Hypoxia-Mediated Regulation of Histone Demethylases Affects Angiogenesis-Associated Functions in Endothelial Cells

Abstract

Objective: Previous studies have demonstrated that the expression of several lysine (K)-specific demethylases (KDMs) is induced by hypoxia. Here, we sought to investigate the exact mechanisms underlying this regulation and its functional implications for endothelial cell function, such as angiogenesis. Approach and Results: We analyzed the expression changes of KDMs under hypoxia and modulation of HIF (hypoxia-inducible factor) expression using GRO-Seq and RNA-Seq in endothelial cells. We provide evidence that the majority of the KDMs are induced at the level of nascent transcription mediated by the action of HIF-1α and HIF-2α. Importantly, we show that transcriptional changes at the level of initiation represent the major mechanism of gene activation. To delineate the epigenetic effects of hypoxia and HIF activation in normoxia, we analyzed the genome-wide changes of H3K27me3 using chromosome immunoprecipitation-Seq. We discovered a redistribution of H3K27me3 at ≈2000 to 3000 transcriptionally active loci nearby genes implicated in angiogenesis. Among these, we demonstrate that vascular endothelial growth factor A ( VEGFA ) expression is partly induced by KDM4B- and KDM6B-mediated demethylation of nearby regions. Knockdown of KDM4B and KDM6B decreased cell proliferation, tube formation, and endothelial sprouting while affecting hundreds of genes associated with angiogenesis. These findings provide novel insights into the regulation of KDMs by hypoxia and the epigenetic regulation of VEGFA-mediated angiogenesis. Conclusions: Our study describes an additional level of epigenetic regulation where hypoxia induces redistribution of H3K27me3 around genes implicated in proliferation and angiogenesis. More specifically, we demonstrate that KDM4B and KDM6B play a key role in modulating the expression of the major angiogenic driver VEGFA.

Therapeutic potential of inhibiting histone 3 lysine 27 demethylases: a review of the literature

“…It remains to be addressed, for example, whether KDM6A/B inhibition with GSK-J4 alters the microenvironment of solid tumours, including their stroma, vasculature and immune cell infiltration. Interestingly, Liu et al (2020) demonstrated an essential role for KDM6B-mediated H3K27 demethylation in the hypoxic induction of the gene encoding the pro-angiogenic mediator VEGFA [ 98 ]. Moreover, KDM6B knockdown or inhibition with GSK-J4 was found to inhibit endothelial cell proliferation and tube formation under hypoxic conditions [ 98 ].…”

Identifying Obstructive Sleep Apnea Syndrome-Associated Genes and Pathways through Weighted Gene Coexpression Network Analysis

“…The so-called epigenetics refers to heritable phenotypic changes without those in DNA sequence [ 16 ]. In recent years, hypoxia-mediated epigenetic regulation has had a major function in the mechanism of OSAS [ 17 ]. Under chronic intermittent hypoxia-reoxygenation circumstances, the epigenetic process influences the adaptive potential and phenotypic variability, which contributes to the development of numerous deleterious effects of OSAS [ 18 , 19 ].…”

Systems approaches to understand oxygen sensing: how multi-omics has driven advances in understanding oxygen-based signalling

“…A limitation of microarrays and RNA sequencing is they only provide a measure of steady state RNA levels without any information on the relative contributions of RNA transcription and decay rates. Methods detecting nascent RNA, namely metabolic RNA pulse labelling sequencing, GRO-seq and precision run-on (PRO)-seq, have elucidated direct transcriptional changes in response to low oxygen [36,38,[42][43][44][45], and determined the relative contributions of transcription and decay to changes in mRNA levels [44]. These data find that transcription is the major contributor to changes in transcript levels in response to hypoxia and that these changes are mainly HIF dependent.…”

“…ChIP-seq studies have shown hypoxia induces redistribution of the histone methylation landscape co-ordinating changes in hypoxia gene expression [ 40 , 61–64 ]. This work has contributed to the identification of specific JmjC histone demethylases, namely lysine demethylase 6A (KDM6A) and KDM5A, as oxygen sensors [ 62 , 64 ], determining the dependence of SET1B on H3K4me3 and gene expression changes in hypoxia [ 40 ], and elucidating the role of KDM4B and KDM6B in regulating hypoxic VEGFA expression and angiogenesis [ 43 ]. Furthermore, genome wide mapping of H3K27ac, a histone modification associated with transcriptionally active/poised genes, finds hypoxia induces changes in H3K27ac at gene loci correlating with effects of hypoxia on gene expression [ 42 ].…”