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Beyene MB, Visvanathan R, Ahmed M, Benyamin B, Beard JR, Amare AT. Development and validation of an intrinsic capacity score in the UK Biobank study. Maturitas 2024; 185:107976. [PMID: 38537388 DOI: 10.1016/j.maturitas.2024.107976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/06/2024] [Accepted: 03/14/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND In 2015, the World Health Organization introduced the concept of intrinsic capacity (IC) to define the individual-level characteristics that enable an older person to be and do the things they value. This study developed an intrinsic capacity score for UK Biobank study participants and validated its use as a tool for health outcome prediction, understanding healthy aging trajectories, and genetic research. METHODS Our analysis included data from 45,208 UK biobank participants who had a complete record of the ten variables included in the analysis. Factor adequacy was tested using Kaiser-Meyer-Olkin, Barthelt's, and the determinant of matrix tests, and the number of factors was determined by the parallel analysis method. Exploratory and confirmatory factor analyses were employed to determine the structure and dimensionality of indicators. Finally, the intrinsic capacity score was generated, and its construct and predictive validities as well as reliability were assessed. RESULTS The factor analysis identified a multidimensional construct comprising one general factor (intrinsic capacity) and five specific factors (locomotor, vitality, cognitive, psychological, and sensory). The bifactor structure showed a better fit (comparative fit index = 0.995, Tucker Lewis index = 0.976, root mean square error of approximation = 0.025, root mean square residual = 0.009) than the conventional five-factor structure. The intrinsic capacity score generated using the bifactor confirmatory factor analysis has good construct validity, as demonstrated by an inverse association with age (lower intrinsic capacity in older age; (β) =-0.035 (95%CI: -0.036, -0.034)), frailty (lower intrinsic capacity score in prefrail participants, β = -0.104 (95%CI: (-0.114, -0.094)) and frail participants, β = -0.227 (95%CI: -0.267, -0.186) than robust participants), and comorbidity (a lower intrinsic capacity score associated with increased Charlson's comorbidity index, β =-0.019 (95%CI: -0.022, -0.015)). The intrinsic capacity score also predicted comorbidity (a one-unit increase in baseline intrinsic capacity score led to a lower Charlson's comorbidity index, β = 0.147 (95%CI: -0.173, -0.121)) and mortality (a one-unit increase in baseline intrinsic capacity score led to 25 % lower risk of death, odds ratio = 0.75(95%CI: 0.663, 0.848)). CONCLUSION The bifactor structure showed a better fit in all goodness of fit tests. The intrinsic capacity construct has strong structural, construct, and predictive validities and is a promising tool for monitoring aging trajectories.
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Affiliation(s)
- Melkamu Bedimo Beyene
- Discipline of Psychiatry, School of Medicine, University of Adelaide, Adelaide, SA, Australia; Adelaide Geriatrics Training and Research with Aged Care Centre (GTRAC), Faculty of Health and Medical Sciences, University of Adelaide, Woodville, SA, 5011, Australia
| | - Renuka Visvanathan
- Adelaide Geriatrics Training and Research with Aged Care Centre (GTRAC), Faculty of Health and Medical Sciences, University of Adelaide, Woodville, SA, 5011, Australia; Aged and Extended Care Services, The Queen Elizabeth Hospital, Central Adelaide Local Health Network, Adelaide, SA, Australia
| | - Muktar Ahmed
- Discipline of Psychiatry, School of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Beben Benyamin
- Australian Centre for Precision Health, Allied Health and Human Performance, University of South Australia, Adelaide 5000, Australia; South Australian Health and Medical Research Institute, Adelaide 5000, Australia
| | - John R Beard
- International Longevity Centre USA, Columbia University Mailman School of Public Health, NY, USA
| | - Azmeraw T Amare
- Discipline of Psychiatry, School of Medicine, University of Adelaide, Adelaide, SA, Australia; Adelaide Geriatrics Training and Research with Aged Care Centre (GTRAC), Faculty of Health and Medical Sciences, University of Adelaide, Woodville, SA, 5011, Australia.
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Polesskaya O, Boussaty E, Cheng R, Lamonte O, Zhou T, Du E, Sanches TM, Nguyen KM, Okamoto M, Palmer AA, Friedman R. Genome-wide association study for age-related hearing loss in CFW mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598304. [PMID: 38915500 PMCID: PMC11195089 DOI: 10.1101/2024.06.10.598304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
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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Affiliation(s)
- Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Ely Boussaty
- Department of Otolaryngology - Head and Neck Surgery, University of California San Diego, La Jolla, CA, 92093, USA
| | - Riyan Cheng
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Olivia Lamonte
- Department of Otolaryngology - Head and Neck Surgery, University of California San Diego, La Jolla, CA, 92093, USA
| | - Thomas Zhou
- Department of Otolaryngology - Head and Neck Surgery, University of California San Diego, La Jolla, CA, 92093, USA
| | - Eric Du
- Department of Otolaryngology - Head and Neck Surgery, University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Khai-Minh Nguyen
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Mika Okamoto
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Rick Friedman
- Department of Otolaryngology - Head and Neck Surgery, University of California San Diego, La Jolla, CA, 92093, USA
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3
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Ninoyu Y, Friedman RA. The genetic landscape of age-related hearing loss. Trends Genet 2024; 40:228-237. [PMID: 38161109 DOI: 10.1016/j.tig.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 12/03/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024]
Abstract
Age-related hearing loss (ARHL) is a prevalent concern in the elderly population. Recent genome-wide and phenome-wide association studies (GWASs and PheWASs) have delved into the identification of causative variants and the understanding of pleiotropy, highlighting the polygenic intricacies of this complex condition. While recent large-scale GWASs have pinpointed significant SNPs and risk variants associated with ARHL, the detailed mechanisms, encompassing both genetic and epigenetic modifications, remain to be fully elucidated. This review presents the latest advances in association studies, integrating findings from both human studies and model organisms. By juxtaposing historical perspectives with contemporary genomics, we aim to catalyze innovative research and foster the development of novel therapeutic strategies for ARHL.
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Affiliation(s)
- Yuzuru Ninoyu
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, USA; Department of Otolaryngology-Head and Neck Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Rick A Friedman
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, USA.
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4
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Xu K, Chen S, Bai X, Xie L, Qiu Y, Liu X, Wang X, Kong W, Sun Y. Degradation of cochlear Connexin26 accelerate the development of age-related hearing loss. Aging Cell 2023; 22:e13973. [PMID: 37681746 PMCID: PMC10652327 DOI: 10.1111/acel.13973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/03/2023] [Accepted: 08/15/2023] [Indexed: 09/09/2023] Open
Abstract
The GJB2 gene, encoding Connexin26 (Cx26), is one of the most common causes of inherited deafness. Clinically, mutations in GJB2 cause congenital deafness or late-onset progressive hearing loss. Recently, it has been reported that Cx26 haploid deficiency accelerates the development of age-related hearing loss (ARHL). However, the roles of cochlear Cx26 in the hearing function of aged animals remain unclear. In this study, we revealed that the Cx26 expression was significantly reduced in the cochleae of aged mice, and further explored the underlying molecular mechanism for Cx26 degradation. Immunofluorescence co-localization results showed that Cx26 was internalized and degraded by lysosomes, which might be one of the important ways for Cx26 degradation in the cochlea of aged mice. Currently, whether the degradation of Cx26 in the cochlea leads directly to ARHL, as well as the mechanism of Cx26 degradation-related hearing loss are still unclear. To address these questions, we generated mice with Cx26 knockout in the adult cochlea as a model for the natural degradation of Cx26. Auditory brainstem response (ABR) results showed that Cx26 knockout mice exhibited high-frequency hearing loss, which gradually progressed over time. Pathological examination also revealed the degeneration of hair cells and spiral ganglions, which is similar to the phenotype of ARHL. In summary, our findings suggest that degradation of Cx26 in the cochlea accelerates the occurrence of ARHL, which may be a novel mechanism of ARHL.
