Selective Inhibition of Histone Deacetylase 2 Silences Progesterone Receptor–Mediated Signaling
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Interplay Between Epigenetics and Metabolism in Oncogenesis: Mechanisms and Therapeutic Approaches
OPEN Oncogene (2017) 36, 3359–3374 www.nature.com/onc REVIEW Interplay between epigenetics and metabolism in oncogenesis: mechanisms and therapeutic approaches CC Wong1, Y Qian2,3 and J Yu1 Epigenetic and metabolic alterations in cancer cells are highly intertwined. Oncogene-driven metabolic rewiring modifies the epigenetic landscape via modulating the activities of DNA and histone modification enzymes at the metabolite level. Conversely, epigenetic mechanisms regulate the expression of metabolic genes, thereby altering the metabolome. Epigenetic-metabolomic interplay has a critical role in tumourigenesis by coordinately sustaining cell proliferation, metastasis and pluripotency. Understanding the link between epigenetics and metabolism could unravel novel molecular targets, whose intervention may lead to improvements in cancer treatment. In this review, we summarized the recent discoveries linking epigenetics and metabolism and their underlying roles in tumorigenesis; and highlighted the promising molecular targets, with an update on the development of small molecule or biologic inhibitors against these abnormalities in cancer. Oncogene (2017) 36, 3359–3374; doi:10.1038/onc.2016.485; published online 16 January 2017 INTRODUCTION metabolic genes have also been identified as driver genes It has been appreciated since the early days of cancer research mutated in some cancers, such as isocitrate dehydrogenase 1 16 17 that the metabolic profiles of tumor cells differ significantly from and 2 (IDH1/2) in gliomas and acute myeloid leukemia (AML), 18 normal cells. Cancer cells have high metabolic demands and they succinate dehydrogenase (SDH) in paragangliomas and fuma- utilize nutrients with an altered metabolic program to support rate hydratase (FH) in hereditary leiomyomatosis and renal cell 19 their high proliferative rates and adapt to the hostile tumor cancer (HLRCC). -
The Roles of Histone Deacetylase 5 and the Histone Methyltransferase Adaptor WDR5 in Myc Oncogenesis
The Roles of Histone Deacetylase 5 and the Histone Methyltransferase Adaptor WDR5 in Myc oncogenesis By Yuting Sun This thesis is submitted in fulfilment of the requirements for the degree of Doctor of Philosophy at the University of New South Wales Children’s Cancer Institute Australia for Medical Research School of Women’s and Children’s Health, Faculty of Medicine University of New South Wales Australia August 2014 PLEASE TYPE THE UNIVERSITY OF NEW SOUTH WALES Thesis/Dissertation Sheet Surname or Family name: Sun First name: Yuting Other name/s: Abbreviation for degree as given in the University calendar: PhD School : School of·Women's and Children's Health Faculty: Faculty of Medicine Title: The Roles of Histone Deacetylase 5 and the Histone Methyltransferase Adaptor WDR5 in Myc oncogenesis. Abstract 350 words maximum: (PLEASE TYPE) N-Myc Induces neuroblastoma by regulating the expression of target genes and proteins, and N-Myc protein is degraded by Fbxw7 and NEDD4 and stabilized by Aurora A. The class lla histone deacetylase HDAC5 suppresses gene transcription, and blocks myoblast and leukaemia cell differentiation. While histone H3 lysine 4 (H3K4) trimethylation at target gene promoters is a pre-requisite for Myc· induced transcriptional activation, WDRS, as a histone H3K4 methyltransferase presenter, is required for H3K4 methylation and transcriptional activation mediated by a histone H3K4 methyltransferase complex. Here, I investigated the roles of HDAC5 and WDR5 in N-Myc overexpressing neuroblastoma. I have found that N-Myc upregulates HDAC5 protein expression, and that HDAC5 represses NEDD4 gene expression, increases Aurora A gene expression and consequently upregulates N-Myc protein expression in neuroblastoma cells. -
The Histone Deacetylase HDA15 Interacts with MAC3A and MAC3B to Regulate Intron
