2017年3月14日火曜日

KDM & Oxygen Concentration ASAP


KDM4A is Highly Sensitive to Oxygen Concentrations

† Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
‡ Radcliffe Department of Medicine, Division of Cardiovascular Medicine, BHF Centre of Research Excellence, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
§ Target Discovery Institute, NDM Research Building, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
ACS Chem. Biol., Article ASAP
DOI: 10.1021/acschembio.6b00958
Publication Date (Web): January 4, 2017
Copyright © 2017 American Chemical Society

Abstract

Abstract Image
 
 
 
The JmjC histone lysine demethylases (KDMs) are epigenetic regulators involved in the removal of methyl groups from post-translationally modified lysyl residues within histone tails, modulating gene transcription. These enzymes require molecular oxygen for catalytic activity and, as 2-oxoglutarate (2OG)-dependent oxygenases, are related to the cellular oxygen sensing HIF hydroxylases PHD2 and FIH. Recent studies have indicated that the activity of some KDMs, including the pseudogene-encoded KDM4E, may be sensitive to changing oxygen concentrations. Here, we report detailed analysis of the effect of oxygen availability on the activity of the KDM4 subfamily member KDM4A, importantly demonstrating a high level of O2 sensitivity both with isolated protein and in cells. Kinetic analysis of the recombinant enzyme revealed a high KMapp(O2) of 173 ± 23 μM, indicating that the activity of the enzyme is able to respond sensitively to a reduction in oxygen concentration. Furthermore, immunofluorescence experiments in U2OS cells conditionally overexpressing KDM4A showed that the cellular activity of KDM4A against its primary substrate, H3K9me3, displayed a graded response to depleting oxygen concentrations in line with the data obtained using isolated protein. These results suggest that KDM4A possesses the potential to act as an oxygen sensor in the context of chromatin modifications, with possible implications for epigenetic regulation in hypoxic disease states. Importantly, this correlation between the oxygen sensitivity of the catalytic activity of KDM4A in biochemical and cellular assays demonstrates the utility of biochemical studies in understanding the factors contributing to the diverse biological functions and varied activity of the 2OG oxygenases.

Supporting Information

The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acschembio.6b00958.
  • Figures showing a consensus mechanism, in vitro O2 calibration, validation of the U2OS F-KDM4A cell line, and calculation of KDM4A activity. Tables showing antibodies used in immunofluorescence and Western blot experiments and sequences of primers. (PDF)

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Article Views: 326 Times
Received 31 October 2016
Date accepted 4 January 2017
Published online 4 January 2017
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KDM Inhibitors 2017


1.  http://epigeneticsandchromatin.biomedcentral.com/articles/10.1186/s13072-017-0116-6



2.

 

http://pubs.acs.org/action/doSearch?AllField=Histone+lysine+demethylases+KDMs&startPage=&sortBy=Earliest

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KDM Inhibitors 2016


Perspective


Previous Article
Table of Contents

Recent Progress in Histone Demethylase Inhibitors

† Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, U.K.
‡ Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7BN, U.K.
§ Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, U.K.
∥ Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Headington, OX3 7FZ, U.K.
J. Med. Chem., 2016, 59 (4), pp 1308–1329
DOI: 10.1021/acs.jmedchem.5b01758
Publication Date (Web): December 28, 2015
Copyright © 2015 American Chemical Society
*For C.J.S.: E-mail, christopher.schofield@chem.ox.ac.uk Phone, +44 (0)1865 285000, fax, +44 (0)1865 275674., *For A.K.: E-mail, akane.kawamura@chem.ox.ac.uk.
This article is part of the Epigenetics special issue.
Biography
Tom E. McAllister completed his Ph.D. in chemical biology at the University of Leeds in 2013 under the supervision of Dr. Michael E. Webb, developing methods to study labile protein post-translational modifications. He then worked as a postdoctoral fellow with Assoc. Prof. W. Bruce Turnbull, also at Leeds, to produce virus-like particles through defined protein–carbohydrate interactions. After a brief spell as a teaching fellow at the University of York, Tom began his postdoctoral position with Dr. Akane Kawamura at the University of Oxford in 2014. His current work focusses on the development of highly selective inhibitors for histone demethylases.
Biography
Katherine S. England completed an M.Chem. degree at the University of Oxford, working under the supervision of Prof. Jeremy Robertson for her final year research project. In 2002, she joined the Medicinal Chemistry department at Pfizer in Sandwich, UK, where she worked in drug discovery across a variety of disease areas and drug classes. Katherine joined the Structural Genomics Consortium at the University of Oxford in 2011, where she designed and synthesized inhibitors of epigenetic proteins and was awarded a D.Phil. in Organic Chemistry under the supervision of Prof. Christopher Schofield and Prof. Paul Brennan. In 2015, she joined the newly formed Alzheimer’s Research UK Oxford Drug Discovery Institute, where she is engaged in the design and synthesis of new molecules as potential treatments for dementia.
Biography
Richard J. Hopkinson received his D.Phil. in organic chemistry (2012) from the University of Oxford under the supervision of Prof. Christopher J. Schofield FRS, where his work focused on studying the mechanisms of histone demethylases. Following postdoctoral work on demethylase inhibition, he was elected to the William R. Miller Junior Research Fellowship in Molecular Aspects of Biology at St. Edmund Hall, Oxford, where his current research investigates the (bio)chemistry of formaldehyde in cellular systems.
Biography
Paul E. Brennan received his Ph.D. in organic chemistry from UC Berkeley, working on combinatorial chemistry and antibiotics. Following postdoctoral research in Cambridge University on total synthesis, Paul returned to California to take a position at Amgen. His research was focused on kinase inhibitors for oncology. After two years at Amgen, Paul moved to Pfizer in Sandwich, UK. In 2011, Paul joined the Structural Genomics Consortium as the Associate Professor of Medicinal Chemistry to discover chemical probes for epigenetic proteins. Since 2015, Paul has been the Head of Chemistry at the ARUK ODDI. His current research is focused on epigenetic proteins and new dementia targets.
Biography
Akane Kawamura completed her M.Chem. in Chemistry in 2000 and received her D.Phil. in Pharmacology from University of Oxford in 2005. She spent three years at Summit PLC, a biotechnology company, where she led a number of drug discovery projects across multiple therapeutic areas. In 2009, she joined Professor Chris Schofield’s laboratory to work on developing chemical probes for epigenetic proteins. She was awarded a BHF CRE Senior Fellowship in 2012 and a Royal Society Dorothy Hodgkin Research Fellowship in 2013. Her current research focuses on understanding the molecular mechanisms of epigenetic regulation by chromatin modifying enzymes.
Biography
Christopher J. Schofield’s research is driven by a desire to apply chemical principles and techniques to understanding biology. His research focuses on the functions, mechanisms, and structures of “chemically interesting” metallo-enzymes with roles ranging from antibiotic resistance to the oxygen dependent regulation of protein biosynthesis in humans.

Abstract

Abstract Image
 
 
 
There is increasing interest in targeting histone N-methyl-lysine demethylases (KDMs) with small molecules both for the generation of probes for target exploration and for therapeutic purposes. Here we update on previous reviews on the inhibition of the lysine-specific demethylases (LSDs or KDM1s) and JmjC families of N-methyl-lysine demethylases (JmjC KDMs, KDM2–7), focusing on the academic and patent literature from 2014 to date. We also highlight recent biochemical, biological, and structural studies which are relevant to KDM inhibitor development.
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Article Views: 3,209 Times
Received 10 November 2015
Published online 28 December 2015
Published in print 25 February 2016
Learn more about these metrics Article Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.

The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated.
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