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Affiliation(s)
- Kai Xu
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Sen Chen
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Xue Bai
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Le Xie
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Yue Qiu
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Xiao‐zhou Liu
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Xiao‐hui Wang
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Wei‐jia Kong
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
| | - Yu Sun
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanChina
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and RegenerationWuhanChina
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5
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Du EY, Boussaty EC, La Monte OA, Dixon PR, Zhou TY, Friedman RA. Large-scale phenotyping and characterization of age-related hearing loss in outbred CFW mice. Hear Res 2022; 424:108605. [PMID: 36088865 DOI: 10.1016/j.heares.2022.108605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/27/2022] [Accepted: 09/03/2022] [Indexed: 11/18/2022]
Abstract
Age-related hearing loss (ARHL), or presbycusis, is one of the most prevalent conditions affecting the global population. A substantial fraction of patients with ARHL have no identifiable mutation despite over a hundred having been discovered, suggesting unidentified monogenic or polygenic causes. In this study, we investigated the hearing function of the aging outbred CFW mice through auditory brainstem response (ABR) thresholds. Through the characterization of 1,132 ABRs, we observed significant variation in both absolute thresholds and the effect of aging. We identify eight distinct patterns of hearing loss and were able to categorize nearly all data within these eight categories. Proportions within each category varied immensely between aging timepoints. We observe a small but consistent hearing deficit in female CFW mice. The resulting phenotypic data are a necessity for ARHL association mapping at a higher resolution than has previously been achieved and provides a new resource for studying ARHL.
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Affiliation(s)
- Eric Y Du
- Department of Otolaryngology - Head and Neck Surgery, University of California, San Diego, La Jolla, CA, USA
| | - Ely C Boussaty
- Department of Otolaryngology - Head and Neck Surgery, University of California, San Diego, La Jolla, CA, USA
| | - Olivia A La Monte
- Department of Otolaryngology - Head and Neck Surgery, University of California, San Diego, La Jolla, CA, USA; University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Peter R Dixon
- Department of Otolaryngology - Head and Neck Surgery, University of California, San Diego, La Jolla, CA, USA
| | - Thomas Y Zhou
- University of California, San Diego, La Jolla, CA, USA
| | - Rick A Friedman
- Department of Otolaryngology - Head and Neck Surgery, University of California, San Diego, La Jolla, CA, USA.
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6
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Mathias SR, Knowles EE, Mollon J, Rodrigue AL, Woolsey MK, Hernandez AM, Garrett AS, Fox PT, Olvera RL, Peralta JM, Kumar S, Göring HH, Duggirala R, Curran JE, Blangero J, Glahn DC. The Genetic contribution to solving the cocktail-party problem. iScience 2022; 25:104997. [PMID: 36111257 PMCID: PMC9468408 DOI: 10.1016/j.isci.2022.104997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 07/19/2022] [Accepted: 08/18/2022] [Indexed: 11/25/2022] Open
Abstract
Communicating in everyday situations requires solving the cocktail-party problem, or segregating the acoustic mixture into its constituent sounds and attending to those of most interest. Humans show dramatic variation in this ability, leading some to experience real-world problems irrespective of whether they meet criteria for clinical hearing loss. Here, we estimated the genetic contribution to cocktail-party listening by measuring speech-reception thresholds (SRTs) in 425 people from large families and ranging in age from 18 to 91 years. Roughly half the variance of SRTs was explained by genes (h 2 = 0.567). The genetic correlation between SRTs and hearing thresholds (HTs) was medium (ρ G = 0.392), suggesting that the genetic factors influencing cocktail-party listening were partially distinct from those influencing sound sensitivity. Aging and socioeconomic status also strongly influenced SRTs. These findings may represent a first step toward identifying genes for "hidden hearing loss," or hearing problems in people with normal HTs.
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Affiliation(s)
- Samuel R. Mathias
- Department of Psychiatry, Boston Children’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Emma E.M. Knowles
- Department of Psychiatry, Boston Children’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Josephine Mollon
- Department of Psychiatry, Boston Children’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Amanda L. Rodrigue
- Department of Psychiatry, Boston Children’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Mary K. Woolsey
- Research Imaging Institute, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Alyssa M. Hernandez
- Research Imaging Institute, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Amy S. Garrett
- Research Imaging Institute, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Peter T. Fox
- Research Imaging Institute, University of Texas Health Science Center, San Antonio, TX 78229, USA
- South Texas Veterans Health Care System, San Antonio, TX 78229, USA
| | - Rene L. Olvera
- South Texas Diabetes and Obesity Institute and Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
| | - Juan M. Peralta
- South Texas Diabetes and Obesity Institute and Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
| | - Satish Kumar
- South Texas Diabetes and Obesity Institute and Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
| | - Harald H.H. Göring
- South Texas Diabetes and Obesity Institute and Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
| | - Ravi Duggirala
- South Texas Diabetes and Obesity Institute and Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
| | - Joanne E. Curran
- South Texas Diabetes and Obesity Institute and Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
| | - John Blangero
- South Texas Diabetes and Obesity Institute and Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
| | - David C. Glahn
- Department of Psychiatry, Boston Children’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
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7
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Yasuda SP, Miyasaka Y, Hou X, Obara Y, Shitara H, Seki Y, Matsuoka K, Takahashi A, Wakai E, Hibino H, Takada T, Shiroishi T, Kominami R, Kikkawa Y. Two Loci Contribute to Age-Related Hearing Loss Resistance in the Japanese Wild-Derived Inbred MSM/Ms Mice. Biomedicines 2022; 10:biomedicines10092221. [PMID: 36140322 PMCID: PMC9496148 DOI: 10.3390/biomedicines10092221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/30/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
An MSM/Ms strain was established using Japanese wild mice, which exhibit resistance to several phenotypes associated with aging, such as obesity, inflammation, and tumorigenesis, compared to common inbred mouse strains. MSM/Ms strain is resistant to age-related hearing loss, and their auditory abilities are sustained for long durations. The age-related hearing loss 3 (ahl3) locus contributes to age-related hearing in MSM/Ms strain. We generated ahl3 congenic strains by transferring a genomic region on chromosome 17 from MSM/Ms mice into C57BL/6J mice. Although C57BL/6J mice develop age-related hearing loss because of the ahl allele of the cadherin 23 gene, the development of middle- to high-frequency hearing loss was significantly delayed in an ahl3 congenic strain. Moreover, the novel age-related hearing loss 10 (ahl10) locus associated with age-related hearing resistance in MSM/Ms strain was mapped to chromosome 12. Although the resistance effects in ahl10 congenic strain were slightly weaker than those in ahl3 congenic strain, slow progression of age-related hearing loss was confirmed in ahl10 congenic strain despite harboring the ahl allele of cadherin 23. These results suggest that causative genes and polymorphisms of the ahl3 and ahl10 loci are important targets for the prevention and treatment of age-related hearing loss.
