Macrophage-specific targeting of histone demethylases with small-molecule inhibitors suppresses inflammatory responses in vivo [RNA-seq]

ABSTRACT: Macrophages are versatile immune cells, with the ability to respond to varied intrinsic and extrinsic cues, and transition between inflammatory and pro-reparative phenotypes. A complex network of epigenetic processes, such as DNA methylation, histone methylation, and acetylation, play key roles in modulating macrophage polarization and inflammatory gene expression. Transcriptional analysis in patients with respiratory failure, long COVID-19, and influenza revealed an augmented expression of chromatin-modifiers including histone demethylases, broadly defined as lysine demethylases (KDMs), in lung macrophages. Therefore, macrophage-specific pharmacological perturbation of these enzymes in vivo holds therapeutic promise in abating inflammation. To investigate the role of KDMs in inflammation, we screened a panel of small-molecule inhibitors of chromatin modifiers for their efficacy in inducing anti-inflammatory macrophage polarization in vitro. We demonstrate that pretreatment with the broad spectrum KDM inhibitor n-octyl-IOX1, KDM5-specific inhibitor PB-IT resulted in a significant decrease of lipopolysaccharide (LPS)-induced expression of the inflammatory genes Il1b, Il6, Tnfa, and iNos in bone marrow-derived macrophages (BMDM). Subsequent RNA sequencing and CUT&RUN analyses revealed that LPS activation led to distinct transcriptomic and epigenomic alterations including expression of master transcription factors (TFs) BLIMP-1 and GFI1 whereas n-octyl-IOX1 and PB-IT treatments rewired these regulatory networks, thereby impeding inflammatory gene expression and response. To further probe the merit of KDM inhibition in perturbing macrophage-mediated inflammation in vivo, we delivered n-octyl-IOX1 selectively to macrophages in mice using a cell-specific, targeted lipidoid nanoparticles. n-octyl-IOX1 loaded nanoparticles significantly diminished LPS-mediated peritoneal macrophage expansion and inflammatory gene expression in this cell population, underscoring the importance of macrophage-specific targeting of KDMs with small-molecule inhibitors in inflammatory disease.

ORGANISM(S): Mus musculus

PROVIDER: GSE292494 | GEO | 2026/08/11

REPOSITORIES: GEO