Regulatory variants of blood pressure genes

Genome-wide association studies (GWAS) have identified blood pressure-related loci, but functional insights into causality and related molecular mechanisms lag behind. We functionally characterize 4608 genetic variants in linkage with blood pressure loci in vascular smooth muscle cells (VSMCs) and cardiomyocytes (CMs) by massively parallel reporter assays (MPRAs). Regulatory variants are in non-conserved loci, enriched in repeats, and alter trait-relevant transcription factor binding sites. Higher-order genome organization indicates that loci harboring regulatory variants converge in spatial hubs to control specific signaling pathways required for proper cardiovascular function. Modelling different variant allele frequencies by CRISPR prime editing led to expression changes of KCNK9, SFXN2, and PCGF6. We provide mechanistic insights into how regulatory variants converge their effects on blood pressure genes (i.e. ULK4, MAP4, CFDP1, PDE5A, 10q24.32), and cardiovascular pathways. Our findings support advances in molecular precision medicine to define functionally relevant variants and the genetic architecture of blood pressure genes. Overall design: MPRA pool of 232,975 oligonucleotides, 1 sample for input library and then 5 replicates for CMs and 4 for VSMCs. The plasmid pool as DNA input and each TagSeq replicate (CMs = 5 replicates, VSMCs = 4 replicates) was sequenced on the HiSeq 2500 platform (Illumina), single end with 50 bp. Prime Editing (CRISPR/Cas9) using HEK293 with 3 replicates per allelic frequency of each SNP.