Setdb2 Regulates Inflammatory Trigger-Induced Trained Immunity of Macrophages Through Two Different Epigenetic Mechanisms

"Trained immunity" of innate immune cells occurs through a two-step response pattern where an initial pathogenic or sterile inflammatory trigger is followed by an augmented response to a later un-related secondary pathogen challenge. The memory effect is mediated at least in part through epigenetic modifications of the chromatin landscape. Here, we investigated the role of the epigenetic modifier Setdb2 in microbial (β-glucan) or sterile trigger (Western-diet-WD/oxidized-LDL-oxLDL)-induced trained immunity of macrophages. Using genetic mouse models and genomic analysis, we uncovered a critical role of Setdb2 in regulating proinflammatory and metabolic pathway reprogramming. We further showed that Setdb2 regulates trained immunity through two different complementary mechanisms: one where it positively regulates glycolytic and inflammatory pathway genes via enhancer-promoter looping, which is independent of its enzymatic activity; and a second mechanism that requires its SET domain and is associated with both elevated H3K9 methylation changes and repression of interferon response pathway gene promoters. Interestingly, while both mechanisms occur in response to pathogenic training, only the chromatin-looping mechanism operates in response to the sterile inflammatory stimulus. These results reveal a previously unknown bifurcation in the downstream pathways that distinguishes between pathogenic and sterile inflammatory signaling responses associated with the innate immune memory response and may provide potential therapeutic opportunities to target cytokine vs. interferon these pathways to limit complications of chronic inflammation. Gene expression (RNA-seq, n = 24) and chromatin accessibility (ATAC-seq, n = 24) were analyzed in wild-type (WT) and Setdb2 knockout (Setdb2KO) bone marrow-derived macrophages (BMDMs) under four different treatment conditions: control (CTRL), β-glucan (GLU), lipopolysaccharide (LPS), and a combination of β-glucan and lipopolysaccharide (GLULPS).