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Abstract
During aging, the mechanisms that normally maintain health and stress resistance strikingly decline, resulting in decrepitude, frailty, and ultimately death. Exactly when and how this decline occurs is unknown. Changes in transcriptional networks and chromatin state lie at the heart of age-dependent decline. These epigenomic changes are not only observed during aging but also profoundly affect cellular function and stress resistance, thereby contributing to the progression of aging. We propose that the dysregulation of transcriptional and chromatin networks is a crucial component of aging. Understanding age-dependent epigenomic changes will yield key insights into how aging begins and progresses and should lead to the development of new therapeutics that delay or even reverse aging and age-related diseases.
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Affiliation(s)
- Lauren N Booth
- Department of Genetics, Stanford University, 300 Pasteur Drive, Stanford, CA 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, 300 Pasteur Drive, Stanford, CA 94305, USA; Glenn Laboratories for the Biology of Aging, Stanford University, 300 Pasteur Drive, Stanford, CA 94305, USA.
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152
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Chen M, Zhang M, Zhai L, Hu H, Liu P, Tan M. Tryptic Peptides Bearing C-Terminal Dimethyllysine Need to Be Considered during the Analysis of Lysine Dimethylation in Proteomic Study. J Proteome Res 2017; 16:3460-3469. [PMID: 28730820 DOI: 10.1021/acs.jproteome.7b00373] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lysine methylation plays important roles in structural and functional regulation of chromatin. Although trypsin is the most widely used protease in mass spectrometry-based proteomic analysis for lysine methylation substrates, the proteolytic activity of trypsin on dimethylated lysine residues remains an arguable issue. In this study, we tested the ability of trypsin to cleave dimethylated lysine residues in synthetic peptides, purified albumin, and whole cell lysate, and found that the C-terminal of dimethylated lysine residue could be cleaved in a protein sequence-dependent manner. Kinetic studies revealed that the optimal digestion time and enzyme-to-substrate ratio for the cleavage of dimethylated lysine by trypsin was around 16 h and 1:50, respectively. We further showed the tryptic C-terminal lysine-dimethylated (C-Kme2) peptides could contribute to a significant portion of substrate identification in the proteomic study, which utilizes the chemical dimethylation labeling approach. More than 120 tryptic C-Kme2 peptides (7% of total peptides identified) were identified in chemically lysine-dimethyl-labeled HeLa whole cell lysate by a single-shot nanoflow high performance liquid chromatography with tandem mass spectrometry (nano-HPLC-MS/MS) analysis. Moreover, in an assay for substrate identification of protease Glu-C using stable isotope dimethyl labeling approach, our data showed the tryptic C-Kme2 peptides accounted for more than 13% of total tryptic peptides. Additionally, our in vivo methylome profiling data revealed some C-Kme2 peptides, which is of importance to identification and quantification of biologically relevant protein and lysine-methylated site. Therefore, we reason that the tryptic peptides bearing C-terminal dimethylated lysine need to be considered in the mass spectrometric analysis of lysine dimethylation.
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Affiliation(s)
- Ming Chen
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, PR China.,University of Chinese Academy of Sciences , Beijing 100049, PR China
| | - Min Zhang
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, PR China.,University of Chinese Academy of Sciences , Beijing 100049, PR China
| | - Linhui Zhai
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, PR China
| | - Hao Hu
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, PR China
| | - Ping Liu
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, PR China
| | - Minjia Tan
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, PR China.,University of Chinese Academy of Sciences , Beijing 100049, PR China
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153
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Long W, Yi Y, Chen S, Cao Q, Zhao W, Liu Q. Potential New Therapies for Pediatric Diffuse Intrinsic Pontine Glioma. Front Pharmacol 2017; 8:495. [PMID: 28790919 PMCID: PMC5525007 DOI: 10.3389/fphar.2017.00495] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 07/11/2017] [Indexed: 12/20/2022] Open
Abstract
Diffuse intrinsic pontine glioma (DIPG) is an extensively invasive malignancy with infiltration into other regions of the brainstem. Although large numbers of specific targeted therapies have been tested, no significant progress has been made in treating these high-grade gliomas. Therefore, the identification of new therapeutic approaches is of great importance for the development of more effective treatments. This article reviews the conventional therapies and new potential therapeutic approaches for DIPG, including epigenetic therapy, immunotherapy, and the combination of stem cells with nanoparticle delivery systems.
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Affiliation(s)
- Wenyong Long
- Department of Neurosurgery, Xiangya Hospital, Central South UniversityChangsha, China
| | - Yang Yi
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen UniversityGuangzhou, China.,Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen UniversityGuangzhou, China
| | - Shen Chen
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen UniversityGuangzhou, China.,Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen UniversityGuangzhou, China
| | - Qi Cao
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, HoustonTX, United States
| | - Wei Zhao
- Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-sen UniversityGuangzhou, China.,Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen UniversityGuangzhou, China
| | - Qing Liu
- Department of Neurosurgery, Xiangya Hospital, Central South UniversityChangsha, China
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154
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Foma AM, Aslani S, Karami J, Jamshidi A, Mahmoudi M. Epigenetic involvement in etiopathogenesis and implications in treatment of systemic lupus erythematous. Inflamm Res 2017; 66:1057-1073. [DOI: 10.1007/s00011-017-1082-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/22/2017] [Accepted: 07/13/2017] [Indexed: 10/19/2022] Open
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155
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Jiang Y, Mao C, Yang R, Yan B, Shi Y, Liu X, Lai W, Liu Y, Wang X, Xiao D, Zhou H, Cheng Y, Yu F, Cao Y, Liu S, Yan Q, Tao Y. EGLN1/c-Myc Induced Lymphoid-Specific Helicase Inhibits Ferroptosis through Lipid Metabolic Gene Expression Changes. Am J Cancer Res 2017; 7:3293-3305. [PMID: 28900510 PMCID: PMC5595132 DOI: 10.7150/thno.19988] [Citation(s) in RCA: 200] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/15/2017] [Indexed: 12/24/2022] Open
Abstract
Ferroptosis is a newly discovered form of non-apoptotic cell death in multiple human diseases. However, the epigenetic mechanisms underlying ferroptosis remain poorly defined. First, we demonstrated that lymphoid-specific helicase (LSH), which is a DNA methylation modifier, interacted with WDR76 to inhibit ferroptosis by activating lipid metabolism-associated genes, including GLUT1, and ferroptosis related genes SCD1 and FADS2, in turn, involved in the Warburg effect. WDR76 targeted these genes expression in dependent manner of LSH and chromatin modification in DNA methylation and histone modification. These effects were dependent on iron and lipid reactive oxygen species. We further demonstrated that EGLN1 and c-Myc directly activated the expression of LSH by inhibiting HIF-1α. Finally, we demonstrated that LSH functioned as an oncogene in lung cancer in vitro and in vivo. Therefore, our study elucidates the molecular basis of the c-Myc/EGLN1-mediated induction of LSH expression that inhibits ferroptosis, which can be exploited for the development of therapeutic strategies targeting ferroptosis for the treatment of cancer.
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156
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Andrei SA, Sijbesma E, Hann M, Davis J, O’Mahony G, Perry MWD, Karawajczyk A, Eickhoff J, Brunsveld L, Doveston RG, Milroy LG, Ottmann C. Stabilization of protein-protein interactions in drug discovery. Expert Opin Drug Discov 2017; 12:925-940. [DOI: 10.1080/17460441.2017.1346608] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Sebastian A. Andrei
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Eline Sijbesma
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Michael Hann
- Platform Technology and Science, Medicines Research Centre, GlaxoSmithKline R&D, Stevenage, UK
| | - Jeremy Davis
- Department of Chemistry, UCB Celltech, Slough, UK
| | - Gavin O’Mahony
- CVMD Medicinal Chemistry, Innovative Medicines and Early Development, AstraZeneca Gothenburg, Pepparedsleden, Mölndal, Sweden
| | - Matthew W. D. Perry
- RIA Medicinal Chemistry, Innovative Medicines and Early Development, AstraZeneca Gothenburg, Pepparedsleden, Mölndal, Sweden
| | - Anna Karawajczyk
- Medicinal Chemistry, Taros Chemicals GmbH & Co. KG, Dortmund, Germany
| | - Jan Eickhoff
- Assay development & screening, Lead Discovery Center GmbH, Dortmund, Germany
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Richard G. Doveston
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Lech-Gustav Milroy
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Chemistry, University of Duisburg-Essen, Essen, Germany
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157
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Terranova-Barberio M, Thomas S, Munster PN. Epigenetic modifiers in immunotherapy: a focus on checkpoint inhibitors. Immunotherapy 2017; 8:705-19. [PMID: 27197539 DOI: 10.2217/imt-2016-0014] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Immune surveillance should be directed to suppress tumor development and progression, involving a balance of coinhibitory and costimulatory signals that amplify immune response without overwhelming the host. Immunotherapy confers durable clinical benefit in 'immunogenic tumors', whereas in other tumors the responses are modest. Thus, immune checkpoint inhibitors may need to be combined with strategies to boost immune response or increase the tumor immune profile. Epigenetic aberrations contribute significantly to carcinogenesis. Recent findings suggest that epigenetic drugs prime the immune response by increasing expression of tumor-associated antigens and immune-related genes, as well as modulating chemokines and cytokines involved in immune system activation. This review describes our current understanding regarding epigenetic and immunotherapy combination, focusing on immune response priming to checkpoint blockade.
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Affiliation(s)
- Manuela Terranova-Barberio
- Department of Medicine, Division of Hematology & Oncology, University of California, Room A722, 1600 Divisadero St, Box 1770, San Francisco, CA 94115, USA
| | - Scott Thomas
- Department of Medicine, Division of Hematology & Oncology, University of California, Room A722, 1600 Divisadero St, Box 1770, San Francisco, CA 94115, USA
| | - Pamela N Munster
- Department of Medicine, Division of Hematology & Oncology, University of California, Room A722, 1600 Divisadero St, Box 1770, San Francisco, CA 94115, USA
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158
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Miller TE, Liau BB, Wallace LC, Morton AR, Xie Q, Dixit D, Factor DC, Kim LJY, Morrow JJ, Wu Q, Mack SC, Hubert CG, Gillespie SM, Flavahan WA, Hoffmann T, Thummalapalli R, Hemann MT, Paddison PJ, Horbinski CM, Zuber J, Scacheri PC, Bernstein BE, Tesar PJ, Rich JN. Transcription elongation factors represent in vivo cancer dependencies in glioblastoma. Nature 2017; 547:355-359. [PMID: 28678782 PMCID: PMC5896562 DOI: 10.1038/nature23000] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 06/05/2017] [Indexed: 12/23/2022]
Abstract
Glioblastoma is a universally lethal cancer with a median survival time of approximately 15 months. Despite substantial efforts to define druggable targets, there are no therapeutic options that notably extend the lifespan of patients with glioblastoma. While previous work has largely focused on in vitro cellular models, here we demonstrate a more physiologically relevant approach to target discovery in glioblastoma. We adapted pooled RNA interference (RNAi) screening technology for use in orthotopic patient-derived xenograft models, creating a high-throughput negative-selection screening platform in a functional in vivo tumour microenvironment. Using this approach, we performed parallel in vivo and in vitro screens and discovered that the chromatin and transcriptional regulators needed for cell survival in vivo are non-overlapping with those required in vitro. We identified transcription pause-release and elongation factors as one set of in vivo-specific cancer dependencies, and determined that these factors are necessary for enhancer-mediated transcriptional adaptations that enable cells to survive the tumour microenvironment. Our lead hit, JMJD6, mediates the upregulation of in vivo stress and stimulus response pathways through enhancer-mediated transcriptional pause-release, promoting cell survival specifically in vivo. Targeting JMJD6 or other identified elongation factors extends survival in orthotopic xenograft mouse models, suggesting that targeting transcription elongation machinery may be an effective therapeutic strategy for glioblastoma. More broadly, this study demonstrates the power of in vivo phenotypic screening to identify new classes of 'cancer dependencies' not identified by previous in vitro approaches, and could supply new opportunities for therapeutic intervention.
