Identification of key genes for esophageal squamous cell carcinoma via integrated bioinformatics analysis and experimental confirmation.

Abstract

BackgroundEsophageal squamous cell carcinoma (ESCC) as the main subtype of esophageal cancer (EC) is a leading cause of cancer-related death worldwide. Despite advances in early diagnosis and clinical management, the long-term survival of ESCC patients remains disappointing, due to a lack of full understanding of the molecular mechanisms.MethodsIn order to identify the differentially expressed genes (DEGs) in ESCC, the microarray datasets GSE20347 and GSE26886 from Gene Expression Omnibus (GEO) database were analyzed. The enrichment analyses of gene ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Set Enrichment Analysis (GSEA) were performed for the DEGs. The protein-protein interaction (PPI) network of these DEGs was constructed using the Cytoscape software based on the STRING database to select as hub genes for weighted co-expression network analysis (WGCNA) with ESCC samples from TCGA database.ResultsA total of 746 DEGs were commonly shared in the two datasets including 286 upregulated genes and 460 downregulated genes in ESCC. The DEGs were enriched in biological processes such as extracellular matrix organization, proliferation and keratinocyte differentiation, and were enriched in biological pathways such as ECM-receptor interaction and cell cycle. GSEA analysis also indicated the enrichment of upregulated DEGs in cell cycle. The 40 DEGs were selected as hub genes. The MEblack module was found to be enriched in the cell cycle, Spliceosome, DNA replication and Oocyte meiosis. Among the hub genes correlated with MEblack module, GSEA analysis indicated that DEGs of TCGA samples with DLGAP5 upregulation was enriched in cell cycle. Moreover, the highly endogenous expression of DLGAP5 was confirmed in ESCC cells. DLGAP5 knockdown significantly inhibited the proliferation of ESCC cells.ConclusionsDEGs and hub genes such as DLGAP5 from independent datasets in the current study will provide clues to elucidate the molecular mechanisms involved in development and progression of ESCC.