From organoids to human inner ear development — and back again

Abstract

Hearing and balance depend on the coordinated development and function of diverse specialized cell types in the human inner ear. However, scarce human tissue and imperfect models have limited mechanistic insight and translation into therapeutic strategies. This thesis establishes human pluripotent stem cell–derived inner ear organoids (IEOs) and couples them to single-cell and single-nucleus transcriptomics to resolve cell identity, lineage trajectories, and signaling environments during otic development. A high-resolution temporal atlas of organoid differentiation defines key fate decisions and reveals where in vitro programs diverge from in vivo development. Systematic benchmarking against fetal and adult human inner ear tissue shows that IEOs reproducibly generate multiple otic lineages (predominantly vestibular sensory epithelia, neurons, and periotic mesenchyme), while exposing the absence of secretory epithelia crucial for endolymph homeostasis. To address this gap, a developmental atlas spanning the first and second trimesters maps the full cochlear and vestibular human inner ear. This atlas identifies Hedgehog signaling suppression as a driver of secretory fate. Implementing this insight enables organoids to produce secretory, sensory, and neuronal cell types within a single platform. The thesis provides detailed protocols, emphasizes validation, and outlines translational applications for modeling genetic disorders and evaluating emerging therapies.