Nicotine

Nicotine acts on nicotinic acetylcholine receptors in the brain. People who smoke adjust how many cigarettes they smoke and how deeply they inhale, and slower nicotine clearance is associated with smoking fewer cigarettes [1].

The liver converts 70 to 80% of nicotine to cotinine, and CYP2A6 carries out about 90% of that step. CYP2A6 also converts cotinine to 3'-hydroxycotinine, and the ratio of the two (the nicotine metabolite ratio) is used in research as a measure of how fast a person clears nicotine [1]. Nicotine's half-life in blood averages about 2 hours; cotinine's is about 16 hours [2].

Genes are not the only influence. Nicotine is cleared faster in women than in men, faster again with estrogen-containing contraceptives, and fastest in pregnancy, when nicotine clearance rises by about 60%. Menthol cigarettes slow it, and kidney failure reduces clearance [2]. The drug methoxsalen inhibits CYP2A6 [1].

CYP2A6 has many variant alleles. Gene2Rx reads six of them: *2 (rs1801272, Leu160His), *17 (rs28399454, Val365Met) and *20 (a two-letter deletion that cuts the protein short), which greatly reduce or remove activity toward nicotine; *9, a change in the gene's promoter that lowers how much enzyme is made; and *18 and *21, which reduce activity moderately [1]. The report counts *20 as no function and the other five as decreased function, and combines your two copies into a metabolizer group.

Several important alleles are structural. CYP2A6 sits next to a near copy of itself, CYP2A7, and uneven crossing-over between them produces the *4 whole-gene deletion, the *12 hybrid gene and gene duplications [1]. Gene2Rx does not detect these. A person with one *4 deletion can appear to have two normal copies, and someone with *4/*4, who makes no CYP2A6 at all, cannot be identified.

The human evidence is consistent. In a meta-analysis of 18 studies across ancestries, people with reduced-function CYP2A6 genotypes smoked fewer cigarettes per day, and *4/*4 smokers smoked fewer than people with a working copy [1]. In lighter smokers the link with cigarettes per day can disappear, because people also change how deeply and how often they inhale [1]. In European-ancestry smokers, CYP2A6 normal metabolizers who also carried the CHRNA5-region risk genotype smoked the most and had about twice the odds of lung cancer (odds ratio 2.03) [3]. In two studies of African American smokers, reduced CYP2A6 activity genotypes were associated with lower lung cancer risk (pooled odds ratio 0.64) [4].

CYP2A6 and quitting

The strongest treatment evidence comes from a randomized trial of 1,246 smokers grouped by their nicotine metabolite ratio, a blood measure of CYP2A6 activity rather than a genotype. Varenicline worked better than the nicotine patch in normal metabolizers (odds ratio 2.17 for quitting at the end of treatment), but not in slow metabolizers, who also reported more side effects with varenicline [5]. In that trial the number of slow metabolizers who needed the patch for one extra person to quit was 10.3, close to 8.1 for varenicline; in normal metabolizers it was 26.0 for the patch against 4.9 for varenicline [1]. Bupropion's effect did not differ by CYP2A6 genotype in an earlier trial [1].

How often reduced CYP2A6 function occurs depends on ancestry. About 50% of CYP2A6 gene copies in Japanese people carry a decrease- or loss-of-function allele, against 12% in White people, and 38% of African Americans have a reduced-function genotype against 21% of White people. The *4 deletion is about 1% of gene copies in White people and nearly 15% in Yupik Alaska Native people [1]. Because *4 and *12 are not read, Gene2Rx will miss more reduced metabolizers in East Asian and Alaska Native populations than in European ones.

CHRNA5 makes the alpha-5 subunit of some nicotinic receptors. At rs16969968 the G allele codes for aspartic acid at position 398 (Asp398) and the A allele for asparagine (Asn398). In laboratory tests, receptors containing the Asn398 form responded less to a nicotine-like agonist [6]. That is a reduced response, not an increased one. Mouse work suggests why it matters: alpha-5 receptors in the habenula, a small brain region, send a signal that limits nicotine intake at higher doses, and mice without alpha-5 took far more nicotine [7]. Whether the human variant acts the same way is not proven.

