GSE195656
Trans-interaction of risk loci 6p24.1 and 10q11.21 is associated with endothelial damage in coronary artery disease
The variant rs6903956 has been identified as one of the Asian-specific genetic risk factors for coronary artery disease (CAD). However, rs6903956 lies in a non-coding locus on chromosome 6p24.1, hampering efforts of functional annotation. We produced induced pluripotent stem cells (iPSCs) from CAD patients (AA risk genotype at rs6903956) and normal controls (GG non-risk genotype at rs6903956). CRIPSR-Cas9-based deletions (?63-89bp) on 6p24.1 including rs6903956 were performed to generate isogenic iPSC-derived endothelial cells. Edited CAD endothelial cells exhibited a global transcriptional downregulation of pathways relating to abnormal vascular physiology and activated endothelial processes. Surprisingly, deletions on either risk or non-risk 6p24.1 locus had minimal influence on cis gene expressions. Instead, a CXC chemokine ligand on chromosome 10q11.21, CXCL12, was uncovered as a potential effector gene in CAD endothelial cells. Underlying this effect was the preferential inter-chromosomal interaction of 6p24.1 risk locus to a weak promoter of CXCL12, confirmed by chromatin conformation capture assays on our iPSC-derived endothelial cells. Functionally, risk genotypes AA/ AG at rs6903956 were associated significantly with elevated levels of circulating damaged endothelial cells in CAD patients. Circulating endothelial cells isolated from patients with risk genotypes AA/ AG were also found to have 10 folds higher CXCL12 transcript copies/ cell than those with non-risk genotype GG. Our study reveals the trans-acting impact of 6p24.1 risk locus, involving the atherosclerosis-implicated gene CXCL12, and is associated with intensified endothelial injury. Overall design: RNA-seq of endothelial cells differentiated from patient derived induced pluripotent stem cells (iPSCs) with CRISPR-Cas9 based deletions (63-89bp) on 6p24.1 including rs6903956