151
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Affiliation(s)
- Christopher J Burns
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
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152
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Dalvi MP, Martinez ED. JumonjiC demethylase inhibitors show potential for targeting chemotherapy-resistant lung cancers. Mol Cell Oncol 2017; 4:e1345352. [PMID: 29057307 DOI: 10.1080/23723556.2017.1345352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 06/19/2017] [Indexed: 10/19/2022]
Abstract
Resistance to standard taxane-platin chemotherapy and tumor relapse are a major challenge in the treatment of non-small cell lung cancers (NSCLC). Our recent study identified JumonjiC demethylase inhibitors as a highly potent therapeutic strategy for targeting chemoresistant tumors and for preventing the emergence of drug-tolerant clones from taxane-platin treated NSCLCs.
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Affiliation(s)
- Maithili P Dalvi
- Hamon Center for Therapeutic Oncology Research, Simmons Comprehensive Cancer Center, and Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Elisabeth D Martinez
- Hamon Center for Therapeutic Oncology Research, Simmons Comprehensive Cancer Center, and Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
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153
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Jedlicka P. The potential of KDM3A as a therapeutic target in Ewing Sarcoma and other cancers. Expert Opin Ther Targets 2017; 21:997-999. [PMID: 29022407 DOI: 10.1080/14728222.2017.1391791] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Paul Jedlicka
- a Department of Pathology , University of Colorado Denver, Anschutz Medical Campus , Aurora , CO , USA
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154
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SETD2 alterations impair DNA damage recognition and lead to resistance to chemotherapy in leukemia. Blood 2017; 130:2631-2641. [PMID: 29018079 DOI: 10.1182/blood-2017-03-775569] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 09/18/2017] [Indexed: 02/06/2023] Open
Abstract
Mutations in SETD2, encoding the histone 3 lysine 36 trimethyltransferase, are enriched in relapsed acute lymphoblastic leukemia and MLL-rearranged acute leukemia. We investigated the impact of SETD2 mutations on chemotherapy sensitivity in isogenic leukemia cell lines and in murine leukemia generated from a conditional knockout of Setd2. SETD2 mutations led to resistance to DNA-damaging agents, cytarabine, 6-thioguanine, doxorubicin, and etoposide, but not to a non-DNA damaging agent, l-asparaginase. H3K36me3 localizes components of the DNA damage response (DDR) pathway and SETD2 mutation impaired DDR, blunting apoptosis induced by cytotoxic chemotherapy. Consistent with local recruitment of DDR, genomic regions with higher H3K36me3 had a lower mutation rate, which was increased with SETD2 mutation. Heterozygous conditional inactivation of Setd2 in a murine model decreased the latency of MLL-AF9-induced leukemia and caused resistance to cytarabine treatment in vivo, whereas homozygous loss delayed leukemia formation. Treatment with JIB-04, an inhibitor of the H3K9/36me3 demethylase KDM4A, restored H3K36me3 levels and sensitivity to cytarabine. These findings establish SETD2 alteration as a mechanism of resistance to DNA-damaging chemotherapy, consistent with a local loss of DDR, and identify a potential therapeutic strategy to target SETD2-mutant leukemias.
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155
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Kulkarni A, Mateus M, Thinnes CC, McCullagh JS, Schofield CJ, Taylor GP, Bangham CRM. Glucose Metabolism and Oxygen Availability Govern Reactivation of the Latent Human Retrovirus HTLV-1. Cell Chem Biol 2017; 24:1377-1387.e3. [PMID: 28965728 PMCID: PMC5696563 DOI: 10.1016/j.chembiol.2017.08.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/24/2017] [Accepted: 08/17/2017] [Indexed: 12/30/2022]
Abstract
The human retrovirus HTLV-1 causes a hematological malignancy or neuroinflammatory disease in ∼10% of infected individuals. HTLV-1 primarily infects CD4+ T lymphocytes and persists as a provirus integrated in their genome. HTLV-1 appears transcriptionally latent in freshly isolated cells; however, the chronically active anti-HTLV-1 cytotoxic T cell response observed in infected individuals indicates frequent proviral expression in vivo. The kinetics and regulation of HTLV-1 proviral expression in vivo are poorly understood. By using hypoxia, small-molecule hypoxia mimics, and inhibitors of specific metabolic pathways, we show that physiologically relevant levels of hypoxia, as routinely encountered by circulating T cells in the lymphoid organs and bone marrow, significantly enhance HTLV-1 reactivation from latency. Furthermore, culturing naturally infected CD4+ T cells in glucose-free medium or chemical inhibition of glycolysis or the mitochondrial electron transport chain strongly suppresses HTLV-1 plus-strand transcription. We conclude that glucose metabolism and oxygen tension regulate HTLV-1 proviral latency and reactivation in vivo. Physiological (1%) hypoxia enhances HTLV-1 plus-strand transcription HTLV-1 transcription is hypoxia regulated but HIF independent Inhibition of glycolysis or the mitochondrial ETC suppresses HTLV-1 transcription Extracellular glucose concentration regulates HTLV-1 reactivation from latency
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Affiliation(s)
- Anurag Kulkarni
- Section of Virology, Department of Medicine, Imperial College, London W2 1PG, UK
| | - Manuel Mateus
- Section of Virology, Department of Medicine, Imperial College, London W2 1PG, UK
| | - Cyrille C Thinnes
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, UK
| | - James S McCullagh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, UK
| | - Graham P Taylor
- Section of Virology, Department of Medicine, Imperial College, London W2 1PG, UK
| | - Charles R M Bangham
- Section of Virology, Department of Medicine, Imperial College, London W2 1PG, UK.
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156
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Lee HJ, Kim BK, Yoon KB, Kim YC, Han SY. Novel inhibitors of lysine (K)-specific Demethylase 4A with anticancer activity. Invest New Drugs 2017; 35:733-741. [PMID: 28905188 DOI: 10.1007/s10637-017-0496-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 07/20/2017] [Indexed: 10/18/2022]
Abstract
Lysine (K)-specific demethylase 4A (KDM4A) is a histone demethylase that removes methyl residues from trimethylated or dimethylated histone 3 at lysines 9 and 36. Overexpression of KDM4A is found in various cancer types. To identify KDM4A inhibitors with anti-tumor functions, screening with an in vitro KDM4A enzyme activity assay was carried out. The benzylidenehydrazine analogue LDD2269 was selected, with an IC50 of 6.56 μM of KDM4A enzyme inhibition, and the binding mode was investigated using in silico molecular docking. Demethylation inhibition by LDD2269 was confirmed with a cell-based assay using antibodies against methylated histone at lysines 9 and 36. HCT-116 colon cancer cell line proliferation was suppressed by LDD2269, which also interfered with soft-agar growth and migration of HCT-116 cells. AnnexinV staining and PARP cleavage experiments showed apoptosis induction by LDD2269. Derivatives of LDD2269 were synthesized and the structure-activity relationship was explored. LDD2269 is reported here as a strong inhibitor of KDM4A in in vitro and cell-based systems, with anti-tumor functions.
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Affiliation(s)
- Hyo Jeong Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Gyeongsang National University, 501 Jinju-daero, Jinju, Gyeongnam, 52828, Republic of Korea
| | - Bo-Kyoung Kim
- School of Life Sciences, Gwangju Institute of Science & Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Republic of Korea.,New Drug Development Center (NDDC), Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu, Republic of Korea
| | - Kyoung Bin Yoon
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Gyeongsang National University, 501 Jinju-daero, Jinju, Gyeongnam, 52828, Republic of Korea
| | - Yong-Chul Kim
- School of Life Sciences, Gwangju Institute of Science & Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Republic of Korea.
| | - Sun-Young Han
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Gyeongsang National University, 501 Jinju-daero, Jinju, Gyeongnam, 52828, Republic of Korea.
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157
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Dobrynin G, McAllister TE, Leszczynska KB, Ramachandran S, Krieg AJ, Kawamura A, Hammond EM. KDM4A regulates HIF-1 levels through H3K9me3. Sci Rep 2017; 7:11094. [PMID: 28894274 PMCID: PMC5593970 DOI: 10.1038/s41598-017-11658-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 08/25/2017] [Indexed: 01/11/2023] Open
Abstract
Regions of hypoxia (low oxygen) occur in most solid tumours and cells in these areas are the most aggressive and therapy resistant. In response to decreased oxygen, extensive changes in gene expression mediated by Hypoxia-Inducible Factors (HIFs) contribute significantly to the aggressive hypoxic tumour phenotype. In addition to HIFs, multiple histone demethylases are altered in their expression and activity, providing a secondary mechanism to extend the hypoxic signalling response. In this study, we demonstrate that the levels of HIF-1α are directly controlled by the repressive chromatin mark, H3K9me3. In conditions where the histone demethylase KDM4A is depleted or inactive, H3K9me3 accumulates at the HIF-1α locus, leading to a decrease in HIF-1α mRNA and a reduction in HIF-1α stabilisation. Loss of KDM4A in hypoxic conditions leads to a decreased HIF-1α mediated transcriptional response and correlates with a reduction in the characteristics associated with tumour aggressiveness, including invasion, migration, and oxygen consumption. The contribution of KDM4A to the regulation of HIF-1α is most robust in conditions of mild hypoxia. This suggests that KDM4A can enhance the function of HIF-1α by increasing the total available protein to counteract any residual activity of prolyl hydroxylases.
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Affiliation(s)
- Grzegorz Dobrynin
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, The University of Oxford, Oxford, OX3 7DQ, UK
| | - Tom E McAllister
- Department of Chemistry, Chemistry Research Laboratory, The University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Katarzyna B Leszczynska
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, The University of Oxford, Oxford, OX3 7DQ, UK
| | - Shaliny Ramachandran
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, The University of Oxford, Oxford, OX3 7DQ, UK
| | - Adam J Krieg
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, Oregon, USA
| | - Akane Kawamura
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Trust Centre of Human Genetics, Roosevelt Drive, The University of Oxford, Oxford, OX3 7BN, UK
- Department of Chemistry, Chemistry Research Laboratory, The University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Ester M Hammond
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, The University of Oxford, Oxford, OX3 7DQ, UK.