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Affiliation(s)
- Tyler E Miller
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio 44195, USA.,Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Brian B Liau
- Harvard Medical School, Boston, Massachusetts 02114, USA.,Epigenomics Program, Broad Institute, Cambridge, Massachusetts 02142, USA.,Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Lisa C Wallace
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Andrew R Morton
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Qi Xie
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Deobrat Dixit
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Daniel C Factor
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Leo J Y Kim
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio 44195, USA.,Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - James J Morrow
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Qiulian Wu
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Stephen C Mack
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio 44195, USA
| | - Christopher G Hubert
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio 44195, USA
| | - Shawn M Gillespie
- Harvard Medical School, Boston, Massachusetts 02114, USA.,Epigenomics Program, Broad Institute, Cambridge, Massachusetts 02142, USA.,Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - William A Flavahan
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio 44195, USA
| | - Thomas Hoffmann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Rohit Thummalapalli
- Harvard Medical School, Boston, Massachusetts 02114, USA.,Epigenomics Program, Broad Institute, Cambridge, Massachusetts 02142, USA.,Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Michael T Hemann
- The Koch Institute for Integrative Cancer Research at MIT, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Craig M Horbinski
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA.,Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60615, USA
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Bradley E Bernstein
- Harvard Medical School, Boston, Massachusetts 02114, USA.,Epigenomics Program, Broad Institute, Cambridge, Massachusetts 02142, USA.,Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Paul J Tesar
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - Jeremy N Rich
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio 44195, USA
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159
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Bae N, Viviano M, Su X, Lv J, Cheng D, Sagum C, Castellano S, Bai X, Johnson C, Khalil MI, Shen J, Chen K, Li H, Sbardella G, Bedford MT. Developing Spindlin1 small-molecule inhibitors by using protein microarrays. Nat Chem Biol 2017; 13:750-756. [PMID: 28504676 PMCID: PMC5831360 DOI: 10.1038/nchembio.2377] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 02/15/2017] [Indexed: 12/19/2022]
Abstract
The discovery of inhibitors of methyl- and acetyl-binding domains has provided evidence for the 'druggability' of epigenetic effector molecules. The small-molecule probe UNC1215 prevents methyl-dependent protein-protein interactions by engaging the aromatic cage of MBT domains and, with lower affinity, Tudor domains. Using a library of tagged UNC1215 analogs, we screened a protein-domain microarray of human methyllysine effector molecules to rapidly detect compounds with new binding profiles with either increased or decreased specificity. Using this approach, we identified a compound (EML405) that acquired a novel interaction with the Tudor-domain-containing protein Spindlin1 (SPIN1). Structural studies facilitated the rational synthesis of SPIN1 inhibitors with increased selectivity (EML631-633), which engage SPIN1 in cells, block its ability to 'read' H3K4me3 marks and inhibit its transcriptional-coactivator activity. Protein microarrays can thus be used as a platform to 'target-hop' and identify small molecules that bind and compete with domain-motif interactions.
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Affiliation(s)
- Narkhyun Bae
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Monica Viviano
- Dipartimento di Farmacia, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano (SA), Italy
| | - Xiaonan Su
- Beijing Advanced Innovation Center for Structural Biology, MOE Key Laboratory of Protein Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, 100084, P.R. China
| | - Jie Lv
- Center for Regenerative Medicine, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA & Department of Cardiothoracic Surgery, Weill Cornell Medical College, Cornell University
| | - Donghang Cheng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Cari Sagum
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Sabrina Castellano
- Dipartimento di Farmacia, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano (SA), Italy
- Dipartimento di Medicina e Chirurgia, Università degli Studi di Salerno, Via Salvador Allende, I-84081 Baronissi (SA), Italy
| | - Xue Bai
- Beijing Advanced Innovation Center for Structural Biology, MOE Key Laboratory of Protein Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, 100084, P.R. China
| | - Claire Johnson
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Mahmoud Ibrahim Khalil
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
- Molecular Biology Unit, Department of Zoology, Faculty of Science, Alexandria University, Egypt
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Kaifu Chen
- Center for Regenerative Medicine, Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA & Department of Cardiothoracic Surgery, Weill Cornell Medical College, Cornell University
| | - Haitao Li
- Beijing Advanced Innovation Center for Structural Biology, MOE Key Laboratory of Protein Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing, 100084, P.R. China
| | - Gianluca Sbardella
- Dipartimento di Farmacia, Epigenetic Med Chem Lab, Università degli Studi di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano (SA), Italy
| | - Mark T. Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
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160
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Kaniskan HÜ, Jin J. Recent progress in developing selective inhibitors of protein methyltransferases. Curr Opin Chem Biol 2017; 39:100-108. [PMID: 28662389 DOI: 10.1016/j.cbpa.2017.06.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 06/14/2017] [Indexed: 10/19/2022]
Abstract
Mounting evidence suggests that protein methyltransferases (PMTs), which catalyze methylation of histones as well as non-histone proteins, play a crucial role in diverse biological pathways and human diseases. In particular, PMTs have been recognized as major players in regulating gene expression and chromatin state. There has been an increasingly growing interest in these enzymes as potential therapeutic targets and over the past two years tremendous progress has been made in the discovery of selective, small molecule inhibitors of protein lysine and arginine methyltransferases. Inhibitors of PMTs have been used extensively in oncology studies as tool compounds, and inhibitors of EZH2, DOT1L and PRMT5 are currently in clinical trials.
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Affiliation(s)
- H Ümit Kaniskan
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
| | - Jian Jin
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
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161
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Borutinskaitė V, Virkšaitė A, Gudelytė G, Navakauskienė R. Green tea polyphenol EGCG causes anti-cancerous epigenetic modulations in acute promyelocytic leukemia cells. Leuk Lymphoma 2017. [PMID: 28641467 DOI: 10.1080/10428194.2017.1339881] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Green tea (Camellia sinensis) catechin epigallocatechin-3-gallate (EGCG) has been shown to possess diverse anti-cancerous properties. We demonstrated EGCG ability to inhibit acute promyelocytic leukemia (APL) cell proliferation and cause apoptosis. In addition, quantitative real-time polymerase chain reaction (RT-qPCR) analysis revealed elevated expression of genes associated with cell cycle arrest and differentiation (p27, PCAF, C/EBPα, and C/EBPɛ). Furthermore, EGCG caused anti-cancerous epigenetic changes: downregulation of epigenetic modifiers DNMT1, HDAC1, HDAC2, and G9a was observed by RT-qPCR analysis. Reduced amount of H3K9me2 after treatment with EGCG confirmed G9a downregulation. Polycomb repressive complex 2 (PRC2) core components were also shown to be downregulated in gene and protein level. Chromatin immunoprecipitation (ChIP) analysis revealed that EGCG treatment enhanced hyperacetylated H4 and acetylated H3K14 histones binding to the promoter regions of p27, PCAF, C/EBPα, and C/EBPɛ and reduced binding effect to PRC2 core component genes EZH2, SUZ12, and EED. Our results indicate that EGCG, as cell proliferation inhibitor and epigenetic modifier, might be useful for APL treatment.
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Affiliation(s)
- Veronika Borutinskaitė
- a Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center , Vilnius University , Vilnius , Lithuania
| | - Aida Virkšaitė
- a Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center , Vilnius University , Vilnius , Lithuania
| | - Giedrė Gudelytė
- a Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center , Vilnius University , Vilnius , Lithuania
| | - Rūta Navakauskienė
- a Department of Molecular Cell Biology, Institute of Biochemistry, Life Sciences Center , Vilnius University , Vilnius , Lithuania
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162
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Upregulation of CD11b and CD86 through LSD1 inhibition promotes myeloid differentiation and suppresses cell proliferation in human monocytic leukemia cells. Oncotarget 2017; 8:85085-85101. [PMID: 29156705 PMCID: PMC5689595 DOI: 10.18632/oncotarget.18564] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 06/02/2017] [Indexed: 12/11/2022] Open
Abstract
LSD1 (Lysine Specific Demethylase1)/KDM1A (Lysine Demethylase 1A), a flavin adenine dinucleotide (FAD)-dependent histone H3K4/K9 demethylase, sustains oncogenic potential of leukemia stem cells in primary human leukemia cells. However, the pro-differentiation and anti-proliferation effects of LSD1 inhibition in acute myeloid leukemia (AML) are not yet fully understood. Here, we report that small hairpin RNA (shRNA) mediated LSD1 inhibition causes a remarkable transcriptional activation of myeloid lineage marker genes (CD11b/ITGAM and CD86), reduction of cell proliferation and decrease of clonogenic ability of human AML cells. Cell surface expression of CD11b and CD86 is significantly and dynamically increased in human AML cells upon sustained LSD1 inhibition. Chromatin immunoprecipitation and quantitative PCR (ChIP-qPCR) analyses of histone marks revealed that there is a specific increase of H3K4me2 modification and an accompanied increase of H3K4me3 modification at the respective CD11b and CD86 promoter region, whereas the global H3K4me2 level remains constant. Consistently, inhibition of LSD1 in vivo significantly blocks tumor growth and induces a prominent increase of CD11b and CD86. Taken together, our results demonstrate the anti-tumor properties of LSD1 inhibition on human AML cell line and mouse xenograft model. Our findings provide mechanistic insights into the LSD1 functions in controlling both differentiation and proliferation in AML.
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163
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San José-Enériz E, Agirre X, Rabal O, Vilas-Zornoza A, Sanchez-Arias JA, Miranda E, Ugarte A, Roa S, Paiva B, Estella-Hermoso de Mendoza A, Alvarez RM, Casares N, Segura V, Martín-Subero JI, Ogi FX, Soule P, Santiveri CM, Campos-Olivas R, Castellano G, de Barrena MGF, Rodriguez-Madoz JR, García-Barchino MJ, Lasarte JJ, Avila MA, Martinez-Climent JA, Oyarzabal J, Prosper F. Discovery of first-in-class reversible dual small molecule inhibitors against G9a and DNMTs in hematological malignancies. Nat Commun 2017; 8:15424. [PMID: 28548080 PMCID: PMC5458547 DOI: 10.1038/ncomms15424] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 03/29/2017] [Indexed: 02/08/2023] Open
Abstract
The indisputable role of epigenetics in cancer and the fact that epigenetic alterations can be reversed have favoured development of epigenetic drugs. In this study, we design and synthesize potent novel, selective and reversible chemical probes that simultaneously inhibit the G9a and DNMTs methyltransferase activity. In vitro treatment of haematological neoplasia (acute myeloid leukaemia-AML, acute lymphoblastic leukaemia-ALL and diffuse large B-cell lymphoma-DLBCL) with the lead compound CM-272, inhibits cell proliferation and promotes apoptosis, inducing interferon-stimulated genes and immunogenic cell death. CM-272 significantly prolongs survival of AML, ALL and DLBCL xenogeneic models. Our results represent the discovery of first-in-class dual inhibitors of G9a/DNMTs and establish this chemical series as a promising therapeutic tool for unmet needs in haematological tumours. Epigenetic drugs are emerging as a powerful therapeutic option for cancer treatment. Here, the authors synthesized selective chemical probes that simultaneously inhibit the G9a and DNMTs methyltransferase activity and demonstrate their anti-tumour activity using in vitro and in vivo models of haematological neoplasia.
