AUTHOR=Gwilliam Kathleen , Sperber Michal , Perry Katherine , Rose Kevin P. , Ginsberg Laura , Paladugu Nikhil , Song Yang , Milon Beatrice , Elkon Ran , Hertzano Ronna 

TITLE=A cell type–specific approach to elucidate the role of miR-96 in inner ear hair cells

JOURNAL=Frontiers in Audiology and Otology

VOLUME=2

YEAR=2024

URL=https://www.frontiersin.org/journals/audiology-and-otology/articles/10.3389/fauot.2024.1400576

DOI=10.3389/fauot.2024.1400576

ISSN=2813-6055

ABSTRACT=<sec><title>Introduction</title><p>Mutations in microRNA-96 (miR-96), a microRNA expressed within the hair cells (HCs) of the inner ear, result in progressive hearing loss in both mouse models and humans. In this study, we present the first HC-specific RNA-sequencing (RNA-seq) dataset from newborn <italic>Mir96</italic><sup><italic>Dmdo</italic></sup> heterozygous, homozygous mutant, and wildtype mice.</p></sec><sec><title>Methods</title><p>Bulk RNA-seq was performed on HCs of newborn <italic>Mir96</italic><sup><italic>Dmdo</italic></sup> heterozygous, homozygous mutant, and wildtype mice. Differentially expressed gene analysis was conducted on <italic>Mir96</italic><sup><italic>Dmdo</italic></sup> homozygous mutant HCs compared to wildtype littermate controls, followed by GO term and protein-protein interaction analysis on these differentially expressed genes.</p></sec><sec><title>Results</title><p>We identify 215 upregulated and 428 downregulated genes in the HCs of the <italic>Mir96</italic><sup><italic>Dmdo</italic></sup> homozygous mutant mice compared to their wildtype littermate controls. Many of the significantly downregulated genes in <italic>Mir96</italic><sup><italic>Dmdo</italic></sup> homozygous mutant HCs have established roles in HC development and/or known roles in deafness including <italic>Myo15a, Myo7a, Ush1c, Gfi1</italic>, and <italic>Ptprq</italic> and have enrichment in gene ontology (GO) terms with biological functions such as sensory perception of sound. Interestingly, upregulated genes in <italic>Mir96</italic><sup><italic>Dmdo</italic></sup> homozygous mutants, including possible miR-96 direct targets, show higher wildtype expression in supporting cells compared to HCs.</p></sec><sec><title>Conclusion</title><p>Our data further support a role for miR-96 in HC development, possibly as a repressor of supporting cell transcriptional programs in HCs. The HC-specific <italic>Mir96</italic><sup><italic>Dmdo</italic></sup> RNA-seq data set generated from this manuscript are now publicly available in a dedicated profile in the gene expression analysis resource (gEAR-<ext-link ext-link-type="uri" xlink:href="https://umgear.org/p?l=miR96" xmlns:xlink="http://www.w3.org/1999/xlink">https://umgear.org/p?l=miR96</ext-link>).</p></sec>