Integration of WGNCA and PPI networks to identify key genes for oral squamous cell carcinoma

doi:10.19438/j.cjoms.2024.02.003

Abstract

Abstract: PURPOSE: To screen important biomarkers associated with oral squamous cell carcinoma (OSCC) by using bioinformation technology. METHODS: The gene expression profiles of OSCC were obtained from GEO database and differentially expressed genes (DEGs) extracted. WGCNA was used to obtain the core genes in the module with the most significant relationship with OSCC and intersected with DEGs. At the same time, pathway analysis as well as protein network analysis(PPI) were performed. The CytoHubba was used to extract candidate key genes. Secondly, survival analysis was used to identify key genes, and verify expression in OSCC. Furthermore, the association between key genes and immune infiltrating cells and immune checkpoints was explored in OSCC. GraphPad Prism 8 software was used for data analysis. RESULTS: A total of 53 co-expressed DEGs were identified. Enrichment analysis revealed that these genes mainly involved in extracellular matrix, extracellular region, PI3K-Akt and other pathways. Twenty candidate core genes were identified from PPI networks, among which 5 key genes(SERPINE1, SERPINH1, LAMC2, ITGA5 and ITGA3) were identified using survival analysis. GEPIA and GSE30784 showed that these five genes had differential expression in OSCC tissues (P< 0.05). SERPINE1 was not expressed at the protein level of OSCC through HPA database, but SERPINH1, LAMC2, ITGA5 and ITGA3 were highly expressed. They significantly correlated with immune infiltration cells such as CD8⁺ T cells and dendritic cells and immune checkpoints such as CD276, VEGFA, and PDCD1(P< 0.05). CONCLUSIONS: SERPINE1, SERPINH1, LAMC2, ITGA5 and ITGA3 can be used as biomarkers of OSCC, providing new clues for the diagnosis, prognosis and treatment of OSCC.

Key words: Weighted gene co-expression network analysis, Oral squamous cell carcinoma, Survival analysis, Key genes, Immune infiltration

CLC Number:

R739.8

LI Jin-cun, ZHAI Kun, HU Chen, LIU Xu-ying, MA Xing-ping, MA Jian. Integration of WGNCA and PPI networks to identify key genes for oral squamous cell carcinoma[J]. China Journal of Oral and Maxillofacial Surgery, 2024, 22(2): 128-136.

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