bioRxiv preprint doi: https://doi.org/10.1101/2020.11.17.386672; this version posted November 17, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 The histone deacetylase HDA15 interacts with MAC3A and MAC3B to regulate intron 2 retention of ABA-responsive genes 3 4 Yi-Tsung Tu1#, Chia-Yang Chen1#, Yi-Sui Huang1, Ming-Ren Yen2, Jo-Wei Allison Hsieh2,3, 5 Pao-Yang Chen2,3*and Keqiang Wu1* 6 7 1Institute of Plant Biology, National Taiwan University, Taipei 10617, Taiwan 8 2 Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan 9 3 Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan 10 University, Taipei, Taiwan 11 12 # These authors contributed equally to this work. 13 * Corresponding authors: Keqiang Wu ([email protected], +886-2-3366-4546) and Pao-Yang 14 Chen ([email protected], +886-2-2787-1140) 15 16 Short title: HDA15 and MAC3A/MAC3B coregulate intron retention 17 One sentence summary: HDA15 and MAC3A/MAC3B coregulate intron retention and reduce 18 the histone acetylation level of the genomic regions near ABA-responsive retained introns. 19 20 The author responsible for distribution of materials integral to the findings presented in this 21 article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) 22 is: Keqiang Wu ([email protected]) 23 24 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.11.17.386672; this version posted November 17, 2020. -
Determining HDAC8 Substrate Specificity by Noah Ariel Wolfson A
Determining HDAC8 substrate specificity by Noah Ariel Wolfson A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Biological Chemistry) in the University of Michigan 2014 Doctoral Committee: Professor Carol A. Fierke, Chair Professor Robert S. Fuller Professor Anna K. Mapp Associate Professor Patrick J. O’Brien Associate Professor Raymond C. Trievel Dedication My thesis is dedicated to all my family, mentors, and friends who made getting to this point possible. ii Table of Contents Dedication ....................................................................................................................................... ii List of Figures .............................................................................................................................. viii List of Tables .................................................................................................................................. x List of Appendices ......................................................................................................................... xi Abstract ......................................................................................................................................... xii Chapter 1 HDAC8 substrates: Histones and beyond ...................................................................... 1 Overview ..................................................................................................................................... 1 HDAC introduction -
Distinct Contributions of DNA Methylation and Histone Acetylation to the Genomic Occupancy of Transcription Factors
Downloaded from genome.cshlp.org on October 8, 2021 - Published by Cold Spring Harbor Laboratory Press Research Distinct contributions of DNA methylation and histone acetylation to the genomic occupancy of transcription factors Martin Cusack,1 Hamish W. King,2 Paolo Spingardi,1 Benedikt M. Kessler,3 Robert J. Klose,2 and Skirmantas Kriaucionis1 1Ludwig Institute for Cancer Research, University of Oxford, Oxford, OX3 7DQ, United Kingdom; 2Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom; 3Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ, United Kingdom Epigenetic modifications on chromatin play important roles in regulating gene expression. Although chromatin states are often governed by multilayered structure, how individual pathways contribute to gene expression remains poorly under- stood. For example, DNA methylation is known to regulate transcription factor binding but also to recruit methyl-CpG binding proteins that affect chromatin structure through the activity of histone deacetylase complexes (HDACs). Both of these mechanisms can potentially affect gene expression, but the importance of each, and whether these activities are inte- grated to achieve appropriate gene regulation, remains largely unknown. To address this important question, we measured gene expression, chromatin accessibility, and transcription factor occupancy in wild-type or DNA methylation-deficient mouse embryonic stem cells following HDAC inhibition. We observe widespread increases in chromatin accessibility at ret- rotransposons when HDACs are inhibited, and this is magnified when cells also lack DNA methylation. A subset of these elements has elevated binding of the YY1 and GABPA transcription factors and increased expression. The pronounced ad- ditive effect of HDAC inhibition in DNA methylation–deficient cells demonstrates that DNA methylation and histone deacetylation act largely independently to suppress transcription factor binding and gene expression. -