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158
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Tan SQ, Geng X, Liu JH, Pan WHT, Wang LX, Liu HK, Hu L, Chao HM. Xue-fu-Zhu-Yu decoction protects rats against retinal ischemia by downregulation of HIF-1α and VEGF via inhibition of RBP2 and PKM2. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2017; 17:365. [PMID: 28709426 PMCID: PMC5513111 DOI: 10.1186/s12906-017-1857-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 06/23/2017] [Indexed: 12/29/2022]
Abstract
BACKGROUND Retinal ischemia-related eye diseases result in visual dysfunction. This study investigates the protective effects and mechanisms of Xue-Fu-Zhu-Yu decoction (XFZYD) with respect to retinal ischemia. METHODS Retinal ischemia (I) was induced in Wistar rats by a high intraocular pressure (HIOP) of 120 mmHg for 1 h, which was followed by reperfusion of the ischemic eye; the fellow untreated eye acted as a control. Electroretinogram (ERG), biochemistry and histopathology investigations were performed. RESULTS Significant ischemic changes occurred after ischemia including decreased ERG b-wave ratios, less numerous retinal ganglion cells (RGCs), reduced inner retinal thickness, fewer choline acetyltransferase (ChAT) labeled amacrine cell bodies, increased glial fibrillary acidic protein (GFAP) immunoreactivity and increased vimentin Müller immunolabeling. These were accompanied by significant increases in the mRNA/protein concentrations of vascular endothelium growth factor, hypoxia-inducible factor-1α, pyruvate kinase M2 and retinoblastoma-binding protein 2. The ischemic changes were concentration-dependently and significantly altered when XFZYD was given for seven consecutive days before or after retina ischemia, compared to vehicle. These alterations included enhanced ERG b-wave amplitudes, more numerous RGCs, enhanced inner retinal thickness, a greater number of ChAT immunolabeled amacrine cell bodies and decreased GFAP/vimentin immunoreactivity. Furthermore, decreased mRNA levels of VEGF, HIF-1α, PKM2, and RBP2 were also found. Reduced protein concentrations of VEGF, HIF-1α, PKM2, and RBP2 were also demonstrated. Furthermore, there was an inhibition of the ischemia-associated increased ratios (target protein/β-actin) in the protein levels of VEGF, HIF-1α, PKM2, and RBP2, which were induced by Shikonin, JIB-04 or Avastin. CONCLUSION XFZYD would seem to protect against well-known retinal ischemic changes via a synergistic inhibition of RBP2 and PKM2, as well as down-regulation of HIF-1α and a reduction in VEGF secretion.
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Affiliation(s)
- Shu-Qiu Tan
- Department of Ophthalmology, Affiliated Hospital of Taishan Medical University, Taishan, Shandong China
| | - Xue Geng
- Department of Pharmacology, School of Medicine, Shandong University, Jinan, Shandong China
| | - Jorn-Hon Liu
- Department of Ophthalmology, Cheng Hsin General Hospital, Taipei, Taiwan
| | - Wynn Hwai-Tzong Pan
- Institute of Pharmacology, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Li-Xiang Wang
- Department of Pharmacology, School of Medicine, Shandong University, Jinan, Shandong China
| | - Hui-Kang Liu
- Division of Basic Chinese Medicine, National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei, Taiwan
| | - Lei Hu
- Department of Ophthalmology, Affiliated Hospital of Taishan Medical University, Taishan, Shandong China
| | - Hsiao-Ming Chao
- Department of Ophthalmology, Cheng Hsin General Hospital, Taipei, Taiwan
- Institute of Pharmacology, School of Medicine, National Yang-Ming University, Taipei, Taiwan
- Department of Chinese Medicine, School of Chinese Medicine, China Medical University, Taichung, Taiwan
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159
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Yang J, Milasta S, Hu D, AlTahan AM, Interiano RB, Zhou J, Davidson J, Low J, Lin W, Bao J, Goh P, Nathwani AC, Wang R, Wang Y, Ong SS, Boyd VA, Young B, Das S, Shelat A, Wu Y, Li Z, Zheng JJ, Mishra A, Cheng Y, Qu C, Peng J, Green DR, White S, Guy RK, Chen T, Davidoff AM. Targeting Histone Demethylases in MYC-Driven Neuroblastomas with Ciclopirox. Cancer Res 2017; 77:4626-4638. [PMID: 28684529 DOI: 10.1158/0008-5472.can-16-0826] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 11/28/2016] [Accepted: 06/29/2017] [Indexed: 12/21/2022]
Abstract
Histone lysine demethylases facilitate the activity of oncogenic transcription factors, including possibly MYC. Here we show that multiple histone demethylases influence the viability and poor prognosis of neuroblastoma cells, where MYC is often overexpressed. We also identified the approved small-molecule antifungal agent ciclopirox as a novel pan-histone demethylase inhibitor. Ciclopirox targeted several histone demethylases, including KDM4B implicated in MYC function. Accordingly, ciclopirox inhibited Myc signaling in parallel with mitochondrial oxidative phosphorylation, resulting in suppression of neuroblastoma cell viability and inhibition of tumor growth associated with an induction of differentiation. Our findings provide new insights into epigenetic regulation of MYC function and suggest a novel pharmacologic basis to target histone demethylases as an indirect MYC-targeting approach for cancer therapy. Cancer Res; 77(17); 4626-38. ©2017 AACR.
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Affiliation(s)
- Jun Yang
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | - Sandra Milasta
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Dongli Hu
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Alaa M AlTahan
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Rodrigo B Interiano
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Junfang Zhou
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jesse Davidson
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jonathan Low
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Wenwei Lin
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ju Bao
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Pollyanna Goh
- Department of Oncology, University College London Cancer Institute, London, United Kingdom
| | - Amit C Nathwani
- Department of Oncology, University College London Cancer Institute, London, United Kingdom
| | - Ruoning Wang
- Department of Pediatrics, The Ohio State University School of Medicine, The Research Institute at Nationwide Children's Hospital, Center for Childhood Cancer and Blood Disease, Columbus, Ohio
| | - Yingdi Wang
- Yale Cardiovascular Research Center, Yale School of Medicine, New Haven, Connecticut
| | - Su Sien Ong
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Vincent A Boyd
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Brandon Young
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sourav Das
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Anang Shelat
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Yinan Wu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Zhenmei Li
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jie J Zheng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Ashutosh Mishra
- Department of Structural Biology, Department of Developmental Neurobiology and St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Yong Cheng
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Chunxu Qu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Junmin Peng
- Department of Structural Biology, Department of Developmental Neurobiology and St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Douglas R Green
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Stephen White
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - R Kiplin Guy
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Andrew M Davidoff
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, Tennessee
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160
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Sdelci S, Kubicek S. Generation of a Cellular Reporter for Functional BRD4 Inhibition. Bio Protoc 2017; 7:e2368. [PMID: 34541110 DOI: 10.21769/bioprotoc.2368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 05/21/2017] [Accepted: 05/30/2017] [Indexed: 11/02/2022] Open
Abstract
The ubiquitously expressed bromodomain-containing protein 4 (BRD4) is an epigenetic reader, which recruits transcriptional regulatory complexes to acetylated chromatin. Because of its role in enhancing proliferation, BRD4 has become a therapeutic target in oncology, as the inhibition of this protein leads to the reduction of the growth of many tumours. Even though BRD4 is more and more studied, its mechanism of action has not been fully described yet. Therefore, we aimed at generating a cellular reporter system to monitor BRD4 inhibition. Such reporter can be potentially used in high throughput chemical and genetic screenings, in order to uncover new possible BRD4 functional pathways. The deeper understanding of the mechanism of action of BRD4 activity will certainly help in developing new therapy strategies for those cancers so called BRD4-dependent.
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Affiliation(s)
- Sara Sdelci
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, Vienna, Austria
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, Vienna, Austria.,Christian Doppler Laboratory for Chemical Epigenetics and Antiinfectives, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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161
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Wang X, Wang S, Yao G, Yu D, Chen K, Tong Q, Ye L, Wu C, Sun Y, Li H, Hermann DM, Doeppner TR, Jin F, Dai Y, Wu J. Identification of the histone lysine demethylase KDM4A/JMJD2A as a novel epigenetic target in M1 macrophage polarization induced by oxidized LDL. Oncotarget 2017; 8:114442-114456. [PMID: 29383092 PMCID: PMC5777704 DOI: 10.18632/oncotarget.17748] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 04/12/2017] [Indexed: 02/05/2023] Open
Abstract
Oxidized low density lipoprotein (oxLDL) induces macrophage activation, an event essential for atherosclerosis. Emerging evidence supports that epigenetic regulation plays important roles in macrophage activation and function. However, it remains unclear which epigenetic modulator is responsible for oxLDL-induced macrophage activation. Here, we identify for the first time KDM4A (JMJD2A) as an epigenetic modifying enzyme that controls oxLDL-induced pro-inflammatory M1 polarization of macrophages. OxLDL triggered M1 polarization of murine and human macrophages, characterized by expression of iNOS and robust production of inflammatory cytokines (e.g., TNF-α, MCP-1, IL-1β). In contrast, protein level of the M2 marker Arg1 was clearly decreased after treated with oxLDL. Notably, exposure to oxLDL resulted in markedly increased expression of KDM4A in macrophages. Functionally, shRNA knockdown of KDM4A significantly impaired M1 polarization and expression of inflammatory cytokines induced by oxLDL, accompanied by increased expression of Arg1 and VEGF. However, inhibition of KDM4A by shRNA or the pan-selective KDM inhibitor JIB-04 did not affect oxLDL-mediated activation of the NF-κB and hypoxia inducible factor (HIF) pathways, and vice versa. In addition, JIB-04 induced apoptosis of macrophages in a dose-dependent manner, an event attenuated by oxLDL. Together, these findings argue that KDM4A might represent a novel epigenetic modulator that acts to direct oxLDL-induced M1 polarization of macrophages, while its up-regulation is independent of NF-κB and HIF activation, two signals critical for pro-inflammatory activation of macrophages. They also suggest that KDM4A might serve as a potential target for epigenetic therapy in prevention and treatment of inflammatory diseases such as atherosclerosis.
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Affiliation(s)
- Xue Wang
- Department of Neurology, the First Hospital of Jilin University, Changchun, Jilin, China
| | - Siqing Wang
- Department of Cancer Immunology, Institute of Translational Medicine, the First Hospital of Jilin University, Changchun, Jilin, China
| | - Gang Yao
- Department of Neurology, the Second Hospital of Jilin University, Changchun, Jilin, China
| | - Dehai Yu
- Cancer Center, the First Hospital of Jilin University, Changchun, Jilin, China
| | - Kexin Chen
- Department of Immunology, Institute of Translational Medicine, the First Hospital of Jilin University, Changchun, Jilin, China
| | - Qian Tong
- Department of Cardiology, the First Hospital of Jilin University, Changchun, Jilin, China
| | - Long Ye
- Department of Spine Surgery, the First Hospital of Jilin University, Changchun, Jilin, China
| | - Chuan Wu
- Department of Hematology, Cancer Center, the First Hospital of Jilin University, Changchun, Jilin, China
| | - Yue Sun
- Laboratory of Cancer Precision Medicine, Cancer Center, the First Hospital of Jilin University, Changchun, Jilin, China
| | - Haixia Li
- Department of Neurology, the First Hospital of Jilin University, Changchun, Jilin, China
| | - Dirk M Hermann
- Department of Neurology, University of Duisburg-Essen, Essen, Germany
| | - Thorsten R Doeppner
- Department of Neurology, University of Göttingen Medical School, Göttingen, Germany
| | - Fengyan Jin
- Department of Hematology, Cancer Center, the First Hospital of Jilin University, Changchun, Jilin, China
| | - Yun Dai
- Laboratory of Cancer Precision Medicine, Cancer Center, the First Hospital of Jilin University, Changchun, Jilin, China
| | - Jiang Wu
- Department of Neurology, the First Hospital of Jilin University, Changchun, Jilin, China
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162
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Carter DM, Specker E, Przygodda J, Neuenschwander M, von Kries JP, Heinemann U, Nazaré M, Gohlke U. Identification of a Novel Benzimidazole Pyrazolone Scaffold That Inhibits KDM4 Lysine Demethylases and Reduces Proliferation of Prostate Cancer Cells. SLAS DISCOVERY 2017; 22:801-812. [PMID: 28346812 DOI: 10.1177/2472555217699157] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Human lysine demethylase (KDM) enzymes (KDM1-7) constitute an emerging class of therapeutic targets, with activities that support growth and development of metastatic disease. By interacting with and co-activating the androgen receptor, the KDM4 subfamily (KDM4A-E) promotes aggressive phenotypes of prostate cancer (PCa). Knockdown of KDM4 expression or inhibition of KDM4 enzyme activity reduces the proliferation of PCa cell lines and highlights inhibition of lysine demethylation as a possible therapeutic method for PCa treatment. To address this possibility, we screened the ChemBioNet small molecule library for inhibitors of the human KDM4E isoform and identified several compounds with IC50 values in the low micromolar range. Two hits, validated as active by an orthogonal enzyme-linked immunosorbent assay, displayed moderate selectivity toward the KDM4 subfamily and exhibited antiproliferative effects in cellular models of PCa. These compounds were further characterized by their ability to maintain the transcriptionally silent histone H3 tri-methyl K9 epigenetic mark at subcytotoxic concentrations. Taken together, these efforts identify and validate a hydroxyquinoline scaffold and a novel benzimidazole pyrazolone scaffold as tractable for entry into hit-to-lead chemical optimization campaigns.
