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Pippa S, Mannironi C, Licursi V, Bombardi L, Colotti G, Cundari E, Mollica A, Coluccia A, Naccarato V, La Regina G, Silvestri R, Negri R. Small Molecule Inhibitors of KDM5 Histone Demethylases Increase the Radiosensitivity of Breast Cancer Cells Overexpressing JARID1B. Molecules 2019; 24:molecules24091739. [PMID: 31060229 PMCID: PMC6540222 DOI: 10.3390/molecules24091739] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 04/24/2019] [Accepted: 05/01/2019] [Indexed: 12/18/2022] Open
Abstract
Background: KDM5 enzymes are H3K4 specific histone demethylases involved in transcriptional regulation and DNA repair. These proteins are overexpressed in different kinds of cancer, including breast, prostate and bladder carcinomas, with positive effects on cancer proliferation and chemoresistance. For these reasons, these enzymes are potential therapeutic targets. Methods: In the present study, we analyzed the effects of three different inhibitors of KDM5 enzymes in MCF-7 breast cancer cells over-expressing one of them, namely KDM5B/JARID1B. In particular we tested H3K4 demethylation (western blot); radio-sensitivity (cytoxicity and clonogenic assays) and damage accumulation (COMET assay and kinetics of H2AX phosphorylation). Results: we show that all three compounds with completely different chemical structures can selectively inhibit KDM5 enzymes and are capable of increasing sensitivity of breast cancer cells to ionizing radiation and radiation-induced damage. Conclusions: These findings confirm the involvement of H3K4 specific demethylases in the response to DNA damage, show a requirement of the catalytic function and suggest new strategies for the therapeutic use of their inhibitors.
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Affiliation(s)
- Simone Pippa
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy.
| | - Cecilia Mannironi
- Institute of Molecular Biology and Pathology, Italian National Research Council, 00185 Rome, Italy.
| | - Valerio Licursi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy.
- Institute for Systems Analysis and Computer Science "A. Ruberti", Italian National Research Council, 00185 Rome, Italy.
| | - Luca Bombardi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy.
| | - Gianni Colotti
- Institute of Molecular Biology and Pathology, Italian National Research Council, 00185 Rome, Italy.
| | - Enrico Cundari
- Institute of Molecular Biology and Pathology, Italian National Research Council, 00185 Rome, Italy.
| | - Adriano Mollica
- Department of Pharmacy, University "G. d' Annunzio" of Chieti, Via dei Vestini 31, 66100 Chieti, Italy.
| | - Antonio Coluccia
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy.
| | - Valentina Naccarato
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy.
| | - Giuseppe La Regina
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy.
| | - Romano Silvestri
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia Cenci Bolognetti Foundation, Sapienza University of Rome, 00185 Rome, Italy.
| | - Rodolfo Negri
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy.
- Institute of Molecular Biology and Pathology, Italian National Research Council, 00185 Rome, Italy.
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Mizukami H, Kim JD, Tabara S, Lu W, Kwon C, Nakashima M, Fukamizu A. KDM5D-mediated H3K4 demethylation is required for sexually dimorphic gene expression in mouse embryonic fibroblasts. J Biochem 2019; 165:335-342. [PMID: 30541083 DOI: 10.1093/jb/mvy106] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 12/10/2018] [Indexed: 11/14/2022] Open
Abstract
Males and females share the same genetic code, but gene expression profile often displays differences between two sexes. Mouse embryonic fibroblasts (MEFs) have been used to experiment as a useful tool to test gene function. They have also been characterized by gender-based differences in expressed genes such as Y-linked Sry or X-linked Hprt. However, there is no report on sex differences in global gene expression. Here, using the next-generation RNA sequencing, we compared the comprehensive transcriptome of MEFs derived from two sexes. In comparison with the female group, the male group up-regulated 27 differentially expressed genes (DEGs), in which a male-specific histone demethylase KDM5D gene is included, and 7 DEGs were down-regulated. Based on the results by searching the ENCODE analysis, it was shown that the expression of 15 genes identified is potentially regulated by the methylation of H3K4me1 or H3K4me3. Interestingly, we demonstrated that both of H3K4 methylation are induced by knocking down KDM5D, which causes changes in patterns of eight DEGs found in male MEFs. Collectively, these data not only suggest an importance of KDM5D-mediated demethylation of H3K4 involved in the sexually dimorphic gene expression in male MEFs, but also may provide information regarding sex-dependent changes in gene expression when MEFs are used for experiments.
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Affiliation(s)
- Hayase Mizukami
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA).,Graduate School of Life and Environmental Sciences
| | - Jun-Dal Kim
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA)
| | | | - Weizhe Lu
- Ph.D. Program in Human Biology, School of Integrative Global Majors (SIGMA)
| | - Chulwon Kwon
- Graduate School of Life and Environmental Sciences
| | | | - Akiyoshi Fukamizu
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA).,International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, Japan
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53
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Post-translational modifications and chromatin dynamics. Essays Biochem 2019; 63:89-96. [DOI: 10.1042/ebc20180067] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 12/21/2022]
Abstract
Abstract
The dynamic structure of chromatin is linked to gene regulation and many other biological functions. Consequently, it is of importance to understand the factors that regulate chromatin dynamics. While the in vivo analysis of chromatin has verified that histone post-translational modifications play a role in modulating DNA accessibility, the complex nuclear environment and multiplicity of modifications prevents clear conclusions as to how individual modifications influence chromatin dynamics in the cell. For this reason, in vitro analyses of model reconstituted nucleosomal arrays has been pivotal in understanding the dynamic nature of chromatin compaction and the affects that specific post-translational modifications can have on the higher order chromatin structure. In this mini-review, we briefly describe the dynamic chromatin structures that have been observed in vitro and the environmental conditions that give rise to these various conformational states. Our focus then turns to a discussion of the specific histone post-translational modifications that have been shown to alter formation of these higher order chromatin structures in vitro and how this may relate to the biological state and accessibility of chromatin in vivo.
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54
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Shen X, Hu K, Cheng G, Xu L, Chen Z, Du P, Zhuang Z. KDM5D inhibit epithelial‐mesenchymal transition of gastric cancer through demethylation in the promoter of Cul4A in male. J Cell Biochem 2019; 120:12247-12258. [PMID: 30864186 DOI: 10.1002/jcb.27308] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 06/27/2018] [Indexed: 01/19/2023]
Affiliation(s)
- Xudong Shen
- Department of Oncology The Second Affiliated Hospital of Soochow University Suzhou China
| | - Kewei Hu
- Department of gastroenterology The Second Affiliated Hospital of Soochow University Suzhou China
| | - Guilian Cheng
- Department of gastroenterology The Second Affiliated Hospital of Soochow University Suzhou China
| | - Liming Xu
- Department of gastroenterology The Second Affiliated Hospital of Soochow University Suzhou China
| | - Zhengrong Chen
- Department of General Surgery The Second Affiliated Hospital of Soochow University Suzhou China
| | - Peng Du
- Department of General Surgery The Second Affiliated Hospital of Soochow University Suzhou China
| | - Zhixiang Zhuang
- Department of Oncology The Second Affiliated Hospital of Soochow University Suzhou China
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55
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Liu X, Zhang SM, McGeary MK, Krykbaeva I, Lai L, Jansen DJ, Kales SC, Simeonov A, Hall MD, Kelly DP, Bosenberg MW, Yan Q. KDM5B Promotes Drug Resistance by Regulating Melanoma-Propagating Cell Subpopulations. Mol Cancer Ther 2019; 18:706-717. [PMID: 30523048 PMCID: PMC6397704 DOI: 10.1158/1535-7163.mct-18-0395] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 10/09/2018] [Accepted: 11/26/2018] [Indexed: 12/19/2022]
Abstract
Tumor heterogeneity is a major challenge for cancer treatment, especially due to the presence of various subpopulations with stem cell or progenitor cell properties. In mouse melanomas, both CD34+p75- (CD34+) and CD34-p75- (CD34-) tumor subpopulations were characterized as melanoma-propagating cells (MPC) that exhibit some of those key features. However, these two subpopulations differ from each other in tumorigenic potential, ability to recapitulate heterogeneity, and chemoresistance. In this study, we demonstrate that CD34+ and CD34- subpopulations carrying the BRAFV600E mutation confer differential sensitivity to targeted BRAF inhibition. Through elevated KDM5B expression, melanoma cells shift toward a more drug-tolerant, CD34- state upon exposure to BRAF inhibitor or combined BRAF inhibitor and MEK inhibitor treatment. KDM5B loss or inhibition shifts melanoma cells to the more BRAF inhibitor-sensitive CD34+ state. These results support that KDM5B is a critical epigenetic regulator that governs the transition of key MPC subpopulations with distinct drug sensitivity. This study also emphasizes the importance of continuing to advance our understanding of intratumor heterogeneity and ultimately develop novel therapeutics by altering the heterogeneous characteristics of melanoma.
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Affiliation(s)
- Xiaoni Liu
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut
| | - Shang-Min Zhang
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut
| | - Meaghan K McGeary
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut
| | - Irina Krykbaeva
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut
| | - Ling Lai
- Penn Cardiovascular Institute, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Daniel J Jansen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
| | - Stephen C Kales
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland
| | - Daniel P Kelly
- Penn Cardiovascular Institute, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Marcus W Bosenberg
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut.
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut.
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56
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Yang GJ, Ko CN, Zhong HJ, Leung CH, Ma DL. Structure-Based Discovery of a Selective KDM5A Inhibitor that Exhibits Anti-Cancer Activity via Inducing Cell Cycle Arrest and Senescence in Breast Cancer Cell Lines. Cancers (Basel) 2019; 11:E92. [PMID: 30650517 PMCID: PMC6360022 DOI: 10.3390/cancers11010092] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 12/24/2018] [Accepted: 01/10/2019] [Indexed: 12/13/2022] Open
Abstract
Breast cancer is the one of the most frequent causes of female cancer mortality. KDM5A, a histone demethylase, can increase the proliferation, metastasis, and drug resistance of cancers, including breast cancer, and is thus an important therapeutic target. In the present work, we performed hierarchical virtual screening towards the KDM5A catalytic pocket from a chemical library containing 90,000 compounds. Using multiple biochemical methods, the cyclopenta[c]chromen derivative 1 was identified as the top candidate for KDM5A demethylase inhibitory activity. Compared with the well-known KDM5 inhibitor CPI-455 (18), 1 exhibited higher potency against KDM5A and much higher selectivity for KDM5A over both KDM4A and other KDM5 family members (KDM5B and KDM5C). Additionally, compound 1 repressed the proliferation of various KDM5A-overexpressing breast cancer cell lines. Mechanistically, 1 promoted accumulation of p16 and p27 by blocking KDM5A-mediated H3K4me3 demethylation, leading to cell cycle arrest and senescence. To date, compound 1 is the first cyclopenta[c]chromen-based KDM5A inhibitor reported, and may serve as a novel motif for developing more selective and efficacious pharmacological molecules targeting KDM5A. In addition, our research provides a possible anti-cancer mechanism of KDM5A inhibitors and highlights the feasibility and significance of KDM5A as a therapeutic target for KDM5A-overexpressing breast cancer.
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Affiliation(s)
- Guan-Jun Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China.
| | - Chung-Nga Ko
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong 999077, China.
| | - Hai-Jing Zhong
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China.
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China.
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong 999077, China.
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57
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Horton JR, Woodcock CB, Chen Q, Liu X, Zhang X, Shanks J, Rai G, Mott BT, Jansen DJ, Kales SC, Henderson MJ, Cyr M, Pohida K, Hu X, Shah P, Xu X, Jadhav A, Maloney DJ, Hall MD, Simeonov A, Fu H, Vertino PM, Cheng X. Structure-Based Engineering of Irreversible Inhibitors against Histone Lysine Demethylase KDM5A. J Med Chem 2018; 61:10588-10601. [PMID: 30392349 PMCID: PMC6467790 DOI: 10.1021/acs.jmedchem.8b01219] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The active sites of hundreds of human α-ketoglutarate (αKG) and Fe(II)-dependent dioxygenases are exceedingly well preserved, which challenges the design of selective inhibitors. We identified a noncatalytic cysteine (Cys481 in KDM5A) near the active sites of KDM5 histone H3 lysine 4 demethylases, which is absent in other histone demethylase families, that could be explored for interaction with the cysteine-reactive electrophile acrylamide. We synthesized analogs of a thienopyridine-based inhibitor chemotype, namely, 2-((3-aminophenyl)(2-(piperidin-1-yl)ethoxy)methyl)thieno[3,2- b]pyridine-7-carboxylic acid (N70) and a derivative containing a (dimethylamino)but-2-enamido)phenyl moiety (N71) designed to form a covalent interaction with Cys481. We characterized the inhibitory and binding activities against KDM5A and determined the cocrystal structures of the catalytic domain of KDM5A in complex with N70 and N71. Whereas the noncovalent inhibitor N70 displayed αKG-competitive inhibition that could be reversed after dialysis, inhibition by N71 was dependent on enzyme concentration and persisted even after dialysis, consistent with covalent modification.
