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

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

JOURNAL=Frontiers in Pharmacology

VOLUME=15

YEAR=2024

URL=https://www.frontiersin.org/journals/pharmacology/articles/10.3389/fphar.2024.1498295

DOI=10.3389/fphar.2024.1498295

ISSN=1663-9812

ABSTRACT=<sec><title>Background</title><p>Colorectal cancer (CRC) is the leading cancer among Saudis, and mutations in <italic>BRAF</italic>, <italic>KRAS</italic>, and <italic>NRAS</italic> 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.</p></sec><sec><title>Methodology</title><p>The study employed the TruSight Tumor 15 next-generation sequencing (NGS) panel on 86 colorectal cancer (CRC) samples to detect somatic mutations in <italic>BRAF</italic>, <italic>KRAS</italic>, and <italic>NRAS</italic> 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 <italic>BRAF</italic> proteins, providing insights into the therapeutic relevance of pathogenic variants.</p></sec><sec><title>Results</title><p>Out of 86 tumor samples, 40 (46.5%) harbored somatic mutations within actionable genes (<italic>BRAF</italic>: 2.3%, <italic>KRAS</italic>: 43%, <italic>NRAS</italic>: 2.3%). Fourteen missense variants were identified (<italic>BRAF</italic>: n = 1, <italic>KRAS</italic>: n = 11, <italic>NRAS</italic>: n = 2). Variants with strong clinical significance included <italic>BRAF</italic> V600E (2.32%) and <italic>KRAS</italic> G12D (18.60%). Variants with potential clinical significance included several <italic>KRAS</italic> and an <italic>NRAS</italic> mutation, while variants of unknown significance included <italic>KRAS</italic> E49K and <italic>NRAS</italic> R102Q. One variant was novel: <italic>NRAS</italic> R102Q, and two were rare: <italic>KRAS</italic> 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.</p></sec><sec><title>Conclusion</title><p>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.</p></sec>