Deep Sequencing of Three Loci Implicated in Large-Scale Genome-Wide Association Study Smoking Meta-Analyses

Investigation of the genetic effect of 56 tobacco-smoking susceptibility genes on DNA methylation and RNA expression in human brain

Although various susceptibility genes have been revealed to influence tobacco smoking, the underlying regulatory mechanisms between genetic variants and smoking are poorly understood. In this study, we investigated cis-expression quantitative trait loci (cis-eQTLs) and methylation quantitative trait loci (mQTLs) for 56 candidate smoking-linked genes using the BrainCloud cohort samples. An eQTL was revealed to significantly affect EGLN2 expression in the European sample and two mQTLs were respectively detected in CpG sites in NRXN1 and CYP2A7. Interestingly, we found for the first time that the minor allele of the single nucleotide polymorphism (SNP) rs3745277 located in CYP2A7P1 (downstream of CYP2B6) significantly decreased methylation at the CpG site for CYP2A7 (cg25427638; P = 5.31 × 10^-7), reduced expression of CYP2B6 (P = 0.03), and lowered the percentage of smokers (8.8% vs. 42.3%; Odds Ratio (OR) = 0.14, 95% Confidence Interval (CI): 0.02-0.62; P = 4.47 × 10^-3) in a dominant way for the same cohort sample. Taken together, our findings resulted from analyzing genetic variation, DNA methylation, mRNA expression, and smoking status together using the same participants revealed a regulatory mechanism linking mQTLs to the smoking phenotype. Moreover, we demonstrated the presence of different regulatory effects of low-frequency and common variants on mRNA expression and DNA methylation.

Functional characterization of novel rare CYP2A6 variants and potential implications for clinical outcomes

CYP2A6 activity, phenotyped by the nicotine metabolite ratio (NMR), is a predictor of several smoking behaviors, including cessation and smoking‐related disease risk. The heritability of the NMR is 60–80%, yet weighted genetic risk scores (wGRSs) based on common variants explain only 30–35%. Rare variants (minor allele frequency <1%) are hypothesized to explain some of this missing heritability. We present two targeted sequencing studies where rare protein‐coding variants are functionally characterized in vivo, in silico, and in vitro to examine this hypothesis. In a smoking cessation trial, 1687 individuals were sequenced; characterization measures included the in vivo NMR, in vitro protein expression, and metabolic activity measured from recombinant proteins. In a human liver bank, 312 human liver samples were sequenced; measures included RNA expression, protein expression, and metabolic activity from extracted liver tissue. In total, 38 of 47 rare coding variants identified were novel; characterizations ranged from gain‐of‐function to loss‐of‐function. On a population level, the portion of NMR variation explained by the rare coding variants was small (~1%). However, upon incorporation, the accuracy of the wGRS was improved for individuals with rare protein‐coding variants (i.e., the residuals were reduced), and approximately one‐third of these individuals (12/39) were re‐assigned from normal to slow metabolizer status. Rare coding variants can alter an individual’s CYP2A6 activity; their integration into wGRSs through precise functional characterization is necessary to accurately assess clinical outcomes and achieve precision medicine for all. Investigation into noncoding variants is warranted to further explain the missing heritability in the NMR.

The Role of Pharmacogenetics in Smoking

Smoking continues to be the leading preventable contributor to death worldwide. Twin studies have suggested a significant genetic contribution underlying most smoking behaviors (40-70% heritability estimates). Candidate gene studies of smoking phenotypes have identified several pharmacogenes implicated in nicotine's pharmacokinetics (CYP2A6, CYP2B6, CYP2A13, FMOs, UGTs, and OCT2), and nicotine's pharmacodynamic response in the central nervous system (nicotinic acetylcholine receptors, as well as through the dopaminergic and serotonergic systems). Subsequent genome-wide association studies (GWAS) have confirmed the role of certain pharmacogenes through hypothesis-free approaches. Furthermore, pharmacogenes that alter the efficacy of smoking cessation pharmacotherapies, including nicotine replacement therapies, bupropion, and varenicline, may also impact quitting success. In this brief review we highlight the role of pharmacogenes in smoking behaviors, such as smoking status, consumption, nicotine dependence, spontaneous quitting, and altered abstinence to pharmacotherapies; We provide examples from initial candidate gene associations and subsequent GWAS. The genes CYP2A6 and the CHRNA5-A3-B4 confer the most replicated sources of genetic variation in smoking behaviors, likely due to their importance in nicotine's pharmacology. We will also provide examples of genetic scoring approaches, and the role of rare variants in explaining a portion of the missing heritability in smoking behaviors.

Genetic susceptibility to nicotine addiction: Advances and shortcomings in our understanding of the CHRNA5/A3/B4 gene cluster contribution

Over the last decade, robust human genetic findings have been instrumental in elucidating the heritable basis of nicotine addiction (NA). They highlight coding and synonymous polymorphisms in a cluster on chromosome 15, encompassing the CHRNA5, CHRNA3 and CHRNB4 genes, coding for three subunits of the nicotinic acetylcholine receptor (nAChR). They have inspired an important number of preclinical studies, and will hopefully lead to the definition of novel drug targets for treating NA. Here, we review these candidate gene and genome-wide association studies (GWAS) and their direct implication in human brain function and NA-related phenotypes. We continue with a description of preclinical work in transgenic rodents that has led to a mechanistic understanding of several of the genetic hits. We also highlight important issues with regards to CHRNA3 and CHRNB4 where we are still lacking a dissection of their role in NA, including even in preclinical models. We further emphasize the use of human induced pluripotent stem cell-derived models for the analysis of synonymous and intronic variants on a human genomic background. Finally, we indicate potential avenues to further our understanding of the role of this human genetic variation. This article is part of the special issue on 'Contemporary Advances in Nicotine Neuropharmacology'.