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Affiliation(s)
- John R. Horton
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Clayton B. Woodcock
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Qin Chen
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Xu Liu
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Xing Zhang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - John Shanks
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Bryan T. Mott
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Daniel J. Jansen
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Stephen C. Kales
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Mark J. Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Matthew Cyr
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Katherine Pohida
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Pranav Shah
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Xin Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - David J. Maloney
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Haian Fu
- Departments of Pharmacology, Emory University, Atlanta, Georgia 30322, United States
- Hematology and Medical Oncology, Emory University, Atlanta, Georgia 30322, United States
- Emory Chemical Biology Discovery Center, Emory University, Atlanta, Georgia 30322, United States
- The Winship Cancer Institute, Emory University, Atlanta, Georgia 30322, United States
| | - Paula M. Vertino
- The Winship Cancer Institute, Emory University, Atlanta, Georgia 30322, United States
- Department of Radiation Oncology, Emory University, Atlanta, Georgia 30322, United States
| | - Xiaodong Cheng
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
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De Smedt E, Lui H, Maes K, De Veirman K, Menu E, Vanderkerken K, De Bruyne E. The Epigenome in Multiple Myeloma: Impact on Tumor Cell Plasticity and Drug Response. Front Oncol 2018; 8:566. [PMID: 30619733 PMCID: PMC6297718 DOI: 10.3389/fonc.2018.00566] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/13/2018] [Indexed: 01/19/2023] Open
Abstract
Multiple myeloma (MM) is a clonal plasma cell malignancy that develops primarily in the bone marrow (BM), where reciprocal interactions with the BM niche foster MM cell survival, growth, and drug resistance. MM cells furthermore reshape the BM to their own needs by affecting the different BM stromal cell types resulting in angiogenesis, bone destruction, and immune suppression. Despite recent advances in treatment modalities, MM remains most often incurable due to the development of drug resistance to all standard of care agents. This underscores the unmet need for these heavily treated relapsed/refractory patients. Disruptions in epigenetic regulation are a well-known hallmark of cancer cells, contributing to both cancer onset and progression. In MM, sequencing and gene expression profiling studies have also identified numerous epigenetic defects, including locus-specific DNA hypermethylation of cancer-related and B cell specific genes, genome-wide DNA hypomethylation and genetic defects, copy number variations and/or abnormal expression patterns of various chromatin modifying enzymes. Importantly, these so-called epimutations contribute to genomic instability, disease progression, and a worse outcome. Moreover, the frequency of mutations observed in genes encoding for histone methyltransferases and DNA methylation modifiers increases following treatment, indicating a role in the emergence of drug resistance. In support of this, accumulating evidence also suggest a role for the epigenetic machinery in MM cell plasticity, driving the differentiation of the malignant cells to a less mature and drug resistant state. This review discusses the current state of knowledge on the role of epigenetics in MM, with a focus on deregulated histone methylation modifiers and the impact on MM cell plasticity and drug resistance. We also provide insight into the potential of epigenetic modulating agents to enhance clinical drug responses and avoid disease relapse.
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Affiliation(s)
- Eva De Smedt
- Department of Hematology and Immunology-Myeloma Center Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Hui Lui
- Department of Hematology and Immunology-Myeloma Center Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Department of Hematology, Tianjin Medical University General Hospital, Tianjin, China
| | - Ken Maes
- Department of Hematology and Immunology-Myeloma Center Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Kim De Veirman
- Department of Hematology and Immunology-Myeloma Center Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Eline Menu
- Department of Hematology and Immunology-Myeloma Center Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Karin Vanderkerken
- Department of Hematology and Immunology-Myeloma Center Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Elke De Bruyne
- Department of Hematology and Immunology-Myeloma Center Brussels, Vrije Universiteit Brussel, Brussels, Belgium
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59
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Physiological effects of KDM5C on neural crest migration and eye formation during vertebrate development. Epigenetics Chromatin 2018; 11:72. [PMID: 30522514 PMCID: PMC6282277 DOI: 10.1186/s13072-018-0241-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 11/22/2018] [Indexed: 02/07/2023] Open
Abstract
Background Lysine-specific histone demethylase 5C (KDM5C) belongs to the jumonji family of demethylases and is specific for the di- and tri-demethylation of lysine 4 residues on histone 3 (H3K4 me2/3). KDM5C is expressed in the brain and skeletal muscles of humans and is associated with various biologically significant processes. KDM5C is known to be associated with X-linked mental retardation and is also involved in the development of cancer. However, the developmental significance of KDM5C has not been explored yet. In the present study, we investigated the physiological roles of KDM5C during Xenopus laevis embryonic development. Results Loss-of-function analysis using kdm5c antisense morpholino oligonucleotides indicated that kdm5c knockdown led to small-sized heads, reduced cartilage size, and malformed eyes (i.e., small-sized and deformed eyes). Molecular analyses of KDM5C functional roles using whole-mount in situ hybridization, β-galactosidase staining, and reverse transcription-polymerase chain reaction revealed that loss of kdm5c resulted in reduced expression levels of neural crest specifiers and genes involved in eye development. Furthermore, transcriptome analysis indicated the significance of KDM5C in morphogenesis and organogenesis. Conclusion Our findings indicated that KDM5C is associated with embryonic development and provided additional information regarding the complex and dynamic gene network that regulates neural crest formation and eye development. This study emphasizes the functional significance of KDM5C in Xenopus embryogenesis; however, further analysis is needed to explore the interactions of KDM5C with specific developmental genes. Electronic supplementary material The online version of this article (10.1186/s13072-018-0241-x) contains supplementary material, which is available to authorized users.
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60
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Hu D, Jablonowski C, Cheng PH, AlTahan A, Li C, Wang Y, Palmer L, Lan C, Sun B, Abu-Zaid A, Fan Y, Brimble M, Gamboa NT, Kumbhar RC, Yanishevski D, Miller KM, Kang G, Zambetti GP, Chen T, Yan Q, Davidoff AM, Yang J. KDM5A Regulates a Translational Program that Controls p53 Protein Expression. iScience 2018; 9:84-100. [PMID: 30388705 PMCID: PMC6214872 DOI: 10.1016/j.isci.2018.10.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 09/01/2018] [Accepted: 10/10/2018] [Indexed: 12/14/2022] Open
Abstract
The p53 tumor suppressor pathway is frequently inactivated in human cancers. However, there are some cancer types without commonly recognized alterations in p53 signaling. Here we report that histone demethylase KDM5A is involved in the regulation of p53 activity. KDM5A is significantly amplified in multiple types of cancers, an event that tends to be mutually exclusive to p53 mutation. We show that KDM5A acts as a negative regulator of p53 signaling through inhibition of p53 translation via suppression of a subgroup of eukaryotic translation initiation genes. Genetic deletion of KDM5A results in upregulation of p53 in multiple lineages of cancer cells and inhibits tumor growth in a p53-dependent manner. In addition, we have identified a regulatory loop between p53, miR-34, and KDM5A, whereby the induction of miR-34 leads to suppression of KDM5A. Thus, our findings reveal a mechanism by which KDM5A inhibits p53 translation to modulate cancer progression.
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Affiliation(s)
- Dongli Hu
- Department of Surgery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Carolyn Jablonowski
- Department of Surgery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Pei-Hsin Cheng
- Department of Surgery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Alaa AlTahan
- Department of Surgery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Chunliang Li
- Department of Tumor Cell Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yingdi Wang
- Department of Oncology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Lance Palmer
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Cuixia Lan
- Department of Clinical Laboratory, Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao 266033, China
| | - Bingmei Sun
- Department of Clinical Laboratory, Qingdao Central Hospital, Affiliated Hospital of Qingdao University, Qingdao 266042, China
| | - Ahmed Abu-Zaid
- Department of Surgery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yiping Fan
- Department of Computational Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Mark Brimble
- Department of Surgery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Nicolas T Gamboa
- Department of Surgery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Ramhari C Kumbhar
- Department of Molecular Biosciences, University of Texas at Austin, 100 E 24th St NHB 2.606 Stop A5000, Austin, TX 78712, USA
| | - David Yanishevski
- Department of Surgery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Kyle M Miller
- Department of Molecular Biosciences, University of Texas at Austin, 100 E 24th St NHB 2.606 Stop A5000, Austin, TX 78712, USA
| | - Guolian Kang
- Department of Biostatistics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Gerard P Zambetti
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, 310 Cedar St, New Haven, CT 06520, USA
| | - Andrew M Davidoff
- Department of Surgery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jun Yang
- Department of Surgery, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
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Plch J, Hrabeta J, Eckschlager T. KDM5 demethylases and their role in cancer cell chemoresistance. Int J Cancer 2018; 144:221-231. [PMID: 30246379 DOI: 10.1002/ijc.31881] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 09/03/2018] [Accepted: 09/13/2018] [Indexed: 12/28/2022]
Abstract
Histone methylation is important in the regulation of genes expression, and thus its dysregulation has been observed in various cancers. KDM5 enzymes are capable of removing tri- and di- methyl marks from lysine 4 on histone H3 (H3K4) which makes them potential players in the downregulation of tumor suppressors, but could also suggest that their activity repress oncogenes. Depending on the methylation site, their effect on transcription can be either activating or repressing. There is emerging evidence for deregulation of KDM5A/B/C/D and important phenotypic consequences in various types of cancer. It has been suggested that the KDM5 family of demethylases plays a role in the appearance of drug tolerance. Drug resistance remains a challenge to successful cancer treatment. This review summarizes recent advances in understanding the functions of KDM5 histone demethylases in cancer chemoresistance and potential therapeutic targeting of these enzymes, which seems to prevent the emergence of a drug-resistant population.
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Affiliation(s)
- Johana Plch
- Department of Pediatric Hematology and Oncology, 2nd Medical Faculty and University Hospital Motol, Prague, Czech Republic
| | - Jan Hrabeta
- Department of Pediatric Hematology and Oncology, 2nd Medical Faculty and University Hospital Motol, Prague, Czech Republic
| | - Tomas Eckschlager
- Department of Pediatric Hematology and Oncology, 2nd Medical Faculty and University Hospital Motol, Prague, Czech Republic
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Wu L, Cao J, Cai WL, Lang SM, Horton JR, Jansen DJ, Liu ZZ, Chen JF, Zhang M, Mott BT, Pohida K, Rai G, Kales SC, Henderson MJ, Hu X, Jadhav A, Maloney DJ, Simeonov A, Zhu S, Iwasaki A, Hall MD, Cheng X, Shadel GS, Yan Q. KDM5 histone demethylases repress immune response via suppression of STING. PLoS Biol 2018; 16:e2006134. [PMID: 30080846 PMCID: PMC6095604 DOI: 10.1371/journal.pbio.2006134] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 08/16/2018] [Accepted: 07/19/2018] [Indexed: 12/15/2022] Open
Abstract
Cyclic GMP-AMP (cGAMP) synthase (cGAS) stimulator of interferon genes (STING) senses pathogen-derived or abnormal self-DNA in the cytosol and triggers an innate immune defense against microbial infection and cancer. STING agonists induce both innate and adaptive immune responses and are a new class of cancer immunotherapy agents tested in multiple clinical trials. However, STING is commonly silenced in cancer cells via unclear mechanisms, limiting the application of these agonists. Here, we report that the expression of STING is epigenetically suppressed by the histone H3K4 lysine demethylases KDM5B and KDM5C and is activated by the opposing H3K4 methyltransferases. The induction of STING expression by KDM5 blockade triggered a robust interferon response in a cytosolic DNA-dependent manner in breast cancer cells. This response resulted in resistance to infection by DNA and RNA viruses. In human tumors, KDM5B expression is inversely associated with STING expression in multiple cancer types, with the level of intratumoral CD8+ T cells, and with patient survival in cancers with a high level of cytosolic DNA, such as human papilloma virus (HPV)-positive head and neck cancer. These results demonstrate a novel epigenetic regulatory pathway of immune response and suggest that KDM5 demethylases are potential targets for antipathogen treatment and anticancer immunotherapy.
