201
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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: 104] [Impact Index Per Article: 11.6] [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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202
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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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203
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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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204
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Liu K, Liu Y, Lau JL, Min J. Epigenetic targets and drug discovery Part 2: Histone demethylation and DNA methylation. Pharmacol Ther 2015; 151:121-40. [PMID: 25857453 DOI: 10.1016/j.pharmthera.2015.04.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 03/31/2015] [Indexed: 02/06/2023]
Abstract
Chromatin structure is dynamically modulated by various chromatin modifications, such as histone/DNA methylation and demethylation. We have reviewed histone methyltransferases and methyllysine binders in terms of small molecule screening and drug discovery in the first part of this review series. In this part, we will summarize recent progress in chemical probe and drug discovery of histone demethylases and DNA methyltransferases. Histone demethylation and DNA methylation have attracted a lot of attention regarding their biology and disease implications. Correspondingly, many small molecule compounds have been designed to modulate the activity of histone demethylases and DNA methyltransferases, and some of them have been developed into therapeutic drugs or put into clinical trials.
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Affiliation(s)
- Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Yanli Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Johnathan L Lau
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada; Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada; Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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205
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Rasmussen PB, Staller P. The KDM5 family of histone demethylases as targets in oncology drug discovery. Epigenomics 2015; 6:277-86. [PMID: 25111482 DOI: 10.2217/epi.14.14] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
There is growing evidence for a causal role of the KDM5 family of histone demethylases in human cancer. In particular, KDM5A (JARID1A/RBP2) and KDM5B (JARID1B/PLU1) contribute to cancer cell proliferation, reduce the expression of tumor suppressor genes, promote the development of drug tolerance and maintain tumor-initiating cells. KDM5 enzymes remove tri- and di-methylations of lysine 4 of histone H3 - modifications that occur at the start site of transcription in actively transcribed genes. However, the importance of the histone demethylase activity of KDM5 proteins for cancer cells has not been resolved so far. The currently available approaches suppress or remove the targeted proteins and thereby affect their putative functions as structural components and recruitment factors for other chromatin-associated proteins. Therefore, the development of specific enzymatic inhibitors for KDM5 will promote our understanding of the biological role of their catalytic activity and yield potential novel anticancer therapeutics.
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206
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Van Rechem C, Black JC, Boukhali M, Aryee MJ, Gräslund S, Haas W, Benes CH, Whetstine JR. Lysine demethylase KDM4A associates with translation machinery and regulates protein synthesis. Cancer Discov 2015; 5:255-63. [PMID: 25564516 PMCID: PMC4355328 DOI: 10.1158/2159-8290.cd-14-1326] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
UNLABELLED Chromatin-modifying enzymes are predominantly nuclear; however, these factors are also localized to the cytoplasm, and very little is known about their role in this compartment. In this report, we reveal a non-chromatin-linked role for the lysine-specific demethylase KDM4A. We demonstrate that KDM4A interacts with the translation initiation complex and affects the distribution of translation initiation factors within polysome fractions. Furthermore, KDM4A depletion reduced protein synthesis and enhanced the protein synthesis suppression observed with mTOR inhibitors, which paralleled an increased sensitivity to these drugs. Finally, we demonstrate that JIB-04, a JmjC demethylase inhibitor, suppresses translation initiation and enhances mTOR inhibitor sensitivity. These data highlight an unexpected cytoplasmic role for KDM4A in regulating protein synthesis and suggest novel potential therapeutic applications for this class of enzyme. SIGNIFICANCE This report documents an unexpected cytoplasmic role for the lysine demethylase KDM4A. We demonstrate that KDM4A interacts with the translation initiation machinery, regulates protein synthesis and, upon coinhibition with mTOR inhibitors, enhances the translation suppression and cell sensitivity to these therapeutics.
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Affiliation(s)
- Capucine Van Rechem
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts
| | - Joshua C Black
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts
| | - Myriam Boukhali
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts
| | - Martin J Aryee
- Massachusetts General Hospital Department of Pathology and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts
| | - Susanne Gräslund
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Wilhelm Haas
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts
| | - Cyril H Benes
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts
| | - Johnathan R Whetstine
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts.
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207
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Chen Y, Terajima M, Yang Y, Sun L, Ahn YH, Pankova D, Puperi DS, Watanabe T, Kim MP, Blackmon SH, Rodriguez J, Liu H, Behrens C, Wistuba II, Minelli R, Scott KL, Sanchez-Adams J, Guilak F, Pati D, Thilaganathan N, Burns AR, Creighton CJ, Martinez ED, Zal T, Grande-Allen KJ, Yamauchi M, Kurie JM. Lysyl hydroxylase 2 induces a collagen cross-link switch in tumor stroma. J Clin Invest 2015; 125:1147-62. [PMID: 25664850 DOI: 10.1172/jci74725] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 01/05/2015] [Indexed: 01/08/2023] Open
Abstract
Epithelial tumor metastasis is preceded by an accumulation of collagen cross-links that heighten stromal stiffness and stimulate the invasive properties of tumor cells. However, the biochemical nature of collagen cross-links in cancer is still unclear. Here, we postulated that epithelial tumorigenesis is accompanied by changes in the biochemical type of collagen cross-links. Utilizing resected human lung cancer tissues and a p21CIP1/WAF1-deficient, K-rasG12D-expressing murine metastatic lung cancer model, we showed that, relative to normal lung tissues, tumor stroma contains higher levels of hydroxylysine aldehyde-derived collagen cross-links (HLCCs) and lower levels of lysine aldehyde-derived cross-links (LCCs), which are the predominant types of collagen cross-links in skeletal tissues and soft tissues, respectively. Gain- and loss-of-function studies in tumor cells showed that lysyl hydroxylase 2 (LH2), which hydroxylates telopeptidyl lysine residues on collagen, shifted the tumor stroma toward a high-HLCC, low-LCC state, increased tumor stiffness, and enhanced tumor cell invasion and metastasis. Together, our data indicate that LH2 enhances the metastatic properties of tumor cells and functions as a regulatory switch that controls the relative abundance of biochemically distinct types of collagen cross-links in the tumor stroma.
