A Single-Nucleus Atlas of Human Prenatal Inner Ear Development

Hearing and balance rely on the coordinated activity of diverse cell types in the human inner ear. However, the mechanisms driving the formation and specialization of these cells during development remain poorly understood. This knowledge gap limits our ability to interpret the impact of pathogenic variants in the hundreds of genes associated with hearing and balance disorders, and hinders the design of targeted therapies. To address this, we present HIEDRA (Human Inner Ear Development single-nucleus RNAseq Atlas), a transcriptomic atlas of the developing human inner ear spanning the first and second trimesters. This resource maps the molecular identity and developmental trajectories of sensory and nonsensory epithelial cells, neurons, and mesenchymal populations. Notably, we define transcriptional signatures and regulatory networks of previously under-characterized epithelial secretory cells essential for ionic homeostasis and inner ear function. By evaluating inner ear disease-related gene expression, we reveal that sensory and secretory lineages exhibit genetic susceptibilities. We further uncover that suppression of Hedgehog signaling is a key requirement for the differentiation of secretory cells. Functional validation in human inner ear organoids confirms this mechanism and enables the generation of organoids that faithfully recapitulate all three major cell types found in vivo. HIEDRA provides a foundational resource for understanding human inner ear development, refining in vitro models, and guiding the development of targeted therapies for hearing and balance disorders.