Identification of novel stage-specific key biomarkers gene for early stage, advanced stage, and metastatic oral squamous cell carcinoma using systems biology approach

Abstract

Abstract Background: The present study aimed to identify biomarker genes associated with disease progression from an early and advanced stage to metastatic oral squamous cell carcinoma (OSCC) and to explore their regulatory mechanism. Materials and Methods: Three microarray datasets, GSE85195, GSE78060, and GSE70604, were used for differential analysis using a limma package of R language. The thresholds for identifying differential expression analyses (DEGs) were an adjusted P value of 0.05 and a |log 2 fold change (FC)| >1. The final annotated genes were extracted by comparing the differentially expressed genes to disease-specific genes in DisGeNET. Further, gene prioritization was performed for DEGs. After that, prioritized DEGs were used to analyze functional enrichment using the database for annotation, visualization, and integrated discovery (DAVID) database. Furthermore, the prioritized DEGs were also used to construct protein–protein interaction (PPI) network using STRING database and visualized by the Cytoscape, and further analyzed by molecular complex detection (MCODE) and CytoHubba plugins to obtain essential hub genes and modules. Subsequently, the Kaplan–Meier plot was constructed for the hub gene using a publicly available dataset to analyze overall survival (OS) and to assess whether candidate molecules are prognosticators. Results: The study identified 10 hub genes for all three stages of OSCC. Top 10 highest-scored early-stage genes are AURKA, CDCA3, CDC45, CENPN, CDC6, MAD2L1, KIF4A, CDT1, PLK1, and CDC20; for advance stage, KIF4A, MAD2L1, AURKA, DTL, ESPL1, ECT2, CDC45, CDC20, CENPN, and CDC6; for metastatic stage, MFAP5, IRF6, P4HA2, COL11A2, COL10A1, LOXL2, BMP1, COL5A2, COL5A1, and ADAMTS14. Hub genes were enriched in the biological process associated gene ontology term: Positive regulation of the apoptotic process, positive regulation of cell proliferation, negative regulation of the apoptotic process, and angiogenesis Wnt signaling pathway, FoxO signaling pathway, and pathways in cancer. Except for ESPL1 and COL11A2, all hub genes were highly elevated in OSCC compared with normal tissues. According to the survival analysis results, low expression levels of CNPEN and MFAP5 were significantly linked to worse OSCC patients out of the 23 hub genes studied. Conclusion: Several putative biomarker genes were associated with OSCC patients’ staging and OS. Therefore, they may have clinical use as diagnostic biomarkers and therapeutic targets.