Image: A diagram of a genetic variant associated with five vascular diseases is a distal regulator of endothelin-1 gene expression (Photo courtesy of the Broad Institute of MIT and Harvard University).
Genome-wide association studies have implicated a common genetic variant in chromosome 6p24 in coronary artery disease, as well as four other vascular diseases: migraine headache, cervical artery dissection, fibromuscular dysplasia, and hypertension.
However, it has not been clear how this polymorphism affects the risk for so many diseases. Scientists have now shown how this DNA variant enhances the activity of a gene called endothelin-1, which is known to promote vasoconstriction and hardening of the arteries.
Scientists at Broad Institute of MIT and Harvard University, (Cambridge, MA, USA) and their colleagues examined genetic variants associated with an increased risk for coronary artery disease and myocardial infarction in nearly 200,000 individuals using data from the CARDIOGRAMplusC4D consortium and the 1000 Genomes Project. Specifically, they focused on single-nucleotide polymorphisms (SNPs), variations that affect a single DNA building block.
Their analysis revealed that a SNP called rs9349379, located hundreds of kilobases away, was the strongest risk factor for cardiovascular disease at chromosome 6p24. Additional analysis of UK Biobank data from 112,338 people of European ancestry revealed that a specific form of rs9349379 known as the G allele, which was present in 36% of these individuals, was associated with an increased risk of coronary artery disease.
The investigators then used CRISPR/Cas9 gene editing to delete a small region of DNA at rs9349379 in human pluripotent stem cells and then converted these immature cells into vascular cell to study how rs9349379 regulates the activity of the physically distant endothelin 1 (EDN1) gene. Importantly, analysis of blood samples from 99 healthy individuals showed that the G allele at rs9349379 is associated with higher levels of Big endothelin-1 (ET-1), a precursor protein product of the EDN1 gene. Epigenomic data from human tissue revealed an enhancer signature at rs9349379 exclusively in aorta, suggesting a regulatory function for this SNP in the vasculature. CRISPR-edited stem cell-derived endothelial cells demonstrate rs9349379 regulates expression of EDN1; a gene located 600 kb upstream of Phosphatase And Actin Regulator 1 (PHACTR1).
The authors concluded that overall, these data illustrate the integration of genetic, phenotypic, and epigenetic analysis to identify the biologic mechanism by which a common, non-coding variant can distally regulate a gene and contribute to the pathogenesis of multiple vascular diseases. Sekar Kathiresan, MD, a cardiologist and senior author of the study said, “The main value of our study is the pinpointing of the importance of endothelin-1 and blood vessel constriction to multiple vascular diseases. We also show how to identify a core gene for multiple diseases through genome editing in cells.” The study was published on July 27, 2017, in the journal Cell.