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Affiliation(s)
- Shumpei P. Yasuda
- Deafness Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Yuki Miyasaka
- Deafness Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
- Division of Experimental Animals, Graduate School of Medicine, Nagoya University, Nagoya 466-8550, Japan
| | - Xuehan Hou
- Deafness Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
- Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan
| | - Yo Obara
- Deafness Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Hiroshi Shitara
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
- Laboratory for Transgenic Technology, Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Yuta Seki
- Deafness Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Kunie Matsuoka
- Deafness Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Ai Takahashi
- Deafness Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Eri Wakai
- Deafness Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
- Division of Glocal Pharmacology, Department of Pharmacology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Hiroshi Hibino
- Division of Glocal Pharmacology, Department of Pharmacology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Toyoyuki Takada
- Integrated Bioresource Information Division, RIKEN BioResource Research Center, Tsukuba 305-0074, Japan
| | | | - Ryo Kominami
- Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan
| | - Yoshiaki Kikkawa
- Deafness Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
- Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan
- Correspondence:
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Population-scale analysis of common and rare genetic variation associated with hearing loss in adults. Commun Biol 2022; 5:540. [PMID: 35661827 PMCID: PMC9166757 DOI: 10.1038/s42003-022-03408-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 04/23/2022] [Indexed: 12/29/2022] Open
Abstract
To better understand the genetics of hearing loss, we performed a genome-wide association meta-analysis with 125,749 cases and 469,497 controls across five cohorts. We identified 53/c loci affecting hearing loss risk, including common coding variants in COL9A3 and TMPRSS3. Through exome sequencing of 108,415 cases and 329,581 controls, we observed rare coding associations with 11 Mendelian hearing loss genes, including additive effects in known hearing loss genes GJB2 (Gly12fs; odds ratio [OR] = 1.21, P = 4.2 × 10-11) and SLC26A5 (gene burden; OR = 1.96, P = 2.8 × 10-17). We also identified hearing loss associations with rare coding variants in FSCN2 (OR = 1.14, P = 1.9 × 10-15) and KLHDC7B (OR = 2.14, P = 5.2 × 10-30). Our results suggest a shared etiology between Mendelian and common hearing loss in adults. This work illustrates the potential of large-scale exome sequencing to elucidate the genetic architecture of common disorders where both common and rare variation contribute to risk.
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9
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Boussaty EC, Friedman RA, Clifford RE. Hearing loss and tinnitus: association studies for complex-hearing disorders in mouse and man. Hum Genet 2022; 141:981-990. [PMID: 34318347 PMCID: PMC8792513 DOI: 10.1007/s00439-021-02317-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/13/2021] [Indexed: 12/29/2022]
Abstract
Genome-wide association studies (GWAS) provide an unbiased first look at genetic loci involved in aging and noise-induced sensorineural hearing loss and tinnitus. The hearing phenotype, whether audiogram-based or self-report, is regressed against genotyped information at representative single nucleotide polymorphisms (SNPs) across the genome. Findings include the fact that both hearing loss and tinnitus are polygenic disorders, with up to thousands of genes, each of effect size of < 0.02. Smaller human GWAS' were able to use objective measures and identified a few loci; however, hundreds of thousands of participants have been required for the statistical power to identify significant variants, and GWAS is unable to assess rare variants with mean allele frequency < 1%. Animal studies are required as well because of inability to access the human cochlea. Mouse GWAS builds on linkage techniques and the known phenotypic differences in auditory function between inbred strains. With the advantage that the laboratory environment can be controlled for noise and aging, the Hybrid Mouse Diversity Panel (HDMP) combines 100 strains sequenced at high resolution. Lift-over regions between mice and humans have identified over 17,000 homologous genes. Since most significant SNPs are either intergenic or in introns, and binding sites between species are poorly preserved between species, expression quantitative trait locus information is required to bring humans and mice into agreement. Transcriptome-wide analysis studies (TWAS) can prioritize putative causal genes and tissues. Diverse species, each making a distinct contribution, carry a synergistic advantage in the quest for treatment and ultimate cure of sensorineural hearing difficulties.
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Affiliation(s)
- Ely Cheikh Boussaty
- School of Health Sciences, Division of Otolaryngology, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Rick Adam Friedman
- School of Health Sciences, Division of Otolaryngology, University of California San Diego, La Jolla, San Diego, CA, USA
| | - Royce E Clifford
- School of Health Sciences, Division of Otolaryngology, University of California San Diego, La Jolla, San Diego, CA, USA.
- Research Department, VA Hospitals San Diego, San Diego, CA, USA.
- Visiting Scientist, Department of Environmental Health, Harvard School of Public Health, Boston, MA, USA.
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Hearing Function: Identification of New Candidate Genes Further Explaining the Complexity of This Sensory Ability. Genes (Basel) 2021; 12:genes12081228. [PMID: 34440402 PMCID: PMC8394865 DOI: 10.3390/genes12081228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 11/16/2022] Open
Abstract
To date, the knowledge of the genetic determinants behind the modulation of hearing ability is relatively limited. To investigate this trait, we performed Genome-Wide Association Study (GWAS) meta-analysis using genotype and audiometric data (hearing thresholds at 0.25, 0.5, 1, 2, 4, and 8 kHz, and pure-tone averages of thresholds at low, medium, and high frequencies) collected in nine cohorts from Europe, South-Eastern USA, Caucasus, and Central Asia, for an overall number of ~9000 subjects. Three hundred seventy-five genes across all nine analyses were tagged by single nucleotide polymorphisms (SNPs) reaching a suggestive p-value (p < 10−5). Amongst these, 15 were successfully replicated using a gene-based approach in the independent Italian Salus in the Apulia cohort (n = 1774) at the nominal significance threshold (p < 0.05). In addition, the expression level of the replicated genes was assessed in published human and mouse inner ear datasets. Considering expression patterns in humans and mice, eleven genes were considered particularly promising candidates for the hearing function: BNIP3L, ELP5, MAP3K20, MATN2, MTMR7, MYO1E, PCNT, R3HDM1, SLC9A9, TGFB2, and YTHDC2. These findings represent a further contribution to our understanding of the genetic basis of hearing function and its related diseases.
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11
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Schmitz J, Abbondanza F, Paracchini S. Genome-wide association study and polygenic risk score analysis for hearing measures in children. Am J Med Genet B Neuropsychiatr Genet 2021; 186:318-328. [PMID: 34476894 DOI: 10.1002/ajmg.b.32873] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 06/11/2021] [Accepted: 08/10/2021] [Indexed: 01/04/2023]
Abstract
An efficient auditory system contributes to cognitive and psychosocial development. A right ear advantage in hearing thresholds (HTs) has been described in adults and atypical patterns of left/right hearing threshold asymmetry (HTA) have been described for psychiatric and neurodevelopmental conditions. Previous genome-wide association studies (GWASs) on HT have mainly been conducted in elderly participants whose hearing is more likely to be affected by external environmental factors. Here, we investigated HT and HTA in a children population cohort (ALSPAC, n = 6,743). Better hearing was associated with better cognitive performance and higher socioeconomic status. At the group level, HTA suggested a left ear advantage (mean = -0.28 dB) that was mainly driven by females. SNP heritability for HT and HTA was 0.13 and 0.02, respectively (n = 4,989). We found a modest negative genetic correlation between HT and reading ability. GWAS for HT (n = 5,344) did not yield significant hits but polygenic risk scores for higher educational attainment (EA, ß = -1,564.72, p = .008) and schizophrenia (ß = -241.14, p = .004) were associated with lower HT, that is, better hearing. In summary, we report new data supporting associations between hearing measures and cognitive abilities at the behavioral level. Genetic analysis suggests shared biological pathways between cognitive and sensory systems and provides evidence for a positive outcome of genetic risk for schizophrenia.
