CYP2C9 Promoter Variable Number Tandem Repeat Polymorphism Regulates mRNA Expression in Human Livers

Abstract

ABSTRACT:CYP2C9 is involved in metabolism of nearly 25% of clinically used drugs. Coding region polymorphisms CYP2C9*2 and *3 contribute to interperson variability in drug dosage and clinical outcomes, whereas the role of a regulatory polymorphism remains uncertain. Measuring allelic RNA expression in 87 human liver samples, combined with genotyping, sequencing, and reporter gene assays, we identified a promoter variable number tandem repeat polymorphism (pVNTR) that fully accounted for allelic CYP2C9 mRNA expression differences. Present in three different variant forms [short (pVNTR-S), medium (pVNTR-M), and long (pVNTR-L)], only the pVNTR-S allele reduced the CYP2C9 mRNA level compared with the pVNTR-M (reference) allele. pVNTR-S is in linkage disequilibrium with *3, with linkage disequilibrium r 2 of 0.53 to 0.75 in different populations. In patients who were taking a maintenance dose of warfarin, the mean warfarin dose was associated with the copies of pVNTR-S (p ‫؍‬ 0.0001). However, in multivariate regression models that included the CYP2C9*3, pVNTR-S was no longer a significant predictor of the warfarin dose (p ‫؍‬ 0.60). These results indicate that although pVNTR-S reduced CYP2C9 mRNA expression, the in vivo effects of pVNTR-S on warfarin metabolism cannot be separated from the effects of *3. Therefore, it is not necessary to consider pVNTR-S as an additional biomarker for warfarin dosing. Larger clinical studies are needed to define whether the pVNTR-S has a minimal effect in vivo, or whether the effect attributed to *3 is really a combination of effects on expression by the pVNTR-S along with effects on catalytic activity from the nonsynonymous *3 variant.

Pharmacogenomics of Drug Metabolizing Enzymes and Transporters: Relevance to Precision Medicine

“…CYP2C9 constitutes approximately 18% of the total CYP protein in the human liver microsomes [62]. CYP2C9 metabolizes approximately 25% of clinically-administered drugs including anti-inflammatory agents such as flurbiprofen, hypoglycemic agents such as glipizide and tolbutamide, the anticoagulant S-warfarin, and the anticonvulsant phenytoin [63], [64]. More than 60 variant alleles have been identified for the CYP2C9 gene (http://www.cypalleles.ki.se/cyp2c9.htm).…”

Pharmacogenomics of CYP2C9: Functional and Clinical Considerations

“…Three patterns that were termed short, medium and long were identified. The medium repeat pattern was the most common and taken as the reference sequence [ 115 ]. The short allele appeared to be associated with decreased levels of CYP2C9 transcription in the liver, based on allelic imbalance studies and reporter gene assays.…”

“…The short allele appeared to be associated with decreased levels of CYP2C9 transcription in the liver, based on allelic imbalance studies and reporter gene assays. In addition, homozygosity for the short allele was associated with a lower warfarin dose but the overall effect on dose of this variant was less than that seen with CYP2C9*2 and *3 and was not significant in a multiple regression model [ 115 ].…”

Effects of coagulation factor VII polymorphisms on warfarin sensitivity and responsiveness in Jordanian cardiovascular patients during the initiation and maintenance phases of warfarin therapy

“…Exactly 25% of clinically used medications are metabolized by CYP2C9 , which is located on chromosome 10q24.2 and spans 55 kb 11,12. The genetic variability of CYP2C9 influences the treatment regimens of drugs with a narrow therapeutic index, including warfarin 13…”