A single-nucleus transcriptomic atlas of human inner ear development.
Hearing and balance rely on coordinated activity of multiple inner ear cell types, yet the mechanisms governing their development and specification in humans remain unclear. Consequently, this limits our understanding of how disease genes affect cell type formation and function, limiting the development of targeted treatments, including gene therapies. Here we present the Human Inner Ear Development snRNA-seq Atlas (HIEDRA), a single-nucleus transcriptomic atlas of the human inner ear spanning the first and second trimesters. HIEDRA maps sensory and nonsensory epithelia, neurons and mesenchyme-associated populations, including undercharacterized secretory cells required for ion homeostasis. We identify selective vulnerability in sensory and secretory lineages to disease-associated genes, infer regulatory networks and show that Hedgehog signaling suppression is required for secretory cell specification. We validate this mechanism in human inner ear organoids, expanding the model to include all major cell types. Altogether, these findings provide insights into human inner ear cell type specification, improve in vitro models and establish HIEDRA as a resource for investigating human inner ear development.