NEW YORK – A research team from Canada, Spain, and the US has used systems biology to functionally characterize noncoding genetic variants at loci linked to high blood pressure (BP) through prior genome-wide association studies.
"Our approach represents a roadmap of how to use functional genomics to determine causal variants in the noncoding genome that regulate genes in complex genetic traits, such as blood pressure," co-senior and corresponding author Philipp Maass, a researcher affiliated with the Hospital for Sick Children and the University of Toronto, explained in an email.
As they reported in Cell Genomics on Wednesday, the researchers used massively parallel reporter assays to functionally assess more than 4,600 variants in two cardiovascular-relevant cell types, focusing on variants in linkage disequilibrium with 135 high BP-associated loci. Their results highlighted BP-related regulatory variants in vascular smooth muscle cells and cardiomyocytes — particularly those influencing transcription factors with cardiovascular effects — and revealed an overrepresentation of BP-linked regulatory variants in less evolutionarily conserved repeat sequences.
"Unexpectedly, we uncovered high densities of hundreds of regulatory variants at genes relevant for blood pressure," Maass said, noting that such high-density variants "may act in concert to regulate target genes."
By combining cis-regulatory element maps, DNase-hypersensitive sites, and chromatin immunoprecipitation sequencing data from an effort known as EpiMap, meanwhile, the team incorporated active or repressed sequence profiles in cardiac, brain vascular smooth muscle, smooth muscle, and coronary artery tissues to focus in on apparent causal variants. These causal variants were subsequently explored further with the help of CRISPR prime editing experiments.
"We substituted highly likely causal variants to alternative sequences and showed that they affect genes which are not necessarily the closest, but which are relevant for blood pressure regulation," Maass explained.
Based on these and other follow-up analyses, the researchers flagged a set of candidate genes such as KCNK9, SFXN2, and PCGF6 that are suspected of contributing to high BP development. Their results also provided a look at the architecture of gene regulatory networks influencing BP, including interrelated and interacting regulatory variants that mediate BP-related processes.
"Our findings underscore that genomic mechanisms and gene regulation in complex traits are not linear," Maass said. "They rather consist of synergistic [three-dimensional] regulatory hubs involving many regions of the noncoding genome."
More broadly, the study is expected to serve as a foundation for future studies of hypertension and related cardiovascular conditions.
In particular, the team's systematic BP variant characterization approach "provides a valuable resource for cardiac and hypertension genomics and for cardiovascular biology," Maass said, "and can facilitate determining genomic markers for molecular precision medicine in the future."