Jin Xiang, Liu Xingang, Li Xiaodan, Guan Yinghui
Department of Respiration, The First Hospital of Jilin University, Changchun 130021, China.
ICU Department, The First Hospital of Jilin University, Changchun 130021, China.
Biomed Res Int. 2016;2016:4369431. doi: 10.1155/2016/4369431. Epub 2016 Aug 17.
Introduction. Lung adenocarcinoma (LAC) is the most frequent type of lung cancer and has a high metastatic rate at an early stage. This study is aimed at identifying LAC-associated genes. Materials and Methods. GSE62950 downloaded from Gene Expression Omnibus included a DNA methylation dataset and an mRNA expression profiles dataset, both of which included 28 LAC tissue samples and 28 adjacent normal tissue samples. The differentially expressed genes (DEGs) were screened by Limma package in R, and their functions were predicted by enrichment analysis using TargetMine online tool. Then, protein-protein interaction (PPI) network was constructed using STRING and Cytoscape. Finally, LAC-associated methylation sites were identified by CpGassoc package in R and mapped to the DEGs to obtain LAC-associated DEGs. Results. Total 913 DEGs were identified in LAC tissues. In the PPI networks, MAD2L1, AURKB, CCNB2, CDC20, and WNT3A had higher degrees, and the first four genes might be involved in LAC through interaction. Total 8856 LAC-associated methylation sites were identified and mapped to the DEGs. And there were 29 LAC-associated methylation sites located in 27 DEGs (e.g., SH3GL2, BAI3, CDH13, JAM2, MT1A, LHX6, and IGFBP3). Conclusions. These key genes might play a role in pathogenesis of LAC.
引言。肺腺癌（LAC）是肺癌最常见的类型，且早期转移率高。本研究旨在鉴定与肺腺癌相关的基因。
材料与方法。从基因表达综合数据库下载的GSE62950包含一个DNA甲基化数据集和一个mRNA表达谱数据集，两者均包含28个肺腺癌组织样本和28个相邻正常组织样本。使用R语言中的Limma软件包筛选差异表达基因（DEG），并使用TargetMine在线工具通过富集分析预测其功能。然后，使用STRING和Cytoscape构建蛋白质-蛋白质相互作用（PPI）网络。最后，使用R语言中的CpGassoc软件包鉴定与肺腺癌相关的甲基化位点，并将其映射到差异表达基因上以获得与肺腺癌相关的差异表达基因。
结果。在肺腺癌组织中总共鉴定出913个差异表达基因。在PPI网络中，MAD2L1、AURKB、CCNB2、CDC20和WNT3A具有较高的连接度，前四个基因可能通过相互作用参与肺腺癌的发生。总共鉴定出8856个与肺腺癌相关的甲基化位点，并将其映射到差异表达基因上。并且有29个与肺腺癌相关的甲基化位点位于27个差异表达基因中（例如，SH3GL2、BAI3、CDH13、JAM2、MT1A、LHX6和IGFBP3）。
结论。这些关键基因可能在肺腺癌的发病机制中发挥作用。