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Affiliation(s)
- Lizhen Wu
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Jian Cao
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Wesley L. Cai
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Sabine M. Lang
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - John R. Horton
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Daniel J. Jansen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Zongzhi Z. Liu
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Jocelyn F. Chen
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Meiling Zhang
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Bryan T. Mott
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Katherine Pohida
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Stephen C. Kales
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Mark J. Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - David J. Maloney
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Shu Zhu
- Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences and Medical Center, University of Science and Technology of China, Hefei, China
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Xiaodong Cheng
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Gerald S. Shadel
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
- Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
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The Histone Demethylase KDM5 Is Essential for Larval Growth in Drosophila. Genetics 2018; 209:773-787. [PMID: 29764901 PMCID: PMC6028249 DOI: 10.1534/genetics.118.301004] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 05/11/2018] [Indexed: 02/07/2023] Open
Abstract
Regulated gene expression is necessary for developmental and homeostatic processes. The KDM5 family of transcriptional regulators are histone H3 lysine 4 demethylases that can function through both demethylase-dependent and -independent mechanisms. While loss and overexpression of KDM5 proteins are linked to intellectual disability and cancer, respectively, their normal developmental functions remain less characterized. Drosophila melanogaster provides an ideal system to investigate KDM5 function, as it encodes a single ortholog in contrast to the four paralogs found in mammalian cells. To examine the consequences of complete loss of KDM5, we generated a null allele of Drosophila kdm5, also known as little imaginal discs (lid), and show that it is essential for viability. Animals lacking KDM5 show a dramatically delayed larval development that coincides with decreased proliferation and increased cell death in wing imaginal discs. Interestingly, this developmental delay is independent of the well-characterized Jumonji C (JmjC) domain-encoded histone demethylase activity of KDM5, suggesting key functions for less characterized domains. Consistent with the phenotypes observed, transcriptome analyses of kdm5 null mutant wing imaginal discs revealed the dysregulation of genes involved in several cellular processes, including cell cycle progression and DNA repair. Together, our analyses reveal KDM5 as a key regulator of larval growth and offer an invaluable tool for defining the biological activities of KDM5 family proteins.
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Nie Z, Shi L, Lai C, O'Connell SM, Xu J, Stansfield RK, Hosfield DJ, Veal JM, Stafford JA. Structure-based design and discovery of potent and selective KDM5 inhibitors. Bioorg Med Chem Lett 2018; 28:1490-1494. [DOI: 10.1016/j.bmcl.2018.03.083] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/27/2018] [Accepted: 03/29/2018] [Indexed: 12/16/2022]
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Shokri G, Doudi S, Fathi-Roudsari M, Kouhkan F, Sanati MH. Targeting histone demethylases KDM5A and KDM5B in AML cancer cells: A comparative view. Leuk Res 2018; 68:105-111. [DOI: 10.1016/j.leukres.2018.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 01/23/2018] [Accepted: 02/05/2018] [Indexed: 02/07/2023]
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Horton JR, Liu X, Wu L, Zhang K, Shanks J, Zhang X, Rai G, Mott BT, Jansen DJ, Kales SC, Henderson MJ, Pohida K, Fang Y, Hu X, Jadhav A, Maloney DJ, Hall MD, Simeonov A, Fu H, Vertino PM, Yan Q, Cheng X. Insights into the Action of Inhibitor Enantiomers against Histone Lysine Demethylase 5A. J Med Chem 2018; 61:3193-3208. [PMID: 29537847 PMCID: PMC6322411 DOI: 10.1021/acs.jmedchem.8b00261] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Isomers of chiral drugs can exhibit marked differences in biological activities. We studied the binding and inhibitory activities of 12 compounds against KDM5A. Among them are two pairs of enantiomers representing two distinct inhibitor chemotypes, namely, ( R)- and ( S)-2-((2-chlorophenyl)(2-(piperidin-1-yl)ethoxy)methyl)-1 H-pyrrolo[3,2- b]pyridine-7-carboxylic acid (compounds N51 and N52) and ( R) - and ( S) -N-(1-(3-isopropyl-1 H-pyrazole-5-carbonyl)pyrrolidin-3-yl)cyclopropanecarboxamide (compounds N54 and N55). In vitro, the S enantiomer of the N51/N52 pair (N52) and the R enantiomer of the N54/N55 pair (N54) exhibited about 4- to 5-fold greater binding affinity. The more potent enzyme inhibition of KDM5A by the R-isoform for the cell-permeable N54/N55 pair translated to differences in growth inhibitory activity. We determined structures of the KDM5A catalytic domain in complex with all 12 inhibitors, which revealed the interactions (or lack thereof) responsible for the differences in binding affinity. These results provide insights to guide improvements in binding potency and avenues for development of cell permeable inhibitors of the KDM5 family.
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Affiliation(s)
- John R. Horton
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Xu Liu
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Lizhen Wu
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut 06520, United States
| | - Kai Zhang
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut 06520, United States
| | - John Shanks
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Xing Zhang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Bryan T. Mott
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Daniel J. Jansen
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Stephen C. Kales
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Mark J. Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Katherine Pohida
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Yuhong Fang
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - David J. Maloney
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Haian Fu
- Department of Pharmacology, Emory University, Atlanta, Georgia 30322, United States
- Department of Hematology and Medical Oncology, Emory University, Atlanta, Georgia 30322, United States
- Emory Chemical Biology Discovery Center, Emory University, Atlanta, Georgia 30322, United States
- The Winship Cancer Institute, Emory University, Atlanta, Georgia 30322, United States
| | - Paula M. Vertino
- The Winship Cancer Institute, Emory University, Atlanta, Georgia 30322, United States
- Department of Radiation Oncology, Emory University, Atlanta, Georgia 30322, United States
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut 06520, United States
| | - Xiaodong Cheng
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, United States
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Gale M, Sayegh J, Cao J, Norcia M, Gareiss P, Hoyer D, Merkel JS, Yan Q. Screen-identified selective inhibitor of lysine demethylase 5A blocks cancer cell growth and drug resistance. Oncotarget 2018; 7:39931-39944. [PMID: 27224921 PMCID: PMC5129982 DOI: 10.18632/oncotarget.9539] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/05/2016] [Indexed: 11/25/2022] Open
Abstract
Lysine demethylase 5A (KDM5A/RBP2/JARID1A) is a histone lysine demethylase that is overexpressed in several human cancers including lung, gastric, breast and liver cancers. It plays key roles in important cancer processes including tumorigenesis, metastasis, and drug tolerance, making it a potential cancer therapeutic target. Chemical tools to analyze KDM5A demethylase activity are extremely limited as available inhibitors are not specific for KDM5A. Here, we characterized KDM5A using a homogeneous luminescence-based assay and conducted a screen of about 9,000 small molecules for inhibitors. From this screen, we identified several 3-thio-1,2,4-triazole compounds that inhibited KDM5A with low μM in vitro IC50 values. Importantly, these compounds showed great specificity and did not inhibit its close homologue KDM5B (PLU1/JARID1B) or the related H3K27 demethylases KDM6A (UTX) and KDM6B (JMJD3). One compound, named YUKA1, was able to increase H3K4me3 levels in human cells and selectively inhibit the proliferation of cancer cells whose growth depends on KDM5A. As KDM5A was shown to mediate drug tolerance, we investigated the ability of YUKA1 to prevent drug tolerance in EGFR-mutant lung cancer cells treated with gefitinib and HER2+ breast cancer cells treated with trastuzumab. Remarkably, this compound hindered the emergence of drug-tolerant cells, highlighting the critical role of KDM5A demethylase activity in drug resistance. The small molecules presented here are excellent tool compounds for further study of KDM5A's demethylase activity and its contributions to cancer.
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Affiliation(s)
- Molly Gale
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Joyce Sayegh
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA.,Current address: Department of Biology and Chemistry, Azusa Pacific University, Azusa, CA, USA
| | - Jian Cao
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Michael Norcia
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, USA
| | - Peter Gareiss
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, USA
| | - Denton Hoyer
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, USA
| | - Jane S Merkel
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
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68
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Hayes A, Mok NY, Liu M, Thai C, Henley AT, Atrash B, Lanigan RM, Sejberg J, Le Bihan YV, Bavetsias V, Blagg J, Raynaud FI. Pyrido[3,4-d]pyrimidin-4(3H)-one metabolism mediated by aldehyde oxidase is blocked by C2-substitution. Xenobiotica 2017; 47:771-777. [PMID: 27618572 PMCID: PMC5526139 DOI: 10.1080/00498254.2016.1230245] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 08/24/2016] [Accepted: 08/25/2016] [Indexed: 12/14/2022]
Abstract
1. We have previously described C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-one derivatives as cell permeable inhibitors of the KDM4 and KDM5 subfamilies of JmjC histone lysine demethylases. 2. Although exemplar compound 1 exhibited moderate clearance in mouse liver microsomes, it was highly cleared in vivo due to metabolism by aldehyde oxidase (AO). Similar human and mouse AO-mediated metabolism was observed with the pyrido[3,4-d]pyrimidin-4(3H)-one scaffold and other C8-substituted derivatives. 3. We identified the C2-position as the oxidation site by LC-MS and 1H-NMR and showed that C2-substituted derivatives are no longer AO substrates. 4. In addition to the experimental data, these observations are supported by molecular modelling studies in the human AO protein crystal structure.
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Affiliation(s)
- Angela Hayes
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - N. Yi Mok
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Manjuan Liu
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Ching Thai
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Alan T. Henley
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Butrus Atrash
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Rachel M. Lanigan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Jimmy Sejberg
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Yann-Vaï Le Bihan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Vassilios Bavetsias
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Florence I. Raynaud
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
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69
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Xie Q, Li C, Song X, Wu L, Jiang Q, Qiu Z, Cao H, Yu K, Wan C, Li J, Yang F, Huang Z, Niu B, Jiang Z, Zhang T. Folate deficiency facilitates recruitment of upstream binding factor to hot spots of DNA double-strand breaks of rRNA genes and promotes its transcription. Nucleic Acids Res 2017; 45:2472-2489. [PMID: 27924000 PMCID: PMC5389733 DOI: 10.1093/nar/gkw1208] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 11/22/2016] [Indexed: 12/24/2022] Open
Abstract
The biogenesis of ribosomes in vivo is an essential process for cellular functions. Transcription of ribosomal RNA (rRNA) genes is the rate-limiting step in ribosome biogenesis controlled by environmental conditions. Here, we investigated the role of folate antagonist on changes of DNA double-strand breaks (DSBs) landscape in mouse embryonic stem cells. A significant DSB enhancement was detected in the genome of these cells and a large majority of these DSBs were found in rRNA genes. Furthermore, spontaneous DSBs in cells under folate deficiency conditions were located exclusively within the rRNA gene units, representing a H3K4me1 hallmark. Enrichment H3K4me1 at the hot spots of DSB regions enhanced the recruitment of upstream binding factor (UBF) to rRNA genes, resulting in the increment of rRNA genes transcription. Supplement of folate resulted in a restored UBF binding across DNA breakage sites of rRNA genes, and normal rRNA gene transcription. In samples from neural tube defects (NTDs) with low folate level, up-regulation of rRNA gene transcription was observed, along with aberrant UBF level. Our results present a new view by which alterations in folate levels affects DNA breakage through epigenetic control leading to the regulation of rRNA gene transcription during the early stage of development.
