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

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 to 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.

Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response

“…11a ). A low signal for histone H3 trimethylated at lysine 27 (H3K27me3, repressive mark) 37 was found throughout the O-GlcNAz sites in both MCF-7 and ADR cells, whereas a high H3K27ac signal 38 was measured in all these regions, which suggests that the binding of OCTFs is associated with transcriptional activation (Fig. 3d ).…”

Site-specific phosphorylation of histone H1.4 is associated with transcription activation

“…peaks were associated with 'active' promoters, we also found significant overlap with another 'active' promoter mark; H3K27ac [20] ( Figure 1C) (log ratio: 4.94) thereby providing multiple points of corroboration.…”

“…In order to further characterize the status of the promoters associated with pS187-H1.4 peaks, we used H3K4me3 ChIP-Seq data from a separate study conducted on MCF7 cells [20]. The H3K4me3 epigenetic mark has widely been associated with 'active' transcription state or the 'transcription readiness' of nearby promoters [21,22].…”

Evidence for context-dependent functions of KDM5B in prostate development and prostate cancer

“…Though the role of KDM5B in tumorigenesis is not well understood, its higher expression in cancer cells may regulate the distribution of H3K4me3 near promoter regions of tumor suppressors and modulate their expression, thus affecting cancer cell proliferation [6]. Recently, several KDM5B inhibitors have been identified and reported in different cancers such as the breast and prostate cancers [46,47]. In all these studies, genetic or pharmacologic inhibition of KDM5B upregulates the expression of tumor suppressor genes and caused growth arrest and apoptotic cell death in cancer cells suggesting that KDM5B may mostly act as a repressor of tumor suppressor genes.…”