Resident Macrophages are Locally Programmed for Silent Clearance of Apoptotic Cells

Although apoptotic cells (ACs) contain nucleic acids that can be recognized by Toll-like receptors (TLRs), engulfment of ACs does not initiate inflammation in healthy organisms. To better understand this phenomenon, we identified and characterized macrophage populations that continually engulf ACs in several distinct tissues. These macrophages share characteristics compatible with immunologically silent clearance of ACs, including high expression of AC recognition receptors, low expression of TLR9, and reduced TLR responsiveness to nucleic acids. When removed from tissues, these macrophages lose many of these characteristics and generate inflammatory responses to AC-derived nucleic acids, suggesting that cues from the tissue microenvironment are required to program macrophages for silent AC clearance. We show that KLF2 and KLF4 control expression of many genes within this AC clearance program. Coordinated expression of AC receptors with genes that limit responses to nucleic acids may represent a central feature of tissue macrophages that ensures maintenance of homeostasis. RNA sequencing on purified Tim-4+ peritoneal macrophages was performed on RNA isolated from macrophages immediately ex vivo (n=1) or after tissue culture for 60 hours (n=2) in two independent experiments. Tim-4+ peritoneal macrophages were stimulated + apoptotic cells (ACs) after tissue culture for 2 or 60 hours n=2 per experimental condition.