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Affiliation(s)
- Qiu Xie
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics-Peking University Teaching Hospital, Beijing 100020, China
| | - Caihua Li
- Genesky Biotechnologies Inc, Shanghai 200120, China
| | - Xiaozhen Song
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics-Peking University Teaching Hospital, Beijing 100020, China
| | - Lihua Wu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics-Peking University Teaching Hospital, Beijing 100020, China
| | - Qian Jiang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics-Peking University Teaching Hospital, Beijing 100020, China
| | - Zhiyong Qiu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics-Peking University Teaching Hospital, Beijing 100020, China
| | - Haiyan Cao
- Department of Laboratory Medicine, The Fourth Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Kaihui Yu
- Department of Pathophysiology, Guangxi Medical University, Guangxi 530021, China
| | - Chunlei Wan
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics-Peking University Teaching Hospital, Beijing 100020, China
| | - Jianting Li
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan 030001, China
| | - Feng Yang
- Genesky Biotechnologies Inc, Shanghai 200120, China
| | - Zebing Huang
- Genesky Biotechnologies Inc, Shanghai 200120, China
| | - Bo Niu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics-Peking University Teaching Hospital, Beijing 100020, China
| | | | - Ting Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics-Peking University Teaching Hospital, Beijing 100020, China
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Gong F, Clouaire T, Aguirrebengoa M, Legube G, Miller KM. Histone demethylase KDM5A regulates the ZMYND8-NuRD chromatin remodeler to promote DNA repair. J Cell Biol 2017; 216:1959-1974. [PMID: 28572115 PMCID: PMC5496618 DOI: 10.1083/jcb.201611135] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 03/14/2017] [Accepted: 04/13/2017] [Indexed: 12/15/2022] Open
Abstract
Upon DNA damage, histone modifications are reshaped to accommodate DNA damage signaling and repair. Gong et al. report that the histone demethylase KDM5A promotes loading of the chromatin remodeling complex ZMYND8–NuRD to double-strand DNA breaks through H3K4me3 demethylation, thereby allowing repair of the lesion. Upon DNA damage, histone modifications are dynamically reshaped to accommodate DNA damage signaling and repair within chromatin. In this study, we report the identification of the histone demethylase KDM5A as a key regulator of the bromodomain protein ZMYND8 and NuRD (nucleosome remodeling and histone deacetylation) complex in the DNA damage response. We observe KDM5A-dependent H3K4me3 demethylation within chromatin near DNA double-strand break (DSB) sites. Mechanistically, demethylation of H3K4me3 is required for ZMYND8–NuRD binding to chromatin and recruitment to DNA damage. Functionally, KDM5A deficiency results in impaired transcriptional silencing and repair of DSBs by homologous recombination. Thus, this study identifies a crucial function for KDM5A in demethylating H3K4 to allow ZMYND8–NuRD to operate within damaged chromatin to repair DSBs.
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Affiliation(s)
- Fade Gong
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
| | - Thomas Clouaire
- Laboratoire de Biologie Cellulaire et Moléculaire du Controle de la Prolifération, Centre de Biologie Intégrative, Centre National de la Recherche Scientifique, Université de Toulouse, Toulouse, France
| | - Marion Aguirrebengoa
- Laboratoire de Biologie Cellulaire et Moléculaire du Controle de la Prolifération, Centre de Biologie Intégrative, Centre National de la Recherche Scientifique, Université de Toulouse, Toulouse, France
| | - Gaëlle Legube
- Laboratoire de Biologie Cellulaire et Moléculaire du Controle de la Prolifération, Centre de Biologie Intégrative, Centre National de la Recherche Scientifique, Université de Toulouse, Toulouse, France
| | - Kyle M Miller
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX
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Maggi EC, Crabtree JS. Novel targets in the treatment of neuroendocrine tumors: RBP2. INTERNATIONAL JOURNAL OF ENDOCRINE ONCOLOGY 2017. [DOI: 10.2217/ije-2016-0022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Retinoblastoma binding protein 2, also known as RBP2, JARID1A or KDM5A, is an H3K4 demethylase implicated in a variety of non-neuroendocrine, and more recently, neuroendocrine tumors (NETs). NETs are tumors that form from neuroendocrine cells in tissues of the GI tract, endocrine pancreas, lung, skin and other tissues. RBP2 is expressed at abnormally high levels in NETs and recent work demonstrates that modulation of RBP2 in vitro and in vivo impacts end points of tumorigenesis. Interestingly, the demethylase activity of RBP2 is not exclusively responsible for these changes, as RBP2's binding partners may mediate its activity in a tissue- or context-dependent manner. Here, we discuss the features of RBP2 and its role in cell cycle regulation, angiogenesis and drug resistance in cancer.
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Affiliation(s)
- Elaine C Maggi
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Judy S Crabtree
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, USA
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72
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Theisen ER, Pishas KI, Saund RS, Lessnick SL. Therapeutic opportunities in Ewing sarcoma: EWS-FLI inhibition via LSD1 targeting. Oncotarget 2017; 7:17616-30. [PMID: 26848860 PMCID: PMC4951237 DOI: 10.18632/oncotarget.7124] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 01/23/2016] [Indexed: 11/25/2022] Open
Abstract
Ewing sarcoma is an aggressive primary pediatric bone tumor, often diagnosed in adolescents and young adults. A pathognomonic reciprocal chromosomal translocation results in a fusion gene coding for a protein which derives its N-terminus from a FUS/EWS/TAF15 (FET) protein family member, commonly EWS, and C-terminus containing the DNA-binding domain of an ETS transcription factor, commonly FLI1. Nearly 85% of cases express the EWS-FLI protein which functions as a transcription factor and drives oncogenesis. As the primary genomic lesion and a protein which is not expressed in normal cells, disrupting EWS-FLI function is an attractive therapeutic strategy for Ewing sarcoma. However, transcription factors are notoriously difficult targets for the development of small molecules. Improved understanding of the oncogenic mechanisms employed by EWS-FLI to hijack normal cellular programming has uncovered potential novel approaches to pharmacologically block EWS-FLI function. In this review we examine targeting the chromatin regulatory enzymes recruited to conspire in oncogenesis with a focus on the histone lysine specific demethylase 1 (LSD1). LSD1 inhibitors are being aggressively investigated in acute myeloid leukemia and the results of early clinical trials will help inform the future use of LSD1 inhibitors in sarcoma. High LSD1 expression is observed in Ewing sarcoma patient samples and mechanistic and preclinical data suggest LSD1 inhibition globally disrupts the function of EWS-ETS proteins.
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Affiliation(s)
- Emily R Theisen
- Center for Childhood Cancer and Blood Disorders, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Kathleen I Pishas
- Center for Childhood Cancer and Blood Disorders, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Cancer Therapeutics Laboratory, Centre for Personalized Cancer Medicine, Discipline of Medicine, University of Adelaide, Adelaide, South Australia, Australia
| | - Ranajeet S Saund
- Center for Childhood Cancer and Blood Disorders, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Stephen L Lessnick
- Center for Childhood Cancer and Blood Disorders, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Division of Pediatric Hematology/Oncology/Bone Marrow Transplant at The Ohio State University, Columbus, Ohio, USA
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73
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Affiliation(s)
- Joyce Taylor-Papadimitriou
- a Breast Cancer Biology , Division of Cancer Studies, King's College London , Guy's Hospital, London , UK
| | - Joy Burchell
- a Breast Cancer Biology , Division of Cancer Studies, King's College London , Guy's Hospital, London , UK
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74
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Cao J, Wu L, Zhang SM, Lu M, Cheung WKC, Cai W, Gale M, Xu Q, Yan Q. An easy and efficient inducible CRISPR/Cas9 platform with improved specificity for multiple gene targeting. Nucleic Acids Res 2016; 44:e149. [PMID: 27458201 PMCID: PMC5100567 DOI: 10.1093/nar/gkw660] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/11/2016] [Accepted: 07/12/2016] [Indexed: 12/26/2022] Open
Abstract
The CRISPR/Cas9 system is a powerful genome editing tool and has been widely used for biomedical research. However, many challenges, such as off-target effects and lack of easy solutions for multiplex targeting, are still limiting its applications. To overcome these challenges, we first developed a highly efficient doxycycline-inducible Cas9-EGFP vector. This vector allowed us to track the cells for uniform temporal control and efficient gene disruption, even in a polyclonal setting. Furthermore, the inducible CRISPR/Cas9 system dramatically decreased off-target effects with a pulse exposure of the genome to the Cas9/sgRNA complex. To target multiple genes simultaneously, we established simple one-step cloning approaches for expression of multiple sgRNAs with improved vectors. By combining our inducible and multiplex genome editing approaches, we were able to simultaneously delete Lysine Demethylase (KDM) 5A, 5B and 5C efficiently in vitro and in vivo This user friendly and highly efficient toolbox provides a solution for easy genome editing with tight temporal control, minimal off-target effects and multiplex targeting.
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Affiliation(s)
- Jian Cao
- 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
| | - Shang-Min Zhang
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520 USA
| | - Min Lu
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520 USA
- Harbin Institute of Technology, Harbin, 150001 China
| | - William K C Cheung
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520 USA
| | - Wesley Cai
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520 USA
| | - Molly Gale
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520 USA
| | - Qi Xu
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520 USA
- Department of Oncology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127 China
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520 USA
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75
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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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76
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Gehling VS, Bellon SF, Harmange JC, LeBlanc Y, Poy F, Odate S, Buker S, Lan F, Arora S, Williamson KE, Sandy P, Cummings RT, Bailey CM, Bergeron L, Mao W, Gustafson A, Liu Y, VanderPorten E, Audia JE, Trojer P, Albrecht BK. Identification of potent, selective KDM5 inhibitors. Bioorg Med Chem Lett 2016; 26:4350-4. [DOI: 10.1016/j.bmcl.2016.07.026] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 07/08/2016] [Accepted: 07/09/2016] [Indexed: 12/26/2022]
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77
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Shen H, Xu W, Guo R, Rong B, Gu L, Wang Z, He C, Zheng L, Hu X, Hu Z, Shao ZM, Yang P, Wu F, Shi YG, Shi Y, Lan F. Suppression of Enhancer Overactivation by a RACK7-Histone Demethylase Complex. Cell 2016; 165:331-42. [PMID: 27058665 DOI: 10.1016/j.cell.2016.02.064] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 12/14/2015] [Accepted: 02/22/2016] [Indexed: 12/29/2022]
Abstract
Regulation of enhancer activity is important for controlling gene expression programs. Here, we report that a biochemical complex containing a potential chromatin reader, RACK7, and the histone lysine 4 tri-methyl (H3K4me3)-specific demethylase KDM5C occupies many active enhancers, including almost all super-enhancers. Loss of RACK7 or KDM5C results in overactivation of enhancers, characterized by the deposition of H3K4me3 and H3K27Ac, together with increased transcription of eRNAs and nearby genes. Furthermore, loss of RACK7 or KDM5C leads to de-repression of S100A oncogenes and various cancer-related phenotypes. Our findings reveal a RACK7/KDM5C-regulated, dynamic interchange between histone H3K4me1 and H3K4me3 at active enhancers, representing an additional layer of regulation of enhancer activity. We propose that RACK7/KDM5C functions as an enhancer "brake" to ensure appropriate enhancer activity, which, when compromised, could contribute to tumorigenesis.
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Affiliation(s)
- Hongjie Shen
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Key Laboratory of Epigenetics, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Key Laboratory of Birth Defect, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Wenqi Xu
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Key Laboratory of Epigenetics, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Key Laboratory of Birth Defect, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Rui Guo
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Key Laboratory of Epigenetics, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Bowen Rong
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Key Laboratory of Epigenetics, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Lei Gu
- Newborn Medicine Division, Boston Children's Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Zhentian Wang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Key Laboratory of Epigenetics, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Chenxi He
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Key Laboratory of Epigenetics, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Lijuan Zheng
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Key Laboratory of Epigenetics, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Xin Hu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Shanghai Cancer Center, Fudan University, Shanghai 200032, China
| | - Zhen Hu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Shanghai Cancer Center, Fudan University, Shanghai 200032, China
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Shanghai Cancer Center, Fudan University, Shanghai 200032, China
| | - Pengyuan Yang
- Department of System Biology, Institutes of Biomedical Sciences, Fudan University, 138 Yixue Yuan Road, Shanghai 200032, China
| | - Feizhen Wu
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Key Laboratory of Epigenetics, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yujiang Geno Shi
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Key Laboratory of Epigenetics, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Key Laboratory of Birth Defect, Children's Hospital of Fudan University, Shanghai 201102, China; Division of Endocrinology, Brigham and Women Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yang Shi
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Key Laboratory of Epigenetics, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Key Laboratory of Birth Defect, Children's Hospital of Fudan University, Shanghai 201102, China; Newborn Medicine Division, Boston Children's Hospital and Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
| | - Fei Lan
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, and Key Laboratory of Epigenetics, Department of Cellular and Genetic Medicine, School of Basic Medical Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Key Laboratory of Birth Defect, Children's Hospital of Fudan University, Shanghai 201102, China; Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Shanghai Cancer Center, Fudan University, Shanghai 200032, China.