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Affiliation(s)
- Judith Schmitz
- School of Medicine, University of St Andrews, St Andrews, UK
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12
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Ivarsdottir EV, Holm H, Benonisdottir S, Olafsdottir T, Sveinbjornsson G, Thorleifsson G, Eggertsson HP, Halldorsson GH, Hjorleifsson KE, Melsted P, Gylfason A, Arnadottir GA, Oddsson A, Jensson BO, Jonasdottir A, Jonasdottir A, Juliusdottir T, Stefansdottir L, Tragante V, Halldorsson BV, Petersen H, Thorgeirsson G, Thorsteinsdottir U, Sulem P, Hinriksdottir I, Jonsdottir I, Gudbjartsson DF, Stefansson K. The genetic architecture of age-related hearing impairment revealed by genome-wide association analysis. Commun Biol 2021; 4:706. [PMID: 34108613 PMCID: PMC8190123 DOI: 10.1038/s42003-021-02224-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 05/17/2021] [Indexed: 02/05/2023] Open
Abstract
Age-related hearing impairment (ARHI) is the most common sensory disorder in older adults. We conducted a genome-wide association meta-analysis of 121,934 ARHI cases and 591,699 controls from Iceland and the UK. We identified 21 novel sequence variants, of which 13 are rare, under either additive or recessive models. Of special interest are a missense variant in LOXHD1 (MAF = 1.96%) and a tandem duplication in FBF1 covering 4 exons (MAF = 0.22%) associating with ARHI (OR = 3.7 for homozygotes, P = 1.7 × 10-22 and OR = 4.2 for heterozygotes, P = 5.7 × 10-27, respectively). We constructed an ARHI genetic risk score (GRS) using common variants and showed that a common variant GRS can identify individuals at risk comparable to carriers of rare high penetrance variants. Furthermore, we found that ARHI and tinnitus share genetic causes. This study sheds a new light on the genetic architecture of ARHI, through several rare variants in both Mendelian deafness genes and genes not previously linked to hearing.
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Affiliation(s)
- Erna V Ivarsdottir
- deCODE Genetics/Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Hilma Holm
- deCODE Genetics/Amgen, Reykjavik, Iceland
| | | | | | | | | | | | - Gisli H Halldorsson
- deCODE Genetics/Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Kristjan E Hjorleifsson
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Pall Melsted
- deCODE Genetics/Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | | | | | | | | | - Bjarni V Halldorsson
- deCODE Genetics/Amgen, Reykjavik, Iceland
- School of Technology, Reykjavik University, Reykjavik, Iceland
| | - Hannes Petersen
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Akureyri Hospital, Akureyri, Iceland
| | - Gudmundur Thorgeirsson
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Division of Cardiology, Department of Internal Medicine, Landspitali University Hospital, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | - Ingileif Jonsdottir
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Department of Immunology, Landspitali University Hospital, Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Reykjavik, Iceland.
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland.
| | - Kari Stefansson
- deCODE Genetics/Amgen, Reykjavik, Iceland.
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
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13
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Ultrarare heterozygous pathogenic variants of genes causing dominant forms of early-onset deafness underlie severe presbycusis. Proc Natl Acad Sci U S A 2020; 117:31278-31289. [PMID: 33229591 DOI: 10.1073/pnas.2010782117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Presbycusis, or age-related hearing loss (ARHL), is a major public health issue. About half the phenotypic variance has been attributed to genetic factors. Here, we assessed the contribution to presbycusis of ultrarare pathogenic variants, considered indicative of Mendelian forms. We focused on severe presbycusis without environmental or comorbidity risk factors and studied multiplex family age-related hearing loss (mARHL) and simplex/sporadic age-related hearing loss (sARHL) cases and controls with normal hearing by whole-exome sequencing. Ultrarare variants (allele frequency [AF] < 0.0001) of 35 genes responsible for autosomal dominant early-onset forms of deafness, predicted to be pathogenic, were detected in 25.7% of mARHL and 22.7% of sARHL cases vs. 7.5% of controls (P = 0.001); half were previously unknown (AF < 0.000002). MYO6, MYO7A, PTPRQ, and TECTA variants were present in 8.9% of ARHL cases but less than 1% of controls. Evidence for a causal role of variants in presbycusis was provided by pathogenicity prediction programs, documented haploinsufficiency, three-dimensional structure/function analyses, cell biology experiments, and reported early effects. We also established Tmc1 N321I/+ mice, carrying the TMC1:p.(Asn327Ile) variant detected in an mARHL case, as a mouse model for a monogenic form of presbycusis. Deafness gene variants can thus result in a continuum of auditory phenotypes. Our findings demonstrate that the genetics of presbycusis is shaped by not only well-studied polygenic risk factors of small effect size revealed by common variants but also, ultrarare variants likely resulting in monogenic forms, thereby paving the way for treatment with emerging inner ear gene therapy.
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14
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Wonkam A, Manyisa N, Bope CD, Dandara C, Chimusa ER. Whole exome sequencing reveals pathogenic variants in MYO3A, MYO15A and COL9A3 and differential frequencies in ancestral alleles in hearing impairment genes among individuals from Cameroon. Hum Mol Genet 2020; 29:3729-3743. [PMID: 33078831 PMCID: PMC7861016 DOI: 10.1093/hmg/ddaa225] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 10/01/2020] [Accepted: 10/12/2020] [Indexed: 12/30/2022] Open
Abstract
There is scarcity of known gene variants of hearing impairment (HI) in African populations. This knowledge deficit is ultimately affecting the development of genetic diagnoses. We used whole exome sequencing to investigate gene variants, pathways of interactive genes and the fractions of ancestral overderived alleles for 159 HI genes among 18 Cameroonian patients with non-syndromic HI (NSHI) and 129 ethnically matched controls. Pathogenic and likely pathogenic (PLP) variants were found in MYO3A, MYO15A and COL9A3, with a resolution rate of 50% (9/18 patients). The study identified significant genetic differentiation in novel population-specific gene variants at FOXD4L2, DHRS2L6, RPL3L and VTN between HI patients and controls. These gene variants are found in functional/co-expressed interactive networks with other known HI-associated genes and in the same pathways with VTN being a hub protein, that is, focal adhesion pathway and regulation of the actin cytoskeleton (P-values <0.05). The results suggest that these novel population-specific gene variants are possible modifiers of the HI phenotypes. We found a high proportion of ancestral allele versus derived at low HI patients-specific minor allele frequency in the range of 0.0–0.1. The results showed a relatively low pickup rate of PLP variants in known genes in this group of Cameroonian patients with NSHI. In addition, findings may signal an evolutionary enrichment of some variants of HI genes in patients, as the result of polygenic adaptation, and suggest the possibility of multigenic influence on the phenotype of congenital HI, which deserves further investigations.
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Affiliation(s)
- Ambroise Wonkam
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa.,Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Noluthando Manyisa
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa
| | - Christian D Bope
- Department of Mathematics and Department of Computer Science, Faculty of Sciences, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Collet Dandara
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa
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15
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Kalra G, Milon B, Casella AM, Herb BR, Humphries E, Song Y, Rose KP, Hertzano R, Ament SA. Biological insights from multi-omic analysis of 31 genomic risk loci for adult hearing difficulty. PLoS Genet 2020; 16:e1009025. [PMID: 32986727 PMCID: PMC7544108 DOI: 10.1371/journal.pgen.1009025] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 10/08/2020] [Accepted: 08/04/2020] [Indexed: 12/13/2022] Open
Abstract
Age-related hearing impairment (ARHI), one of the most common medical conditions, is strongly heritable, yet its genetic causes remain largely unknown. We conducted a meta-analysis of GWAS summary statistics from multiple hearing-related traits in the UK Biobank (n = up to 330,759) and identified 31 genome-wide significant risk loci for self-reported hearing difficulty (p < 5x10-8), of which eight have not been reported previously in the peer-reviewed literature. We investigated the regulatory and cell specific expression for these loci by generating mRNA-seq, ATAC-seq, and single-cell RNA-seq from cells in the mouse cochlea. Risk-associated genes were most strongly enriched for expression in cochlear epithelial cells, as well as for genes related to sensory perception and known Mendelian deafness genes, supporting their relevance to auditory function. Regions of the human genome homologous to open chromatin in epithelial cells from the mouse were strongly enriched for heritable risk for hearing difficulty, even after adjusting for baseline effects of evolutionary conservation and cell-type non-specific regulatory regions. Epigenomic and statistical fine-mapping most strongly supported 50 putative risk genes. Of these, 39 were expressed robustly in mouse cochlea and 16 were enriched specifically in sensory hair cells. These results reveal new risk loci and risk genes for hearing difficulty and suggest an important role for altered gene regulation in the cochlear sensory epithelium.
