ltd, China
| | - Linda Hu
- Upstate Medical University, Syracuse, NY, USA
| | - Yao Zhao
- Laboratory for Stem Cell and Regenerative Medicine & Clinical Research Center, The Affiliated Hospital of Weifang Medical University, China
| | - Haihua Wang
- Laboratory for Stem Cell and Regenerative Medicine & Clinical Research Center, The Affiliated Hospital of Weifang Medical University, China
| | - Zhanju Wang
- The Department of Hematology, the Affiliated Hospital of Weifang Medical University, China
| | - Haiying Wang
- The Department of Hematology, the Affiliated Hospital of Weifang Medical University, China
| | - Lin Wang
- The School of Physics and Optoelectronic Engineering, Weifang University, China
| | - Wilhelm G Dirks
- Department of Human and Animal Cell Culture, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G Drexler
- Department of Human and Animal Cell Culture, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Xin Xu
- Laboratory for Stem Cell and Regenerative Medicine & Clinical Research Center, The Affiliated Hospital of Weifang Medical University, China.,School of Life Science and Technology, Weifang Medical University, China
| | - Zhenbo Hu
- Laboratory for Stem Cell and Regenerative Medicine & Clinical Research Center, The Affiliated Hospital of Weifang Medical University, China
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15
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Liu Z, He Y, Xu C, Li J, Zeng S, Yang X, Han Q. The role of PHF8 and TLR4 in osteogenic differentiation of periodontal ligament cells in inflammatory environment. J Periodontol 2020; 92:1049-1059. [PMID: 33040333 DOI: 10.1002/jper.20-0285] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 12/28/2022]
Abstract
BACKGROUND Histone methylation is considered to play an important role in the occurrence and development of periodontitis. Plant homeodomain finger protein 8 (PHF8), a histone demethylase, has been shown to regulate inflammation and osteogenic differentiation of bone marrow stromal cells (BMSCs). This study aimed to detect the functions of PHF8 and TLR4 in osteogenic differentiation in an inflammatory environment induced by Porphyromonas gingivalis lipopolysaccharide (Pg-LPS) METHODS: A periodontitis mouse model was established, and the mice were treated with TAK-242. Immunohistochemical staining was used to detect the expression of PHF8 in periodontal tissue. Periodontal ligament cells (PDLCs) were treated with mineralization induction medium supplemented with Pg-LPS and/or TAK-242, and a Cell Counting Kit-8 (CCK-8) assay was used to detect the proliferation of PDLCs. Real-time PCR and western blotting were used to detect the mRNA and protein expression levels, respectively, of PHF8, toll-like receptor 4 (TLR4) and the other osteogenic markers alkaline phosphatase (ALP), osteocalcin (OCN), Special AT-rich sequence-binding protein 2 (Satb2) and Runt-related transcription factor 2 (Runx2) RESULTS: Periodontitis reduced PHF8 expression in periodontal tissue, and TAK-242 partially reversed this downregulation. An in vitro experiment revealed that the mRNA and protein expression levels of PHF8 were significantly upregulated during the osteogenic differentiation of PDLCs. Alizarin red staining showed that the mineralized nodules of PDLCs in osteogenic induction group were more than those in control group. Real-time PCR and western blot results indicated that Pg-LPS inhibited PHF8 expression and upregulated TLR4 expression in PDLCs. TAK-242 inhibited TLR4 and partially reversed the inhibition of PHF8 expression and osteogenic differentiation induced by Pg-LPS in PDLCs CONCLUSION: PHF8 and TLR4 play important roles in periodontitis. Pg-LPS inhibits the expression of PHF8 via upregulation of TLR4 and might further inhibit the osteogenic differentiation of PDLCs. However, the specific mechanisms involved remain to be explored.
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Affiliation(s)
- Zhao Liu
- Department of endodontics, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Yiheng He
- School of Stomatology, Southern Medical University, Guangzhou, P.R. China
| | - Chenrong Xu
- Department of Periodontics, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Jianjia Li
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Shuguang Zeng
- Department of Oral and Maxillofacial Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Xi Yang
- Department of Periodontics, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Qianqian Han
- Department of Periodontics, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
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16
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Fioravanti R, Romanelli A, Mautone N, Di Bello E, Rovere A, Corinti D, Zwergel C, Valente S, Rotili D, Botrugno OA, Dessanti P, Vultaggio S, Vianello P, Cappa A, Binda C, Mattevi A, Minucci S, Mercurio C, Varasi M, Mai A. Tranylcypromine-Based LSD1 Inhibitors: Structure-Activity Relationships, Antiproliferative Effects in Leukemia, and Gene Target Modulation. ChemMedChem 2020; 15:643-658. [PMID: 32003940 DOI: 10.1002/cmdc.201900730] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Indexed: 01/07/2023]
Abstract
LSD1 is a lysine demethylase highly involved in initiation and development of cancer. To design highly effective covalent inhibitors, a strategy is to fill its large catalytic cleft by designing tranylcypromine (TCP) analogs decorated with long, hindered substituents. We prepared three series of TCP analogs, carrying aroyl- and arylacetylamino (1 a-h), Z-amino acylamino (2 a-o), or double-substituted benzamide (3 a-n) residues at the C4 or C3 position of the phenyl ring. Further fragments obtained by chemical manipulation applied on the TCP scaffold (compounds 4 a-i) were also prepared. When tested against LSD1, most of 1 and 3 exhibited IC50 values in the low nanomolar range, with 1 e and 3 a,d,f,g being also the most selective respect to monoamine oxidases. In MV4-11 AML and NB4 APL cells compounds 3 were the most potent, displaying up to sub-micromolar cell growth inhibition against both cell lines (3 a) or against NB4 cells (3 c). The most potent compounds in cellular assays were also able to induce the expression of LSD1 target genes, such as GFI-1b, ITGAM, and KCTD12, as functional read-out for LSD1 inhibition. Mouse and human intrinsic clearance data highlighted the high metabolic stability of compounds 3 a, 3 d and 3 g. Further studies will be performed on the new compounds 3 a and 3 c to assess their anticancer potential in different cancer contexts.
