Time-resolved phosphoproteomics reveals scaffolding and catalysis-responsive patterns of SHP2-dependent signaling

• DOI: 10.7554/elife.64251
• Publication Date: 2021-03-23T13:00:56Z
• Authors: Vidyasiri Vemulap...; Lily A Chylek; Alison Erickson; Anamarija Pfeiffer; Khal-Hentz Gabriel; Jonathan LaRochelle; Kartik Subramanian; Ruili Cao; Kimberley Stegmaier; Morvarid Mohseni; Matthew J LaMarche; Michael G Acker; Peter K Sorger; Steven P Gygi; Stephen C Blacklow
• Keywords: Proteomics; 572; QH301-705.5; Science; Protein Tyrosine Phosphatase, Non-Receptor Type 11; PTPN11; Catalysis; phosphatase; src Homology Domains; 03 medical and health sciences; Piperidines; Biochemistry and Chemical Biology; Cell Line, Tumor; Occludin; Guanine Nucleotide Exchange Factors; Humans; Biology (General); Phosphorylation; Phosphotyrosine; mass spectrometry; 0303 health sciences; Epidermal Growth Factor; Phospholipase C gamma; Q; R; Phosphoproteins; 3. Good health; ErbB Receptors; Repressor Proteins; Pyrimidines; Medicine; epidermal growth factor receptor; signal transduction; Protein Binding; Signal Transduction

SHP2 is a protein tyrosine phosphatase that normally potentiates intracellular signaling by growth factors, antigen receptors, and some cytokines, yet is frequently mutated in human cancer. Here, we examine the role of SHP2 in the responses of breast cancer cells to EGF by monitoring phosphoproteome dynamics when SHP2 is allosterically inhibited by SHP099. The dynamics of phosphotyrosine abundance at more than 400 tyrosine residues reveal six distinct response signatures following SHP099 treatment and washout. Remarkably, in addition to newly identified substrate sites on proteins such as occludin, ARHGAP35, and PLCγ2, another class of sites shows reduced phosphotyrosine abundance upon SHP2 inhibition. Sites of decreased phospho-abundance are enriched on proteins with two nearby phosphotyrosine residues, which can be directly protected from dephosphorylation by the paired SH2 domains of SHP2 itself. These findings highlight the distinct roles of the scaffolding and catalytic activities of SHP2 in effecting a transmembrane signaling response.