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Affiliation(s)
- Gurmannat Kalra
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
- Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Beatrice Milon
- Department of Otorhinolaryngology-Head & Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Alex M. Casella
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
- Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD, United States of America
- Physician Scientist Training Program, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Brian R. Herb
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Elizabeth Humphries
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
- Program in Molecular Epidemiology, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Yang Song
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Kevin P. Rose
- Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, MD, United States of America
- Department of Otorhinolaryngology-Head & Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Ronna Hertzano
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
- Department of Otorhinolaryngology-Head & Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States of America
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, United States of America
| | - Seth A. Ament
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States of America
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, United States of America
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16
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Nolan LS. Age-related hearing loss: Why we need to think about sex as a biological variable. J Neurosci Res 2020; 98:1705-1720. [PMID: 32557661 DOI: 10.1002/jnr.24647] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 04/28/2020] [Accepted: 04/28/2020] [Indexed: 12/12/2022]
Abstract
It has long been known that age-related hearing loss (ARHL) is more common, more severe, and with an earlier onset in men compared to women. Even in the absence of confounding factors such as noise exposure, these sexdifferences in susceptibility to ARHL remain. In the last decade, insight into the pleiotrophic nature by which estrogen signaling can impact multiple signaling mechanisms to mediate downstream changes in gene expression and/or elicit rapid changes in cellular function has rapidly gathered pace, and a role for estrogen signaling in the biological pathways that confer neuroprotection is becoming undeniable. Here I review the evidence why we need to consider sex as a biological variable (SABV) when investigating the etiology of ARHL. Loss of auditory function with aging is frequency-specific and modulated by SABV. Evidence also suggests that differences in cochlear physiology between women and men are already present from birth. Understanding the molecular basis of these sex differences in ARHL will accelerate the development of precision medicine therapies for ARHL.
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Affiliation(s)
- Lisa S Nolan
- Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
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17
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Di Stazio M, Morgan A, Brumat M, Bassani S, Dell'Orco D, Marino V, Garagnani P, Giuliani C, Gasparini P, Girotto G. New age-related hearing loss candidate genes in humans: an ongoing challenge. Gene 2020; 742:144561. [PMID: 32173538 DOI: 10.1016/j.gene.2020.144561] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/08/2020] [Indexed: 01/18/2023]
Abstract
Age-related hearing loss (ARHL) is the most frequent sensory disorder in the elderly, affecting approximately one-third of people aged more than 65 years. Despite a large number of people affected, ARHL is still an area of unmet clinical needs, and only a few ARHL susceptibility genes have been detected so far. In order to further investigate the genetics of ARHL, we analyzed a series of 46 ARHL candidate genes, selected according to previous Genome Wide Association Studies (GWAS) data, literature updates and animal models, in a large cohort of 464 Italian ARHL patients. We have filtered the variants according to a) pathogenicity prediction, b) allele frequency in public databases, c) allele frequency in an internal cohort of 113 healthy matched controls, and 81 healthy semi-supercentenarians. After data analysis, all the variants of interest have been tested by functional "in silico" or "in vitro" experiments (i.e., molecular dynamics simulations and protein translation analysis) to assess their pathogenic role, and the expression of the mutated genes have been checked in mouse or zebrafish inner ear. This multi-step approach led to the characterization of a series of ultra-rare likely pathogenic variants in DCLK1, SLC28A3, CEP104, and PCDH20 genes, contributing to describe the first association of these genes with ARHL in humans. These results provide essential insights on the understanding of the molecular bases of such a complex, heterogeneous and frequent disorder, unveiling new possible targets for the future development of innovative therapeutic and preventive approaches that could improve the quality of life of the millions of people affected worldwide.
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Affiliation(s)
- M Di Stazio
- Institute for Maternal and Child Health - IRCCS, Burlo Garofolo, Trieste, Italy.
| | - A Morgan
- Institute for Maternal and Child Health - IRCCS, Burlo Garofolo, Trieste, Italy; Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - M Brumat
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - S Bassani
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - D Dell'Orco
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Verona, Italy
| | - V Marino
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biological Chemistry, University of Verona, Verona, Italy
| | - P Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Italy; Interdepartimental Centre L. Galvani (CIG), University of Bologna, Italy; Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden
| | - C Giuliani
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Italy; School of Anthropology and Museum Ethnography, University of Oxford, United Kingdom
| | - P Gasparini
- Institute for Maternal and Child Health - IRCCS, Burlo Garofolo, Trieste, Italy; Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - G Girotto
- Institute for Maternal and Child Health - IRCCS, Burlo Garofolo, Trieste, Italy; Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
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18
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Ingham NJ, Rook V, Di Domenico F, James E, Lewis MA, Girotto G, Buniello A, Steel KP. Functional analysis of candidate genes from genome-wide association studies of hearing. Hear Res 2020; 387:107879. [PMID: 31927188 PMCID: PMC6996162 DOI: 10.1016/j.heares.2019.107879] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/23/2019] [Accepted: 12/27/2019] [Indexed: 10/27/2022]
Abstract
The underlying causes of age-related hearing loss (ARHL) are not well understood, but it is clear from heritability estimates that genetics plays a role in addition to environmental factors. Genome-wide association studies (GWAS) in human populations can point to candidate genes that may be involved in ARHL, but follow-up analysis is needed to assess the role of these genes in the disease process. Some genetic variants may contribute a small amount to a disease, while other variants may have a large effect size, but the genetic architecture of ARHL is not yet well-defined. In this study, we asked if a set of 17 candidate genes highlighted by early GWAS reports of ARHL have detectable effects on hearing by knocking down expression levels of each gene in the mouse and analysing auditory function. We found two of the genes have an impact on hearing. Mutation of Dclk1 led to late-onset progressive increase in ABR thresholds and the A430005L14Rik (C1orf174) mutants showed worse recovery from noise-induced damage than controls. We did not detect any abnormal responses in the remaining 15 mutant lines either in thresholds or from our battery of suprathreshold ABR tests, and we discuss the possible reasons for this.
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Affiliation(s)
- Neil J Ingham
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, UK; Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.
| | - Victoria Rook
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, UK
| | | | - Elysia James
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, UK
| | - Morag A Lewis
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, UK; Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Giorgia Girotto
- Clinical Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy; Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Annalisa Buniello
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, UK; Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Karen P Steel
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, UK; Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
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19
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Hirose F, Takai S, Takahashi I, Shigemura N. Expression of protocadherin-20 in mouse taste buds. Sci Rep 2020; 10:2051. [PMID: 32029864 PMCID: PMC7005180 DOI: 10.1038/s41598-020-58991-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 01/23/2020] [Indexed: 11/25/2022] Open
Abstract
Taste information is detected by taste cells and then transmitted to the brain through the taste nerve fibers. According to our previous data, there may be specific coding of taste quality between taste cells and nerve fibers. However, the molecular mechanisms underlying this coding specificity remain unclear. The purpose of this study was to identify candidate molecules that may regulate the specific coding. GeneChip analysis of mRNA isolated from the mice taste papillae and taste ganglia revealed that 14 members of the cadherin superfamily, which are important regulators of synapse formation and plasticity, were expressed in both tissues. Among them, protocadherin-20 (Pcdh20) was highly expressed in a subset of taste bud cells, and co-expressed with taste receptor type 1 member 3 (T1R3, a marker of sweet- or umami-sensitive taste cells) but not gustducin or carbonic anhydrase-4 (markers of bitter/sweet- and sour-sensitive taste cells, respectively) in circumvallate papillae. Furthermore, Pcdh20 expression in taste cells occurred later than T1R3 expression during the morphogenesis of taste papillae. Thus, Pcdh20 may be involved in taste quality-specific connections between differentiated taste cells and their partner neurons, thereby acting as a molecular tag for the coding of sweet and/or umami taste.