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Affiliation(s)
- Rossella Fioravanti
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185, Rome, Italy
| | - Annalisa Romanelli
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185, Rome, Italy
| | - Nicola Mautone
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185, Rome, Italy
| | - Elisabetta Di Bello
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185, Rome, Italy
| | - Annarita Rovere
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185, Rome, Italy
| | - Davide Corinti
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185, Rome, Italy
| | - Clemens Zwergel
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185, Rome, Italy.,Department of Medicine of Precision, University of Studi della Campania Luigi Vanvitelli, Vico L. De Crecchio 7, 80138, Naples, Italy
| | - Sergio Valente
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185, Rome, Italy
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185, Rome, Italy
| | - Oronza A Botrugno
- Department of Experimental Oncology, IEO - European Institute of Oncology IRCCS, via Adamello 16, 20139, Milan, Italy.,IRCCS San Raffaele Scientific Institute, Via Olgettina Milano, 58, 20132, Milan, Italy
| | - Paola Dessanti
- Department of Experimental Oncology, IEO - European Institute of Oncology IRCCS, via Adamello 16, 20139, Milan, Italy.,Oryzon Genomics S.A., Sant Ferran, 08940 Cornellà de Llobregat, Barcelona, Spain
| | - Stefania Vultaggio
- Department of Experimental Oncology, IEO - European Institute of Oncology IRCCS, via Adamello 16, 20139, Milan, Italy
| | - Paola Vianello
- Department of Experimental Oncology, IEO - European Institute of Oncology IRCCS, via Adamello 16, 20139, Milan, Italy
| | - Anna Cappa
- Department of Experimental Oncology, IEO - European Institute of Oncology IRCCS, via Adamello 16, 20139, Milan, Italy.,Experimental Therapeutics Program, IFOM-FIRC Institute of Molecular Oncology Foundation, via Adamello 16, 20139, Milan, Italy
| | - Claudia Binda
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Saverio Minucci
- Department of Experimental Oncology, IEO - European Institute of Oncology IRCCS, via Adamello 16, 20139, Milan, Italy.,Department of Biosciences, University of Milan, Via Festa del Perdono 7, 20122, Milano, Italy
| | - Ciro Mercurio
- Department of Experimental Oncology, IEO - European Institute of Oncology IRCCS, via Adamello 16, 20139, Milan, Italy.,Experimental Therapeutics Program, IFOM-FIRC Institute of Molecular Oncology Foundation, via Adamello 16, 20139, Milan, Italy
| | - Mario Varasi
- Department of Experimental Oncology, IEO - European Institute of Oncology IRCCS, via Adamello 16, 20139, Milan, Italy.,Experimental Therapeutics Program, IFOM-FIRC Institute of Molecular Oncology Foundation, via Adamello 16, 20139, Milan, Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, P. le A. Moro 5, 00185, Rome, Italy
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17
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Xu X, Wang L, Hu L, Dirks WG, Zhao Y, Wei Z, Chen D, Li Z, Wang Z, Han Y, Wei L, Drexler HG, Hu Z. Small molecular modulators of JMJD1C preferentially inhibit growth of leukemia cells. Int J Cancer 2019; 146:400-412. [PMID: 31271662 DOI: 10.1002/ijc.32552] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 06/25/2019] [Accepted: 06/27/2019] [Indexed: 01/08/2023]
Abstract
Histone demethylases are promising therapeutic targets as they play fundamental roles for survival of Mixed lineage leukemia rearranged acute leukemia (MLLr AL). Here we focused on the catalytic Jumonji domain of histone H3 lysine 9 (H3K9) demethylase JMJD1C to screen for potential small molecular modulators from 149,519 natural products and 33,765 Chinese medicine components via virtual screening. JMJD1C Jumonji domain inhibitor 4 (JDI-4) and JDI-12 that share a common structural backbone were detected within the top 15 compounds. Surface plasmon resonance analysis showed that JDI-4 and JDI-12 bind to JMJD1C and its family homolog KDM3B with modest affinity. In vitro demethylation assays showed that JDI-4 can reverse the H3K9 demethylation conferred by KDM3B. In vivo demethylation assays indicated that JDI-4 and JDI-12 could induce the global increase of H3K9 methylation. Cell proliferation and colony formation assays documented that JDI-4 and JDI-12 kill MLLr AL and other malignant hematopoietic cells, but not leukemia cells resistant to JMJD1C depletion or cord blood cells. Furthermore, JDI-16, among multiple compounds structurally akin to JDI-4/JDI-12, exhibits superior killing activities against malignant hematopoietic cells compared to JDI-4/JDI-12. Mechanistically, JDI-16 not only induces apoptosis but also differentiation of MLLr AL cells. RNA sequencing and quantitative PCR showed that JDI-16 induced gene expression associated with cell metabolism; targeted metabolomics revealed that JDI-16 downregulates lactic acids, NADP+ and other metabolites. Moreover, JDI-16 collaborates with all-trans retinoic acid to repress MLLr AML cells. In summary, we identified bona fide JMJD1C inhibitors that induce preferential death of MLLr AL cells.
