Transcriptomic Analyses of Inner Ear Sensory Epithelia in Zebrafish

Abstract

Analysis of gene expression has the potential to assist in the understanding of multiple cellular processes including proliferation, cell‐fate specification, senesence, and activity in both healthy and disease states. Zebrafish model has been increasingly used to understand the process of hearing and the development of the vertebrate auditory system. Within the zebrafish inner ear, there are three otolith organs, each containing a sensory macula of hair cells. The saccular macula is primarily involved in hearing, the utricular macula is primarily involved in balance and the function of the lagenar macula is not completely understood. The goal of this study is to understand the transcriptional differences in the sensory macula associated with different otolith organs with the intention of understanding the genetic mechanisms responsible for the distinct role each organ plays in sensory perception. The sensory maculae of the saccule, utricle, and lagena were dissected out of adult Et(krt4:GFP)sqet4 zebrafish expressing green fluorescent protein in hair cells for transcriptional analysis. The total RNAs of the maculae were isolated and analyzed by RNA GeneChip microarray. Several of the differentially expressed genes are known to be involved in deafness, otolith development and balance. Gene expression among these otolith organs was very well conserved with less than 10% of genes showing differential expression. Data from this study will help to elucidate which genes are involved in hearing and balance. Furthermore, the findings of this study will assist in the development of the zebrafish model for human hearing and balance disorders. Anat Rec, 303:527–543, 2020. © 2019 American Association for Anatomy

A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish

“…We then identified shared cell states between the regenerating saccule and utricle through integrated clustering analysis and found that gene expression changes are largely conserved between datasets for the three major cell populations that contribute to hair cell regeneration: SC, PC and HC (Figure S2C; Table S5). In agreement with Yao et al (Yao et al, 2020), we observed elevated expression levels of wnt11r , sema3e , otol1a , and nr2f1 in the saccule and identified that these genes are expressed in the support cell clusters specifically. During regeneration, these genes are upregulated only in the saccule.…”

The Genomics of Auditory Function and Disease

“…When such studies are coupled with bioinformatic analyses, groups of genes that underlie processes in cell type–specific development/function, aging, or even regulators of these processes can be identified. As transcriptomic analyses require tissue samples, most such studies to date have used tissues from animal models such as mice ( 71 , 84 , 100 , 145 ), rats ( 125 ), zebrafish ( 183 ), or chickens ( 11 ). Additional model organisms studied include Xenopus ( 130 ), bats ( 103 ), and guinea pigs ( 158 ).…”

Single-Cell Sequencing Applications in the Inner Ear

“…Previous studies have defined some crucial signaling pathways -such as FGF, Notch, and Wnt -and genessuch as Pax2 and Atoh1 -that play essential roles in the development and maintenance of the inner ear (Scheffer et al, 2015;Zhong et al, 2019). Each region of the sensory epithelium is composed of highly heterogeneous populations of cells depending on the physiological and anatomical criteria of that region (Szarama et al, 2012;Jeng et al, 2020;Ono et al, 2020;Yao et al, 2020), and this highlights the importance of examining the expression of a large number of genes at the single cell level.…”