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Affiliation(s)
- Edurne San José-Enériz
- Area de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Ciberonc, Universidad de Navarra, Avenida Pío XII, 55 31008 Pamplona, Spain
| | - Xabier Agirre
- Area de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Ciberonc, Universidad de Navarra, Avenida Pío XII, 55 31008 Pamplona, Spain
| | - Obdulia Rabal
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research, University of Navarra, Avenida Pío XII, 55 31008 Pamplona, Spain
| | - Amaia Vilas-Zornoza
- Area de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Ciberonc, Universidad de Navarra, Avenida Pío XII, 55 31008 Pamplona, Spain
| | - Juan A Sanchez-Arias
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research, University of Navarra, Avenida Pío XII, 55 31008 Pamplona, Spain
| | - Estibaliz Miranda
- Area de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Ciberonc, Universidad de Navarra, Avenida Pío XII, 55 31008 Pamplona, Spain
| | - Ana Ugarte
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research, University of Navarra, Avenida Pío XII, 55 31008 Pamplona, Spain
| | - Sergio Roa
- Area de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Ciberonc, Universidad de Navarra, Avenida Pío XII, 55 31008 Pamplona, Spain
| | - Bruno Paiva
- Area de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Ciberonc, Universidad de Navarra, Avenida Pío XII, 55 31008 Pamplona, Spain
| | - Ander Estella-Hermoso de Mendoza
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research, University of Navarra, Avenida Pío XII, 55 31008 Pamplona, Spain
| | - Rosa María Alvarez
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research, University of Navarra, Avenida Pío XII, 55 31008 Pamplona, Spain
| | - Noelia Casares
- Area de Terapia Génica y Hepatología, Centro de Investigación Médica Aplicada, Universidad de Navarra, Avenida Pío XII, 55 31008 Pamplona, Spain
| | - Victor Segura
- Unidad de Bioinformática, Centro de Investigación Médica Aplicada, Universidad de Navarra, Avenida Pío XII, 55 31008 Pamplona, Spain
| | - José I Martín-Subero
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centre Esther Koplowitz, C/ Rosello 153 2nd floor 08036 Barcelona, Spain
| | | | - Pierre Soule
- Nanotemper Technologies GmbH, Flößergasse 4, Munich, Germany
| | - Clara M Santiveri
- Spectroscopy and NMR Unit, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain
| | - Ramón Campos-Olivas
- Spectroscopy and NMR Unit, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro, 3 28029 Madrid, Spain
| | - Giancarlo Castellano
- Departamento de Fundamentos Clínicos, Universitat de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Centre Esther Koplowitz, C/ Rosello 153 2nd floor 08036 Barcelona, Spain
| | - Maite Garcia Fernandez de Barrena
- Area de Terapia Génica y Hepatología, Centro de Investigación Médica Aplicada, Universidad de Navarra, Avenida Pío XII, 55 31008 Pamplona, Spain
| | - Juan Roberto Rodriguez-Madoz
- Area de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Ciberonc, Universidad de Navarra, Avenida Pío XII, 55 31008 Pamplona, Spain
| | - Maria José García-Barchino
- Area de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Ciberonc, Universidad de Navarra, Avenida Pío XII, 55 31008 Pamplona, Spain
| | - Juan Jose Lasarte
- Area de Terapia Génica y Hepatología, Centro de Investigación Médica Aplicada, Universidad de Navarra, Avenida Pío XII, 55 31008 Pamplona, Spain
| | - Matias A Avila
- Area de Terapia Génica y Hepatología, Centro de Investigación Médica Aplicada, Universidad de Navarra, Avenida Pío XII, 55 31008 Pamplona, Spain
| | - Jose Angel Martinez-Climent
- Area de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Ciberonc, Universidad de Navarra, Avenida Pío XII, 55 31008 Pamplona, Spain
| | - Julen Oyarzabal
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research, University of Navarra, Avenida Pío XII, 55 31008 Pamplona, Spain
| | - Felipe Prosper
- Area de Hemato-Oncología, Centro de Investigación Médica Aplicada, IDISNA, Ciberonc, Universidad de Navarra, Avenida Pío XII, 55 31008 Pamplona, Spain.,Departamento de Hematología, Clínica Universidad de Navarra, Universidad de Navarra, Avenida Pío XII, 36 31008 Pamplona, Spain
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164
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Mayes K, Elsayed Z, Alhazmi A, Waters M, Alkhatib SG, Roberts M, Song C, Peterson K, Chan V, Ailaney N, Malapati P, Blevins T, Lisnić B, Dumur CI, Landry JW. BPTF inhibits NK cell activity and the abundance of natural cytotoxicity receptor co-ligands. Oncotarget 2017; 8:64344-64357. [PMID: 28969075 PMCID: PMC5610007 DOI: 10.18632/oncotarget.17834] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/26/2017] [Indexed: 11/25/2022] Open
Abstract
Using syngeneic BALB/c mouse breast cancer models, we show that the chromatin remodeling subunit bromodomain PHD finger transcription factor (BPTF) suppresses natural killer (NK) cell antitumor activity in the tumor microenvironment (TME). In culture, BPTF suppresses direct natural cytotoxicity receptor (NCR) mediated NK cell cytolytic activity to mouse and human cancer cell lines, demonstrating conserved functions. Blocking mouse NCR1 in vivo rescues BPTF KD tumor weights, demonstrating its importance for the control of tumor growth. We discovered that BPTF occupies heparanase (Hpse) regulatory elements, activating its expression. Increased heparanase activity results in reduced cell surface abundance of the NCR co-ligands: heparan sulfate proteoglycans (HSPGs). Using gain and loss of function approaches we show that elevated heparanase levels suppress NK cell cytolytic activity to tumor cells in culture. These results suggest that BPTF activates heparanase expression, which in turn reduces cell surface HSPGs and NCR co-ligands, inhibiting NK cell activity. Furthermore, gene expression data from human breast cancer tumors shows that elevated BPTF expression correlates with reduced antitumor immune cell signatures, supporting conserved roles for BPTF in suppressing antitumor immunity. Conditional BPTF depletion in established mouse breast tumors enhances antitumor immunity, suggesting that inhibiting BPTF could provide a novel immunotherapy.
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Affiliation(s)
- Kimberly Mayes
- The Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Zeinab Elsayed
- The Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Aiman Alhazmi
- The Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Michael Waters
- The Department of Biochemistry, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Suehyb G Alkhatib
- The Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Mark Roberts
- The Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Carolyn Song
- The Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Kristen Peterson
- The Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Vivian Chan
- The Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Nikhil Ailaney
- The Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Pumoli Malapati
- The Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Tana Blevins
- The Department of Pathology, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Berislav Lisnić
- The Center for Proteomics and Department for Histology and Embryology, University of Rijeka, Faculty of Medicine, 51000 Rijeka, Croatia
| | - Catherine I Dumur
- The Department of Pathology, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Joseph W Landry
- The Department of Human and Molecular Genetics, Virginia Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
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165
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Zacharioudakis E, Agarwal P, Bartoli A, Abell N, Kunalingam L, Bergoglio V, Xhemalce B, Miller KM, Rodriguez R. Chromatin Regulates Genome Targeting with Cisplatin. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Emmanouil Zacharioudakis
- Institut Curie; PSL Research University; Chemical Cell Biology Group; 26 Rue d'Ulm 75248 Paris Cedex 05 France
- CNRS UMR3666; 75005 Paris France
- INSERM U1143; 75005 Paris France
- Institut de Chimie des Substances Naturelles; UPR2301; 1 Avenue de la Terrasse 91198 Gif-sur-Yvette Cedex France
| | - Poonam Agarwal
- Department of Molecular Biosciences; Institute of Cellular and Molecular Biology; University of Texas at Austin; 2506 Speedway Stop A5000 Austin TX 78712 USA
| | - Alexandra Bartoli
- Institut Curie; PSL Research University; Chemical Cell Biology Group; 26 Rue d'Ulm 75248 Paris Cedex 05 France
- CNRS UMR3666; 75005 Paris France
- INSERM U1143; 75005 Paris France
- Institut de Chimie des Substances Naturelles; UPR2301; 1 Avenue de la Terrasse 91198 Gif-sur-Yvette Cedex France
| | - Nathan Abell
- Department of Molecular Biosciences; Institute of Cellular and Molecular Biology; University of Texas at Austin; 2506 Speedway Stop A5000 Austin TX 78712 USA
| | - Lavaniya Kunalingam
- Institut Curie; PSL Research University; Chemical Cell Biology Group; 26 Rue d'Ulm 75248 Paris Cedex 05 France
- CNRS UMR3666; 75005 Paris France
- INSERM U1143; 75005 Paris France
- Institut de Chimie des Substances Naturelles; UPR2301; 1 Avenue de la Terrasse 91198 Gif-sur-Yvette Cedex France
| | - Valérie Bergoglio
- CRCT; University of Toulouse; INSERM, CNRS, UPS; Avenue Hubert Curien 31037 Toulouse France
| | - Blerta Xhemalce
- Department of Molecular Biosciences; Institute of Cellular and Molecular Biology; University of Texas at Austin; 2506 Speedway Stop A5000 Austin TX 78712 USA
| | - Kyle M. Miller
- Department of Molecular Biosciences; Institute of Cellular and Molecular Biology; University of Texas at Austin; 2506 Speedway Stop A5000 Austin TX 78712 USA
| | - Raphaël Rodriguez
- Institut Curie; PSL Research University; Chemical Cell Biology Group; 26 Rue d'Ulm 75248 Paris Cedex 05 France
- CNRS UMR3666; 75005 Paris France
- INSERM U1143; 75005 Paris France
- Institut de Chimie des Substances Naturelles; UPR2301; 1 Avenue de la Terrasse 91198 Gif-sur-Yvette Cedex France
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166
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Zacharioudakis E, Agarwal P, Bartoli A, Abell N, Kunalingam L, Bergoglio V, Xhemalce B, Miller KM, Rodriguez R. Chromatin Regulates Genome Targeting with Cisplatin. Angew Chem Int Ed Engl 2017; 56:6483-6487. [PMID: 28474855 PMCID: PMC5488169 DOI: 10.1002/anie.201701144] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/14/2017] [Indexed: 01/11/2023]
Abstract
Cisplatin derivatives can form various types of DNA lesions (DNA‐Pt) and trigger pleiotropic DNA damage responses. Here, we report a strategy to visualize DNA‐Pt with high resolution, taking advantage of a novel azide‐containing derivative of cisplatin we named APPA, a cellular pre‐extraction protocol and the labeling of DNA‐Pt by means of click chemistry in cells. Our investigation revealed that pretreating cells with the histone deacetylase (HDAC) inhibitor SAHA led to detectable clusters of DNA‐Pt that colocalized with the ubiquitin ligase RAD18 and the replication protein PCNA. Consistent with activation of translesion synthesis (TLS) under these conditions, SAHA and cisplatin cotreatment promoted focal accumulation of the low‐fidelity polymerase Polη that also colocalized with PCNA. Remarkably, these cotreatments synergistically triggered mono‐ubiquitination of PCNA and apoptosis in a RAD18‐dependent manner. Our data provide evidence for a role of chromatin in regulating genome targeting with cisplatin derivatives and associated cellular responses.
