title: Pairwise network mechanisms in the host signaling response to coxsackievirus B3 infection.
abstract: Signal transduction networks can be perturbed biochemically, genetically, and pharmacologically to unravel their functions. But at the systems level, it is not clear how such perturbations are best implemented to extract molecular mechanisms that underlie network function. Here, we combined pairwise perturbations with multiparameter phosphorylation measurements to reveal causal mechanisms within the signaling network response of cardiomyocytes to coxsackievirus B3 (CVB3) infection. Using all possible pairs of six kinase inhibitors, we assembled a dynamic nine-protein phosphorylation signature of perturbed CVB3 infectivity. Cluster analysis of the resulting dataset showed repeatedly that paired inhibitor data were required for accurate data-driven predictions of kinase substrate links in the host network. With pairwise data, we also derived a high-confidence network based on partial correlations, which identified phospho-IκBα as a central "hub" in the measured phosphorylation signature. The reconstructed network helped to connect phospho-IκBα with an autocrine feedback circuit in host cells involving the proinflammatory cytokines, TNF and IL-1. Autocrine blockade substantially inhibited CVB3 progeny release and improved host cell viability, implicating TNF and IL-1 as cell autonomous components of CVB3-induced myocardial damage. We conclude that pairwise perturbations, when combined with network-level intracellular measurements, enrich for mechanisms that would be overlooked by single perturbants.
authors.affiliation: The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, Providence Heart and Lung Institute at St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.
authors.forename: Farshid S
authors.initials: FS
authors.lastname: Garmaroudi
authors.forename: David
authors.initials: D
authors.lastname: Marchant
authors.forename: Xiaoning
authors.initials: X
authors.lastname: Si
authors.forename: Abbas
authors.initials: A
authors.lastname: Khalili
authors.forename: Ali
authors.initials: A
authors.lastname: Bashashati
authors.forename: Brian W
authors.initials: BW
authors.lastname: Wong
authors.forename: Aline
authors.initials: A
authors.lastname: Tabet
authors.forename: Raymond T
authors.initials: RT
authors.lastname: Ng
authors.forename: Kevin
authors.initials: K
authors.lastname: Murphy
authors.forename: Honglin
authors.initials: H
authors.lastname: Luo
authors.forename: Kevin A
authors.initials: KA
authors.lastname: Janes
authors.forename: Bruce M
authors.initials: BM
authors.lastname: McManus
mesh_terms: D002460:Cell Line; D029822:Enterovirus B, Human; D004769:Enterovirus Infections / Q000378:metabolism*; D054884:Host-Pathogen Interactions; D006801:Humans; D007375:Interleukin-1 / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D032383:Myocytes, Cardiac / Q000187:drug effects / Q000378:metabolism / Q000821:virology*; D010766:Phosphorylation; D047428:Protein Kinase Inhibitors / Q000494:pharmacology; D015398:Signal Transduction; D014409:Tumor Necrosis Factor-alpha / Q000378:metabolism
chemical_list: D007375:Interleukin-1; D047428:Protein Kinase Inhibitors; C439524:TNF protein, human; D014409:Tumor Necrosis Factor-alpha