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  • Identification of key genes involved in the development of human oral squamous cell carcinoma using systems biology

  • Navid Motovalibashi,1 Fahimeh Pakravan,2 Zohreh Hojati,3,*
    1. Isfahan University of Medical Sciences, Faculty of Dentistry,
    2. Isfahan University of Medical Sciences, Faculty of Dentistry,
    3. Cell and Molecular Biology Department, Faculty Of Biological Science And Technology , University of Isfahan


  • Introduction: Oral squamous cell carcinoma is one of the most common malignancies of the head and neck region, which is associated with high mortality and recurrence rates. Despite therapeutic advances, late diagnosis and molecular heterogeneity of this cancer have hindered the development of targeted and effective therapies. With the advancement of systems biology and RNA-seq-based transcriptomic analyses, it has become possible to identify genes and molecular pathways involved in OSCC. This study aimed to identify key genes and functional modules involved in the development and progression of OSCC.
  • Methods: In this study, RNA-seq data related to OSCC patients were extracted from the TCGA database. After data quality control and outlier removal using PCA analysis, data normalization was performed using the DESeq2 package in R software. Differentially expressed genes were identified with a threshold of |log2FC > 1.5| and p-value < 0.001. Then, to investigate the biological role of these genes, functional enrichment analysis was performed using the DAVID tool. Subsequently, protein-coding genes were extracted and entered into the STRING database to construct a protein interaction network. The network created in Cytoscape software was plotted and key modules and central genes were identified using the MCODE plugin. Finally, clusters with the highest interaction strength were selected.
  • Results: Differential expression analysis led to the identification of a set of genes differentially expressed in OSCC patients compared to healthy samples. Functional enrichment analysis showed that the mentioned genes are involved in pathways such as cell cycle regulation, apoptosis, inflammatory responses and pathways related to tumor growth and invasion. The structure of the PPI network led to the identification of key modules in which genes such as were identified as the central nodes with the most interactions.
  • Conclusion: The findings of this study show that the combination of gene expression analysis, protein network analysis, and functional module extraction can identify key genes involved in OSCC cancer with high accuracy. These genes, as potential biomarkers and therapeutic targets, have the potential to be further investigated in experimental and clinical studies and can pave the way for the design of targeted therapies in the future. Two genes, SGO1 and KIF20A, were identified as new candidate genes that had the highest correlation with key cancer-related pathways.
  • Keywords: Systems biology, human oral squamous cell carcinoma, gene expression bus, differentially express

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