Original Research ARTICLE
Next generation sequencing and animal models reveal SLC9A3R1 as a new gene involved in human age-related hearing loss.
- 1IRCCS Materno Infantile Burlo Garofolo (IRCCS), Italy
- 2Dipartimento di Clinical University of Medical and Surgical Medical Sciences, Università di Trieste, Italy
- 3Sidra Medical and Research Center, Qatar
- 4Heart Science, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, United Kingdom
Age-related hearing loss (ARHL) is the most common sensory impairment in the elderly affecting millions of people worldwide. To shed light on the genetics of ARHL, a large cohort of 464 Italian patients has been deeply characterized at clinical and molecular level. In particular, 46 candidate genes, selected on the basis of genome-wide association studies (GWAS), animal models and literature updates, were analyzed by targeted re-sequencing. After filtering and prioritization steps, SLC9A3R1 has been identified as a strong candidate and then validated by “in vitro” and “in vivo” studies. Briefly, a rare (MAF: 2.886e-5) missense variant c.539G>A, p.(R180Q) was detected in two unrelated male patients affected by ARHL characterised by a severe to profound high-frequency hearing loss. The variant, predicted as damaging, was not present in healthy matched controls. Protein modelling confirmed the pathogenic effect of p.(R180Q) variant on protein’s structure leading to a change in the total number of hydrogen bonds. In situ hybridization showed slc9a3r1 expression in zebrafish inner ear. A zebrafish knock-in model, generated by CRISPR-Cas9 technology, revealed a reduced auditory response at all frequencies in slc9a3r1R180Q/R180Q mutants compared to slc9a3r1+/+ and slc9a3r1+/R180Q animals. Moreover, a significant reduction (5.8%) in the total volume of the saccular otolith (which is responsible for sound detection) was observed in slc9a3r1R180Q/R180Q compared to slc9a3r1+/+ (P=0.0014), while the utricular otolith, necessary for balance, was not affected in agreement with the human phenotype.
Overall, these data strongly support the role of SLC9A3R1 gene in the pathogenesis of ARHL opening new perspectives in terms of diagnosis, prevention and treatment.
Keywords: Hearing Loss, CRISPR-Cas9, next-generation sequencing., Zebrafish model, gene-discovery
Received: 21 Aug 2018;
Accepted: 11 Feb 2019.
Edited by:Mike Mikailov, United States Food and Drug Administration, United States
Reviewed by:Theodora Katsila, University of Patras, Greece
GuangJun Zhang, Purdue University, United States
Copyright: © 2019 Girotto, Morgan, Krishnamoorthy, Cocca, Brumat, Bassani, La Bianca, Di Stazio and Gasparini. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Dr. Giorgia Girotto, IRCCS Materno Infantile Burlo Garofolo (IRCCS), Trieste, Italy, firstname.lastname@example.org