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Affiliation(s)
- David M Carter
- 1 Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Edgar Specker
- 2 Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
| | - Jessica Przygodda
- 1 Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,2 Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
| | | | | | - Udo Heinemann
- 1 Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Marc Nazaré
- 2 Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
| | - Ulrich Gohlke
- 1 Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
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163
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Tumber A, Nuzzi A, Hookway ES, Hatch SB, Velupillai S, Johansson C, Kawamura A, Savitsky P, Yapp C, Szykowska A, Wu N, Bountra C, Strain-Damerell C, Burgess-Brown NA, Ruda GF, Fedorov O, Munro S, England KS, Nowak RP, Schofield CJ, La Thangue NB, Pawlyn C, Davies F, Morgan G, Athanasou N, Müller S, Oppermann U, Brennan PE. Potent and Selective KDM5 Inhibitor Stops Cellular Demethylation of H3K4me3 at Transcription Start Sites and Proliferation of MM1S Myeloma Cells. Cell Chem Biol 2017; 24:371-380. [PMID: 28262558 PMCID: PMC5361737 DOI: 10.1016/j.chembiol.2017.02.006] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 10/31/2016] [Accepted: 02/01/2017] [Indexed: 12/16/2022]
Abstract
Methylation of lysine residues on histone tail is a dynamic epigenetic modification that plays a key role in chromatin structure and gene regulation. Members of the KDM5 (also known as JARID1) sub-family are 2-oxoglutarate (2-OG) and Fe2+-dependent oxygenases acting as histone 3 lysine 4 trimethyl (H3K4me3) demethylases, regulating proliferation, stem cell self-renewal, and differentiation. Here we present the characterization of KDOAM-25, an inhibitor of KDM5 enzymes. KDOAM-25 shows biochemical half maximal inhibitory concentration values of <100 nM for KDM5A-D in vitro, high selectivity toward other 2-OG oxygenases sub-families, and no off-target activity on a panel of 55 receptors and enzymes. In human cell assay systems, KDOAM-25 has a half maximal effective concentration of ∼50 μM and good selectivity toward other demethylases. KDM5B is overexpressed in multiple myeloma and negatively correlated with the overall survival. Multiple myeloma MM1S cells treated with KDOAM-25 show increased global H3K4 methylation at transcriptional start sites and impaired proliferation.
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Affiliation(s)
- Anthony Tumber
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Andrea Nuzzi
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Edward S Hookway
- NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | - Stephanie B Hatch
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Srikannathasan Velupillai
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Catrine Johansson
- NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK; Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Akane Kawamura
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Pavel Savitsky
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
| | - Clarence Yapp
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | | | - Na Wu
- NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | - Chas Bountra
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
| | | | | | - Gian Filippo Ruda
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Oleg Fedorov
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Shonagh Munro
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Katherine S England
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Radoslaw P Nowak
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | | | | | - Charlotte Pawlyn
- Division of Cancer Therapeutics, Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Faith Davies
- Division of Cancer Therapeutics, Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK; University of Arkansas for Medical Sciences, Myeloma Institute, 4301 W. Markham #816, Little Rock, AR 72205, USA
| | - Gareth Morgan
- Division of Cancer Therapeutics, Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK; University of Arkansas for Medical Sciences, Myeloma Institute, 4301 W. Markham #816, Little Rock, AR 72205, USA
| | - Nick Athanasou
- NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK
| | - Susanne Müller
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK.
| | - Udo Oppermann
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford OX3 7LD, UK.
| | - Paul E Brennan
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK.
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164
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Hatch SB, Yapp C, Montenegro RC, Savitsky P, Gamble V, Tumber A, Ruda GF, Bavetsias V, Fedorov O, Atrash B, Raynaud F, Lanigan R, Carmichael L, Tomlin K, Burke R, Westaway SM, Brown JA, Prinjha RK, Martinez ED, Oppermann U, Schofield CJ, Bountra C, Kawamura A, Blagg J, Brennan PE, Rossanese O, Müller S. Assessing histone demethylase inhibitors in cells: lessons learned. Epigenetics Chromatin 2017; 10:9. [PMID: 28265301 PMCID: PMC5333395 DOI: 10.1186/s13072-017-0116-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/21/2017] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Histone lysine demethylases (KDMs) are of interest as drug targets due to their regulatory roles in chromatin organization and their tight associations with diseases including cancer and mental disorders. The first KDM inhibitors for KDM1 have entered clinical trials, and efforts are ongoing to develop potent, selective and cell-active 'probe' molecules for this target class. Robust cellular assays to assess the specific engagement of KDM inhibitors in cells as well as their cellular selectivity are a prerequisite for the development of high-quality inhibitors. Here we describe the use of a high-content cellular immunofluorescence assay as a method for demonstrating target engagement in cells. RESULTS A panel of assays for the Jumonji C subfamily of KDMs was developed to encompass all major branches of the JmjC phylogenetic tree. These assays compare compound activity against wild-type KDM proteins to a catalytically inactive version of the KDM, in which residues involved in the active-site iron coordination are mutated to inactivate the enzyme activity. These mutants are critical for assessing the specific effect of KDM inhibitors and for revealing indirect effects on histone methylation status. The reported assays make use of ectopically expressed demethylases, and we demonstrate their use to profile several recently identified classes of KDM inhibitors and their structurally matched inactive controls. The generated data correlate well with assay results assessing endogenous KDM inhibition and confirm the selectivity observed in biochemical assays with isolated enzymes. We find that both cellular permeability and competition with 2-oxoglutarate affect the translation of biochemical activity to cellular inhibition. CONCLUSIONS High-content-based immunofluorescence assays have been established for eight KDM members of the 2-oxoglutarate-dependent oxygenases covering all major branches of the JmjC-KDM phylogenetic tree. The usage of both full-length, wild-type and catalytically inactive mutant ectopically expressed protein, as well as structure-matched inactive control compounds, allowed for detection of nonspecific effects causing changes in histone methylation as a result of compound toxicity. The developed assays offer a histone lysine demethylase family-wide tool for assessing KDM inhibitors for cell activity and on-target efficacy. In addition, the presented data may inform further studies to assess the cell-based activity of histone lysine methylation inhibitors.
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Affiliation(s)
- Stephanie B. Hatch
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
| | - Clarence Yapp
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
| | - Raquel C. Montenegro
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
- Medical Faculty, Research and Drug Development Center, Federal University of Ceará, Rua Cel. Nunes de Melo n.1000—Rodolfo Teófilo, 60, Fortaleza, CE 430-270 Brazil
| | - Pavel Savitsky
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
| | - Vicki Gamble
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
| | - Anthony Tumber
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
| | - Gian Filippo Ruda
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
| | - Vassilios Bavetsias
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - Oleg Fedorov
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
| | - Butrus Atrash
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - Florence Raynaud
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - Rachel Lanigan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - LeAnne Carmichael
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - Kathy Tomlin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - Rosemary Burke
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - Susan M. Westaway
- Epigenetics Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, SG1 2NY UK
| | - Jack A. Brown
- Epigenetics Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, SG1 2NY UK
| | - Rab K. Prinjha
- Epigenetics Discovery Performance Unit, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, SG1 2NY UK
| | - Elisabeth D. Martinez
- Hamon Center for Therapeutic Oncology Research, and Department of Pharmacology, UT Southwestern Medical Center at Dallas, Dallas, TX 75390 USA
| | - Udo Oppermann
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, NIHR Oxford Biomedical Research Unit, University of Oxford, Oxford, OX3 7LD UK
| | | | - Chas Bountra
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
| | - Akane Kawamura
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA UK
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN UK
| | - Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - Paul E. Brennan
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
| | - Olivia Rossanese
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, 15 Cotswold Road, London, SM2 5NG UK
| | - Susanne Müller
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ UK
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ UK
- Buchmann Institute for Molecular Life Science, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany
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165
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Histone Lysine Demethylases of JMJD2 or KDM4 Family are Important Epigenetic Regulators in Reward Circuitry in the Etiopathology of Depression. Neuropsychopharmacology 2017; 42:854-863. [PMID: 27711046 PMCID: PMC5312068 DOI: 10.1038/npp.2016.231] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Revised: 09/01/2016] [Accepted: 09/30/2016] [Indexed: 01/08/2023]
Abstract
Major depressive disorder (MDD) is debilitating mental illness and is one of the leading contributors to global burden of disease, but unfortunately newer and better drugs are not forthcoming. The reason is lack of complete understanding of molecular mechanisms underlying the development of this disorder. Recent research shows dysregulation in epigenetic regulatory mechanisms, particularly the transcriptionally repressive di- and tri-methylation of histone 3 lysine 9 (H3K9me2/me3) in nucleus accumbens (NAc), a critical region of the reward pathway involved in the development of anhedonia, the hallmark of depression. However, the role of histone lysine demethylases, which can remove methylation from H3K9, in particular Jumonji domain containing demethylases 2 or Jmjd2 family, has not been studied. Using social defeat stress-induced mouse model of depression, this study uncovered that transcripts of most of the Jmjd2 members were unchanged after 5 days of defeat during the onset of depression, but were downregulated after 10 days of defeat in full-blown depression. Blocking the Jumonji domain containing demethylases by chronic administration of inhibitors dimethyloxalylglycine (DMOG) and ML324 resulted in depression-like phenotype even in absence of stress exposure, which was associated with an increase in transcriptionally repressive epigenetic marks H3K9me2/me3 in NAc, causing altered neuroplastic changes as reported in NAc in depression models. Thus, we report for the first time that Jmjd2 class demethylases are critical epigenetic regulators involved in etiopathology of depression and related disorders and activation of these demethylases can be a good strategy in the treatment of MDD and related psychiatric disorders.
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166
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Cascella B, Lee SG, Singh S, Jez JM, Mirica LM. The small molecule JIB-04 disrupts O 2 binding in the Fe-dependent histone demethylase KDM4A/JMJD2A. Chem Commun (Camb) 2017; 53:2174-2177. [PMID: 28144654 PMCID: PMC5511625 DOI: 10.1039/c6cc09882g] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
JIB-04, a specific inhibitor of the O2-activating, Fe-dependent histone lysine demethylases, is revealed to disrupt the binding of O2 in KDM4A/JMJD2A through a continuous O2-consumption assay, X-ray crystal structure data, and molecular docking.
