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Li CY, Wang W, Leung CH, Yang GJ, Chen J. KDM5 family as therapeutic targets in breast cancer: Pathogenesis and therapeutic opportunities and challenges. Mol Cancer 2024; 23:109. [PMID: 38769556 PMCID: PMC11103982 DOI: 10.1186/s12943-024-02011-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/29/2024] [Indexed: 05/22/2024] Open
Abstract
Breast cancer (BC) is the most frequent malignant cancer diagnosis and is a primary factor for cancer deaths in women. The clinical subtypes of BC include estrogen receptor (ER) positive, progesterone receptor (PR) positive, human epidermal growth factor receptor 2 (HER2) positive, and triple-negative BC (TNBC). Based on the stages and subtypes of BC, various treatment methods are available with variations in the rates of progression-free disease and overall survival of patients. However, the treatment of BC still faces challenges, particularly in terms of drug resistance and recurrence. The study of epigenetics has provided new ideas for treating BC. Targeting aberrant epigenetic factors with inhibitors represents a promising anticancer strategy. The KDM5 family includes four members, KDM5A, KDM5B, KDM5C, and KDMD, all of which are Jumonji C domain-containing histone H3K4me2/3 demethylases. KDM5 proteins have been extensively studied in BC, where they are involved in suppressing or promoting BC depending on their specific upstream and downstream pathways. Several KDM5 inhibitors have shown potent BC inhibitory activity in vitro and in vivo, but challenges still exist in developing KDM5 inhibitors. In this review, we introduce the subtypes of BC and their current therapeutic options, summarize KDM5 family context-specific functions in the pathobiology of BC, and discuss the outlook and pitfalls of KDM5 inhibitors in this disease.
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Affiliation(s)
- Chang-Yun Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Wanhe Wang
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shaanxi, 710072, China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China.
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macau, China.
- Macao Centre for Research and Development in Chinese Medicine, University of Macau, Macau, China.
- MoE Frontiers Science Centre for Precision Oncology, University of Macau, Macau, China.
| | - Guan-Jun Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China.
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China.
- Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
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Di Nisio E, Danovska S, Condemi L, Cirigliano A, Rinaldi T, Licursi V, Negri R. H3 Lysine 4 Methylation Is Required for Full Activation of Genes Involved in α-Ketoglutarate Availability in the Nucleus of Yeast Cells after Diauxic Shift. Metabolites 2023; 13:metabo13040507. [PMID: 37110165 PMCID: PMC10146420 DOI: 10.3390/metabo13040507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
We show that in S. cerevisiae the metabolic diauxic shift is associated with a H3 lysine 4 tri-methylation (H3K4me3) increase which involves a significant fraction of transcriptionally induced genes which are required for the metabolic changes, suggesting a role for histone methylation in their transcriptional regulation. We show that histone H3K4me3 around the start site correlates with transcriptional induction in some of these genes. Among the methylation-induced genes are IDP2 and ODC1, which regulate the nuclear availability of α-ketoglutarate, which, as a cofactor for Jhd2 demethylase, regulates H3K4 tri-methylation. We propose that this feedback circuit could be used to regulate the nuclear α-ketoglutarate pool concentration. We also show that yeast cells adapt to the absence of Jhd2 by decreasing Set1 methylation activity.
