Computational phosphoproteomic insights into predominant BRAF phosphosites and associated regulatory networks in cancer.

BRAF, a serine/threonine kinase, functions as a key effector of the MAPK signaling cascade and regulates cell proliferation and survival. Oncogenic BRAF mutations disrupt MAPK pathway homeostasis, contributing significantly to cancer progression and pathogenesis. BRAF phosphorylation is pivotal for modulating downstream signaling events. In this study, we performed a comprehensive analysis of global human phosphoproteomic datasets to elucidate BRAF phosphorylation dynamics and associated regulatory networks. The systematic annotation identified BRAF phosphorylation in 912 qualitative profiles across 166 studies and 234 quantitative differential datasets from 73 studies, revealing 44 and 21 distinct phosphosites, respectively. Class I phosphosites with localization probability ≥75% or A-score > 13 were filtered. A fold-change threshold of ≥1.3 for upregulation and ≤ 0.76 for downregulation was applied. Particularly, six predominant phosphorylation sites, S446, S729, S151, T401, S365, and S447, were frequently observed. Further analysis of melanoma-melanoma-specific phosphoproteomic datasets and correlations with gene expression data from melanoma cell lines revealed several key co-regulated proteins associated with the predominant BRAF phosphosites, including STAT3, BAD, CDK16, ITPKB, NPM1, MDC1, CHEK2, PRKDC, EIF3A, TP53BP1, RB1, and CDK14. These co-regulated proteins highlight the integration of BRAF signaling with critical processes, such as cell cycle control, apoptosis, DNA damage response, and protein synthesis in melanoma. Our analysis suggests that targeting BRAF-interacting proteins may also modulate oncogenic signaling pathways and represent promising biomarkers for melanoma diagnosis and therapy.