Epigenetic Regulation of TRAIL Signaling: Implication for Cancer Therapy
cancers Review Epigenetic Regulation of TRAIL Signaling: Implication for Cancer Therapy Mohammed I. Y. Elmallah 1,2,* and Olivier Micheau 1,* 1 INSERM, Université Bourgogne Franche-Comté, LNC UMR1231, F-21079 Dijon, France 2 Chemistry Department, Faculty of Science, Helwan University, Ain Helwan 11795 Cairo, Egypt * Correspondence: [email protected] (M.I.Y.E.); [email protected] (O.M.) Received: 23 May 2019; Accepted: 18 June 2019; Published: 19 June 2019 Abstract: One of the main characteristics of carcinogenesis relies on genetic alterations in DNA and epigenetic changes in histone and non-histone proteins. At the chromatin level, gene expression is tightly controlled by DNA methyl transferases, histone acetyltransferases (HATs), histone deacetylases (HDACs), and acetyl-binding proteins. In particular, the expression level and function of several tumor suppressor genes, or oncogenes such as c-Myc, p53 or TRAIL, have been found to be regulated by acetylation. For example, HATs are a group of enzymes, which are responsible for the acetylation of histone proteins, resulting in chromatin relaxation and transcriptional activation, whereas HDACs by deacetylating histones lead to chromatin compaction and the subsequent transcriptional repression of tumor suppressor genes. Direct acetylation of suppressor genes or oncogenes can affect their stability or function. Histone deacetylase inhibitors (HDACi) have thus been developed as a promising therapeutic target in oncology. While these inhibitors display anticancer properties in preclinical models, and despite the fact that some of them have been approved by the FDA, HDACi still have limited therapeutic efficacy in clinical terms. Nonetheless, combined with a wide range of structurally and functionally diverse chemical compounds or immune therapies, HDACi have been reported to work in synergy to induce tumor regression. -
Cigarette Smoking-Induced Endothelial Dysfunction: Molecular Mechanisms and Therapeutic Approaches
Cigarette Smoking-Induced Endothelial Dysfunction: Molecular Mechanisms and Therapeutic Approaches DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Tamer M. Abdelghany Graduate Program in Molecular, Cellular and Developmental Biology The Ohio State University 2013 Dissertation Committee: Dr. Jay L. Zweier, MD, Advisor Dr. Arthur Strauch III, PhD Dr. Amal Amer, MD PhD Copyright by Tamer M. Abdelghany 2013 Abstract Cigarette smoking (CS) remains the single largest preventable cause of death. Worldwide, smoking causes more than five million deaths annually and, according to the current trends, smoking may cause up to 10 million annual deaths by 2030. In the U.S. alone, approximately half a million adults die from smoking-related illnesses each year which represents ~ 19% of all deaths in the U.S., and among them 50,000 are killed due to exposure to secondhand smoke (SHS). Smoking is a major risk factor for cardiovascular disease (CVD). The crucial event of The CVD is the endothelial dysfunction (ED). Despite of the vast number of studies conducted to address this significant health problem, the exact mechanism by which CS induces ED is not fully understood. The ultimate goal of this thesis; therefore, is to study the mechanisms by which CS induces ED, aiming at the development of new therapeutic strategies that can be used in protection and/or reversal of CS-induced ED. In the first part of this study, we developed a well-characterized animal model for chronic secondhand smoke exposure (SHSE) to study the onset and severity of the disease. -
Antigen-Specific Memory CD4 T Cells Coordinated Changes in DNA