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Affiliation(s)
- Fumie Hirose
- Section of Oral Neuroscience, Faculty of Dental Science, Kyushu University, Fukuoka, Japan.,Section of Orthodontics and Dentofacial Orthopedics, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Shingo Takai
- Section of Oral Neuroscience, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Ichiro Takahashi
- Section of Orthodontics and Dentofacial Orthopedics, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Noriatsu Shigemura
- Section of Oral Neuroscience, Faculty of Dental Science, Kyushu University, Fukuoka, Japan. .,Division of Sensory Physiology, Research and Development Center for Five-Sense Devices Taste and Odor Sensing, Kyushu University, Fukuoka, Japan.
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20
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Wells HRR, Newman TA, Williams FMK. Genetics of age-related hearing loss. J Neurosci Res 2020; 98:1698-1704. [PMID: 31989664 DOI: 10.1002/jnr.24549] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 12/13/2022]
Abstract
Age-related hearing loss (ARHL) has recently been confirmed as a common complex trait, that is, it is heritable with many genetic variants each contributing a small amount of risk, as well as environmental determinants. Historically, attempts to identify the genetic variants underlying the ARHL have been of limited success, relying on the selection of candidate genes based on the limited knowledge of the pathophysiology of the condition, and linkage studies in samples comprising related individuals. More recently genome-wide association studies have been performed, but these require very large samples having consistent and reliable phenotyping for hearing loss (HL), and early attempts suffered from lack of reliable replication of their findings. Replicated variants shown associated with ARHL include those lying in genes GRM7, ISG20, TRIOBP, ILDR1, and EYA4. The availability of large biobanks and the development of collaborative consortia have led to a breakthrough over the last couple of years, and many new genetic variants associated with ARHL are becoming available, through the analysis publicly available bioresources and electronic health records. These findings along with immunohistochemistry and mouse models of HL look set to help disentangle the genetic architecture of ARHL, and highlight the need for standardization of phenotyping methods to facilitate data sharing and collaboration across research networks.
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Affiliation(s)
| | - Tracey A Newman
- CES, Medicine, B85, M55, Life Sciences, University of Southampton, Southampton, UK
| | - Frances M K Williams
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
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21
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Wells HRR, Freidin MB, Zainul Abidin FN, Payton A, Dawes P, Munro KJ, Morton CC, Moore DR, Dawson SJ, Williams FMK. GWAS Identifies 44 Independent Associated Genomic Loci for Self-Reported Adult Hearing Difficulty in UK Biobank. Am J Hum Genet 2019; 105:788-802. [PMID: 31564434 PMCID: PMC6817556 DOI: 10.1016/j.ajhg.2019.09.008] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 09/04/2019] [Indexed: 01/13/2023] Open
Abstract
Age-related hearing impairment (ARHI) is the most common sensory impairment in the aging population; a third of individuals are affected by disabling hearing loss by the age of 65. It causes social isolation and depression and has recently been identified as a risk factor for dementia. The genetic risk factors and underlying pathology of ARHI are largely unknown, meaning that targets for new therapies remain elusive, yet heritability estimates range between 35% and 55%. We performed genome-wide association studies (GWASs) for two self-reported hearing phenotypes, using more than 250,000 UK Biobank (UKBB) volunteers aged between 40 and 69 years. Forty-four independent genome-wide significant loci (p < 5E-08) were identified, considerably increasing the number of established trait loci. Thirty-four loci are novel associations with hearing loss of any form, and only one of the ten known hearing loci has a previously reported association with an ARHI-related trait. Gene sets from these loci are enriched in auditory processes such as synaptic activities, nervous system processes, inner ear morphology, and cognition, while genetic correlation analysis revealed strong positive correlations with multiple personality and psychological traits for the first time. Immunohistochemistry for protein localization in adult mouse cochlea implicate metabolic, sensory, and neuronal functions for NID2, CLRN2, and ARHGEF28. These results provide insight into the genetic landscape underlying ARHI, opening up novel therapeutic targets for further investigation. In a wider context, our study also highlights the viability of using self-report phenotypes for genetic discovery in very large samples when deep phenotyping is unavailable.
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Affiliation(s)
- Helena R R Wells
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London SE1 7EH, UK; UCL Ear Institute, University College London, London WC1X 8EE, UK
| | - Maxim B Freidin
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London SE1 7EH, UK
| | - Fatin N Zainul Abidin
- UCL Ear Institute, University College London, London WC1X 8EE, UK; Centre for Medical Image Computing, Department of Medical Physics and Biomedical Engineering, University College London, London, WC1E 7JE, UK
| | - Antony Payton
- Division of Informatics, Imaging & Data Sciences, The University of Manchester, Manchester M13 9PT, UK
| | - Piers Dawes
- Manchester Centre for Audiology and Deafness, The University of Manchester, Manchester M13 9PL, UK
| | - Kevin J Munro
- Manchester Centre for Audiology and Deafness, The University of Manchester, Manchester M13 9PL, UK; Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
| | - Cynthia C Morton
- Manchester Centre for Audiology and Deafness, The University of Manchester, Manchester M13 9PL, UK; Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK; Departments of Obstetrics and Gynecology and of Pathology, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA 02115, USA
| | - David R Moore
- Manchester Centre for Audiology and Deafness, The University of Manchester, Manchester M13 9PL, UK; Cincinnati Children's Hospital Medical Centre, Department of Otolaryngology, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Sally J Dawson
- UCL Ear Institute, University College London, London WC1X 8EE, UK.
| | - Frances M K Williams
- Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, King's College London, London SE1 7EH, UK.
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22
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Abstract
The older Finnish Twin Cohort (FTC) was established in 1974. The baseline survey was in 1975, with two follow-up health surveys in 1981 and 1990. The fourth wave of assessments was done in three parts, with a questionnaire study of twins born during 1945-1957 in 2011-2012, while older twins were interviewed and screened for dementia in two time periods, between 1999 and 2007 for twins born before 1938 and between 2013 and 2017 for twins born in 1938-1944. The content of these wave 4 assessments is described and some initial results are described. In addition, we have invited twin-pairs, based on response to the cohortwide surveys, to participate in detailed in-person studies; these are described briefly together with key results. We also review other projects based on the older FTC and provide information on the biobanking of biosamples and related phenotypes.
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23
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Abstract
Age-related hearing loss (ARHL) is the most prevalent sensory deficit in the elderly. This progressive hearing impairment leads to social isolation and is also associated with comorbidities, such as frailty, falls, and late-onset depression. Moreover, there is a growing evidence linking it with cognitive decline and increased risk of dementia. Given the large social and welfare burden that results from ARHL, and because ARHL is potentially a modifiable risk factor for dementia, there is an urgent need for therapeutic interventions to ameliorate age-related auditory decline. However, a prerequisite for design of therapies is knowledge of the underlying molecular mechanisms. Currently, our understanding of ARHL is very limited. Here, we review recent findings from research into ARHL from both human and animal studies and discuss future prospects for advances in our understanding of genetic susceptibility, pathology, and potential therapeutic approaches in ARHL.
