Differential Gene Expression Profiling of Oesophageal Squamous Cell Carcinoma by DNA Microarray and Bioinformatics Analysis

Abstract

Differential gene expression profiling was carried out on primary tumour tissues and adjacent non-neoplastic tissues from patients with oesophageal squamous cell carcinoma (ESCC). RNA extracted from ESCC tissues and matched normal oesophageal epithelium of four ESCC patients was analysed using whole-genome microarrays. Bioinformatics analysis was also carried out to ascertain which genes and pathways may be important in the carcinogenesis of ESCC. A total of 570 genes were identified that differed significantly in expression: 303 genes were up-regulated and 267 genes were down-regulated in ESCC tissues compared with normal oesophageal epithelium. Gene ontology analysis showed that the primary molecular functions of these genes were related to the extracellular region, collagen and endopeptidase inhibitor activity. Pathway analysis revealed seven pathways or networks highly associated with the differential expression profile. Gene set analysis showed that the POD1_KO_UP gene set was significantly enriched, containing 15 matching genes. Thus, a large number of genes are involved in the carcinogenesis of ESCC and participate in various cell processes and pathways.