Transcriptomic profiling of inner ear hair cell spontaneous regeneration reveals the key role of dlx5a

Abstract

Sensory hair cells (HCs) are susceptible to damage, typically causing permanent hearing and balance deficits in mammals due to limited regeneration. Understanding spontaneous regeneration in non-mammalian models offers key insights for restoring sensory function. Here, we establish a zebrafish semicircular canal crista HC injury model and characterize subsequent regeneration and functional recovery processes. Lineage tracing demonstrates that regenerated crista HCs derive from preexisting and newly formed supporting cells (SCs) that emerged after crista HC injury via both mitotic and non-mitotic mechanisms. Single-cell transcriptomic sequencing of otic vesicles across a regeneration timeline reveals that transcriptomic dynamics peak at 24 h post-injury and uncovers a coordinated multicellular response, including activated inflammatory signaling in immune cells and regenerative pathways in SC populations. Finally, we identify dlx5a as a key transcription factor required for crista HC regeneration. In this work, we provide a framework for understanding vestibular HC regeneration that may inform regenerative therapies for sensory restoration. This study establishes a zebrafish inner ear hair cell injury model, characterizes hair cell regeneration at cellular and single-cell transcriptomic levels, and identifies dlx5a as a key regulator of spontaneous regeneration.