Association and cis-mQTL analysis of variants in CHRNA3-A5, CHRNA7, CHRNB2, and CHRNB4 in relation to nicotine dependence in a Chinese Han population

Qiang Liu,Maiqiu Wang,Jingjing Li,Rongli Fan,Jundong Wang,Li Wen,Zhongli Yang,Kunkai Su,Yinghao Yao,Xianzhong Jiang,Thomas J Payne,Yunlong Ma,Wenji Yuan,Haijun Han,Keran Jiang,Wenyan Cui,Jiali Chen,Ming D Li

doi:10.1038/s41398-018-0130-x

Abstract

Nicotine dependence (ND) is a worldwide health problem. Numerous genetic studies have demonstrated a significant association of variants in nicotinic acetylcholine receptors (nAChRs) with smoking behaviors. However, most of these studies enrolled only subjects of European or African ancestry. In addition, although an increasing body of evidence implies a causal connection of single-nucleotide polymorphisms (SNPs) and epigenetic regulation of gene expression, few studies of this issue have been reported. In this study, we performed both association and interaction analysis for 67 SNPs in CHRNA3-A5, CHRNA7, CHRNB2, and CHRNB4 with ND in a Chinese Han population (N = 5055). We further analyzed cis-mQTL for the three most significant SNPs and 5580 potential methylation loci within these target gene regions. Our results indicated that the SNPs rs1948 and rs7178270 in CHRNB4 and rs3743075 in CHRNA3 were significantly associated with the Fagerström Test for Nicotine Dependence (FTND) score (p = 6.6 × 10−5; p = 2.0 × 10−4, and p = 7.0 × 10−4, respectively). Haplotype-based association analysis revealed that two major haplotypes, T-G and C-A, formed by rs3743075–rs3743074 in CHRNA3, and other two major haplotypes, A-G-C and G-C-C, formed by rs1948–rs7178270–rs17487223 in CHRNB4, were significantly associated with the FTND score (p ≤ 8.0 × 10−4). Further, we found evidence for the presence of significant interaction among variants within CHRNA3/B4/A5, CHRNA4/B2/A5, and CHRNA7 in affecting ND, with corresponding p values of 5.8 × 10−6, 8.0 × 10−5, and 0.012, respectively. Finally, we identified two CpG sites (CpG_2975 and CpG_3007) in CHRNA3 that are significantly associated with three cis-mQTL SNPs (rs1948, rs7178270, rs3743075) in the CHRNA5/A3/B4 cluster (p ≤ 1.9 × 10−6), which formed four significant CpG–SNP pairs in our sample. Together, we revealed at least three novel SNPs in CHRNA3 and CHRNB4 to be significantly associated with the FTND score. Further, we showed that these significant variants contribute to ND via two methylated sites, and we demonstrated significant interaction affecting ND among variants in CHRNA5/A3/B4, CHRNA7, and CHRNA4/B2/A5. In sum, these findings provide robust evidence that SNPs in nAChR genes convey a risk of ND in the Chinese Han population.

Highlights

Tobacco smoking is a major public health problem that causes nearly 6 million deaths worldwide every year.[1]
Individual single-nucleotide polymorphisms (SNPs)-based association analysis As shown in Table 2, for smoking status, we found that eight variants in CHRNA5 and one variant in CHRNA4 showed significant associations (p = 8.0 × 10−3 to 4.4 × 10−2)
For the FTND measure, we detected five major haplotypes in the CHRNA5/A3/B4 cluster that were significantly associated with nicotine dependence (ND)

Summary

Introduction

Tobacco smoking is a major public health problem that causes nearly 6 million deaths worldwide every year.[1] Because of the lack of effective treatment for smoking addiction, the addictive properties of nicotine in tobacco smoke, and lack of awareness of the consequences of. Liu et al Translational Psychiatry (2018)8:83 smoking in many regions, the worldwide death toll caused by cigarette smoking might well reach 10 million annually by 2020.2 many developed countries have implemented regulations and laws against tobacco smoking, which have led to dramatic reductions in smoking during recent years, smoking remains a significant issue in many developing countries, especially in Asia.[3,4] For example, the prevalence of smoking in Chinese men aged 15 or older is an estimated 52.1%,5 meaning that male Chinese smokers account for almost one of third of the total number of smokers in the world.[6]. The most replicated susceptibility loci for ND are nAChR subunit genes in the CHRNA5/A3/B4 cluster on chromosome 15,12–24 CHRNB3/A6 on chromosome 8,12,25 and CYP2A6/A7 on chromosome 19.12,14,25 In addition, a significant association has been reported of variants in the CHRNA5/A3/B4 cluster with ND and lung cancer.[18]

Methods

Results

Conclusion