Downloaded from http://www.jimmunol.org/ by guest on September 24, 2021 is online at: average * The Journal of Immunology The Journal of Immunology published online 18 March 2013 from submission to initial decision 4 weeks from acceptance to publication http://www.jimmunol.org/content/early/2013/03/17/jimmun ol.1202267 Coordinated Changes in DNA Methylation in Antigen-Specific Memory CD4 T Cells Shin-ichi Hashimoto, Katsumi Ogoshi, Atsushi Sasaki, Jun Abe, Wei Qu, Yoichiro Nakatani, Budrul Ahsan, Kenshiro Oshima, Francis H. W. Shand, Akio Ametani, Yutaka Suzuki, Shuichi Kaneko, Takashi Wada, Masahira Hattori, Sumio Sugano, Shinichi Morishita and Kouji Matsushima J Immunol Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Author Choice option Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Freely available online through http://www.jimmunol.org/content/suppl/2013/03/18/jimmunol.120226 7.DC1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material Permissions Email Alerts Subscription Author Choice Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2013 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 24, 2021. Published March 18, 2013, doi:10.4049/jimmunol.1202267 The Journal of Immunology Coordinated Changes in DNA Methylation in Antigen-Specific Memory CD4 T Cells Shin-ichi Hashimoto,*,†,‡ Katsumi Ogoshi,* Atsushi Sasaki,† Jun Abe,* Wei Qu,† Yoichiro Nakatani,† Budrul Ahsan,x Kenshiro Oshima,† Francis H. -
Pan-Histone Deacetylase Inhibitors Regulate Signaling Pathways
Majumdar et al. BMC Genomics 2012, 13:709 http://www.biomedcentral.com/1471-2164/13/709 RESEARCH ARTICLE Open Access Pan-histone deacetylase inhibitors regulate signaling pathways involved in proliferative and pro-inflammatory mechanisms in H9c2 cells Gipsy Majumdar1, Piyatilake Adris1, Neha Bhargava1, Hao Chen2 and Rajendra Raghow1,2* Abstract Background: We have shown previously that pan-HDAC inhibitors (HDACIs) m-carboxycinnamic acid bis-hydroxamide (CBHA) and trichostatin A (TSA) attenuated cardiac hypertrophy in BALB/c mice by inducing hyper-acetylation of cardiac chromatin that was accompanied by suppression of pro-inflammatory gene networks. However, it was not feasible to determine the precise contribution of the myocytes- and non-myocytes to HDACI-induced gene expression in the intact heart. Therefore, the current study was undertaken with a primary goal of elucidating temporal changes in the transcriptomes of cardiac myocytes exposed to CBHA and TSA. Results: We incubated H9c2 cardiac myocytes in growth medium containing either of the two HDACIs for 6h and 24h and analyzed changes in gene expression using Illumina microarrays. H9c2 cells exposed to TSA for 6h and 24h led to differential expression of 468 and 231 genes, respectively. In contrast, cardiac myocytes incubated with CBHA for 6h and 24h elicited differential expression of 768 and 999 genes, respectively. We analyzed CBHA- and TSA-induced differentially expressed genes by Ingenuity Pathway (IPA), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Core_TF programs and discovered that CBHA and TSA impinged on several common gene networks. Thus, both HDACIs induced a repertoire of signaling kinases (PTEN-PI3K-AKT and MAPK) and transcription factors (Myc, p53, NFkB and HNF4A) representing canonical TGFβ, TNF-α, IFNγ and IL-6 specific networks. -
Histone Deacetylase Inhibitors Synergizes with Catalytic Inhibitors of EZH2 to Exhibit Anti-Tumor Activity in Small Cell Carcinoma of the Ovary, Hypercalcemic Type
Author Manuscript Published OnlineFirst on September 19, 2018; DOI: 10.1158/1535-7163.MCT-18-0348 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Histone deacetylase inhibitors synergizes with catalytic inhibitors of EZH2 to exhibit anti- tumor activity in small cell carcinoma of the ovary, hypercalcemic type Yemin Wang1,2,*, Shary Yuting Chen1,2, Shane Colborne3, Galen Lambert2, Chae Young Shin2, Nancy Dos Santos4, Krystal A. Orlando5, Jessica D. Lang6, William P.D. Hendricks6, Marcel B. Bally4, Anthony N. Karnezis1,2, Ralf Hass7, T. Michael Underhill8, Gregg B. Morin3,9, Jeffrey M. Trent6, Bernard E. Weissman5, David G. Huntsman1,2,10,* 1Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada 2Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada. 3Michael Smith Genome Science Centre, British Columbia Cancer Agency, Vancouver, BC, Canada. 4Department of Experimental Therapeutics, British Columbia Cancer Research Centre, Vancouver, BC, Canada. 5Department of Pathology and Laboratory Medicine and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA. 6Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA. 7Department of Obstetrics and Gynecology, Hannover Medical School, D-30625 Hannover, Germany. 8Department of Cellular and Physiological Sciences and Biomedical Research Centre, University 1 Downloaded from mct.aacrjournals.org on September 26, 2021. © 2018 American Association for Cancer Research. Author Manuscript Published OnlineFirst on September 19, 2018; DOI: 10.1158/1535-7163.MCT-18-0348 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. -