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Affiliation(s)
- Xin Xu
- Laboratory for Stem Cell and Regenerative Medicine, The Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China.,College of Bioscience and Technology, Weifang, Shandong, China
| | - Lin Wang
- The School of Physics and Optoelectronic Engineering, Weifang University, Weifang, Shandong, China
| | - Linda Hu
- Upstate Medical University, Syracuse, NY
| | - Wilhelm G Dirks
- Department of Human and Animal Cell Culture, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Yao Zhao
- Laboratory for Stem Cell and Regenerative Medicine, The Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Zhishuai Wei
- College of Bioscience and Technology, Weifang, Shandong, China
| | - Dexiang Chen
- College of Bioscience and Technology, Weifang, Shandong, China
| | - Zhaoliang Li
- Laboratory for Stem Cell and Regenerative Medicine, The Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Zhanju Wang
- The Department of Hematology, The Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
| | - Yangyang Han
- College of Bioscience and Technology, Weifang, Shandong, China
| | - Liuya Wei
- College of Pharmacy, Weifang Medical University, Weifang, Shandong, China
| | - Hans G Drexler
- Department of Human and Animal Cell Culture, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Zhenbo Hu
- Laboratory for Stem Cell and Regenerative Medicine, The Affiliated Hospital of Weifang Medical University, Weifang, Shandong, China
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18
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Jia Y, Reddy MA, Das S, Oh HJ, Abdollahi M, Yuan H, Zhang E, Lanting L, Wang M, Natarajan R. Dysregulation of histone H3 lysine 27 trimethylation in transforming growth factor-β1-induced gene expression in mesangial cells and diabetic kidney. J Biol Chem 2019; 294:12695-12707. [PMID: 31266808 DOI: 10.1074/jbc.ra119.007575] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 06/13/2019] [Indexed: 12/20/2022] Open
Abstract
Transforming growth factor-β1 (TGF-β)-induced fibrotic and inflammatory genes in renal mesangial cells (MCs) play important roles in glomerular dysfunction associated with diabetic nephropathy (DN). TGF-β regulates gene expression in MCs by altering key chromatin histone modifications at target gene promoters. However, the role of the repressive histone H3 lysine 27 trimethylation (H3K27me3) modification is unclear. Here we show that TGF-β reduces H3K27me3 at the Ctgf, Serpine1, and Ccl2 gene promoters in rat MCs (RMCs) and reciprocally up-regulates the expression of these pro-fibrotic and inflammatory genes. In parallel, TGF-β down-regulates Enhancer of Zeste homolog 2 (Ezh2), an H3K27me3 methyltransferase, and decreases its recruitment at Ctgf and Ccl2 but not Serpine1 promoters. Ezh2 knockdown with siRNAs enhances TGF-β-induced expression of these genes, supporting its repressive function. Mechanistically, Ezh2 down-regulation is mediated by TGF-β-induced microRNA, miR-101b, which targets Ezh2 3'-UTR. TGF-β also up-regulates Jmjd3 and Utx in RMCs, suggesting a key role for these H3K27me3 demethylases in H3K27me3 inhibition. In RMCs, Utx knockdown inhibits hypertrophy, a key event in glomerular dysfunction. The H3K27me3 regulators are similarly altered in human and mouse MCs. High glucose inhibits Ezh2 and increases miR-101b in a TGF-β-dependent manner. Furthermore, in kidneys from rodent models of DN, fibrotic genes, miR-101b, and H3K27me3 demethylases are up-regulated, whereas Ezh2 protein levels as well as enrichment of Ezh2 and H3K27me3 at target genes are decreased, demonstrating in vivo relevance. These results suggest that H3K27me3 inhibition by TGF-β via dysregulation of related histone-modifying enzymes and miRNAs augments pathological genes mediating glomerular mesangial dysfunction and DN.
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Affiliation(s)
- Ye Jia
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, California 91010.,Division of Nephrology, First Hospital of Jilin University, Changchun 130021, China
| | - Marpadga A Reddy
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, California 91010
| | - Sadhan Das
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, California 91010
| | - Hyung Jung Oh
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, California 91010.,Ewha Institute of Convergence Medicine, Ewha Womans University Mokdong Hospital, Seoul 07985, South Korea
| | - Maryam Abdollahi
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, California 91010
| | - Hang Yuan
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, California 91010.,Division of Nephrology, First Hospital of Jilin University, Changchun 130021, China
| | - Erli Zhang
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, California 91010.,Department of Cardiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China
| | - Linda Lanting
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, California 91010
| | - Mei Wang
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, California 91010
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, California 91010
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19
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Abstract
The most common type of head and neck cancer, head and neck squamous cell carcinoma (HNSCC), can develop therapeutic resistance that complicates its treatment. The 5-y survival rate for HNSCC remains at ~50%, and improving these outcomes requires a better understanding of the pathogenesis of HNSCC. Studies of HNSCC using in vitro, ex vivo, and in vivo approaches provide a novel conceptual framework based on epigenetic mechanisms for developing future clinical applications. Normal oral tissues are influenced by environmental factors that induce pathological changes affecting the network of epigenetic enzymes and signaling pathways to induce HNSCC growth and metastasis. Although various epigenetic regulator families, such as DNA methyltransferases, ten-eleven translocation proteins, histone acetyltransferases, histone deacetylases, BET bromodomain proteins, protein arginine methyltransferases, histone lysine methyltransferases, and histone lysine demethylases, have a role in diverse cancers, specific members have a function in HNSCC. Recently, lysine-specific demethylases have been identified as a potential, attractive, and novel target of HNSCC. Lysine-specific demethylase 1 (LSD1) expression is inappropriately upregulated in HNSCC and an orthotopic HNSCC mouse model. LSD1 can demethylate lysine at specific histone positions to repress gene expression or stimulate transcription, indicating a dual and context-dependent role in transcriptional regulation. Our study showed that LSD1 promotes HNSCC growth and metastasis. Pharmacological attenuation of LSD1 inhibits orthotopic and patient-derived HNSCC xenograft growth-specific target genes and signaling pathways. This review provides recent evidence demonstrating the function of epigenetic regulator enzymes in HNSCC progression, including potential therapeutic applications for such enzymes in combination and immunotherapy.
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Affiliation(s)
- M.V. Bais
- Department of Molecular and Cell Biology, Boston University Henry M. Goldman School of Dental Medicine, Boston, MA, USA
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20
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Abstract
Epigenetic changes are well-established contributors to cancer progression and normal developmental processes. The reversible modification of histones plays a central role in regulating the nuclear processes of gene transcription, DNA replication, and DNA repair. The KDM4 family of Jumonj domain histone demethylases specifically target di- and tri-methylated lysine 9 on histone H3 (H3K9me3), removing a modification central to defining heterochromatin and gene repression. KDM4 enzymes are generally over-expressed in cancers, making them compelling targets for study and therapeutic inhibition. One of these family members, KDM4B, is especially interesting due to its regulation by multiple cellular stimuli, including DNA damage, steroid hormones, and hypoxia. In this review, we discuss what is known about the regulation of KDM4B in response to the cellular environment, and how this context-dependent expression may be translated into specific biological consequences in cancer and reproductive biology.
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Affiliation(s)
- Cailin Wilson
- Department of Pathology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Adam J Krieg
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, OR 97239, USA.
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Beaverton, OR 97006, USA.
