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RNA-seq analysis to examine the effect of KDM2B knockdown or overexpression on transcriptional responses in ECs during VEGF-signaling

ABSTRACT: Vascular endothelial growth factor (VEGF) signaling serves a central role in vascular development as well as maintaining vascular homeostasis. In endothelial cells (ECs), VEGF activates gene expression of angiogenic transcription factors (TFs) followed by downstream induction of angiogenic responsive genes. Recent findings support histone modification dynamics contribute to transcriptional control of genes important for EC functions. Lysine demethylase 2B (KDM2B) demethylates histone H3K4me3 and H3K36me2/3 and also mediates monoubiquitylation of histone H2A119K. KDM2B functions as a transcriptional repressor in somatic cell reprograming and tumor development. However, the role of KDM2B during VEGF-signaling remains to be elucidated. Here, we show in cultured human ECs that knockdown of KDM2B enhances VEGF-induced angiogenesis via increased abilities of migration and proliferation. In contrast, ectopic expression of KDM2B has inhibitory effects on angiogenesis. The function of KDM2B is possibly dependent on its catalytic Jumondi C domain. Genome-wide analysis further reveal that KDM2B selectively controls transcription of VEGF-induced angiogenic TFs where increased H3K4me3/H3K36me3 and decreased of H2A119Kub are associated. These findings suggest an essential role of KDM2B during VEGF-signaling in ECs. Because dysregulation of VEGF signaling in ECs is involved in various diseases including cancer, KDM2B may be a potential therapeutic target in VEGF-mediated vasculopathic diseases.

ORGANISM(S): Homo sapiens

PROVIDER: GSE196505 | GEO | 2022/04/01

REPOSITORIES: GEO

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Project description:Although differentiation of mice embryonic stem cells into vascular endothelial cells (ECs) gives a model for investigating molecular mechanisms of vascular development in vivo, temporal dynamics of gene expressions and chromatin modifications have not been studied until now. Here, we interrogated transcriptome and two histone modifications, H3K4me3 and H3K27me3, with a genome-wide scale during ECs differentiation and elucidated epigenetic switch peculiar to ECs. We find Gata2, Fli1, Sox7, and Sox18 are master regulators from genetic and epigenetic data, these genes were induced after Etv2 activation. These genes have specific histone modification pattern which is repressed by H3K27me3 modification at Flk-sorted mesoderm and changed to the bivalent (H3K4me3 and H3K27me3 both positive) state rapidly after vascular endothelial cells growth factor (VEGF) stimuli. Using a previously reported ECs differentiation model, we demonstrate that four transcription factors are critical for ECs specific gene expressions and efficient differentiation. Moreover, from knockdown experiments using si-RNA, we discovered these factors inhibited not only TGFÎ² signaling pathway, that is endothelial mesenchymal transition pathway, but also other near lineage commitment, including blood cells, skeletal muscle cells, vascular smooth muscle cells, and cardiomyocytes. We further identify each factor specific target genes during ECs differentiation by microarray, including both activating and repressing genes. Together, our findings from a detailed epigenetic approach provide a basic understanding temporal regulated chromatin signatures and resulting gene expression profile during ECs commitment, which is applicable to other models of differentiation and production of mature and long lasting ECs for regenerative medicine. Total 17 samples were derived from [1] ES cells, Flk-sorted mesoderm cells, and in the absense or presence of VEGF (6, 12, 24, and 48h) to determine VEGF activated genes during endothelial cells differentiation, [2] control si-RNA, si-Gata2, si-Fli1, si-Sox7, or si-Sox18 transfected cells under VEGF stimuli, [3] control si-RNA or si-Mix (si-Gata2, si-Fli1, si-Sox7, and si-Sox18) transfected cells under VEGF stimuli for the identification of each transcription factor dependent genes during endothelial cells differentiation.

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RNA-seq analysis to examine the effect of KDM2B knockdown or overexpression on transcriptional responses in ECs during VEGF-signaling

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