Genome-wide association study for age-related hearing loss in CFW mice

Polesskaya, O.; Boussaty, E. C.; Cheng, R.; Lamonte, O. A.; Zhou, T.; Du, E.; Sanches, T. M.; Nguyen, K.-M.; Okamoto, M.; Palmer, A. A.; Friedman, R.

doi:10.1101/2024.06.10.598304

bioRxiv · 10.1101/2024.06.10.598304

Genome-wide association study for age-related hearing loss in CFW mice

Polesskaya, O.·Boussaty, E. C.·Cheng, R.·Lamonte, O. A.·Zhou, T.·Du, E.·Sanches, T. M.·Nguyen, K.-M.·Okamoto, M.·Palmer, A. A.·Friedman, R.

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Abstract

Age-related hearing impairment is the most common cause of hearing loss and is one of the most prevalent conditions affecting the elderly globally. It is influenced by a combination of environmental and genetic factors. The mouse and human inner ears are functionally and genetically homologous. Investigating the genetic basis of age-related hearing loss (ARHL) in an outbred mouse model may lead to a better understanding of the molecular mechanisms of this condition. We used Carworth Farms White (CFW) outbred mice, because they are genetically diverse and exhibit variation in the onset and severity of ARHL. The goal of this study was to identify genetic loci involved in regulating ARHL. Hearing at a range of frequencies was measured using Auditory Brainstem Response (ABR) thresholds in 946 male and female CFW mice at the age of 1, 6, and 10 months. We obtained genotypes at 4.18 million single nucleotide polymorphisms (SNP) using low-coverage (mean coverage 0.27x) whole-genome sequencing followed by imputation using STITCH. To determine the accuracy of the genotypes we sequenced 8 samples at >30x coverage and used calls from those samples to estimate the discordance rate, which was 0.45%. We performed genetic analysis for the ABR thresholds for each frequency at each age, and for the time of onset of deafness for each frequency. The SNP heritability ranged from 0 to 42% for different traits. Genome-wide association analysis identified several regions associated with ARHL that contained potential candidate genes, including Dnah11, Rapgef5, Cpne4, Prkag2, and Nek11. We confirmed, using functional study, that Prkag2 deficiency causes age-related hearing loss at high frequency in mice; this makes Prkag2 a candidate gene for further studies. This work helps to identify genetic risk factors for ARHL and to define novel therapeutic targets for the treatment and prevention of ARHL.

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Polesskaya, O., Boussaty, E. C., Cheng, R., Lamonte, O. A., Zhou, T., Du, E., Sanches, T. M., Nguyen, K.-M., Okamoto, M., Palmer, A. A., Friedman, R.. 2024-06-10. Genome-wide association study for age-related hearing loss in CFW mice. https://doi.org/10.1101/2024.06.10.598304

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