Esophageal squamous cell carcinoma: Integrated bioinformatics analysis for differential gene expression with identification of hub genes and lncRNA

F M Yasir Hasib

doi:10.1016/j.bbrep.2022.101262

Esophageal squamous cell carcinoma: Integrated bioinformatics analysis for differential gene expression with identification of hub genes and lncRNA

Biochem Biophys Rep. 2022 Apr 16:30:101262. doi: 10.1016/j.bbrep.2022.101262. eCollection 2022 Jul.

Author

F M Yasir Hasib^{1

2}

Affiliations

¹ Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong SAR, China.
² Department of Pathology and Parasitology, Chattogram Veterinary and Animal Sciences University, Bangladesh.

Abstract

Background: Esophageal squamous cell carcinoma (ESCC) is a typical Gastro-Intestinal (GI) tract neoplasm. This study was conducted to know the Differential Expressed Genes (DEGs) profile of ESCC along with hub gene screening, lncRNA identification, and drug-genes interactions.

Methods: GSE161533, GSE20347, GSE45670 microarray datasets were retrieved from the NCBI Gene Expression Omnibus (GEO) database. GEO2R was used for the DEGs identification, whereas GO (Gene Ontology) and KEGG enrichment analysis were performed in DAVID. PPI network constructed using STRING and visualized with Cytoscape app with the help of MCODE. The top ten connectivity genes were selected as hub genes-further survival analysis was performed in the Kaplan-Meier plotter. Moreover, Boxplot, pathological stage plots were constructed using GEPIA (Gene Expression Profiling Interactive Analysis). The methylation heatmap assembled in the DiseaseMeth version 2.0. lncRNA (Long non-coding RNA) was identified comparing the list of genes in HUGO, and Gene-drug interactions were accumulated from the DgiDB platform.

Results: This experiment showed 16 upregulated, and 59 downregulated DEGs shared among the three datasets. Biological process analysis showed significant terms such as extracellular matrix disassembly and collagen catabolism. The extracellular region was detected as the most crucial cellular compartment. Notably, metalloen dopeptidease and serine-type endopeptidase activity showed significant molecular functions term. In contrast, transcriptional misregulation was a highly substantial KEGG pathway. Kaplan-Meier plotter showed higher expression of CXCL8, SPP1, MMP13, CXCL1, and TOP2A have a significant impact on the overall survival of the patients. Nine out of ten hub genes have significantly different expression levels than normal and cancer tissues. HYMAI was the only lncRNA commonly expressed upregulated among the three datasets. Drug-gene interaction showed multiple genes have no drug options exist till now.

Keywords: DEGs; ESCC; Hub genes; lncRNA.