Genetic variants and risk of lung cancer in never smokers: a genome-wide association study

Abstract

Background: Lung cancer in individuals who have never smoked tobacco products is an increasing medical and public-health issue. We aimed to unravel the genetic basis of lung cancer in never smokers.

Methods: We did a four-stage investigation. First, a genome-wide association study of single nucleotide polymorphisms (SNPs) was done with 754 never smokers (377 matched case-control pairs at Mayo Clinic, Rochester, MN, USA). Second, the top candidate SNPs from the first study were validated in two independent studies among 735 (MD Anderson Cancer Center, Houston, TX, USA) and 253 (Harvard University, Boston, MA, USA) never smokers. Third, further replication of the top SNP was done in 530 never smokers (UCLA, Los Angeles, CA, USA). Fourth, expression quantitative trait loci (eQTL) and gene-expression differences were analysed to further elucidate the causal relation between the validated SNPs and the risk of lung cancer in never smokers.

Findings: 44 top candidate SNPs were identified that might alter the risk of lung cancer in never smokers. rs2352028 at chromosome 13q31.3 was subsequently replicated with an additive genetic model in the four independent studies, with a combined odds ratio of 1.46 (95% CI 1.26-1.70, p=5.94x10(-6)). A cis eQTL analysis showed there was a strong correlation between genotypes of the replicated SNPs and the transcription level of the gene GPC5 in normal lung tissues (p=1.96x10(-4)), with the high-risk allele linked with lower expression. Additionally, the transcription level of GPC5 in normal lung tissue was twice that detected in matched lung adenocarcinoma tissue (p=6.75x10(-11)).

Interpretation: Genetic variants at 13q31.3 alter the expression of GPC5, and are associated with susceptibility to lung cancer in never smokers. Downregulation of GPC5 might contribute to the development of lung cancer in never smokers.

Funding: US National Institutes of Health; Mayo Foundation.

Figure 1. Study design and key findings

eQTL=expression quantitative trait loci. SNP=single nucleotide polymorphism. MDACC=MD Anderson Cancer Center. UCLA=University College Los Angeles.

Figure 2. Scatter plot of chromosome position (x axis) against –log₁₀ (p value; y axis) from conditional logistic regression analyses adjusted for history of chronic obstructive pulmonary disease, exposure to second-hand smoke at adulthood, and family history of lung cancer

(A) Black arrows indicate two SNPs: rs11183940 (p=1·5×10⁻⁶) and rs10880785 (p=7·1×10⁻⁶) on chromosome 12 with strongest significant association in the Mayo genome-wide association study. (B) The arrow indicates two SNPs: rs2352028 (p=4·3×10⁻⁵) and rs2352029 (p=5·3×10⁻⁵) on chromosome 13 replicated in the MD Anderson Cancer Center study.

Figure 3. Association of rs2352028 with lung cancer risk overall (A) and in adenocarcinoma only (B) in never smokers in four independent studies

Black squares indicate the odds ratios, with the size of the square inversely proportional to its variance. Horizontal lines represent 95% CI. The combined results under each genetic model are indicated by the black diamond. Heterogeneity test p values were calculated using a Cochran’s Q test. PAR%=percentage of population attributable risk. MAF=minor allele frequency (case/control). MDACC=MD Anderson Cancer Center. UCLA=University College Los Angeles.

Figure 4. Expression levels of GPC5 in normal lung tissues based on the genotype of rs2352028 and rs2352029

Gene expression is in normalised units. Centre lines are the ranges of expression levels; boxes indicate IQR. The p value was calculated with a linear regression model adjusted for age and sex.