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Identification of key gene signatures and their characterization by expression correlation with drug sensitivity in smoking-associated oral squamous cell carcinoma

1 Central Research Laboratory, K. S. Hegde Medical Academy, Nitte (Deemed to be University), Deralakatte, Mangalore, Karnataka, India
2 Department of Oncology, Justice K S Hegde Charitable Hospital, K. S. Hegde Medical Academy, Nitte (Deemed to be University), Deralakatte, Mangalore, Karnataka, India
3 Department of Biochemistry, K. S. Hegde Medical Academy, Nitte (Deemed to be University), Deralakatte, Mangalore, Karnataka, India

Correspondence Address:
Prakash Patil,
Central Research Laboratory, K S Hegde Medical Academy, Nitte (Deemed to be University), Deralakatte, Mangalore - 575 018, Karnataka
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Source of Support: None, Conflict of Interest: None

DOI: 10.4103/jcrt.jcrt_1120_21

Aims: Oral squamous cell carcinoma (OSCC), a most frequent type of head-and-neck cancer, is becoming more common and posing a substantial health risk. Using a network biology strategy, this study intended to find and investigate critical genes associated with OSCC. Materials and Methods: The extended protein–protein interaction networks for differentially expressed genes related to smoking and nonsmoking conditions of OSCC were constructed and visualized using Cytoscape software. The hub genes/proteins were determined based on degree and betweenness centrality measures and then evaluated and validated for expression using the Gene Expression Profiling Interactive Analysis 2 (GEPIA2), and their relationship to the sensitivity of small molecules was discovered utilizing the Gene Set Cancer Analysis (GSCA) web server. Results: A total of 596 differentially expressed genes were screened, and four genes, interleukin (IL)-6, JUN, tumor necrosis factor (TNF), and vascular endothelial growth factor A (VEGFA), were identified as hub proteins, and their expression and overall survival in head-and-neck cancers were further investigated using GEPIA2. TNF and VEGFA gene expressions were considerably greater in cancers when compared to normal samples, while JUN and IL-6 gene expressions were not statistically significant. Further, these hub proteins are found to have a substantial favorable correlation with overall survival of head-and-neck cancer patients. Finally, GSCA was used to predict gene-specific potential drugs that act on these molecules by combining mRNA expression and drug sensitivity data from the Genomics of Drug Sensitivity in Cancer and the Cancer Therapeutics Response Portal. Conclusions: The hub genes/proteins identified in this study could help researchers better understand the molecular processes involved in the progression and metastasis of oral cancer in smokers.

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