Bioinformatics analysis of screening of differentially expressed genes and related biological characteristics in esophageal squamous cell carcinoma / 中华消化杂志

ABSTRACT

Objective:To analyze the differentially expressed genes in esophageal squamous cell carcinoma (ESCC) by bioinformatics method, to screen the key genes related to the carcinogenesis and development of ESCC and to find out biomarkers for early diagnosis and prognosis of ESCC.Methods:The ESCC microarray datasets GSE26886, GSE77861, GSE100942, GSE20347, GSE23400, GSE38129 and GSE17351 from gene expression omnibus datasets were downloaded. The differentially expressed genes in ESCC and normal esophageal mucosa tissues of each dataset were screened out, and then the common differentially expressed key genes of seven dataset were selected out. After that, the key differentially expressed genes were analyzed by gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway. Cytoscape software and molecular complex detection were used for protein-protein interaction network (PPI), and the critical hub genes were screened out. The expression of hub genes was divided into high-expression group and low-expression group. The relationship between hub genes and the prognosis of patients with ESCC was analyzed by Kaplan-Meier database.Results:A total of 626 differentially expressed key genes of ESCC were screened out from the seven datasets, including 302 up-regulated genes and 324 down-regulated genes. The results of GO analysis showed that the key differentially expressed genes were mainly involved in collagen binding, regulation of cell cycle and epithelial cell differentiation.The results of KEGG analysis indicated that the differentially expressed genes were focused on extracellular matrix-receptor interaction, p53 signaling pathway and arachidonic acid metabolism signaling pathway. Five hub genes were screened out from PPI, which were collagen type Ⅲ α1 chain ( COL3 A1), collagen type Ⅹ α1 chain ( COL10 A1), collagen type Ⅵ α3 chain ( COL6 A3), collagen type Ⅴ α2 chain ( COL5 A2) and collagen type Ⅰ α1 chain ( COL1 A1). The expression levels of COL3 A1, COL10 A1, COL6 A3, COL5 A2 and COL1 A1 in ESCC tissues were higher than those of normal esophageal mucosa tissues. The prognosis of high-expression group was worse than that of low-expression group. Conclusions:There are differentially expressed genes profiles between ESCC tissues and normal mucosa tissues. COL3 A1, COL10 A1, COL6 A3, COL5 A2 and COL1 A1 are key genes in the genesis and development of ESCC and also related to the prognosis of the patients, which may be new molecular markers for the diagnosis and treatment of ESCC.