The human association has been replicated in large studies. Genome-wide studies of more than 140,000 people found that a marker in this CHRNA5-CHRNA3 region was associated with about one more cigarette per day per copy [8]. In a meta-analysis of 24 European-ancestry studies (29,072 people), the A allele was associated with a lower chance of quitting; people with A/A quit a median of four years later than people with G/G, and among smokers who developed lung cancer, A/A was associated with diagnosis a median of four years earlier [9]. A genome-wide study also linked the same region to lung cancer [10].

One finding points toward action. In a cessation trial of 1,073 smokers, people with the high-risk CHRNA5-region haplotype did poorly on placebo but responded to cessation medicines about three times as well as people with the low-risk haplotype, so the extra risk largely disappeared with treatment [11].

Frequencies are from the 1000 Genomes Project as listed in dbSNP [12]; the last column is calculated from them. Because the report counts one or two copies as "Increased Risk", most people of European ancestry receive that result.

COMT breaks down dopamine, particularly in the prefrontal cortex. At rs4680 the G allele codes for valine at position 158 and the A allele for methionine. The Val form gives higher enzyme activity in human brain tissue [13], and the Met form has been described as having three to four times lower activity [14]. The report calls Val/Val Normal Function, Val/Met Intermediate Function and Met/Met Decreased Function. About half of European gene copies carry Met (50%), against 28% in East Asian and African samples [15].

The link to smoking is inconsistent. In two studies of women, Met/Met was associated with better quitting, including about three times the odds of quitting in a nicotine patch trial [14]. A larger UK patch trial also found faster relapse in people with a Val allele [16]. On the other hand, a cohort study and meta-analysis found only weak evidence that Met was associated with heavier smoking and no association with quitting [17]. Taken together, the evidence does not show that Met carriers become more dependent, and some of it suggests they do better with the patch.

Gene2Rx wrote this guideline itself; no guideline body has published one. The report shows each gene separately, and its recommendations are written for a clinician. They are restated here in plain language with the strength the report gives them.

Read these against the evidence above. The CYP2A6 groups rest on well-understood biology and a large treatment trial, although that trial measured enzyme activity in the blood, not genotype. Slow metabolizers in that trial did as well on the patch as on varenicline and had fewer side effects with the patch [5]. Poor metabolizers were not studied separately, so the report's advice to avoid nicotine replacement in that group is a cautious extrapolation rather than a trial finding. The CHRNA5 association with smoking is strong; the reward-and-craving explanation in the report is not established, and the laboratory work shows a weaker receptor response. The COMT rows rest on mixed evidence, and the strong rating for Met/Met is not supported by the studies above.

Smoking is common, quitting is hard, and two of these genes have unusually solid evidence. CYP2A6 sets how fast nicotine is cleared, and that rate was used prospectively to choose between the patch and varenicline in a randomized trial [5]. The CHRNA5 variant has been tied to cigarettes per day, age at quitting and lung cancer in studies of tens of thousands of people [8] [9], and carriers appear to benefit more from cessation medicines [11].

The practical value is mostly for people who want to quit: a result can support a conversation about which cessation medicine to try and why a first attempt may have been harder. It is not a way to judge how much nicotine is safe. The COMT part is included because it has been studied for years, but it is the least reliable result in this guideline.

If you want to stop smoking or vaping, bring your report to your clinician or pharmacist. A CYP2A6 Slow or Poor Metabolizer result is relevant to the choice between the nicotine patch and varenicline, and a CHRNA5 Increased Risk result is a reason to use a cessation medicine rather than trying without one [5] [11]. Do not start, stop or change a cessation medicine on the basis of a genetic result without your prescriber.

Other factors also change nicotine clearance. Estrogen-containing contraceptives and pregnancy speed it up, menthol slows it, and the inhibitor methoxsalen blocks CYP2A6 [2] [1]. Tell your clinician about these too.

No result on this page makes nicotine use safe. A slow CYP2A6 result is associated with smoking fewer cigarettes, but smokers with that result still face the harms of smoking.

Each position Gene2Rx reads is measured directly or inferred by imputation from nearby markers; a variant at a position the data does not cover cannot be seen. For CYP2A6 this matters most. The *4 deletion, the *12 hybrid, duplications and many rarer alleles are not read, so a Normal Metabolizer result does not rule out reduced activity, particularly in people of East Asian or Alaska Native ancestry [1]. Consumer arrays (23andMe, AncestryDNA, MyHeritage) are not clinical-grade tests, and their raw data is labeled not for medical use.

