Periodic Reporting for period 3 - EnDeCAD (Enhancers Decoding the Mechanisms Underlying CAD Risk)
Berichtszeitraum: 2022-01-01 bis 2023-06-30
1) We have extensively investigated the involvement of the liver in the progression of coronary artery disease. We 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 (Ref #1). 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. Another important finding was the discovery that risk variant-containing regulatory elements often seem to regulate many genes, not just one. 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.
2) We have harnessed the potential of single cell genomics techniques to present the first enhancer atlas of human atherosclerotic lesions in the native tissue context. We demonstrated that genetic risk variants associated with CAD are particularly enriched in cis-regulatory elements specific to ECs and SMCs, indicating that these cells play a significant role in transmitting susceptibility to the disease. Based on chromatin accessibility mapping and gene expression data, we were able to identify putative target genes for approximately 30% of all known loci associated with CAD. Finally, we performed experimental fine-mapping of the variants using MPRA and identified the most potential causal SNPs for over 30 CAD loci. We present several CAD loci where chromatin accessibility and gene expression could be assigned to one cell type predicting the cell type of action.
3) Our results above have demonstrated that noncoding regulatory elements are frequently cell-type specific. For these reasons, it is important to measure gene expression, epigenetic profiles and cell phenotypes in pure cell populations. To achieve this, we have collected genetic, transcriptomic, epigenetic and phenotypic data from SMCs and ECs extracted from 150+ multiethnic heart transplant donors. We demonstrate that almost half of the CAD-associated loci were associated with one of the CAD-relevant SMC phenotypes traits, migration, proliferation, and calcification. Furthermore, we found thousands of expression quantitative trait loci (eQTLs) and over 3,000 regulatory elements whose activity is modulated by genetic variants in ECs. Importantly, the regulatory SNPs identified were enriched in CAD loci, as exemplified by PECAM-1, FES, and AXL loci for which experimental evidence supports their contributions to vascular functions. Together our data supports the view that genetic predisposition for CAD is partly manifested through the ECs and SMCs. These findings could improve the interpretation of CAD GWAS and inform candidate targets for therapeutic intervention or risk prediction.
These results will ultimately lead to more complete picture of gene regulatory programs and causal events driving CAD progression. The mechanisms revealing causality of single variant loci will significantly advance the field, while increase in our understanding of the molecular landscape causing CAD across tissues represent a major breakthrough. Shedding light into the molecular mechanisms of these variants has the potential to improve biomarker and drug target identification, risk prediction and treatment selection in clinical practice.