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Affiliation(s)
- Barbara Cascella
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA. and Department of Biology, Washington University, St. Louis, Missouri 63130, USA.
| | - Soon Goo Lee
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA.
| | - Sukrit Singh
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA.
| | - Joseph M Jez
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA.
| | - Liviu M Mirica
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA.
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167
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Zawistowski JS, Bevill SM, Goulet DR, Stuhlmiller TJ, Beltran AS, Olivares-Quintero JF, Singh D, Sciaky N, Parker JS, Rashid NU, Chen X, Duncan JS, Whittle MC, Angus SP, Velarde SH, Golitz BT, He X, Santos C, Darr DB, Gallagher K, Graves LM, Perou CM, Carey LA, Earp HS, Johnson GL. Enhancer Remodeling during Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacologic Targeting of the P-TEFb Complex. Cancer Discov 2017; 7:302-321. [PMID: 28108460 DOI: 10.1158/2159-8290.cd-16-0653] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 01/10/2017] [Accepted: 01/10/2017] [Indexed: 11/16/2022]
Abstract
Targeting the dysregulated BRAF-MEK-ERK pathway in cancer has increasingly emerged in clinical trial design. Despite clinical responses in specific cancers using inhibitors targeting BRAF and MEK, resistance develops often involving nongenomic adaptive bypass mechanisms. Inhibition of MEK1/2 by trametinib in patients with triple-negative breast cancer (TNBC) induced dramatic transcriptional responses, including upregulation of receptor tyrosine kinases (RTK) comparing tumor samples before and after one week of treatment. In preclinical models, MEK inhibition induced genome-wide enhancer formation involving the seeding of BRD4, MED1, H3K27 acetylation, and p300 that drives transcriptional adaptation. Inhibition of the P-TEFb-associated proteins BRD4 and CBP/p300 arrested enhancer seeding and RTK upregulation. BRD4 bromodomain inhibitors overcame trametinib resistance, producing sustained growth inhibition in cells, xenografts, and syngeneic mouse TNBC models. Pharmacologic targeting of P-TEFb members in conjunction with MEK inhibition by trametinib is an effective strategy to durably inhibit epigenomic remodeling required for adaptive resistance.Significance: Widespread transcriptional adaptation to pharmacologic MEK inhibition was observed in TNBC patient tumors. In preclinical models, MEK inhibition induces dramatic genome-wide modulation of chromatin, in the form of de novo enhancer formation and enhancer remodeling. Pharmacologic targeting of P-TEFb complex members at enhancers is an effective strategy to durably inhibit such adaptation. Cancer Discov; 7(3); 302-21. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 235.
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Affiliation(s)
- Jon S Zawistowski
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Samantha M Bevill
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Daniel R Goulet
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Timothy J Stuhlmiller
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Adriana S Beltran
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Jose F Olivares-Quintero
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Darshan Singh
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Noah Sciaky
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Joel S Parker
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Naim U Rashid
- Department of Biostatistics, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Xin Chen
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - James S Duncan
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Martin C Whittle
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Steven P Angus
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Sara Hanna Velarde
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Brian T Golitz
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Xiaping He
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Charlene Santos
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - David B Darr
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Kristalyn Gallagher
- Department of Surgery, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Lee M Graves
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Charles M Perou
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Lisa A Carey
- Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - H Shelton Earp
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina.,Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Gary L Johnson
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina.
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168
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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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169
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Sun L, Fang J. Epigenetic regulation of epithelial-mesenchymal transition. Cell Mol Life Sci 2016; 73:4493-4515. [PMID: 27392607 PMCID: PMC5459373 DOI: 10.1007/s00018-016-2303-1] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 06/10/2016] [Accepted: 06/30/2016] [Indexed: 12/12/2022]
Abstract
Epithelial-mesenchymal transition (EMT) is an essential process for morphogenesis and organ development which reversibly enables polarized epithelial cells to lose their epithelial characteristics and to acquire mesenchymal properties. It is now evident that the aberrant activation of EMT is also a critical mechanism to endow epithelial cancer cells with migratory and invasive capabilities associated with metastatic competence. This dedifferentiation program is mediated by a small cohort of pleiotropic transcription factors which orchestrate a complex array of epigenetic mechanisms for the wide-spread changes in gene expression. Here, we review major epigenetic mechanisms with an emphasis on histone modifications and discuss their implications in EMT and tumor progression. We also highlight mechanisms underlying transcription regulation concerted by various chromatin-modifying proteins and EMT-inducing transcription factors at different molecular layers. Owing to the reversible nature of epigenetic modifications, a thorough understanding of their functions in EMT will not only provide new insights into our knowledge of cancer progression and metastasis, but also facilitate the development of diagnostic and therapeutic strategies for human malignancy.
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Affiliation(s)
- Lidong Sun
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Jia Fang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.
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170
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Wang J, Wang H, Wang LY, Cai D, Duan Z, Zhang Y, Chen P, Zou JX, Xu J, Chen X, Kung HJ, Chen HW. Silencing the epigenetic silencer KDM4A for TRAIL and DR5 simultaneous induction and antitumor therapy. Cell Death Differ 2016; 23:1886-1896. [PMID: 27612013 PMCID: PMC5071577 DOI: 10.1038/cdd.2016.92] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 07/06/2016] [Accepted: 07/21/2016] [Indexed: 02/05/2023] Open
Abstract
Recombinant TRAIL and agonistic antibodies to death receptors (DRs) have been in clinical trial but displayed limited anti-cancer efficacy. Lack of functional DR expression in tumors is a major limiting factor. We report here that chromatin regulator KDM4A/JMJD2A, not KDM4B, has a pivotal role in silencing tumor cell expression of both TRAIL and its receptor DR5. In TRAIL-sensitive and -resistant cancer cells of lung, breast and prostate, KDM4A small-molecule inhibitor compound-4 (C-4) or gene silencing strongly induces TRAIL and DR5 expression, and causes TRAIL-dependent apoptotic cell death. KDM4A inhibition also strongly sensitizes cells to TRAIL. C-4 alone potently inhibits tumor growth with marked induction of TRAIL and DR5 expression in the treated tumors and effectively sensitizes them to the newly developed TRAIL-inducer ONC201. Mechanistically, C-4 does not appear to act through the Akt-ERK-FOXO3a pathway. Instead, it switches histone modifying enzyme complexes at promoters of TRAIL and DR5 transcriptional activator CHOP gene by dissociating KDM4A and nuclear receptor corepressor (NCoR)-HDAC complex and inducing the recruitment of histone acetylase CBP. Thus, our results reveal KDM4A as a key epigenetic silencer of TRAIL and DR5 in tumors and establish inhibitors of KDM4A as a novel strategy for effectively sensitizing tumors to TRAIL pathway-based therapeutics.
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Affiliation(s)
- Junjian Wang
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Sacramento, CA, USA
| | - Haibin Wang
- First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ling-Yu Wang
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Sacramento, CA, USA
| | - Demin Cai
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Sacramento, CA, USA
| | - Zhijian Duan
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Sacramento, CA, USA
| | - Yanhong Zhang
- Comparative Oncology Laboratory, Schools of Medicine and Veterinary Medicine, University of California, Davis, CA, USA
| | - Peng Chen
- First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - June X Zou
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Sacramento, CA, USA
| | - Jianzhen Xu
- Shantou University Medical College, No. 22 Xinling Road, Shantou, China
| | - Xinbin Chen
- Comparative Oncology Laboratory, Schools of Medicine and Veterinary Medicine, University of California, Davis, CA, USA
| | - Hsing-Jien Kung
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Sacramento, CA, USA
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan Town, Miaoli County 350, Taiwan
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Research 3 Bldg, 4645, 2nd Avenue, Sacramento, CA 95817, USA. Tel: +1 916 734 3221; Fax: +1 916 734 0190; E-mail: or
| | - Hong-Wu Chen
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Sacramento, CA, USA
- Veterans Affairs Northern California Health Care System, Mather, CA, USA
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Research 3 Bldg, 4645, 2nd Avenue, Sacramento, CA 95817, USA. Tel: +1 916 734 3221; Fax: +1 916 734 0190; E-mail: or
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171
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Blair LP, Liu Z, Labitigan RLD, Wu L, Zheng D, Xia Z, Pearson EL, Nazeer FI, Cao J, Lang SM, Rines RJ, Mackintosh SG, Moore CL, Li W, Tian B, Tackett AJ, Yan Q. KDM5 lysine demethylases are involved in maintenance of 3'UTR length. SCIENCE ADVANCES 2016; 2:e1501662. [PMID: 28138513 PMCID: PMC5262454 DOI: 10.1126/sciadv.1501662] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 10/20/2016] [Indexed: 06/06/2023]
Abstract
The complexity by which cells regulate gene and protein expression is multifaceted and intricate. Regulation of 3' untranslated region (UTR) processing of mRNA has been shown to play a critical role in development and disease. However, the process by which cells select alternative mRNA forms is not well understood. We discovered that the Saccharomyces cerevisiae lysine demethylase, Jhd2 (also known as KDM5), recruits 3'UTR processing machinery and promotes alteration of 3'UTR length for some genes in a demethylase-dependent manner. Interaction of Jhd2 with both chromatin and RNA suggests that Jhd2 affects selection of polyadenylation sites through a transcription-coupled mechanism. Furthermore, its mammalian homolog KDM5B (also known as JARID1B or PLU1), but not KDM5A (also known as JARID1A or RBP2), promotes shortening of CCND1 transcript in breast cancer cells. Consistent with these results, KDM5B expression correlates with shortened CCND1 in human breast tumor tissues. In contrast, both KDM5A and KDM5B are involved in the lengthening of DICER1. Our findings suggest both a novel role for this family of demethylases and a novel targetable mechanism for 3'UTR processing.
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Affiliation(s)
- Lauren P. Blair
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Zongzhi Liu
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | | | - Lizhen Wu
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Dinghai Zheng
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Zheng Xia
- Division of Biostatistics, Dan L Duncan Comprehensive Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Erica L. Pearson
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Fathima I. Nazeer
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Jian Cao
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Sabine M. Lang
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Rachel J. Rines
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Samuel G. Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72032, USA
| | - Claire L. Moore
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Wei Li
- Division of Biostatistics, Dan L Duncan Comprehensive Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Alan J. Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72032, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
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172
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The Gut Microbiota and their Metabolites: Potential Implications for the Host Epigenome. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 902:33-44. [PMID: 27161349 DOI: 10.1007/978-3-319-31248-4_3] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The gut microbiota represents a metabolically active biomass of up to 2 kg in adult humans. Microbiota-derived molecules significantly contribute to the host metabolism. Large amounts of bacterial metabolites are taken up by the host and are subsequently utilized by the human body. For instance, short chain fatty acids produced by the gut microbiota are a major energy source of humans.It is widely accepted that microbiota-derived metabolites are used as fuel for beta-oxidation (short chain fatty acids) and participate in many metabolic processes (vitamins, such as folic acid). Apart from these direct metabolic effects, it also becomes more and more evident that these metabolites can interact with the mammalian epigenetic machinery. By interacting with histones and DNA they may be able to manipulate the host's chromatin state and functionality and hence its physiology and health.In this chapter, we summarize the current knowledge on possible interactions of different bacterial metabolites with the mammalian epigenetic machinery, mostly based on in vitro data. We discuss the putative impact on chromatin marks, for example histone modifications and DNA methylation. Subsequently, we speculate about possible beneficial and adverse consequences for the epigenome, the physiology and health of the host, as well as plausible future applications of this knowledge for in vivo translation to support personal health.