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21
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Thinnes CC, Lohans CT, Abboud MI, Yeh T, Tumber A, Nowak RP, Attwood M, Cockman ME, Oppermann U, Loenarz C, Schofield CJ. Selective Inhibitors of a Human Prolyl Hydroxylase (OGFOD1) Involved in Ribosomal Decoding. Chemistry 2019; 25:2019-2024. [PMID: 30427558 PMCID: PMC6471485 DOI: 10.1002/chem.201804790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Indexed: 12/12/2022]
Abstract
Human prolyl hydroxylases are involved in the modification of transcription factors, procollagen, and ribosomal proteins, and are current medicinal chemistry targets. To date, there are few reports on inhibitors selective for the different types of prolyl hydroxylases. We report a structurally informed template-based strategy for the development of inhibitors selective for the human ribosomal prolyl hydroxylase OGFOD1. These inhibitors did not target the other human oxygenases tested, including the structurally similar hypoxia-inducible transcription factor prolyl hydroxylase, PHD2.
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Affiliation(s)
| | | | | | - Tzu‐Lan Yeh
- Department of ChemistryUniversity of OxfordOxfordOX1 3TAUK
| | - Anthony Tumber
- Department of ChemistryUniversity of OxfordOxfordOX1 3TAUK
- Structural Genomics ConsortiumUniversity of OxfordHeadingtonOX3 7DQUK
| | - Radosław P. Nowak
- Structural Genomics ConsortiumUniversity of OxfordHeadingtonOX3 7DQUK
- Department of Cancer BiologyDana-Farber Cancer InstituteBoston, MA02215USA
| | - Martin Attwood
- Centre for Cellular and Molecular PhysiologyUniversity of OxfordOxfordOX3 7BNUK
| | - Matthew E. Cockman
- Centre for Cellular and Molecular PhysiologyUniversity of OxfordOxfordOX3 7BNUK
| | - Udo Oppermann
- Structural Genomics ConsortiumUniversity of OxfordHeadingtonOX3 7DQUK
| | - Christoph Loenarz
- Department of ChemistryUniversity of OxfordOxfordOX1 3TAUK
- Institute of Pharmaceutical SciencesAlbert-Ludwigs-Universität Freiburg79104FreiburgGermany
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22
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Martignago D, Bernardini B, Polticelli F, Salvi D, Cona A, Angelini R, Tavladoraki P. The Four FAD-Dependent Histone Demethylases of Arabidopsis Are Differently Involved in the Control of Flowering Time. Front Plant Sci 2019; 10:669. [PMID: 31214214 PMCID: PMC6558185 DOI: 10.3389/fpls.2019.00669] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/02/2019] [Indexed: 05/18/2023]
Abstract
In Arabidopsis thaliana, four FAD-dependent lysine-specific histone demethylases (LDL1, LDL2, LDL3, and FLD) are present, bearing both a SWIRM and an amine oxidase domain. In this study, a comparative analysis of gene structure, evolutionary relationships, tissue- and organ-specific expression patterns, physiological roles and target genes for the four Arabidopsis LDL/FLDs is reported. Phylogenetic analysis evidences a different evolutionary history for the four LDL/FLDs, while promoter activity data show that LDL/FLDs are strongly expressed during plant development and embryogenesis, with some gene-specific expression patterns. Furthermore, phenotypical analysis of loss-of-function mutants indicates a role of all four Arabidopsis LDL/FLD genes in the control of flowering time, though for some of them with opposing effects. This study contributes toward a better understanding of the LDL/FLD physiological roles and may provide biotechnological strategies for crop improvement.
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Affiliation(s)
- Damiano Martignago
- Department of Science, Roma Tre University, Rome, Italy
- Centre for Research in Agricultural Genomics, Spanish National Research Council–Institute for Food and Agricultural Research and Technology–Autonomous University of Barcelona–University of Barcelona, Barcelona, Spain
| | | | - Fabio Polticelli
- Department of Science, Roma Tre University, Rome, Italy
- ‘Roma Tre’ Section, National Institute of Nuclear Physics, Rome, Italy
| | - Daniele Salvi
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| | | | | | - Paraskevi Tavladoraki
- Department of Science, Roma Tre University, Rome, Italy
- *Correspondence: Paraskevi Tavladoraki,
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23
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De Smedt E, Lui H, Maes K, De Veirman K, Menu E, Vanderkerken K, De Bruyne E. The Epigenome in Multiple Myeloma: Impact on Tumor Cell Plasticity and Drug Response. Front Oncol 2018; 8:566. [PMID: 30619733 PMCID: PMC6297718 DOI: 10.3389/fonc.2018.00566] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/13/2018] [Indexed: 01/19/2023] Open
Abstract
Multiple myeloma (MM) is a clonal plasma cell malignancy that develops primarily in the bone marrow (BM), where reciprocal interactions with the BM niche foster MM cell survival, growth, and drug resistance. MM cells furthermore reshape the BM to their own needs by affecting the different BM stromal cell types resulting in angiogenesis, bone destruction, and immune suppression. Despite recent advances in treatment modalities, MM remains most often incurable due to the development of drug resistance to all standard of care agents. This underscores the unmet need for these heavily treated relapsed/refractory patients. Disruptions in epigenetic regulation are a well-known hallmark of cancer cells, contributing to both cancer onset and progression. In MM, sequencing and gene expression profiling studies have also identified numerous epigenetic defects, including locus-specific DNA hypermethylation of cancer-related and B cell specific genes, genome-wide DNA hypomethylation and genetic defects, copy number variations and/or abnormal expression patterns of various chromatin modifying enzymes. Importantly, these so-called epimutations contribute to genomic instability, disease progression, and a worse outcome. Moreover, the frequency of mutations observed in genes encoding for histone methyltransferases and DNA methylation modifiers increases following treatment, indicating a role in the emergence of drug resistance. In support of this, accumulating evidence also suggest a role for the epigenetic machinery in MM cell plasticity, driving the differentiation of the malignant cells to a less mature and drug resistant state. This review discusses the current state of knowledge on the role of epigenetics in MM, with a focus on deregulated histone methylation modifiers and the impact on MM cell plasticity and drug resistance. We also provide insight into the potential of epigenetic modulating agents to enhance clinical drug responses and avoid disease relapse.