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MESH Headings
- Adenocarcinoma/enzymology
- Adenocarcinoma/mortality
- Adenocarcinoma/secondary
- Animals
- Carcinoma, Squamous Cell/enzymology
- Carcinoma, Squamous Cell/mortality
- Carcinoma, Squamous Cell/secondary
- Cell Line, Tumor
- Cells, Cultured
- Collagen/metabolism
- Enzyme Induction
- Extracellular Matrix/metabolism
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Kaplan-Meier Estimate
- Lung Neoplasms/enzymology
- Lung Neoplasms/mortality
- Lung Neoplasms/pathology
- Male
- Mice, 129 Strain
- Mice, Transgenic
- Neoplasm Transplantation
- Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase/physiology
- Promoter Regions, Genetic
- STAT3 Transcription Factor/metabolism
- Tumor Microenvironment
- Up-Regulation
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208
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Hamamoto R, Saloura V, Nakamura Y. Critical roles of non-histone protein lysine methylation in human tumorigenesis. Nat Rev Cancer 2015; 15:110-24. [PMID: 25614009 DOI: 10.1038/nrc3884] [Citation(s) in RCA: 264] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Several protein lysine methyltransferases and demethylases have been identified to have critical roles in histone modification. A large body of evidence has indicated that their dysregulation is involved in the development and progression of various diseases, including cancer, and these enzymes are now considered to be potential therapeutic targets. Although most studies have focused on histone methylation, many reports have revealed that these enzymes also regulate the methylation dynamics of non-histone proteins such as p53, RB1 and STAT3 (signal transducer and activator of transcription 3), which have important roles in human tumorigenesis. In this Review, we summarize the molecular functions of protein lysine methylation and its involvement in human cancer, with a particular focus on lysine methylation of non-histone proteins.
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Affiliation(s)
- Ryuji Hamamoto
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, 5841 S. Maryland Avenue, MC 2115 Chicago, Illinois 60637, USA
| | - Vassiliki Saloura
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, 5841 S. Maryland Avenue, MC 2115 Chicago, Illinois 60637, USA
| | - Yusuke Nakamura
- Section of Hematology/Oncology, Department of Medicine, The University of Chicago, 5841 S. Maryland Avenue, MC 2115 Chicago, Illinois 60637, USA
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209
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Wade MA, Jones D, Wilson L, Stockley J, Coffey K, Robson CN, Gaughan L. The histone demethylase enzyme KDM3A is a key estrogen receptor regulator in breast cancer. Nucleic Acids Res 2014; 43:196-207. [PMID: 25488809 PMCID: PMC4288188 DOI: 10.1093/nar/gku1298] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Endocrine therapy has successfully been used to treat estrogen receptor (ER)-positive breast cancer, but this invariably fails with cancers becoming refractory to treatment. Emerging evidence has suggested that fluctuations in ER co-regulatory protein expression may facilitate resistance to therapy and be involved in breast cancer progression. To date, a small number of enzymes that control methylation status of histones have been identified as co-regulators of ER signalling. We have identified the histone H3 lysine 9 mono- and di-methyl demethylase enzyme KDM3A as a positive regulator of ER activity. Here, we demonstrate that depletion of KDM3A by RNAi abrogates the recruitment of the ER to cis-regulatory elements within target gene promoters, thereby inhibiting estrogen-induced gene expression changes. Global gene expression analysis of KDM3A-depleted cells identified gene clusters associated with cell growth. Consistent with this, we show that knockdown of KDM3A reduces ER-positive cell proliferation and demonstrate that KDM3A is required for growth in a model of endocrine therapy-resistant disease. Crucially, we show that KDM3A catalytic activity is required for both ER-target gene expression and cell growth, demonstrating that developing compounds which target demethylase enzymatic activity may be efficacious in treating both ER-positive and endocrine therapy-resistant disease.
