The widespread regulatory role of the phosphorylation of RNA-binding proteins (RBPs) in RNA abnormalities

Abstract

Protein phosphorylation is a pervasive post-translational modification that orchestrates cellular signal transduction and functional control during tumorigenesis. By charting a pan-cancer phosphoproteomic atlas with a focus on RNA-binding proteins (RBPs), we found that differentially phosphorylated sites between tumors and matched non-tumor tissues are strongly enriched on RBPs. These data suggest that phosphorylation can amplify oncogenic signals through RBP-mediated RNA dysregulation. Among all RBPs, phosphorylation of Nucleolin (NCL) at threonine 76 (NCL T76) is upregulated across multiple cancer types and is tightly associated with poor patient prognosis and widespread abnormalities in RNA processing. We systematically mapped the upstream kinase–substrate landscape and actionable compounds for this key RBP phosphosite and the downstream classes of RNA dysregulation linked to these modifications. Integrative analyses and in vitro experiments identify cyclin-dependent kinase 2 (CDK2) as the upstream kinase for NCL T76. The small molecule inhibitor TG-02 effectively suppresses CDK2-mediated phosphorylation at NCL T76. Our study establishes RBP phosphorylation as a prevalent regulatory layer across cancers that reshapes RNA regulatory networks. It further defines NCL T76 as a critical functional site, elucidates its upstream control, and highlights the CDK2–NCL T76 axis as a tractable therapeutic avenue.