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Lavinsky J, Kasperbauer G, Bento RF, Mendonça A, Wang J, Crow AL, Allayee H, Friedman RA. Noise Exposure and Distortion Product Otoacoustic Emission Suprathreshold Amplitudes: A Genome-Wide Association Study. Audiol Neurootol 2021; 26:445-453. [PMID: 34280920 DOI: 10.1159/000514143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 11/25/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Although several candidate-gene association studies have been conducted to investigate noise-induced hearing loss (NIHL) in humans, most are underpowered, unreplicated, and account for only a fraction of the genetic risk. Mouse genome-wide association studies (GWASs) have revolutionized the field of genetics and have led to the discovery of hundreds of genes involved in complex traits. The hybrid mouse diversity panel (HMDP) is a collection of classic inbred and recombinant inbred strains whose genomes have been either genotyped at high resolution or sequenced. To further investigate the genetics of NIHL, we report the first GWAS based on distortion product otoacoustic emission (DPOAE) measurements and the HMDP. METHODS A total of 102 strains (n = 635) from the HMDP were evaluated based on DPOAE suprathreshold amplitudes before and after noise exposure. DPOAE amplitude variation was set at 60 and 70 dB SPL of the primary tones for each frequency separately (8, 11.3, 16, 22.6, and 32 kHz). These values provided an indirect assessment of outer hair cell integrity. Six-week-old mice were exposed for 2 h to 10 kHz octave-band noise at 108 dB SPL. To perform local expression quantitative trait locus (eQTL) analysis, gene expression microarray profiles were generated using cochlear RNA from 64 hybrid mouse strains (n = 3 arrays per strain). RESULTS Several new loci were identified and positional candidate-genes associated with NIHL were prioritized, especially after noise exposure (1 locus at baseline and 5 loci after exposure). A total of 35 candidate genes in these 6 loci were identified with at least 1 probe whose expression was regulated by a significant cis-eQTL in the cochlea. After careful analysis of the candidate genes based on cochlear gene expression, 2 candidate genes were prioritized: Eya1 (baseline) and Efr3a (post-exposure). DISCUSSION AND CONCLUSION For the first time, an association analysis with correction for population structure was used to map several loci for hearing traits in inbred strains of mice based on DPOAE suprathreshold amplitudes before and after noise exposure. Our results identified a number of novel loci and candidate genes for susceptibility to NIHL, especially the Eya1 and Efr3a genes. Our findings validate the power of the HMDP for detecting NIHL susceptibility genes.
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Affiliation(s)
- Joel Lavinsky
- Postgraduate Program in Medicine: Surgical Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Guilherme Kasperbauer
- Postgraduate Program in Medicine: Surgical Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Ricardo F Bento
- Department of Otolaryngology, University of São Paulo, La Jolla, California, USA
| | - Aline Mendonça
- Postgraduate Program in Medicine: Surgical Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Juemei Wang
- Keck School of Medicine of USC, Los Angeles, California, USA
| | - Amanda L Crow
- Keck School of Medicine of USC, Los Angeles, California, USA
| | - Hooman Allayee
- Keck School of Medicine of USC, Los Angeles, California, USA
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Maazi H, Hartiala JA, Suzuki Y, Crow AL, Shafiei Jahani P, Lam J, Patel N, Rigas D, Han Y, Huang P, Eskin E, Lusis AJ, Gilliland FD, Akbari O, Allayee H. A GWAS approach identifies Dapp1 as a determinant of air pollution-induced airway hyperreactivity. PLoS Genet 2019; 15:e1008528. [PMID: 31869344 PMCID: PMC6944376 DOI: 10.1371/journal.pgen.1008528] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/06/2020] [Accepted: 11/15/2019] [Indexed: 02/07/2023] Open
Abstract
Asthma is a chronic inflammatory disease of the airways with contributions from genes, environmental exposures, and their interactions. While genome-wide association studies (GWAS) in humans have identified ~200 susceptibility loci, the genetic factors that modulate risk of asthma through gene-environment (GxE) interactions remain poorly understood. Using the Hybrid Mouse Diversity Panel (HMDP), we sought to identify the genetic determinants of airway hyperreactivity (AHR) in response to diesel exhaust particles (DEP), a model traffic-related air pollutant. As measured by invasive plethysmography, AHR under control and DEP-exposed conditions varied 3-4-fold in over 100 inbred strains from the HMDP. A GWAS with linear mixed models mapped two loci significantly associated with lung resistance under control exposure