Dissecting Non-Coding GWAS Loci with High-Resolution 3D Chromatin Interactions Reveals Causal Genes with Relevance to Heart Failure [Perturb-seq]
Heart failure is caused in part by cardiac remodeling processes that include the death of cardiac myocytes and their replacement by cardiac fibroblasts. We hypothesized that these two cell types may harbor epigenetic contexts in which heart disease-associated non-coding SNPs perturb gene expression relevant to disease. Accordingly, we generated high-resolution Hi-C data layered with functional genomic information to annotate and link putative distal regulatory elements in heart disease-associated loci to gene promoters. Our analysis identified several target genes with established roles in cardiac fibrosis and/or heart disease (GJA1, TBC1D32, CXCL12, IL6R, and FURIN). Perturb-seq in cardiac fibroblasts after knocking out putative regulatory elements confirmed regulatory relationships involving GJA1, CXCL12, and FURIN, in addition to changes in transcriptomic signatures associated with fibroblasts in heart failure. Our results demonstrate how integrative multi-omic approaches can delineate pathophysiologically relevant regulatory circuits that connect protein-coding genes to non-coding genetic variants associated with disease. Overall design: Hi-C, ATAC-seq, and RNA-seq data were generated from primary cells--human cardiac myocytes (HCM) and normal human cardiac fibroblasts--ventricular (NHCFV). ATAC-seq and RNA-seq were also generated for immortalized human cardiac fibroblasts (iHCF), which were additionally used for gene editing experiments to validate SNP-gene predictions.