Single-cell transcriptomic profiling of the zebrafish inner ear reveals molecularly distinct hair cell and supporting cell subtypes

Abstract

A major cause of human deafness and vestibular dysfunction is permanent loss of the mechanosensory hair cells of the inner ear. In non-mammalian vertebrates such as zebrafish, regeneration of missing hair cells can occur throughout life. While a comparative approach has the potential to reveal the basis of such differential regenerative ability, the degree to which the inner ears of fish and mammals share common hair cells and supporting cell types remains unresolved. Here we perform single-cell RNA sequencing of the zebrafish inner ear at embryonic through adult stages to catalog the diversity of hair cells and non-sensory supporting cells. We identify a putative progenitor population for hair cells and supporting cells, as well as distinct hair and supporting cell types in the maculae versus cristae. The hair cell and supporting cell types differ from those described for the lateral line system, a distributed mechanosensory organ in zebrafish in which most studies of hair cell regeneration have been conducted. In the maculae, we identify two subtypes of hair cells that share gene expression with mammalian striolar or extrastriolar hair cells. In situ hybridization reveals that these hair cell subtypes occupy distinct spatial domains within the three macular organs, the utricle, saccule, and lagena, consistent with the reported distinct electrophysiological properties of hair cells within these domains. These findings suggest that primitive specialization of spatially distinct striolar and extrastriolar hair cells likely arose in the last common ancestor of fish and mammals. The similarities of inner ear cell type composition between fish and mammals validate zebrafish as a relevant model for understanding inner ear-specific hair cell function and regeneration.

Future Pharmacotherapy for Sensorineural Hearing Loss by Protection and Regeneration of Auditory Hair Cells

“…For this purpose, precise analyses of the process for naturally occurring HC regeneration in the avian and fish auditory epithelia may be useful. Recent studies using single-cell RNA sequencing provide gene expression profiles of chick and zebrafish auditory epithelial cells in quiescent, degenerative, and regenerative status [ 90 , 92 , 93 , 94 , 95 , 96 , 97 ]. In contrast to mammalian cochleae, mammalian vestibular sensory organs retain the capacity for HC regeneration.…”

Vestibular physiology and function in zebrafish

“…Top, end organs in the horizontal plane; Bottom end organs in the saggital plane. Arrow heads indicate the general polarity of the hair cells in the epithelia, which change direction along the line of polarity reversal (LPR, dashed black line) in the otolith maculae ( Platt, 1993 ; Liu et al, 2022 ; Shi et al, 2023 ). There is no LPR in the cristae or macula neglecta.…”

“…Zebrafish inner ear hair cells vary in their molecular signatures ( Barta et al, 2018 ; Hoffman et al, 2018 ; Shi et al, 2023 ). Using single-cell RNA sequencing, Shi et al, 2023 showed that hair cells from the inner ear have distinct genetic profiles.…”

“…Zebrafish inner ear hair cells vary in their molecular signatures ( Barta et al, 2018 ; Hoffman et al, 2018 ; Shi et al, 2023 ). Using single-cell RNA sequencing, Shi et al, 2023 showed that hair cells from the inner ear have distinct genetic profiles. Using unsupervised clustering, hair cells from the maculae and cristae were distinctly separated, as were striolar and extrastriolar cells.…”

“…Using unsupervised clustering, hair cells from the maculae and cristae were distinctly separated, as were striolar and extrastriolar cells. Striolar hair cells expressed cabp2b+ , which overlaps with pvalb9 , an orthologue of the mammalian striolar marker oncomodulin ( Hoffman et al, 2018 ), while extrastriolar cells expressed capb1b+ in a domain that is exclusive of pvalb9 ( Shi et al, 2023 ). Similarly, central and peripheral zones of cristae were molecularly distinct.…”