Large-scale phosphoproteomics reveals Shp-2 phosphatase-dependent regulators of Pdgf-receptor signaling

Despite its low cellular abundance, tyrosine phosphorylation (pTyr) regulates numerous cell signaling pathways in health and disease. We applied comprehensive phosphoproteomics to unravel differential regulators of receptor tyrosine kinase (RTK)–initiated signaling networks upon activation by Pdgf-ββ, Fgf-2, or Igf-1, and identified over 40,000 phosphorylation sites, including many phosphotyrosine sites without additional enrichment. The analysis revealed RTK-specific regulation of hundreds of pTyr sites on key signaling molecules. We found the tyrosine phosphatase Shp2 to be the master regulator of Pdgfr pTyr signaling. Application of a recently introduced allosteric Shp2 inhibitor revealed global regulation of the Pdgf-dependent tyrosine phosphoproteome, which significantly impaired cell migration. Additionally, we present a list of hundreds of Shp2-dependent targets and putative substrates including Rasa1 and Cortactin with increased tyrosine phosphorylation, and Gab1 and Erk1/2 with decreased tyrosine phosphorylation. Our study demonstrates that large-scale quantitative phosphoproteomics can precisely dissect tightly regulated kinase-phosphatase signaling networks.