A Brief Report of Smoking Behaviors in Patients with Incidental Pulmonary Nodules: Associations with Communication and Risk Perception

Introduction:

Incidental pulmonary nodules (IPNs) are commonly found on routine chest imaging. Little is known about smoking behaviors among patients with IPNs or characteristics of patient-clinician communication that may contribute to these behaviors. We assessed the association of patient characteristics and communication quality with smoking behaviors and stage of change for tobacco cessation among patients with IPNs.

Materials and methods:

Prospective, repeated-measures, cohort study of current smokers and past-year quitters with IPNs treated within the Veterans Affairs Portland Health Care System. Eligible patients had newly reported, incidental nodules <3 cm planned for non-urgent computed tomography (CT) follow-up. Our primary outcomes were changes in amount smoked and stage of change for tobacco cessation throughout the follow-up period. We used multivariable-adjusted generalized estimating equations for analyses.

Results:

We identified 37 current smokers and 9 recent quitters. By the final visit, 8 of 36 (22%) baseline smokers had quit and 2 of 7 (29%) recent quitters had resumed smoking. Of 40 respondents, 23 (58%) reported receiving any tobacco treatment (recommendation to quit, medication, and/or behavioral treatment) at least once during follow-up. We found no significant associations of high-quality communication, patient distress, self-perceived risk of lung cancer, and self-reported clinician-recommended smoking cessation interventions with decrease in amount smoked or positive stage of change.

Conclusions:

Many smokers and recent quitters with IPNs quit during follow-up, though nearly half reported no quit support. We found no association between communication quality or quit support and decreased smoking. The intensity of tobacco treatment offered may have been insufficient to affect behavior.

Lung cancer screening-low dose CT for lung cancer screening: recent trial results and next steps

Screening for lung cancer using low-dose CT has already been implemented in North America following the results of the National Lung Screening Trial. Outside North America, clinicians and researchers are addressing issues that may have a major impact on the success of screening programmes by reviewing results of existing trials and by designing new research and pilot programmes. This review summarizes the work that has been done to try to answer the remaining questions and highlights potential barriers which may affect screening uptake and cost-effectiveness.

Implementation of lung cancer CT screening in the Nordic countries

INTRODUCTION

We review the current knowledge of CT screening for lung cancer and present an expert-based, joint protocol for the proper implementation of screening in the Nordic countries.

MATERIALS AND METHODS

Experts representing all the Nordic countries performed literature review and concensus for a joint protocol for lung cancer screening.

RESULTS AND DISCUSSION

Areas of concern and caution are presented and discussed. We suggest to perform CT screening pilot studies in the Nordic countries in order to gain experience and develop specific and safe protocols for the implementation of such a program.

The Association between Smoking Abstinence and Mortality in the National Lung Screening Trial

RATIONALE

Smoking is the largest contributor to lung cancer risk, and those who continue to smoke after diagnosis have a worse survival. Screening for lung cancer with low-dose computed tomography (LDCT) reduces mortality in high-risk individuals. Smoking cessation is an essential component of a high-quality screening program.

OBJECTIVES

To quantify the effects of smoking history and abstinence on mortality in high-risk individuals who participated in the NLST (National Lung Screening Trial).

METHODS

This is a secondary analysis of a randomized controlled trial (NLST).

MEASUREMENTS AND MAIN RESULTS

Measurements included self-reported demographics, medical and smoking history, and lung cancer-specific and all-cause mortality. Cox regression was used to study the association of mortality with smoking status and pack-years. Kaplan-Meier survival curves were examined for differences in survival based on trial arm and smoking status. Current smokers had an increased lung cancer-specific (hazard ratio [HR], 2.14-2.29) and all-cause mortality (HR, 1.79-1.85) compared with former smokers irrespective of screening arm. Former smokers in the control arm abstinent for 7 years had a 20% mortality reduction comparable with the benefit reported with LDCT screening in the NLST. The maximum benefit was seen with the combination of smoking abstinence at 15 years and LDCT screening, which resulted in a 38% reduction in lung cancer-specific mortality (HR, 0.62; 95% confidence interval, 0.51-0.76).

CONCLUSIONS

Seven years of smoking abstinence reduced lung cancer-specific mortality at a magnitude comparable with LDCT screening. This reduction was greater when abstinence was combined with screening, highlighting the importance of smoking cessation efforts in screening programs.

Nicotinic acetylcholine receptors: upregulation, age-related effects and associations with drug use

Nicotinic acetylcholine receptors are ligand-gated ion channels that exogenously bind nicotine. Nicotine produces rewarding effects by interacting with these receptors in the brain's reward system. Unlike other receptors, chronic stimulation by an agonist induces an upregulation of receptor number that is not due to increased gene expression in adults; while upregulation also occurs during development and adolescence there have been some opposing findings regarding a change in corresponding gene expression. These receptors have also been well studied with regard to human genetic associations and, based on evidence suggesting shared genetic liabilities between substance use disorders, numerous studies have pointed to a role for this system in comorbid drug use. This review will focus on upregulation of these receptors in adulthood, adolescence and development, as well as the findings from human genetic association studies which point to different roles for these receptors in risk for initiation and continuation of drug use.