Single-cell transcriptomic profiling reveals cellular heterogeneity and organ-specific signatures in the vestibular system

The vestibular sensory epithelia, comprising the utricle, saccule, and ampullary cristae, exhibit distinct regenerative capacities and physiological specializations, yet the cellular heterogeneity and regulatory logic governing their development remain incompletely understood. Here, we generated a single-cell transcriptomic atlas of postnatal day 1 mouse vestibular organs, identifying nine transcriptionally distinct epithelial subpopulations with marked organ-specific distributions. Trajectory reconstruction revealed a conserved tri-phase differentiation cascade ( Sox2 → Atoh1 → Myo7a ) but divergent topologies: linear progenitor progression in ampulla/saccule versus branched paths in utricle. Single-cell regulatory network inference and clustering analysis uncovered 16 regulons, including Pou4f3 -driven programs in hair cells. Wilcoxon testing additionally identified Nfib as a differentially expressed transcription factor in saccule-predominant dark-cell precursors ( Kcne1 -negative at postnatal day 1). CellChat analysis further demonstrated distinct interactomic architectures: the saccule employs high-capacity plastic signaling (insulin-like growth factor), the ampulla emphasizes extracellular matrix remodeling (collagen/thrombospondin), and the utricle and ampulla share neural adhesion signatures (neuronal growth regulator/cell adhesion molecule), with quantitative enrichment in the utricle. These findings establish a molecular framework linking transcriptional programs to organ-specific communication strategies, providing mechanistic insights into vestibular functional diversification and targeted regenerative strategies.