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3
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Taylor-Papadimitriou J, Burchell JM. Histone Methylases and Demethylases Regulating Antagonistic Methyl Marks: Changes Occurring in Cancer. Cells 2022; 11:cells11071113. [PMID: 35406676 PMCID: PMC8997813 DOI: 10.3390/cells11071113] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 02/06/2023] Open
Abstract
Epigenetic regulation of gene expression is crucial to the determination of cell fate in development and differentiation, and the Polycomb (PcG) and Trithorax (TrxG) groups of proteins, acting antagonistically as complexes, play a major role in this regulation. Although originally identified in Drosophila, these complexes are conserved in evolution and the components are well defined in mammals. Each complex contains a protein with methylase activity (KMT), which can add methyl groups to a specific lysine in histone tails, histone 3 lysine 27 (H3K27), by PcG complexes, and H3K4 and H3K36 by TrxG complexes, creating transcriptionally repressive or active marks, respectively. Histone demethylases (KDMs), identified later, added a new dimension to histone methylation, and mutations or changes in levels of expression are seen in both methylases and demethylases and in components of the PcG and TrX complexes across a range of cancers. In this review, we focus on both methylases and demethylases governing the methylation state of the suppressive and active marks and consider their action and interaction in normal tissues and in cancer. A picture is emerging which indicates that the changes which occur in cancer during methylation of histone lysines can lead to repression of genes, including tumour suppressor genes, or to the activation of oncogenes. Methylases or demethylases, which are themselves tumour suppressors, are highly mutated. Novel targets for cancer therapy have been identified and a methylase (KMT6A/EZH2), which produces the repressive H3K27me3 mark, and a demethylase (KDM1A/LSD1), which demethylates the active H3K4me2 mark, are now under clinical evaluation.
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Botta L, Filippi S, Zippilli C, Cesarini S, Bizzarri BM, Cirigliano A, Rinaldi T, Paiardini A, Fiorucci D, Saladino R, Negri R, Benedetti P. Artemisinin Derivatives with Antimelanoma Activity Show Inhibitory Effect against Human DNA Topoisomerase 1. ACS Med Chem Lett 2020; 11:1035-1040. [PMID: 32435422 DOI: 10.1021/acsmedchemlett.0c00131] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 04/10/2020] [Indexed: 02/07/2023] Open
Abstract
Artesunic acid and artemisinin are natural substances with promiscuous anticancer activity against different types of cancer cell lines. The mechanism of action of these compounds is associated with the formation of reactive radical species by cleavage of the sesquiterpene pharmacophore endoperoxide bridge. Here we suggested topoisomerase 1 as a possible molecular target for the improvement of the anticancer activity of these compounds. In this context, we report that novel hybrid and dimer derivatives of artesunic acid and artemisinin, bearing camptothecin and SN38 as side-chain biological effectors, can inhibit growth of yeast cells overexpressing human topoisomerase 1 and its enzymatic activity in vitro. These derivatives showed also anticancer activity in melanoma cell lines higher than camptothecin and paclitaxel. In silico molecular docking calculations highlighted a common binding mode for the novel derivatives, with the sesquiterpene lactone scaffold being located near the traditional recognition site for camptothecin, while the bioactive side-chain effector laid in the camptothecin cleft.
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Affiliation(s)
- Lorenzo Botta
- Department of Ecological and Biological Sciences, University of Tuscia, via S. C. De Lellis 44, 01100 Viterbo, Italy
| | - Silvia Filippi
- Department of Ecological and Biological Sciences, University of Tuscia, via S. C. De Lellis 44, 01100 Viterbo, Italy
| | - Claudio Zippilli
- Department of Ecological and Biological Sciences, University of Tuscia, via S. C. De Lellis 44, 01100 Viterbo, Italy
| | - Silvia Cesarini
- Department of Ecological and Biological Sciences, University of Tuscia, via S. C. De Lellis 44, 01100 Viterbo, Italy
| | - Bruno Mattia Bizzarri
- Department of Ecological and Biological Sciences, University of Tuscia, via S. C. De Lellis 44, 01100 Viterbo, Italy
| | - Angela Cirigliano
- Istituto di Biologia e Patologia Molecolari, CNR Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Teresa Rinaldi
- Sapienza University of Rome, Department of Biology and Biotechnology, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Alessandro Paiardini
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Diego Fiorucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Raffaele Saladino
- Department of Ecological and Biological Sciences, University of Tuscia, via S. C. De Lellis 44, 01100 Viterbo, Italy
| | - Rodolfo Negri
