Phosphorylation site dynamics of early T-cell receptor signaling

• Published in: PloS one Vol. 9; no. 8; p. e104240
• Main Authors: Chylek, Lily A, Akimov, Vyacheslav, Dengjel, Jörn, Rigbolt, Kristoffer T G, Hu, Bin, Hlavacek, William S, Blagoev, Blagoy
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 22.08.2014; Public Library of Science (PLoS)
• Subjects: Actin; Adaptive immunity; BASIC BIOLOGICAL SCIENCES; Binding sites; Biochemistry; Biology and Life Sciences; CD28 antigen; Cell differentiation; Cell Line; Cellular biology; Cellular manufacture; Chemistry; Computer applications; Dermatology; Differentiation (biology); Humans; Hypotheses; Immune response; Immunology; INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Kinases; Laboratories; Lymphocytes; Lymphocytes T; Mathematical models; Models, Biological; Molecular biology; Ordinary differential equations; Phosphoproteins - metabolism; Phosphorylation; Protein interaction; Protein Interaction Maps; Protein Tyrosine Phosphatase, Non-Receptor Type 6 - metabolism; Proteins; Proteome; Proteomics; Proteomics - methods; Receptors, Antigen, T-Cell - metabolism; Regulatory mechanisms (biology); Science & Technology - Other Topics; SHP-1 protein; Signal Transduction; Signaling; Stimulation; Studies; Systems analysis; T cell receptors; T-cell receptor; T-Lymphocytes - metabolism; Tyrosine - metabolism; Wiskott-Aldrich Syndrome Protein Family - metabolism; Denmark; New Mexico; United States > US; Germany
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0104240

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.