| Summary: | Summary: Muscle regeneration relies on the regulation of muscle stem cells (MuSCs) through paracrine signaling interactions. We analyzed muscle regeneration in mice using single-cell RNA sequencing (scRNA-seq) and generated over 34,000 single-cell transcriptomes spanning four time-points. We identified 15 distinct cell types including heterogenous populations of muscle stem and progenitor cells. We resolved a hierarchical map of these myogenic cells by trajectory inference and observed stage-specific regulatory programs within this continuum. Through ligand-receptor interaction analysis, we identified over 100 candidate regeneration-associated paracrine communication pairs between MuSCs and non-myogenic cells. We show that myogenic stem/progenitor cells exhibit heterogeneous expression of multiple Syndecan proteins in cycling myogenic cells, suggesting that Syndecans may coordinate myogenic fate regulation. We performed ligand stimulation in vitro and confirmed that three paracrine factors (FGF2, TGFβ1, and RSPO3) regulate myogenic cell proliferation in a Syndecan-dependent manner. Our study provides a scRNA-seq reference resource to investigate cell communication interactions in muscle regeneration. : De Micheli et al. present an annotated, time-resolved single-cell transcriptomic atlas of muscle regeneration in adult mice. They observe a hierarchy of muscle stem and progenitor cells that exhibit stage-specific expression programs and show that Syndecan proteins regulate muscle progenitor cell fates by interaction with newly discovered paracrine communication factors. Keywords: muscle stem cells, single-cell RNA-sequencing, skeletal muscle regeneration, myogenic differentiation, ligand receptor interaction, syndecans
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