- Sapienza University of Rome, Department of Biology and Biotechnology, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Pietro Benedetti
- Dipartimento di Biologia, Università di Padova Distaccato presso il “Centro Linceo Beniamino Segre” Accademia Nazionale dei Lincei, Palazzo Corsini, Via della Lungara 10, 00165 Rome, Italy
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Pippa S, Mannironi C, Licursi V, Bombardi L, Colotti G, Cundari E, Mollica A, Coluccia A, Naccarato V, La Regina G, Silvestri R, Negri R. Small Molecule Inhibitors of KDM5 Histone Demethylases Increase the Radiosensitivity of Breast Cancer Cells Overexpressing JARID1B. Molecules 2019; 24:molecules24091739. [PMID: 31060229 PMCID: PMC6540222 DOI: 10.3390/molecules24091739] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 04/24/2019] [Accepted: 05/01/2019] [Indexed: 12/18/2022] Open
Abstract
Background: KDM5 enzymes are H3K4 specific histone demethylases involved in transcriptional regulation and DNA repair. These proteins are overexpressed in different kinds of cancer, including breast, prostate and bladder carcinomas, with positive effects on cancer proliferation and chemoresistance. For these reasons, these enzymes are potential therapeutic targets. Methods: In the present study, we analyzed the effects of three different inhibitors of KDM5 enzymes in MCF-7 breast cancer cells over-expressing one of them, namely KDM5B/JARID1B. In particular we tested H3K4 demethylation (western blot); radio-sensitivity (cytoxicity and clonogenic assays) and damage accumulation (COMET assay and kinetics of H2AX phosphorylation). Results: we show that all three compounds with completely different chemical structures can selectively inhibit KDM5 enzymes and are capable of increasing sensitivity of breast cancer cells to ionizing radiation and radiation-induced damage. Conclusions: These findings confirm the involvement of H3K4 specific demethylases in the response to DNA damage, show a requirement of the catalytic function and suggest new strategies for the therapeutic use of their inhibitors.
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Affiliation(s)
- Simone Pippa
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy.
| | - Cecilia Mannironi
- Institute of Molecular Biology and Pathology, Italian National Research Council, 00185 Rome, Italy.
| | - Valerio Licursi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy.
- Institute for Systems Analysis and Computer Science "A. Ruberti", Italian National Research Council, 00185 Rome, Italy.
| | - Luca Bombardi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy.
| | - Gianni Colotti
- Institute of Molecular Biology and Pathology, Italian National Research Council, 00185 Rome, Italy.
| | - Enrico Cundari
- Institute of Molecular Biology and Pathology, Italian National Research Council, 00185 Rome, Italy.
| | - Adriano Mollica
- Department of Pharmacy, University "G. d' Annunzio" of Chieti, Via dei Vestini 31, 66100 Chieti, Italy.
| | - Antonio Coluccia
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy.
| | - Valentina Naccarato
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy.
| | - Giuseppe La Regina
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy.
| | - Romano Silvestri
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy.
| | - Rodolfo Negri
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy.
- Institute of Molecular Biology and Pathology, Italian National Research Council, 00185 Rome, Italy.
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6
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Mocavini I, Pippa S, Licursi V, Paci P, Trisciuoglio D, Mannironi C, Presutti C, Negri R. JARID1B expression and its function in DNA damage repair are tightly regulated by miRNAs in breast cancer. Cancer Sci 2019; 110:1232-1243. [PMID: 30588710 PMCID: PMC6447846 DOI: 10.1111/cas.13925] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 12/13/2018] [Accepted: 12/16/2018] [Indexed: 12/18/2022] Open
Abstract
JARID1B/KDM5B histone demethylase's mRNA is markedly overexpressed in breast cancer tissues and cell lines and the protein has been shown to have a prominent role in cancer cell proliferation and DNA repair. However, the mechanism of its post‐transcriptional regulation in cancer cells remains elusive. We performed a computational analysis of transcriptomic data from a set of 103 breast cancer patients, which, along with JARID1B upregulation, showed a strong downregulation of 2 microRNAs (miRNAs), mir‐381 and mir‐486, potentially targeting its mRNA. We showed that both miRNAs can target JARID1B 3′UTR and reduce luciferase's activity in a complementarity‐driven repression assay. Moreover, MCF7 breast cancer cells overexpressing JARID1B showed a strong protein reduction when transfected with mir‐486. This protein's decrease is accompanied by accumulation of DNA damage, enhanced radiosensitivity and increase of BRCA1 mRNA, 3 features previously correlated with JARID1B silencing. These results enlighten an important role of a miRNA’s circuit in regulating JARID1B's activity and suggest new perspectives for epigenetic therapies.
