Journal Article

Exploring somatic mutations in BRAF, KRAS, and NRAS as therapeutic targets in Saudi colorectal cancer patients through massive parallel sequencing and variant classification

Aljuhani, Thamer Abdulhamid, Banaganapalli, Babajan, Awan, Zuhier Ahmad, Bokhary, Rana Y., Elango, Ramu, Al Mahdi, Hadiah Bassam, Al-Rayes, Nuha, Shaik, Noor Ahmad, Alqawas, Rahaf Talal, Al-Mutadares, Mahmood, El-Harouni, Ashraf AbdulRahman

2024

Overview

Colorectal cancer (CRC) is the leading cancer among Saudis, and mutations in , , and genes are therapeutically significant due to their association with pathways critical for cell cycle regulation. This study evaluates the prevalence and frequency of somatic mutations in these actionable genes in Saudi CRC patients and assesses their pathogenicity with bioinformatics methods. The study employed the TruSight Tumor 15 next-generation sequencing (NGS) panel on 86 colorectal cancer (CRC) samples to detect somatic mutations in , , and genes. Bioinformatic analyses of NGS sequences included variant annotation with ANNOVAR, pathogenicity prediction, variant reclassification with CancerVar, and extensive structural analysis. Additionally, molecular docking assessed the binding of Encorafenib to wild-type and mutant proteins, providing insights into the therapeutic relevance of pathogenic variants. Out of 86 tumor samples, 40 (46.5%) harbored somatic mutations within actionable genes ( : 2.3%, : 43%, : 2.3%). Fourteen missense variants were identified ( : n = 1, : n = 11, : n = 2). Variants with strong clinical significance included V600E (2.32%) and G12D (18.60%). Variants with potential clinical significance included several and an mutation, while variants of unknown significance included E49K and R102Q. One variant was novel: R102Q, and two were rare: E49K and G138E. We further extended the CancerVar prediction capability by adding new pathogenicity prediction tools. Molecular docking demonstrated that Encorafenib inhibits the V600E variant BRAF protein less effectively compared to its wild-type counterpart. Overall, this study highlights the importance of comprehensive molecular screening and bioinformatics in understanding the mutational landscape of CRC in the Saudi population, ultimately improving targeted drug treatments.

• Publisher: Frontiers Media SA,Frontiers Media S.A
• Subject: Bioinformatics / Biomarkers / BRAF V600E / Cancer / Cell cycle / Chemotherapy / Colorectal cancer / Colorectal carcinoma / Genes / Genetic testing / Genomes / Hospitals / K-Ras protein / Mutation / Next-generation sequencing / Oncology / Pathogenicity / Patients / Pharmacology / Predictions / somatic mutations / targeted drug therapy / Therapeutic targets / TruSight tumor 15 panel / Tumors