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Affiliation(s)
- Mark A Wade
- Northen Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Dominic Jones
- Northen Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Laura Wilson
- Northen Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Jacqueline Stockley
- The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Kelly Coffey
- Northen Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Craig N Robson
- Northen Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Luke Gaughan
- Northen Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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210
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Thinnes CC, England KS, Kawamura A, Chowdhury R, Schofield CJ, Hopkinson RJ. Targeting histone lysine demethylases - progress, challenges, and the future. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1839:1416-32. [PMID: 24859458 PMCID: PMC4316176 DOI: 10.1016/j.bbagrm.2014.05.009] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 05/06/2014] [Accepted: 05/13/2014] [Indexed: 12/20/2022]
Abstract
N-Methylation of lysine and arginine residues has emerged as a major mechanism of transcriptional regulation in eukaryotes. In humans, N(ε)-methyllysine residue demethylation is catalysed by two distinct subfamilies of demethylases (KDMs), the flavin-dependent KDM1 subfamily and the 2-oxoglutarate- (2OG) dependent JmjC subfamily, which both employ oxidative mechanisms. Modulation of histone methylation status is proposed to be important in epigenetic regulation and has substantial medicinal potential for the treatment of diseases including cancer and genetic disorders. This article provides an introduction to the enzymology of the KDMs and the therapeutic possibilities and challenges associated with targeting them, followed by a review of reported KDM inhibitors and their mechanisms of action from kinetic and structural perspectives.
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Affiliation(s)
- Cyrille C Thinnes
- The Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | | | - Akane Kawamura
- The Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
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211
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England KS, Tumber A, Krojer T, Scozzafava G, Ng SS, Daniel M, Szykowska A, Che K, von Delft F, Burgess-Brown NA, Kawamura A, Schofield CJ, Brennan PE. Optimisation of a triazolopyridine based histone demethylase inhibitor yields a potent and selective KDM2A (FBXL11) inhibitor. MEDCHEMCOMM 2014; 5:1879-1886. [PMID: 26682034 PMCID: PMC4678576 DOI: 10.1039/c4md00291a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A potent inhibitor of the JmjC histone lysine demethylase KDM2A (compound 35, pIC50 7.2) with excellent selectivity over representatives from other KDM subfamilies has been developed; the discovery that a triazolopyridine compound binds to the active site of JmjC KDMs was followed by optimisation of the triazole substituent for KDM2A inhibition and selectivity.
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Affiliation(s)
- Katherine S. England
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Anthony Tumber
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
| | - Giuseppe Scozzafava
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Stanley S. Ng
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
| | - Michelle Daniel
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
| | - Aleksandra Szykowska
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
| | - KaHing Che
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
| | - Frank von Delft
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Nicola A. Burgess-Brown
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
| | - Akane Kawamura
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | | | - Paul E. Brennan
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, UK
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212
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Tran TA, Wichterman-Kouznetsova J, Varghese D, Huang R, Huang W, Becker M, Austin CP, Inglese J, Johnson RL, Martinez ED. Identification of small molecule modulators of gene transcription with anticancer activity. ACS Chem Biol 2014; 9:2603-11. [PMID: 25188650 PMCID: PMC4245161 DOI: 10.1021/cb500532x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Epigenetic regulation of gene expression is essential in many biological processes, and its deregulation contributes to pathology including tumor formation. We used an image-based cell assay that measures the induction of a silenced GFP-estrogen receptor reporter to identify novel classes of small molecules involved in the regulation of gene expression. Using this Locus Derepression assay, we queried 283,122 compounds by quantitative high-throughput screening evaluating compounds at multiple concentrations. After confirmation and independent validation, the Locus Derepression assay identified 19 small molecules as new actives that induce the GFP message over 2-fold. Viability assays demonstrated that 17 of these actives have anti-proliferative activity, and two of them show selectivity for cancer versus patient-matched normal cells and cause unique changes in gene expression patterns in cancer cells by altering histone marks. Hence, these compounds represent chemical tools for understanding the molecular mechanisms of epigenetic control of transcription and for modulating cell growth pathways.
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Affiliation(s)
| | | | | | - Ruili Huang
- NIH
Chemical Genomics Center, NCATS, NIH, Rockville, Maryland 20850, United States
| | - Wenwei Huang
- NIH
Chemical Genomics Center, NCATS, NIH, Rockville, Maryland 20850, United States
| | - Matthias Becker
- Laboratory
of Receptor Biology and Gene Expression, NCI, NIH, Bethesda, Maryland 20892, United States
| | | | - James Inglese
- NIH
Chemical Genomics Center, NCATS, NIH, Rockville, Maryland 20850, United States
| | - Ronald L. Johnson
- NIH
Chemical Genomics Center, NCATS, NIH, Rockville, Maryland 20850, United States
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213
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Rodriguez R, Miller KM. Unravelling the genomic targets of small molecules using high-throughput sequencing. Nat Rev Genet 2014; 15:783-96. [PMID: 25311424 DOI: 10.1038/nrg3796] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Small molecules--including various approved and novel cancer therapeutics--can operate at the genomic level by targeting the DNA and protein components of chromatin. Emerging evidence suggests that functional interactions between small molecules and the genome are non-stochastic and are influenced by a dynamic interplay between DNA sequences and chromatin states. The establishment of genome-wide maps of small-molecule targets using unbiased methodologies can help to characterize and exploit drug responses. In this Review, we discuss how high-throughput sequencing strategies, such as ChIP-seq (chromatin immunoprecipitation followed by sequencing) and Chem-seq (chemical affinity capture and massively parallel DNA sequencing), are enabling the comprehensive identification of small-molecule target sites throughout the genome, thereby providing insights into unanticipated drug effects.
