In Vivo Functional Effects of CYP2C9 M1L, a Novel and Common Variant in the Yup’ik Alaska Native Population

Abstract

Alaska Native people are under-represented in genetic research but have unique gene variation that may critically impact their response to pharmacotherapy. Full resequencing of CYP2C9 in a cross-section of this population identified CYP2C9 Met1Leu ( M1L) , a novel, relatively common single nucleotide polymorphism hypothesized to confer CYP2C9 poor metabolizer phenotype by disrupting the start codon. M1L is present at a minor allele frequency of 6.3% in Yup’ik Alaska Native people and thus can contribute to the risk of an adverse drug response from narrow-therapeutic-index CYP2C9 substrates such as ( S) -warfarin. This study’s objective was to characterize the catalytic efficiency of the Leu1 variant enzyme in vivo by evaluating the pharmacokinetic behavior of naproxen, a probe substrate for CYP2C9 activity, in genotyped Yup’ik participants. We first confirmed the selectivity of ( S)-naproxen O-demethylation by CYP2C9 using activity-phenotyped human liver microsomes and selective cytochrome P450 inhibitors and then developed and validated a novel liquid chromatography mass spectrometry method for simultaneous quantification of ( S) -naproxen, ( S) -O-desmethylnaproxen, and naproxen acyl glucuronide in human urine. The average ratio of ( S) -O-desmethylnaproxen to unchanged ( S) -naproxen in urine was 18.0 ± 8.0 ( n = 11) for the homozygous CYP2C9 Met1 reference group and 10.3 ± 6.6 ( n = 11) for the Leu1 variant carrier group ( P = 0.011). The effect of M1L variation on CYP2C9 function and its potential to alter the pharmacokinetics of drugs metabolized by the enzyme has clinical implications and should be included in a variant screening panel when pharmacogenetic testing in the Alaska Native population is warranted.

Significance Statement

The novel CYP2C9 Met1Leu variant in Alaska Native people was recently identified. This study validated ( S) -naproxen as a CYP2C9 probe substrate to characterize the in vivo functional activity of the CYP2C9 Leu1 variant. The results of this pharmacogenetic-pharmacokinetic study suggest that the CYP2C9 Leu1 variant exhibits loss of enzyme activity. This finding may be important to consider when administering narrow-therapeutic-index medications metabolized by CYP2C9 and also compels further investigation to characterize novel genetic variation in understudied populations.