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173
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Horton JR, Liu X, Gale M, Wu L, Shanks JR, Zhang X, Webber PJ, Bell JSK, Kales SC, Mott BT, Rai G, Jansen DJ, Henderson MJ, Urban DJ, Hall MD, Simeonov A, Maloney DJ, Johns MA, Fu H, Jadhav A, Vertino PM, Yan Q, Cheng X. Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse Compounds. Cell Chem Biol 2016; 23:769-781. [PMID: 27427228 PMCID: PMC4958579 DOI: 10.1016/j.chembiol.2016.06.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 05/15/2016] [Accepted: 06/04/2016] [Indexed: 12/12/2022]
Abstract
The KDM5/JARID1 family of Fe(II)- and α-ketoglutarate-dependent demethylases removes methyl groups from methylated lysine 4 of histone H3. Accumulating evidence supports a role for KDM5 family members as oncogenic drivers. We compare the in vitro inhibitory properties and binding affinity of ten diverse compounds with all four family members, and present the crystal structures of the KDM5A-linked Jumonji domain in complex with eight of these inhibitors in the presence of Mn(II). All eight inhibitors structurally examined occupy the binding site of α-ketoglutarate, but differ in their specific binding interactions, including the number of ligands involved in metal coordination. We also observed inhibitor-induced conformational changes in KDM5A, particularly those residues involved in the binding of α-ketoglutarate, the anticipated peptide substrate, and intramolecular interactions. We discuss how particular chemical moieties contribute to inhibitor potency and suggest strategies that might be utilized in the successful design of selective and potent epigenetic inhibitors.
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Affiliation(s)
- John R Horton
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Xu Liu
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Molly Gale
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Lizhen Wu
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - John R Shanks
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Xing Zhang
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Philip J Webber
- Department of Pharmacology, Emory University, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA 30322, USA
| | - Joshua S K Bell
- Department of Radiation Oncology, Emory University, Atlanta, GA 30322, USA
| | - Stephen C Kales
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Bryan T Mott
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Daniel J Jansen
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Mark J Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Daniel J Urban
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - David J Maloney
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Margaret A Johns
- Department of Pharmacology, Emory University, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA 30322, USA
| | - Haian Fu
- Department of Pharmacology, Emory University, Atlanta, GA 30322, USA; Department of Hematology and Medical Oncology, Emory University, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University, Atlanta, GA 30322, USA; The Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Paula M Vertino
- Department of Radiation Oncology, Emory University, Atlanta, GA 30322, USA; The Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA.
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA; The Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA.
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174
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Kim TD, Oh S, Lightfoot SA, Shin S, Wren JD, Janknecht R. Upregulation of PSMD10 caused by the JMJD2A histone demethylase. Int J Clin Exp Med 2016; 9:10123-10134. [PMID: 28883898 PMCID: PMC5584593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
PSMD10, also known as gankyrin, is associated with the proteasome and has been shown to be an oncoprotein in the liver. Here, we report that PSMD10 expression is stimulated by the histone demethylase JMJD2A/KDM4A and its interaction partner, the ETV1 transcription factor, in LNCaP prostate cancer cells. Global analysis of expression patterns revealed that PSMD10 mRNA levels are positively correlated with those of both JMJD2A and ETV1. In human prostate tumors, PSMD10 is highly overexpressed at the protein level and correlates with JMJD2A overexpression; further, PSMD10 expression is enhanced in the prostates of transgenic JMJD2A mice. Moreover, PSMD10 is particularly overexpressed in high Gleason score prostate tumors. Downregulation of PSMD10 in LNCaP prostate cancer cells impaired their growth, indicating that PSMD10 may exert a pro-oncogenic function in the prostate. Lastly, we observed that PSMD10 expression is correlated to YAP1, a component of the Hippo signaling pathway and whose gene promoter is regulated by JMJD2A, and that PSMD10 can cooperate with YAP1 in stimulating LNCaP cell growth. Altogether, these data indicate that PSMD10 is a novel downstream effector of JMJD2A and suggest that inhibition of the JMJD2A histone demethylase by small molecule drugs may be effective to curtail the oncogenic activity of PSMD10 in various PSMD10-overexpressing tumors.
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Affiliation(s)
- Tae-Dong Kim
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Sangphil Oh
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Stan A Lightfoot
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Sook Shin
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Jonathan D Wren
- Arthritis & Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
- Stephenson Cancer Center, Oklahoma City, OK 73104, USA
| | - Ralf Janknecht
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Stephenson Cancer Center, Oklahoma City, OK 73104, USA
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175
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Agger K, Miyagi S, Pedersen MT, Kooistra SM, Johansen JV, Helin K. Jmjd2/Kdm4 demethylases are required for expression of Il3ra and survival of acute myeloid leukemia cells. Genes Dev 2016; 30:1278-88. [PMID: 27257215 PMCID: PMC4911927 DOI: 10.1101/gad.280495.116] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 05/04/2016] [Indexed: 12/04/2022]
Abstract
Agger et al. show that Jmjd2/Kdm4 activities are required for MLL-AF9 translocated AML. Expression of the interleukin 3 receptor α (Il3ra) subunit is dependent on Jmjd2/Kdm4 through a mechanism involving removal of H3K9me3 from the promoter of the Il3ra gene. Acute myeloid leukemias (AMLs) with a rearrangement of the mixed-linage leukemia (MLL) gene are aggressive hematopoietic malignancies. Here, we explored the feasibility of using the H3K9- and H3K36-specific demethylases Jmjd2/Kdm4 as putative drug targets in MLL-AF9 translocated leukemia. Using Jmjd2a, Jmjd2b, and Jmjd2c conditional triple-knockout mice, we show that Jmjd2/Kdm4 activities are required for MLL-AF9 translocated AML in vivo and in vitro. We demonstrate that expression of the interleukin 3 receptor α (Il3ra also known as Cd123) subunit is dependent on Jmjd2/Kdm4 through a mechanism involving removal of H3K9me3 from the promoter of the Il3ra gene. Importantly, ectopic expression of Il3ra in Jmjd2/Kdm4 knockout cells alleviates the requirement of Jmjd2/Kdm4 for the survival of AML cells, showing that Il3ra is a critical downstream target of Jmjd2/Kdm4 in leukemia. These results suggest that the JMJD2/KDM4 proteins are promising drug targets for the treatment of AML.
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Affiliation(s)
- Karl Agger
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Satoru Miyagi
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark; The Danish Stem Cell Center (DanStem), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Marianne Terndrup Pedersen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Susanne M Kooistra
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jens Vilstrup Johansen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark; The Danish Stem Cell Center (DanStem), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
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176
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Li Q, Huang Y, Liu X, Gan J, Chen H, Yang CG. Rhein Inhibits AlkB Repair Enzymes and Sensitizes Cells to Methylated DNA Damage. J Biol Chem 2016; 291:11083-93. [PMID: 27015802 PMCID: PMC4900258 DOI: 10.1074/jbc.m115.711895] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Indexed: 01/07/2023] Open
Abstract
The AlkB repair enzymes, including Escherichia coli AlkB and two human homologues, ALKBH2 and ALKBH3, are iron(II)- and 2-oxoglutarate-dependent dioxygenases that efficiently repair N(1)-methyladenine and N(3)-methylcytosine methylated DNA damages. The development of small molecule inhibitors of these enzymes has seen less success. Here we have characterized a previously discovered natural product rhein and tested its ability to inhibit AlkB repair enzymes in vitro and to sensitize cells to methyl methane sulfonate that mainly produces N(1)-methyladenine and N(3)-methylcytosine lesions. Our investigation of the mechanism of rhein inhibition reveals that rhein binds to AlkB repair enzymes in vitro and promotes thermal stability in vivo In addition, we have determined a new structural complex of rhein bound to AlkB, which shows that rhein binds to a different part of the active site in AlkB than it binds to in fat mass and obesity-associated protein (FTO). With the support of these observations, we put forth the hypothesis that AlkB repair enzymes would be effective pharmacological targets for cancer treatment.
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Affiliation(s)
- Qi Li
- From the Laboratory of Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yue Huang
- From the Laboratory of Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xichun Liu
- the Coordination Chemistry Institute and State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China, and
| | - Jianhua Gan
- the School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Hao Chen
- the Coordination Chemistry Institute and State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China, and
| | - Cai-Guang Yang
- From the Laboratory of Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China, , To whom correspondence should be addressed. Tel.: 86-21-50806029; Fax: 86-21-50807088; E-mail:
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177
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Sdelci S, Lardeau CH, Tallant C, Klepsch F, Klaiber B, Bennett J, Rathert P, Schuster M, Penz T, Fedorov O, Superti-Furga G, Bock C, Zuber J, Huber KVM, Knapp S, Müller S, Kubicek S. Mapping the chemical chromatin reactivation landscape identifies BRD4-TAF1 cross-talk. Nat Chem Biol 2016; 12:504-10. [PMID: 27159579 DOI: 10.1038/nchembio.2080] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 03/18/2016] [Indexed: 12/14/2022]
Abstract
Bromodomain-containing proteins of the BET family recognize histone lysine acetylation and mediate transcriptional activation of target genes such as the MYC oncogene. Pharmacological inhibitors of BET domains promise therapeutic benefits in a variety of cancers. We performed a high-diversity chemical compound screen for agents capable of modulating BRD4-dependent heterochromatization of a generic reporter in human cells. In addition to known and new compounds targeting BRD4, we identified small molecules that mimic BRD4 inhibition without direct engagement. One such compound was a potent inhibitor of the second bromodomain of TAF1. Using this inhibitor, we discovered that TAF1 synergizes with BRD4 to control proliferation of cancer cells, making TAF1 an attractive epigenetic target in cancers driven by MYC.
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Affiliation(s)
- Sara Sdelci
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Charles-Hugues Lardeau
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Christian Doppler Laboratory for Chemical Epigenetics and Antiinfectives, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Cynthia Tallant
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Freya Klepsch
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Björn Klaiber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - James Bennett
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Philipp Rathert
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Michael Schuster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Thomas Penz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Oleg Fedorov
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria.,Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Kilian V M Huber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Stefan Knapp
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.,Johann Wolfgang Goethe-University, Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Susanne Müller
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Christian Doppler Laboratory for Chemical Epigenetics and Antiinfectives, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
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178
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Lillico R, Stesco N, Khorshid Amhad T, Cortes C, Namaka MP, Lakowski TM. Inhibitors of enzymes catalyzing modifications to histone lysine residues: structure, function and activity. Future Med Chem 2016; 8:879-97. [PMID: 27173004 DOI: 10.4155/fmc-2016-0021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Gene expression is partly controlled by epigenetic mechanisms including histone-modifying enzymes. Some diseases are caused by changes in gene expression that can be mitigated by inhibiting histone-modifying enzymes. This review covers the enzyme inhibitors targeting histone lysine modifications. We summarize the enzymatic mechanisms of histone lysine acetylation, deacetylation, methylation and demethylation and discuss the biochemical roles of these modifications in gene expression and in disease. We discuss inhibitors of lysine acetylation, deacetylation, methylation and demethylation defining their structure-activity relationships and their potential mechanisms. We show that there are potentially indiscriminant off-target effects on gene expression even with the use of selective epigenetic enzyme inhibitors.