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Affiliation(s)
- Raphaël Rodriguez
- 1] Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles du CNRS, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France. [2] Institut Curie Research Center, Organic Synthesis and Cell Biology Group, 26 rue d'Ulm, 75248, Paris Cedex 05, France. [3]
| | - Kyle M Miller
- 1] Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, University of Texas at Austin, 2506 Speedway Stop A5000, Austin, Texas 78712, USA. [2]
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214
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Yu W, Eram MS, Hajian T, Szykowska A, Burgess-Brown N, Vedadi M, Brown PJ. A scintillation proximity assay for histone demethylases. Anal Biochem 2014; 463:54-60. [DOI: 10.1016/j.ab.2014.06.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Revised: 06/22/2014] [Accepted: 06/28/2014] [Indexed: 10/25/2022]
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215
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Katz TA, Huang Y, Davidson NE, Jankowitz RC. Epigenetic reprogramming in breast cancer: from new targets to new therapies. Ann Med 2014; 46:397-408. [PMID: 25058177 DOI: 10.3109/07853890.2014.923740] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Breast cancer is the most commonly diagnosed cancer and the second leading cause of cancer death among women in the United States. Recently, interest has grown in the role of epigenetics in breast cancer development and progression. Epigenetic changes such as DNA methylation, histone modifications, and abnormal expression of non-coding RNAs emerged as novel biomarkers in breast cancer diagnosis, therapy, and prevention. This review focuses on the most recent mechanistic findings underlying epigenetic changes in breast cancer development and their role as predictors of breast cancer risk. The rapid progress in our understanding of epigenetic findings in breast cancer has opened new avenues for potential therapeutic approaches via identification of epigenetic targets. We highlight the development of novel epigenetically targeted drugs, relevant clinical trials in breast cancer patients, and recent approaches combining epigenetic agents with chemotherapy and/or endocrine therapy that may incrementally improve long-term outcomes in appropriately selected breast cancer patients. Biomarkers of response are needed, however, to identify patient subsets that are most likely to benefit from epigenetic treatment strategies.
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Affiliation(s)
- Tiffany A Katz
- Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, The Women's Cancer Research Center , Pittsburgh, PA , USA
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216
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Blagg J, Workman P. Chemical biology approaches to target validation in cancer. Curr Opin Pharmacol 2014; 17:87-100. [PMID: 25175311 DOI: 10.1016/j.coph.2014.07.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 07/15/2014] [Accepted: 07/16/2014] [Indexed: 02/06/2023]
Abstract
Target validation is a crucial element of drug discovery. Especially given the wealth of potential targets emerging from cancer genome sequencing and functional genetic screens, and also considering the time and cost of downstream drug discovery efforts, it is essential to build confidence in a proposed target, ideally using different technical approaches. We argue that complementary biological and chemical biology strategies are essential for robust target validation. We discuss recent progress in the discovery and application of high quality chemical tools and other chemical biology approaches to target validation in cancer. Among other topical examples, we highlight the emergence of designed irreversible chemical tools to study potential target proteins and oncogenic pathways that were hitherto regarded as poorly druggable.
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Affiliation(s)
- Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK.
| | - Paul Workman
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK.
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217
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Chu CH, Wang LY, Hsu KC, Chen CC, Cheng HH, Wang SM, Wu CM, Chen TJ, Li LT, Liu R, Hung CL, Yang JM, Kung HJ, Wang WC. KDM4B as a target for prostate cancer: structural analysis and selective inhibition by a novel inhibitor. J Med Chem 2014; 57:5975-85. [PMID: 24971742 PMCID: PMC4216216 DOI: 10.1021/jm500249n] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Indexed: 12/17/2022]
Abstract
The KDM4/JMJD2 Jumonji C-containing histone lysine demethylases (KDM4A-KDM4D), which selectively remove the methyl group(s) from tri/dimethylated lysine 9/36 of H3, modulate transcriptional activation and genome stability. The overexpression of KDM4A/KDM4B in prostate cancer and their association with androgen receptor suggest that KDM4A/KDM4B are potential progression factors for prostate cancer. Here, we report the crystal structure of the KDM4B·pyridine 2,4-dicarboxylic acid·H3K9me3 ternary complex, revealing the core active-site region and a selective K9/K36 site. A selective KDM4A/KDM4B inhibitor, 4, that occupies three subsites in the binding pocket is identified by virtual screening. Pharmacological and genetic inhibition of KDM4A/KDM4B significantly blocks the viability of cultured prostate cancer cells, which is accompanied by increased H3K9me3 staining and transcriptional silencing of growth-related genes. Significantly, a substantial portion of differentially expressed genes are AR-responsive, consistent with the roles of KDM4s as critical AR activators. Our results point to KDM4 as a useful therapeutic target and identify a new inhibitor scaffold.
