Large-Scale Phosphoproteomics Reveals Shp-2 Phosphatase-Dependent Regulators of Pdgf Receptor Signaling

• Published in: Cell reports (Cambridge) 2018-03, Vol.22 (10), p.2784-2796
• Main Authors: Batth, Tanveer S., Papetti, Moreno, Pfeiffer, Anamarija, Tollenaere, Maxim A.X., Francavilla, Chiara, Olsen, Jesper V.
• Format: Article
• Language: English
• Subjects: label-free quantitation; mass spectrometry; orbitrap; PDGF; phosphoproteomics; Q exactive; Shp-2; SHP099; TiO2; tyrosine phosphorylation
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2018.02.038

Despite its low cellular abundance, phosphotyrosine (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 more than 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 Shp-2 to be the master regulator of Pdgfr pTyr signaling. Application of a recently introduced allosteric Shp-2 inhibitor revealed global regulation of the Pdgf-dependent tyrosine phosphoproteome, which significantly impaired cell migration. In addition, we present a list of hundreds of Shp-2-dependent targets and putative substrates, including Rasa1 and Cortactin with increased pTyr and Gab1 and Erk1/2 with decreased pTyr. Our study demonstrates that large-scale quantitative phosphoproteomics can precisely dissect tightly regulated kinase-phosphatase signaling networks. [Display omitted] •Study of global phosphoproteome response after activation of different RTKs•Shp-2 is highly phosphorylated upon Pdgf, but not Fgf-2, stimulation•Application of an allosteric Shp-2 inhibitor reveals phosphotyrosine targets of Shp-2•Pdgf-receptor-dependent cell migration is controlled by Shp-2 Batth et al. use mass spectrometry-based phosphoproteomics to analyze receptor tyrosine kinase signaling activated by different ligands, identifying hundreds of differentially regulated phosphotyrosine sites. Tyrosine phosphatase Shp-2 regulates global tyrosine phosphorylation in a Pdgf-receptor-dependent manner, affecting cellular outcomes.