Single-Cell RNA-Seq Analysis of the Endolymphatic Sac of the Mouse Inner Ear

Authors

• K Honda
• J Burns
• M Kelly
• M Hoa
• M Kelley
• P Wangemann
• R Morell
• A Griffith

Abstract

Mutations of the SLC26A4 gene are a common cause of hearing loss associated with enlargement of the endolymphatic sac and duct (EES) of the inner ear. SLC26A4 encodes a transmembrane anion exchanger, pendrin, which is expressed in a subset of nonsensory epithelial cells in the endolymphatic sac (ES). For normal development and acquisition of hearing in mice, Slc26a4 expression is required only in the ES and only between embryonic day 16.5 (E16.5) and postnatal day 2 (P2). The physiological function of the ES is poorly understood but thought to involve homeostasis of endolymph. Histological analysis suggested that there are two major ES epithelial cell types: mitochondria-rich cells (MRCs) that express pendrin, and ribosome-rich cells (RRCs). In order to define the molecular and cellular architecture of the ES epithelium, we performed single-cell RNA-seq analysis of C57BL/6J ES epithelium harvested at E16.5 or P5. Principal component analysis and hierarchical clustering identified two major clusters of samples. The first cluster was characterized by the expression of four genes (Slc26a4, Foxi1, Atp6v0a4, Atp6v1b1) known to be expressed in MRCs. Mutations of these four genes are also known to cause EES. This cluster also expressed many other genes encoding transporters, ion channels and pumps. The second major sample cluster lacked expression of the four MRC-specific genes or other genes encoding transporters or ion channels or pumps. This sample cluster corresponds to RRCs. Our results provide a molecular-cellular model for regulation of ionic, pH and fluid homeostasis by the ES.

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