Dynamic Phosphoproteomic Profiling Identifies CK2 as a Critical Survival Kinase in Quiescent Breast Cancer Cells and a Therapeutic Target for Minimal Residual Disease

Quiescent cancer cells (QCCs) evade conventional therapies and contribute to minimal residual disease (MRD) and relapse, yet the signaling pathways governing their survival remain poorly understood. Here, we performed integrative proteomic and phosphoproteomic profiling of triple-negative breast cancer cells transitioning between proliferation and serum withdrawal-induced quiescence, followed by reactivation. We identified dynamic remodeling of both proteome and phosphoproteome, with quiescent cells showing downregulation of mitotic drivers and upregulation of extracellular matrix components. Notably, phosphorylation of CK2 substrates was increased during quiescence, and CK2 inhibition using CX-4945 impaired cell survival under nutrient and genotoxic stress, disrupted autophagy, microtubule dynamics, and protein synthesis. Phospho-enrichment and functional assays identified Death-associated protein kinase 3 (DAPK3) as a CK2-regulated effector mediating stress-induced apoptosis. In silico analysis confirmed a link between high CK2 expression and poor chemotherapy response in basal breast cancer. These findings establish CK2 as a critical survival kinase in QCCs and a potential therapeutic target for MRD eradication in breast cancer.