Cell-type identity of the avian cochlea

Abstract

Highlights d Single-cell transcriptomic characterization of the avian cochlear sensory epithelium d Distinct hair cell and supporting cell types d Tonotopic gene expression dynamics of hair cells d Resource of cell-type-specific gene expression in the mature avian cochlea

Transcriptomic characterization of dying hair cells in the avian cochlea

“…We propose that the transcriptional changes during the demise of hair cells are an important component of the first triggers of cell regeneration. The chicken cochlea harbors two major hair cell types: tall hair cells located in the neural (superior) region of the chicken cochlea and short hair cells located along the abneural (inferior) side (Figures 1A and 1B) (Hirokawa, 1978;Janesick et al, 2021). We found that the neural tall and abneural short hair cells die synchronously through apoptosis within 24 h of aminoglycoside exposure.…”

“…We found a large group of genes that is initially downregulated in dying tall and short hair cells, and only 19 genes in tall hair cells and 148 genes in short hair cells were transiently upregulated. The number and specificity of upregulated genes in short hair cells revealed a complex response to aminoglycoside-induced damage and apoptosis, which we speculate is owed to the distinct physiological differences between the two major cochlear sensory hair cell types (Janesick et al, 2021).…”

“…Using the spectral clustering algorithm of the CellTrails package (Ellwanger et al, 2018), we classified hair cells, supporting cells, and homogene cells based on expression of established cell-specific marker genes (Janesick et al, 2021). We identified 316 hair cells in total, expressing 15,748 genes (Table S2A).…”

“…Clustering revealed seven distinct groups of hair cells (Figure S4A, S1-S7). We hypothesized that this heterogeneity, which is beyond the expected major grouping into tall and short hair cells (Janesick et al, 2021), is caused by distinct changes in gene expression that occur PST. When we visualized individual cells by each time point (Figures S4B-S4F), we noticed that the majority of cells in clusters S1 (15 out of 22) and S2 (51 out of 76) came from the P7 control group, whereas clusters S3-S6 were derived almost exclusively from PST cells.…”

“…In basic research, aminoglycosides are used to eliminate hair cells to study regenerative responses or the lack of regeneration in various animal models (Abbas and Rivolta, 2015;Cafaro et al, 2007;Scheibinger et al, 2018;Yorgason et al, 2011). Since the discovery that the avian basilar papilla, which is equivalent to the mammalian organ of Corti (Hirokawa, 1978;Janesick et al, 2021), is capable of naturally regenerating lost hair cells (Corwin and Cotanche, 1988;Ryals and Rubel, 1988), the chicken inner ear has emerged as a major model system to study inner ear hair cell regeneration (Janesick and Heller, 2019).…”