Identifying expression and DNA methylation biomarkers for lung adenocarcinoma risk in East Asia

Lung adenocarcinoma (LUAD) is the most common type of lung cancer. A recent genome-wide association study of lung adenocarcinoma in East Asia reported 28 independent susceptibility variants across 25 loci and identified 2 genes whose genetically predicted expression levels are associated with lung adenocarcinoma risk, using an ancestry-matched lung tissue expression quantitative trait loci (QTL) dataset. It is desirable to identify additional susceptibility loci and to understand their underlying biological mechanisms.

Using an expanded genome-wide association study of lung adenocarcinoma in East Asia and ancestry-matched lung tissue expression QTL and DNA methylation QTL datasets, we performed transcriptome-wide association studies and DNA methylome-wide association studies simultaneously and examined the association between measured expression of genes and DNA methylation of nearby CpGs. Genes and nearby CpGs are termed CpG-gene-LUAD trios if these 3 associations hold simultaneously.

At a Bonferroni-corrected P value less than .05, we identified a new susceptibility locus (6p21.31; lead single-nucleotide polymorphism rs7772643), 10 lung adenocarcinoma-associated genes, and 86 lung adenocarcinoma-associated CpGs. At a false discovery rate q value less than 0.05, we identified 28 lung adenocarcinoma-associated genes, 220 lung adenocarcinoma-associated CpGs, and 45 CpG-gene-LUAD trios; among them, 43 were direction-matched regarding these 3 associations. These show that 23 of the known 28 susceptibility variants for lung adenocarcinoma in East Asia are near these genes or CpGs and MARCH3, ELF5, IKZF3, GSDMB, CCDC116, and DSP are putative novel candidate genes. Few of them were reported in lung adenocarcinoma in European populations.

This study substantially advances our understanding of the etiology of lung adenocarcinoma in East Asia and could be useful in developing translational applications.