Cis-methylation quantitative trait loci mapping of chromosome 15q25.1 in human brain reveals novel genetic associations with nicotine dependence. D. B. Hancock1, J. C. Wang2, N. C. Gaddis1, N. L. Saccone2, J. A. Stitzel3, A. Goate2, L. J. Bierut2, E. O. Johnson1 1) RTI International, Research Triangle Park, NC; 2) Washington University, St. Louis, MO; 3) University of Colorado, Boulder, CO.
Genome-wide association studies have unequivocally found that single nucleotide polymorphisms (SNPs) on chromosome 15q25.1 contribute to nicotine dependence and other smoking behaviors. The associated SNPs span genes that encode iron-responsive element binding protein 2 (IREB2), hydroxylysine kinase (HYKK), proteasome subunit alpha type-4 (PSMA4), and three nicotinic acetylcholine receptors (CHRNA5, CHRNA3, and CHRNB4). Prior analyses of this region found that the associated SNPs have important biological functions in human brain: the missense SNP rs16969968 alters the receptor function of CHRNA5, and several upstream and intronic SNPs tag expression quantitative trait loci (eQTL) regulating CHRNA5 mRNA expression. To identify other biologically important SNPs that may contribute to nicotine dependence, we conducted cis-methylation QTL (cis-meQTL) mapping using SNP genotypes and DNA methylation levels measured across the IREB2-HYKK-PSMA4-CHRNA5-CHRNA3-CHRNB4 gene region in the BrainCloud and Brain QTL cohorts (total N=175 European Americans and 65 African Americans). We found significant associations between 8 SNPs and CHRNA5 methylation (5.75x10-5 < P < 6.04x10-10) and between 2 SNPs and CHRNA3 methylation (1.29x10-4 < P < 7.67x10-6) in prefrontal cortex. We also observed significant associations of these SNPs with CHRNA5 methylation in frontal cortex, temporal cortex, and pons (3.42x10-3 < P < 4.92x10-12). We tested the newly identified cis-meQTL SNPs for association with nicotine dependence in a meta-analysis across four independent cohorts with total N=9,815 (5,549 European Americans, 2,309 Italians, and 1,957 African Americans). All of the CHRNA5-implicated SNPs were nominally to significantly associated with nicotine dependence (7.99x10-3 < P < 8.83x10-4): rs2292117, rs6495306, rs680244 and rs621849 tagged known cis-eQTL SNPs associated with nicotine dependence, whereas rs12915366, rs3743077, rs950776, and rs11636753 represent new association signals. The SNP minor alleles were associated with higher CHRNA5 DNA methylation and mRNA expression levels and decreased risk of nicotine dependence. This inverse relationship is consistent with previously reported rodent models. Our findings are the first to connect previously observed differences in CHRNA5 mRNA expression and nicotine dependence risk to underlying differences in DNA methylation.
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