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Affiliation(s)
- Ryan Lillico
- Faculty of Health Sciences, College of Pharmacy, University of Manitoba, Winnipeg, Manitoba, Canada
- Pharmaceutical Analysis Laboratory, College of Pharmacy, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Nicholas Stesco
- Faculty of Health Sciences, College of Pharmacy, University of Manitoba, Winnipeg, Manitoba, Canada
- Pharmaceutical Analysis Laboratory, College of Pharmacy, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Tina Khorshid Amhad
- Faculty of Health Sciences, College of Pharmacy, University of Manitoba, Winnipeg, Manitoba, Canada
- Joint Laboratory of Biological Psychiatry Between Shantou University Medical College and College of Medicine, University of Manitoba, Winnipeg, MB, Canada
- Department of Human Anatomy and Cell Science, College of Medicine, University of Manitoba, Winnipeg, MB, Canada
- Department of Rehabilitation Medicine, Health Sciences Centre (HSC), Winnipeg, MB, Canada
| | - Claudia Cortes
- Joint Laboratory of Biological Psychiatry Between Shantou University Medical College and College of Medicine, University of Manitoba, Winnipeg, MB, Canada
- Department of Human Anatomy and Cell Science, College of Medicine, University of Manitoba, Winnipeg, MB, Canada
- Department of Rehabilitation Medicine, Health Sciences Centre (HSC), Winnipeg, MB, Canada
| | - Mike P Namaka
- Faculty of Health Sciences, College of Pharmacy, University of Manitoba, Winnipeg, Manitoba, Canada
- Joint Laboratory of Biological Psychiatry Between Shantou University Medical College and College of Medicine, University of Manitoba, Winnipeg, MB, Canada
- Department of Human Anatomy and Cell Science, College of Medicine, University of Manitoba, Winnipeg, MB, Canada
- Department of Rehabilitation Medicine, Health Sciences Centre (HSC), Winnipeg, MB, Canada
| | - Ted M Lakowski
- Faculty of Health Sciences, College of Pharmacy, University of Manitoba, Winnipeg, Manitoba, Canada
- Pharmaceutical Analysis Laboratory, College of Pharmacy, University of Manitoba, Winnipeg, Manitoba, Canada
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179
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Kim TD, Shin S, Janknecht R. ETS transcription factor ERG cooperates with histone demethylase KDM4A. Oncol Rep 2016; 35:3679-88. [PMID: 27109047 PMCID: PMC4869937 DOI: 10.3892/or.2016.4747] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 01/11/2016] [Indexed: 12/20/2022] Open
Abstract
ERG (ETS-related gene) is a member of the ETS (erythroblast transformation-specific) family of transcription factors. Overexpression of the ERG transcription factor is observed in half of all prostate tumors and is an underlying cause of this disease. However, the mechanisms involved in the functions of ERG are still not fully understood. In the present study, we showed that ERG can directly bind to KDM4A (also known as JMJD2A), a histone demethylase that particularly demethylates lysine 9 on histone H3. ERG and KDM4A cooperated in upregulating the promoter of Yes-associated protein 1 (YAP1), a downstream effector in the Hippo signaling pathway and crucial growth regulator. Multiple ERG binding sites within the human YAP1 gene promoter were identified and their impact on transcription was determined through mutational analysis. Furthermore, we found that ERG expression reduced histone H3 lysine 9 trimethylation at the YAP1 gene promoter, consistent with its epigenetic regulation through the ERG interaction partner, KDM4A. Finally, downregulation of YAP1 phenocopied the growth-retarding effect of ERG or KDM4A depletion in human VCaP prostate cancer cells. Collectively, these results elucidated a novel mechanism - ERG promotes prostate tumorigenesis together with KDM4A through the upregulation of YAP1. A corollary is that KDM4A as well as YAP1 inhibitors may prove beneficial for the therapy of ERG-overexpressing prostate tumors.
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Affiliation(s)
- Tae-Dong Kim
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Sook Shin
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Ralf Janknecht
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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180
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Signalling couples hair follicle stem cell quiescence with reduced histone H3 K4/K9/K27me3 for proper tissue homeostasis. Nat Commun 2016; 7:11278. [PMID: 27080563 PMCID: PMC4835553 DOI: 10.1038/ncomms11278] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 03/09/2016] [Indexed: 12/14/2022] Open
Abstract
Mechanisms of plasticity to acquire different cell fates are critical for adult stem cell (SC) potential, yet are poorly understood. Reduced global histone methylation is an epigenetic state known to mediate plasticity in cultured embryonic SCs and T-cell progenitors. Here we find histone H3 K4/K9/K27me3 levels actively reduced in adult mouse skin and hair follicle stem cells (HFSCs) during G0 quiescence. The level of marks over specific gene promoters did not correlate to mRNA level changes in quiescent HFSCs. Skin hypomethylation during quiescence was necessary for subsequent progression of hair homeostasis (cycle). Inhibiting BMP signal, a known HFSC anti-proliferative factor, elevated HFSC methylation in vivo during quiescence prior to proliferation onset. Furthermore, removal of proliferation factors and addition of BMP4 reduced histone methylases and increased demethylases mRNAs in cultured skin epithelial cells. We conclude that signalling couples hair follicle stem cell quiescence with reduced H3 K4/K9/K27me3 levels for proper tissue homeostasis. Changes in global histone trimethylation have been linked to embryonic but not adult stem cell plasticity. Here, Lee et al. find H3 K4/K9/K27me3 levels actively reduced in adult mouse skin and hair follicle stem cells during quiescence (catagen) and link this to active bone morphogen protein signalling.
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181
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Martinez ED, Gazdar AF. Inhibiting the Jumonji family: a potential new clinical approach to targeting aberrant epigenetic mechanisms. Epigenomics 2016; 8:313-6. [PMID: 26918824 DOI: 10.2217/epi.15.115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Elisabeth D Martinez
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA.,Harold C Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Adi F Gazdar
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA.,Harold C Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA
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182
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Korczynska M, Le DD, Younger N, Gregori-Puigjané E, Tumber A, Krojer T, Velupillai S, Gileadi C, Nowak RP, Iwasa E, Pollock SB, Torres IO, Oppermann U, Shoichet BK, Fujimori DG. Docking and Linking of Fragments To Discover Jumonji Histone Demethylase Inhibitors. J Med Chem 2016; 59:1580-98. [PMID: 26699912 PMCID: PMC5080985 DOI: 10.1021/acs.jmedchem.5b01527] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Development of tool molecules that inhibit Jumonji demethylases allows for the investigation of cancer-associated transcription. While scaffolds such as 2,4-pyridinedicarboxylic acid (2,4-PDCA) are potent inhibitors, they exhibit limited selectivity. To discover new inhibitors for the KDM4 demethylases, enzymes overexpressed in several cancers, we docked a library of 600,000 fragments into the high-resolution structure of KDM4A. Among the most interesting chemotypes were the 5-aminosalicylates, which docked in two distinct but overlapping orientations. Docking poses informed the design of covalently linked fragment compounds, which were further derivatized. This combined approach improved affinity by ∼ 3 log-orders to yield compound 35 (Ki = 43 nM). Several hybrid inhibitors were selective for KDM4C over the related enzymes FIH, KDM2A, and KDM6B while lacking selectivity against the KDM3 and KDM5 subfamilies. Cocrystal structures corroborated the docking predictions. This study extends the use of structure-based docking from fragment discovery to fragment linking optimization, yielding novel KDM4 inhibitors.
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Affiliation(s)
- Magdalena Korczynska
- Department of Pharmaceutical Chemistry, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Daniel D. Le
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Noah Younger
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Elisabet Gregori-Puigjané
- Department of Pharmaceutical Chemistry, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Anthony Tumber
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
- Nuffield Department of Clinical Medicine, Target Discovery Institute (TDI), University of Oxford, Oxford OX3 7BN, U.K
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
| | | | - Carina Gileadi
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
| | - Radosław P. Nowak
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
| | - Eriko Iwasa
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Samuel B. Pollock
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Idelisse Ortiz Torres
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Udo Oppermann
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, U.K
- Botnar Research Center, University of Oxford, Oxford OX3 7LD, U.K
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
| | - Danica Galonić Fujimori
- Department of Pharmaceutical Chemistry, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, Genentech Hall, 600 16th Street, MC2280, San Francisco, California 94158-2280, United States
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183
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Horton JR, Engstrom A, Zoeller EL, Liu X, Shanks JR, Zhang X, Johns MA, Vertino PM, Fu H, Cheng X. Characterization of a Linked Jumonji Domain of the KDM5/JARID1 Family of Histone H3 Lysine 4 Demethylases. J Biol Chem 2016; 291:2631-46. [PMID: 26645689 PMCID: PMC4742734 DOI: 10.1074/jbc.m115.698449] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 11/17/2015] [Indexed: 12/18/2022] Open
Abstract
The KDM5/JARID1 family of Fe(II)- and α-ketoglutarate-dependent demethylases remove methyl groups from tri- and dimethylated lysine 4 of histone H3. Accumulating evidence from primary tumors and model systems supports a role for KDM5A (JARID1A/RBP2) and KDM5B (JARID1B/PLU1) as oncogenic drivers. The KDM5 family is unique among the Jumonji domain-containing histone demethylases in that there is an atypical insertion of a DNA-binding ARID domain and a histone-binding PHD domain into the Jumonji domain, which separates the catalytic domain into two fragments (JmjN and JmjC). Here we demonstrate that internal deletion of the ARID and PHD1 domains has a negligible effect on in vitro enzymatic kinetics of the KDM5 family of enzymes. We present a crystal structure of the linked JmjN-JmjC domain from KDM5A, which reveals that the linked domain fully reconstitutes the cofactor (metal ion and α-ketoglutarate) binding characteristics of other structurally characterized Jumonji domain demethylases. Docking studies with GSK-J1, a selective inhibitor of the KDM6/KDM5 subfamilies, identify critical residues for binding of the inhibitor to the reconstituted KDM5 Jumonji domain. Further, we found that GSK-J1 inhibited the demethylase activity of KDM5C with 8.5-fold increased potency compared with that of KDM5B at 1 mm α-ketoglutarate. In contrast, JIB-04 (a pan-inhibitor of the Jumonji demethylase superfamily) had the opposite effect and was ~8-fold more potent against KDM5B than against KDM5C. Interestingly, the relative selectivity of JIB-04 toward KDM5B over KDM5C in vitro translates to a ~10-50-fold greater growth-inhibitory activity against breast cancer cell lines. These data define the minimal requirements for enzymatic activity of the KDM5 family to be the linked JmjN-JmjC domain coupled with the immediate C-terminal helical zinc-binding domain and provide structural characterization of the linked JmjN-JmjC domain for the KDM5 family, which should prove useful in the design of KDM5 demethylase inhibitors with improved potency and selectivity.