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Affiliation(s)
- Michael R Bowl
- Mammalian Genetics Unit, MRC Harwell Institute, Oxford OX11 0RD, United Kingdom
| | - Sally J Dawson
- UCL Ear Institute, University College London, London WC1X 8EE, United Kingdom
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24
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Ingham NJ, Pearson SA, Vancollie VE, Rook V, Lewis MA, Chen J, Buniello A, Martelletti E, Preite L, Lam CC, Weiss FD, Powis Z, Suwannarat P, Lelliott CJ, Dawson SJ, White JK, Steel KP. Mouse screen reveals multiple new genes underlying mouse and human hearing loss. PLoS Biol 2019; 17:e3000194. [PMID: 30973865 PMCID: PMC6459510 DOI: 10.1371/journal.pbio.3000194] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 03/07/2019] [Indexed: 11/23/2022] Open
Abstract
Adult-onset hearing loss is very common, but we know little about the underlying molecular pathogenesis impeding the development of therapies. We took a genetic approach to identify new molecules involved in hearing loss by screening a large cohort of newly generated mouse mutants using a sensitive electrophysiological test, the auditory brainstem response (ABR). We review here the findings from this screen. Thirty-eight unexpected genes associated with raised thresholds were detected from our unbiased sample of 1,211 genes tested, suggesting extreme genetic heterogeneity. A wide range of auditory pathophysiologies was found, and some mutant lines showed normal development followed by deterioration of responses, revealing new molecular pathways involved in progressive hearing loss. Several of the genes were associated with the range of hearing thresholds in the human population and one, SPNS2, was involved in childhood deafness. The new pathways required for maintenance of hearing discovered by this screen present new therapeutic opportunities. This study uses an electrophysiological screen of over a thousand new mutant mouse lines to identify 38 new genes underlying deafness, some associated with human hearing function, revealing a wide range of molecular and pathological mechanisms. Progressive hearing loss with age is extremely common in the population, leading to difficulties in understanding speech, increased social isolation, and associated depression. We know it has a significant heritability, but so far we know very little about the molecular pathways leading to hearing loss, hampering the development of treatments. Here, we describe a large-scale screen of 1,211 new targeted mouse mutant lines, resulting in the identification of 38 genes underlying hearing loss that were not previously suspected of involvement in hearing. Some of these genes reveal molecular pathways that may be useful targets for drug development. Our further analysis of the genes identified and the varied pathological mechanisms within the ear resulting from the mutations suggests that hearing loss is an extremely heterogeneous disorder and may have as many as 1,000 genes involved.
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Affiliation(s)
- Neil J. Ingham
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | | | | | - Victoria Rook
- Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Morag A. Lewis
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Jing Chen
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Annalisa Buniello
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Elisa Martelletti
- Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Lorenzo Preite
- Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Chi Chung Lam
- Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Felix D. Weiss
- Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
| | - Zӧe Powis
- Department of Emerging Genetics Medicine, Ambry Genetics, Aliso Viejo, California, United States of America
| | - Pim Suwannarat
- Mid-Atlantic Permanente Medical Group, Rockville, Maryland, United States of America
| | | | - Sally J. Dawson
- UCL Ear Institute, University College London, London, United Kingdom
| | | | - Karen P. Steel
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Wolfson Centre for Age-Related Diseases, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, United Kingdom
- * E-mail:
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25
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Girotto G, Morgan A, Krishnamoorthy N, Cocca M, Brumat M, Bassani S, La Bianca M, Di Stazio M, Gasparini P. Next Generation Sequencing and Animal Models Reveal SLC9A3R1 as a New Gene Involved in Human Age-Related Hearing Loss. Front Genet 2019; 10:142. [PMID: 30863428 PMCID: PMC6399162 DOI: 10.3389/fgene.2019.00142] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 02/11/2019] [Indexed: 01/29/2023] Open
Abstract
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 characterized by a severe to profound high-frequency hearing loss. The variant, predicted as damaging, was not present in healthy matched controls. Protein modeling 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 slc9a3r1 R180Q/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 slc9a3r1 R180Q/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.
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Affiliation(s)
- Giorgia Girotto
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy.,Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Anna Morgan
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy.,Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Navaneethakrishnan Krishnamoorthy
- Sidra Medical and Research Center, Doha, Qatar.,Heart Science Centre, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Massimiliano Cocca
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Marco Brumat
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy.,Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Sissy Bassani
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy.,Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Martina La Bianca
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Mariateresa Di Stazio
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy.,Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Paolo Gasparini
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy.,Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
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26
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Fetoni AR, Zorzi V, Paciello F, Ziraldo G, Peres C, Raspa M, Scavizzi F, Salvatore AM, Crispino G, Tognola G, Gentile G, Spampinato AG, Cuccaro D, Guarnaccia M, Morello G, Van Camp G, Fransen E, Brumat M, Girotto G, Paludetti G, Gasparini P, Cavallaro S, Mammano F. Cx26 partial loss causes accelerated presbycusis by redox imbalance and dysregulation of Nfr2 pathway. Redox Biol 2018; 19:301-317. [PMID: 30199819 PMCID: PMC6129666 DOI: 10.1016/j.redox.2018.08.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/26/2018] [Accepted: 08/05/2018] [Indexed: 11/29/2022] Open
Abstract
Mutations in GJB2, the gene that encodes connexin 26 (Cx26), are the most common cause of sensorineural hearing impairment. The truncating variant 35delG, which determines a complete loss of Cx26 protein function, is the prevalent GJB2 mutation in several populations. Here, we generated and analyzed Gjb2+/- mice as a model of heterozygous human carriers of 35delG. Compared to control mice, auditory brainstem responses (ABRs) and distortion product otoacoustic emissions (DPOAEs) worsened over time more rapidly in Gjb2+/- mice, indicating they were affected by accelerated age-related hearing loss (ARHL), or presbycusis. We linked causally the auditory phenotype of Gjb2+/- mice to apoptosis and oxidative damage in the cochlear duct, reduced release of glutathione from connexin hemichannels, decreased nutrient delivery to the sensory epithelium via cochlear gap junctions and deregulated expression of genes that are under transcriptional control of the nuclear factor erythroid 2-related factor 2 (Nrf2), a pivotal regulator of tolerance to redox stress. Moreover, a statistically significant genome-wide association with two genes (PRKCE and TGFB1) related to the Nrf2 pathway (p-value < 4 × 10-2) was detected in a very large cohort of 4091 individuals, originating from Europe, Caucasus and Central Asia, with hearing phenotype (including 1076 presbycusis patients and 1290 healthy matched controls). We conclude that (i) elements of the Nrf2 pathway are essential for hearing maintenance and (ii) their dysfunction may play an important role in the etiopathogenesis of human presbycusis.
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Affiliation(s)
- Anna Rita Fetoni
- CNR Institute of Cell Biology and Neurobiology, Monterotondo 00015, Italy; Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Rome, Italy; Institute of Otolaryngology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo F. Vito 1, 00168 Rome, Italy
| | - Veronica Zorzi
- CNR Institute of Cell Biology and Neurobiology, Monterotondo 00015, Italy; Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Rome, Italy
| | - Fabiola Paciello
- CNR Institute of Cell Biology and Neurobiology, Monterotondo 00015, Italy; Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Rome, Italy
| | - Gaia Ziraldo
- CNR Institute of Cell Biology and Neurobiology, Monterotondo 00015, Italy; Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Rome, Italy
| | - Chiara Peres
- CNR Institute of Cell Biology and Neurobiology, Monterotondo 00015, Italy
| | - Marcello Raspa
- CNR Institute of Cell Biology and Neurobiology, Monterotondo 00015, Italy
| | | | | | - Giulia Crispino
- CNR Institute of Cell Biology and Neurobiology, Monterotondo 00015, Italy
| | - Gabriella Tognola
- CNR Institute of Electronics, Computer and Telecommunication Engineering, 20133 Milano, Italy
| | - Giulia Gentile
- CNR Institute of Neurological Sciences, 95126 Catania, Italy
| | | | - Denis Cuccaro
- CNR Institute of Neurological Sciences, 95126 Catania, Italy
| | | | | | - Guy Van Camp
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, 2610 Antwerp, Belgium
| | - Erik Fransen
- Department of Biomedical Sciences, University of Antwerp, 2650 Antwerp, Belgium
| | - Marco Brumat
- Dept Med Surg & Hlth Sci, University of Trieste, Trieste, Italy; IRCCS Burlo Garofolo, Inst Maternal & Child Hlth, Trieste, Italy
| | - Giorgia Girotto
- Dept Med Surg & Hlth Sci, University of Trieste, Trieste, Italy; IRCCS Burlo Garofolo, Inst Maternal & Child Hlth, Trieste, Italy
| | - Gaetano Paludetti
- Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Rome, Italy; Institute of Otolaryngology, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo F. Vito 1, 00168 Rome, Italy
| | - Paolo Gasparini
- Dept Med Surg & Hlth Sci, University of Trieste, Trieste, Italy; IRCCS Burlo Garofolo, Inst Maternal & Child Hlth, Trieste, Italy.