The research was done mostly in cigarette smokers, mainly of European ancestry. Much less is known about e-cigarettes or nicotine pouches. The genes also explain only part of the difference between people: hormones, menthol, other medicines and the way a person smokes all change nicotine exposure [2].

Does a CHRNA5 risk result mean I cannot quit?

No. The effect on quitting is modest, and in a cessation trial the extra risk largely went away when people used a cessation medicine [11].

I am a slow CYP2A6 metabolizer. Should I use a lower-strength patch?

Not on your own. In the trial, slow metabolizers did as well on the standard patch as on varenicline [5]. If you notice nausea, dizziness or a racing heart on the patch, tell your pharmacist or clinician rather than changing the dose yourself.

Is a test of my nicotine metabolism better than a gene test?

The nicotine metabolite ratio measured in blood or saliva reflects CYP2A6 activity including deletions, hormones and menthol, and it was the measure used in the treatment trial [5]. It can only be measured in people who currently use nicotine [1].

1. Tanner JA, Tyndale RF. Variation in CYP2A6 activity and personalized medicine. J Pers Med (2017). CYP2A6 alleles, ancestry differences, smoking behavior and cessation trials.
2. Benowitz NL, Hukkanen J, Jacob P. Nicotine chemistry, metabolism, kinetics and biomarkers. Handb Exp Pharmacol (2009). Half-lives and non-genetic influences on nicotine clearance.
3. Wassenaar CA et al. Relationship between CYP2A6 and CHRNA5-CHRNA3-CHRNB4 variation and smoking behaviors and lung cancer risk. J Natl Cancer Inst (2011). Combined effects in European-ancestry smokers.
4. Wassenaar CA et al. CYP2A6 reduced activity gene variants confer reduction in lung cancer risk in African American smokers: findings from two independent populations. Carcinogenesis (2015). CYP2A6 and lung cancer in African American smokers.
5. Lerman C et al. Use of the nicotine metabolite ratio as a genetically informed biomarker of response to nicotine patch or varenicline for smoking cessation: a randomised, double-blind placebo-controlled trial. Lancet Respir Med (2015). Patch versus varenicline by nicotine metabolism rate.
6. Bierut LJ et al. Variants in nicotinic receptors and risk for nicotine dependence. Am J Psychiatry (2008). Replication and receptor function of rs16969968.
7. Fowler CD et al. Habenular alpha5 nicotinic receptor subunit signalling controls nicotine intake. Nature (2011). Mouse evidence for how alpha-5 limits nicotine intake.
8. Tobacco and Genetics Consortium. Genome-wide meta-analyses identify multiple loci associated with smoking behavior. Nat Genet (2010). CHRNA5-CHRNA3 region and cigarettes per day.
9. Chen LS et al. CHRNA5 risk variant predicts delayed smoking cessation and earlier lung cancer diagnosis: a meta-analysis. J Natl Cancer Inst (2015). Age at quitting and at lung cancer diagnosis by genotype.
10. Hung RJ et al. A susceptibility locus for lung cancer maps to nicotinic acetylcholine receptor subunit genes on 15q25. Nature (2008). Lung cancer genome-wide association.
11. Chen LS et al. Interplay of genetic risk factors (CHRNA5-CHRNA3-CHRNB4) and cessation treatments in smoking cessation success. Am J Psychiatry (2012). Cessation medicines offset the genetic risk.
12. dbSNP: rs16969968 (CHRNA5). Allele frequencies, including 1000 Genomes populations.
13. Chen J et al. Functional analysis of genetic variation in catechol-O-methyltransferase (COMT): effects on mRNA, protein, and enzyme activity in postmortem human brain. Am J Hum Genet (2004). Val158Met and enzyme activity.
14. Colilla S et al. Association of catechol-O-methyltransferase with smoking cessation in two independent studies of women. Pharmacogenet Genomics (2005). Met/Met and quitting.
15. dbSNP: rs4680 (COMT). Allele frequencies, including 1000 Genomes populations.
16. Munafo MR et al. Association of COMT Val108/158Met genotype with smoking cessation. Pharmacogenet Genomics (2008). Relapse on the nicotine patch by genotype.
17. Munafo MR et al. Association of COMT Val(108/158)Met genotype and cigarette smoking in pregnant women. Nicotine Tob Res (2011). Cohort and meta-analysis with weak or null findings.