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Affiliation(s)
| | - Simone Pippa
- Department of Biology and Biotechnology "C. Darwin,", "Sapienza" - University of Rome, Rome, Italy
| | - Valerio Licursi
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Paola Paci
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Daniela Trisciuoglio
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Cecilia Mannironi
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Carlo Presutti
- Department of Biology and Biotechnology "C. Darwin,", "Sapienza" - University of Rome, Rome, Italy.,Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Rodolfo Negri
- Department of Biology and Biotechnology "C. Darwin,", "Sapienza" - University of Rome, Rome, Italy.,Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
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7
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Abstract
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Post-translational
modifications of histones by protein methyltransferases
(PMTs) and histone demethylases (KDMs) play an important role in the
regulation of gene expression and transcription and are implicated
in cancer and many other diseases. Many of these enzymes also target
various nonhistone proteins impacting numerous crucial biological
pathways. Given their key biological functions and implications in
human diseases, there has been a growing interest in assessing these
enzymes as potential therapeutic targets. Consequently, discovering
and developing inhibitors of these enzymes has become a very active
and fast-growing research area over the past decade. In this review,
we cover the discovery, characterization, and biological application
of inhibitors of PMTs and KDMs with emphasis on key advancements in
the field. We also discuss challenges, opportunities, and future directions
in this emerging, exciting research field.
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Affiliation(s)
- H Ümit Kaniskan
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Michael L Martini
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Jian Jin
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
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8
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Jambhekar A, Anastas JN, Shi Y. Histone Lysine Demethylase Inhibitors. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026484. [PMID: 28049654 DOI: 10.1101/cshperspect.a026484] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The dynamic regulation of covalent modifications to histones is essential for maintaining genomic integrity and cell identity and is often compromised in cancer. Aberrant expression of histone lysine demethylases has been documented in many types of blood and solid tumors, and thus demethylases represent promising therapeutic targets. Recent advances in high-throughput chemical screening, structure-based drug design, and structure-activity relationship studies have improved both the specificity and the in vivo efficacy of demethylase inhibitors. This review will briefly outline the connection between demethylases and cancer and will provide a comprehensive overview of the structure, specificity, and utility of currently available demethylase inhibitors. To date, a select group of demethylase inhibitors is being evaluated in clinical trials, and additional compounds may soon follow from the bench to the bedside.
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Affiliation(s)
- Ashwini Jambhekar
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115
| | - Jamie N Anastas
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Yang Shi
- Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts 02115.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
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9
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Discovery of resveratrol derivatives as novel LSD1 inhibitors: Design, synthesis and their biological evaluation. Eur J Med Chem 2017; 126:246-258. [DOI: 10.1016/j.ejmech.2016.11.035] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/14/2016] [Accepted: 11/15/2016] [Indexed: 01/06/2023]
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10
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Penterling C, Drexler GA, Böhland C, Stamp R, Wilke C, Braselmann H, Caldwell RB, Reindl J, Girst S, Greubel C, Siebenwirth C, Mansour WY, Borgmann K, Dollinger G, Unger K, Friedl AA. Depletion of Histone Demethylase Jarid1A Resulting in Histone Hyperacetylation and Radiation Sensitivity Does Not Affect DNA Double-Strand Break Repair. PLoS One 2016; 11:e0156599. [PMID: 27253695 PMCID: PMC4890786 DOI: 10.1371/journal.pone.0156599] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 05/17/2016] [Indexed: 12/31/2022] Open
Abstract
Histone demethylases have recently gained interest as potential targets in cancer treatment and several histone demethylases have been implicated in the DNA damage response. We investigated the effects of siRNA-mediated depletion of histone demethylase Jarid1A (KDM5A, RBP2), which demethylates transcription activating tri- and dimethylated lysine 4 at histone H3 (H3K4me3/me2), on growth characteristics and cellular response to radiation in several cancer cell lines. In unirradiated cells Jarid1A depletion lead to histone hyperacetylation while not affecting cell growth. In irradiated cells, depletion of Jarid1A significantly increased cellular radiosensitivity. Unexpectedly, the hyperacetylation phenotype did not lead to disturbed accumulation of DNA damage response and repair factors 53BP1, BRCA1, or Rad51 at damage sites, nor did it influence resolution of radiation-induced foci or rejoining of reporter constructs. We conclude that the radiation sensitivity observed following depletion of Jarid1A is not caused by a deficiency in repair of DNA double-strand breaks.
