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Coronary artery disease (CAD) is the leading cause of death in the United States. There is a need for novel therapeutic targets that prevent life-threatening consequences directly associated with plaque accumulation in the vascular wall—the underlying cause of CAD. During the progression of atherosclerosis, vascular smooth muscle cells (VSMCs) transdifferentiate from a contractile to a synthetic phenotype that can either promote fibrous cap stability (fibroblast-like) or contribute to inflammation and plaque accumulation (macrophage or osteoblast-like).The molecular mechanisms driving the functional phenotypic switching of VSMCs are not fully understood and represent a unique opportunity for discovering new treatments directly targeting plaque formation in the vascular wall. We measured gene expression regulation during VSMC dedifferentiation using time-course chromatin remodeling (ATACseq) and nascent transcription data (PROseq). We stimulated VSMCs from three healthy heart transplant donors with PDGF-BB for 0, 4, 8, 12, and 16 hours and performed sequencing in duplicate for each donor at each time point for a total of 30 PROseq and 30 ATACseq libraries. We identified 231,315 regions of accessible chromatin (peaks) in the ATACseq data and 12,954 genes in the PROseq data across the five time points. Likelihood ratio testing detected 13,285 peaks and 7,438 genes with time-dynamic changes in read counts representing six patterns of variable accessibility and nascent transcription following PDGF-BB stimulation: gradual increase/decrease (I/D), immediate I/D, and transient I/D. Transcription factor binding site (TFBS) motif enrichment of dynamic peaks revealed 31 TFs unique to one time dynamic. We identified 157 genes directly downstream of peaks enriched for the 31 TFBSs sharing similar time-specific fold changes. THAP1 binding site motifs had the highest number of cis-regulatory connections (596) and downstream genes (80). Our results capture the first ever time-course ATACseq and PROseq analysis conducted in human VSMCs and provide the ability to predict regulatory edges between TFs and genes in order to map the regulatory cascading events occurring during VSMC switching from a contractile to a synthetic state.
Perry et al. (Wed,) studied this question.