Selective loss of specific subsets of hair cell and spiral ganglion cell types in an outbred mouse model of age-related hearing loss

Abstract

Age□related hearing loss (ARHL) is the most common cause of hearing loss and is one of the most prevalent conditions affecting the elderly globally. Despite evidence from our lab and others about its polygenic nature, little is known about the genes, cell types and pathways involved, preventing the development of therapeutic intervention. In this manuscript we describe, for the first time, the complete cell-type specific cochlear transcriptome of the aging mouse cochlea in outbred mice, using snRNA-seq, in relation to auditory threshold variation. We annotated cochlear cell types identified using unsupervised clustering via a three-tiered approach. First, we annotated clusters by linking to expression of known marker genes. Second, we used the NS-Forest algorithm to select minimum cluster-specific marker genes, which were first used to reduce dimensional feature space for statistical comparison of our clusters with existing publicly available data sets on the gEAR website (https://umgear.org/). Finally, we validated and refined our annotation using Multiplexed Error Robust Fluorescence In Situ Hybridization (MERFISH) and the cluster-specific marker genes as probes. We report on 60 unique cell-types (clusters) expanding the number of defined cochlear cell types by more than two times. Additionally, we show cluster variation with hearing thresholds demonstrating specific cell type increases and decrease in response to hearing loss implicating hair cell (HC) subtypes, ganglion cell subtypes, and cell subtypes withing the stria vascularis in this model of ARHL. These results provide a view into the cellular and molecular mechanisms responsible for age-related hearing loss and pathways for therapeutic targeting.