Analysis of tissue-specific differentially methylated genes with differential gene expression in non-small cell lung cancers

Adenocarcinoma (ADC) and squamous cell carcinomas (SCC) are two subtypes of non-small cell lung carcinomas which are regarded as the leading cause of cancer-related malignancy worldwide. The aim of this study was to detect the differentially methylated loci (DML) and differentially methylated genes (DMGs) of these two tumor sets, and then to illustrate the different expression levels of specific methylated genes. Using the TCGA database and Illumina HumanMethylation 27 arrays, we first screened the DMGs and DML in tumor samples. Then, we explored the Biological Process terms of hypermethylated and hypomethylated genes using Functional Gene Ontology (GO) catalogues. Hypermethylation intensively occurred in the CpG-island, whereas hypomethylation was located in the non-CpG-island. Most SCC and ADC hypermethylated genes involved GO function of DNA dependent regulation of transcription, and hypomethylated genes mainly enriched in the term of immune responses. Additionally, the expression levels of specific differentially methylated genes are distinct between ADC and SCC. It was concluded that ADC and SCC have a different methylation status that might play an important role in carcinogenesis.