title: Phosphorylation site dynamics of early T-cell receptor signaling.
abstract: In adaptive immune responses, T-cell receptor (TCR) signaling impacts multiple cellular processes and results in T-cell differentiation, proliferation, and cytokine production. Although individual protein-protein interactions and phosphorylation events have been studied extensively, we lack a systems-level understanding of how these components cooperate to control signaling dynamics, especially during the crucial first seconds of stimulation. Here, we used quantitative proteomics to characterize reshaping of the T-cell phosphoproteome in response to TCR/CD28 co-stimulation, and found that diverse dynamic patterns emerge within seconds. We detected phosphorylation dynamics as early as 5 s and observed widespread regulation of key TCR signaling proteins by 30 s. Development of a computational model pointed to the presence of novel regulatory mechanisms controlling phosphorylation of sites with central roles in TCR signaling. The model was used to generate predictions suggesting unexpected roles for the phosphatase PTPN6 (SHP-1) and shortcut recruitment of the actin regulator WAS. Predictions were validated experimentally. This integration of proteomics and modeling illustrates a novel, generalizable framework for solidifying quantitative understanding of a signaling network and for elucidating missing links.
authors.affiliation: Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America; Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States of America.
authors.forename: Lily A
authors.initials: LA
authors.lastname: Chylek
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark.
authors.forename: Vyacheslav
authors.initials: V
authors.lastname: Akimov
authors.affiliation: Department of Dermatology, Medical Center; Freiburg Institute for Advanced Studies (FRIAS); BIOSS Centre for Biological Signalling Studies; ZBSA Center for Biological Systems Analysis, University of Freiburg, Freiburg, Germany.
authors.forename: Jörn
authors.initials: J
authors.lastname: Dengjel
authors.affiliation: Department of Dermatology, Medical Center; Freiburg Institute for Advanced Studies (FRIAS); BIOSS Centre for Biological Signalling Studies; ZBSA Center for Biological Systems Analysis, University of Freiburg, Freiburg, Germany.
authors.forename: Kristoffer T G
authors.initials: KT
authors.lastname: Rigbolt
authors.affiliation: Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America; Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America.
authors.forename: Bin
authors.initials: B
authors.lastname: Hu
authors.affiliation: Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America; Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America; Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America.
authors.forename: William S
authors.initials: WS
authors.lastname: Hlavacek
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark.
authors.forename: Blagoy
authors.initials: B
authors.lastname: Blagoev
mesh_terms: D002460:Cell Line; D006801:Humans; D008954:Models, Biological; D010750:Phosphoproteins / Q000378:metabolism; D010766:Phosphorylation; D060066:Protein Interaction Maps; D053824:Protein Tyrosine Phosphatase, Non-Receptor Type 6 / Q000378:metabolism; D020543:Proteome; D040901:Proteomics / Q000379:methods; D011948:Receptors, Antigen, T-Cell / Q000378:metabolism*; D015398:Signal Transduction; D013601:T-Lymphocytes / Q000378:metabolism*; D014443:Tyrosine / Q000378:metabolism; D051300:Wiskott-Aldrich Syndrome Protein Family / Q000378:metabolism
chemical_list: D010750:Phosphoproteins; D020543:Proteome; D011948:Receptors, Antigen, T-Cell; D051300:Wiskott-Aldrich Syndrome Protein Family; D014443:Tyrosine; C509249:PTPN6 protein, human; D053824:Protein Tyrosine Phosphatase, Non-Receptor Type 6