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Affiliation(s)
- Eva De Smedt
- Department of Hematology and Immunology-Myeloma Center Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Hui Lui
- Department of Hematology and Immunology-Myeloma Center Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Ken Maes
- Department of Hematology and Immunology-Myeloma Center Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Kim De Veirman
- Department of Hematology and Immunology-Myeloma Center Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Eline Menu
- Department of Hematology and Immunology-Myeloma Center Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Karin Vanderkerken
- Department of Hematology and Immunology-Myeloma Center Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Elke De Bruyne
- Department of Hematology and Immunology-Myeloma Center Brussels, Vrije Universiteit Brussel, Brussels, Belgium
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24
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Walport LJ, Schofield CJ. Adventures in Defining Roles of Oxygenases in the Regulation of Protein Biosynthesis. CHEM REC 2018; 18:1760-1781. [PMID: 30151867 DOI: 10.1002/tcr.201800056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/17/2018] [Indexed: 12/19/2022]
Abstract
The 2-oxoglutarate (2OG) dependent oxygenases were first identified as having roles in the post-translational modification of procollagen in animals. Subsequently in plants and microbes, they were shown to have roles in the biosynthesis of many secondary metabolites, including signalling molecules and the penicillin/cephalosporin antibiotics. Crystallographic studies of microbial 2OG oxygenases and related enzymes, coupled to DNA sequence analyses, led to the prediction that 2OG oxygenases are widely distributed in aerobic biology. This personal account begins with examples of the roles of 2OG oxygenases in antibiotic biosynthesis, and then describes efforts to assign functions to other predicted 2OG oxygenases. In humans, 2OG oxygenases have been found to have roles in small molecule metabolism, as well as in the epigenetic regulation of protein and nucleic acid biosynthesis and function. The roles and functions of human 2OG oxygenases are compared, focussing on discussion of their substrate and product selectivities. The account aims to emphasize how scoping the substrate selectivity of, sometimes promiscuous, enzymes can provide insights into their functions and so enable therapeutic work.
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Affiliation(s)
- Louise J Walport
- Department of Chemistry, University of Oxford Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Christopher J Schofield
- Department of Chemistry, University of Oxford Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK
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25
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Jones SE, Olsen L, Dorosz J, Seger ST, Andersson JL, Kristensen LH, Gajhede M. Peptides Derived from Histone 3 and Modified at Position 18 Inhibit Histone Demethylase KDM6 Enzymes. Chembiochem 2018; 19:1817-1822. [PMID: 29878441 DOI: 10.1002/cbic.201800185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Indexed: 11/12/2022]
Abstract
The KDM6 subfamily of histone lysine demethylases has recently been implicated as a putative target in the treatment of a number of diseases; this makes the availability of potent and selective inhibitors important. Due to high sequence similarity of the catalytic domain of Jumonji C histone demethylases, the development of small-molecule, family-specific inhibitors has, however, proven challenging. One approach to achieve the selective inhibition of these enzymes is the use of peptides derived from the substrate, the histone 3 C terminus. Here we used computational methods to optimize such inhibitors of the KDM6 family. Through natural amino acid substitution, it is shown that a K18I variant of a histone H3 derived peptide significantly increases affinity towards the KDM6 enzymes. The crystal structure of KDM6B in complex with a histone 3 derived K18I peptide reveals a tighter fit of the isoleucine side chain, compared with that of the arginine. As a consequence, the peptide R17 residue also has increased hydrophilic interactions. These interactions of the optimized peptide are likely to be responsible for the increased affinity to the KDM6 enzymes.
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Affiliation(s)
- Sarah E Jones
- Biostructural Research, Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Lars Olsen
- Biostructural Research, Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Jerzy Dorosz
- Biostructural Research, Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Signe T Seger
- Novo Nordisk Pharmatech, Københavnsvej 216, 4600, Køge, Denmark
| | - Jan L Andersson
- Nuevolution AB (publ.), Rønnegade 8, 2100, Copenhagen, Denmark
| | | | - Michael Gajhede
- Biostructural Research, Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
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26
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Bonnici J, Tumber A, Kawamura A, Schofield CJ. Inhibitors of both the N-methyl lysyl- and arginyl-demethylase activities of the JmjC oxygenases. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170071. [PMID: 29685975 PMCID: PMC5915715 DOI: 10.1098/rstb.2017.0071] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2017] [Indexed: 12/22/2022] Open
Abstract
The Jumonji C (JmjC) family of 2-oxoglutarate (2OG)-dependent oxygenases have established roles in the regulation of transcription via the catalysis of demethylation of Nε-methylated lysine residues in histone tails, especially the N-terminal tail of histone H3. Most human JmjC Nɛ -methyl lysine demethylases (KDMs) are complex enzymes, with 'reader domains' in addition to their catalytic domains. Recent biochemical evidence has shown that some, but not all, JmjC KDMs also have Nω-methyl arginyl demethylase (RDM) activity. JmjC KDM activity has been linked to multiple cancers and some JmjC proteins are therapeutic targets. It is, therefore, important to test not only whether compounds in development inhibit the KDM activity of targeted JmjC demethylases, but also whether they inhibit other activities of these proteins. Here we report biochemical studies on the potential dual inhibition of JmjC KDM and RDM activities using a model JmjC demethylase, KDM4E (JMJD2E). The results reveal that all of the tested compounds inhibit both the KDM and RDM activities, raising questions about the in vivo effects of the inhibitors.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
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Affiliation(s)
- Joanna Bonnici
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Anthony Tumber
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Akane Kawamura
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Christopher J Schofield
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
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27
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Levin M, Stark M, Assaraf YG. The JmjN domain as a dimerization interface and a targeted inhibitor of KDM4 demethylase activity. Oncotarget 2018; 9:16861-16882. [PMID: 29682190 PMCID: PMC5908291 DOI: 10.18632/oncotarget.24717] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 02/25/2018] [Indexed: 12/14/2022] Open
Abstract
Histone methylation is regulated to shape the epigenome by modulating DNA compaction, thus playing central roles in fundamental chromatin-based processes including transcriptional regulation, DNA repair and cell proliferation. Histone methylation is erased by demethylases including the well-established KDM4 subfamily members, however, little is known about their dimerization capacity and its impact on their demethylase activity. Using the powerful bimolecular fluorescence complementation technique, we herein show the in situ formation of human KDM4A and KDM4C homodimers and heterodimers in nuclei of live transfectant cells and evaluate their H3K9me3 demethylation activity. Using size exclusion HPLC as well as Western blot analysis, we show that endogenous KDM4C undergoes dimerization under physiological conditions. Importantly, we identify the JmjN domain as the KDM4C dimerization interface and pin-point specific charged residues therein to be essential for this dimerization. We further demonstrate that KDM4A/C dimerization is absolutely required for their demethylase activity which was abolished by the expression of free JmjN peptides. In contrast, KDM4B does not dimerize and functions as a monomer, and hence was not affected by free JmjN expression. KDM4 proteins are overexpressed in numerous malignancies and their pharmacological inhibition or depletion in cancer cells was shown to impair tumor cell proliferation, invasion and metastasis. Thus, the KDM4 dimer-interactome emerging from the present study bears potential implications for cancer therapeutics via selective inhibition of KDM4A/C demethylase activity using JmjN-based peptidomimetics.