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Affiliation(s)
- Emmanouil Zacharioudakis
- Institut Curie, PSL Research University, Chemical Cell Biology Group, 26 Rue d'Ulm, 75248, Paris Cedex 05, France.,CNRS UMR3666, 75005, Paris, France.,INSERM U1143, 75005, Paris, France.,Institut de Chimie des Substances Naturelles, UPR2301, 1 Avenue de la Terrasse, 91198, Gif-sur-Yvette Cedex, France
| | - Poonam Agarwal
- Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, University of Texas at Austin, 2506 Speedway Stop A5000, Austin, TX, 78712, USA
| | - Alexandra Bartoli
- Institut Curie, PSL Research University, Chemical Cell Biology Group, 26 Rue d'Ulm, 75248, Paris Cedex 05, France.,CNRS UMR3666, 75005, Paris, France.,INSERM U1143, 75005, Paris, France.,Institut de Chimie des Substances Naturelles, UPR2301, 1 Avenue de la Terrasse, 91198, Gif-sur-Yvette Cedex, France
| | - Nathan Abell
- Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, University of Texas at Austin, 2506 Speedway Stop A5000, Austin, TX, 78712, USA
| | - Lavaniya Kunalingam
- Institut Curie, PSL Research University, Chemical Cell Biology Group, 26 Rue d'Ulm, 75248, Paris Cedex 05, France.,CNRS UMR3666, 75005, Paris, France.,INSERM U1143, 75005, Paris, France.,Institut de Chimie des Substances Naturelles, UPR2301, 1 Avenue de la Terrasse, 91198, Gif-sur-Yvette Cedex, France
| | - Valérie Bergoglio
- CRCT, University of Toulouse, INSERM, CNRS, UPS, Avenue Hubert Curien, 31037, Toulouse, France
| | - Blerta Xhemalce
- Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, University of Texas at Austin, 2506 Speedway Stop A5000, Austin, TX, 78712, USA
| | - Kyle M Miller
- Department of Molecular Biosciences, Institute of Cellular and Molecular Biology, University of Texas at Austin, 2506 Speedway Stop A5000, Austin, TX, 78712, USA
| | - Raphaël Rodriguez
- Institut Curie, PSL Research University, Chemical Cell Biology Group, 26 Rue d'Ulm, 75248, Paris Cedex 05, France.,CNRS UMR3666, 75005, Paris, France.,INSERM U1143, 75005, Paris, France.,Institut de Chimie des Substances Naturelles, UPR2301, 1 Avenue de la Terrasse, 91198, Gif-sur-Yvette Cedex, France
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167
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Andrews FH, Strahl BD, Kutateladze TG. Insights into newly discovered marks and readers of epigenetic information. Nat Chem Biol 2017; 12:662-8. [PMID: 27538025 DOI: 10.1038/nchembio.2149] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 07/11/2016] [Indexed: 02/06/2023]
Abstract
The field of chromatin biology has been advancing at an accelerated pace. Recent discoveries of previously uncharacterized sites and types of post-translational modifications (PTMs) and the identification of new sets of proteins responsible for the deposition, removal, and reading of these marks continue raising the complexity of an already exceedingly complicated biological phenomenon. In this Perspective article we examine the biological importance of new types and sites of histone PTMs and summarize the molecular mechanisms of chromatin engagement by newly discovered epigenetic readers. We also highlight the imperative role of structural insights in understanding PTM-reader interactions and discuss future directions to enhance the knowledge of PTM readout.
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Affiliation(s)
- Forest H Andrews
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, the University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, USA
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168
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Abstract
![]()
Post-translational
modifications of histones by protein methyltransferases
(PMTs) and histone demethylases (KDMs) play an important role in the
regulation of gene expression and transcription and are implicated
in cancer and many other diseases. Many of these enzymes also target
various nonhistone proteins impacting numerous crucial biological
pathways. Given their key biological functions and implications in
human diseases, there has been a growing interest in assessing these
enzymes as potential therapeutic targets. Consequently, discovering
and developing inhibitors of these enzymes has become a very active
and fast-growing research area over the past decade. In this review,
we cover the discovery, characterization, and biological application
of inhibitors of PMTs and KDMs with emphasis on key advancements in
the field. We also discuss challenges, opportunities, and future directions
in this emerging, exciting research field.
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Affiliation(s)
- H Ümit Kaniskan
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Michael L Martini
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Jian Jin
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
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169
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Precision cancer therapy is impacted by oncogene-dependent epigenome remodeling. NPJ Precis Oncol 2017. [PMID: 29872691 DOI: 10.1038/s41698‐017‐0005‐2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The cancer genome provides the blueprint for identifying oncogenic mutations driving tumor growth and these mutant proteins and pathways are the targets for precision cancer therapies. However, many oncogenes are capable of reprogramming the landscape of active portion of the genome, commonly known as the epigenome. This creates fluidity, and thereby heterogeneity, that demands consideration of this additional layer of complexity for effective therapeutic design and application. Molecular dissection of the epigenome may identify oncogene-induced, actionable vulnerabilities, broadening the spectrum of precision oncology treatments.
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170
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Liu F, Mischel PS, Cavenee WK. Precision cancer therapy is impacted by oncogene-dependent epigenome remodeling. NPJ Precis Oncol 2017; 1:1. [PMID: 29872691 PMCID: PMC5871882 DOI: 10.1038/s41698-017-0005-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 08/30/2016] [Accepted: 09/01/2016] [Indexed: 12/11/2022] Open
Abstract
The cancer genome provides the blueprint for identifying oncogenic mutations driving tumor growth and these mutant proteins and pathways are the targets for precision cancer therapies. However, many oncogenes are capable of reprogramming the landscape of active portion of the genome, commonly known as the epigenome. This creates fluidity, and thereby heterogeneity, that demands consideration of this additional layer of complexity for effective therapeutic design and application. Molecular dissection of the epigenome may identify oncogene-induced, actionable vulnerabilities, broadening the spectrum of precision oncology treatments.
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Affiliation(s)
- Feng Liu
- 1National Research Center for Translational Medicine (Shanghai), State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Paul S Mischel
- 2Ludwig Institute for Cancer Research, La Jolla, CA 92093 USA.,3Department of Pathology, UCSD School of Medicine, La Jolla, CA 92093 USA.,4Moores Cancer Center, UCSD School of Medicine, La Jolla, CA 92093 USA
| | - Webster K Cavenee
- 2Ludwig Institute for Cancer Research, La Jolla, CA 92093 USA.,4Moores Cancer Center, UCSD School of Medicine, La Jolla, CA 92093 USA.,5Department of Medicine, UCSD School of Medicine, La Jolla, CA 92093 USA
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171
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Khyzha N, Alizada A, Wilson MD, Fish JE. Epigenetics of Atherosclerosis: Emerging Mechanisms and Methods. Trends Mol Med 2017; 23:332-347. [PMID: 28291707 DOI: 10.1016/j.molmed.2017.02.004] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/13/2017] [Accepted: 02/16/2017] [Indexed: 12/26/2022]
Abstract
Atherosclerosis is a vascular pathology characterized by inflammation and plaque build-up within arterial vessel walls. Vessel occlusion, often occurring after plaque rupture, can result in myocardial and cerebral infarction. Epigenetic changes are increasingly being associated with atherosclerosis and are of interest from both therapeutic and biomarker perspectives. Emerging genomic approaches that profile DNA methylation, chromatin accessibility, post-translational histone modifications, transcription factor binding, and RNA expression in low or single cell populations are poised to enhance our spatiotemporal understanding of atherogenesis. Here, we review recent therapeutically relevant epigenetic discoveries and emerging technologies that may generate new opportunities for atherosclerosis research.
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Affiliation(s)
- Nadiya Khyzha
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Heart & Stroke Richard Lewar Centre of Excellence in Cardiovascular Research, Toronto, Canada
| | - Azad Alizada
- Heart & Stroke Richard Lewar Centre of Excellence in Cardiovascular Research, Toronto, Canada; Genetics and Genome Biology, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Michael D Wilson
- Heart & Stroke Richard Lewar Centre of Excellence in Cardiovascular Research, Toronto, Canada; Genetics and Genome Biology, Hospital for Sick Children, Toronto, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Canada.
| | - Jason E Fish
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Heart & Stroke Richard Lewar Centre of Excellence in Cardiovascular Research, Toronto, Canada.
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172
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Abstract
The organization of the chromatin structure is essential for maintaining cell-type-specific gene expression and therefore for cell identity. This structure is highly dynamic and is regulated by a large number of chromatin-associated proteins that are required for normal development and differentiation. Recurrent somatic mutations have been found with high frequency in genes coding for chromatin-associated proteins in cancer, and several of these are required for cancer maintenance. In this review, we discuss recent advances in understanding the role of chromatin-associated proteins in transcription, development, and cancer. Specifically, we focus on selected examples of proteins belonging to the histone methyltransferase, histone demethylase, or bromodomain families, for which specific small molecule inhibitors have been developed and are in either preclinical or clinical trials.
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Affiliation(s)
- Kristian Helin
- Biotech Research and Innovation Centre (BRIC),
- Centre for Epigenetics, and
- The Danish Stem Cell Center (DanStem), University of Copenhagen, 2200 Copenhagen, Denmark
| | - Saverio Minucci
- Department of Experimental Oncology,
- Drug Development Program, European Institute of Oncology, 20139 Milan, Italy
- Department of Biosciences, University of Milan, 20100 Milan, Italy
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173
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Yang C, Wang W, Liang JX, Li G, Vellaisamy K, Wong CY, Ma DL, Leung CH. A Rhodium(III)-Based Inhibitor of Lysine-Specific Histone Demethylase 1 as an Epigenetic Modulator in Prostate Cancer Cells. J Med Chem 2017; 60:2597-2603. [DOI: 10.1021/acs.jmedchem.7b00133] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Chao Yang
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University of Macau, Macau, China
| | - Wanhe Wang
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Jia-Xin Liang
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University of Macau, Macau, China
| | - Guodong Li
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University of Macau, Macau, China
| | - Kasipandi Vellaisamy
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Chun-Yuen Wong
- Department
of Biology and Chemistry, City University of Hong Kong, Tat Chee
Avenue, Kowloon, Hong Kong
SAR, China
| | - Dik-Lung Ma
- Department
of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Chung-Hang Leung
- State
Key Laboratory of Quality Research in Chinese Medicine, Institute
of Chinese Medical Sciences, University of Macau, Macau, China
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174
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Mohammad F, Weissmann S, Leblanc B, Pandey DP, Højfeldt JW, Comet I, Zheng C, Johansen JV, Rapin N, Porse BT, Tvardovskiy A, Jensen ON, Olaciregui NG, Lavarino C, Suñol M, de Torres C, Mora J, Carcaboso AM, Helin K. EZH2 is a potential therapeutic target for H3K27M-mutant pediatric gliomas. Nat Med 2017; 23:483-492. [DOI: 10.1038/nm.4293] [Citation(s) in RCA: 308] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/08/2017] [Indexed: 12/14/2022]
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175
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Leucker TM, Nomura Y, Kim JH, Bhatta A, Wang V, Wecker A, Jandu S, Santhanam L, Berkowitz D, Romer L, Pandey D. Cystathionine γ-lyase protects vascular endothelium: a role for inhibition of histone deacetylase 6. Am J Physiol Heart Circ Physiol 2017; 312:H711-H720. [PMID: 28188215 DOI: 10.1152/ajpheart.00724.2016] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 02/01/2017] [Accepted: 02/03/2017] [Indexed: 01/21/2023]
Abstract
Endothelial cystathionine γ-lyase (CSEγ) contributes to cardiovascular homeostasis, mainly through production of H2S. However, the molecular mechanisms that control CSEγ gene expression in the endothelium during cardiovascular diseases are unclear. The aim of the current study is to determine the role of specific histone deacetylases (HDACs) in the regulation of endothelial CSEγ. Reduced CSEγ mRNA expression and protein abundance were observed in human aortic endothelial cells (HAEC) exposed to oxidized LDL (OxLDL) and in aortas from atherogenic apolipoprotein E knockout (ApoE-/-) mice fed a high-fat diet compared with controls. Intact murine aortic rings exposed to OxLDL (50 μg/ml) for 24 h exhibited impaired endothelium-dependent vasorelaxation that was blocked by CSEγ overexpression or the H2S donor NaHS. CSEγ expression was upregulated by pan-HDAC inhibitors and by class II-specific HDAC inhibitors, but not by other class-specific inhibitors. The HDAC6 selective inhibitor tubacin and HDAC6-specific siRNA increased CSEγ expression and blocked OxLDL-mediated reductions in endothelial CSEγ expression and CSEγ promoter activity, indicating that HDAC6 is a specific regulator of CSEγ expression. Consistent with this finding, HDAC6 mRNA, protein expression, and activity were upregulated in OxLDL-exposed HAEC, but not in human aortic smooth muscle cells. HDAC6 protein levels in aortas from high-fat diet-fed ApoE-/- mice were comparable to those in controls, whereas HDAC6 activity was robustly upregulated. Together, our findings indicate that HDAC6 is upregulated by atherogenic stimuli via posttranslational modifications and is a critical regulator of CSEγ expression in vascular endothelium. Inhibition of HDAC6 activity may improve endothelial function and prevent or reverse the development of atherosclerosis.NEW & NOTEWORTHY Oxidative injury to endothelial cells by oxidized LDL reduced cystathionine γ-lyase (CSEγ) expression and H2S production, leading to endothelial dysfunction, which was prevented by histone deacetylase 6 (HDAC6) inhibition. Our data suggest HDAC6 as a novel therapeutic target to prevent the development of atherosclerosis.
