Transcriptome Sequencing to Identify Transcription Factor Regulatory Network and Alternative Splicing in Endothelial...

This study aims to investigate the mechanisms underlying the response of human umbilical vein vascular endothelial cells (HUVECs) to vascular endothelial growth factor (VEGF) stimulation. HUVECs were treated with or without 16 ng/mL VEGF for 4 days, and RNA was extracted from HUVECs. After sequencing and data filtering (tool: NGS QC Toolkit), clean data were mapped to genome hg19 (tool: TopHat2). Thereafter, 154 differentially expressed genes (DEGs) were identified between VEGF group and control group (tool: Cuffdiff), and DEGs were enriched in 11 pathways associated with cytokine receptor interaction and chemokine signaling. Protein-protein interaction network of DEGs was constructed (tool: STRING), and ISG15 and MX1 were hub DEGs. The regulatory network of DEGs and transcription factors (TFs) (tool: TRED database) was also constructed, and CCL2 and FN1 (hub DEGs) were co-regulated by NFKB1 and RELA (hub TFs). Moreover, exon usage and alternative splicing were analyzed (tool: DEXSeq), and the splicing of ADORA2A was altered under VEGF stimulation. VEGF might influence HUVECs proliferation and migration, as well as angiogenesis process by regulating the expression of ISG15, MX1, CCL2, FN1, and ADORA2A. However, more research studies are still required to verify these predictions.