PO19 An interplay of non-coding RNAs regulates CDH13 expression and affects endothelial function and coronary artery disease risk

Background Many common diseases have a polygenic architecture. The responsible alleles are thought to mediate risk by disturbing gene regulation in most cases; however, the precise mechanisms have been elucidated only for a few. Purpose We investigated the 16q23.3 genomic locus, which genome-wide significantly associates with coronary artery disease, a globally leading cause of death caused by the accumulation of lipid-rich inflammatory plaques in the arterial wall. Methods and Results The 16q23.3 locus harbors CDH13, whose mRNA and protein we found to be suppressed in atherosclerotic human and mouse arteries. Loss-of-function (LoF) variants of CDH13 were associated with detrimental cardiovascular phenotypes in the UK Biobank. Its knock-out increased plaque sizes in Cdh13-/-/Apoe-/- mice compared to Apoe-/- mice on a Western diet. After establishing an atheroprotective role of CDH13, we studied its regulation. Integration of population genomic and transcriptomic datasets by GWAS-eQTL colocalization analysis identified CDH13 and four long non-coding RNAs (lncRNAs) as candidate causal genes at the 16q23.3 locus. dCas13-mediated RNA immunoprecipitation revealed that the lncRNA CDH13-AS2 binds to CDH13 mRNA in human endothelial cells (ECs). Its CRISPR/Cas9-based knockout in ECs was atherogenic, whereas dCas9-based transcriptional activation (CRISPRa) of CDH13-AS2 was atheroprotective; effects that were found to be mediated by the stability of CDH13 mRNA. To further understand how the CDH13-AS2 protects the mRNA, we searched in silico and screened in vitro for microRNAs (miRNAs) that bind to CDH13 3’UTR. Indeed, four miRNAs, miR-19b-3p, miR-125b-2-3p, miR-433-3p, and miR-7b-5p, were found experimentally to accelerate CDH13 mRNA degradation, an effect that was neutralized by CRISPRa of CDH13-AS2. Conclusions Our study reveals an interplay among miRNAs, lncRNAs, and mRNA that modulates the abundance of the atheroprotective protein CDH13 in endothelial cells, potentially offering new therapeutic targets for RNA-based interventions in coronary artery disease.