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78
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Lussi YC, Mariani L, Friis C, Peltonen J, Myers TR, Krag C, Wong G, Salcini AE. Impaired removal of H3K4 methylation affects cell fate determination and gene transcription. Development 2016; 143:3751-3762. [PMID: 27578789 DOI: 10.1242/dev.139139] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 08/20/2016] [Indexed: 01/30/2023]
Abstract
Methylation of histone 3 lysine 4 (H3K4) is largely associated with promoters and enhancers of actively transcribed genes and is finely regulated during development by the action of histone methyltransferases and demethylases. H3K4me3 demethylases of the KDM5 family have been previously implicated in development, but how the regulation of H3K4me3 level controls developmental processes is not fully established. Here, we show that the H3K4 demethylase RBR-2, the unique member of the KDM5 family in C. elegans, acts cell-autonomously and in a catalytic-dependent manner to control vulva precursor cells fate acquisition, by promoting the LIN-12/Notch pathway. Using genome-wide approaches, we show that RBR-2 reduces the H3K4me3 level at transcription start sites (TSSs) and in regions upstream of the TSSs, and acts both as a transcription repressor and activator. Analysis of the lin-11 genetic locus, a direct RBR-2 target gene required for vulva precursor cell fate acquisition, shows that RBR-2 controls the epigenetic signature of the lin-11 vulva-specific enhancer and lin-11 expression, providing in vivo evidence that RBR-2 can positively regulate transcription and cell fate acquisition by controlling enhancer activity.
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Affiliation(s)
- Yvonne C Lussi
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen DK-2200, Denmark.,Centre for Epigenetics, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Luca Mariani
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen DK-2200, Denmark.,Centre for Epigenetics, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Carsten Friis
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen DK-2200, Denmark.,Centre for Epigenetics, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Juhani Peltonen
- A. I. Virtanen Institute for Molecular Sciences, Department of Neurobiology, University of Eastern Finland, Kuopio 70211, Finland
| | - Toshia R Myers
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen DK-2200, Denmark.,Centre for Epigenetics, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Claudia Krag
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Garry Wong
- A. I. Virtanen Institute for Molecular Sciences, Department of Neurobiology, University of Eastern Finland, Kuopio 70211, Finland
| | - Anna Elisabetta Salcini
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen DK-2200, Denmark .,Centre for Epigenetics, University of Copenhagen, Copenhagen DK-2200, Denmark
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79
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Zhou D, Kannappan V, Chen X, Li J, Leng X, Zhang J, Xuan S. RBP2 induces stem-like cancer cells by promoting EMT and is a prognostic marker for renal cell carcinoma. Exp Mol Med 2016; 48:e238. [PMID: 27282106 PMCID: PMC4929691 DOI: 10.1038/emm.2016.37] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 12/30/2015] [Accepted: 01/06/2016] [Indexed: 12/13/2022] Open
Abstract
Renal cell carcinoma (RCC), one of the most common kidney cancers, has a poor prognosis. Epithelial to mesenchymal transition (EMT) is a hallmark of carcinoma invasion and metastasis. Several studies have examined the molecular regulation of EMT, but the relationship between histone demethylases and EMT is little understood. In this study, we investigated the role of retinoblastoma-binding protein-2 (RBP2), a histone demethylase that is highly expressed in RCC and is positively correlated with poor RCC prognosis in the regulation of EMT. We found that ectopic overexpression of RBP2 can induce cancer stem cell-like (CSC) phenotypes through EMT in RCC cells by converting them to a more mesenchymal phenotype. This results in increased resistance to apoptosis, which leads to enhanced tumor growth in xenograft models. Together, our data show that RBP2 is an epigenetic regulator that has an important role in the initiation of CSC phenotypes through EMT, leading to tumor progression. RBP2 is also a novel biomolecule for RCC diagnosis, and prognosis and may be a therapeutic target.
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MESH Headings
- Animals
- Biomarkers, Tumor/analysis
- Biomarkers, Tumor/metabolism
- Carcinogenesis/metabolism
- Carcinogenesis/pathology
- Carcinoma, Renal Cell/diagnosis
- Carcinoma, Renal Cell/metabolism
- Carcinoma, Renal Cell/pathology
- Cell Line, Tumor
- Epithelial-Mesenchymal Transition
- Follow-Up Studies
- Humans
- Kidney/metabolism
- Kidney/pathology
- Kidney Neoplasms/diagnosis
- Kidney Neoplasms/metabolism
- Kidney Neoplasms/pathology
- Mice, Inbred BALB C
- Mice, Nude
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/pathology
- Prognosis
- Retinol-Binding Proteins, Cellular/analysis
- Retinol-Binding Proteins, Cellular/metabolism
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Affiliation(s)
- Dahai Zhou
- College of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Department of Urology, 401 Hospital of PLA, Qingdao, China
| | - Vinodh Kannappan
- Research Institute in Healthcare Science, Faculty of Science & Engineering, University of Wolverhampton, Wolverhampton, UK
| | | | - Jingqin Li
- Department of Urology, 401 Hospital of PLA, Qingdao, China
| | - Xuefeng Leng
- Department of Urology, 401 Hospital of PLA, Qingdao, China
| | - Jinping Zhang
- Department of Urology, 401 Hospital of PLA, Qingdao, China
| | - Shiying Xuan
- College of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Qingdao Municipal Hospital, Qingdao, China
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80
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Wu X, Fang Z, Yang B, Zhong L, Yang Q, Zhang C, Huang S, Xiang R, Suzuki T, Li LL, Yang SY. Discovery of KDM5A inhibitors: Homology modeling, virtual screening and structure-activity relationship analysis. Bioorg Med Chem Lett 2016; 26:2284-8. [PMID: 27020306 DOI: 10.1016/j.bmcl.2016.03.048] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 03/01/2016] [Accepted: 03/14/2016] [Indexed: 02/05/2023]
Abstract
Herein we report the discovery of a series of new KDM5A inhibitors. A three-dimensional (3D) structure model of KDM5A jumonji domain was firstly established based on homology modeling. Molecular docking-based virtual screening was then performed against commercial chemical databases. A number of hit compounds were retrieved. Further structural optimization and structure-activity relationship (SAR) analysis were carried out to the most active hit compound, 9 (IC50: 2.3 μM), which led to the discovery of several new KDM5A inhibitors. Among them, compound 15e is the most potent one with an IC50 value of 0.22 μM against KDM5A. This compound showed good selectivity for KDM5A and considerable ability to suppress the demethylation of H3K4me3 in intact cells. Compound 15e could be taken as a good lead compound for further studies.
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Affiliation(s)
- Xiaoai Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center for Biotherapy, Sichuan University, Sichuan 610041, China; Department of Nuclear Medicine, West China Hospital, Sichuan University, Sichuan 610041, China
| | - Zhen Fang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center for Biotherapy, Sichuan University, Sichuan 610041, China
| | - Bo Yang
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China; Department of Pharmacy, Panzhihua Central Hospital, Panzhihua, Sichuan 617067, China
| | - Lei Zhong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center for Biotherapy, Sichuan University, Sichuan 610041, China
| | - Qiuyuan Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center for Biotherapy, Sichuan University, Sichuan 610041, China
| | - Chunhui Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center for Biotherapy, Sichuan University, Sichuan 610041, China
| | - Shenzhen Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center for Biotherapy, Sichuan University, Sichuan 610041, China
| | - Rong Xiang
- Department of Clinical Medicine, School of Medicine, Nankai University, Tianjin 300071, China
| | - Takayoshi Suzuki
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Taishogun Nishitakatsukasa-Cho, Kita-ku, Kyoto 403-8334, Japan
| | - Lin-Li Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, China.
| | - Sheng-Yong Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center for Biotherapy, Sichuan University, Sichuan 610041, China.
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81
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Bavetsias V, Lanigan RM, Ruda GF, Atrash B, McLaughlin MG, Tumber A, Mok NY, Le Bihan YV, Dempster S, Boxall K, Jeganathan F, Hatch SB, Savitsky P, Velupillai S, Krojer T, England K, Sejberg J, Thai C, Donovan A, Pal A, Scozzafava G, Bennett J, Kawamura A, Johansson C, Szykowska A, Gileadi C, Burgess-Brown N, von Delft F, Oppermann U, Walters Z, Shipley J, Raynaud FI, Westaway SM, Prinjha RK, Fedorov O, Burke R, Schofield C, Westwood IM, Bountra C, Müller S, van Montfort RL, Brennan PE, Blagg J. 8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors. J Med Chem 2016; 59:1388-409. [PMID: 26741168 PMCID: PMC4770324 DOI: 10.1021/acs.jmedchem.5b01635] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Indexed: 11/29/2022]
Abstract
We report the discovery of N-substituted 4-(pyridin-2-yl)thiazole-2-amine derivatives and their subsequent optimization, guided by structure-based design, to give 8-(1H-pyrazol-3-yl)pyrido[3,4-d]pyrimidin-4(3H)-ones, a series of potent JmjC histone N-methyl lysine demethylase (KDM) inhibitors which bind to Fe(II) in the active site. Substitution from C4 of the pyrazole moiety allows access to the histone peptide substrate binding site; incorporation of a conformationally constrained 4-phenylpiperidine linker gives derivatives such as 54j and 54k which demonstrate equipotent activity versus the KDM4 (JMJD2) and KDM5 (JARID1) subfamily demethylases, selectivity over representative exemplars of the KDM2, KDM3, and KDM6 subfamilies, cellular permeability in the Caco-2 assay, and, for 54k, inhibition of H3K9Me3 and H3K4Me3 demethylation in a cell-based assay.
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Affiliation(s)
- Vassilios Bavetsias
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Rachel M. Lanigan
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Gian Filippo Ruda
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Butrus Atrash
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Mark G. McLaughlin
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Anthony Tumber
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - N. Yi Mok
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Yann-Vaï Le Bihan
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Sally Dempster
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Katherine
J. Boxall
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Fiona Jeganathan
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Stephanie B. Hatch
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Pavel Savitsky
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Srikannathasan Velupillai
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Tobias Krojer
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Katherine
S. England
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Jimmy Sejberg
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Ching Thai
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Adam Donovan
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Akos Pal
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Giuseppe Scozzafava
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - James
M. Bennett
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Akane Kawamura
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Catrine Johansson
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Botnar Research
Centre, NIHR Oxford Biomedical Research
Unit, Oxford OX3 7LD, U.K.
| | - Aleksandra Szykowska
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Carina Gileadi
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Nicola
A. Burgess-Brown
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Frank von Delft
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Diamond Light Source (DLS), Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K.
- Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
| | - Udo Oppermann
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Botnar Research
Centre, NIHR Oxford Biomedical Research
Unit, Oxford OX3 7LD, U.K.
| | - Zoe Walters
- Divisions of Molecular Pathology and Cancer
Therapeutics, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Janet Shipley
- Divisions of Molecular Pathology and Cancer
Therapeutics, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Florence I. Raynaud
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Susan M. Westaway
- Epinova Discovery Performance Unit, Medicines
Research Centre, GlaxoSmithKline R&D, Stevenage SG1 2NY, U.K.
| | - Rab K. Prinjha
- Epinova Discovery Performance Unit, Medicines
Research Centre, GlaxoSmithKline R&D, Stevenage SG1 2NY, U.K.
| | - Oleg Fedorov
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Rosemary Burke
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | | | - Isaac M. Westwood
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Chas Bountra
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Susanne Müller
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Rob L.
