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Peer-reviewedCC BY-NC-ND 4.0Nature Neuroscience

A single-nucleus transcriptomic atlas of human inner ear development

  • Wouter H. van der Valk1,2
  • Shantha Devi Udayappan1,2
  • Edward S. A. van Beelen1
  • Jermaine Goveia3
  • Aleksandar Beatovic3
  • Matthieu Moisse3
  • Roberta Menafra4
  • John C. M. J. de Groot1,2
  • Karl R. Koehler5,6
  • Peter Paul G. van Benthem1
  • Heiko Locher1,2
6 affiliations
  1. 1OtoBiology Leiden, Department of Otorhinolaryngology and Head and Neck Surgery, Leiden University Medical Center, Leiden, the Netherlands
  2. 2The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, the Netherlands
  3. 3Unicle Biomedical Data Science, Leuven, Belgium
  4. 4Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
  5. 5Department of Otolaryngology, Department of Dermatology, Department of Plastic and Oral Surgery, F.M. Kirby Neurobiology Center, Boston Children’s Hospital, Boston, MA USA
  6. 6Department of Otolaryngology—Head and Neck Surgery, Department of Dermatology, Harvard Medical School, Boston, MA USA
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Abstract

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.

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Cite

BibTeXRIS
BibTeX
@article{valk2026singlenucleus,
  title = {{A single-nucleus transcriptomic atlas of human inner ear development}},
  author = {Wouter H. van der Valk and Shantha Devi Udayappan and Edward S. A. van Beelen and Jermaine Goveia and Aleksandar Beatovic and Matthieu Moisse and Roberta Menafra and John C. M. J. de Groot and Karl R. Koehler and Peter Paul G. van Benthem and Heiko Locher},
  journal = {Nature Neuroscience},
  year = {2026},
  month = sep,
  doi = {10.1038/s41593-026-02432-8},
  url = {https://doi.org/10.1038/s41593-026-02432-8},
  note = {CC BY-NC-ND 4.0},
}
RIS
TY  - JOUR
TI  - A single-nucleus transcriptomic atlas of human inner ear development
AU  - Wouter H. van der Valk
AU  - Shantha Devi Udayappan
AU  - Edward S. A. van Beelen
AU  - Jermaine Goveia
AU  - Aleksandar Beatovic
AU  - Matthieu Moisse
AU  - Roberta Menafra
AU  - John C. M. J. de Groot
AU  - Karl R. Koehler
AU  - Peter Paul G. van Benthem
AU  - Heiko Locher
PY  - 2026
DA  - 2026/09/09
JO  - Nature Neuroscience
DO  - 10.1038/s41593-026-02432-8
UR  - https://doi.org/10.1038/s41593-026-02432-8
AB  - 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.
SN  - 1097-6256
SN  - 1546-1726
ER  -