Genome-wide meta-analysis reveals common splice site acceptor variant in CHRNA4 associated with nicotine dependence.

Dana B Hancock ,J Chen,X Chen,Peter Kraft ,Gunnar W Reginsson ,Simon Stacey ,Henry R Kranzler ,Eric O Johnson ,Timothy B Baker ,Joel Gelernter ,Sharon M Lutz ,Daníel F Guðbjartsson ,Nathan Gaddis ,Fangyi Gu ,Heike Bickeböller ,John E Hokanson ,Maria Teresa Landi ,Laura J Bierut ,Anu Loukola ,Jaakko Kaprio ,Stacy Steinberg ,Christopher I Amos ,Cristie Glasheen ,Irene Brüske ,Thorgeir E Thorgeirsson ,Nancy L Saccone ,Pamela A F Madden ,Beenish Qaiser ,Florian Zink ,Brittni N Frederiksen ,Lindsay A Farrer ,Neil E Caporaso ,Richard Sherva ,Kāri Stefánsson

doi:10.1038/tp.2015.149

Abstract

We conducted a 1000 Genomes–imputed genome-wide association study (GWAS) meta-analysis for nicotine dependence, defined by the Fagerström Test for Nicotine Dependence in 17 074 ever smokers from five European-ancestry samples. We followed up novel variants in 7469 ever smokers from five independent European-ancestry samples. We identified genome-wide significant association in the alpha-4 nicotinic receptor subunit (CHRNA4) gene on chromosome 20q13: lowest P=8.0 × 10−9 across all the samples for rs2273500-C (frequency=0.15; odds ratio=1.12 and 95% confidence interval=1.08–1.17 for severe vs mild dependence). rs2273500-C, a splice site acceptor variant resulting in an alternate CHRNA4 transcript predicted to be targeted for nonsense-mediated decay, was associated with decreased CHRNA4 expression in physiologically normal human brains (lowest P=7.3 × 10−4). Importantly, rs2273500-C was associated with increased lung cancer risk (N=28 998, odds ratio=1.06 and 95% confidence interval=1.00–1.12), likely through its effect on smoking, as rs2273500-C was no longer associated with lung cancer after adjustment for smoking. Using criteria for smoking behavior that encompass more than the single ‘cigarettes per day' item, we identified a common CHRNA4 variant with important regulatory properties that contributes to nicotine dependence and smoking-related consequences.

Highlights

Cigarette smoking is a major contributor to cancer, vascular disease and lung disease, and the leading cause of preventable mortality worldwide.[1]
To evaluate the regulatory potential of novel intronic single nucleotide polymorphism (SNP) in CHRNA4 associated with nicotine dependence, we first used RNA-seq and genotype data from the pilot phase of the Genotype-Tissue Expression (GTEx) project to investigate SNP effects on splicing
We focused on the liver tissue, which had the highest CHRNA4 expression levels among the GTEx tissues, and all brain tissues combined, which had lower CHRNA4 expression levels but high relevance for nicotine dependence

Summary

Introduction

Cigarette smoking is a major contributor to cancer, vascular disease and lung disease, and the leading cause of preventable mortality worldwide.[1] Nicotine dependence is heritable,[2] and genome-wide association study (GWAS) analyses of smoking behaviors and nicotine dependence have unequivocally identified single nucleotide polymorphism (SNP) associations within nicotinic acetylcholine receptor gene clusters on chromosomes 15q25 (CHRNA5-CHRNA3-CHRNB4) and 8p11 (CHRNB3CHRNA6).[3,4,5,6,7,8,9] The largest prior GWAS of smoking behavior was conducted using very large sample sizes (N up to 74 053) and phenotypes such as smoking history (ever vs never), age of onset, smoking cessation (former vs current) and cigarettes per day (CPD).[5,6,7]. East Cornwallis Road, P.O. Box 12194, Research Triangle Park, NC 27709, USA.

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Results

Conclusion