M. van Montfort
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Paul E. Brennan
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Julian Blagg
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
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82
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Wang D, Han S, Peng R, Jiao C, Wang X, Yang X, Yang R, Li X. Depletion of histone demethylase KDM5B inhibits cell proliferation of hepatocellular carcinoma by regulation of cell cycle checkpoint proteins p15 and p27. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2016; 35:37. [PMID: 26911146 PMCID: PMC4766611 DOI: 10.1186/s13046-016-0311-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 02/19/2016] [Indexed: 01/12/2023]
Abstract
Background KDM5B is a jmjc domain-containing histone demethylase which remove tri-, di-, and monomethyl groups from histone H3 lysine 4 (H3K4). KDM5B has been determined as an oncogene in many malignancies. However, its expression and role in hepatocellular carcinoma (HCC) remain unknown. Methods We detected the expression of KDM5B in HCC tissues and cell lines. Cell proliferation was performed to reveal the role of KDM5B depletion on HCC cells both in vivo and in vitro. Flow cytometry was used to analyze the cell cycle and chip analysis was conducted to determine the direct target of KDM5B. Results KDM5B is frequently up-regulated in HCC specimens compared with adjacent normal tissues and its expression level was significantly correlated with tumor size, TNM stage, and Edmondson grade. Moreover, Kaplan-Meier survival analysis showed that patients with high levels of KDM5B expression had a relatively poor prognosis. Knockdown of KDM5B notably inhibits HCC cell proliferation both in vivo and in vitro via arresting the cell cycle at G1/S phase partly through up-regulation of p15 and p27. Further molecular mechanism study indicates that silencing of KDM5B promotes p15 and p27 expression by increasing histone H3K4 trimethylation in their promoters. Conclusions KDM5B could be a potentially therapeutic target, which provides a rationale for the development of histone demethylase inhibitors as a strategy against HCC. Electronic supplementary material The online version of this article (doi:10.1186/s13046-016-0311-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dong Wang
- Liver Transplantation Center, Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Sheng Han
- Liver Transplantation Center, Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Rui Peng
- Department of General Surgery, Nanjing Medical University Affiliated Cancer Hospital, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Chenyu Jiao
- Liver Transplantation Center, Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Xing Wang
- Liver Transplantation Center, Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Xinxiang Yang
- Liver Transplantation Center, Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Renjie Yang
- Liver Transplantation Center, Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Xiangcheng Li
- Liver Transplantation Center, Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
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83
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Gajan A, Barnes VL, Liu M, Saha N, Pile LA. The histone demethylase dKDM5/LID interacts with the SIN3 histone deacetylase complex and shares functional similarities with SIN3. Epigenetics Chromatin 2016; 9:4. [PMID: 26848313 PMCID: PMC4740996 DOI: 10.1186/s13072-016-0053-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 01/14/2016] [Indexed: 01/01/2023] Open
Abstract
Background Regulation of gene expression by histone-modifying enzymes is essential to control cell fate decisions and developmental processes. Two histone-modifying enzymes, RPD3, a deacetylase, and dKDM5/LID, a demethylase, are present in a single complex, coordinated through the SIN3 scaffold protein. While the SIN3 complex has been demonstrated to have functional histone deacetylase activity, the role of the demethylase dKDM5/LID as part of the complex has not been investigated. Results Here, we analyzed the developmental and transcriptional activities of dKDM5/LID in relation to SIN3. Knockdown of either Sin3A or lid resulted in decreased cell proliferation in S2 cells and wing imaginal discs. Conditional knockdown of either Sin3A or lid resulted in flies that displayed wing developmental defects. Interestingly, overexpression of dKDM5/LID rescued the wing developmental defect due to reduced levels of SIN3 in female flies, indicating a major role for dKDM5/LID in cooperation with SIN3 during development. Together, these observed phenotypes strongly suggest that dKDM5/LID as part of the SIN3 complex can impact previously uncharacterized transcriptional networks. Transcriptome analysis revealed that SIN3 and dKDM5/LID regulate many common genes. While several genes implicated in cell cycle and wing developmental pathways were affected upon altering the level of these chromatin factors, a significant affect was also observed on genes required to mount an effective stress response. Further, under conditions of induced oxidative stress, reduction of SIN3 and/or dKDM5/LID altered the expression of a greater number of genes involved in cell cycle-related processes relative to normal conditions. This highlights an important role for SIN3 and dKDM5/LID proteins to maintain proper progression through the cell cycle in environments of cellular stress. Further, we find that target genes are bound by both SIN3 and dKDM5/LID, however, histone acetylation, not methylation, plays a predominant role in gene regulation by the SIN3 complex. Conclusions We have provided genetic evidence to demonstrate functional cooperation between the histone demethylase dKDM5/LID and SIN3. Biochemical and transcriptome data further support functional links between these proteins. Together, the data provide a solid framework for analyzing the gene regulatory pathways through which SIN3 and dKDM5/LID control diverse biological processes in the organism. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0053-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ambikai Gajan
- Department of Biological Sciences, Wayne State University, Detroit, MI USA
| | - Valerie L Barnes
- Department of Biological Sciences, Wayne State University, Detroit, MI USA
| | - Mengying Liu
- Department of Biological Sciences, Wayne State University, Detroit, MI USA
| | - Nirmalya Saha
- Department of Biological Sciences, Wayne State University, Detroit, MI USA
| | - Lori A Pile
- Department of Biological Sciences, Wayne State University, Detroit, MI USA
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84
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Davie JR, Xu W, Delcuve GP. Histone H3K4 trimethylation: dynamic interplay with pre-mRNA splicing. Biochem Cell Biol 2016; 94:1-11. [DOI: 10.1139/bcb-2015-0065] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Histone H3 lysine 4 trimethylation (H3K4me3) is often stated as a mark of transcriptionally active promoters. However, closer study of the positioning of H3K4me3 shows the mark locating primarily after the first exon at the 5′ splice site and overlapping with a CpG island in mammalian cells. There are several enzyme complexes that are involved in the placement of the H3K4me3 mark, including multiple protein complexes containing SETD1A, SETD1B, and MLL1 enzymes (writers). CXXC1, which is associated with SETD1A and SETD1B, target these enzymes to unmethylated CpG islands. Lysine demethylases (KDM5 family members, erasers) demethylate H3K4me3. The H3K4me3 mark is recognized by several proteins (readers), including lysine acetyltransferase complexes, chromatin remodelers, and RNA bound proteins involved in pre-mRNA splicing. Interestingly, attenuation of H3K4me3 impacts pre-mRNA splicing, and inhibition of pre-mRNA splicing attenuates H3K4me3.
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Affiliation(s)
- James R. Davie
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Wayne Xu
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Genevieve P. Delcuve
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
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85
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Gelato KA, Shaikhibrahim Z, Ocker M, Haendler B. Targeting epigenetic regulators for cancer therapy: modulation of bromodomain proteins, methyltransferases, demethylases, and microRNAs. Expert Opin Ther Targets 2016; 20:783-99. [DOI: 10.1517/14728222.2016.1134490] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | | | - Matthias Ocker
- Global Drug Discovery, Bayer Pharma AG, Berlin, Germany
- Department of Gastroenterology/Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Berlin, Germany
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86
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Jangravi Z, Najafi M, Shabani M. Investigation of Histone Lysine-Specific Demethylase 5D KDM5D) Isoform Expression in Prostate Cancer Cell Lines: a System Approach. IRANIAN BIOMEDICAL JOURNAL 2016; 20:117-21. [PMID: 26728332 PMCID: PMC4726892 DOI: 10.7508/ibj.2016.02.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Background: It is now well-demonstrated that histone demethylases play an important role in developmental controls, cell-fate decisions, and a variety of diseases such as cancer. Lysine-specific demethylase 5D (KDM5D) is a male-specific histone demethylase that specifically demethylates di- and tri-methyl H3K4 at the start site of active gene. In this light, the aim of this study was to investigate isoform/transcript-specific expression profiles of KDM5D in three prostate cancer cell lines, Du-145, LNCaP, and PC3. Methods: Real-time PCR analysis was performed to determine the expression levels of different KDM5D transcripts in the prostate cell lines. A gene regulatory network was established to analyze the gene expression profile. Results: Significantly different expression levels of both isoforms were found among the three cell lines. Interestingly, isoform I was expressed in three cell lines while isoform III did only in DU-145. The expression levels of both isoforms were higher in DU-145 when compared to other cell lines (P<0.0001). The observed expression profile was determined by using regulatory network analyses. Conclusion: The present study, for the first time, not only showed the expression profiles of KDM5D isoforms in prostate cancer cell lines but also evaluated the effects of the gene regulatory network on the expression profile of this gene.
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Affiliation(s)
- Zohreh Jangravi
- Dept. of Biochemistry, Iran University of Medical Sciences, Tehran, Iran.,Dept. of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mohammad Najafi
- Dept. of Biochemistry, Iran University of Medical Sciences, Tehran, Iran.,Dept. of Biochemistry, Razi Drug Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammd Shabani
- Dept. of Biochemistry, Iran University of Medical Sciences, Tehran, Iran
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87
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Wang H, Song C, Ding Y, Pan X, Ge Z, Tan BH, Gowda C, Sachdev M, Muthusami S, Ouyang H, Lai L, Francis OL, Morris CL, Abdel-Azim H, Dorsam G, Xiang M, Payne KJ, Dovat S. Transcriptional Regulation of JARID1B/KDM5B Histone Demethylase by Ikaros, Histone Deacetylase 1 (HDAC1), and Casein Kinase 2 (CK2) in B-cell Acute Lymphoblastic Leukemia. J Biol Chem 2015; 291:4004-18. [PMID: 26655717 DOI: 10.1074/jbc.m115.679332] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Indexed: 12/26/2022] Open
Abstract
Impaired function of the Ikaros (IKZF1) protein is associated with the development of high-risk B-cell precursor acute lymphoblastic leukemia (B-ALL). The mechanisms of Ikaros tumor suppressor activity in leukemia are unknown. Ikaros binds to the upstream regulatory elements of its target genes and regulates their transcription via chromatin remodeling. Here, we report that Ikaros represses transcription of the histone H3K4 demethylase, JARID1B (KDM5B). Transcriptional repression of JARID1B is associated with increased global levels of H3K4 trimethylation. Ikaros-mediated repression of JARID1B is dependent on the activity of the histone deacetylase, HDAC1, which binds to the upstream regulatory element of JARID1B in complex with Ikaros. In leukemia, JARID1B is overexpressed, and its inhibition results in cellular growth arrest. Ikaros-mediated repression of JARID1B in leukemia is impaired by pro-oncogenic casein kinase 2 (CK2). Inhibition of CK2 results in increased binding of the Ikaros-HDAC1 complex to the promoter of JARID1B, with increased formation of trimethylated histone H3 lysine 27 and decreased histone H3 Lys-9 acetylation. In cases of high-risk B-ALL that carry deletion of one Ikaros (IKZF1) allele, targeted inhibition of CK2 restores Ikaros binding to the JARID1B promoter and repression of JARID1B. In summary, the presented data suggest a mechanism through which Ikaros and HDAC1 regulate the epigenetic signature in leukemia: via regulation of JARID1B transcription. The presented data identify JARID1B as a novel therapeutic target in B-ALL and provide a rationale for the use of CK2 inhibitors in the treatment of high-risk B-ALL.
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Affiliation(s)
- Haijun Wang
- From the Department of Pathology, Xinxiang Medical University, Xinxiang 453003, Henan, China, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033
| | - Chunhua Song
- Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033
| | - Yali Ding
- Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033
| | - Xiaokang Pan
- Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033
| | - Zheng Ge
- Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033
| | - Bi-Hua Tan
- Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033
| | - Chandrika Gowda
- Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033
| | - Mansi Sachdev
- Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033
| | - Sunil Muthusami
- Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033
| | - Hongsheng Ouyang
- From the Department of Pathology, Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Liangxue Lai
- From the Department of Pathology, Xinxiang Medical University, Xinxiang 453003, Henan, China
| | | | | | - Hisham Abdel-Azim
- the Division of Hematology, Oncology, and Blood and Marrow Transplantation, Children's Hospital Los Angeles, University of Southern California Keck School of Medicine, Los Angeles, California 90027
| | - Glenn Dorsam
- North Dakota State University, Fargo, North Dakota 58108, and
| | - Meixian Xiang
- the College of Pharmacy, South-Central University for Nationalities, Wuhan 430074, China
| | | | - Sinisa Dovat
- Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033,
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88
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Liu X, Secombe J. The Histone Demethylase KDM5 Activates Gene Expression by Recognizing Chromatin Context through Its PHD Reader Motif. Cell Rep 2015; 13:2219-31. [PMID: 26673323 DOI: 10.1016/j.celrep.2015.11.007] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 10/05/2015] [Accepted: 10/31/2015] [Indexed: 12/22/2022] Open
Abstract
KDM5 family proteins are critically important transcriptional regulators whose physiological functions in the context of a whole animal remain largely unknown. Using genome-wide gene expression and binding analyses in Drosophila adults, we demonstrate that KDM5 (Lid) is a direct regulator of genes required for mitochondrial structure and function. Significantly, this occurs independently of KDM5's well-described JmjC domain-encoded histone demethylase activity. Instead, it requires the PHD motif of KDM5 that binds to histone H3 that is di- or trimethylated on lysine 4 (H3K4me2/3). Genome-wide, KDM5 binding overlaps with the active chromatin mark H3K4me3, and a fly strain specifically lacking H3K4me2/3 binding shows defective KDM5 promoter recruitment and gene activation. KDM5 therefore plays a central role in regulating mitochondrial function by utilizing its ability to recognize specific chromatin contexts. Importantly, KDM5-mediated regulation of mitochondrial activity is likely to be key in human diseases caused by dysfunction of this family of proteins.
