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Bhatt IS, Raygoza Garay JA, Bhagavan SG, Ingalls V, Dias R, Torkamani A. Polygenic Risk Score-Based Association Analysis Identifies Genetic Comorbidities Associated with Age-Related Hearing Difficulty in Two Independent Samples. J Assoc Res Otolaryngol 2024; 25:387-406. [PMID: 38782831 PMCID: PMC11349729 DOI: 10.1007/s10162-024-00947-0] [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: 01/16/2024] [Accepted: 04/18/2024] [Indexed: 05/25/2024] Open
Abstract
PURPOSE Age-related hearing loss is the most common form of permanent hearing loss that is associated with various health traits, including Alzheimer's disease, cognitive decline, and depression. The present study aims to identify genetic comorbidities of age-related hearing loss. Past genome-wide association studies identified multiple genomic loci involved in common adult-onset health traits. Polygenic risk scores (PRS) could summarize the polygenic inheritance and quantify the genetic susceptibility of complex traits independent of trait expression. The present study conducted a PRS-based association analysis of age-related hearing difficulty in the UK Biobank sample (N = 425,240), followed by a replication analysis using hearing thresholds (HTs) and distortion-product otoacoustic emissions (DPOAEs) in 242 young adults with self-reported normal hearing. We hypothesized that young adults with genetic comorbidities associated with age-related hearing difficulty would exhibit subclinical decline in HTs and DPOAEs in both ears. METHODS A total of 111,243 participants reported age-related hearing difficulty in the UK Biobank sample (> 40 years). The PRS models were derived from the polygenic risk score catalog to obtain 2627 PRS predictors across the health spectrum. HTs (0.25-16 kHz) and DPOAEs (1-16 kHz, L1/L2 = 65/55 dB SPL, F2/F1 = 1.22) were measured on 242 young adults. Saliva-derived DNA samples were subjected to low-pass whole genome sequencing, followed by genome-wide imputation and PRS calculation. The logistic regression analyses were performed to identify PRS predictors of age-related hearing difficulty in the UK Biobank cohort. The linear mixed model analyses were performed to identify PRS predictors of HTs and DPOAEs. RESULTS The PRS-based association analysis identified 977 PRS predictors across the health spectrum associated with age-related hearing difficulty. Hearing difficulty and hearing aid use PRS predictors revealed the strongest association with the age-related hearing difficulty phenotype. Youth with a higher genetic predisposition to hearing difficulty revealed a subclinical elevation in HTs and a decline in DPOAEs in both ears. PRS predictors associated with age-related hearing difficulty were enriched for mental health, lifestyle, metabolic, sleep, reproductive, digestive, respiratory, hematopoietic, and immune traits. Fifty PRS predictors belonging to various trait categories were replicated for HTs and DPOAEs in both ears. CONCLUSION The study identified genetic comorbidities associated with age-related hearing loss across the health spectrum. Youth with a high genetic predisposition to age-related hearing difficulty and other related complex traits could exhibit sub-clinical decline in HTs and DPOAEs decades before clinically meaningful age-related hearing loss is observed. We posit that effective communication of genetic risk, promoting a healthy lifestyle, and reducing exposure to environmental risk factors at younger ages could help prevent or delay the onset of age-related hearing difficulty at older ages.
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Affiliation(s)
- Ishan Sunilkumar Bhatt
- Department of Communication Sciences & Disorders, University of Iowa, 250 Hawkins Dr, Iowa City, IA, 52242, USA.