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Affiliation(s)
- Thorsten M Leucker
- Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Yohei Nomura
- Division of Cardiothoracic Surgery, Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland; and
| | - Jae Hyung Kim
- Department of Anesthesiology and Pain Medicine, Ajou University School of Medicine, Suwon, South Korea
| | - Anil Bhatta
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Victor Wang
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Andrea Wecker
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sandeep Jandu
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lakshmi Santhanam
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Dan Berkowitz
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lewis Romer
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Deepesh Pandey
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland;
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176
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Bromberg KD, Mitchell TRH, Upadhyay AK, Jakob CG, Jhala MA, Comess KM, Lasko LM, Li C, Tuzon CT, Dai Y, Li F, Eram MS, Nuber A, Soni NB, Manaves V, Algire MA, Sweis RF, Torrent M, Schotta G, Sun C, Michaelides MR, Shoemaker AR, Arrowsmith CH, Brown PJ, Santhakumar V, Martin A, Rice JC, Chiang GG, Vedadi M, Barsyte-Lovejoy D, Pappano WN. The SUV4-20 inhibitor A-196 verifies a role for epigenetics in genomic integrity. Nat Chem Biol 2017; 13:317-324. [DOI: 10.1038/nchembio.2282] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 11/23/2016] [Indexed: 12/30/2022]
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177
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Pietanza MC, Zimmerman S, Peters S, Curran WJ. Seeking New Approaches to Patients With Small Cell Lung Cancer. Am Soc Clin Oncol Educ Book 2017; 35:e477-82. [PMID: 27249756 DOI: 10.1200/edbk_158710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The fundamental approach to the treatment of small cell lung cancer (SCLC) has not changed in the last several decades, with most advances being restricted to improved radiation approaches. The standard first-line chemotherapy regimen in the United States and Europe remains cisplatin or carboplatin plus etoposide in the treatment of limited stage (LS-SCLC) and extensive stage (ES-SCLC) disease. Radiation therapy is administered to those patients with LS-SCLC, whose cancer is confined to the chest in a single tolerable radiation field. This article will summarize a number of exciting observations regarding the biology of SCLC and how a deeper understanding of newly integrated targets and target pathways may lead to new and better therapeutic approaches in the near future.
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Affiliation(s)
- Marie Catherine Pietanza
- From the Merck Research Laboratories, Rahway, NJ; Department of Oncology, HFR Fribourg, Fribourg, Switzerland; Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland; Winship Cancer Institute of Emory University, Atlanta, GA
| | - Stefan Zimmerman
- From the Merck Research Laboratories, Rahway, NJ; Department of Oncology, HFR Fribourg, Fribourg, Switzerland; Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland; Winship Cancer Institute of Emory University, Atlanta, GA
| | - Solange Peters
- From the Merck Research Laboratories, Rahway, NJ; Department of Oncology, HFR Fribourg, Fribourg, Switzerland; Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland; Winship Cancer Institute of Emory University, Atlanta, GA
| | - Walter J Curran
- From the Merck Research Laboratories, Rahway, NJ; Department of Oncology, HFR Fribourg, Fribourg, Switzerland; Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland; Winship Cancer Institute of Emory University, Atlanta, GA
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178
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Hess J. Predictive Factors for Outcome and Quality of Life in HPV-Positive and HPV-Negative HNSCC. Recent Results Cancer Res 2017; 206:233-242. [PMID: 27699543 DOI: 10.1007/978-3-319-43580-0_18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Infection with high-risk types of the human papilloma virus (HPV) is an etiological risk factor for oropharyngeal squamous cell carcinoma (OPSCC) and associated with a better response to therapy and improved survival. A better understanding of the molecular principles underlying the differences in clinical behavior could pave the way to establish more effective and less toxic therapy for HPV-positive OPSCC and their HPV-negative counterparts. Compelling experimental evidence demonstrates that extensive global reprogramming of epigenetic profiles is as important as genetic mutations during neoplastic transformation and malignant progression, including HPV-positive OPSCC. In this chapter, the current knowledge on HPV-related alterations in DNA methylation, histone modification, and chromosome remodeling will be summarized and assessment of cancer-related profiles will be discussed as a valuable tool to gain important diagnostic or prognostic information for therapeutic decision-making and clinical management of HNSCC patients.
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Affiliation(s)
- Jochen Hess
- Department of Otolaryngology, Head and Neck Surgery, University Hospital and Research Group Molecular Mechanisms of Head and Neck Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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179
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Comet I, Riising EM, Leblanc B, Helin K. Maintaining cell identity: PRC2-mediated regulation of transcription and cancer. Nat Rev Cancer 2016; 16:803-810. [PMID: 27658528 DOI: 10.1038/nrc.2016.83] [Citation(s) in RCA: 316] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Enhancer of zeste homologue 2 (EZH2), the catalytic subunit of Polycomb repressive complex 2 (PRC2), has attracted broad research attention in the past few years because of its involvement in the development and maintenance of many types of cancer and the use of specific EZH2 inhibitors in clinical trials. Several observations show that PRC2 can have both oncogenic and tumour-suppressive functions. We propose that these apparently opposing roles of PRC2 in cancer are a consequence of the molecular function of the complex in maintaining, rather than specifying, the transcriptional repression state of its several thousand target genes.
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Affiliation(s)
- Itys Comet
- Biotech Research and Innovation Centre (BRIC) and the Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Eva M Riising
- Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Benjamin Leblanc
- Biotech Research and Innovation Centre (BRIC) and the Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
- The Danish Stem Cell Center (Danstem), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC) and the Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
- The Danish Stem Cell Center (Danstem), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
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180
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Investigation of EZH2 pathways for novel epigenetic treatment strategies in oropharyngeal cancer. J Otolaryngol Head Neck Surg 2016; 45:54. [PMID: 27793210 PMCID: PMC5084374 DOI: 10.1186/s40463-016-0168-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 10/21/2016] [Indexed: 12/22/2022] Open
Abstract
Background In recent decades, the incidence of oropharyngeal squamous cell carcinoma (OPSCC) has been rising worldwide as a result of increasing oncogenic human papillomavirus (HPV) infections in the oropharynx. EZH2 is an epigenetic regulatory protein associated with tumor aggressiveness and negative survival outcomes in several human cancers. We aimed to determine the role of EZH2 as a potential therapeutic epigenetic target in HPV-positive and negative OPSCC. Methods The expression of EZH2 was measured by immunohistochemistry (IHC) and droplet digital PCR (ddPCR) in 2 HPV-positive and 2 HPV-negative cell lines. The cell lines were then cultured and treated with one of 3 EZH2 epigenetic inhibitors (3-deazaneplanocin A, GSK-343 and EPZ005687) or DMSO (control). Following 2, 4 and 7 days of treatment, cells were analyzed and compared by gene expression, cell survival and proliferation assays. Results EZH2 targeting resulted in greater inhibition of growth and survival in HPV-positive compared to HPV-negative cells lines. The expression profile of genes important in OPSCC also differed according to HPV-positivity for Ki67, CCND1, MET and PTEN/PIK3CA, but remained unchanged for EGFR, CDKN2A and p53. Conclusion Inhibition of EZH2 has anti-tumorigenic effects on OPSCC cells in culture that is more pronounced in HPV-positive cell lines. EZH2 is a promising epigenetic target for the treatment of OPSCC.
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181
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Zhen CY, Tatavosian R, Huynh TN, Duc HN, Das R, Kokotovic M, Grimm JB, Lavis LD, Lee J, Mejia FJ, Li Y, Yao T, Ren X. Live-cell single-molecule tracking reveals co-recognition of H3K27me3 and DNA targets polycomb Cbx7-PRC1 to chromatin. eLife 2016; 5. [PMID: 27723458 PMCID: PMC5056789 DOI: 10.7554/elife.17667] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/29/2016] [Indexed: 12/11/2022] Open
Abstract
The Polycomb PRC1 plays essential roles in development and disease pathogenesis. Targeting of PRC1 to chromatin is thought to be mediated by the Cbx family proteins (Cbx2/4/6/7/8) binding to histone H3 with a K27me3 modification (H3K27me3). Despite this prevailing view, the molecular mechanisms of targeting remain poorly understood. Here, by combining live-cell single-molecule tracking (SMT) and genetic engineering, we reveal that H3K27me3 contributes significantly to the targeting of Cbx7 and Cbx8 to chromatin, but less to Cbx2, Cbx4, and Cbx6. Genetic disruption of the complex formation of PRC1 facilitates the targeting of Cbx7 to chromatin. Biochemical analyses uncover that the CD and AT-hook-like (ATL) motif of Cbx7 constitute a functional DNA-binding unit. Live-cell SMT of Cbx7 mutants demonstrates that Cbx7 is targeted to chromatin by co-recognizing of H3K27me3 and DNA. Our data suggest a novel hierarchical cooperation mechanism by which histone modifications and DNA coordinate to target chromatin regulatory complexes. DOI:http://dx.doi.org/10.7554/eLife.17667.001
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Affiliation(s)
- Chao Yu Zhen
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Roubina Tatavosian
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Thao Ngoc Huynh
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Huy Nguyen Duc
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Raibatak Das
- Department of Integrative Biology, University of Colorado Denver, Denver, United States
| | - Marko Kokotovic
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Jun Lee
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Frances J Mejia
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Yang Li
- Department of Chemistry, University of Colorado Denver, Denver, United States
| | - Tingting Yao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Xiaojun Ren
- Department of Chemistry, University of Colorado Denver, Denver, United States
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182
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Seol JH, Song TY, Oh SE, Jo C, Choi A, Kim B, Park J, Hong S, Song I, Jung KY, Yang JH, Park H, Ahn JH, Han JW, Cho EJ. Identification of small molecules that inhibit the histone chaperone Asf1 and its chromatin function. BMB Rep 2016; 48:685-90. [PMID: 26058396 PMCID: PMC4791324 DOI: 10.5483/bmbrep.2015.48.12.063] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Indexed: 12/01/2022] Open
Abstract
The eukaryotic genome is packed into chromatin, which is important for the genomic integrity and gene regulation. Chromatin structures are maintained through assembly and disassembly of nucleosomes catalyzed by histone chaperones. Asf1 (anti-silencing function 1) is a highly conserved histone chaperone that mediates histone transfer on/off DNA and promotes histone H3 lysine 56 acetylation at globular core domain of histone H3. To elucidate the role of Asf1 in the modulation of chromatin structure, we screened and identified small molecules that inhibit Asf1 and H3K56 acetylation without affecting other histone modifications. These pyrimidine-2,4,6-trione derivative molecules inhibited the nucleosome assembly mediated by Asf1 in vitro, and reduced the H3K56 acetylation in HeLa cells. Furthermore, production of HSV viral particles was reduced by these compounds. As Asf1 is implicated in genome integrity, cell proliferation, and cancer, current Asf1 inhibitor molecules may offer an opportunity for the therapeutic development for treatment of diseases. [BMB Reports 2015; 48(12): 685-690]
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Affiliation(s)
- Ja-Hwan Seol
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Tae-Yang Song
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Se Eun Oh
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea
| | - Chanhee Jo
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Ahreum Choi
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Byungho Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Jinyoung Park
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Suji Hong
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Ilrang Song
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Kwan Young Jung
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Jae-Hyun Yang
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Hwangseo Park
- Department of Bioscience and Biotechnology, Sejong University, Seoul 05006, Korea
| | - Jin-Hyun Ahn
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea
| | - Jeung-Whan Han
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Eun-Jung Cho
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
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183
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Rossi A, Ferrari KJ, Piunti A, Jammula S, Chiacchiera F, Mazzarella L, Scelfo A, Pelicci PG, Pasini D. Maintenance of leukemic cell identity by the activity of the Polycomb complex PRC1 in mice. SCIENCE ADVANCES 2016; 2:e1600972. [PMID: 27730210 PMCID: PMC5055382 DOI: 10.1126/sciadv.1600972] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 08/24/2016] [Indexed: 06/01/2023]
Abstract
Leukemia is a complex heterogeneous disease often driven by the expression of oncogenic fusion proteins with different molecular and biochemical properties. Whereas several fusion proteins induce leukemogenesis by activating Hox gene expression (Hox-activating fusions), others impinge on different pathways that do not involve the activation of Hox genes (non-Hox-activating fusions). It has been postulated that one of the main oncogenic properties of the HOXA9 transcription factor is its ability to control the expression of the p16/p19 tumor suppressor locus (Cdkn2a), thereby compensating Polycomb-mediated repression, which is dispensable for leukemias induced by Hox-activating fusions. We show, by genetically depleting the H2A ubiquitin ligase subunits of the Polycomb repressive complex 1 (PRC1), Ring1a and Ring1b, that Hoxa9 activation cannot repress Cdkn2a expression in the absence of PRC1 and its dependent deposition of H2AK119 monoubiquitination (H2AK119Ub). This demonstrates the essential role of PRC1 activity in supporting the oncogenic potential of Hox-activating fusion proteins. By combining genetic tools with genome-wide location and transcription analyses, we further show that PRC1 activity is required for the leukemogenic potential of both Hox-activating and non-Hox-activating fusions, thus preventing the differentiation of leukemic cells independently of the expression of the Cdkn2a locus. Overall, our results genetically demonstrate that PRC1 activity and the deposition of H2AK119Ub are critical factors that maintain the undifferentiated identity of cancer cells, positively sustaining the progression of different types of leukemia.