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Affiliation(s)
- Xingyin Liu
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
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89
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Mutations in the KDM5C ARID Domain and Their Plausible Association with Syndromic Claes-Jensen-Type Disease. Int J Mol Sci 2015; 16:27270-87. [PMID: 26580603 PMCID: PMC4661880 DOI: 10.3390/ijms161126022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/01/2015] [Accepted: 11/04/2015] [Indexed: 11/30/2022] Open
Abstract
Mutations in KDM5C gene are linked to X-linked mental retardation, the syndromic Claes-Jensen-type disease. This study focuses on non-synonymous mutations in the KDM5C ARID domain and evaluates the effects of two disease-associated missense mutations (A77T and D87G) and three not-yet-classified missense mutations (R108W, N142S, and R179H). We predict the ARID domain’s folding and binding free energy changes due to mutations, and also study the effects of mutations on protein dynamics. Our computational results indicate that A77T and D87G mutants have minimal effect on the KDM5C ARID domain stability and DNA binding. In parallel, the change in the free energy unfolding caused by the mutants A77T and D87G were experimentally measured by urea-induced unfolding experiments and were shown to be similar to the in silico predictions. The evolutionary conservation analysis shows that the disease-associated mutations are located in a highly-conserved part of the ARID structure (N-terminal domain), indicating their importance for the KDM5C function. N-terminal residues’ high conservation suggests that either the ARID domain utilizes the N-terminal to interact with other KDM5C domains or the N-terminal is involved in some yet unknown function. The analysis indicates that, among the non-classified mutations, R108W is possibly a disease-associated mutation, while N142S and R179H are probably harmless.
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90
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Zhang Y, Xu Q, Liu G, Huang H, Lin W, Huang Y, Chi Z, Chen S, Lan K, Lin J, Zhang Y. Effect of histone deacetylase on prostate carcinoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:15030-15034. [PMID: 26823840 PMCID: PMC4713626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 10/26/2015] [Indexed: 06/05/2023]
Abstract
Commonly occurred in aged males, the incidence of prostate carcinoma is increasing by years. Histone deacetylase (HDACs) as one key enzyme in regulating gene transcription has been found to be related with cancer occurrence. Trichostatin A (TSA) is one HDAC inhibitor for suppressing tumor growth. This study thus treated prostate carcinoma cell line PC3 with TSA, to analyze the effect of HDAC on the occurrence and progression of HDAC. PC3 cells were treated with gradient concentrations of TSA. MTT assay was employed to detect the proliferation of PC3 cells, while flow cytometry was used to detect the cell apoptosis and cell cycle. Apoptotic proteins including caspase-3, caspase-9 and bcl-2 were further quantified by Western blotting. MTT assays showed a dose- and time-dependent manner of TSA in inhibiting PC3 cell proliferation. Most of PC3 cells were arrested at G1 phase after treating with TSA. The apoptotic ratio of cells was also elevated by higher concentrations of drugs. Apoptotic proteins including caspase-3, caspase-9 and bcl-2 were all up-regulated by TSA. HDAC inhibitor can effectively suppress the proliferation of prostate carcinoma cells, which can be arrested at G1 phase. The elevated apoptotic ratio was caused by up-regulation of apoptosis-related proteins caspase-3, caspase-9 and bcl-2, in both dose- and time-dependent manners.
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Affiliation(s)
- Yuanfeng Zhang
- Department of Urology, Shantou Central Hospital Swatow 515031, Guangdong, China
| | - Qingchun Xu
- Department of Urology, Shantou Central Hospital Swatow 515031, Guangdong, China
| | - Guoyuan Liu
- Department of Urology, Shantou Central Hospital Swatow 515031, Guangdong, China
| | - Hong Huang
- Department of Urology, Shantou Central Hospital Swatow 515031, Guangdong, China
| | - Weiqiang Lin
- Department of Urology, Shantou Central Hospital Swatow 515031, Guangdong, China
| | - Yueying Huang
- Department of Urology, Shantou Central Hospital Swatow 515031, Guangdong, China
| | - Zepai Chi
- Department of Urology, Shantou Central Hospital Swatow 515031, Guangdong, China
| | - Shaochuan Chen
- Department of Urology, Shantou Central Hospital Swatow 515031, Guangdong, China
| | - Kaijian Lan
- Department of Urology, Shantou Central Hospital Swatow 515031, Guangdong, China
| | - Jiahua Lin
- Department of Urology, Shantou Central Hospital Swatow 515031, Guangdong, China
| | - Yonghai Zhang
- Department of Urology, Shantou Central Hospital Swatow 515031, Guangdong, China
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91
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Escape from Mitotic Arrest: An Unexpected Connection Between Microtubule Dynamics and Epigenetic Regulation of Centromeric Chromatin in Schizosaccharomyces pombe. Genetics 2015; 201:1467-78. [PMID: 26510788 DOI: 10.1534/genetics.115.181792] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/23/2015] [Indexed: 01/02/2023] Open
Abstract
Accurate chromosome segregation is necessary to ensure genomic integrity. Segregation depends on the proper functioning of the centromere, kinetochore, and mitotic spindle microtubules and is monitored by the spindle assembly checkpoint (SAC). In the fission yeast Schizosaccharomyces pombe, defects in Dis1, a microtubule-associated protein that influences microtubule dynamics, lead to mitotic arrest as a result of an active SAC and consequent failure to grow at low temperature. In a mutant dis1 background (dis1-288), loss of function of Msc1, a fission yeast homolog of the KDM5 family of proteins, suppresses the growth defect and promotes normal mitosis. Genetic analysis implicates a histone deacetylase (HDAC)-linked pathway in suppression because HDAC mutants clr6-1, clr3∆, and sir2∆, though not hos2∆, also promote normal mitosis in the dis1-288 mutant. Suppression of the dis phenotype through loss of msc1 function requires the spindle checkpoint protein Mad2 and is limited by the presence of the heterochromatin-associated HP1 protein homolog Swi6. We speculate that alterations in histone acetylation promote a centromeric chromatin environment that compensates for compromised dis1 function by allowing for successful kinetochore-microtubule interactions that can satisfy the SAC. In cells arrested in mitosis by mutation of dis1, loss of function of epigenetic determinants such as Msc1 or specific HDACs can promote cell survival. Because the KDM5 family of proteins has been implicated in human cancers, an appreciation of the potential role of this family of proteins in chromosome segregation is warranted.
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92
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Keenan MM, Liu B, Tang X, Wu J, Cyr D, Stevens RD, Ilkayeva O, Huang Z, Tollini LA, Murphy SK, Lucas J, Muoio DM, Kim SY, Chi JT. ACLY and ACC1 Regulate Hypoxia-Induced Apoptosis by Modulating ETV4 via α-ketoglutarate. PLoS Genet 2015; 11:e1005599. [PMID: 26452058 PMCID: PMC4599891 DOI: 10.1371/journal.pgen.1005599] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 09/21/2015] [Indexed: 12/13/2022] Open
Abstract
In order to propagate a solid tumor, cancer cells must adapt to and survive under various tumor microenvironment (TME) stresses, such as hypoxia or lactic acidosis. To systematically identify genes that modulate cancer cell survival under stresses, we performed genome-wide shRNA screens under hypoxia or lactic acidosis. We discovered that genetic depletion of acetyl-CoA carboxylase (ACACA or ACC1) or ATP citrate lyase (ACLY) protected cancer cells from hypoxia-induced apoptosis. Additionally, the loss of ACLY or ACC1 reduced levels and activities of the oncogenic transcription factor ETV4. Silencing ETV4 also protected cells from hypoxia-induced apoptosis and led to remarkably similar transcriptional responses as with silenced ACLY or ACC1, including an anti-apoptotic program. Metabolomic analysis found that while α-ketoglutarate levels decrease under hypoxia in control cells, α-ketoglutarate is paradoxically increased under hypoxia when ACC1 or ACLY are depleted. Supplementation with α-ketoglutarate rescued the hypoxia-induced apoptosis and recapitulated the decreased expression and activity of ETV4, likely via an epigenetic mechanism. Therefore, ACC1 and ACLY regulate the levels of ETV4 under hypoxia via increased α-ketoglutarate. These results reveal that the ACC1/ACLY-α-ketoglutarate-ETV4 axis is a novel means by which metabolic states regulate transcriptional output for life vs. death decisions under hypoxia. Since many lipogenic inhibitors are under investigation as cancer therapeutics, our findings suggest that the use of these inhibitors will need to be carefully considered with respect to oncogenic drivers, tumor hypoxia, progression and dormancy. More broadly, our screen provides a framework for studying additional tumor cell stress-adaption mechanisms in the future. During the development of most solid tumors, there are characteristic physiological differences in the tumor that result from tumor cells outgrowing their local blood supply. Two of these physiological differences, or “stresses,” that occur in the tumor are low oxygen levels (hypoxia) and an accumulation of lactic acidic (lactic acidosis). Cancer cells experiencing hypoxia and lactic acidosis tend to be more resistant to chemo- and radio-therapy and metastasize more readily. Therefore, it is important to understand how tumor cells adapt to and survive these stresses. We used a large scale screening experiment in order to find which genes and proteins are involved in tumor cell adaptation and survival under hypoxia or lactic acidosis. We found that inhibiting either of two genes involved in lipid synthesis allowed tumor cells to survive hypoxia. This occurred because silencing these genes led to an increase in the metabolite α-ketoglutarate, which repressed a transcription factor that contributed to cell death under hypoxia. This research specifically advances our understanding of how tumor cells survive hypoxia and lactic acidosis and more broadly enhances our understanding of the cellular biology of solid tumors.
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Affiliation(s)
- Melissa M. Keenan
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Beiyu Liu
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Xiaohu Tang
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Jianli Wu
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Derek Cyr
- Department of Electrical and Computer Engineering, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Robert D. Stevens
- Sarah W Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, North Carolina, United States of America
- Duke Institute of Molecular Physiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Olga Ilkayeva
- Sarah W Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, North Carolina, United States of America
- Duke Institute of Molecular Physiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Zhiqing Huang
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Laura A. Tollini
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Susan K. Murphy
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Joseph Lucas
- Department of Electrical and Computer Engineering, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Deborah M. Muoio
- Sarah W Stedman Nutrition and Metabolism Center, Duke University Medical Center, Durham, North Carolina, United States of America
- Duke Institute of Molecular Physiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - So Young Kim
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Jen-Tsan Chi
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Center for Genomic and Computational Biology, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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93
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Kong LL, Man DM, Wang T, Zhang GA, Cui W. siRNA targeting RBP2 inhibits expression, proliferation, tumorigenicity and invasion in thyroid carcinoma cells. Oncol Lett 2015; 10:3393-3398. [PMID: 26788140 PMCID: PMC4665154 DOI: 10.3892/ol.2015.3782] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 08/17/2015] [Indexed: 12/21/2022] Open
Abstract
In order to estimate the effects of small interfering RNA (siRNA) targeting retinoblastoma binding protein 2 (RBP2) on the proliferation, expression, invasion, migration and tumorigenicity abilities of papillary thyroid carcinoma K1 cells, siRNA targeting RBP2 (RBP2-siRNA) and negative control siRNA were transfected into K1 cells. The mRNA levels of RBP2 in the transfected cells were estimated by reverse transcription-quantitative polymerase chain reaction (RT-qPCR), and the protein levels of RBP2 in these cells were evaluated by western blot analysis and immunocytochemical (ICC) analyses. The growth, tumorigenicity, migration and invasion abilities of the transfected cells were measured by Cell Counting Kit-8 (CCK-8), soft agar colony formation and transwell chamber assay, respectively. The ICC results demonstrated that the protein expression levels of RBP2 were lower in the RBP2-siRNA-transfected cells than in the blank and control cells (analysis of variance, F=26.754, P<0.01). RBP2-siRNA downregulated RBP2 at the mRNA (t=8.869) and protein level (F=60.835) (P=0.000 vs. control cells). In addition, the transfection of RBP2-siRNA into K1 cells also suppressed cell proliferation at 24, 48 and 72 h post-transfection (t=7.650, P<0.01; t=2.606, P=0.016; and t=2.377, P=0.027, respectively). Compared with the control group, the number of invasive and migrated cells were significantly reduced in the RBP2-siRNA-transfected group (t=4.774 and t=6.366, respectively; P<0.01). Furthermore, the tumorigenic potential of the cells transfected with RBP2-siRNA was markedly reduced, as indicated by the soft agar formation assay (t=2.749, P=0.014 vs. control cells). In conclusion, the transfection of RBP2-siRNA into papillary thyroid carcinoma K1 cells suppressed the expression of RBP2 in these cells, and reduced their proliferation, invasion, migration and tumorigenic potential. Therefore, targeting RBP2 may be an efficient approach to control thyroid carcinoma.
