Identification of potentially critical differentially methylated genes in nasopharyngeal carcinoma: A comprehensive analysis of methylation profiling and gene expression profiling

The present study aimed to identify potentially critical differentially methylated genes associated with the progression of nasopharyngeal carcinoma (NPC). Methylation profiling data of GSE62336 deposited in the Gene Expression Omnibus database were used to identify differentially methylated regions (DMRs) and differentially methylated CpG islands (DMIs). Concurrently, differentially expressed genes (DEGs) were identified using a meta-analysis of three gene expression datasets (GSE53819, GSE13597 and GSE12452). Subsequently, methylated DEGs were identified by comparing DMRs and DEGs. Furthermore, functional associations of these methylated DEGs were analyzed via constructing a functional network using GeneMANIA prediction server. In total, 1,676 hypermethylated genes, 28 hypomethylated genes, 17 DMIs and 2,983 DEGs (1,655 upregulated and 1,328 downregulated) were identified. Among these DEGs, 135 downregulated genes were hypermethylated; of these, dual specificity phosphatase 6 (DUSP6) and tenascin XB (TNXB) contained DMIs. In the functional network, 154 genes and 1,651 association pairs were included. DUSP6 was predicted to exhibit genetic interactions with other hypermethylated DEGs such as malic enzyme 3 and ST3 beta-galactoside alpha-2,3-sialyltransferase 5; TNXB was predicted to be co-expressed with a set of hypermethylated DEGs, including EPH receptor B6, aldehyde dehydrogenase 1 family, member L1 and glutathione peroxidase 3. The hypermethylated DEGs may be involved in the progression of NPC, and they may become novel therapeutic targets for NPC.