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The Genetic Architecture of Hearing Impairment in Mice: Evidence for Frequency Specific 2 Genetic Determinants

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The Genetic Architecture of Hearing Impairment in Mice: Evidence for Frequency Specific 2 Genetic Determinants G3: Genes|Genomes|Genetics Early Online, published on September 4, 2015 as doi:10.1534/g3.115.021592 1 The genetic architecture of hearing impairment in mice: evidence for frequency specific 2 genetic determinants. 3 4 Amanda L. Crow1, Jeffrey Ohmen2, Juemei Wang3, Joel Lavinsky3, Jaana Hartiala1, Qingzhong 5 Li4, Xin Li5, Pezhman Salehide 3, Eleazar Eskin6, Calvin Pan7, Aldons J. Lusis7, Hooman 6 Allayee1, Rick A. Friedman3 7 8 1Department of Preventive Medicine and Institute for Genetic Medicine, Keck School of 9 Medicine, University of Southern California, Los Angeles, CA 90033 10 2House Ear Institute, Los Angeles, CA 90057 11 3Department of Otolaryngology and Zilkha Neurogenetic Institute, Keck School of Medicine, 12 University of Southern California, Los Angeles, CA, 90033 13 4Department of Otolaryngology - Head and Neck Surgery, Eye & ENT Hospital of Fudan 14 University, Shanghai 200031, China 15 5Clinical Laboratory Department, First Affiliated Hospital of Nanchang University, Nanchang, 16 Jiangxi Province 330006, China 17 6Department of Computer Science and Inter-Departmental Program in Bioinformatics, 18 University of California, Los Angeles, Los Angeles, CA 90095 19 7Departments of Human Genetics, Medicine, and Microbiology, Immunology, and Molecular 20 Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095 21 © The Author(s) 2013. Published by the Genetics Society of America. 1 Short Title 2 Genetics of Hearing in Mice 3 4 Keywords 5 Genome-wide association study (GWAS), Hybrid Mouse Diversity Panel (HMDP), genetics, 6 genomics, ABR, hearing, cochlear function 7 8 9 Corresponding Author: 10 Rick A. Friedman 11 USC Keck School of Medicine 12 Zilkha Neurogenetic Institute 13 1501 San Pablo Street (ZNI 231) 14 Los Angeles, CA 90033 15 Tel: (323) 442-4843 16 Fax: (323) 442-2059 17 Email: [email protected] 18 19 1 Abstract 2 Genome-wide association studies (GWAS) have been successfully applied in humans for 3 the study of many complex phenotypes. However, identification of the genetic determinants of 4 hearing in adults has been hampered, in part, by the relative inability to control for 5 environmental factors that might affect hearing throughout the lifetime, as well as a large degree 6 of phenotypic heterogeneity. These and other factors have limited the number of large-scale 7 studies performed in humans that have identified candidate genes that contribute to the etiology 8 of this complex trait. In order to address these limitations, we performed a GWAS analysis using 9 a set of inbred mouse strains from the Hybrid Mouse Diversity Panel. Among 99 strains 10 characterized, we observed ~2 to 5-fold variation in hearing at six different frequencies, which 11 are differentiated biologically from each other by the location in the cochlea where each 12 frequency is registered. Among all frequencies tested, we identified a total of nine significant 13 loci, several of which contained promising candidate genes for follow-up study. Taken together, 14 our results indicate the existence of both genes that affect global cochlear function, as well as 15 anatomical- - and frequency-specific genes, and further demonstrate the complex nature of 16 mammalian hearing variation. 17 1 Introduction 2 Genome-wide association studies (GWAS) have been successfully applied to numerous 3 complex traits in humans (Welter, MacArthur et al. 2014). These GWAS leverage natural genetic 4 variation in an unbiased approach that is advantageous for studying complex traits. We and 5 others have shown that audiometric threshold elevation secondary to aging in humans is 6 continuously distributed throughout the population (Friedman, Van Laer et al. 2009) and that the 7 human cochlea has a perceptual frequency spectrum of 20 Hz to 20 kHz. Heritability studies 8 have shown that the sources of this variance are both genetic and environmental, with 9 approximately half of the variance attributable to hereditary factors (Huang and Tang 2010). As 10 such, a major impediment to progress in the discovery of risk loci for hearing in humans is the 11 lack of control of the many environmental factors that affect hearing during the lifetime, and, to 12 date, only a limited number of large-scale GWAS for hearing phenotypes have been undertaken 13 in humans. We recently reported an association between age-related hearing loss and SNPs 14 within the GRM7 gene and subsequently demonstrated, in a more comprehensive study, the 15 polygeneic nature of this disease (Fransen, Bonneux et al. 2014). Despite these successes, 16 association studies in humans – particularly for common forms of hearing loss and baseline 17 hearing ability – are still plagued by small sample sizes and phenotypic heterogeneity. 