Early downregulation of HC-specific genes in the vestibular sensory epithelium during chronic ototoxicity

Exposure of mammals to ototoxic compounds causes hair cell (HC) loss in the vestibular sensory epithelia of the inner ear. In chronic exposure models, this loss often occurs by extrusion of the HC from the sensory epithelium towards the luminal cavity. HC extrusion is preceded by several steps that begin by detachment and synaptic uncoupling of the cells from the afferent terminals of their postsynaptic vestibular ganglion neurons. To identify gene expression programs driving these responses to chronic ototoxic stress, we performed five RNA-seq control versus treated comparisons involving two species (rat and mouse), two compounds (streptomycin and 3,3’-iminodipropionitrile, IDPN), and three time points in the rat/IDPN model. By comparing the differentially expressed genes and their associated Gene Ontology terms, we identified both common and model-unique expression responses. The earliest and most robust common response was a downregulation of HC-specific genes, including stereocilium ( Atp2b2, Xirp2 ), synaptic (Nsg2), and ion channel genes ( Kcnab1 , Kcna10 ), together with new potential biomarkers of HC stress ( Vsig10l2 ). This response was validated by in-situ hybridisation and immunofluorescence analyses. A second common response across species and compounds was the upregulation of the stress mediator Atf3 . Model- or time-restricted responses included downregulation of cell-cell adhesion and mitochondrial ATP synthesis genes, and upregulation of interferon response, unfolded protein response and tRNA aminoacylation genes. The present results provide key insights on the responses of the vestibular sensory epithelium to chronic ototoxic stress, potentially relevant to other types of chronic stress.