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Affiliation(s)
- Chia-Han Chu
- Institute of Molecular and Cellular Biology
and Department of Life
Sciences and Biomedical Science and Engineering Center, National Tsing-Hua University, Hsinchu, 30013, Taiwan
| | - Ling-Yu Wang
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, University of
California Davis Cancer Center, Sacramento, California 95817, United States
| | - Kai-Cheng Hsu
- Institute
of Bioinformatics and Systems Biology, National
Chiao Tung University, Hsinchu, 30050, Taiwan
| | - Chung-Chin Chen
- Institute of Molecular and Cellular Biology
and Department of Life
Sciences and Biomedical Science and Engineering Center, National Tsing-Hua University, Hsinchu, 30013, Taiwan
| | - Hsing-Hung Cheng
- Institute of Molecular and Cellular Biology
and Department of Life
Sciences and Biomedical Science and Engineering Center, National Tsing-Hua University, Hsinchu, 30013, Taiwan
| | - Szu-Min Wang
- Institute of Molecular and Cellular Biology
and Department of Life
Sciences and Biomedical Science and Engineering Center, National Tsing-Hua University, Hsinchu, 30013, Taiwan
| | - Chien-Ming Wu
- Institute of Molecular and Cellular Biology
and Department of Life
Sciences and Biomedical Science and Engineering Center, National Tsing-Hua University, Hsinchu, 30013, Taiwan
| | - Tsan-Jan Chen
- Institute of Molecular and Cellular Biology
and Department of Life
Sciences and Biomedical Science and Engineering Center, National Tsing-Hua University, Hsinchu, 30013, Taiwan
| | - Ling-Ting Li
- Institute
of Bioinformatics and Systems Biology, National
Chiao Tung University, Hsinchu, 30050, Taiwan
| | - Ruiwu Liu
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, University of
California Davis Cancer Center, Sacramento, California 95817, United States
| | - Chiu-Lien Hung
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, University of
California Davis Cancer Center, Sacramento, California 95817, United States
| | - Jing-Moon Yang
- Institute
of Bioinformatics and Systems Biology, National
Chiao Tung University, Hsinchu, 30050, Taiwan
| | - Hsing-Jien Kung
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, University of
California Davis Cancer Center, Sacramento, California 95817, United States
- National
Health Research Institutes, Miaoli, 35053, Taiwan
| | - Wen-Ching Wang
- Institute of Molecular and Cellular Biology
and Department of Life
Sciences and Biomedical Science and Engineering Center, National Tsing-Hua University, Hsinchu, 30013, Taiwan
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218
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Dhanak D, Jackson P. Development and classes of epigenetic drugs for cancer. Biochem Biophys Res Commun 2014; 455:58-69. [PMID: 25016182 DOI: 10.1016/j.bbrc.2014.07.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/23/2014] [Accepted: 07/01/2014] [Indexed: 12/16/2022]
Abstract
Emerging evidence supports an important, etiologic role for epigenetic modifications in cancer. Various post translational modifications of histone proteins together with DNA methylation constitute an 'epigenetic code' regulating the transcriptional status of the cell and aberrant writing and/or interpretation of the code can contribute to a dysregulated, hyperproliferative state. In some cases, epigenetic deregulation has also been reported to result in tumor initiation. The discovery of somatic mutations in some chromatin binding proteins associated with subtypes of lymphomas and the ability to regulate expression of proto oncogenes such as Myc has spurred the development of specific small molecule modulators of histone binding proteins. Several of these compounds have entered clinical development for the treatment of heme malignancies. This review summarizes progress in the discovery and advancement of epigenetic therapeutics for cancer and provides a perspective for future development.
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Affiliation(s)
- Dashyant Dhanak
- Discovery Sciences, Janssen Pharmaceuticals, 1400 McKean Road, Spring House, PA 19477, USA.
| | - Paul Jackson
- Discovery Sciences, Janssen Pharmaceuticals, 1400 McKean Road, Spring House, PA 19477, USA
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219
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Stein J, Majores M, Rohde M, Lim S, Schneider S, Krappe E, Ellinger J, Dietel M, Stephan C, Jung K, Perner S, Kristiansen G, Kirfel J. KDM5C is overexpressed in prostate cancer and is a prognostic marker for prostate-specific antigen-relapse following radical prostatectomy. THE AMERICAN JOURNAL OF PATHOLOGY 2014; 184:2430-7. [PMID: 25016185 DOI: 10.1016/j.ajpath.2014.05.022] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 05/16/2014] [Accepted: 05/27/2014] [Indexed: 10/25/2022]
Abstract
Currently, few prognostic factors are available to predict the emergence of castration-resistant prostate cancer and no curative options are available. Epigenetic gene regulation has been shown to trigger prostate cancer metastasis and androgen independence. Histone lysine demethylases (KDMs) are epigenetic enzymes that can remove both repressive and activating histone marks. KDM5 family members are capable of removing the histone H3 lysine 4 dimethylation-activating mark, rendering them potential players in the down-regulation of tumor suppressors and suggesting that their activity could repress oncogenes. Here, we systematically investigated KDM5C expression patterns in two independent radical prostatectomy cohorts (822 prostate tumors in total) by immunohistochemistry. Positive nuclear KDM5C staining was significantly associated with a reduced prostate-specific antigen relapse-free survival. Our study confirmed that nuclear KDM5C expression is an independent prognostic parameter. Most strikingly, the prognostic value of nuclear KDM5C expression for progression-free survival was exclusively pronounced for the Gleason group 7. In addition, KDM5C knockdown resulted in growth retardation of prostate cancer cells in vitro and induced regulation of several proliferation-associated genes. Our data indicate that KDM5C is functionally involved in proliferation control of prostate cancer cells and might represent a novel attractive therapy target. Moreover, overexpression of KDM5C is an independent new predictive marker for therapy failure as determined by biochemical recurrence in patients after prostatectomy.
