Novel genes identified in a high-density genome-wide association study for nicotine dependence. Hum Mol Genet

Department of Psychiatry, Washington University School of Medicine, 660 South Euclid, Box 8134, St Louis, MO 63110, USA.
Human Molecular Genetics (Impact Factor: 6.68). 02/2007; 16(1):24-35. DOI: 10.1093/hmg/ddl441
Source: PubMed

ABSTRACT Tobacco use is a leading contributor to disability and death worldwide, and genetic factors contribute in part to the development of nicotine dependence. To identify novel genes for which natural variation contributes to the development of nicotine dependence, we performed a comprehensive genome wide association study using nicotine dependent smokers as cases and non-dependent smokers as controls. To allow the efficient, rapid, and cost effective screen of the genome, the study was carried out using a two-stage design. In the first stage, genotyping of over 2.4 million single nucleotide polymorphisms (SNPs) was completed in case and control pools. In the second stage, we selected SNPs for individual genotyping based on the most significant allele frequency differences between cases and controls from the pooled results. Individual genotyping was performed in 1050 cases and 879 controls using 31 960 selected SNPs. The primary analysis, a logistic regression model with covariates of age, gender, genotype and gender by genotype interaction, identified 35 SNPs with P-values less than 10(-4) (minimum P-value 1.53 x 10(-6)). Although none of the individual findings is statistically significant after correcting for multiple tests, additional statistical analyses support the existence of true findings in this group. Our study nominates several novel genes, such as Neurexin 1 (NRXN1), in the development of nicotine dependence while also identifying a known candidate gene, the beta3 nicotinic cholinergic receptor. This work anticipates the future directions of large-scale genome wide association studies with state-of-the-art methodological approaches and sharing of data with the scientific community.

