Background:
Cholesterol 7α-hydroxylase (CYP7A1) catalyzes the rate-limiting step in bile acid biosynthesis from cholesterol, a main pathway for cholesterol removal from the body. CYP7A1 SNPs are associated with total cholesterol and LDL levels, risk of cardiovascular diseases, and other phenotypes; however, results are inconsistent, and causative variants remain uncertain, except for a frequent promoter SNP (rs3808607).
Methods:
We employed chromatin conformation capture (4C assay), chromatin immunoprecipitation (ChIP-qPCR assay) in hepatocytes, and CRISPR-mediated genome editing in HepG2 cells to identify regulatory regions for CYP7A1. We then screened for SNPs located in regulatory regions, testing effects on reporter gene assays and on hpatic CYP7A1 expression by measuring allelic mRNA expression imbalance.
Results:
4C assays showed several regions interacting with CYP7A1promoter. CRISPR-mediated genome editing in HepG2 cells revealed a novel CYP7A1 enhancer and a repressor region, located >10 kb downstream of the CYP7A1 promoter. SNP screening with an allelic mRNA expression imbalance in human livers and reporter gene assays identified a frequent functional SNP (rs9297994) located in the downstream CYP7A1 enhancer region. SNP rs9297994 is in high linkage disequilibrium with promoter SNP rs3808607, but has opposite effects on CYP7A1 mRNA expression. Their combined effects using a 2-SNP model robustly associate with hepatic CYP7A1 mRNA expression, ranging over two orders of magnitude. Moreover, only the 2-SNP model, but not each single SNP alone, is significantly associated with LDL levels, risk of CAD, statin response, and diabetes in several clinical cohorts, including CATHGEN and Framingham.
Conclusion:
Two interacting regulatory SNPs modulate CYP7A1 expression and are associated with risk of coronary artery disease and diabetes.