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Affiliation(s)
- Johannes Stein
- Institute of Pathology, University of Bonn, Bonn, Germany
| | | | | | - Soyoung Lim
- Institute of Pathology, University of Cologne, Köln, Germany
| | | | - Eliana Krappe
- Institute of Pathology, University of Bonn, Bonn, Germany
| | - Jörg Ellinger
- Department of Urology, University of Bonn, Bonn, Germany
| | - Manfred Dietel
- Institute of Pathology, Charité University Hospital, Berlin, Germany
| | - Carsten Stephan
- Department of Urology, Charité University Hospital, Berlin, Germany
| | - Klaus Jung
- Berlin Institute of Urologic Research, Charité University Hospital, Berlin, Germany
| | - Sven Perner
- Institute of Pathology, University of Bonn, Bonn, Germany
| | | | - Jutta Kirfel
- Institute of Pathology, University of Bonn, Bonn, Germany.
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220
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Easmon J, Pürstinger G, Heinisch G, Fiebig HH, Roth T, Hofmann J. Synthesis, cytotoxic, and antitumor activities of 2-pyridylhydrazones derived from 3-benzoylpyridazines. Arch Pharm (Weinheim) 2014; 347:599-608. [PMID: 24917378 DOI: 10.1002/ardp.201400137] [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: 04/07/2014] [Revised: 04/07/2014] [Accepted: 04/23/2014] [Indexed: 11/10/2022]
Abstract
A series of 2-pyridylhydrazones derived from phenyl-pyridazin-3-yl-methanones were prepared in search for potential novel antitumor agents. The stereochemistry of these compounds was established by means of NMR spectroscopy. Whereas hydrazones derived from 3-benzoylpyridazines (IC50 = 0.99-8.74 µM) inhibited the proliferation of the tumor cell lines tested, the non-fully aromatic 3-benzoylpyridazinone hydrazones (IC50 >10 µM) turned out to be inactive. Compounds E-1b (IC50 = 0.12 µM) and E-1d (IC50 = 0.18 µM) exert high cytotoxic activities in clonogenic assays involving human tumor cells of different tissue origins. In vivo application of compound E-1b (300 mg/kg/day) resulted in a 66% reduction in tumor burden.
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Affiliation(s)
- Johnny Easmon
- Pharmaceutical Chemistry-Institute of Pharmacy, Centrum für Chemie und Biomedizin, Leopold-Franzens-Universität, Innsbruck, Austria
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221
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Kim TD, Fuchs JR, Schwartz E, Abdelhamid D, Etter J, Berry WL, Li C, Ihnat MA, Li PK, Janknecht R. Pro-growth role of the JMJD2C histone demethylase in HCT-116 colon cancer cells and identification of curcuminoids as JMJD2 inhibitors. Am J Transl Res 2014; 6:236-247. [PMID: 24936217 PMCID: PMC4058306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Accepted: 03/17/2014] [Indexed: 06/03/2023]
Abstract
Colon tumors are a major cause of cancer death, yet their molecular intricacies are not fully understood. We demonstrate that the histone demethylases JMJD2A, JMJD2B and JMJD2C are overexpressed in colon cancer cell lines, whereas another related protein, JMJD2D, is not. Interestingly, despite their high homology, the intracellular localization of JMJD2A-C is different in colon and other cancer cells, with JMJD2A being present comparably in the cytoplasm and nucleus, JMJD2B more prevalent in the nucleus and JMJD2C strongly associated with chromatin. This suggests that each of these three proteins performs different, non-redundant functions. Moreover, we show that JMJD2C (also called KDM4C) forms complexes with β-catenin, an oncoprotein whose overexpression is crucial for the development of most colonic tumors. In addition, JMJD2C downregulation reduced both growth and clonogenic capacity of HCT-116 colon cancer cells. Further, JMJD2C was required for efficient expression of the growth stimulatory proteins FRA1 and cyclin D1 as well as the survival factor BCL2. Lastly, we identified derivatives of curcumin as in vitro inhibitors of JMJD2 enzymes, suggesting that these curcuminoids could be useful for decreasing JMJD2 activity in vivo. In conclusion, our data highlight that overexpression of JMJD2C confers a pro-growth effect on colon cancer cells and, therefore, its inhibition by curcuminoids or other small molecules could be beneficial as an adjuvant therapy for colon cancer patients.