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Affiliation(s)
- Corina Penterling
- Department of Radiation Oncology, Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Guido A. Drexler
- Department of Radiation Oncology, Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Claudia Böhland
- Department of Radiation Oncology, Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Ramona Stamp
- Department of Radiation Oncology, Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Christina Wilke
- Research Unit Radiation Cytogenetics, Helmholtz Center Munich, Neuherberg, Germany
| | - Herbert Braselmann
- Research Unit Radiation Cytogenetics, Helmholtz Center Munich, Neuherberg, Germany
| | - Randolph B. Caldwell
- Research Unit Radiation Cytogenetics, Helmholtz Center Munich, Neuherberg, Germany
| | - Judith Reindl
- Institut für Angewandte Physik und Messtechnik, Universität der Bundeswehr München, Neubiberg, Germany
| | - Stefanie Girst
- Institut für Angewandte Physik und Messtechnik, Universität der Bundeswehr München, Neubiberg, Germany
| | - Christoph Greubel
- Institut für Angewandte Physik und Messtechnik, Universität der Bundeswehr München, Neubiberg, Germany
| | | | - Wael Y. Mansour
- Laboratory of Radiobiology & Experimental Radiooncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Tumor Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Kerstin Borgmann
- Laboratory of Radiobiology & Experimental Radiooncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Günther Dollinger
- Institut für Angewandte Physik und Messtechnik, Universität der Bundeswehr München, Neubiberg, Germany
| | - Kristian Unger
- Research Unit Radiation Cytogenetics, Helmholtz Center Munich, Neuherberg, Germany
- Clinical Cooperation Group ‘Personalized Radiotherapy of Head and Neck Cancer’, Helmholtz Center Munich, Neuherberg, Germany
| | - Anna A. Friedl
- Department of Radiation Oncology, Ludwig-Maximilians-University of Munich, Munich, Germany
- Clinical Cooperation Group ‘Personalized Radiotherapy of Head and Neck Cancer’, Helmholtz Center Munich, Neuherberg, Germany
- * E-mail:
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11
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McAllister TE, England KS, Hopkinson RJ, Brennan PE, Kawamura A, Schofield CJ. Recent Progress in Histone Demethylase Inhibitors. J Med Chem 2016; 59:1308-29. [PMID: 26710088 DOI: 10.1021/acs.jmedchem.5b01758] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
There is increasing interest in targeting histone N-methyl-lysine demethylases (KDMs) with small molecules both for the generation of probes for target exploration and for therapeutic purposes. Here we update on previous reviews on the inhibition of the lysine-specific demethylases (LSDs or KDM1s) and JmjC families of N-methyl-lysine demethylases (JmjC KDMs, KDM2-7), focusing on the academic and patent literature from 2014 to date. We also highlight recent biochemical, biological, and structural studies which are relevant to KDM inhibitor development.