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Affiliation(s)
| | - Amanda Engstrom
- the Graduate Program in Biochemistry, Cell and Developmental Biology
| | | | - Xu Liu
- From the Departments of Biochemistry
| | | | | | | | - Paula M Vertino
- Radiation Oncology, the Winship Cancer Institute, Emory University, Atlanta, Georgia 30322
| | - Haian Fu
- the Winship Cancer Institute, Emory University, Atlanta, Georgia 30322 Radiation Oncology, the Emory Chemical Biology Discovery Center, and Hematology and Medical Oncology, and
| | - Xiaodong Cheng
- From the Departments of Biochemistry, the Winship Cancer Institute, Emory University, Atlanta, Georgia 30322
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184
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Kim TD, Jin F, Shin S, Oh S, Lightfoot SA, Grande JP, Johnson AJ, van Deursen JM, Wren JD, Janknecht R. Histone demethylase JMJD2A drives prostate tumorigenesis through transcription factor ETV1. J Clin Invest 2016; 126:706-20. [PMID: 26731476 DOI: 10.1172/jci78132] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 11/13/2015] [Indexed: 02/06/2023] Open
Abstract
Histone demethylase upregulation has been observed in human cancers, yet it is unknown whether this is a bystander event or a driver of tumorigenesis. We found that overexpression of lysine-specific demethylase 4A (KDM4A, also known as JMJD2A) was positively correlated with Gleason score and metastasis in human prostate tumors. Overexpression of JMJD2A resulted in the development of prostatic intraepithelial neoplasia in mice, demonstrating that JMJD2A can initiate prostate cancer development. Moreover, combined overexpression of JMJD2A and the ETS transcription factor ETV1, a JMJD2A-binding protein, resulted in prostate carcinoma formation in mice haplodeficient for the phosphatase and tensin homolog (Pten) tumor-suppressor gene. Additionally, JMJD2A cooperated with ETV1 to increase expression of yes associated protein 1 (YAP1), a Hippo pathway component that itself was associated with prostate tumor aggressiveness. ETV1 facilitated the recruitment of JMJD2A to the YAP1 promoter, leading to changes in histone lysine methylation in a human prostate cancer cell line. Further, YAP1 expression largely rescued the growth inhibitory effects of JMJD2A depletion in prostate cancer cells, indicating that YAP1 is a downstream effector of JMJD2A. Taken together, these data reveal a JMJD2A/ETV1/YAP1 axis that promotes prostate cancer initiation and that may be a suitable target for therapeutic inhibition.
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185
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Abstract
Histone modifications (methylation, acetylation, phosphorylation, sumoylation, etc.,) are at the heart of cellular regulatory mechanisms, which control expression of genes in an orderly fashion and control the entire cellular regulatory networks. Histone lysine methylation has been identified as one of the several posttranslational histone modifications that plays crucial role in regulating gene expressions in facultative heterochromatic DNA regions while maintaining structural integrity in constitutive heterochromatic DNA regions. Since histone methylation is dysregulated in various cellular diseases, it has been considered a potential therapeutic target for drug development. Currently there is no simple method available to screen and preclinically evaluate drugs modulating this cellular process, we recently developed two different methods by adopting reporter gene technology to screen drugs and to preclinically evaluate them in living animals. Method detects and quantitatively monitors the level of histone methylations in intact cells, is of a prerequisite to screen small molecules that modulate histone lysine methylation. Here, we describe two independent optical imaging sensors developed to image histone methylations in cells and in living animals. Since we used standard PCR-based cloning strategies to construct different plasmid vectors shown in this chapter, we are not providing any details regarding the construction methods, instead, we focus on detailing various methods used for measuring histone methylation-assisted luciferase quantitation in cells and imaging in living animals.
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Affiliation(s)
- Thillai V Sekar
- Molecular Imaging Program at Stanford, Bio-X Program, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ramasamy Paulmurugan
- Molecular Imaging Program at Stanford, Bio-X Program, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Radiology, Stanford University School of Medicine, 3155, Porter Drive, #2236, Palo Alto, CA, 94304, USA.
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186
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Wang L, Kofler M, Brosch G, Melesina J, Sippl W, Martinez ED, Easmon J. 2-Benzazolyl-4-Piperazin-1-Ylsulfonylbenzenecarbohydroxamic Acids as Novel Selective Histone Deacetylase-6 Inhibitors with Antiproliferative Activity. PLoS One 2015; 10:e0134556. [PMID: 26698121 PMCID: PMC4689404 DOI: 10.1371/journal.pone.0134556] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 07/13/2015] [Indexed: 11/19/2022] Open
Abstract
We have screened our compound collection in an established cell based assay that measures the derepression of an epigenetically silenced transgene, the locus derepression assay. The screen led to the identification of 4-[4-(1-methylbenzimidazol-2-yl)piperazin-1-yl]sulfonylbenzenecarbohydroxamic acid (9b) as an active which was found to inhibit HDAC1. In initial structure activity relationships study, the 1-methylbenzimidazole ring was replaced by the isosteric heterocycles benzimidazole, benzoxazole, and benzothiazole and the position of the hydroxamic acid substituent on the phenyl ring was varied. Whereas compounds bearing a para substituted hydroxamic acid (9a-d) were active HDAC inhibitors, the meta substituted analogues (8a-d) were appreciably inactive. Compounds 9a-d selectively inhibited HDAC6 (IC50 = 0.1-1.0 μM) over HDAC1 (IC50 = 0.9-6 μM) and moreover, also selectively inhibited the growth of lung cancer cells vs. patient matched normal cells. The compounds induce a cell cycle arrest in the S-phase while induction of apoptosis is neglible as compared to controls. Molecular modeling studies uncovered that the MM-GBSA energy for interaction of 9a-d with HDAC6 was higher than for HDAC1 providing structural rationale for the HDAC6 selectivity.
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Affiliation(s)
- Lei Wang
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, United States of America
| | - Marina Kofler
- Institute of Pharmacy, Department of Pharmaceutical Chemistry, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80–82, A-6020 Innsbruck, Austria
| | - Gerald Brosch
- Division of Molecular Biology, Center for Chemistry and Biomedicine, Innsbruck Medical University Innrain 80–82, A-6020 Innsbruck Austria
| | - Jelena Melesina
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-Universität Halle-Wittenberg, D-06099 Halle/Saale, Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-Universität Halle-Wittenberg, D-06099 Halle/Saale, Germany
| | - Elisabeth D. Martinez
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, United States of America
- Department of Pharmacology, UT Southwestern Medical center, Dallas, TX, United States of America
- * E-mail: (JE); (EM)
| | - Johnny Easmon
- Institute of Pharmacy, Department of Pharmaceutical Chemistry, Center for Chemistry and Biomedicine, University of Innsbruck, Innrain 80–82, A-6020 Innsbruck, Austria
- * E-mail: (JE); (EM)
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187
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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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188
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Thinnes CC, Tumber A, Yapp C, Scozzafava G, Yeh T, Chan MC, Tran TA, Hsu K, Tarhonskaya H, Walport LJ, Wilkins SE, Martinez ED, Müller S, Pugh CW, Ratcliffe PJ, Brennan PE, Kawamura A, Schofield CJ. Betti reaction enables efficient synthesis of 8-hydroxyquinoline inhibitors of 2-oxoglutarate oxygenases. Chem Commun (Camb) 2015; 51:15458-61. [PMID: 26345662 DOI: 10.1039/c5cc06095h] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2024]
Abstract
There is interest in developing potent, selective, and cell-permeable inhibitors of human ferrous iron and 2-oxoglutarate (2OG) oxygenases for use in functional and target validation studies. The 3-component Betti reaction enables efficient one-step C-7 functionalisation of modified 8-hydroxyquinolines (8HQs) to produce cell-active inhibitors of KDM4 histone demethylases and other 2OG oxygenases; the work exemplifies how a template-based metallo-enzyme inhibitor approach can be used to give biologically active compounds.
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Affiliation(s)
- C C Thinnes
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.
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189
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Successful strategies in the discovery of small-molecule epigenetic modulators with anticancer potential. Future Med Chem 2015; 7:2243-61. [DOI: 10.4155/fmc.15.140] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
As a class, epigenetic enzymes have been identified as clear targets for cancer therapeutics based on their broad hyperactivity in solid and hematological malignancies. The search for effective inhibitors of histone writers and of histone erasers has been a focus of drug discovery efforts both in academic and pharmaceutical laboratories and has led to the identification of some promising leads. This review focuses on the discovery strategies and preclinical evaluation studies of a subset of the more advanced compounds that target histone writers or histone erasers. The specificity and anticancer potential of these small molecules is discussed within the context of their development pipeline.
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190
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Casciello F, Windloch K, Gannon F, Lee JS. Functional Role of G9a Histone Methyltransferase in Cancer. Front Immunol 2015; 6:487. [PMID: 26441991 PMCID: PMC4585248 DOI: 10.3389/fimmu.2015.00487] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 09/07/2015] [Indexed: 11/13/2022] Open
Abstract
Post-translational modifications of DNA and histones are epigenetic mechanisms, which affect the chromatin structure, ultimately leading to gene expression changes. A number of different epigenetic enzymes are actively involved in the addition or the removal of various covalent modifications, which include acetylation, methylation, phosphorylation, ubiquitination, and sumoylation. Deregulation of these processes is a hallmark of cancer. For instance, G9a, a histone methyltransferase responsible for histone H3 lysine 9 (H3K9) mono- and dimethylation, has been observed to be upregulated in different types of cancer and its overexpression has been associated with poor prognosis. Key roles played by these enzymes in various diseases have led to the hypothesis that these molecules represent valuable targets for future therapies. Several small molecule inhibitors have been developed to specifically block the epigenetic activity of these enzymes, representing promising therapeutic tools in the treatment of human malignancies, such as cancer. In this review, the role of one of these epigenetic enzymes, G9a, is discussed, focusing on its functional role in regulating gene expression as well as its implications in cancer initiation and progression. We also discuss important findings from recent studies using epigenetic inhibitors in cell systems in vitro as well as experimental tumor growth and metastasis assays in vivo.
