Gene4HL: An Integrated Genetic Database for Hearing Loss

Single-cell atlas comparison across vertebrates reveals auditory cell evolution and mechanisms for hair cell regeneration

Mammals suffer permanent hearing impairment from the loss of auditory hair cells due to their inability to regenerate. In contrast, lower vertebrates exhibit extraordinary capacity for hair cell regeneration and hearing restoration, but the mechanisms remain unclear. Here we characterize the single-cell atlas of Xenopus laevis inner ear and perform a comprehensive comparison with mouse model. An exceptionally conserved inner ear neuronal cell type is discovered. The results reveal that the outer hair cells (OHCs) exist exclusively in mammals. Importantly, our analyses reveal an orchestrated gene expression program in Xenopus, characterized by upregulation of hair cell regeneration-related genes, coupled with downregulation of proliferation inhibitory genes. These findings unveil a natural feature of regenerative capacity in Xenopus, and provide molecular and evolutionary evidences for differential regenerative capacities across vertebrates. This work offers insights from amphibians into developing strategies to solve the challenges of hair cell regeneration in humans.

Classification and prediction of variants associated with hearing loss using sequence information in the vicinity of mutation sites

Hearing impairment is a major global health problem, affecting more than 5 % of the world's population at various ages, from neonates to the elderly. Among the common genetic variations in humans, single nucleotide variations and small insertions or deletions predominate. The study of hearing loss resulting from these variations is proving invaluable in the analysis and diagnosis of hearing disorders. The identification of pathogenic mutations is frequently a lengthy and laborious process. Existing computational prediction tools have been developed primarily for common diseases and genome-wide analyses, with less focus on deafness. This study proposes a novel approach that focuses on the regions surrounding mutation sites. Mutation sites associated with deafness and their flanking regions of different lengths were extracted from relevant databases and combined into seven distinct segments of different lengths. The information-theoretic features of these segments were computed. Five machine learning algorithms were then used for training, resulting in the construction of a model capable of classifying and predicting deafness-related mutations. For fragments encompassing the 250 bp regions upstream and downstream of the mutations, the average AUC of the five classifiers on the independent test set is 0.89 and the average ACC is 0.85, indicating that the model has a high recognition rate of the pathogenic deafness mutation site. An ensemble approach was also applied to predict variants of uncertain significance (VUS) that may be associated with deafness. These variants were then scored and ranked to assess their likelihood of contributing to the condition.

Transcriptional response to mild therapeutic hypothermia in noise-induced cochlear injury

Introduction

Prevention or treatment for acoustic injury has been met with many translational challenges, resulting in the absence of FDA-approved interventions. Localized hypothermia following noise exposure mitigates acute cochlear injury and may serve as a potential avenue for therapeutic approaches. However, the mechanisms by which hypothermia results in therapeutic improvements are poorly understood.

Methods

This study performs the transcriptomic analysis of cochleae from juvenile rats that experienced noise-induced hearing loss (NIHL) followed by hypothermia or control normothermia treatment.

Results

Differential gene expression results from RNA sequencing at 24 h post-exposure to noise suggest that NIHL alone results in increased inflammatory and immune defense responses, involving complement activation and cytokine-mediated signaling. Hypothermia treatment post-noise, in turn, may mitigate the acute inflammatory response.

Discussion

This study provides a framework for future research to optimize hypothermic intervention for ameliorating hearing loss and suggests additional pathways that could be targeted for NIHL therapeutic intervention.

Predicting the Impact of OTOF Gene Missense Variants on Auditory Neuropathy Spectrum Disorder

Auditory neuropathy spectrum disorder (ANSD) associated with mutations of the OTOF gene is one of the common types of sensorineural hearing loss of a hereditary nature. Due to its high genetic heterogeneity, ANSD is considered one of the most difficult hearing disorders to diagnose. The dataset from 270 known annotated single amino acid substitutions (SAV) related to ANSD was created. It was used to estimate the accuracy of pathogenicity prediction using the known (from dbNSFP4.4) method and a new one. The new method (ConStruct) for the creation of the protein-centric classification model is based on the use of Random Forest for the analysis of missense variants in exons of the OTOF gene. A system of predictor variables was developed based on the modern understanding of the structure and function of the otoferlin protein and reflecting the location of changes in the tertiary structure of the protein due to mutations in the OTOF gene. The conservation values of nucleotide substitutions in genomes of 100 vertebrates and 30 primates were also used as variables. The average prediction of balanced accuracy and the AUC value calculated by the 5-fold cross-validation procedure were 0.866 and 0.903, respectively. The model shows good results for interpreting data from the targeted sequencing of the OTOF gene and can be implemented as an auxiliary tool for the diagnosis of ANSD in the early stages of ontogenesis. The created model, together with the results of the pathogenicity prediction of SAVs via other known accurate methods, were used for the evaluation of a manually created set of 1302 VUS related to ANSD. Based on the analysis of predicted results, 16 SAVs were selected as the new most probable pathogenic variants.