An international research team reports that more than one-third of genetic variants that increase the risk of coronary artery disease (CAD) regulate the expression of genes in the liver. These variants also have an impact on the expression of genes regulating cholesterol metabolism.
The findings provide valuable new insight into the genetics of coronary artery disease, according to the scientists, who published their study “Integrative analysis of liver-specific non-coding regulatory SNPs associated with the risk of coronary artery disease” in the American Journal of Human Genetics.
“Genetic factors underlying coronary artery disease (CAD) have been widely studied using genome-wide association studies (GWASs). However, the functional understanding of the CAD loci has been limited by the fact that a majority of GWAS variants are located within non-coding regions with no functional role. High cholesterol and dysregulation of the liver metabolism such as non-alcoholic fatty liver disease confer an increased risk of CAD,” write the investigators.
“Here, we studied the function of non-coding single-nucleotide polymorphisms in CAD GWAS loci located within liver-specific enhancer elements by identifying their potential target genes using liver cis-eQTL analysis and promoter Capture Hi-C in HepG2 cells. Altogether, 734 target genes were identified of which 121 exhibited correlations to liver-related traits. To identify potentially causal regulatory SNPs, the allele-specific enhancer activity was analyzed by (1) sequence-based computational predictions, (2) quantification of allele-specific transcription factor binding, and (3) STARR-seq massively parallel reporter assay.”
“Altogether, our analysis identified 1,277 unique SNPs that display allele-specific regulatory activity. Among these, susceptibility enhancers near important cholesterol homeostasis genes (APOB, APOC1, APOE, and LIPA) were identified, suggesting that altered gene regulatory activity could represent another way by which genetic variation regulates serum lipoprotein levels.
“Using CRISPR-based perturbation, we demonstrate how the deletion/activation of a single enhancer leads to changes in the expression of many target genes located in a shared chromatin interaction domain.”
“Our integrative genomics approach represents a comprehensive effort in identifying putative causal regulatory regions and target genes that could predispose to clinical manifestation of CAD by affecting liver function.”
Both genetic and environmental factors contribute to CAD and recent genome-wide association studies have identified approximately 200 risk loci for CAD. However, the vast majority of such variants are located in the non-coding regions of the genome and have no known biological function. Even though the functional characterization of such variants has been difficult in the past, new and advanced genomics techniques such as RNA-seq, ChIP-seq, STARR-seq and HiC, and computational analysis, have made understanding the variants’ functions possible.
The involvement of the liver in the progression of coronary artery disease is not completely understood. In the new study, the researchers show that over one third of risk variants for CAD are located in regulatory elements specific to liver, and they act to regulate the expression of genes implicated in traditional risk factors, such as glucose and cholesterol related traits.
“Our results not only confirm the correlation of cholesterol levels and the risk of coronary artery disease but also pinpoint for the first time the causal single nucleotide polymorphisms and the potential target genes that mediate the risk,” says Minna Kaikkonen-Määttä, PhD, Academy Research Fellow and associate professor from the University of Eastern Finland.
The team also included researchers from Kuopio University Hospital, the University of California Los Angeles, and the University of Arizona.
Another important finding was the discovery that risk variant-containing regulatory elements often seem to regulate many genes, not just one.
“Overall, our findings expand the list of genes and regulatory mechanisms acting in the liver and governing the risk of CAD development. Deciphering gene regulatory networks is becoming increasingly important in understanding disease mechanisms and developing next generation drug therapies,” adds Kaikkonen-Määttä.