A Computational Approach to Identify the Mutations in the Genes of the RTK Signaling Pathway and their Possible Association with Oral Squamous Cell Carcinoma

Abstract

Background: We aimed to determine the role of receptor tyrosine kinases (RTK) signaling family genes in the development of oral squamous cell carcinoma (OSCC). Method: In the present in silico study, 40 whole genome sequences of patients with OSCC from the cBioPortal was analysed to identify the mutations in the genes of the RTK signaling pathway. Using the STRING v10.5, we further checked the gene with the highest frequency of mutations for its protein interactions. The obtained protein interaction network was used to identify the possible pathways related to disease phenotype. Results: Epidermal growth factor receptor (EGFR) gene showed the highest frequency of mutation (5%) among the 16 genes clustered in the RTK signaling pathway as available in the cBioportal database. Missense mutations viz., G203E, R521K were identified in the EGFR gene. The other genes which returned positive results during analysis were ERBB4 (D245N, L993S), PDGFB (R100H), and PDGFRB (L667M). Conclusion: The in silico method of analysis can be a contemporary approach for identifying possible mutations or pathways associated with the development of OSCC. Further high throughput strategies should be applied to substantiate the role of the genes identified in the present study and draw conclusive evidence as to their association with the disease phenotype.

Keywords

• oral squamous cell carcinoma
• receptor tyrosine kinases
• cbioportal
• mutations