Phosphate Availability and Ectomycorrhizal Symbiosis with Pinus Sylvestris Have Independent Effects on the Paxillus Involutus Transcriptome
This is a repository copy of Phosphate availability and ectomycorrhizal symbiosis with Pinus sylvestris have independent effects on the Paxillus involutus transcriptome. White Rose Research Online URL for this paper: http://eprints.whiterose.ac.uk/168854/ Version: Published Version Article: Paparokidou, C., Leake, J.R. orcid.org/0000-0001-8364-7616, Beerling, D.J. et al. (1 more author) (2020) Phosphate availability and ectomycorrhizal symbiosis with Pinus sylvestris have independent effects on the Paxillus involutus transcriptome. Mycorrhiza. ISSN 0940- 6360 https://doi.org/10.1007/s00572-020-01001-6 Reuse This article is distributed under the terms of the Creative Commons Attribution (CC BY) licence. This licence allows you to distribute, remix, tweak, and build upon the work, even commercially, as long as you credit the authors for the original work. More information and the full terms of the licence here: https://creativecommons.org/licenses/ Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ Mycorrhiza https://doi.org/10.1007/s00572-020-01001-6 ORIGINAL ARTICLE Phosphate availability and ectomycorrhizal symbiosis with Pinus sylvestris have independent effects on the Paxillus involutus transcriptome Christina Paparokidou1 & Jonathan R. Leake1 & David J. Beerling1 & Stephen A. Rolfe1 Received: 16 June 2020 /Accepted: 29 October 2020 # The Author(s) 2020 Abstract Many plant species form symbioses with ectomycorrhizal fungi, which help them forage for limiting nutrients in the soil such as inorganic phosphate (Pi). -
SET-Induced Calcium Signaling and MAPK/ERK Pathway Activation Mediate Dendritic Cell-Like Differentiation of U937 Cells
Leukemia (2005) 19, 1439–1445 & 2005 Nature Publishing Group All rights reserved 0887-6924/05 $30.00 www.nature.com/leu SET-induced calcium signaling and MAPK/ERK pathway activation mediate dendritic cell-like differentiation of U937 cells A Kandilci1 and GC Grosveld1 1Department of Genetics and Tumor Cell Biology, Mail Stop 331, St Jude Children’s Research Hospital, 332 N. Lauderdale, Memphis, TN 38105, USA Human SET, a target of chromosomal translocation in human G1/S transition by allowing cyclin E–CDK2 activity in the leukemia encodes a highly conserved, ubiquitously expressed, presence of p21.11 Second, SET interacts with cyclin B–CDK1.19 nuclear phosphoprotein. SET mediates many functions includ- ing chromatin remodeling, transcription, apoptosis and cell Overexpression of SET inhibits cyclin B-CDK1 activity, which in cycle control. We report that overexpression of SET directs turn, blocks the G2/M transition; this finding suggests a negative 13 differentiation of the human promonocytic cell line U937 along regulatory role for SET in G2/M transition. Overexpression of the dendritic cell (DC) pathway, as cells display typical cell division autoantigen-1 (CDA1), another member of the morphologic changes associated with DC fate and express NAP/SET family, inhibits proliferation and decreases bromo- the DC surface markers CD11b and CD86. Differentiation occurs deoxyuridine uptake in HeLa cells.20 Acidic and basic domains via a calcium-dependent mechanism involving the CaMKII and 20 MAPK/ERK pathways. Similar responses are elicited by inter- of CDA1 show 40% identity and 68% similarity to SET. feron-c (IFN-c) treatment with the distinction that IFN-c signaling We have recently shown that overexpression of SET in the activates the DNA-binding activity of STAT1 whereas SET human promonocytic cell line U937 causes G0/G1 arrest and overexpression does not.