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Affiliation(s)
- May Levin
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Michal Stark
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
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28
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Dalvi MP, Wang L, Zhong R, Kollipara RK, Park H, Bayo J, Yenerall P, Zhou Y, Timmons BC, Rodriguez-Canales J, Behrens C, Mino B, Villalobos P, Parra ER, Suraokar M, Pataer A, Swisher SG, Kalhor N, Bhanu NV, Garcia BA, Heymach JV, Coombes K, Xie Y, Girard L, Gazdar AF, Kittler R, Wistuba II, Minna JD, Martinez ED. Taxane-Platin-Resistant Lung Cancers Co-develop Hypersensitivity to JumonjiC Demethylase Inhibitors. Cell Rep 2018; 19:1669-1684. [PMID: 28538184 DOI: 10.1016/j.celrep.2017.04.077] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 03/06/2017] [Accepted: 04/27/2017] [Indexed: 12/30/2022] Open
Abstract
Although non-small cell lung cancer (NSCLC) patients benefit from standard taxane-platin chemotherapy, many relapse, developing drug resistance. We established preclinical taxane-platin-chemoresistance models and identified a 35-gene resistance signature, which was associated with poor recurrence-free survival in neoadjuvant-treated NSCLC patients and included upregulation of the JumonjiC lysine demethylase KDM3B. In fact, multi-drug-resistant cells progressively increased the expression of many JumonjiC demethylases, had altered histone methylation, and, importantly, showed hypersensitivity to JumonjiC inhibitors in vitro and in vivo. Increasing taxane-platin resistance in progressive cell line series was accompanied by progressive sensitization to JIB-04 and GSK-J4. These JumonjiC inhibitors partly reversed deregulated transcriptional programs, prevented the emergence of drug-tolerant colonies from chemo-naive cells, and synergized with standard chemotherapy in vitro and in vivo. Our findings reveal JumonjiC inhibitors as promising therapies for targeting taxane-platin-chemoresistant NSCLCs.
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Affiliation(s)
- Maithili P Dalvi
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lei Wang
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rui Zhong
- Department of Clinical Science, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rahul K Kollipara
- Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hyunsil Park
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Juan Bayo
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Paul Yenerall
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yunyun Zhou
- Department of Clinical Science, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Brenda C Timmons
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jaime Rodriguez-Canales
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Barbara Mino
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pamela Villalobos
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Edwin R Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Milind Suraokar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Apar Pataer
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Stephen G Swisher
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Neda Kalhor
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Natarajan V Bhanu
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin A Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kevin Coombes
- Department of Biomedical Informatics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Yang Xie
- Department of Clinical Science, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Luc Girard
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adi F Gazdar
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ralf Kittler
- Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Elisabeth D Martinez
- Hamon Center for Therapeutic Oncology Research, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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29
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Abstract
Histone methylation plays a key role in the regulation of chromatin structure, and its dynamics regulates important cellular processes. The investigation of the role of alterations in histone methylation in cancer has led to the identification of histone methyltransferases and demethylases as promising novel targets for therapy. Lysine-specific demethylase 1(LSD1, also known as KDM1A) is the first discovered histone lysine demethylase, with the ability to demethylase H3K4me1/2 and H3K9me1/2 at target loci in a context-dependent manner. LSD1 regulates the balance between self-renewal and differentiation of stem cells, and is highly expressed in various cancers, playing an important role in differentiation and self-renewal of tumor cells. In this review, we summarize recent studies about the LSD1, its role in normal and tumor cells, and the potential use of small molecule LSD1 inhibitors in therapy.
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Affiliation(s)
- Amir Hosseini
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Saverio Minucci
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy.,Department of Biosciences, University of Milan, Milan, Italy
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30
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Abstract
Renal cell carcinoma (RCC), the most common kidney cancer, is responsible for more than 100,000 deaths per year worldwide. The molecular mechanism of RCC is poorly understood. Many studies have indicated that epigenetic changes such as DNA methylation, noncoding RNAs, and histone modifications are central to the pathogenesis of cancer. Histone demethylases (KDMs) play a central role in histone modifications. There is emerging evidence that KDMs such as KDM3A, KDM5C, KDM6A, and KDM6B play important roles in RCC. The available literature suggests that KDMs could promote RCC development and progression via hypoxia-mediated angiogenesis pathways. Small-molecule inhibitors of KDMs are being developed and used in preclinical studies; however, their clinical relevance is yet to be established. In this mini review, we summarize our current knowledge on the putative role of histone demethylases in RCC.
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31
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Cencioni C, Spallotta F, Farsetti A, Zeiher AM, Gaetano C. Deciphering Histone Code Enigmas Sheds New Light on Cardiac Regeneration. Circ Res 2017; 120:1370-1372. [PMID: 28450354 DOI: 10.1161/circresaha.117.310919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Chiara Cencioni
- From the National Research Council (CNR), Institute of Cell Biology and Neurobiology, Rome, Italy (C.C., A.F.); and Division of Cardiovascular Epigenetics, Department of Cardiology (C.C., F.S., C.G.) and Internal Medicine Clinic III, Department of Cardiology (F.S., A.F., A.M.Z., C.G.), Goethe University, Frankfurt am Main, Germany
| | - Francesco Spallotta
- From the National Research Council (CNR), Institute of Cell Biology and Neurobiology, Rome, Italy (C.C., A.F.); and Division of Cardiovascular Epigenetics, Department of Cardiology (C.C., F.S., C.G.) and Internal Medicine Clinic III, Department of Cardiology (F.S., A.F., A.M.Z., C.G.), Goethe University, Frankfurt am Main, Germany
| | - Antonella Farsetti
- From the National Research Council (CNR), Institute of Cell Biology and Neurobiology, Rome, Italy (C.C., A.F.); and Division of Cardiovascular Epigenetics, Department of Cardiology (C.C., F.S., C.G.) and Internal Medicine Clinic III, Department of Cardiology (F.S., A.F., A.M.Z., C.G.), Goethe University, Frankfurt am Main, Germany
| | - Andreas M Zeiher
- From the National Research Council (CNR), Institute of Cell Biology and Neurobiology, Rome, Italy (C.C., A.F.); and Division of Cardiovascular Epigenetics, Department of Cardiology (C.C., F.S., C.G.) and Internal Medicine Clinic III, Department of Cardiology (F.S., A.F., A.M.Z., C.G.), Goethe University, Frankfurt am Main, Germany
| | - Carlo Gaetano
- From the National Research Council (CNR), Institute of Cell Biology and Neurobiology, Rome, Italy (C.C., A.F.); and Division of Cardiovascular Epigenetics, Department of Cardiology (C.C., F.S., C.G.) and Internal Medicine Clinic III, Department of Cardiology (F.S., A.F., A.M.Z., C.G.), Goethe University, Frankfurt am Main, Germany .
