Stem cells tightly regulate dead cell clearance to maintain tissue fitness [scRNA-seq]

Macrophages and dendritic cells have long been appreciated for their ability to migrate to and engulf dying cells and debris, including some of the billions of cells that are naturally eliminated from our body daily. However, a substantial amount of these dying cells are cleared by local tissue cells, so-called 'non-professional phagocytes', critical to preserve organismal fitness. How non-professional phagocytes are able to sense and digest nearby apoptotic corpses while still performing their normal tissue functions is unclear. Here, we explore the molecular mechanisms underlying this balancing act. Exploiting the cyclical bouts of tissue regeneration and degeneration during the hair cycle, we show that stem cells can transiently become non-professional phagocytes when confronted with dying cells. Adoption of this phagocytic state requires not only local lipids produced by apoptotic corpses, which are necessary for RXRa activation, but also tissue-specific retinoids able to activate RARg. The dual factor dependency enables tight regulation of the genes requisite to activate phagocytic apoptotic clearance. The tunable phagocytic program we describe here offers an attractive mechanism to offset phagocytic duties against the primary stem cell function of replenishing differentiated cells to preserve tissue integrity during homeostasis. Our findings have broad implications for other non-motile stem or progenitor cells which experience cell death in an immune-privileged niche. Overall design: For each hair cycle stage, wild type hair follicle stem cells (HFSCs) from 3-6 wild type animals were pooled and FACS sorted directly into SMARTSeq2 lysis buffer in 96-well plates and snap frozen. SMART-Seq2 was performed as described in Picelli, S. et al. Full-length RNA-seq from single cells using Smart-seq2. Nature Protocols 9, 171-181 (2014). Modifications were made as in Yang, H., Adam, R. C., Ge, Y., Hua, Z. L. & Fuchs, E. Epithelial-Mesenchymal Micro-niches Govern Stem Cell Lineage Choices. Cell 169, 483-496.e413 (2017).