A Single-Cell Level Comparison of Human Inner Ear Organoids and the Human Cochlea and Vestibular Organs

Abstract

Genetic inner ear disorders are among the most common congenital abnormalities and lead to hearing loss and balance disorders. Ideally, tissue culture models of the inner ear should contain a functional unit combining otic sensory and nonsensory cell types to recapitulate the varied etiologies of inner ear disorders. Here, we evaluated cell type diversity of late-stage human pluripotent stem cell-derived inner ear organoids using single-cell transcriptomic analysis, electron microscopy and immunohistochemistry. We observed the induction of on-target inner ear-related periotic mesenchymal cells alongside off-target induction of skeletal myocytes, endothelial cells, and ependymal cells. By constructing a single-cell transcriptomic atlas of the human fetal and adult inner ear, we show that epithelium in the inner ear organoids contains cochlear and vestibular identities similar to the developing human inner ear. Moreover, the inner ear organoids contain immature type I and type II vestibular hair cells. Within these putative inner ear cell types, we confirmed the expression of genes and proteins linked to sensorineural hearing loss. This approach using human inner ear organoids would allow for disease modeling of specific genetic inner ear pathologies in the sensory and nonsensory domains of the inner ear.

Cochlear transcript diversity and its role in auditory functions implied by an otoferlin short isoform

“…According to previous studies 26,27 , we annotated cell types based on the known cell-type-specific markers (Supplementary Fig. 1a), including Tympanic border cell (TBC, Emilin2 + ) 28 , Fibroblast cell (FC, Coch + , Otos + ) 29,30 , Inner phalangeal cell/Inner border cell (IPhC/IBC, Slc1a3 + , S100a6 + ) [31][32][33] , Deiter cell/Pillar cell/Inner sulcus cell/Outer sulcus cell (DC/PC/ ISC/OSC, Gata3 + , Fbxo2 + , Skp1a + , Epyc + , Bmp4 + ) 26,34-37 , Reissner's membrane cell (RMC, Vom1 + ) 38 , Capillary endothelial cells (CEC, Ly6c1 + ) 39 , Capillary pericytes (Rgs5 + ) 30 , OHC (Ocm + , Slc26a5 + ) 40,41 , and IHC (Otof + , Slc17a8 + ) 25,42 . The marker genes expressed in each cluster are listed in Supplementary Data 1.…”