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Liau BB, Sievers C, Donohue LK, Gillespie SM, Flavahan WA, Miller TE, Venteicher AS, Hebert CH, Carey CD, Rodig SJ, Shareef SJ, Najm FJ, van Galen P, Wakimoto H, Cahill DP, Rich JN, Aster JC, Suvà ML, Patel AP, Bernstein BE. Adaptive Chromatin Remodeling Drives Glioblastoma Stem Cell Plasticity and Drug Tolerance. Cell Stem Cell 2017; 20:233-246.e7. [PMID: 27989769 PMCID: PMC5291795 DOI: 10.1016/j.stem.2016.11.003] [Citation(s) in RCA: 322] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/06/2016] [Accepted: 10/31/2016] [Indexed: 12/17/2022]
Abstract
Glioblastoma, the most common and aggressive malignant brain tumor, is propagated by stem-like cancer cells refractory to existing therapies. Understanding the molecular mechanisms that control glioblastoma stem cell (GSC) proliferation and drug resistance may reveal opportunities for therapeutic interventions. Here we show that GSCs can reversibly transition to a slow-cycling, persistent state in response to targeted kinase inhibitors. In this state, GSCs upregulate primitive developmental programs and are dependent upon Notch signaling. This transition is accompanied by widespread redistribution of repressive histone methylation. Accordingly, persister GSCs upregulate, and are dependent on, the histone demethylases KDM6A/B. Slow-cycling cells with high Notch activity and histone demethylase expression are present in primary glioblastomas before treatment, potentially contributing to relapse. Our findings illustrate how cancer cells may hijack aspects of native developmental programs for deranged proliferation, adaptation, and tolerance. They also suggest strategies for eliminating refractory tumor cells by targeting epigenetic and developmental pathways.
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Affiliation(s)
- Brian B Liau
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Cem Sievers
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Laura K Donohue
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Shawn M Gillespie
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - William A Flavahan
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Tyler E Miller
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
| | - Andrew S Venteicher
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Christine H Hebert
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Christopher D Carey
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Sarah J Shareef
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Fadi J Najm
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Peter van Galen
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Hiroaki Wakimoto
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Daniel P Cahill
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jeremy N Rich
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
| | - Jon C Aster
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Mario L Suvà
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Anoop P Patel
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
| | - Bradley E Bernstein
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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Affiliation(s)
- Joyce Taylor-Papadimitriou
- a Breast Cancer Biology , Division of Cancer Studies, King's College London , Guy's Hospital, London , UK
| | - Joy Burchell
- a Breast Cancer Biology , Division of Cancer Studies, King's College London , Guy's Hospital, London , UK
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Abstract
The response to hypoxia is primarily mediated by the hypoxia-inducible transcription factor (HIF). Levels of HIF are regulated by the oxygen-sensing HIF hydroxylases, members of the 2-oxoglutarate (2OG) dependent oxygenase family. JmjC-domain containing histone lysine demethylases (JmjC-KDMs), also members of the 2OG oxygenase family, are key epigenetic regulators that modulate the methylation levels of histone tails. Kinetic studies of the JmjC-KDMs indicate they could also act in an oxygen-sensitive manner. This may have important implications for epigenetic regulation in hypoxia. In this review we examine evidence that the levels and activity of JmjC-KDMs are sensitive to oxygen availability, and consider how this may influence their roles in early development and hypoxic disease states including cancer and cardiovascular disease.
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Affiliation(s)
- Rebecca L Hancock
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
- Radcliffe Department of Medicine, Division of Cardiovascular Medicine, BHF Centre of Research Excellence, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Kate Dunne
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
- Radcliffe Department of Medicine, Division of Cardiovascular Medicine, BHF Centre of Research Excellence, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Louise J Walport
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Emily Flashman
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Akane Kawamura
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
- Radcliffe Department of Medicine, Division of Cardiovascular Medicine, BHF Centre of Research Excellence, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
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Casati L, Sendra R, Sibilia V, Celotti F. Endocrine disrupters: the new players able to affect the epigenome. Front Cell Dev Biol 2015; 3:37. [PMID: 26151052 PMCID: PMC4471431 DOI: 10.3389/fcell.2015.00037] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 05/17/2015] [Indexed: 01/27/2023] Open
Abstract
Epigenetics represents the way by which the environment is able to program the genome; there are three main levels of epigenetic control on genome: DNA methylation, post-translational histone modification and microRNA expression. The term Epigenetics has been widened by NIH to include “both heritable changes in gene activity and expression but also stable, long-term alterations in the transcriptional potential of a cell that are not necessarily heritable.” These changes might be produced mostly by the early life environment and might affect health influencing the susceptibility to develop diseases, from cancer to mental disorder, during the entire life span. The most studied environmental influences acting on epigenome are diet, infections, wasting, child care, smoking and environmental pollutants, in particular endocrine disrupters (EDs). These are environmental xenobiotics able to interfere with the normal development of the male and female reproductive systems of wildlife, of experimental animals and possibly of humans, disrupting the normal reproductive functions. Data from literature indicate that EDs can act at different levels of epigenetic control, in some cases transgenerationally, in particular when the exposure to these compounds occurs during the prenatal and earliest period of life. Some of the best characterized EDs will be considered in this review. Among the EDs, vinclozolin (VZ), and methoxychlor (MXC) promote epigenetic transgenerational effects. Polychlorinated biphenils (PCBs), the most widespread environmental EDs, affect histone post-translational modifications in a dimorphic way, possibly as the result of an alteration of gene expression of the enzymes involved in histone modification, as the demethylase Jarid1b, an enzyme also involved in regulating the interaction of androgens with their receptor.