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Affiliation(s)
- Tom E McAllister
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford, OX1 3TA, U.K
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford , Old Road Campus, Roosevelt Drive, Headington, OX3 7BN, U.K
| | - Katherine S England
- Structural Genomics Consortium, University of Oxford , Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, U.K
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Headington, OX3 7FZ, U.K
| | - Richard J Hopkinson
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford, OX1 3TA, U.K
| | - Paul E Brennan
- Structural Genomics Consortium, University of Oxford , Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, U.K
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Headington, OX3 7FZ, U.K
| | - Akane Kawamura
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford, OX1 3TA, U.K
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford , Old Road Campus, Roosevelt Drive, Headington, OX3 7BN, U.K
| | - Christopher J Schofield
- Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford, OX1 3TA, U.K
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12
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Martinez NJ, Simeonov A. Cell-based assays to support the profiling of small molecules with histone methyltransferase and demethylase modulatory activity. DRUG DISCOVERY TODAY. TECHNOLOGIES 2015; 18:9-17. [PMID: 26723887 DOI: 10.1016/j.ddtec.2015.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 10/07/2015] [Indexed: 02/07/2023]
Abstract
Histone methylation is a prevalent and dynamic chromatin modification, executed by the action of histone methyltransferases (HMTs) and demethylases (HDMs). Aberrant activity of many of these enzymes is associated with human disease, hence, there is a growing interest in identifying corresponding small molecule inhibitors with therapeutic potential. To date, most of the technologies supporting the identification of these inhibitors constitute in vitro biochemical assays which, although robust and sensitive, do not study HMTs and HDMs in their native cellular state nor provide information of inhibitor's cell permeability and toxicity. The evident need for complementary cellular approaches has recently propelled the development of cell-based assays that enable screening of HMT and HDM enzymes in a more relevant environment. Here, we highlight current cellular methodologies for HMT and HDM drug discovery support. We anticipate that implementation of these cell-based assays will positively impact the discovery of pharmacologically potent HMT and HDM inhibitors.
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Affiliation(s)
- Natalia J Martinez
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, United States.
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Keenan MM, Liu B, Tang X, Wu J, Cyr D, Stevens RD, Ilkayeva O, Huang Z, Tollini LA, Murphy SK, Lucas J, Muoio DM, Kim SY, Chi JT. ACLY and ACC1 Regulate Hypoxia-Induced Apoptosis by Modulating ETV4 via α-ketoglutarate. PLoS Genet 2015; 11:e1005599. [PMID: 26452058 PMCID: PMC4599891 DOI: 10.1371/journal.pgen.1005599] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 09/21/2015] [Indexed: 12/13/2022] Open
Abstract
In order to propagate a solid tumor, cancer cells must adapt to and survive under various tumor microenvironment (TME) stresses, such as hypoxia or lactic acidosis. To systematically identify genes that modulate cancer cell survival under stresses, we performed genome-wide shRNA screens under hypoxia or lactic acidosis. We discovered that genetic depletion of acetyl-CoA carboxylase (ACACA or ACC1) or ATP citrate lyase (ACLY) protected cancer cells from hypoxia-induced apoptosis. Additionally, the loss of ACLY or ACC1 reduced levels and activities of the oncogenic transcription factor ETV4. Silencing ETV4 also protected cells from hypoxia-induced apoptosis and led to remarkably similar transcriptional responses as with silenced ACLY or ACC1, including an anti-apoptotic program. Metabolomic analysis found that while α-ketoglutarate levels decrease under hypoxia in control cells, α-ketoglutarate is paradoxically increased under hypoxia when ACC1 or ACLY are depleted. Supplementation with α-ketoglutarate rescued the hypoxia-induced apoptosis and recapitulated the decreased expression and activity of ETV4, likely via an epigenetic mechanism. Therefore, ACC1 and ACLY regulate the levels of ETV4 under hypoxia via increased α-ketoglutarate. These results reveal that the ACC1/ACLY-α-ketoglutarate-ETV4 axis is a novel means by which metabolic states regulate transcriptional output for life vs. death decisions under hypoxia. Since many lipogenic inhibitors are under investigation as cancer therapeutics, our findings suggest that the use of these inhibitors will need to be carefully considered with respect to oncogenic drivers, tumor hypoxia, progression and dormancy. More broadly, our screen provides a framework for studying additional tumor cell stress-adaption mechanisms in the future. During the development of most solid tumors, there are characteristic physiological differences in the tumor that result from tumor cells outgrowing their local blood supply. Two of these physiological differences, or “stresses,” that occur in the tumor are low oxygen levels (hypoxia) and an accumulation of lactic acidic (lactic acidosis). Cancer cells experiencing hypoxia and lactic acidosis tend to be more resistant to chemo- and radio-therapy and metastasize more readily. Therefore, it is important to understand how tumor cells adapt to and survive these stresses. We used a large scale screening experiment in order to find which genes and proteins are involved in tumor cell adaptation and survival under hypoxia or lactic acidosis. We found that inhibiting either of two genes involved in lipid synthesis allowed tumor cells to survive hypoxia. This occurred because silencing these genes led to an increase in the metabolite α-ketoglutarate, which repressed a transcription factor that contributed to cell death under hypoxia. This research specifically advances our understanding of how tumor cells survive hypoxia and lactic acidosis and more broadly enhances our understanding of the cellular biology of solid tumors.
