BET protein inhibition regulates macrophage chromatin accessibility and microbiota-dependent colitis [ATAC-seq]

In colitis, macrophage functionality is altered compared to normal homeostatic conditions. Loss of IL-10 signaling results in an inappropriate chronic inflammatory response to bacterial stimulation. It remains unknown if inhibition of bromodomain and extra-terminal domain (BET) proteins alters usage of DNA regulatory elements responsible for driving inflammatory gene expression. We determined if the BET inhibitor, (+)-JQ1, could suppress inflammatory activation of macrophages in Il10-/- mice. We performed ATAC-seq and RNA-seq on Il10-/- bone marrow-derived macrophages (BMDMs) cultured in the presence and absence of lipopolysaccharide (LPS) with and without treatment with (+)-JQ1 and evaluated changes in chromatin accessibility and gene expression. Treatment with (+)-JQ1 suppressed LPS-induced changes in chromatin at distal regulatory elements associated with inflammatory genes, particularly in regions that contain motifs for AP-1 and IRF transcription factors. Mature bone marrow derived macrophages were cultured and biologically matched samples (n=3 biological replicates/condition) were generated for the following conditions: 1) unstimulated and no treatment, 2) unstimulated and (+)-JQ1 treatment (500nM), 3) unstimulated and IL-10 treatment (10ng/mL), 4) lipopolysaccharide (LPS) stimulation (50ng/mL) and no treatment, 5) LPS stimulation and (+)-JQ1 treatment, and 6) LPS stimulation and IL-10 treatment. Samples were treated with (+)-JQ1 or IL-10 or remained untreated in culture for 12 hours followed by LPS stimulation for 4 hours in for appropriate conditions (with PBS serving as a control).