The discovery and simulation analysis of a novel mutation c.40 G < T (V14F) in the NRAS gene in patients with colorectal cancer in Saudi Arabia

Abstract

Background: Colorectal cancer (CRC) is the most diagnosed cancer in men and the second most common cancer in women and remains associated with high morbidity and mortality in Saudi Arabia. The current understanding of genetic heterogeneity of CRC biology encourages the identification of the genetic causes of CRC in the Saudi population. Methods: In this study, we obtained 89 CRC patients’ tumor samples from Saudi Arabia and investigated the molecular alterations of the NRAS proto-oncogene, GTPase (NRAS) gene in the collected CRC tumor tissue samples to identify gene mutations using DNA sequencing using an automated DNA sequencer ABI 3730xl. The impact of mutations was analyzed using different bioinformatics tools including SwissModel, Missense3D, molecular dynamics simulations using YASARA DYNAMICS and Protein Variation Effect Analyzer (PROVEAN) tool. Results: We identified a novel mutation c.40 G > T, in one patient in whom valine was replaced by phenylalanine (V14F). Notably, we also identified another mutation in the same codon c.40 G > A where valine is replaced by isoleucine (V14I). Our in-silico analysis revealed that this novel mutation alters the binding affinity of the NRAS gene substantially, and as a result, could have lethal consequences on the downstream signaling genes and pathways including MAPK and PI3K involved in regulating CRC growth and progression. Conclusions: These findings provide insights into the molecular etiology of CRC in general and particularly in the Saudi population. Thus, these findings in NRAS mutation testing may also guide further treatment modalities, and more personalized therapy may be optimized.

Keywords

• NRAS
• V14F
• Colorectal cancer
• Novel mutation
• 3D homology modeling