Abstract
Activation of macrophage proinflammatory and antimicrobial phenotypes is regulated by IFN-γ and LPS via synergistic induction of canonical, inflammatory NF-κB target genes. However, whether IFN-γ negatively regulates components of the LPS response, and how this may affect macrophage activation, is still unclear. Here we use combined transcriptomic and epigenomic approaches to find that IFN-γ selectively abrogates LPS-induced feedback and alters macrophage metabolic pathways by suppressing TLR4-mediated gene activation. In contrast to superinduction of inflammatory genes via enhancers that bind IRF1 and STAT1, IFN-γ represses target enhancers that bind STAT3. TLR4-activated but IFN-γ-suppressed enhancers comprise two subsets discernable by differential regulation of histone acetylation and recruitment of STAT3, CDK8 and cohesin. Our findings thus show that IFN-γ suppresses feedback inhibitory and metabolic components of TLR responses to enhance macrophage activation; they also provide insights for IFN-γ-mediated selective inhibition of TLR4-induced transcription. Such inhibition can contribute to severe and sustained inflammatory responses.
Highlights
Activation of macrophage proinflammatory and antimicrobial phenotypes is regulated by IFN-γ and LPS via synergistic induction of canonical, inflammatory NF-κB target genes
During TLR4 response, autocrine IFN-β signals through the interferon-stimulated gene factor 3 (ISGF3) complex composed of STAT1/STAT2/IRF9 that binds to interferon-stimulated response elements (ISREs), to induce a feedforward loop in LPS-induced gene expression promoting macrophage activation[11]
We find that LPS-induced genes that are repressed by IFN-γ priming can be subdivided into at least two subsets: those regulated by an IL-10-STAT3 negative feedback loop, and those that function in metabolic pathways and are regulated independently of IL-10
Summary
Selective inhibition of LPS-induced transcription by IFN-γ. A well-established function of IFN-γ is augmentation of LPSinduced inflammatory gene expression, but little is known about the overall effects of IFN-γ on TLR4-induced transcriptional responses. LPSinducible genes repressed by IFN-γ (cluster IV) were associated with negative regulation of inflammatory responses, metabolism, and iron transport (Fig. 1d) Closer examination of these genes and comparison to one public dataset (GSE4370028) revealed that cluster IV contains IL10 and approximately 30% (239/770) of genes in cluster IV correspond to IL-10-inducible genes (Fig. 1e, left, representative genes are shown, and Supplementary Fig. 1c). These results suggest that IFN-γ broadly interrupts the IL-10mediated LPS-induced negative feedback-loop that negatively regulates inflammation, at least in part by suppressing IL10 induction. R: Resting macrophages G: IFN-γ-primed macrophages L: LPS-stimulated macrophages GL: IFN-γ-primed LPS-stimulated macrophages
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