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Affiliation(s)
- Alessandra Rossi
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Karin J. Ferrari
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Andrea Piunti
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - SriGanesh Jammula
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Fulvio Chiacchiera
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Luca Mazzarella
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Andrea Scelfo
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milan, Italy
| | - Diego Pasini
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
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184
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Yao X, Xing M, Ooi WF, Tan P, Teh BT. Epigenomic Consequences of Coding and Noncoding Driver Mutations. Trends Cancer 2016; 2:585-605. [PMID: 28741489 DOI: 10.1016/j.trecan.2016.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/30/2016] [Accepted: 09/02/2016] [Indexed: 12/27/2022]
Abstract
Chromatin alterations are integral to the pathogenic process of cancer, as demonstrated by recent discoveries of frequent mutations in chromatin-modifier genes and aberrant DNA methylation states in different cancer types. Progress is being made on elucidating how chromatin alterations, and how proteins catalyzing these alterations, mechanistically contribute to tissue-specific tumorigenesis. In parallel, technologies enabling the genome-wide profiling of histone modifications have revealed the existence of noncoding driver genetic alterations in cancer. In this review, we survey the current knowledge of coding and noncoding cancer drivers, and discuss their impact on the chromatin landscape. Translational implications of these findings for novel cancer therapies are also presented.
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Affiliation(s)
- Xiaosai Yao
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Manjie Xing
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 5 Lower Kent Ridge Road, Singapore 119074, Singapore; Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Wen Fong Ooi
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Patrick Tan
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; National Cancer Centre, 11 Hospital Drive, Singapore 169610, Singapore; Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, #12-01, Singapore 117599, Singapore; SingHealth/Duke-NUS Precision Medicine Institute, Singapore 168752, Singapore.
| | - Bin Tean Teh
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; National Cancer Centre, 11 Hospital Drive, Singapore 169610, Singapore; Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, #12-01, Singapore 117599, Singapore; SingHealth/Duke-NUS Precision Medicine Institute, Singapore 168752, Singapore; Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673.
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185
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Kung PP, Rui E, Bergqvist S, Bingham P, Braganza J, Collins M, Cui M, Diehl W, Dinh D, Fan C, Fantin VR, Gukasyan HJ, Hu W, Huang B, Kephart S, Krivacic C, Kumpf RA, Li G, Maegley KA, McAlpine I, Nguyen L, Ninkovic S, Ornelas M, Ryskin M, Scales S, Sutton S, Tatlock J, Verhelle D, Wang F, Wells P, Wythes M, Yamazaki S, Yip B, Yu X, Zehnder L, Zhang WG, Rollins RA, Edwards M. Design and Synthesis of Pyridone-Containing 3,4-Dihydroisoquinoline-1(2H)-ones as a Novel Class of Enhancer of Zeste Homolog 2 (EZH2) Inhibitors. J Med Chem 2016; 59:8306-25. [DOI: 10.1021/acs.jmedchem.6b00515] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Michael Ryskin
- Pfizer Global Research and Development, 401 North Middletown Road, Pearl River, New York 10965, United States
| | | | | | | | | | | | | | | | | | | | | | | | - Wei-Guo Zhang
- Pfizer Global Research and Development, 401 North Middletown Road, Pearl River, New York 10965, United States
| | - Robert A. Rollins
- Pfizer Global Research and Development, 401 North Middletown Road, Pearl River, New York 10965, United States
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186
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Banelli B, Carra E, Barbieri F, Würth R, Parodi F, Pattarozzi A, Carosio R, Forlani A, Allemanni G, Marubbi D, Florio T, Daga A, Romani M. The histone demethylase KDM5A is a key factor for the resistance to temozolomide in glioblastoma. Cell Cycle 2016; 14:3418-29. [PMID: 26566863 DOI: 10.1080/15384101.2015.1090063] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Notwithstanding current multimodal treatment, including surgery, radiotherapy and chemotherapy with temozolomide (TMZ), median survival of glioblastoma (GBM) patients is about 14 months, due to the rapid emergence of cell clones resistant to treatment. Therefore, understanding the mechanisms underlying chemoresistance is mandatory to improve treatments' outcome. We generated TMZ resistant cells (TMZ-R) from a GBM cell line and from cancer stem cell-enriched cultures isolated from human GBMs. We demonstrated that TMZ resistance is partially reverted by "drug wash-out" suggesting the contribution of epigenetic mechanisms in drug resistance and supporting the possibility of TMZ rechallenge in GBM patients after prior drug exposure. The expression of histone lysine demethylase genes (KDMs) was increased in TMZ-R cells compared to parental cells, and TMZ resistance or restored sensitivity was mimicked by over-expressing or inactivating KDM5A. Methylation and expression of O6-methylguanine-DNA methyltransferase (MGMT) and drug efflux mechanisms were not altered in TMZ-R cells compared to parental TMZ sensitive cells. TMZ-R cells transiently acquired morphologic and molecular characteristics of differentiated tumor cells, features that were lost after drug wash-out. In conclusion, we demonstrated that treatment-induced TMZ resistance in GBM involves epigenetic mechanisms in a subset of slow-cycling and transiently partially differentiated cells that escape drug cytotoxicity, overcome G2 checkpoint and sustain clonal growth. We found that TMZ-R cells are sensitive to histone deacethylase inhibitors (HDACi) that synergize with TMZ. This strong synergism could be exploited to develop novel combined adjuvant therapies for this rapidly progressing and invariably lethal cancer.
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Affiliation(s)
- Barbara Banelli
- a Laboratory of Tumor Epigenetics; IRCCS AOU San Martino - IST ; Genova , Italy
| | - Elisa Carra
- b Laboratory of Regenerative Medicine; IRCCS AOU San Martino - IST ; Genova , Italy
| | - Federica Barbieri
- c Section of Pharmacology ; Department of Internal Medicine and Center of Excellence for Biomedical Research (CEBR); University of Genova ; Genova , Italy
| | - Roberto Würth
- c Section of Pharmacology ; Department of Internal Medicine and Center of Excellence for Biomedical Research (CEBR); University of Genova ; Genova , Italy
| | - Federica Parodi
- a Laboratory of Tumor Epigenetics; IRCCS AOU San Martino - IST ; Genova , Italy
| | - Alessandra Pattarozzi
- c Section of Pharmacology ; Department of Internal Medicine and Center of Excellence for Biomedical Research (CEBR); University of Genova ; Genova , Italy
| | - Roberta Carosio
- a Laboratory of Tumor Epigenetics; IRCCS AOU San Martino - IST ; Genova , Italy
| | - Alessandra Forlani
- a Laboratory of Tumor Epigenetics; IRCCS AOU San Martino - IST ; Genova , Italy
| | - Giorgio Allemanni
- a Laboratory of Tumor Epigenetics; IRCCS AOU San Martino - IST ; Genova , Italy
| | - Daniela Marubbi
- b Laboratory of Regenerative Medicine; IRCCS AOU San Martino - IST ; Genova , Italy.,d Department of Experimental Medicine (DIMES) ; University of Genova ; Genova , Italy
| | - Tullio Florio
- c Section of Pharmacology ; Department of Internal Medicine and Center of Excellence for Biomedical Research (CEBR); University of Genova ; Genova , Italy
| | - Antonio Daga
- b Laboratory of Regenerative Medicine; IRCCS AOU San Martino - IST ; Genova , Italy
| | - Massimo Romani
- a Laboratory of Tumor Epigenetics; IRCCS AOU San Martino - IST ; Genova , Italy
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187
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Initiation of diverse epigenetic states during nuclear programming of the Drosophila body plan. Proc Natl Acad Sci U S A 2016; 113:8735-40. [PMID: 27439862 DOI: 10.1073/pnas.1516450113] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Epigenetic patterns of histone modifications contribute to the maintenance of tissue-specific gene expression. Here, we show that such modifications also accompany the specification of cell identities by the NF-κB transcription factor Dorsal in the precellular Drosophila embryo. We provide evidence that the maternal pioneer factor, Zelda, is responsible for establishing poised RNA polymerase at Dorsal target genes before Dorsal-mediated zygotic activation. At the onset of cell specification, Dorsal recruits the CBP/p300 coactivator to the regulatory regions of defined target genes in the presumptive neuroectoderm, resulting in their histone acetylation and transcriptional activation. These genes are inactive in the mesoderm due to transcriptional quenching by the Snail repressor, which precludes recruitment of CBP and prevents histone acetylation. By contrast, inactivation of the same enhancers in the dorsal ectoderm is associated with Polycomb-repressed H3K27me3 chromatin. Thus, the Dorsal morphogen gradient produces three distinct histone signatures including two modes of transcriptional repression, active repression (hypoacetylation), and inactivity (H3K27me3). Whereas histone hypoacetylation is associated with a poised polymerase, H3K27me3 displaces polymerase from chromatin. Our results link different modes of RNA polymerase regulation to separate epigenetic patterns and demonstrate that developmental determinants orchestrate differential chromatin states, providing new insights into the link between epigenetics and developmental patterning.