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Affiliation(s)
- Tae-Dong Kim
- Department of Cell Biology, University of Oklahoma Health Sciences CenterOklahoma City, OK 73104, USA
| | - James R Fuchs
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State UniversityColumbus, OH 43210, USA
| | - Eric Schwartz
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State UniversityColumbus, OH 43210, USA
| | - Dalia Abdelhamid
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State UniversityColumbus, OH 43210, USA
| | - Jonathan Etter
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State UniversityColumbus, OH 43210, USA
| | - William L Berry
- Department of Cell Biology, University of Oklahoma Health Sciences CenterOklahoma City, OK 73104, USA
| | - Chenglong Li
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State UniversityColumbus, OH 43210, USA
| | - Michael A Ihnat
- Department of Pharmaceutical Sciences, University of Oklahoma Health Sciences CenterOklahoma City, OK 73104, USA
- Peggy and Charles Stephenson Cancer CenterOklahoma City, OK 73104, USA
| | - Pui-Kai Li
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State UniversityColumbus, OH 43210, USA
| | - Ralf Janknecht
- Department of Cell Biology, University of Oklahoma Health Sciences CenterOklahoma City, OK 73104, USA
- Peggy and Charles Stephenson Cancer CenterOklahoma City, OK 73104, USA
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222
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Van der Meulen J, Speleman F, Van Vlierberghe P. The H3K27me3 demethylase UTX in normal development and disease. Epigenetics 2014; 9:658-68. [PMID: 24561908 PMCID: PMC4063824 DOI: 10.4161/epi.28298] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In 2007, the Ubiquitously Transcribed Tetratricopeptide Repeat on chromosome X (UTX) was identified as a histone demethylase that specifically targets di- and tri-methyl groups on lysine 27 of histone H3 (H3K27me2/3). Since then, UTX has been proven essential during normal development, as it is critically required for correct reprogramming, embryonic development and tissue-specific differentiation. UTX is a member of the MLL2 H3K4 methyltransferase complex and its catalytic activity has been linked to regulation of HOX and RB transcriptional networks. In addition, an H3K27me2/3 demethylase independent function for UTX was uncovered in promoting general chromatin remodeling in concert with the BRG1-containing SWI/SNF remodeling complex. Constitutional inactivation of UTX causes a specific hereditary disorder called the Kabuki syndrome, whereas somatic loss of UTX has been reported in a variety of human cancers. Here, we compile the breakthrough discoveries made from the first disclosure of UTX as a histone demethylase till the identification of disease-related UTX mutations and specific UTX inhibitors.
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Affiliation(s)
| | - Frank Speleman
- Center for Medical Genetics; Ghent University; Ghent, Belgium
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223
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Mannironi C, Proietto M, Bufalieri F, Cundari E, Alagia A, Danovska S, Rinaldi T, Famiglini V, Coluccia A, La Regina G, Silvestri R, Negri R. An high-throughput in vivo screening system to select H3K4-specific histone demethylase inhibitors. PLoS One 2014; 9:e86002. [PMID: 24489688 PMCID: PMC3906020 DOI: 10.1371/journal.pone.0086002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 12/03/2013] [Indexed: 12/15/2022] Open
Abstract
Background Histone demethylases (HDMs) have a prominent role in epigenetic regulation and are emerging as potential therapeutic cancer targets. The search for small molecules able to inhibit HDMs in vivo is very active but at the present few compounds were found to be specific for defined classes of these enzymes. Methodology/Principal Findings In order to discover inhibitors specific for H3K4 histone demethylation we set up a screening system which tests the effects of candidate small molecule inhibitors on a S.cerevisiae strain which requires Jhd2 demethylase activity to efficiently grow in the presence of rapamycin. In order to validate the system we screened a library of 45 structurally different compounds designed as competitive inhibitors of α -ketoglutarate (α-KG) cofactor of the enzyme, and found that one of them inhibited Jhd2 activity in vitro and in vivo. The same compound effectively inhibits human Jumonji AT-Rich Interactive Domain (JARID) 1B and 1D in vitro and increases H3K4 tri-methylation in HeLa cell nuclear extracts (NEs). When added in vivo to HeLa cells, the compound leads to an increase of tri-methyl-H3K4 (H3K4me3) but does not affect H3K9 tri-methylation. We describe the cytostatic and toxic effects of the compound on HeLa cells at concentrations compatible with its inhibitory activity. Conclusions/Significance Our screening system is proved to be very useful in testing putative H3K4-specific HDM inhibitors for the capacity of acting in vivo without significantly altering the activity of other important 2-oxoglutarate oxygenases.
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Affiliation(s)
- Cecilia Mannironi
- Istituto di Biologia e Patologia Molecolari Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Marco Proietto
- Istituto Pasteur Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Francesca Bufalieri
- Istituto Pasteur Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Enrico Cundari
- Istituto di Biologia e Patologia Molecolari Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Angela Alagia
- Istituto Pasteur Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Svetlana Danovska
- Istituto Pasteur Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Teresa Rinaldi
- Istituto Pasteur Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Valeria Famiglini
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Rome, Italy
| | - Antonio Coluccia
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Rome, Italy
| | - Giuseppe La Regina
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Rome, Italy
| | - Romano Silvestri
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Rome, Italy
| | - Rodolfo Negri
- Istituto Pasteur Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Rome, Italy
- * E-mail:
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224
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Cho Y, Kim KH, Cho YS, Xu W, Wang X, Kwon HJ. A histone demethylase inhibitor, methylstat, inhibits angiogenesis in vitro and in vivo. RSC Adv 2014. [DOI: 10.1039/c4ra07154a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Histone methylation has been highlighted in the regulation of gene expression. Methylstat, a Jumonji C domain containing histone demethylase inhibitor, inhibitedin vitroandin vivoangiogenesis at nontoxic dose. Collectively, methylstat could be a promising chemical probe for addressing its role in angiogenesis
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Affiliation(s)
- Yumi Cho
- Chemical Genomics National Research Laboratory
- Department of Biotechnology
- Translational Research Center for Protein Function Control
- College of Life Science & Biotechnology
- Yonsei University
| | - Ki Hyun Kim
- Chemical Genomics National Research Laboratory
- Department of Biotechnology
- Translational Research Center for Protein Function Control
- College of Life Science & Biotechnology
- Yonsei University
| | - Yoon Sun Cho
- Chemical Genomics National Research Laboratory
- Department of Biotechnology
- Translational Research Center for Protein Function Control
- College of Life Science & Biotechnology
- Yonsei University
| | - Wenqing Xu
- Department of Chemistry and Biochemistry
- University of Colorado
- Boulder, USA
| | - Xiang Wang
- Department of Chemistry and Biochemistry
- University of Colorado
- Boulder, USA
| | - Ho Jeong Kwon
- Chemical Genomics National Research Laboratory
- Department of Biotechnology
- Translational Research Center for Protein Function Control
- College of Life Science & Biotechnology
- Yonsei University
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225
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Labbé RM, Holowatyj A, Yang ZQ. Histone lysine demethylase (KDM) subfamily 4: structures, functions and therapeutic potential. Am J Transl Res 2013; 6:1-15. [PMID: 24349617 PMCID: PMC3853420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 11/25/2013] [Indexed: 06/03/2023]
Abstract
KDM4 histone demethylases catalyze the removal of methyl marks from histone lysine residues to epigenetically regulate chromatin structure and gene expression. KDM4 expression is tightly regulated to insure proper function in diverse biological processes, such as cellular differentiation. Mounting evidence has shown that disrupting KDM4 expression is implicated in the establishment and progression of multiple diseases including cancer. In particular, genomic regions encoding the KDM4A, B and C genes are often amplified, disrupting normal cellular proliferation. Furthermore, KDM4 demethylases are promising druggable targets. In this review, we highlight the latest advances in characterizing the structures and regulatory mechanisms of KDM4 proteins, as well as our current understanding of their alterations and roles in tumorigenesis. We also review the reported KDM4 inhibitors and discuss their potential as therapeutic agents.
