Screening pathogenic genes in oral squamous cell carcinoma based on the mRNA expression microarray data

Area of Science:

• Genomics and Molecular Biology
• Oncology
• Bioinformatics

Background:

• Oral squamous cell carcinoma (OSCC) is a prevalent cancer with stagnant survival rates.
• Identifying novel pathogenic genes is crucial for improving OSCC diagnosis and treatment.
• Microarray analysis offers a powerful tool for comprehensive gene expression profiling.

Purpose of the Study:

• To screen for pathogenic genes associated with oral squamous cell carcinoma (OSCC) using gene expression data.
• To identify differentially expressed genes (DEGs) between metastatic and non-metastatic OSCC, and between OSCC and normal tissues.
• To construct a microRNA (miRNA)-gene regulatory network for OSCC.

Main Methods:

• Downloaded and analyzed mRNA expression microarray datasets (GSE2280, GSE3524) from the Gene Expression Omnibus (GEO) database.
• Utilized the limma package to identify differentially expressed genes (DEGs) in OSCC samples.
• Performed functional enrichment analyses using DAVID and constructed a miRNA-gene regulatory network with Cytoscape.

Main Results:

• Identified 233 DEGs between metastatic and non-metastatic OSCC (DEGs-1) and 410 DEGs between OSCC and normal tissues (DEGs-2).
• DEGs-1 were enriched in 188 Gene Ontology (GO) terms and 8 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways; DEGs-2 in 228 GO terms and 6 KEGG pathways.
• Constructed a miRNA-gene network involving 126 nodes and 135 regulated pairs, highlighting potential biomarkers like TGM2 and ISL1, and pathogenic genes such as P2RY2 and RAPGEFL1.

Conclusions:

• Transglutaminase 2 (TGM2) and Islet 1 (ISL1) are proposed as potential biomarkers for OSCC and its lymph node metastases.
• Identified several potential pathogenic genes, including P2RY2 and RAPGEFL1, contributing to OSCC development.
• The study provides a foundation for further investigation into the molecular mechanisms and therapeutic targets for OSCC.