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188
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Torigata K, Daisuke O, Mukai S, Hatanaka A, Ohka F, Motooka D, Nakamura S, Ohkawa Y, Yabuta N, Kondo Y, Nojima H. LATS2 Positively Regulates Polycomb Repressive Complex 2. PLoS One 2016; 11:e0158562. [PMID: 27434182 PMCID: PMC4951031 DOI: 10.1371/journal.pone.0158562] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/19/2016] [Indexed: 11/19/2022] Open
Abstract
LATS2, a pivotal Ser/Thr kinase of the Hippo pathway, plays important roles in many biological processes. LATS2 also function in Hippo-independent pathway, including mitosis, DNA damage response and epithelial to mesenchymal transition. However, the physiological relevance and molecular basis of these LATS2 functions remain obscure. To understand novel functions of LATS2, we constructed a LATS2 knockout HeLa-S3 cell line using TAL-effector nuclease (TALEN). Integrated omics profiling of this cell line revealed that LATS2 knockout caused genome-wide downregulation of Polycomb repressive complex 2 (PRC2) and H3K27me3. Cell-cycle analysis revealed that downregulation of PRC2 was not due to cell cycle aberrations caused by LATS2 knockout. Not LATS1, a homolog of LATS2, but LATS2 bound PRC2 on chromatin and phosphorylated it. LATS2 positively regulates histone methyltransferase activity of PRC2 and their expression at both the mRNA and protein levels. Our findings reveal a novel signal upstream of PRC2, and provide insight into the crucial role of LATS2 in coordinating the epigenome through regulation of PRC2.
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Affiliation(s)
- Kosuke Torigata
- Department of Molecular Genetics, Research Institute for Microbial Diseases, Osaka University, Suita City, Osaka, Japan
| | - Okuzaki Daisuke
- Department of Molecular Genetics, Research Institute for Microbial Diseases, Osaka University, Suita City, Osaka, Japan
- DNA-chip Development Center for Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, Suita City, Osaka, Japan
| | - Satomi Mukai
- Department of Molecular Genetics, Research Institute for Microbial Diseases, Osaka University, Suita City, Osaka, Japan
| | - Akira Hatanaka
- Department of Epigenomics, Nagoya City University Graduate School of Medical Sciences, Nagoya City, Aichi, Japan
| | - Fumiharu Ohka
- Department of Epigenomics, Nagoya City University Graduate School of Medical Sciences, Nagoya City, Aichi, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita City, Osaka, Japan
| | - Shota Nakamura
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita City, Osaka, Japan
| | - Yasuyuki Ohkawa
- Department of Advanced Medical Initiatives, Graduate School of Medical Sciences, Kyushu University, Fukuoka City, Fukuoka, Japan
| | - Norikazu Yabuta
- Department of Molecular Genetics, Research Institute for Microbial Diseases, Osaka University, Suita City, Osaka, Japan
| | - Yutaka Kondo
- Department of Epigenomics, Nagoya City University Graduate School of Medical Sciences, Nagoya City, Aichi, Japan
| | - Hiroshi Nojima
- Department of Molecular Genetics, Research Institute for Microbial Diseases, Osaka University, Suita City, Osaka, Japan
- DNA-chip Development Center for Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, Suita City, Osaka, Japan
- * E-mail:
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189
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Kim H, Ramirez CN, Su ZY, Kong ANT. Epigenetic modifications of triterpenoid ursolic acid in activating Nrf2 and blocking cellular transformation of mouse epidermal cells. J Nutr Biochem 2016; 33:54-62. [PMID: 27260468 PMCID: PMC4895202 DOI: 10.1016/j.jnutbio.2015.09.014] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 09/15/2015] [Accepted: 09/17/2015] [Indexed: 01/10/2023]
Abstract
Ursolic acid (UA), a well-known natural triterpenoid found in abundance in blueberries, cranberries and apple peels, has been reported to possess many beneficial health effects. These effects include anticancer activity in various cancers, such as skin cancer. Skin cancer is the most common cancer in the world. Nuclear factor E2-related factor 2 (Nrf2) is a master regulator of antioxidative stress response with anticarcinogenic activity against UV- and chemical-induced tumor formation in the skin. Recent studies show that epigenetic modifications of Nrf2 play an important role in cancer prevention. However, the epigenetic impact of UA on Nrf2 signaling remains poorly understood in skin cancer. In this study, we investigated the epigenetic effects of UA on mouse epidermal JB6 P+ cells. UA inhibited cellular transformation by 12-O-tetradecanoylphorbol-13-acetate at a concentration at which the cytotoxicity was no more than 25%. Under this condition, UA induced the expression of the Nrf2-mediated detoxifying/antioxidant enzymes heme oxygenase-1, NAD(P)H:quinone oxidoreductase 1 and UDP-glucuronosyltransferase 1A1. DNA methylation analysis revealed that UA demethylated the first 15 CpG sites of the Nrf2 promoter region, which correlated with the reexpression of Nrf2. Furthermore, UA reduced the expression of epigenetic modifying enzymes, including the DNA methyltransferases DNMT1 and DNMT3a and the histone deacetylases (HDACs) HDAC1, HDAC2, HDAC3 and HDAC8 (Class I) and HDAC6 and HDAC7 (Class II), and HDAC activity. Taken together, these results suggest that the epigenetic effects of the triterpenoid UA could potentially contribute to its beneficial effects, including the prevention of skin cancer.
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Affiliation(s)
- Hyuck Kim
- Center for Cancer Prevention Research, Ernest Mario School of Pharmacy, Piscataway, NJ 08854, USA; Department of Pharmaceutics, Earnest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Christina N Ramirez
- Department of Pharmaceutics, Earnest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Cellular and Molecular Pharmacology Program, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Zheng-Yuan Su
- Department of Bioscience Technology, Chung Yuan Christian University, Taoyuan City, Taiwan (Republic of China) 32023
| | - Ah-Ng Tony Kong
- Center for Cancer Prevention Research, Ernest Mario School of Pharmacy, Piscataway, NJ 08854, USA; Department of Pharmaceutics, Earnest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
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190
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Richter K, Kietzmann T. Reactive oxygen species and fibrosis: further evidence of a significant liaison. Cell Tissue Res 2016; 365:591-605. [PMID: 27345301 PMCID: PMC5010605 DOI: 10.1007/s00441-016-2445-3] [Citation(s) in RCA: 211] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 06/02/2016] [Indexed: 02/06/2023]
Abstract
Age-related diseases such as obesity, diabetes, non-alcoholic fatty liver disease, chronic kidney disease and cardiomyopathy are frequently associated with fibrosis. Work within the last decade has improved our understanding of the pathophysiological mechanisms contributing to fibrosis development. In particular, oxidative stress and the antioxidant system appear to be crucial modulators of processes such as transforming growth factor-β1 (TGF-β1) signalling, metabolic homeostasis and chronic low-grade inflammation, all of which play important roles in fibrosis development and persistence. In the current review, we discuss the connections between reactive oxygen species, antioxidant enzymes and TGF-β1 signalling, together with functional consequences, reflecting a concept of redox-fibrosis that can be targeted in future therapies. ᅟ ![]()
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Affiliation(s)
- Kati Richter
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Aapistie 7A, FI-90230, Oulu, Finland
| | - Thomas Kietzmann
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Aapistie 7A, FI-90230, Oulu, Finland.
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191
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Walport LJ, Hopkinson RJ, Chowdhury R, Schiller R, Ge W, Kawamura A, Schofield CJ. Arginine demethylation is catalysed by a subset of JmjC histone lysine demethylases. Nat Commun 2016; 7:11974. [PMID: 27337104 PMCID: PMC4931022 DOI: 10.1038/ncomms11974] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 05/17/2016] [Indexed: 12/11/2022] Open
Abstract
While the oxygen-dependent reversal of lysine N(ɛ)-methylation is well established, the existence of bona fide N(ω)-methylarginine demethylases (RDMs) is controversial. Lysine demethylation, as catalysed by two families of lysine demethylases (the flavin-dependent KDM1 enzymes and the 2-oxoglutarate- and oxygen-dependent JmjC KDMs, respectively), proceeds via oxidation of the N-methyl group, resulting in the release of formaldehyde. Here we report detailed biochemical studies clearly demonstrating that, in purified form, a subset of JmjC KDMs can also act as RDMs, both on histone and non-histone fragments, resulting in formaldehyde release. RDM catalysis is studied using peptides of wild-type sequences known to be arginine-methylated and sequences in which the KDM's methylated target lysine is substituted for a methylated arginine. Notably, the preferred sequence requirements for KDM and RDM activity vary even with the same JmjC enzymes. The demonstration of RDM activity by isolated JmjC enzymes will stimulate efforts to detect biologically relevant RDM activity.
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Affiliation(s)
- Louise J. Walport
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Richard J. Hopkinson
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Rasheduzzaman Chowdhury
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Rachel Schiller
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Wei Ge
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Akane Kawamura
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Christopher J. Schofield
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
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192
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Johnson A, Morosini D, Vergilio JA, Yelensky R, Rosenzweig M, Khaira D, Ali SM, Palma N, Lipson D, Juhn F, Erlich R, Stephens PJ, Ross JS, Miller VA, Wang K. Unique genomic features in adolescent and young adult, as compared to older adult, non-Hodgkin lymphoma and potential therapeutic targets. Br J Haematol 2016; 178:640-642. [PMID: 27291498 DOI: 10.1111/bjh.14157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | | | | | | | | | | | - Siraj M Ali
- Foundation Medicine, Inc., Cambridge, MA, USA
| | - Norma Palma
- Foundation Medicine, Inc., Cambridge, MA, USA
| | | | - Frank Juhn
- Foundation Medicine, Inc., Cambridge, MA, USA
| | | | | | - Jeffrey S Ross
- Foundation Medicine, Inc., Cambridge, MA, USA.,Albany Medical College, Albany, NY, USA
| | | | - Kai Wang
- Foundation Medicine, Inc., Cambridge, MA, USA.,Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
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193
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Nwosu ZC, Alborzinia H, Wölfl S, Dooley S, Liu Y. Evolving Insights on Metabolism, Autophagy, and Epigenetics in Liver Myofibroblasts. Front Physiol 2016; 7:191. [PMID: 27313533 PMCID: PMC4887492 DOI: 10.3389/fphys.2016.00191] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 05/12/2016] [Indexed: 12/14/2022] Open
Abstract
Liver myofibroblasts (MFB) are crucial mediators of extracellular matrix (ECM) deposition in liver fibrosis. They arise mainly from hepatic stellate cells (HSCs) upon a process termed “activation.” To a lesser extent, and depending on the cause of liver damage, portal fibroblasts, mesothelial cells, and fibrocytes may also contribute to the MFB population. Targeting MFB to reduce liver fibrosis is currently an area of intense research. Unfortunately, a clog in the wheel of antifibrotic therapies is the fact that although MFB are known to mediate scar formation, and participate in liver inflammatory response, many of their molecular portraits are currently unknown. In this review, we discuss recent understanding of MFB in health and diseases, focusing specifically on three evolving research fields: metabolism, autophagy, and epigenetics. We have emphasized on therapeutic prospects where applicable and mentioned techniques for use in MFB studies. Subsequently, we highlighted uncharted territories in MFB research to help direct future efforts aimed at bridging gaps in current knowledge.
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Affiliation(s)
- Zeribe C Nwosu
- Molecular Hepatology Section, Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg Mannheim, Germany
| | - Hamed Alborzinia
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg Heidelberg, Germany
| | - Stefan Wölfl
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg Heidelberg, Germany
| | - Steven Dooley
- Molecular Hepatology Section, Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg Mannheim, Germany
| | - Yan Liu
- Molecular Hepatology Section, Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg Mannheim, Germany
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194
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Morera L, Lübbert M, Jung M. Targeting histone methyltransferases and demethylases in clinical trials for cancer therapy. Clin Epigenetics 2016; 8:57. [PMID: 27222667 PMCID: PMC4877953 DOI: 10.1186/s13148-016-0223-4] [Citation(s) in RCA: 291] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/04/2016] [Indexed: 12/13/2022] Open
Abstract
The term epigenetics is defined as heritable changes in gene expression that are not due to alterations of the DNA sequence. In the last years, it has become more and more evident that dysregulated epigenetic regulatory processes have a central role in cancer onset and progression. In contrast to DNA mutations, epigenetic modifications are reversible and, hence, suitable for pharmacological interventions. Reversible histone methylation is an important process within epigenetic regulation, and the investigation of its role in cancer has led to the identification of lysine methyltransferases and demethylases as promising targets for new anticancer drugs. In this review, we describe those enzymes and their inhibitors that have already reached the first stages of clinical trials in cancer therapy, namely the histone methyltransferases DOT1L and EZH2 as well as the demethylase LSD1.
