Vascular smooth muscle cell state trajectories mediate molecular mechanisms of coronary disease risk [RNA-seq]

To investigate the genetic basis of SMC cell state trajectories that underlie the SMC component of CAD causality, we developed a dense timecourse single cell transcriptomic and epigenomic mapping of atherosclerosis in a murine disease model with additional high throughput spatial RNA in situ hybridization to localize . We further performed parallel knockout studies with single cell transcriptomics and epigenomics of validated CAD gene Tcf21 to understand its molecular mechanisms in SMC transition. We identified TEAD1 and CEBPB to share significant binding sites with coronary artery disease risk gene TCF21 at enhancer sites across the genome and characterize their genomic relationships through a combination of chromatin immunoprecipitation sequencing for TEAD1, CEBPB, and marker of enhancer activation H3K27ac. We further perform bulk RNAseq to understand the functional effects of TEAD1 knockdown in immortalized smooth muscle cells. Overall design: For siRNA experiments,SMCs were transfected with siRNAs targeting TEAD1 (Dharmacon ON-TARGETplus SMARTpool siRNA L-012603-00-0005;Horizon Discovery) or Silencer Select negative control siRNA (ThermoFisher 4390844) using Lipofectamine RNAiMax Transfection Reagent (ThermoFisher 13778150) according to manufacturer's instructions and incubated for 12 hours post-transfection in serum free media followed by an additional 12 hours of recovery in SmBM supplemented media prior to RNA collection.