Systems Genetics in Human Endothelial Cells Identifies Non-coding Variants Modifying Enhancers, Expression, and Complex Disease Traits

Single-Cell Epigenomics and Functional Fine-Mapping of Atherosclerosis GWAS Loci

“…The epigenetic assays were carried out using bulk epigenomics methods on a panel of human aortic EC cultures derived from genetically diverse donors. Dot size corresponds to statistical significance (false discovery rate [FDR]<0.05, determined by RASQUAL, 33 n=21–44 34 ) and dot color corresponds to the allele-specific ratio (blue, more reference allele reads; red, more alternative allele reads). The most potential predicted target genes, which demonstrate peak-promoter coaccessibility score >0.5, peak accessibility–gene expression correlation > 0.5, or cis–expression quantitative trait loci (eQTL) association in Genotype-Tissue Expression (GTEX) v8 arterial tissues ( Q value≤0.05) or HAECs (FDR<0.05), 34 are shown.…”

“…We have previously identified thousands of genetic variants associated with differential read abundance (allelic bias) in ATAC-seq, histone 3 lysine 27 acetylation (H3K27ac) chromatin immunoprecipitation sequencing (ChIP-Seq), or TF ChIP-Seq data by collecting data from primary cultures of ECs originating from aortic explants and subsequently cultured in 2 different conditions: control (untreated) and proinflammatory cytokine IL (interleukin) 1β treatment. 34 We, therefore, sought to overlay this information with the CAD/MI GWAS SNPs that were located in snATAC-Seq peaks and for which both the SNP-containing peak and a coaccessible promoter were open (cuts per cell >0.1) in atherosclerotic lesion ECs. Altogether, 32 SNPs with significant epigenetic molecular quantitative trait loci were identified, corresponding to 19 peaks (Figure 5 B).…”

CRISPR perturbations at many coronary artery disease loci impair vascular endothelial cell functions

“…rs12906125 is located in the FES promoter and overlaps an ATAC-seq peak as well as a H3K27ac-defined enhancer that physically interacts with the FURIN promoter ( Figure 4A ) 9 . The same SNP is an eQTL for FES in human primary aortic endothelial cells 23 and arterial tissues from GTEx. In the CRISPRa experiments, we found a significant up-regulation of both FES (log2(fold-change (FC))=3.75, adjusted P =8.5×10 −173 ) and FURIN (log2FC=0.78, adjusted P =1.5×10 −10 ) ( Figure 4B ).…”

“…MIA3/AIDA 9 ). At the FURIN/FES locus, we found a candidate regulatory variant that was also prioritized using orthogonal methodologies ( Figure 4 ) 23 . However, it is also likely that some of the findings from our CRISPR screens result from loss- or gain-of-function effects on causal genes independently of the causal variants.…”

“…It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted February 11, 2021. ; https://doi.org/10.1101/2021.02.10.430527 doi: bioRxiv preprint 9 in the FES promoter and overlaps an ATAC-seq peak as well as a H3K27ac-defined enhancer that physically interacts with the FURIN promoter ( Figure 4A) 9 . The same SNP is an eQTL for FES in human primary aortic endothelial cells 23 and arterial tissues from GTEx. In the CRISPRa experiments, we found a significant up-regulation of both FES (log2(fold-change (FC))=3.75, adjusted P=8.5x10 -173 ) and FURIN (log2FC=0.78, adjusted P=1.5x10 -10 ) ( Figure 4B).…”