IFN?-induced memory in human macrophages is not sustained by epigenetic changes but the durability of the cytokine itself [ATAC-Seq]

Macrophages, as key sentinel cells of the innate immune system, can retain memory of prior stimulus exposure. Interferon gamma (IFN?) plays a central role in maintaining trained immunity in vivo and can induce potent memory in macrophages. Such memory is associated with the formation of de novo enhancers that alter gene expression responses to subsequent stimuli. However, how such enhancers are maintained after cytokine exposure remains unclear. We report that durable IFN?-induced enhancers can last for days after cytokine washout, yet the underlying persistence mechanism is not cell-intrinsic. IFN?-treated macrophages continue to exhibit JAK/STAT signaling days after cytokine removal. Blocking IFN? signaling with a JAK inhibitor or anti-IFN? neutralizing antibodies after cytokine removal is sufficient to reverse IFN?-induced enhancers and erase the potentiated state of the treated macrophages. Our findings suggest that epigenetic changes in macrophages do not inherently encode innate immune memory or a “potentiated” macrophage state, but that rather epigenetic changes are themselves dependent on ongoing cytokine signaling. These findings suggest new possibilities for pharmacologic interventions to reverse aberrantly trained immune states associated with pathology. Overall design: ATACseq was performed to identify chromatin opening induced by interferon gamma in human macrophages and assay the necessity of continued JAK/STAT signaling on chromatin accessibility after interferon withdrawal.