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Affiliation(s)
- Ling-Ling Kong
- Department of Pathology, Basic Science School, Jining Medical University, Jining, Shandong 272067, P.R. China
| | - Dong-Mei Man
- Department of Gynecology, Affiliated Hospital of Jining Medical University, Jining, Shandong 272029, P.R. China
| | - Tian Wang
- Department of Electrocardiogram, The First Affiliated Hospital of Jining Medical University, Jining, Shandong 272111, P.R. China
| | - Guo-An Zhang
- Department of Pathology, Basic Science School, Jining Medical University, Jining, Shandong 272067, P.R. China
| | - Wen Cui
- Department of Pathology, Basic Science School, Jining Medical University, Jining, Shandong 272067, P.R. China
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94
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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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95
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The Drosophila histone demethylase dKDM5/LID regulates hematopoietic development. Dev Biol 2015; 405:260-8. [DOI: 10.1016/j.ydbio.2015.07.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 06/12/2015] [Accepted: 07/12/2015] [Indexed: 01/08/2023]
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96
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Abstract
Hydroxylation is an emerging modification generally catalyzed by a family of ∼70 enzymes that are dependent on oxygen, Fe(II), ascorbate, and the Kreb's cycle intermediate 2-oxoglutarate (2OG). These "2OG oxygenases" sit at the intersection of nutrient availability and metabolism where they have the potential to regulate gene expression and growth in response to changes in co-factor abundance. Characterized 2OG oxygenases regulate fundamental cellular processes by catalyzing the hydroxylation or demethylation (via hydroxylation) of DNA, RNA, or protein. As such they have been implicated in various syndromes and diseases, but particularly cancer. In this review we discuss the emerging role of 2OG oxygenases in gene expression control, examine the regulation of these unique enzymes by nutrient availability and metabolic intermediates, and describe these properties in relation to the expanding role of these enzymes in cancer.
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97
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Jangravi Z, Tabar MS, Mirzaei M, Parsamatin P, Vakilian H, Alikhani M, Shabani M, Haynes PA, Goodchild AK, Gourabi H, Baharvand H, Salekdeh GH. Two Splice Variants of Y Chromosome-Located Lysine-Specific Demethylase 5D Have Distinct Function in Prostate Cancer Cell Line (DU-145). J Proteome Res 2015. [PMID: 26215926 DOI: 10.1021/acs.jproteome.5b00333] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the major objectives of the Human Y Chromosome Proteome Project is to characterize sets of proteins encoded from the human Y chromosome. Lysine (K)-specific demethylase 5D (KDM5D) is located on the AZFb region of the Y chromosome and encodes a JmjC-domain-containing protein. KDM5D, the least well-documented member of the KDM5 family, is capable of demethylating di- and trimethyl H3K4. In this study, we detected two novel splice variants of KDM5D with lengths of 2650bp and 2400bp that correspond to the 100 and 80 kDa proteins in the human prostate cancer cell line, DU-145. The knockdown of two variants using the short interfering RNA (siRNA) approach increased the growth rate of prostate cancer cells and reduced cell apoptosis. To explore the proteome pattern of the cells after KDM5D downregulation, we applied a shotgun label-free quantitative proteomics approach. Of 820 proteins present in all four replicates of two treatments, the abundance of 209 proteins changed significantly in response to KDM5D suppression. Of these, there were 102 proteins observed to be less abundant and 107 more abundant in KDM5D knockdown cells compared with control cells. The results revealed that KDM5D knockdown altered the abundance of proteins involved in RNA processing, protein synthesis, apoptosis, the cell cycle, and growth and proliferation. In conjunction, these results provided new insights into the function of KDM5D and its splice variants. The proteomics data are available at PRIDE with ProteomeXchange identifier PXD000416.
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Affiliation(s)
- Zohreh Jangravi
- Molecular Systems Biology Department at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran, Iran.,Biochemistry Department, Iran University of Medical Sciences , Tehran, Iran
| | - Mehdi Sharif Tabar
- Molecular Systems Biology Department at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran, Iran
| | - Mehdi Mirzaei
- The Australian School of Advanced Medicine, Faculty of Human Sciences, Macquarie University , Sydney, New South Wales 2109, Australia
| | - Pouria Parsamatin
- Molecular Systems Biology Department at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran, Iran
| | - Haghighat Vakilian
- Molecular Systems Biology Department at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran, Iran
| | - Mehdi Alikhani
- Molecular Systems Biology Department at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran, Iran
| | - Mohammad Shabani
- Biochemistry Department, Iran University of Medical Sciences , Tehran, Iran
| | - Paul A Haynes
- Department of Chemistry and Biomolecular Sciences, Macquarie University , Sydney, New South Wales 2109, Australia
| | - Ann K Goodchild
- The Australian School of Advanced Medicine, Faculty of Human Sciences, Macquarie University , Sydney, New South Wales 2109, Australia
| | - Hamid Gourabi
- Department of Genetics at Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR , Tehran, Iran
| | - Hossein Baharvand
- Department of Developmental Biology, University of Science and Culture, ACECR , Tehran, Iran.,Department of Stem Cells and Developmental Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- Molecular Systems Biology Department at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran, Iran.,Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran , Karaj, Iran
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98
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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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99
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Epigenetic modifications in cutaneous malignant melanoma: EZH2, H3K4me2, and H3K27me3 immunohistochemical expression is enhanced at the invasion front of the tumor. Am J Dermatopathol 2015; 37:138-44. [PMID: 25614949 DOI: 10.1097/dad.0b013e31828a2d54] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cancer stem cells and the misregulation of epigenetic modifications have been identified to possess a determinative role in carcinogenesis. The purpose of this study was to investigate the expression profile of EZH2 and H3K4me2 and H3K27me3, which constitute stem cell-like "bivalent" domains, in cutaneous malignant melanoma. A comparative analysis of their immunohistochemical expression between the invasion front (IF) and the inner tumor mass was also evaluated. Immunohistochemical methodology was performed on sections of 89 melanoma lesions from 79 patients. The 3 markers studied were identified in the cell nuclei of melanoma cells, nevus cells, and normal epidermal keratinocytes. A specific distribution pattern of H3K4me2 and H3K27me3 was found, as stronger levels were localized at the IF of the tumor (P = 0.034 and P < 0.01, respectively). In general, H3K4me2 and H3K27me3 levels were lower in metastatic with respect to primary melanoma cases (P = 0.0065 and P = 0.027, respectively). Advanced melanoma demonstrated significantly lower H3K4 immunohistochemical expression than did cases of lowest Clark level (I) (P = 0.038) or low Breslow depth (≤1 mm; P < 0.001). Furthermore, EZH2 expression in melanoma cells was higher compared with that in nevus cells (P = 0.02). A positive correlation between EZH2-H3K27me3 (P = 0.03) and H3K4me2-H3K27me3 (P < 0.01) in melanoma cells was also found. Our results suggest the possibility that combined immunohistochemical expression of EZH2, H3K4me2, and H3K27me3 might identify cancer cells with potential stem cell properties, particularly at the IF of this malignancy. This hypothesis should be further investigated, as many of the epigenetic changes are reversible via pharmacologic manipulations and new therapies, overpassing the resistance of advanced melanoma, may be developed.
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100
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Dun MD, Chalkley RJ, Faulkner S, Keene S, Avery-Kiejda KA, Scott RJ, Falkenby LG, Cairns MJ, Larsen MR, Bradshaw RA, Hondermarck H. Proteotranscriptomic Profiling of 231-BR Breast Cancer Cells: Identification of Potential Biomarkers and Therapeutic Targets for Brain Metastasis. Mol Cell Proteomics 2015; 14:2316-30. [PMID: 26041846 DOI: 10.1074/mcp.m114.046110] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Indexed: 11/06/2022] Open
Abstract
Brain metastases are a devastating consequence of cancer and currently there are no specific biomarkers or therapeutic targets for risk prediction, diagnosis, and treatment. Here the proteome of the brain metastatic breast cancer cell line 231-BR has been compared with that of the parental cell line MDA-MB-231, which is also metastatic but has no organ selectivity. Using SILAC and nanoLC-MS/MS, 1957 proteins were identified in reciprocal labeling experiments and 1584 were quantified in the two cell lines. A total of 152 proteins were confidently determined to be up- or down-regulated by more than twofold in 231-BR. Of note, 112/152 proteins were decreased as compared with only 40/152 that were increased, suggesting that down-regulation of specific proteins is an important part of the mechanism underlying the ability of breast cancer cells to metastasize to the brain. When matched against transcriptomic data, 43% of individual protein changes were associated with corresponding changes in mRNA, indicating that the transcript level is a limited predictor of protein level. In addition, differential miRNA analyses showed that most miRNA changes in 231-BR were up- (36/45) as compared with down-regulations (9/45). Pathway analysis revealed that proteome changes were mostly related to cell signaling and cell cycle, metabolism and extracellular matrix remodeling. The major protein changes in 231-BR were confirmed by parallel reaction monitoring mass spectrometry and consisted in increases (by more than fivefold) in the matrix metalloproteinase-1, ephrin-B1, stomatin, myc target-1, and decreases (by more than 10-fold) in transglutaminase-2, the S100 calcium-binding protein A4, and l-plastin. The clinicopathological significance of these major proteomic changes to predict the occurrence of brain metastases, and their potential value as therapeutic targets, warrants further investigation.
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Affiliation(s)
- Matthew D Dun
- From the ‡School of Biomedical Sciences & Pharmacy and §Hunter Medical Research Institute, Faculty of Health and Medicine, University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Robert J Chalkley
- ¶Department of Pharmaceutical Chemistry, University of California San Francisco, California 94158
| | - Sam Faulkner
- From the ‡School of Biomedical Sciences & Pharmacy and §Hunter Medical Research Institute, Faculty of Health and Medicine, University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Sheridan Keene
- From the ‡School of Biomedical Sciences & Pharmacy and §Hunter Medical Research Institute, Faculty of Health and Medicine, University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Kelly A Avery-Kiejda
- From the ‡School of Biomedical Sciences & Pharmacy and §Hunter Medical Research Institute, Faculty of Health and Medicine, University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Rodney J Scott
- From the ‡School of Biomedical Sciences & Pharmacy and §Hunter Medical Research Institute, Faculty of Health and Medicine, University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Lasse G Falkenby
- ‖Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Murray J Cairns
- From the ‡School of Biomedical Sciences & Pharmacy and §Hunter Medical Research Institute, Faculty of Health and Medicine, University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Martin R Larsen
- ‖Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Ralph A Bradshaw
- ¶Department of Pharmaceutical Chemistry, University of California San Francisco, California 94158
| | - Hubert Hondermarck
- From the ‡School of Biomedical Sciences & Pharmacy and §Hunter Medical Research Institute, Faculty of Health and Medicine, University of Newcastle, Callaghan, New South Wales 2308, Australia
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