Single-cell RNA-sequencing of zebrafish hair cells reveals novel genes potentially involved in hearing loss

Abstract

Hair cells play key roles in hearing and balance, and hair cell loss would result in hearing loss or vestibular dysfunction. Cellular and molecular research in hair cell biology provide us a better understanding of hearing and deafness. Zebra sh, owing to their hair cell-enriched organs, have been widely applied in hair cell-related research worldwide. Similar to mammals, zebra sh have inner ear hair cells. In addition, they also have lateral line neuromast hair cells. These different hair cells vary in morphology and function. However, systematic analysis of their molecular characteristics remains lacking. In this study, we analyzed the GFP+ cells isolated from Tg(Brn3c:mGFP) larvae using single cell RNA-sequencing (scRNA-seq). Three subtypes of hair cells, namely macula hair cell (MHC), crista hair cell (CHC) and neuromast hair cell (NHC) were characterized and validated by whole-mount in situ hybridization analysis of marker genes. Furthermore, we carried out the morphological comparison of these hair cells. Based on the hair cell scRNA-seq data, we obtained hair cell-enriched genes pool, including hearing loss genes that have been identi ed in humans and novel genes potentially involved in hair cell formation and function. Two novel genes were discovered to speci cally function in NHCs and MHCs, corresponding to their speci c expression in NHCs and MHCs. This study allows us to understand the speci c genes in hair cell subpopulations of zebra sh, which will shed light on the genetics of both human vestibular and cochlear hair cell function.

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

“…These molecular signatures are conserved across larval and adult stages. However, consistent with other recent work ( Jimenez et al, 2022 ; Qian et al, 2022 ), we were not able to resolve distinct clusters of hair cells or supporting cells corresponding to the distinct types of maculae: i.e. utricle, saccule, and lagena.…”

“…Recent single-cell and single-nucleus RNA-sequencing efforts have generated a wealth of transcriptomic data from hair cells in several model systems, facilitating more direct comparison of cell types and gene regulatory networks between species. Although single-cell transcriptomic data have recently been published for the zebrafish inner ear ( Jimenez et al, 2022 ; Qian et al, 2022 ), the diversity of hair cell and supporting cell subtypes has not been thoroughly analyzed. In order to better understand the diversification of cell types in the zebrafish inner ear, and their relationships to those in mammals, here we perform single-cell and single-nucleus RNA sequencing of the zebrafish inner ear from embryonic through adult stages.…”

Spatially resolved single-cell atlas of ascidian endostyle provides insight into the origin of vertebrate pharyngeal organs

“…S7G). Consequently, we conducted a cross-species comparison between the HCLC cluster to hair cell–related tissues in zebrafish ( 39 ). The results indicated that the HCLC cluster in zone 3 exhibits a high similarity with hair cell populations and hair cell progenitors of the acoustico-lateralis system in zebrafish (Fig.…”

“…To investigate the similarity between the endostyle cell types and vertebrate tissues, we collected scRNA-seq data of zebrafish from Farnsworth et al ( 30 ), Qian et al ( 39 ), and Gillotay et al ( 40 ) as reference datasets. Before comparing the endostyle and zebrafish tissues, we preprocess the zebrafish datasets to unify the annotations and eliminate batch effects between different samples.…”

Single-Cell Transcriptomic Profiling of the Zebrafish Inner Ear Reveals Molecularly Distinct Hair Cell and Supporting Cell Subtypes

“…Recent single-cell and single-nucleus RNA-sequencing efforts have generated a wealth of transcriptomic data from hair cells in several model systems, facilitating more direct comparison of cell types and gene regulatory networks between species. Although single-cell transcriptomic data have recently been published for the zebrafish inner ear (Jimenez et al, 2022;Qian et al, 2022), the diversity of hair cell and supporting cell subtypes has not been thoroughly analyzed.…”