Cis-Regulatory Variants Affect CHRNA5 mRNA Expression in Populations of African and European Ancestry

Oscar Harari,Noah Spiegel,Bryan J Traynor,Tatiana Foroud,Laura J Bierut,Jay Tischfield,Howard J Edenberg,John P Budde,Dana Hancock,Sarah Bertelsen,Joe Henry Steinbach,Andrew Brooks,Nicholas Mckenna,Jen-Chyong Wang,Alison M Goate,Manav Kapoor,Nhung Le

doi:10.1371/journal.pone.0080204

Abstract

Variants within the gene cluster encoding α3, α5, and β4 nicotinic receptor subunits are major risk factors for substance dependence. The strongest impact on risk is associated with variation in the CHRNA5 gene, where at least two mechanisms are at work: amino acid variation and altered mRNA expression levels. The risk allele of the non-synonymous variant (rs16969968; D398N) primarily occurs on the haplotype containing the low mRNA expression allele. In populations of European ancestry, there are approximately 50 highly correlated variants in the CHRNA5-CHRNA3-CHRNB4 gene cluster and the adjacent PSMA4 gene region that are associated with CHRNA5 mRNA levels. It is not clear which of these variants contribute to the changes in CHRNA5 transcript level. Because populations of African ancestry have reduced linkage disequilibrium among variants spanning this gene cluster, eQTL mapping in subjects of African ancestry could potentially aid in defining the functional variants that affect CHRNA5 mRNA levels. We performed quantitative allele specific gene expression using frontal cortices derived from 49 subjects of African ancestry and 111 subjects of European ancestry. This method measures allele-specific transcript levels in the same individual, which eliminates other biological variation that occurs when comparing expression levels between different samples. This analysis confirmed that substance dependence associated variants have a direct cis-regulatory effect on CHRNA5 transcript levels in human frontal cortices of African and European ancestry and identified 10 highly correlated variants, located in a 9 kb region, that are potential functional variants modifying CHRNA5 mRNA expression levels.

Highlights

Several genome-wide association studies have linked chromosome 15q24-q25.1, a region containing the genes encoding the a3, a5, and b4 subunits of neuronal nicotinic receptors, with nicotine dependence and smoking-related illnesses such as lung cancer, airflow obstruction, and chronic obstructive pulmonary disease [1,2,3,4,5,6]
CHRNA5 mRNA expression in normal lung tissue was significantly associated with the genotype of rs16969968. mRNA expression level was about 2.5-fold lower in patients who are homozygous for the minor allele of rs16969968 than patients who are homozygous for the major allele [22]
Total CHRNA5 mRNA level in frontal cortex is strongly associated with variants located upstream of the gene in individuals of both African and European ancestry Similar to our previous study in human brains of European ancestry [19,20], the variability in CHRNA5 total mRNA expression levels in frontal cortices of African ancestry is significantly associated with rs880395 (p = 7.2761027), rs3841324 (p = 6.9461023), and rs588765 (p = 1.1061024) (Table 1)

Summary

Introduction

Several genome-wide association studies have linked chromosome 15q24-q25.1, a region containing the genes encoding the a3, a5, and b4 subunits of neuronal nicotinic receptors, with nicotine dependence and smoking-related illnesses such as lung cancer, airflow obstruction, and chronic obstructive pulmonary disease [1,2,3,4,5,6]. In European American populations, the nicotine dependence risk allele (minor allele) of the non-synonymous variant (rs16969968; D398N) primarily occurs on the haplotype containing the low mRNA expression allele of CHRNA5. The major allele at rs16969968 occurs on both high and low expression haplotypes. When the major allele occurs on the low mRNA expression haplotype of CHRNA5, the risk for nicotine dependence and lung cancer is significantly lower when compared to major alleles on the higher mRNA expression haplotype [19]. CHRNA5 mRNA expression in normal lung tissue was significantly associated with the genotype of rs16969968. MRNA expression level was about 2.5-fold lower in patients who are homozygous for the minor allele of rs16969968 than patients who are homozygous for the major allele [22] CHRNA5 mRNA expression in normal lung tissue was significantly associated with the genotype of rs16969968. mRNA expression level was about 2.5-fold lower in patients who are homozygous for the minor allele of rs16969968 than patients who are homozygous for the major allele [22]

Methods

Results

Conclusion