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Identification of Key Genes and Pathways in Tongue Squamous Cell Carcinoma Using Bioinformatics Analysis
Huayong Zhang1,2, Jianmin Liu3, Xiaoyan Fu1
1Department of Head and Neck Surgery, Sun Yan-sen University Cancer Centre, Guangzhou, Guangdong, China (mainland).
Abstract:
BACKGROUND Tongue squamous cell carcinoma (TSCC) is a major type of oral cancers and has remained an intractable cancer over the past decades. The aim of this study was to identify differentially expressed genes (DEGs) during TSCC and reveal their potential mechanisms. MATERIAL AND METHODS The gene expression profiles of GSE13601 were downloaded from the GEO database. The GSE13601 dataset contains 57 samples, including 31 tongue SCC samples and 26 matched normal mucosa samples. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses were performed; Cytoscape software was used for the protein-protein interaction (PPI) network and module analysis of the DEGs. RESULTS We identified a total of 1,050 upregulated DEGs (uDEGs) and 702 downregulated DEGs (dDEGs) of TSCC. The GO analysis results showed that uDEGs were significantly enriched in the following biological processes (BP): signal transduction, positive or negative regulation of cell proliferation, and negative regulation of cell proliferation. The dDEGs were significantly enriched in the following biological processes: signal transduction, cell adhesion, and apoptotic process. The KEGG pathway analysis showed that uDEGs were enriched in metabolic pathways, pathways in cancer, and PI3K-Akt signaling pathway, while the dDEGs were enriched in focal adhesion and ECM-receptor interaction. The top centrality hub genes RAC1, APP, EGFR, KNG1, AGT, and HRAS were identified from the PPI network. Module analysis revealed that TSCC was associated with significant pathways, including neuroactive ligand-receptor interaction, calcium signaling pathway, and chemokine signaling pathway. CONCLUSIONS The present study identified key genes and signal pathways, which deepen our understanding of the molecular mechanisms of carcinogenesis and development of the disease, and might be used as diagnostic and therapeutic molecular biomarkers for TSCC.
Insights
This study identified key genes and pathways involved in tongue squamous cell carcinoma (TSCC) by analyzing gene expression data. Findings offer potential molecular biomarkers for diagnosing and treating this intractable oral cancer.
Area of Science:
- Oncology
- Genomics
- Molecular Biology
Background:
- Tongue squamous cell carcinoma (TSCC) is a challenging oral cancer with limited treatment options.
- Understanding the molecular mechanisms of TSCC is crucial for developing effective therapies.
Purpose of the Study:
- To identify differentially expressed genes (DEGs) in TSCC.
- To elucidate the potential molecular mechanisms underlying TSCC development.
Main Methods:
- Analyzed gene expression profiles from the GSE13601 dataset (31 TSCC vs. 26 normal samples).
- Utilized Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses.
- Constructed protein-protein interaction (PPI) networks and performed module analysis using Cytoscape.
Main Results:
- Identified 1,050 upregulated and 702 downregulated DEGs in TSCC.
- Upregulated genes are enriched in cell proliferation and PI3K-Akt signaling pathways.
- Downregulated genes are associated with cell adhesion, apoptosis, focal adhesion, and ECM-receptor interactions.
- Key hub genes (e.g., RAC1, APP, EGFR) and pathways (e.g., neuroactive ligand-receptor interaction) were identified.
Conclusions:
- The study identified critical genes and signaling pathways implicated in TSCC pathogenesis.
- These findings enhance the understanding of TSCC molecular mechanisms.
- Identified genes and pathways may serve as potential diagnostic and therapeutic biomarkers for TSCC.