18 In order to harness the same investigative power of the GWAS approach in a more 19 controlled environment that addresses some limitations of human studies, several groups have 20 proposed mouse GWAS (Valdar, Solberg et al. 2006, Bennett, Farber et al. 2010, Flint and Eskin 21 2012, Ghazalpour, Rau et al. 2012, Mott and Flint 2013). For obvious reasons, mouse models 22 have several advantages over human studies. The environment can be more carefully controlled, 23 measurements can be replicated in genetically identical animals, and the proportion of the 1 variability explained by genetic variation is increased. Complex traits in mouse strains have been 2 shown to have higher heritability and genetic loci often have stronger effects on the trait 3 compared to humans (Lindblad-Toh, Winchester et al. 2000, Wiltshire, Pletcher et al. 2003, 4 Yalcin, Fullerton et al. 2004). Furthermore, several recently developed strategies for mouse 5 genetic studies, such as use of the Hybrid Mouse Diversity Panel (HMDP), provide much higher 6 resolution for associated loci than traditional approaches with quantitative trait loci (QTL) 7 mapping (Bennett, Farber et al. 2010, Ghazalpour, Rau et al. 2012). The genetic and functional 8 similarities of the mouse and human ear coupled with the ability to control environmental 9 exposure make the mouse the ideal model for the study of age-related hearing loss. 10 Both naturally occurring and experimentally induced mutations in mice have provided 11 much of our current understanding of many diseases of the ear. It has long been our hypothesis 12 that common forms of hearing impairment in both mice and humans is a complex trait resulting 13 from susceptibility loci throughout the genome that contribute to the natural variation in hearing 14 over time. Based upon literature suggesting that most common disease phenotypes result from 15 sequence variation, often regulatory, in genes that are different from those underlying Mendelian 16 traits, e.g., non-syndromic hearing loss, we undertook a study to characterize the genetics of 17 hearing by performing an association analysis that exploits the natural genetic and phenotypic 18 variation of hearing levels in inbred strains of mice. 19 20 Experimental Methods 21 Animals. Five week-old female mice of 99 inbred strains (n=3-8) from the HMDP (Jackson 22 Laboratories) were obtained and used in accordance with the University of Southern California 23 Institutional Animal Care and Use Committee (IACUC) guidelines. Mice were housed in 1 sterilized microisolator cages and received autoclaved food and water ad libitum. 2 Hearing assessment using auditory brainstem response thresholds (ABR). Mice were 3 anesthetized with an intraperitoneal injection of a mixture of ketamine (80 mg/kg body weight) 4 and xylazine (16 mg/kg body weight). Mouse body temperature was maintained through the use 5 of a TCAT-2DF temperature controller and the HP-4 M heating plate (Physitemp Instruments 6 Inc., Clifton, NJ). Artificial tear ointment was applied to the eyes during anesthesia. Lastly, mice 7 recovered from anesthesia on a heating pad. Stainless-steel electrodes were placed subcutaneously 8 at the vertex of the head and the left mastoid. A ground electrode was placed at the base of the 9 tail. Test sounds were presented using an Intelligent Hearing Systems speaker attached to an 8–in. 10 long tube that was inserted into the ear canal. Due to time and equipment constraints, only the left 11 ear was assessed. 12 Auditory signals were presented as tone pips (4, 8, 16, 24, and 32 kHz) in the form of a 13 hamming wave with a 0.3-ms rise and fall time (total time of 1 ms). These signals were presented 14 at a rate of 40 per second. They were then sent to an amplifier and then to the sound transducer 15 from Intelligent Hearing Systems. Physiologic responses were recorded with a 20,000 analog-to- 16 digital rate and sent to an 8 channel 150-gain AC/DC headbox and then onto a secondary 17 Synamps signal amplifier of 2500 gain before analysis. Filter settings were set at a low-pass of 18 3000 Hz and a high-pass of 100 Hz with an artifact rejection of signals with amplitudes exceeding 19 ± 50 μV. Three thousand waveforms were averaged at each stimulus intensity. Tone bursts were 20 first presented at a high intensity to elicit a waveform. Next, the intensity was decreased by 20 dB 21 until nearing threshold. Intensity was then decreased in smaller steps of 10, 5, and 2 dB as 22 threshold was approached. Hearing threshold was determined by visual inspection of ABR 23 waveforms and was defined as the intensity at which two peaks could be distinguished. 1 Experiments were duplicated at low intensities when the peaks were not apparent. 2 RNA isolation and microarray analysis. We isolated cochlea from 64 HMDP strains (2-4 mice 3 per strain) mice at 6 weeks of age. RNA was purified after decapitation, the inner ear micro- 4 dissected, all soft tissue removed from the cochlear capsule, and the vestibular labyrinth removed 5 at the level of the round and oval windows.
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