Genome-wide DNA methylation signature in lung adenocarcinomas has prognostic impact [gene expression]

Purpose: DNA methylation alterations are early events in tumorigenesis and important in the regulation of gene expression in cancer cells. Lung cancer has in general a poor prognosis, and a deeper insight into the epigenetic landscape in lung adenocarcinoma tumors and its prognostic implications is needed. Experimental Design: We determined whole-genome DNA methylation profiles of 164 lung adenocarcinoma samples and 19 samples of matched normal lung tissue samples using the Illumina Infinium 450K array [GSE66836]. The methylation levels were correlated with gene expression levels analyzed by the Agilent 60K mRNA expression array. Methylation changes were studied specifically in tumors from never-smoking patients, and in tumors with mutations in the EGFR-, KRAS- or TP53 genes, and survival analyses were performed. Results: We identified a large number of differentially methylated CpGs in lung adenocarcinoma tissue, and different methylation profiles in tumors from smokers and never-smokers. Specific methylation profiles were observed in tumors with mutations in the EGFR-, KRAS- or TP53 gene. Both positive and negeative correlations between DNA methylation levels and mRNA expression levels were seen. Methylation profiles of the tumor samples identified clusters of patients with distinct prognosis. A prognostic index based on the methylation levels of 33 CpGs was established, and validated in an independent cohort of lung adenocarcinoma patients from the TCGA project. Among the CpGs in the prognostic signature, some were localized in the HOX B and HOX C gene clusters. Conclusions: Methylation differences mirror biological important features the etiology of lung adenocarcinomas and influence prognosis. We determined mRNA expression in 121 lung adenocarcinoma samples using the Agilent 60K mRNA expression array. These data was correlated with the whole-genome DNA methylation profiles of matched lung adenocarcinomas to investigate the correlation of the CpG methylation to the mRNA expression. We identified a large number of both negative and positive correlations. Negative correlations between gene expression and DNA methylation were most often found when the methylated loci were located in the promoter region, while positive correlations were most often found outside promoter regions Please note that the sample numbers are matched between the methylation study [GSE66836] and this study.

研究目的：DNA甲基化改变是肿瘤发生的早期事件，对癌细胞内基因表达的调控具有关键作用。肺癌整体预后不佳，目前亟需更深入地解析肺腺癌肿瘤的表观遗传图谱及其预后关联。
实验设计：本研究利用Illumina Infinium 450K芯片[GSE66836]，对164份肺腺癌样本及19份匹配的正常肺组织样本进行全基因组DNA甲基化谱分析。将甲基化水平与通过Agilent 60K mRNA表达芯片检测得到的基因表达水平进行关联分析。此外，本研究重点针对从不吸烟者的肿瘤样本、携带EGFR、KRAS或TP53基因突变的肿瘤样本开展甲基化变化研究，并完成了生存分析。
研究结果：本研究在肺腺癌组织中鉴定出大量差异甲基化CpG位点，且吸烟者与从不吸烟者的肿瘤具有不同的甲基化图谱。携带EGFR、KRAS或TP53基因突变的肿瘤均呈现特异性甲基化谱。DNA甲基化水平与mRNA表达水平之间存在正、负双向关联。通过肿瘤样本的甲基化谱可鉴定出具有不同预后特征的患者亚群。本研究构建了基于33个CpG位点甲基化水平的预后指数，并在来自癌症基因组图谱（TCGA）项目的独立肺腺癌患者队列中对该指数进行了验证。该预后特征中的部分CpG位点定位于HOX B和HOX C基因簇。
研究结论：甲基化差异可反映肺腺癌病因学相关的重要生物学特征，并影响患者预后。本研究利用Agilent 60K mRNA表达芯片对121份肺腺癌样本的mRNA表达水平进行了检测，将这些数据与匹配的肺腺癌全基因组DNA甲基化谱进行关联分析，以探究CpG甲基化与mRNA表达之间的相关性，最终鉴定出大量正负双向的关联信号。当甲基化位点位于启动子区域时，最常观察到基因表达与DNA甲基化之间的负相关；而正相关则多发生于启动子区域之外。
备注：请注意本研究与甲基化研究[GSE66836]的样本数量匹配一致。