Macrophage efferocytosis is controlled by epigenetic modifications mediated by RBPJ

Efferocytosis, phagocytic clearance of apoptotic cells, is crucial for inflammation resolution and maintenance of tissue homeostasis. However, it is not known how epigenetic alterations govern macrophage-mediated efferocytosis. A Cleavage Under Targets and Release Using Nuclease (CUT&RUN) sequencing revealed a genome-wide selective suppression of H3K9me3, a heterochromatin mark that represses gene activity, in macrophages undergoing efferocytosis. Moreover, Recombination Signal Binding Protein for Immunoglobulin Kappa J region (RBPJ), which is a transcription factor typically involved in the canonical Notch signaling process, dampened this epigenetic modification, enhanced apoptotic cell clearance, and suppressed inflammation by mouse atherosclerotic plaque, alveolar, peritoneal, and bone marrow-derived macrophages and human primary macrophages. Inhibition of the Notch signaling in macrophages significantly reduced efferocytosis whereas activation of this signaling augmented apoptotic debris clearance. Mechanistically, RBPJ upregulated Stard13 and Arsg by diminishing H3K9me3 on their promoters. Stard13 promoted efferocytosis by magnifying actin polymerization via inhibition and activation of Rho and RAC GTPases, respectively. Genetic and pharmacological inhibitions of SUV39H1/H2, the methyltransferases that are responsible for H3K9 trimethylation, amplified the expression of Stard13 and Arsg, and augmented efferocytosis by RBPJ-/- macrophages. In sum, this study shows epigenetic regulation of efferocytosis in tissue macrophages.