to chromosomes 2 (p = 3.0x10-6) and 19 (p = 5.6x10-7). The chromosome 19 locus harbors Il33 and is syntenic to asthma association signals observed at the IL33 locus in humans. A GxE GWAS for post-DEP exposure lung resistance identified a significantly associated locus on chromosome 3 (p = 2.5x10-6). Among the genes at this locus is Dapp1, an adaptor molecule expressed in immune-related and mucosal tissues, including the lung. Dapp1-deficient mice exhibited significantly lower AHR than control mice but only after DEP exposure, thus functionally validating Dapp1 as one of the genes underlying the GxE association at this locus. In summary, our results indicate that some of the genetic determinants for asthma-related phenotypes may be shared between mice and humans, as well as the existence of GxE interactions in mice that modulate lung function in response to air pollution exposures relevant to humans. The genetic factors that modulate risk of asthma through gene-environment (GxE) interactions are poorly understood, due in large part to the inherent difficulties in carrying out such studies in humans. To address these challenges, we used the Hybrid Mouse Diversity Panel to elucidate the genetic architecture of asthma-related phenotypes in mice and identify loci that are associated with airway hyperreactivity (AHR) under control exposure conditions and in response to diesel exhaust particles (DEP), as a model traffic-related air pollutant. In the absence of exposure, we identified two loci on chromosomes 2 and 19 for AHR. The locus on chromosome 19 harbors Il33 and is syntenic to association signals observed for asthma at the IL33 locus in humans. In response to DEP exposure, we mapped AHR to a region on chromosome 3 and used a genetically modified mouse model to functionally demonstrate that Dapp1 is one of the genes underlying the GxE association at this locus. Collectively, our results support the concept that some of the genetic determinants for asthma-related phenotypes may be shared between mice and humans as well as the existence of GxE interactions in mice that modulate lung function in response to air pollution exposures relevant to humans.
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Affiliation(s)
- Hadi Maazi
- Departments of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Jaana A. Hartiala
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Yuzo Suzuki
- Departments of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Amanda L. Crow
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Pedram Shafiei Jahani
- Departments of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Jonathan Lam
- Departments of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Nisheel Patel
- Departments of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Diamanda Rigas
- Departments of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Yi Han
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Pin Huang
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Eleazar Eskin
- Department of Computer Science and Inter-Departmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Aldons. J. Lusis
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Frank D. Gilliland
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Omid Akbari
- Departments of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- * E-mail: (OA); (HA)
| | - Hooman Allayee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- * E-mail: (OA); (HA)
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Myint A, White CH, Ohmen JD, Li X, Wang J, Lavinsky J, Salehi P, Crow AL, Ohyama T, Friedman RA. Large-scale phenotyping of noise-induced hearing loss in 100 strains of mice. Hear Res 2015; 332:113-120. [PMID: 26706709 DOI: 10.1016/j.heares.2015.12.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 12/06/2015] [Accepted: 12/07/2015] [Indexed: 01/13/2023]
Abstract
A cornerstone technique in the study of hearing is the Auditory Brainstem Response (ABR), an electrophysiologic technique that can be used as a quantitative measure of hearing function. Previous studies have published databases of baseline ABR thresholds for mouse strains, providing a valuable resource for the study of baseline hearing function and genetic mapping of hearing traits in mice. In this study, we further expand upon the existing literature by characterizing the baseline ABR characteristics of 100 inbred mouse strains, 47 of which are newly characterized for hearing function. We identify several distinct patterns of baseline hearing deficits and provide potential avenues for further investigation. Additionally, we characterize the sensitivity of the same 100 strains to noise exposure using permanent thresholds shifts, identifying several distinct patterns of noise-sensitivity. The resulting data provides a new resource for studying hearing loss and noise-sensitivity in mice.
