IFN-γ selectively suppresses a subset ofTLR4-activated genes and enhancers to potentiate M1-like macrophage polarization

Complete polarization of macrophages towards an M1-like proinflammatory and antimicrobial state requires combined action of IFN-{gamma} and LPS. Synergistic activation of canonical inflammatory NF-{kappa}B target genes by IFN-{gamma} and LPS is well appreciated, but less is known about whether IFN-{gamma} negatively regulates components of the LPS response, and how this affects polarization. A combined transcriptomic and epigenomic approach revealed that IFN-{gamma} selectively abrogates LPS-induced feedback and select metabolic pathways by suppressing TLR4-mediated activation of gene enhancers. In contrast to superinduction of inflammatory genes via enhancers that harbor IRF sequences and bind STAT1, IFN-{gamma}-mediated repression targeted enhancers with STAT sequences that bound STAT3. TLR4-activated IFN-{gamma}-suppressed enhancers comprised two subsets distinguished by differential regulation of histone acetylation and recruitment of STAT3, CDK8 and cohesin, and were functionally inactivated by IFN-{gamma}. These findings reveal that IFN-{gamma} suppresses feedback inhibitory and metabolic components of the TLR response to achieve full M1 polarization, and provide insights into mechanisms by which IFN-{gamma} selectively inhibits TLR4-induced transcription.