Comprehensive analysis of aberrant alternative splicing and RNA binding proteins associated with age-related sensorineural hearing loss

TL;DR

This study explores how RNA binding proteins and alternative splicing contribute to age-related hearing loss in mice and humans.

Contribution

The study identifies novel RNA binding proteins and alternative splicing events linked to age-related hearing loss and their regulatory networks.

Findings

Identified 198 and 187 deregulated alternative splicing events in severe and mild age-related hearing loss, respectively.

Found 25 and 14 differentially expressed RNA binding proteins in severe and mild age-related hearing loss.

Demonstrated that ISG15 regulates alternative splicing of UAP1 in human cells.

Abstract

The prevalence of RNA binding proteins (RBPs) in regulating alternative splicing (AS) in age-related sensorineural hearing loss (SNHL) is unclear. To address this question, we comprehensively analyzing RNA-seq data from a mouse model to identify deregulated AS events (RASEs) and differentially expressed RNA binding proteins (DERBPs) associated with age-related SNHL, and constructed the networks between these two levels of changes. We have identified 198 and 187 RASEs related to severe and mild symptoms, respectively. Genes harboring these RASEs are significantly enriched in positive regulation of GTPase activity and cytoskeleton organization. We further identified 25 and 14 DERBPs related to severe and mild symptoms, respectively, and constructed the regulatory network between DERBPs and RASEs. Among these DERBPs, the significantly increased expression of Isg15 and Myom1, the decreased expression of Acan, as well as some of their regulated RASEs including two in Uap1 also demonstrated in cochlear transcriptomes obtained from the age-related SNHL mouse model constructed in this study. Analysis of human pluripotent stem cell-derived macrophages containing ISG15 knockout samples revealed that ISG15 is a key splicing regulator, and can directly regulate the alternative splicing of UAP1 in human cells. These findings prove insights into the involvement of a large number of alternative splicing events driven by RNA-binding proteins (RBPs) in the pathogenesis of age-related SNHL, and suggest their potentials as therapeutic targets and disease markers.

The online version contains supplementary material available at 10.1038/s41598-025-20843-8.

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