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Affiliation(s)
- Anthony Myint
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90089-2821, USA
| | - Cory H White
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90089-2821, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0419, USA
| | - Jeffrey D Ohmen
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90089-2821, USA; Department of Cell Biology and Genetics, House Research Institute, Los Angeles, CA 90057, USA
| | - Xin Li
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90089-2821, USA; Department of Cell Biology and Genetics, House Research Institute, Los Angeles, CA 90057, USA
| | - Juemei Wang
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90089-2821, USA; Department of Cell Biology and Genetics, House Research Institute, Los Angeles, CA 90057, USA
| | - Joel Lavinsky
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90089-2821, USA
| | - Pezhman Salehi
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90089-2821, USA
| | - Amanda L Crow
- Department of Preventive Medicine, Keck School of Medicine of USC, 2250 Alcazar St, Los Angeles, CA 90089-9073, USA
| | - Takahiro Ohyama
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90089-2821, USA; Department of Cell Biology and Genetics, House Research Institute, Los Angeles, CA 90057, USA
| | - Rick A Friedman
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90089-2821, USA; Department of Cell Biology and Genetics, House Research Institute, Los Angeles, CA 90057, USA.
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Zhou X, Crow AL, Hartiala J, Spindler TJ, Ghazalpour A, Barsky LW, Bennett BJ, Parks BW, Eskin E, Jain R, Epstein JA, Lusis AJ, Adams GB, Allayee H. The Genetic Landscape of Hematopoietic Stem Cell Frequency in Mice. Stem Cell Reports 2015; 5:125-38. [PMID: 26050929 PMCID: PMC4618249 DOI: 10.1016/j.stemcr.2015.05.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 05/07/2015] [Accepted: 05/08/2015] [Indexed: 12/31/2022] Open
Abstract
Prior efforts to identify regulators of hematopoietic stem cell physiology have relied mainly on candidate gene approaches with genetically modified mice. Here we used a genome-wide association study (GWAS) strategy with the hybrid mouse diversity panel to identify the genetic determinants of hematopoietic stem/progenitor cell (HSPC) frequency. Among 108 strains, we observed ∼120- to 300-fold variation in three HSPC populations. A GWAS analysis identified several loci that were significantly associated with HSPC frequency, including a locus on chromosome 5 harboring the homeodomain-only protein gene (Hopx). Hopx previously had been implicated in cardiac development but was not known to influence HSPC biology. Analysis of the HSPC pool in Hopx−/− mice demonstrated significantly reduced cell frequencies and impaired engraftment in competitive repopulation assays, thus providing functional validation of this positional candidate gene. These results demonstrate the power of GWAS in mice to identify genetic determinants of the hematopoietic system. Genetic variation across mouse strains influences hematopoietic stem cell frequency This variation can be exploited for genome-wide association studies Hopx is a regulator of hematopoietic stem/progenitor cell function This approach can be used to identify genetic determinants of other stem cell systems
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Affiliation(s)
- Xiaoying Zhou
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Amanda L Crow
- Department of Preventive Medicine and Institute for Genetic Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jaana Hartiala
- Department of Preventive Medicine and Institute for Genetic Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Tassja J Spindler
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Anatole Ghazalpour
- Departments of Human Genetics, Medicine, and Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Lora W Barsky
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Brian J Bennett
- Department of Genetics and Nutrition Research Institute, University of North Carolina, Chapel Hill, Kannapolis, NC 28081, USA
| | - Brian W Parks
- Departments of Human Genetics, Medicine, and Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Eleazar Eskin
- Department of Computer Science and Inter-Departmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Rajan Jain
- Department of Cell and Developmental Biology and Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan A Epstein
- Department of Cell and Developmental Biology and Penn Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aldons J Lusis
- Departments of Human Genetics, Medicine, and Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Gregor B Adams
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
| | - Hooman Allayee
- Department of Preventive Medicine and Institute for Genetic Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
