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

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. Here, we investigated the 16q23.3 genomic locus, which genome-wide significantly associates with coronary artery disease, a globally leading cause of death caused by accumulation of lipid-rich inflammatory plaques in the arterial wall. The 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 . Taken together, our study demonstrates an interplay of miRNAs, lncRNAs, and mRNA, which modulates the abundance of an atheroprotective protein in endothelial cells, which may offer a new therapeutic target for coronary artery disease.