Regulatory variants in a novel distal enhancer regulate the expression of CYP3A4 and CYP3A5

Abstract

The cytochrome P450 3As (CYP3As) are abundantly expressed in the liver and metabolize many commonly prescribed medications. Their expression is highly variable between individuals with little known genetic cause. Despite extensive investigation, cis-acting genetic elements that control the expression of the CYP3As remain uncharacterized. Using chromatin conformation capture (4C assays), we detected reciprocal interaction between a distal regulatory region (DRR) and the CYP3A4 promoter. The DRR colocalizes with a variety of enhancer marks and was found to promote transcription in reporter assays. CRISPR-mediated deletion of the DRR decreased expression of CYP3A4, CYP3A5, and CYP3A7, supporting its role as a shared enhancer regulating the expression of three CYP3A genes. Using reporter gene assays, we identified two single-nucleotide polymorphisms (rs115025140 and rs776744/rs776742) that increased DRR-driven luciferase reporter expression. In a liver cohort (n = 246), rs115025140 was associated with increased expression of CYP3A4 mRNA (1.8-fold) and protein (1.6-fold) and rs776744/rs776742 was associated with 1.39-fold increased expression of CYP3A5 mRNA. The rs115025140 is unique to the African population and in a clinical cohort of African Americans taking statins for lipid control rs115025140 carriers showed a trend toward reduced statin-mediated lipid reduction. In addition, using a published cohort of Chinese patients who underwent renal transplantation taking tacrolimus, rs776744/rs776742 carriers were associated with reduced tacrolimus concentration after adjusting for CYP3A5*3. Our results elucidate a complex regulatory network controlling expression of three CYP3A genes and identify two novel regulatory variants with potential clinical relevance for predicting CYP3A4 and CYP3A5 expression. Study Highlights WHAT IS THE CURRENT KNOWLEDGE ON THE TOPIC?There is limited knowledge concerning distal cis-acting regulatory elements and genetic variants controlling expression of the CYP3As.

Extreme Phenotype Sampling and Next Generation Sequencing to Identify Genetic Variants Associated with Tacrolimus in African American Kidney Transplant Recipients

“…The rs115025140 variant also showed a trend towards reduced statin e cacy. While rs111266634 variant showed a reduced reporter expression in luciferase reporter assay without affecting CYP3A4 and CYP3A5 gene expression [20]. This study also reported that the rs776744 and rs776742 variants, which are not exclusive in AAs, were associated with TAC trough concentrations in Chinese KTRs.…”

“…Collins and colleagues [20] reported variants in the CYP3A DRR that increased expression of CYP3A4 and CYP3A5 mRNA and/or protein. The rs115025140 variant also showed a trend towards reduced statin e cacy.…”

“…Two of these variants were exclusively present in AAs (rs115025140 and rs111266634). Additionally, the rs776744 and rs776742 variants were reported to be associated with TAC troughs in Chinese KTRs [20].…”

“…Within CYB5R2, rs61733057 was predicted to disrupt protein function. Recently, Collins et al, [20] discovered novel genetic variants in the distal regulatory region (DRR) of CYP3A locus. These variants were reported to in uence CYP3A4 and CYP3A5 expression and may impact drug metabolism in humans.…”

Pharmacogenomics Beyond Single Common Genetic Variants: The Way Forward

“…Thus, mutations in the neighboring CYP2C18 gene are associated with ultrarapid metabolism of escitalopram, which is associated with decreased escitalopram levels at a similar or greater extent to those caused by the wellestablished ultrarapid CYP2C19 * 17 allele. Analogous cases have been described for a haplotype within the UGT2B locus, which associates with decreased glucuronidation of clozapine (67), and for a novel distal enhancer in the CYP3A locus that impacts statin efficacy and tacrolimus clearance (68). It is of utmost importance to identify the functionally important genetic variants within the novel CYP2C:TG and UGT2B haplotypes, as the linkage of marker SNPs could drastically differ between ethnic groups.…”