Identifying expression and DNA methylation biomarkers for lung adenocarcinoma risk in East Asia [RNA-seq]

Lung adenocarcinoma (LUAD) is the most common type of lung cancer. A recent genome-wide association study (GWAS) of LUAD in East Asia reported 28 independent susceptibility variants across 25 loci and identified 2 genes whose genetically predicted expression levels are associated with LUAD risk, using an ancestry-matched lung tissue expression quantitative trait loci (eQTL) dataset. It is desirable to identify additional susceptibility loci and to understand their underlying biological mechanisms. Using an expanded GWAS of LUAD in East Asia and ancestry-matched lung tissue eQTL 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 (eQTM). Genes and nearby CpGs are termed CpG–gene–LUAD trios if these three associations hold simultaneously. At Bonferroni-corrected P<0.05, we identified a new susceptibility locus (6p21.31; lead SNP rs7772643), 10 LUAD-associated genes and 86 LUAD-associated CpGs. At false discovery rate q<0.05, we identified 28 LUAD-associated genes, 220 LUAD-associated CpGs, and 45 CpG–gene–LUAD trios; among them, 43 were direction-matched regarding these three associations. These show that 23 of the known 28 susceptibility variants for LUAD in East Asia are near these genes or CpGs and MARCH3, ELF5, IKZF3, GSDMB, CCDC116, and DSP are putative novel susceptibility loci. Few of them was reported in LUAD in European populations. This study substantially advances our understanding of the etiology of LUAD in East Asia and could be useful in developing translational applications. Overall design: From the Lung Cancer Tissue Core, 61 non-smoking subjects of lung adenocarcinoma were selected, after data preprocessing, to have obtained the gene expression profiles of the normal lung tissues adjacent to tumor, using Illumina RNA Access library kit.

肺腺癌（Lung adenocarcinoma, LUAD）是最为常见的肺癌类型。此前一项针对东亚人群肺腺癌的全基因组关联研究（genome-wide association study, GWAS），借助族群匹配的肺组织表达数量性状位点（expression quantitative trait loci, eQTL）数据集，在25个基因座上鉴定出28个独立的易感变异，并发现2个基因的遗传预测表达水平与肺腺癌发病风险相关。进一步挖掘更多易感基因座并阐明其潜在生物学机制，具有重要研究价值。本研究基于扩大样本量的东亚人群肺腺癌GWAS数据集，以及族群匹配的肺组织eQTL与DNA甲基化数量性状位点（DNA methylation QTL）数据集，同步开展转录组全关联研究与甲基化组全关联研究，并分析了基因实测表达水平与邻近CpG位点的DNA甲基化水平之间的关联（expression quantitative trait methylation, eQTM）。若上述三项关联同时成立，则将对应基因、邻近CpG位点与肺腺癌构成的组合称为“CpG-基因-肺腺癌三联体”。在邦费罗尼校正后P<0.05的阈值下，本研究鉴定出1个全新的易感基因座（6p21.31；领先单核苷酸多态性（single nucleotide polymorphism, SNP）rs7772643）、10个肺腺癌关联基因与86个肺腺癌关联CpG位点。在错误发现率（false discovery rate, FDR）q<0.05的阈值下，本研究共鉴定出28个肺腺癌关联基因、220个肺腺癌关联CpG位点以及45个CpG-基因-肺腺癌三联体，其中43个三联体的三项关联方向一致。分析显示，东亚人群肺腺癌已知的28个易感变异中有23个位于上述关联基因或CpG位点附近；同时鉴定出MARCH3、ELF5、IKZF3、GSDMB、CCDC116与DSP作为潜在全新易感基因座。上述潜在易感基因座在欧洲人群肺腺癌研究中鲜有报道。本研究大幅深化了我们对东亚人群肺腺癌病因学的认知，可为后续转化应用研究提供重要依据。实验设计：从肺癌组织核心库中筛选出61名非吸烟肺腺癌患者，经数据预处理后，采用Illumina RNA Access文库构建试剂盒对其肿瘤旁正常肺组织进行基因表达谱检测。