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Affiliation(s)
- Ludovica Morera
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Michael Lübbert
- Department of Hematology and Oncology, University of Freiburg Medical Center, Hugstetter Straße 55, 79106 Freiburg, Germany ; German Cancer Consortium (DKTK), Freiburg, Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-University Freiburg, Albertstraße 25, 79104 Freiburg, Germany ; German Cancer Consortium (DKTK), Freiburg, Germany
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195
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Jullien D, Vignard J, Fedor Y, Béry N, Olichon A, Crozatier M, Erard M, Cassard H, Ducommun B, Salles B, Mirey G. Chromatibody, a novel non-invasive molecular tool to explore and manipulate chromatin in living cells. J Cell Sci 2016; 129:2673-83. [PMID: 27206857 PMCID: PMC4958301 DOI: 10.1242/jcs.183103] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 05/13/2016] [Indexed: 12/25/2022] Open
Abstract
Chromatin function is involved in many cellular processes, its visualization or modification being essential in many developmental or cellular studies. Here, we present the characterization of chromatibody, a chromatin-binding single-domain, and explore its use in living cells. This non-intercalating tool specifically binds the heterodimer of H2A–H2B histones and displays a versatile reactivity, specifically labeling chromatin from yeast to mammals. We show that this genetically encoded probe, when fused to fluorescent proteins, allows non-invasive real-time chromatin imaging. Chromatibody is a dynamic chromatin probe that can be modulated. Finally, chromatibody is an efficient tool to target an enzymatic activity to the nucleosome, such as the DNA damage-dependent H2A ubiquitylation, which can modify this epigenetic mark at the scale of the genome and result in DNA damage signaling and repair defects. Taken together, these results identify chromatibody as a universal non-invasive tool for either in vivo chromatin imaging or to manipulate the chromatin landscape. Summary: Chromatibody is a chromatin-binding single-domain antibody, derived from llama nanobodies, that can be used as a novel non-invasive molecular tool to explore and manipulate chromatin in living cells.
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Affiliation(s)
- Denis Jullien
- Toxalim, Université de Toulouse, INRA, Université de Toulouse 3 Paul Sabatier, 31027 Toulouse, France ITAV, Université de Toulouse, CNRS, UPS, 31106 Toulouse, France
| | - Julien Vignard
- Toxalim, Université de Toulouse, INRA, Université de Toulouse 3 Paul Sabatier, 31027 Toulouse, France
| | - Yoann Fedor
- Toxalim, Université de Toulouse, INRA, Université de Toulouse 3 Paul Sabatier, 31027 Toulouse, France
| | - Nicolas Béry
- CRCT-UMR1037, Université de Toulouse, INSERM, 31037 Toulouse, France
| | - Aurélien Olichon
- CRCT-UMR1037, Université de Toulouse, INSERM, 31037 Toulouse, France
| | | | - Monique Erard
- IPBS-UMR5089, Université de Toulouse, CNRS, 31077 Toulouse, France
| | - Hervé Cassard
- IHAP, Université de Toulouse, INRA, ENVT, 31076 Toulouse, France
| | - Bernard Ducommun
- ITAV, Université de Toulouse, CNRS, UPS, 31106 Toulouse, France CHU de Toulouse, 31106 Toulouse, France
| | - Bernard Salles
- Toxalim, Université de Toulouse, INRA, Université de Toulouse 3 Paul Sabatier, 31027 Toulouse, France
| | - Gladys Mirey
- Toxalim, Université de Toulouse, INRA, Université de Toulouse 3 Paul Sabatier, 31027 Toulouse, France
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196
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Seuter S, Neme A, Carlberg C. Epigenome-wide effects of vitamin D and their impact on the transcriptome of human monocytes involve CTCF. Nucleic Acids Res 2016; 44:4090-104. [PMID: 26715761 PMCID: PMC4872072 DOI: 10.1093/nar/gkv1519] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 12/15/2015] [Accepted: 12/19/2015] [Indexed: 11/13/2022] Open
Abstract
The physiological functions of vitamin D are mediated by its metabolite 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3) activating the transcription factor vitamin D receptor (VDR). In THP-1 human monocytes we demonstrated epigenome-wide effects of 1,25(OH)2D3 at 8979 loci with significantly modulated chromatin accessibility. Maximal chromatin opening was observed after 24 h, while after 48 h most sites closed again. The chromatin-organizing protein CTCF bound to 14% of the 1,25(OH)2D3-sensitive chromatin regions. Interestingly, 1,25(OH)2D3 affected the chromatin association of CTCF providing an additional mechanism for the epigenome-wide effects of the VDR ligand. The 1,25(OH)2D3-modulated transcriptome of THP-1 cells comprised 1284 genes, 77.5% of which responded only 24 h after stimulation. During the 1,25(OH)2D3 stimulation time course the proportion of down-regulated genes increased from 0% to 44.9% and the top-ranking physiological function of the respective genes shifted from anti-microbial response to connective tissue disorders. The integration of epigenomic and transcriptomic data identified 165 physiologically important 1,25(OH)2D3 target genes, including HTT and NOD2, whose expression can be predicted primarily from epigenomic data of their genomic loci. Taken together, a large number of 1,25(OH)2D3-triggered epigenome-wide events precede and accompany the transcriptional activation of target genes of the nuclear hormone.
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Affiliation(s)
- Sabine Seuter
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Antonio Neme
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Carsten Carlberg
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland
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197
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Song X, Zhang L, Gao T, Ye T, Zhu Y, Lei Q, Feng Q, He B, Deng H, Yu L. Selective inhibition of EZH2 by ZLD10A blocks H3K27 methylation and kills mutant lymphoma cells proliferation. Biomed Pharmacother 2016; 81:288-294. [PMID: 27261606 DOI: 10.1016/j.biopha.2016.04.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 04/08/2016] [Accepted: 04/08/2016] [Indexed: 02/05/2023] Open
Abstract
EZH2 (Enhancer of zeste homolog 2) is the catalytic subunit of the polycomb repressive complex 2 (PRC2), which is involved in repressing gene expression by methylating lysine 27 of histone H3 (H3K27) and regulates cell proliferation. EZH2 overexpression is implicated in tumorigenesis and has been a candidate oncogene in several tumor types. Recently, point mutations of EZH2 at Tyr641 and Ala677 were identified in diffuse large B cell lymphoma and follicular lymphoma, where they drive H3K27 hypertrimethylation and cancer progression. Here, we reported a novel, highly potent and selective small molecule inhibitor of EZH2, ZLD10A, which inhibited wild-type and mutant versions of EZH2 with nanomolar potency and had greater than 1000-fold selectivity against 10 other histone methyltransferases. Our results have shown that the compound suppressed global H3K27 methylation and cause the anti-proliferation effects in a concentration- and time-dependent manner in DLBCL cell lines. These results demonstrated that ZLD10A, as a novel EZH2 inhibitor, could be a potential promising agent for the treatment of EZH2 mutant lymphoma.
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Affiliation(s)
- Xuejiao Song
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Lidan Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China.
| | - Tiantao Gao
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Tinghong Ye
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Yongxia Zhu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Qian Lei
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Qiang Feng
- College of Chemistry and Life Science, Chengdu Normal University, Chengdu 611130, China
| | - Bing He
- College of Chemistry and Life Science, Chengdu Normal University, Chengdu 611130, China
| | - Hongxia Deng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Luoting Yu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China.
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Latysheva NS, Babu MM. Discovering and understanding oncogenic gene fusions through data intensive computational approaches. Nucleic Acids Res 2016; 44:4487-503. [PMID: 27105842 PMCID: PMC4889949 DOI: 10.1093/nar/gkw282] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 03/24/2016] [Indexed: 12/21/2022] Open
Abstract
Although gene fusions have been recognized as important drivers of cancer for decades, our understanding of the prevalence and function of gene fusions has been revolutionized by the rise of next-generation sequencing, advances in bioinformatics theory and an increasing capacity for large-scale computational biology. The computational work on gene fusions has been vastly diverse, and the present state of the literature is fragmented. It will be fruitful to merge three camps of gene fusion bioinformatics that appear to rarely cross over: (i) data-intensive computational work characterizing the molecular biology of gene fusions; (ii) development research on fusion detection tools, candidate fusion prioritization algorithms and dedicated fusion databases and (iii) clinical research that seeks to either therapeutically target fusion transcripts and proteins or leverages advances in detection tools to perform large-scale surveys of gene fusion landscapes in specific cancer types. In this review, we unify these different-yet highly complementary and symbiotic-approaches with the view that increased synergy will catalyze advancements in gene fusion identification, characterization and significance evaluation.
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Affiliation(s)
- Natasha S Latysheva
- MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge CB2 0QH, United Kingdom
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge CB2 0QH, United Kingdom
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199
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BRCA1 positively regulates FOXO3 expression by restricting FOXO3 gene methylation and epigenetic silencing through targeting EZH2 in breast cancer. Oncogenesis 2016; 5:e214. [PMID: 27043660 PMCID: PMC4848836 DOI: 10.1038/oncsis.2016.23] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/12/2016] [Accepted: 02/17/2016] [Indexed: 01/09/2023] Open
Abstract
BRCA1 mutation or depletion correlates with basal-like phenotype and poor prognosis in breast cancer but the underlying reason remains elusive. RNA and protein analysis of a panel of breast cancer cell lines revealed that BRCA1 deficiency is associated with downregulation of the expression of the pleiotropic tumour suppressor FOXO3. Knockdown of BRCA1 by small interfering RNA (siRNA) resulted in downregulation of FOXO3 expression in the BRCA1-competent MCF-7, whereas expression of BRCA1 restored FOXO3 expression in BRCA1-defective HCC70 and MDA-MB-468 cells, suggesting a role of BRCA1 in the control of FOXO3 expression. Treatment of HCC70 and MDA-MB-468 cells with either the DNA methylation inhibitor 5-aza-2'-deoxycitydine, the N-methyltransferase enhancer of zeste homologue 2 (EZH2) inhibitor GSK126 or EZH2 siRNA induced FOXO3 mRNA and protein expression, but had no effect on the BRCA1-competent MCF-7 cells. Chromatin immunoprecipitation (ChIP) analysis demonstrated that BRCA1, EZH2, DNMT1/3a/b and histone H3 lysine 27 trimethylation (H3K27me3) are recruited to the endogenous FOXO3 promoter, further advocating that these proteins interact to modulate FOXO3 methylation and expression. In addition, ChIP results also revealed that BRCA1 depletion promoted the recruitment of the DNA methyltransferases DNMT1/3a/3b and the enrichment of the EZH2-mediated transcriptional repressive epigenetic marks H3K27me3 on the FOXO3 promoter. Methylated DNA immunoprecipitation assays also confirmed increased CpG methylation of the FOXO3 gene on BRCA1 depletion. Analysis of the global gene methylation profiles of a cohort of 33 familial breast tumours revealed that FOXO3 promoter methylation is significantly associated with BRCA1 mutation. Furthermore, immunohistochemistry further suggested that FOXO3 expression was significantly associated with BRCA1 status in EZH2-positive breast cancer. Consistently, high FOXO3 and EZH2 mRNA levels were significantly associated with good and poor prognosis in breast cancer, respectively. Together, these data suggest that BRCA1 can prevent and reverse FOXO3 suppression via inhibiting EZH2 and, consequently, its ability to recruit the transcriptional repressive H3K27me3 histone marks and the DNA methylases DNMT1/3a/3b, to induce DNA methylation and gene silencing on the FOXO3 promoter.
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200
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Kutateladze TG, Kiessling LL. Focus on Epigenetics. ACS Chem Biol 2016; 11:541-2. [PMID: 26987448 DOI: 10.1021/acschembio.6b00218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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