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Affiliation(s)
- Lavinia Casati
- Department of Medical Biotechnology and Translational Medicine, University of Milan Milan, Italy
| | - Ramon Sendra
- Departament de Bioquímica i Biologia Molecular, Universitat de València Valencia, Spain
| | - Valeria Sibilia
- Department of Medical Biotechnology and Translational Medicine, University of Milan Milan, Italy
| | - Fabio Celotti
- Department of Pharmacological and Biomolecular Sciences, University of Milan Milan, Italy
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Wang H, Zhou X, Wu M, Wang C, Zhang X, Tao Y, Chen N, Zang J. Structure of the JmjC-domain-containing protein JMJD5. Acta Crystallogr D Biol Crystallogr 2013; 69:1911-20. [PMID: 24100311 DOI: 10.1107/s0907444913016600] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 06/14/2013] [Indexed: 11/10/2022]
Abstract
The post-translational modification of histone tails is the principal process controlling epigenetic regulation in eukaryotes. The lysine methylation of histones is dynamically regulated by two distinct classes of enzymes: methyltransferases and demethylases. JMJD5, which plays an important role in cell-cycle progression, circadian rhythms and embryonic cell proliferation, has been shown to be a JmjC-domain-containing histone demethylase with enzymatic activity towards H3K36me2. Here, the crystal structure of human JMJD5 lacking the N-terminal 175 amino-acid residues is reported. The structure showed that the Gln275, Trp310 and Trp414 side chains might block the insertion of methylated lysine into the active centre of JMJD5, suppressing the histone demethylase activity of the truncated JMJD5 construct. A comparison of the structure of JMJD5 with that of FIH, a well characterized protein hydroxylase, revealed that human JMJD5 might function as a protein hydroxylase. The interaction between JMJD5 and the core histone octamer proteins indicated that the histone proteins could be potential substrates for JMJD5.
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Affiliation(s)
- Haipeng Wang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
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Harrison IF, Dexter DT. Epigenetic targeting of histone deacetylase: therapeutic potential in Parkinson's disease? Pharmacol Ther 2013; 140:34-52. [PMID: 23711791 DOI: 10.1016/j.pharmthera.2013.05.010] [Citation(s) in RCA: 150] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/09/2013] [Indexed: 12/12/2022]
Abstract
Parkinson's disease (PD) is the most common movement disorder affecting more than 4million people worldwide. The primary motor symptoms of the disease are due to degeneration of dopaminergic nigrostriatal neurons. Dopamine replacement therapies have therefore revolutionised disease management by partially controlling these symptoms. However these drugs can produce debilitating side effects when used long term and do not protect degenerating neurons against death. Recent evidence has highlighted a pathological imbalance in PD between the acetylation and deacetylation of the histone proteins around which deoxyribonucleic acid (DNA) is coiled, in favour of excessive histone deacetylation. This mechanism of adding/removing acetyl groups to histone lysine residues is one of many epigenetic regulatory processes which control the expression of genes, many of which will be essential for neuronal survival. Hence, such epigenetic modifications may have a pathogenic role in PD. It has therefore been hypothesised that if this pathological imbalance can be corrected with the use of histone deacetylase inhibiting agents then neurodegeneration observed in PD can be ameliorated. This article will review the current literature with regard to epigenetic changes in PD and the use of histone deacetylase inhibitors (HDACIs) in PD: examining the evidence of the neuroprotective effects of numerous HDACIs in cellular and animal models of Parkinsonian cell death. Ultimately answering the question: does epigenetic targeting of histone deacetylases hold therapeutic potential in PD?
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Affiliation(s)
- Ian F Harrison
- Parkinson's Disease Research Group, Centre for Neuroinflammation and Neurodegeneration, Division of Brain Sciences, Department of Medicine, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK.
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Hou J, Wu J, Dombkowski A, Zhang K, Holowatyj A, Boerner JL, Yang ZQ. Genomic amplification and a role in drug-resistance for the KDM5A histone demethylase in breast cancer. Am J Transl Res 2012; 4:247-256. [PMID: 22937203 PMCID: PMC3426386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 06/11/2012] [Indexed: 06/01/2023]
Abstract
Lysine-specific demethylase 5A (KDM5A), an enzyme that removes activating H3K4 di- and trimethylation marks, plays critical roles in controlling transcription and chromatin architecture, yet its biological functions largely remain uncharacterized, particularly in the context of human cancer. In the present study, we found that the KDM5A gene was significantly amplified and over-expressed in various human tumors, including breast cancer. Reducing the expression of KDM5A by shRNA knockdown inhibited proliferation of KDM5A-amplified breast cancer cells. More importantly, we demonstrated that KDM5A over-expression was associated with breast cancer drug resistance. Furthermore, knockdown of KDM5A gene expression altered H3K4 methylation and induced upregulation of CDK inhibitors as well as genes mediating apoptotic cell death. Taken together, our study strongly links KDM5A histone demethylase activity to breast cancer proliferation and drug resistance, and suggests KDM5A is a potential target for breast cancer therapy.
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Affiliation(s)
- Jinling Hou
- Karmanos Cancer Institute, Department of Oncology, Wayne State UniversityDetroit, MI 48201, USA
| | - Jack Wu
- Karmanos Cancer Institute, Department of Oncology, Wayne State UniversityDetroit, MI 48201, USA
| | - Alan Dombkowski
- Department of Pediatrics, Wayne State UniversityDetroit, MI 48201, USA
| | - Kezhong Zhang
- Karmanos Cancer Institute, Department of Oncology, Wayne State UniversityDetroit, MI 48201, USA
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroit, MI 48201, USA
- Department of Immunology and Microbiology, Wayne State UniversityDetroit, MI 48201, USA
| | - Andreana Holowatyj
- Karmanos Cancer Institute, Department of Oncology, Wayne State UniversityDetroit, MI 48201, USA
| | - Julie L Boerner
- Karmanos Cancer Institute, Department of Oncology, Wayne State UniversityDetroit, MI 48201, USA
| | - Zeng-Quan Yang
- Karmanos Cancer Institute, Department of Oncology, Wayne State UniversityDetroit, MI 48201, USA
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