Single cell RNA-Seq reveals distinct stem cell populations that drive sensory hair cell regeneration in response to loss of Fgf and Notch signaling

Loss of sensory hair cellsleads to deafness and balance deficiencies. In contrast to mammalian hair cells, zebrafish ear and lateral line hair cellsregenerate from poorly characterized, proliferating support cells. Equally ill-defined is the gene regulatory networkunderlying the progression of support cellsto cycling hair cellprogenitors and differentiated hair cells. We used single cellRNA-Sequencing (scRNA-Seq) of lateral line sensory organsand uncovered five different support celltypes, including quiescent and activated stem cells. In silico ordering of support cellsalong a developmental trajectory identified cellsthat self-renew and new groups of genes required for hair celldifferentiation. scRNA-Seq analyses of fgf3 mutants, in which hair cellregeneration is increased, demonstrates that Fgf and Notch signaling inhibit proliferation of support cellsin parallel by inhibiting Wnt signaling. Our scRNA-Seq analyses set the foundation for mechanistic studies of sensory organregeneration and is crucial for identifying factors to trigger hair cellproduction in mammals. To spur advances in the field, we implemented a fully searchable and publicly accessible easy-to-use, web-based interface that reveals celltype specific expression of genes of interest.