Identification of key genes and pathways for esophageal squamous cell carcinoma by bioinformatics analysis

Abstract

The aim of the present study was to identify the differentially expressed genes (DEGs) in esophageal squamous-cellcarcinoma (ESCC) and provide potential therapeutic targets. The microarray dataset GSE20347 was downloaded from the Gene Expression Omnibus (GEO) database, and included 17 tissue samples and 13 normal adjacent tissue samples from patients with ESCC. A total of 22,277 DEGs were identified. A heat map for the DEGs was constructed with the Morpheus online tool and the top 200 genes (100 upregulated and 100 downregulated) were selected for further bioinformatics analysis, including analysis of gene ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, protein-protein interaction networks and Spearman's correlation tests. The results of the GO analysis indicated that the upregulated DEGs were most significantly enriched in membrane-bounded vesicles in the cellular component (CC) category, but were not significantly enriched in any GO terms of the categories biological process (BP) or molecular function (MF); furthermore, the downregulated DEGs were most significantly enriched in regulation of DNA metabolic processes, nucleotide binding and chromosomes in the categories BP, MF and CC, respectively. The KEGG analysis indicated that the downregulated DEGs were enriched in the regulation of cell cycle pathways. The top 10 hub proteins in the protein-protein interaction network were cyclin-dependent kinase 4, budding uninhibited by benzimidazoles 1, cyclin B2, heat shock protein 90AA1, aurora kinase A, H2A histone family member Z, replication factor C subunit 4, and minichromosome maintenance complex component 2, −4 and −7. These proteins are mainly involved in regulating tumor progression. The genes in the four top modules were mainly implicated in regulating cell cycle pathways. Secreted Ly-6/uPAR-related protein (SLURP) was the hub gene, and SLURP and its interacting genes were most enriched in the chromosomal part in the CC category, organelle organization in the BP category and protein binding in the MF category, and were involved in pathways including DNA replication, cell cycle and P53 signaling. The expression of SLURP-1 in fifteen patients with esophageal carcinoma was detected using quantitative polymerase chain reaction analysis, and the results indicated that SLURP-1 expression was significantly decreased in the tumor samples relative to that in normal adjacent tissues. These results suggest that several hub proteins and the hub gene SLURP-1 may serve as potential therapeutic targets, and that gene dysfunction may be involved in the tumorigenesis of ESCC.

Cellular Processes Involved in Jurkat Cells Exposed to Nanosecond Pulsed Electric Field

“…Based on their absolute values of LogFC, a total of 50 genes were selected from the DEGs, followed by analyzing with the Morpheus () online software to construct the heat map (Figure 2) [9]. Furthermore, the biological processes functional enrichment and pathway enrichment analyses for DEGs were investigated using FunRich () software [10].…”

Downregulation of CDCA3 expression inhibits tumor formation in pancreatic cancer

“…CDCA3 is essential to regulate plenty of physiological and pathological processes by stimulating the proteins degradation like transcription factors and signal transduction molecules [33], and exert an important role during various cancer types development [19,22]. Some researches indicated that CDCA3 was markedly overexpressed accompanied by poor prognosis in NSCLC, and exerted a vital part during tumorigenesis and esophageal carcinoma development [34]. Zhang Y et al found that CDCA3 upregulation accelerated the cell proliferation and colony formation, while CDCA3…”

Time series expression pattern of key genes reveals the molecular process of esophageal cancer

“…Till now, with the development of high-throughput sequencing technology, gene expression profiling has been widely used to identify genes or signal pathway related to the development of esophageal cancer [47][48][49][50][51][52]. However, most studies only identified DEGs or signaling pathways, which might be involved in esophageal cancer development based on different GEO datasets.…”