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Lavinsky J, Crow AL, Pan C, Wang J, Aaron KA, Ho MK, Li Q, Salehide P, Myint A, Monges-Hernadez M, Eskin E, Allayee H, Lusis AJ, Friedman RA. Genome-wide association study identifies nox3 as a critical gene for susceptibility to noise-induced hearing loss. PLoS Genet 2015; 11:e1005094. [PMID: 25880434 PMCID: PMC4399881 DOI: 10.1371/journal.pgen.1005094] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Accepted: 02/23/2015] [Indexed: 01/09/2023] Open
Abstract
In the United States, roughly 10% of the population is exposed daily to hazardous levels of noise in the workplace. Twin studies estimate heritability for noise-induced hearing loss (NIHL) of approximately 36%, and strain specific variation in sensitivity has been demonstrated in mice. Based upon the difficulties inherent to the study of NIHL in humans, we have turned to the study of this complex trait in mice. We exposed 5 week-old mice from the Hybrid Mouse Diversity Panel (HMDP) to a 10 kHz octave band noise at 108 dB for 2 hours and assessed the permanent threshold shift 2 weeks post exposure using frequency specific stimuli. These data were then used in a genome-wide association study (GWAS) using the Efficient Mixed Model Analysis (EMMA) to control for population structure. In this manuscript we describe our GWAS, with an emphasis on a significant peak for susceptibility to NIHL on chromosome 17 within a haplotype block containing NADPH oxidase-3 (Nox3). Our peak was detected after an 8 kHz tone burst stimulus. Nox3 mutants and heterozygotes were then tested to validate our GWAS. The mutants and heterozygotes demonstrated a greater susceptibility to NIHL specifically at 8 kHz both on measures of distortion product otoacoustic emissions (DPOAE) and on auditory brainstem response (ABR). We demonstrate that this sensitivity resides within the synaptic ribbons of the cochlea in the mutant animals specifically at 8 kHz. Our work is the first GWAS for NIHL in mice and elucidates the power of our approach to identify tonotopic genetic susceptibility to NIHL. Noise-induced hearing loss (NIHL) is the most common work-related disease in the world and the second cause of hearing loss. Although several candidate gene association studies for NIHL in humans have been conducted, each are underpowered, un-replicated, and account for only a fraction of the genetic risk. Buoyed by the prospects and successes of human association studies, several groups have proposed mouse genome-wide association studies. The environment can be carefully controlled, facilitating the study of complex traits like NIHL. In this manuscript, we describe, for the first time, an association analysis with correction for population structure for the mapping of several loci for susceptibility to NIHL in inbred strains of mice. We identify Nox3 as the associated gene for susceptibility to NIHL that the genetic susceptibility is frequency specific and that it occurs at the level of the cochlear synaptic ribbon.
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Affiliation(s)
- Joel Lavinsky
- Graduate Program in Surgical Sciences, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- Department of Otolaryngology, Zilkha Neurogenetic Institute, USC Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Amanda L. Crow
- Department of Preventive Medicine and Institute for Genetic Medicine, USC Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Calvin Pan
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Juemei Wang
- Department of Otolaryngology, Zilkha Neurogenetic Institute, USC Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Ksenia A. Aaron
- Department of Otolaryngology, Zilkha Neurogenetic Institute, USC Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Maria K. Ho
- Department of Otolaryngology, Zilkha Neurogenetic Institute, USC Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Qingzhong Li
- Department of Otolaryngology, Zilkha Neurogenetic Institute, USC Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Pehzman Salehide
- Department of Otolaryngology, Zilkha Neurogenetic Institute, USC Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Anthony Myint
- Department of Otolaryngology, Zilkha Neurogenetic Institute, USC Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Maya Monges-Hernadez
- Department of Otolaryngology, Zilkha Neurogenetic Institute, USC Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Eleazar Eskin
- Department of Computer Science, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Hooman Allayee
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Aldons J. Lusis
- Department of Preventive Medicine and Institute for Genetic Medicine, USC Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Rick A. Friedman
- Department of Otolaryngology, Zilkha Neurogenetic Institute, USC Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
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