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    • "). In addition, the genotypic groups did not differ with regards to smoking status (Table 2), importantly controlling for previously identified associations of these polymorphisms to smoking dependence in normal individuals (Bierut et al, 2007; Nussbaum et al, 2008). "
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    ABSTRACT: Neurexins are presynaptic neuronal adhesion molecules that interact with postsynaptic neuroligins to form an inter-synaptic complex required for synaptic specification and efficient neurotransmission. Deletions and point mutations in the neurexin 1 (NRXN1) gene are associated with a broad spectrum of neuropsychiatric and neurodevelopmental disorders including, autism, intellectual disability, epilepsy, developmental delay and schizophrenia. Recently, small nucleotide polymorphisms in NRXN1 have been associated with antipsychotic drug response in patients with schizophrenia. Based on prior suggestive evidence of an impact on clozapine response in patients with schizophrenia, we conducted an association study of NRXN1 polymorphisms (rs12467557 and rs10490162) with antipsychotic treatment response in fifty-four patients with schizophrenia in a double blind, placebo-controlled NIMH inpatient crossover trial and examined for association with risk for schizophrenia in independent case-control and family-based clinical cohorts. Pharmacogenetic analysis in the placebo controlled trial revealed significant association of rs12467557and rs10490162 with drug response, whereby individuals homozygous for the A allele, at either SNP, showed significant improvement in positive symptoms, general psychopathology, thought disturbance and negative symptoms, while patients carrying the G allele showed no overall response. While we did not find evidence of the same NRXN1 SNPs being associated with results of the NIMH sponsored CATIE trial, other SNPs showed weakly positive signals. The family and case controls analyses for schizophrenia risk were negative. Our results provide confirmatory evidence of genetically determined differences in drug response in patients with schizophrenia related to NRXN1 variation. Furthermore, these findings potentially implicate NRXN1 in the therapeutic actions of antipsychotic drugs.
    Neuropsychopharmacology: official publication of the American College of Neuropsychopharmacology 03/2014; 39. DOI:10.1038/npp.2014.65 · 7.83 Impact Factor
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    • "Behavioral genetics studies in animal models have been widely used to study the role of specific nicotinic subunits or other genes in nicotine's reward-like properties or other behaviors (Changeux 2010). Additionally, several human studies have associated the genetic variation within multiple nicotinic acetylcholine receptor (nAChR) genes with different nicotine dependence phenotypes (Amos et al. 2008; Berrettini et al. 2008; Bierut et al. 2007; Ehringer et al. 2007; Hung et al. 2008; Saccone et al. 2007; Saccone et al. 2010; Zeiger et al. 2008). However, few forward genetics approaches have been used to identify novel targets for intervention in nicotine behaviors. "
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    ABSTRACT: Mortality from tobacco smoking remains the leading cause of preventable death in the world, yet current cessation therapies are only modestly successful, suggesting new molecular targets are needed. Genetic analysis of gene expression and behavior identified Chrna7 as potentially modulating nicotine place conditioning in the BXD panel of inbred mice. We used gene targeting and pharmacological tools to confirm the role of Chrna7 in nicotine CPP. To identify molecular events downstream of Chrna7 that may modulate nicotine preference, we performed microarray analysis of α7 KO and WT nucleus accumbens tissue, followed by confirmation with quantitative PCR and immunoblotting. In the BXD panel, we found a putative cis eQTL for Chrna7 in nucleus accumbens that correlated inversely to nicotine CPP. We observed that gain-of-function α7 mice did not display nicotine preference at any dose tested, while conversely, α7 KO mice showed nicotine place preference at a dose below that routinely required to produce preference. In B6 mice, the α7 nAChR-selective agonist, PHA-543613, dose-dependently blocked nicotine CPP, which was restored using the α7 nAChR-selective antagonist, MLA. Our genomic studies implicated an mRNA co-expression network regulated by Chrna7 in nucleus accumbens. Mice lacking Chrna7 demonstrate increased insulin signaling in the nucleus accumbens, which may modulate nicotine place preference. Our studies provide novel targets for future work on development of more effective therapeutic approaches to counteract the rewarding properties of nicotine for smoking cessation.
    Genes Brain and Behavior 11/2013; 13(2). DOI:10.1111/gbb.12113 · 3.51 Impact Factor
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    • "Recent meta-analyses sustain these associations (Bierut et al., 2010; Consortium, 2010; Thorgeirsson et al., 2010; Timofeeva et al., 2012). The most well studied single nucleotide polymorphism (SNP) within the cluster has been rs16969968, a missense variant that results in a change from aspartic acid (D) to asparagine (N) in the nAChR α5 subunit and decreased response to agonist when the risk (398N) allele is present (Berrettini and Doyle, 2012; Bierut et al., 2007, 2008; Saccone et al., 2007). Yet, there are other known genetic influences on ND and lung cancer risk within this region, and variants in the cluster have a complex linkage disequilibrium (LD) structure, complicating identification of other functional polymorphism(s) (Pergadia et al., 2009). "
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    ABSTRACT: The cluster of human neuronal nicotinic receptor genes (CHRNA5/A3/B4) (15q25.1) has been associated with a variety of smoking and drug-related behaviors, as well as risk for lung cancer. CHRNA3/B4 intergenic single nucleotide polymorphisms (SNPs) rs1948 and rs8023462 have been associated with early initiation of alcohol and tobacco use, and rs6495309 has been associated with nicotine dependence and risk for lung cancer. An in vitro luciferase expression assay was used to determine whether these SNPs and surrounding sequences contribute to differences in gene expression using cell lines either expressing proteins characteristic of neuronal tissue or derived from lung cancers. Electrophoretic mobility shift assays (EMSAs) were performed to investigate whether nuclear proteins from these cell lines bind SNP alleles differentially. Results from expression assays were dependent on cell culture type and haplotype. EMSAs indicated that rs8023462 and rs6495309 bind nuclear proteins in an allele-specific way. Additionally, GATA transcription factors appeared to bind rs8023462 only when the minor/risk allele was present. Much work has been done to describe the rat Chrnb4/a3 intergenic region, but few studies have examined the human intergenic region effects on expression; therefore, these studies greatly aid human genetic research as it relates to observed nicotine phenotypes, lung cancer risk and potential underlying genetic mechanisms. Data from these experiments support the hypothesis that SNPs associated with human addiction-related phenotypes and lung cancer risk can affect gene expression, and are potential therapeutic targets. Additionally, this is the first evidence that rs8023462 interacts with GATA transcription factors to influence gene expression.
    Brain research 07/2013; 1529. DOI:10.1016/j.brainres.2013.07.017 · 2.83 Impact Factor
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