A stimulus‐contingent positive feedback loop enables IFN‐β dose‐dependent activation of pro‐inflammatory genes

• Published in: Molecular systems biology 2023-05, Vol.19 (5), p.e11294-n/a
• Main Authors: Wilder, Catera L, Lefaudeux, Diane, Mathenge, Raisa, Kishimoto, Kensei, Zuniga Munoz, Alma, Nguyen, Minh A, Meyer, Aaron S, Cheng, Quen J, Hoffmann, Alexander
• Format: Article
• Language: English
• Subjects: Antiviral Agents; Control theory; Cytokines; Datasets; Defense mechanisms; EMBO19; EMBO37; Feedback; Feedback loops; Gene expression; Gene Expression Regulation; IFN‐β; Immune response; Inflammation; inflammatory response; Influenza; Innate immunity; ISGF3; Kinases; Life Sciences; Mathematical models; Positive feedback; Principal components analysis; Signal Transduction; signaling dynamics; Stat2 protein; stimulus‐contingent positive feedback loop; Systems Biology; Transcription activation; Transcription Factors; β-Interferon
• ISSN: 1744-4292; 1744-4292
• DOI: 10.15252/msb.202211294

Type I interferons (IFN) induce powerful antiviral and innate immune responses via the transcription factor, IFN‐stimulated gene factor (ISGF3). However, in some pathological contexts, type I IFNs are responsible for exacerbating inflammation. Here, we show that a high dose of IFN‐β also activates an inflammatory gene expression program in contrast to IFN‐λ3, a type III IFN, which elicits only the common antiviral gene program. We show that the inflammatory gene program depends on a second, potentiated phase in ISGF3 activation. Iterating between mathematical modeling and experimental analysis, we show that the ISGF3 activation network may engage a positive feedback loop with its subunits IRF9 and STAT2. This network motif mediates stimulus‐specific ISGF3 dynamics that are dependent on ligand, dose, and duration of exposure, and when engaged activates the inflammatory gene expression program. Our results reveal a previously underappreciated dynamical control of the JAK–STAT/IRF signaling network that may produce distinct biological responses and suggest that studies of type I IFN dysregulation, and in turn therapeutic remedies, may focus on feedback regulators within it. Synopsis The dose and duration of type I interferon exposure is interpreted by a signaling module that contains a stimulus‐contingent positive feedback loop to specify ISGF3 activation dynamics. A secondary, potentiated phase of ISGF3 activates a pro‐inflammatory gene expression program. High‐dose IFN‐β activates a pro‐inflammatory gene program in epithelial cells. IFN‐β, but not IFN‐λ3, induces a second, potentiated phase in ISGF3 activity. ISGF3 induces its subunits to form a stimulus‐contingent positive feedback loop. The positive feedback motif is required for the pro‐inflammatory gene program. Graphical Abstract The dose and duration of type I interferon exposure is interpreted by a signaling module that contains a stimulus‐contingent positive feedback loop to specify ISGF3 activation dynamics. A secondary, potentiated phase of ISGF3 activates a pro‐inflammatory gene expression program.