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Affiliation(s)
- Roselyne M Labbé
- Karmanos Cancer Institute, Department of Oncology, Wayne State University Detroit, MI 48201, USA
| | - Andreana Holowatyj
- Karmanos Cancer Institute, Department of Oncology, Wayne State University Detroit, MI 48201, USA
| | - Zeng-Quan Yang
- Karmanos Cancer Institute, Department of Oncology, Wayne State University Detroit, MI 48201, USA
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226
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Abstract
It has recently been demonstrated that the genes controlling the epigenetic programmes that are required for maintaining chromatin structure and cell identity include genes that drive human cancer. This observation has led to an increased awareness of chromatin-associated proteins as potentially interesting drug targets. The successful introduction of DNA methylation and histone deacetylase (HDAC) inhibitors for the treatment of specific subtypes of cancer has paved the way for the use of epigenetic therapy. Here, we highlight key biological findings demonstrating the roles of members of the histone lysine demethylase class of enzymes in the development of cancers, discuss the potential and challenges of therapeutically targeting them, and highlight emerging small-molecule inhibitors of these enzymes.
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227
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Huffman K, Martinez ED. Pre-clinical studies of epigenetic therapies targeting histone modifiers in lung cancer. Front Oncol 2013; 3:235. [PMID: 24058902 PMCID: PMC3766830 DOI: 10.3389/fonc.2013.00235] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 08/27/2013] [Indexed: 12/19/2022] Open
Abstract
Treatment options for lung cancer patients have been generally limited to standard therapies or targeted interventions which involve a small number of known mutations. Although the targeted therapies are initially successful, they most often result in drug resistance, relapse, and mortality. We now know that the complexity of lung cancer comes not only from genomic changes, but also from aberrant epigenetic regulatory events. Epigenetic therapies have shown promise as single agents in the treatment of hematological malignancies but have yet to meet this expectation in solid tumors thus fostering researchers to pursue new approaches in the development and use of epigenetic interventions. Here, we review some recent pre-clinical findings involving the use of drugs targeting histone modifying enzymes both as single agents and as co-therapies against lung cancer. A greater understanding of the impact of these epigenetic compounds in lung cancer signaling is needed and further evaluation in vivo is warranted in several cases based on the pre-clinical activity of a subset of compounds discussed in this review, including drugs co-targeting HDACs and EGF receptor, targeting Brd4 and targeting Jumonji histone demethylases.
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Affiliation(s)
- Kenneth Huffman
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center , Dallas, TX , USA
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228
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Dialysis encephalopathy: precipitating factors and improvement in prognosis. Clin Nephrol 1981; 13:60. [PMID: 32456660 PMCID: PMC7249421 DOI: 10.1186/s13045-020-00901-6] [Citation(s) in RCA: 95] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 05/18/2020] [Indexed: 12/16/2022] Open
Abstract
Cancer stem cells (CSCs) contribute to the initiation, recurrence, and metastasis of cancer; however, there are still no drugs targeting CSCs in clinical application. There are several signaling pathways playing critical roles in CSC progression, such as the Wnt, Hedgehog, Notch, Hippo, and autophagy signaling pathways. Additionally, targeting the ferroptosis signaling pathway was recently shown to specifically kill CSCs. Therefore, targeting these pathways may suppress CSC progression. The structure of small-molecule drugs shows a good spatial dispersion, and its chemical properties determine its good druggability and pharmacokinetic properties. These characteristics make small-molecule drugs show a great advantage in drug development, which is increasingly popular in the market. Thus, in this review, we will summarize the current researches on the small-molecule compounds suppressing CSC progression, including inhibitors of Wnt, Notch, Hedgehog, and autophagy pathways, and activators of Hippo and ferroptosis pathways. These small-molecule compounds emphasize CSC importance in tumor progression and propose a new strategy to treat cancer in clinic via targeting CSCs.
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