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Genome and Epigenome

A KDM5 Inhibitor Increases Global H3K4 Trimethylation Occupancy and Enhances the Biological Efficacy of 5-Aza-2′-Deoxycytidine

Benjamin R. Leadem, Ioannis Kagiampakis, Catherine Wilson, Tommy K. Cheung, David Arnott, Patrick Trojer, Marie Classon, Hariharan Easwaran and Stephen B. Baylin
Benjamin R. Leadem
Department of Oncology, the Sidney Kimmel Comprehensive Cancer Research Center at Johns Hopkins University, Baltimore, Maryland.
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Ioannis Kagiampakis
Department of Oncology, the Sidney Kimmel Comprehensive Cancer Research Center at Johns Hopkins University, Baltimore, Maryland.
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Catherine Wilson
Molecular Oncology, Genentech Inc., South San Francisco, California.
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Tommy K. Cheung
Protein Chemistry, Genentech Inc., South San Francisco, California.
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David Arnott
Protein Chemistry, Genentech Inc., South San Francisco, California.
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Patrick Trojer
Constellation Pharmaceuticals, Inc., Cambridge, Massachusetts.
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Marie Classon
Molecular Oncology, Genentech Inc., South San Francisco, California.
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Hariharan Easwaran
Department of Oncology, the Sidney Kimmel Comprehensive Cancer Research Center at Johns Hopkins University, Baltimore, Maryland.
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Stephen B. Baylin
Department of Oncology, the Sidney Kimmel Comprehensive Cancer Research Center at Johns Hopkins University, Baltimore, Maryland.
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  • For correspondence: sbaylin@jhmi.edu
DOI: 10.1158/0008-5472.CAN-17-1453 Published March 2018
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Abstract

The H3K4 demethylase KDM5B is amplified and overexpressed in luminal breast cancer, suggesting it might constitute a potential cancer therapy target. Here, we characterize, in breast cancer cells, the molecular effects of a recently developed small-molecule inhibitor of the KDM5 family of proteins (KDM5i), either alone or in combination with the DNA-demethylating agent 5-aza-2′-deoxycytidine (DAC). KDM5i treatment alone increased expression of a small number of genes, whereas combined treatment with DAC enhanced the effects of the latter for increasing expression of hundreds of DAC-responsive genes. ChIP-seq studies revealed that KDM5i resulted in the broadening of existing H3K4me3 peaks. Furthermore, cells treated with the drug combination exhibited increased promoter and gene body H3K4me3 occupancy at DAC-responsive genes compared with DAC alone. Importantly, treatment with either DAC or DAC+KDM5i induced a dramatic increase in H3K27ac at enhancers with an associated significant increase in target gene expression, suggesting a previously unappreciated effect of DAC on transcriptional regulation. KDM5i synergized with DAC to reduce the viability of luminal breast cancer cells in in vitro assays. Our study provides the first look into the molecular effects of a novel KDM5i compound and suggests that combinatorial inhibition along with DAC represents a new area to explore in translational epigenetics.

Significance: This study offers a first look into the molecular effects of a novel KDM5 inhibitory compound, suggesting how its use in combination with DNA methylation inhibitors presents new opportunities to explore in translational cancer epigenetics. Cancer Res; 78(5); 1127–39. ©2017 AACR.

Footnotes

  • Note: Supplementary data for this article are available at Cancer Research Online (http://cancerres.aacrjournals.org/).

  • Received May 30, 2017.
  • Revision received November 6, 2017.
  • Accepted December 19, 2017.
  • ©2017 American Association for Cancer Research.
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Cancer Research: 78 (5)
March 2018
Volume 78, Issue 5
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A KDM5 Inhibitor Increases Global H3K4 Trimethylation Occupancy and Enhances the Biological Efficacy of 5-Aza-2′-Deoxycytidine
Benjamin R. Leadem, Ioannis Kagiampakis, Catherine Wilson, Tommy K. Cheung, David Arnott, Patrick Trojer, Marie Classon, Hariharan Easwaran and Stephen B. Baylin
Cancer Res March 1 2018 (78) (5) 1127-1139; DOI: 10.1158/0008-5472.CAN-17-1453

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A KDM5 Inhibitor Increases Global H3K4 Trimethylation Occupancy and Enhances the Biological Efficacy of 5-Aza-2′-Deoxycytidine
Benjamin R. Leadem, Ioannis Kagiampakis, Catherine Wilson, Tommy K. Cheung, David Arnott, Patrick Trojer, Marie Classon, Hariharan Easwaran and Stephen B. Baylin
Cancer Res March 1 2018 (78) (5) 1127-1139; DOI: 10.1158/0008-5472.CAN-17-1453
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Cancer Research Online ISSN: 1538-7445
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