Single-cell RNA-Seq resolves cellular complexity in sensory organs from the neonatal inner ear

TLDR

Inner ear sensory epithelia comprise heterogeneous cell populations, but limited cell numbers have hindered comprehensive transcriptional profiling. The study generated single‑cell transcriptomes from 301 cells of newborn mouse utricular and cochlear sensory epithelia to overcome this limitation. Single‑cell RNA‑seq of these cells enabled cluster analysis that distinguished major cochlear and utricular cell types and revealed sub‑populations. The analysis uncovered distinct transcriptional profiles, temporal differentiation trajectories, plasticity at the sensory–nonsensory boundary, and developmental divergence between auditory and vestibular cells.

Abstract

Abstract In the inner ear, cochlear and vestibular sensory epithelia utilize grossly similar cell types to transduce different stimuli: sound and acceleration. Each individual sensory epithelium is composed of highly heterogeneous populations of cells based on physiological and anatomical criteria. However, limited numbers of each cell type have impeded transcriptional characterization. Here we generated transcriptomes for 301 single cells from the utricular and cochlear sensory epithelia of newborn mice to circumvent this challenge. Cluster analysis indicates distinct profiles for each of the major sensory epithelial cell types, as well as less-distinct sub-populations. Asynchrony within utricles allows reconstruction of the temporal progression of cell-type-specific differentiation and suggests possible plasticity among cells at the sensory–nonsensory boundary. Comparisons of cell types from utricles and cochleae demonstrate divergence between auditory and vestibular cells, despite a common origin. These results provide significant insights into the developmental processes that form unique inner ear cell types.