Quantitative phosphoproteomics analysis uncovers CDK1- and PAK2-mediated malignant signaling pathways in clear cell Renal Cell Carcinoma

Clear cell Renal Cell Carcinoma (ccRCC) is among the 10 most common cancers and causes more than 140,000 deaths worldwide every year. In order to elucidate the underlying molecular mechanisms orchestrated by phosphorylation modifications, we performed a comprehensive quantitative phosphoproteomics characterization of ccRCC tumor and normal adjacent tissues. Here, we identified 16,253 phosphopeptides, of which more than 9,000 were quantified. Our in-depth analysis revealed 1,336 phosphopeptides to be differentially regulated between tumor and normal tissues. Moreover, our data reveals that significantly up-regulated phosphoproteins are associated with cytoskeletal re-organization which suggests migratory and invasive behavior of renal tumors. This is supported by a pronounced mesenchymal profile of ccRCC phosphorylation events. Our rigorous characterization of the renal phosphoproteome also revealed that both EGFR and VEGFR are the most important mediators of phospho signaling in RCC pathogenesis. Furthermore, we determined the kinases PAK2, CDK1, Erk1 and Erk2 to be master kinases that are responsible for phosphorylations of many substrates associated with cell proliferation, inflammation and migration. These master kinases are targetable by inhibitory FDA-approved drugs such as fostamatinib and minocycline, which can serve as novel therapeutic agents for ccRCC treatment.