A Genome-Wide Association Study of a Biomarker of Nicotine Metabolism

Individuals with fast nicotine metabolism typically smoke more and thus have a greater risk for smoking-induced diseases. Further, the efficacy of smoking cessation pharmacotherapy is dependent on the rate of nicotine metabolism. Our objective was to use nicotine metabolite ratio (NMR), an established biomarker of nicotine metabolism rate, in a genome-wide association study (GWAS) to identify novel genetic variants influencing nicotine metabolism. A heritability estimate of 0.81 (95% CI 0.70–0.88) was obtained for NMR using monozygotic and dizygotic twins of the FinnTwin cohort. We performed a GWAS in cotinine-verified current smokers of three Finnish cohorts (FinnTwin, Young Finns Study, FINRISK2007), followed by a meta-analysis of 1518 subjects, and annotated the genome-wide significant SNPs with methylation quantitative loci (meQTL) analyses. We detected association on 19q13 with 719 SNPs exceeding genome-wide significance within a 4.2 Mb region. The strongest evidence for association emerged for CYP2A6 (min p = 5.77E-86, in intron 4), the main metabolic enzyme for nicotine. Other interesting genes with genome-wide significant signals included CYP2B6, CYP2A7, EGLN2, and NUMBL. Conditional analyses revealed three independent signals on 19q13, all located within or in the immediate vicinity of CYP2A6. A genetic risk score constructed using the independent signals showed association with smoking quantity (p = 0.0019) in two independent Finnish samples. Our meQTL results showed that methylation values of 16 CpG sites within the region are affected by genotypes of the genome-wide significant SNPs, and according to causal inference test, for some of the SNPs the effect on NMR is mediated through methylation. To our knowledge, this is the first GWAS on NMR. Our results enclose three independent novel signals on 19q13.2. The detected CYP2A6 variants explain a strikingly large fraction of variance (up to 31%) in NMR in these study samples. Further, we provide evidence for plausible epigenetic mechanisms influencing NMR.Author Summary: Nicotine metabolism rate significantly varies between individuals and affects smoking behavior. Individuals with fast nicotine metabolism typically smoke more and thus have a greater risk for smoking-induced diseases. Further, the efficacy of smoking cessation pharmacotherapy is dependent on nicotine metabolism rate. Twin and family studies have shown that genes influence nicotine metabolism; however, only a minor fraction of variance in inter-individual differences in nicotine metabolism is accounted for by known reduced activity variants in CYP2A6, the main metabolic enzyme for nicotine. Here we utilized a biomarker of nicotine metabolism (nicotine metabolite ratio, NMR) in a genome-wide association study of three Finnish cohorts to identify novel genetic variants influencing nicotine metabolism rate. Our results enclose three independent novel signals in CYP2A6. The detected variants explain a strikingly large fraction of variance (up to 31%) in NMR in the study samples. A genetic risk score constructed using the independent signals predicts smoking quantity in two independent Finnish samples. Further, we enclose evidence for plausible epigenetic mechanisms influencing NMR. With the advent of other nicotine delivery devices than tobacco, such as e-cigarettes, the need to understand the long-term consequences and action mechanisms of nicotine and its metabolism are of high public health relevance.