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Affiliation(s)
- Melissa M. Keenan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Beiyu Liu
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Xiaohu Tang
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Jianli Wu
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Derek Cyr
- Department of Electrical and Computer Engineering, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Robert D. Stevens
- Sarah W Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, North Carolina, United States of America
- Duke Institute of Molecular Physiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Olga Ilkayeva
- Sarah W Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, North Carolina, United States of America
- Duke Institute of Molecular Physiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Zhiqing Huang
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Laura A. Tollini
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Susan K. Murphy
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Joseph Lucas
- Department of Electrical and Computer Engineering, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Deborah M. Muoio
- Sarah W Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, North Carolina, United States of America
- Duke Institute of Molecular Physiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - So Young Kim
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Jen-Tsan Chi
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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Gale M, Yan Q. High-throughput screening to identify inhibitors of lysine demethylases. Epigenomics 2015; 7:57-65. [PMID: 25687466 DOI: 10.2217/epi.14.63] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Lysine demethylases (KDMs) are epigenetic regulators whose dysfunction is implicated in the pathology of many human diseases including various types of cancer, inflammation and X-linked intellectual disability. Particular demethylases have been identified as promising therapeutic targets, and tremendous efforts are being devoted toward developing suitable small-molecule inhibitors for clinical and research use. Several High-throughput screening strategies have been developed to screen for small-molecule inhibitors of KDMs, each with advantages and disadvantages in terms of time, cost, effort, reliability and sensitivity. In this Special Report, we review and evaluate the High-throughput screening methods utilized for discovery of novel small-molecule KDM inhibitors.
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Affiliation(s)
- Molly Gale
- Department of Pathology, Yale School of Medicine, New Haven, 310 Cedar St., BML348C, PO Box 208023, New Haven, CT 06520, USA
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Ganai SA, Kalladi SM, Mahadevan V. HDAC inhibition through valproic acid modulates the methylation profiles in human embryonic kidney cells. J Biomol Struct Dyn 2014; 33:1185-97. [PMID: 25012937 DOI: 10.1080/07391102.2014.938247] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Post-translational modifications on the tails of core and linker histones dictate transcription and have vital roles in disease and development. Acetylation and deacetylation events enabled by histone acetyl transferases and histone deacetylases (HDACs) on the chromatin milieu are intricately involved in gene regulation. Inhibition of HDACs is emerging as a powerful strategy in regenerative therapy, transplantation, development and in nuclear reprogramming events. Valproic acid (VPA), belonging to the short-chain fatty acid group of HDAC inhibitors, modulates the epigenome altering gene expression profiles across cell lines. This work attempts to explore the methylation profiles triggered by VPA treatment on human embryonic kidney cells (HEK 293) through a biochemical and computational approach. VPA treatment (for 48 h) has been observed to hypermethylate lysine 4 on the core histone H3 and confers a hypomethylation status of H3 lysine 27 in HEK 293 cells leaving the nuclear area and nuclear contour unaltered. Our structural docking and Binding Free Energy (BFE) calculations establish an active role for VPA in inhibiting the demethylase JARID1A (Jumonji, AT Rich Interactive Domain 1A) and the methyl-transferase EZH2 (Enhancer of Zeste Homologue 2). This work has also proven that VPA can inhibit the activity of proteins like GSK3β and PKCβII involved in developmental disorders. This work establishes a dynamic correlation between histone methylation events and HDAC inhibition and may define newer epigenetic strategies for treating neurodevelopmental and oncological disorders.
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Affiliation(s)
- Shabir Ahmad Ganai
- a Center for Nanotechnology & Advanced Biomaterials, School of Chemical & Biotechnology , SASTRA University , Thanjavur 613401 , India
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