Abstract 413: Lipoprotein SCARB1 Intronic Variant Associated With Increased Coronary Heart Disease Risk Affects Cardio-Protective Gene Networks

Abstract

Introduction: We previously reported a common intronic SCARB1 (12q24.31) variant, rs10846744, located in an enhancer region, to be significantly associated with coronary artery disease (CAD) in the Multi-Ethnic Study of Atherosclerosis (MESA). RNA-Seq showed expression of the immune checkpoint inhibitor lymphocyte activation gene 3 ( LAG3 , 12p13.31), to be 5-fold lower in carriers of the risk allele, while low plasma LAG3 protein levels were also significantly associated with increased CAD risk in MESA, after multivariate regression analysis. Hypothesis: That the SCARB1 rs10846744 variant disrupts long-range transcriptional regulation of LAG3 disturbing cardio-protective and anti-inflammatory gene networks to promote CAD. Methods and Results: Using functional genomics (HiC global chromatin capture, ChIP-Seq and RNA-Seq) in reference and risk EBV-transformed B lymphocytes to assess 3D chromatin architecture and gene-gene interactions at a 2.5kb resolution, we did not observe direct chromatin contacts between SCARB1 and LAG3. In the reference allele, an enhancer-rich intermediate contact (12q13.13) was found containing genes associated with cholesterol ( SOAT2 ) and NR2F2 signaling ( RARG ). This same 12q13.13 region was in direct contact with 22q12.3 ( APOLI) , an apoprotein associated with HDL and innate immunity. Micro-looping within the rs10846744 12q24.31 region showed direct contacts with other enhancers ( NCOR2 ) and cardiovascular loci ( TMEM132B ), while LAG3 micro-looping on 12p13.31 was associated with immune regulatory networks ( CD4 ). Loci associated with viral infection, cytokine production, heart failure and autoimmunity were also identified. NR2F2 disrupted contacts in the risk allele, implicating NR2F2 as a dysfunctional rs10846744 transcriptional repressor altering gene networks. The risk allele included contacts near PCSK9 , VLDLR and 2q33.1, a CAD locus. Conclusion: Functional genomics of the SCARB1 rs10846744 enhancer region identified a number of intra- and inter-chromosomal chromatin contacts in reference cells that were markedly disrupted in risk cells. Perturbing NR2F2 and/or genes disrupted in the SCARB1 -NR2F2 immuno-cardiovascular axis may protect against CAD in the rs10846744 risk population.