| | | | - Fabio Mammano
- CNR Institute of Cell Biology and Neurobiology, Monterotondo 00015, Italy; University of Padova, Department of Physics and Astronomy "G. Galilei", Padova, Italy.
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27
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Lewis MA, Nolan LS, Cadge BA, Matthews LJ, Schulte BA, Dubno JR, Steel KP, Dawson SJ. Whole exome sequencing in adult-onset hearing loss reveals a high load of predicted pathogenic variants in known deafness-associated genes and identifies new candidate genes. BMC Med Genomics 2018; 11:77. [PMID: 30180840 PMCID: PMC6123954 DOI: 10.1186/s12920-018-0395-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/21/2018] [Indexed: 12/22/2022] Open
Abstract
Background Deafness is a highly heterogenous disorder with over 100 genes known to underlie human non-syndromic hearing impairment. However, many more remain undiscovered, particularly those involved in the most common form of deafness: adult-onset progressive hearing loss. Despite several genome-wide association studies of adult hearing status, it remains unclear whether the genetic architecture of this common sensory loss consists of multiple rare variants each with large effect size or many common susceptibility variants each with small to medium effects. As next generation sequencing is now being utilised in clinical diagnosis, our aim was to explore the viability of diagnosing the genetic cause of hearing loss using whole exome sequencing in individual subjects as in a clinical setting. Methods We performed exome sequencing of thirty patients selected for distinct phenotypic sub-types from well-characterised cohorts of 1479 people with adult-onset hearing loss. Results Every individual carried predicted pathogenic variants in at least ten deafness-associated genes; similar findings were obtained from an analysis of the 1000 Genomes Project data unselected for hearing status. We have identified putative causal variants in known deafness genes and several novel candidate genes, including NEDD4 and NEFH that were mutated in multiple individuals. Conclusions The high frequency of predicted-pathogenic variants detected in known deafness-associated genes was unexpected and has significant implications for current diagnostic sequencing in deafness. Our findings suggest that in a clinic setting, efforts should be made to a) confirm key sequence results by Sanger sequencing, b) assess segregations of variants and phenotypes within the family if at all possible, and c) use caution in applying current pathogenicity prediction algorithms for diagnostic purposes. We conclude that there may be a high number of pathogenic variants affecting hearing in the ageing population, including many in known deafness-associated genes. Our findings of frequent predicted-pathogenic variants in both our hearing-impaired sample and in the larger 1000 Genomes Project sample unselected for auditory function suggests that the reference population for interpreting variants for this very common disorder should be a population of people with good hearing for their age rather than an unselected population. Electronic supplementary material The online version of this article (10.1186/s12920-018-0395-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Morag A Lewis
- Wolfson Centre for Age-Related Diseases, King's College London, WC2R 2LS, London, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Lisa S Nolan
- UCL Ear Institute, University College London, WC1X 8EE, London, UK
| | - Barbara A Cadge
- UCL Ear Institute, University College London, WC1X 8EE, London, UK
| | - Lois J Matthews
- Medical University of South Carolina, Charleston, SC, 29425, USA
| | | | - Judy R Dubno
- Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Karen P Steel
- Wolfson Centre for Age-Related Diseases, King's College London, WC2R 2LS, London, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Sally J Dawson
- UCL Ear Institute, University College London, WC1X 8EE, London, UK.
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28
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Morgan A, Vuckovic D, Krishnamoorthy N, Rubinato E, Ambrosetti U, Castorina P, Franzè A, Vozzi D, La Bianca M, Cappellani S, Di Stazio M, Gasparini P, Girotto G. Next-generation sequencing identified SPATC1L as a possible candidate gene for both early-onset and age-related hearing loss. Eur J Hum Genet 2018; 27:70-79. [PMID: 30177775 PMCID: PMC6303261 DOI: 10.1038/s41431-018-0229-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 06/20/2018] [Accepted: 07/17/2018] [Indexed: 11/09/2022] Open
Abstract
Hereditary hearing loss (HHL) and age-related hearing loss (ARHL) are two major sensory diseases affecting millions of people worldwide. Despite many efforts, additional HHL-genes and ARHL genetic risk factors still need to be identified. To fill this gap a large genomic screening based on next-generation sequencing technologies was performed. Whole exome sequencing in a 3-generation Italian HHL family and targeted re-sequencing in 464 ARHL patients were performed. We detected three variants in SPATC1L: a nonsense allele in an HHL family and a frameshift insertion and a missense variation in two unrelated ARHL patients. In silico molecular modelling of all variants suggested a significant impact on the structural stability of the protein itself, likely leading to deleterious effects and resulting in truncated isoforms. After demonstrating Spatc1l expression in mice inner ear, in vitro functional experiments were performed confirming the results of the molecular modelling studies. Finally, a candidate-gene population-based statistical study in cohorts from Caucasus and Central Asia revealed a statistically significant association of SPATC1L with normal hearing function at low and medium hearing frequencies. Overall, the amount of different genetic data presented here (variants with early-onset and late-onset hearing loss in addition to genetic association with normal hearing function), together with relevant functional evidence, likely suggest a role of SPATC1L in hearing function and loss.
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Affiliation(s)
- Anna Morgan
- Department of Medical Sciences, University of Trieste, Trieste, Italy.
| | - Dragana Vuckovic
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Navaneethakrishnan Krishnamoorthy
- Sidra Medical and Research Center, Doha, Qatar.,Heart Science Centre, National Heart and Lung Institute, Imperial College London, London, UK
| | - Elisa Rubinato
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Umberto Ambrosetti
- UO Audiology, Fondazione IRCCS Ca Granda, Ospedale Maggiore Policlinico, Mangiagalli e Regina Elena, Milan, Italy.,Audiology Unit, Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Pierangela Castorina
- UO Audiology, Fondazione IRCCS Ca Granda, Ospedale Maggiore Policlinico, Mangiagalli e Regina Elena, Milan, Italy
| | - Annamaria Franzè
- Ceinge Biotecnologie Avanzate, Naples, Italy; Istituto di Audiologia, Dipartimento di Neuroscienze, Scienze Riproduttive e Odontostomatologiche, Università di Napoli "Federico II", Naples, Italy
| | - Diego Vozzi
- Medical Genetics, Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Martina La Bianca
- Medical Genetics, Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Stefania Cappellani
- Medical Genetics, Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | | | - Paolo Gasparini
- Department of Medical Sciences, University of Trieste, Trieste, Italy.,Medical Genetics, Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Giorgia Girotto
- Department of Medical Sciences, University of Trieste, Trieste, Italy.,Medical Genetics, Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
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