Dynamic cross talk model of the epithelial innate immune response to double-stranded RNA stimulation: coordinated dynamics emerging from cell-level noise

PLoS One. 2014 Apr 7;9(4):e93396. doi: 10.1371/journal.pone.0093396. eCollection 2014.

Abstract

We present an integrated dynamical cross-talk model of the epithelial innate immune response (IIR) incorporating RIG-I and TLR3 as the two major pattern recognition receptors (PRR) converging on the RelA and IRF3 transcriptional effectors. bioPN simulations reproduce biologically relevant gene-and protein abundance measurements in response to time course, gene silencing and dose-response perturbations both at the population and single cell level. Our computational predictions suggest that RelA and IRF3 are under auto- and cross-regulation. We predict, and confirm experimentally, that RIG-I mRNA expression is controlled by IRF7. We also predict the existence of a TLR3-dependent, IRF3-independent transcription factor (or factors) that control(s) expression of MAVS, IRF3 and members of the IKK family. Our model confirms the observed dsRNA dose-dependence of oscillatory patterns in single cells, with periods of 1-3 hr. Model fitting to time series, matched by knockdown data suggests that the NF-κB module operates in a different regime (with different coefficient values) than in the TNFα-stimulation experiments. In future studies, this model will serve as a foundation for identification of virus-encoded IIR antagonists and examination of stochastic effects of viral replication. Our model generates simulated time series, which reproduce the noisy oscillatory patterns of activity (with 1-3 hour period) observed in individual cells. Our work supports the hypothesis that the IIR is a phenomenon that emerged by evolution despite highly variable responses at an individual cell level.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptor Proteins, Signal Transducing / immunology
  • Animals
  • Cells, Cultured
  • Epithelial Cells / cytology
  • Epithelial Cells / immunology*
  • Humans
  • Immunity, Innate / drug effects*
  • Interferon Regulatory Factor-3 / immunology
  • Mice, Knockout
  • RNA, Double-Stranded / immunology
  • RNA, Double-Stranded / pharmacology*
  • Toll-Like Receptor 3 / immunology
  • Transcription Factor RelA / immunology

Substances

  • Adaptor Proteins, Signal Transducing
  • IPS-1 protein, mouse
  • IRF3 protein, human
  • Interferon Regulatory Factor-3
  • Irf3 protein, mouse
  • MAVS protein, human
  • RELA protein, human
  • RNA, Double-Stranded
  • Rela protein, mouse
  • TLR3 protein, human
  • TLR3 protein, mouse
  • Toll-Like Receptor 3
  • Transcription Factor RelA