title: Temporal perturbation of tyrosine phosphoproteome dynamics reveals the system-wide regulatory networks.
abstract: Signal transduction systems are known to widely regulate complex biological events such as cell proliferation and differentiation. Because phosphotyrosine-dependent networks play a key role in transmitting signals, a comprehensive and fine description of their dynamic behavior can lead us to systematically analyze the regulatory mechanisms that result in each biological effect. Here we established a mass spectrometry-based framework for analyzing tyrosine phosphoproteome dynamics through temporal network perturbation. A highly time-resolved description of the epidermal growth factor-dependent signaling pathways in human A431 cells revealed a global view of their multiphase network activation, comprising a spike signal transmission within 1 min of ligand stimulation followed by the prolonged activation of multiple Src-related molecules. Temporal perturbation of Src family kinases with the corresponding inhibitor PP2 in the prolonged activation phase led to the down-regulation of the molecules related to cell adhesion and receptor degradation, whereas the canonical cascades as well as the epidermal growth factor receptor relatively maintained their activities. Our methodology provides a system-wide view of the regulatory network clusters involved in signal transduction that is essential to refine the literature-based network structures for a systems biology analysis.
authors.affiliation: Medical Proteomics Laboratory, Institute of Medical Science, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan. moyama@ims.u-tokyo.ac.jp
authors.forename: Masaaki
authors.initials: M
authors.lastname: Oyama
authors.forename: Hiroko
authors.initials: H
authors.lastname: Kozuka-Hata
authors.forename: Shinya
authors.initials: S
authors.lastname: Tasaki
authors.forename: Kentaro
authors.initials: K
authors.lastname: Semba
authors.forename: Seisuke
authors.initials: S
authors.lastname: Hattori
authors.forename: Sumio
authors.initials: S
authors.lastname: Sugano
authors.forename: Jun-ichiro
authors.initials: J
authors.lastname: Inoue
authors.forename: Tadashi
authors.initials: T
authors.lastname: Yamamoto
mesh_terms: D045744:Cell Line, Tumor; D004815:Epidermal Growth Factor / Q000494:pharmacology; D053263:Gene Regulatory Networks / Q000187:drug effects; D006801:Humans; D010766:Phosphorylation / Q000187:drug effects; D019000:Phosphotyrosine / Q000378:metabolism*; D020543:Proteome / Q000378:metabolism*; D011743:Pyrimidines / Q000494:pharmacology; D013997:Time Factors; D019061:src-Family Kinases / Q000037:antagonists & inhibitors
chemical_list: C412373:AG 1879; D020543:Proteome; D011743:Pyrimidines; D019000:Phosphotyrosine; D004815:Epidermal Growth Factor; D019061:src-Family Kinases