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Affiliation(s)
- Francesco Casciello
- Control of Gene Expression Laboratory, QIMR Berghofer Medical Research Institute , Herston, QLD , Australia ; School of Natural Sciences, Griffith University , Nathan, QLD , Australia
| | - Karolina Windloch
- Control of Gene Expression Laboratory, QIMR Berghofer Medical Research Institute , Herston, QLD , Australia
| | - Frank Gannon
- Control of Gene Expression Laboratory, QIMR Berghofer Medical Research Institute , Herston, QLD , Australia
| | - Jason S Lee
- Control of Gene Expression Laboratory, QIMR Berghofer Medical Research Institute , Herston, QLD , Australia ; Faculty of Health, School of Biomedical Sciences, Queensland University of Technology , Kelvin Grove, QLD , Australia ; School of Chemistry and Molecular Biosciences, University of Queensland , Brisbane, QLD , Australia
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191
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Duan L, Rai G, Roggero C, Zhang QJ, Wei Q, Ma SH, Zhou Y, Santoyo J, Martinez ED, Xiao G, Raj GV, Jadhav A, Simeonov A, Maloney DJ, Rizo J, Hsieh JT, Liu ZP. KDM4/JMJD2 Histone Demethylase Inhibitors Block Prostate Tumor Growth by Suppressing the Expression of AR and BMYB-Regulated Genes. CHEMISTRY & BIOLOGY 2015; 22:1185-96. [PMID: 26364928 PMCID: PMC4578295 DOI: 10.1016/j.chembiol.2015.08.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Revised: 07/18/2015] [Accepted: 08/14/2015] [Indexed: 10/23/2022]
Abstract
Histone lysine demethylase KDM4/JMJD2s are overexpressed in many human tumors including prostate cancer (PCa). KDM4s are co-activators of androgen receptor (AR) and are thus potential therapeutic targets. Yet to date few KDM4 inhibitors that have anti-prostate tumor activity in vivo have been developed. Here, we report the anti-tumor growth effect and molecular mechanisms of three novel KDM4 inhibitors (A1, I9, and B3). These inhibitors repressed the transcription of both AR and BMYB-regulated genes. Compound B3 is highly selective for a variety of cancer cell lines including PC3 cells that lack AR. B3 inhibited the in vivo growth of tumors derived from PC3 cells and ex vivo human PCa explants. We identified a novel mechanism by which KDM4B activates the transcription of Polo-like kinase 1 (PLK1). B3 blocked the binding of KDM4B to the PLK1 promoter. Our studies suggest a potential mechanism-based therapeutic strategy for PCa and tumors with elevated KDM4B/PLK1 expression.
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Affiliation(s)
- Lingling Duan
- Departments of Internal Medicine and Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Carlos Roggero
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry and Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Qing-Jun Zhang
- Departments of Internal Medicine and Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Qun Wei
- Departments of Internal Medicine and Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shi Hong Ma
- Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yunyun Zhou
- Department of Clinical Science, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - John Santoyo
- Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Elisabeth D Martinez
- Department of pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Guanghua Xiao
- Department of Clinical Science, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ganesh V Raj
- Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - David J Maloney
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Josep Rizo
- Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry and Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jer-Tsong Hsieh
- Department of Urology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhi-Ping Liu
- Departments of Internal Medicine and Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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192
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Abstract
Cancer genome sequencing has created an opportunity for precision medicine. Thus far, genetic alterations can only be used to guide treatment for small subsets of certain cancer types with these key alterations. Similar to mutations, epigenetic events are equally suitable for personalized medicine. DNA methylation alterations have been used to identify tumor-specific drug responsive markers. Methylation of MGMT sensitizes gliomas to alkylating agents is an example of epigenetic personalized medicine. Recent studies have revealed that 5-azacytidine and decitabine show activity in myelodysplasia, lung and other cancers. There are currently at least 20 kinds of histone deacetylase inhibitors in clinical testing. Inhibitors targeting other epigenetic regulators are being clinically tested, such as EZH2 inhibitor EPZ-6438.
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Affiliation(s)
- Wenji Yan
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing 100853, China
| | - James G Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Suite 2.18/Research, Pittsburgh, PA 15213, USA
| | - Mingzhou Guo
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing 100853, China
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193
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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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194
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Targeting Chromatin-Mediated Transcriptional Control of Gene Expression in Non-Small Cell Lung Cancer Therapy: Preclinical Rationale and Clinical Results. Drugs 2015; 75:1757-71. [DOI: 10.1007/s40265-015-0461-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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195
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Rüger N, Roatsch M, Emmrich T, Franz H, Schüle R, Jung M, Link A. Tetrazolylhydrazides as Selective Fragment-Like Inhibitors of the JumonjiC-Domain-Containing Histone Demethylase KDM4A. ChemMedChem 2015; 10:1875-83. [DOI: 10.1002/cmdc.201500335] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Nicole Rüger
- Institute of Pharmacy; Ernst-Moritz-Arndt-Universität Greifswald; Friedrich-Ludwig-Jahn-Str. 17 17487 Greifswald Germany
| | - Martin Roatsch
- Institute of Pharmaceutical Sciences; Albert-Ludwigs-Universität Freiburg; Albertstr. 25 79104 Freiburg Germany
| | - Thomas Emmrich
- Institute of Pharmacy; Ernst-Moritz-Arndt-Universität Greifswald; Friedrich-Ludwig-Jahn-Str. 17 17487 Greifswald Germany
| | - Henriette Franz
- University of Freiburg Medical Center; Department of Urology, Women's Hospital and Center for Clinical Research; Breisacher Str. 66 79106 Freiburg Germany
| | - Roland Schüle
- University of Freiburg Medical Center; Department of Urology, Women's Hospital and Center for Clinical Research; Breisacher Str. 66 79106 Freiburg Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences; Albert-Ludwigs-Universität Freiburg; Albertstr. 25 79104 Freiburg Germany
| | - Andreas Link
- Institute of Pharmacy; Ernst-Moritz-Arndt-Universität Greifswald; Friedrich-Ludwig-Jahn-Str. 17 17487 Greifswald Germany
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196
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Schneider P, Miguel Bayo-Fina J, Singh R, Kumar Dhanyamraju P, Holz P, Baier A, Fendrich V, Ramaswamy A, Baumeister S, Martinez ED, Lauth M. Identification of a novel actin-dependent signal transducing module allows for the targeted degradation of GLI1. Nat Commun 2015; 6:8023. [PMID: 26310823 PMCID: PMC4552080 DOI: 10.1038/ncomms9023] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 07/09/2015] [Indexed: 12/12/2022] Open
Abstract
The Down syndrome-associated DYRK1A kinase has been reported as a stimulator of the developmentally important Hedgehog (Hh) pathway, but cells from Down syndrome patients paradoxically display reduced Hh signalling activity. Here we find that DYRK1A stimulates GLI transcription factor activity through phosphorylation of general nuclear localization clusters. In contrast, in vivo and in vitro experiments reveal that DYRK1A kinase can also function as an inhibitor of endogenous Hh signalling by negatively regulating ABLIM proteins, the actin cytoskeleton and the transcriptional co-activator MKL1 (MAL). As a final effector of the DYRK1A-ABLIM-actin-MKL1 sequence, we identify the MKL1 interactor Jumonji domain demethylase 1A (JMJD1A) as a novel Hh pathway component stabilizing the GLI1 protein in a demethylase-independent manner. Furthermore, a Jumonji-specific small-molecule antagonist represents a novel and powerful inhibitor of Hh signal transduction by inducing GLI1 protein degradation in vitro and in vivo.
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Affiliation(s)
- Philipp Schneider
- Department of Medicine, Philipps University, Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology, Hans-Meerwein-Street 3, 35043 Marburg, Germany
| | - Juan Miguel Bayo-Fina
- Department of Pharmacology, UT Southwestern Medical Center, 6000 Harry Hines boulevard, Dallas, Texas 75390-8593, USA
| | - Rajeev Singh
- Department of Medicine, Philipps University, Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology, Hans-Meerwein-Street 3, 35043 Marburg, Germany
| | - Pavan Kumar Dhanyamraju
- Department of Medicine, Philipps University, Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology, Hans-Meerwein-Street 3, 35043 Marburg, Germany
| | - Philipp Holz
- Department of Medicine, Philipps University, Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology, Hans-Meerwein-Street 3, 35043 Marburg, Germany
| | - Aninja Baier
- Department of Surgery, Philipps University, Baldingerstraße 1, 35033 Marburg, Germany
| | - Volker Fendrich
- Department of Surgery, Philipps University, Baldingerstraße 1, 35033 Marburg, Germany
| | - Annette Ramaswamy
- Department of Pathology, Philipps University, Baldingerstraße 1, 35033 Marburg, Germany
| | - Stefan Baumeister
- Department of Biology, Philipps University, Karl-von-Frisch-Straße 8, 35043 Marburg, Germany
| | - Elisabeth D. Martinez
- Department of Pharmacology, UT Southwestern Medical Center, 6000 Harry Hines boulevard, Dallas, Texas 75390-8593, USA
| | - Matthias Lauth
- Department of Medicine, Philipps University, Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology, Hans-Meerwein-Street 3, 35043 Marburg, Germany
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197
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Liu LJ, Lu L, Zhong HJ, He B, Kwong DWJ, Ma DL, Leung CH. An Iridium(III) Complex Inhibits JMJD2 Activities and Acts as a Potential Epigenetic Modulator. J Med Chem 2015. [DOI: 10.1021/acs.jmedchem.5b00375] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Li-Juan Liu
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University of Macau, Taipa, Macao P. R. China
| | - Lihua Lu
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong P. R. China
| | - Hai-Jing Zhong
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University of Macau, Taipa, Macao P. R. China
| | - Bingyong He
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong P. R. China
| | - Daniel W. J. Kwong
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong P. R. China
| | - Dik-Lung Ma
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong P. R. China
| | - Chung-Hang Leung
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University of Macau, Taipa, Macao P. R. China
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198
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Hancock RL, Dunne K, Walport LJ, Flashman E, Kawamura A. Epigenetic regulation by histone demethylases in hypoxia. Epigenomics 2015; 7:791-811. [PMID: 25832587 DOI: 10.2217/epi.15.24] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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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199
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Abstract
Black et al. demonstrate that hypoxia induces transient, site-specific copy gains in primary, nontransformed, and transformed human cells. Hypoxia-driven copy gains are dependent on the KDM4A histone demethylase and are blocked by inhibition of KDM4A with a small molecule or the natural metabolite succinate. Copy number heterogeneity is a prominent feature within tumors. The molecular basis for this heterogeneity remains poorly characterized. Here, we demonstrate that hypoxia induces transient site-specific copy gains (TSSGs) in primary, nontransformed, and transformed human cells. Hypoxia-driven copy gains are not dependent on HIF1α or HIF2α; however, they are dependent on the KDM4A histone demethylase and are blocked by inhibition of KDM4A with a small molecule or the natural metabolite succinate. Furthermore, this response is conserved at a syntenic region in zebrafish cells. Regions with site-specific copy gain are also enriched for amplifications in hypoxic primary tumors. These tumors exhibited amplification and overexpression of the drug resistance gene CKS1B, which we recapitulated in hypoxic breast cancer cells. Our results demonstrate that hypoxia provides a biological stimulus to create transient site-specific copy alterations that could result in heterogeneity within tumors and cell populations. These findings have major implications in our understanding of copy number heterogeneity and the emergence of drug resistance genes in cancer.
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200
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Advances in the development of histone lysine demethylase inhibitors. Curr Opin Pharmacol 2015; 23:52-60. [PMID: 26057211 DOI: 10.1016/j.coph.2015.05.009] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 05/11/2015] [Accepted: 05/15/2015] [Indexed: 11/22/2022]
Abstract
The covalent modification of histones is closely associated with regulation of gene transcription. Chromatin modifications have been suggested to represent an epigenetic code that is dynamically 'written' and 'erased' by specialized proteins, and 'read', or interpreted, by proteins that translate the code into gene expression changes. Initially thought to be an irreversible process, histone methylation is now known to be reversed by demethylases, FAD dependent amineoxidases and by iron(II)-alpha-ketoglutarate dependent deoxygenases of the Jumonji family. Altered histone demethylase activities have been associated with human disease, including cancer. The first wave of novel investigational drugs directed against KDM1A has recently entered the clinic, and the first specific inhibitor targeting a Jumonji KDM is advancing in preclinical regulatory studies.
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