| | - Juan Antonio Raygoza Garay
- Department of Communication Sciences & Disorders, University of Iowa, 250 Hawkins Dr, Iowa City, IA, 52242, USA
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, 52242, USA
| | - Srividya Grama Bhagavan
- Department of Communication Sciences & Disorders, University of Iowa, 250 Hawkins Dr, Iowa City, IA, 52242, USA
| | - Valerie Ingalls
- Department of Communication Sciences & Disorders, University of Iowa, 250 Hawkins Dr, Iowa City, IA, 52242, USA
| | - Raquel Dias
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32608, USA
| | - Ali Torkamani
- Department of Integrative Structural and Computational Biology, Scripps Science Institute, La Jolla, CA, 92037, USA
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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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Zhang X, Wang S, Liu S, Du Z, Wu G, Liang Y, Huang Y, Shang X, Hu Y, Zhu Z, Sun W, Zhang X, Yu H. Epidemiologic association and shared genetic architecture between cataract and hearing difficulties among middle-aged and older adults. Hum Genomics 2024; 18:39. [PMID: 38632618 PMCID: PMC11022469 DOI: 10.1186/s40246-024-00601-z] [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: 08/06/2023] [Accepted: 03/20/2024] [Indexed: 04/19/2024] Open
Abstract
Age-related cataract and hearing difficulties are major sensory disorders that often co-exist in the global-wide elderly and have a tangible influence on the quality of life. However, the epidemiologic association between cataract and hearing difficulties remains unexplored, while little is known about whether the two share their genetic etiology. We first investigated the clinical association between cataract and hearing difficulties using the UK Biobank covering 502,543 individuals. Both unmatched analysis (adjusted for confounders) and a matched analysis (one control matched for each patient with cataract according to confounding factors) were undertaken and confirmed that cataract was associated with hearing difficulties (OR, 2.12; 95% CI, 1.98-2.27; OR, 2.03; 95% CI, 1.86-2.23, respectively). Furthermore, we explored and quantified the shared genetic architecture of these two complex sensory disorders at the common variant level using the bivariate causal mixture model (MiXeR) and conditional/conjunctional false discovery rate method based on the largest available genome-wide association studies of cataract (N = 585,243) and hearing difficulties (N = 323,978). Despite detecting only a negligible genetic correlation, we observe polygenic overlap between cataract and hearing difficulties and identify 6 shared loci with mixed directions of effects. Follow-up analysis of the shared loci implicates candidate genes QKI, STK17A, TYR, NSF, and TCF4 likely contribute to the pathophysiology of cataracts and hearing difficulties. In conclusion, this study demonstrates the presence of epidemiologic association between cataract and hearing difficulties and provides new insights into the shared genetic architecture of these two disorders at the common variant level.
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Affiliation(s)
- Xiayin Zhang
- Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Shan Wang
- Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Shunming Liu
- Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zijing Du
- Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Guanrong Wu
- Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yingying Liang
- Department of Ophthalmology, Guangzhou First people's Hospital, Guangzhou, China
| | - Yu Huang
- Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xianwen Shang
- Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yijun Hu
- Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zhuoting Zhu
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, VIC, East Melbourne, Australia
| | - Wei Sun
- Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China.
| | - Xueli Zhang
- Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China.
| | - Honghua Yu
- Department of Ophthalmology, Guangdong Eye Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangzhou, China.
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Fujikawa T, Ito T, Okada R, Sawada M, Mohri K, Tateishi Y, Takahashi R, Asakage T, Tsutsumi T. Combined genetic polymorphisms of the GSTT1 and NRF2 genes increase susceptibility to cisplatin-induced ototoxicity: A preliminary study. Hear Res 2024; 445:108995. [PMID: 38518393 DOI: 10.1016/j.heares.2024.108995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/01/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
OBJECTIVE The genotype-phenotype relationship in cisplatin-induced ototoxicity remains unclear. By assessing early shifts in distortion product otoacoustic emission (DPOAE) levels after initial cisplatin administration, we aimed to discriminate patients' susceptibility to cisplatin-induced ototoxicity and elucidate their genetic background. STUDY DESIGN A prospective cross-sectional study. SETTING Tertiary referral hospital in Japan. PATIENTS Twenty-six patients with head and neck cancer were undergoing chemoradiotherapy with three cycles of 100 mg/m2 cisplatin. INTERVENTIONS Repetitive pure-tone audiometry and DPOAE measurements, and blood sampling for DNA extraction were performed. Patients were grouped into early ototoxicity presence or absence based on whether DPOAE level shifts exceeded the corresponding reference limits of the 21-day test interval. MAIN OUTCOME MEASURES Hearing thresholds after each cisplatin cycle, severity of other adverse events, and polymorphisms in cisplatin-induced ototoxicity-associated genes were compared. RESULTS Early ototoxicity was present in 14 and absent in 12 patients. Ototoxicity presence on DPOAEs was associated with greater progression of hearing loss in frequencies ≥2 kHz throughout therapy and with higher ototoxicity grades compared with ototoxicity absence. Ototoxicity was further associated with grade ≥2 nausea. Ototoxicity presence was genetically associated with the GSTT1 null genotype and G-allele of NFE2L2 rs6721961, whereas ototoxicity absence was associated with the GSTM1 null genotype. Dose-dependent progression of hearing loss was the greatest in the combined genotype pattern of GSTT1 null and the T/G or G/G variants of rs6721961. CONCLUSION Early DPOAE changes reflected genetic vulnerability to cisplatin-induced ototoxicity. Hereditary insufficiency of the antioxidant defense system causes severe cisplatin-induced hearing loss and nausea.
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Affiliation(s)
- Taro Fujikawa
- Department of Otolaryngology, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo, Tokyo, 113-8510 Japan.
| | - Taku Ito
- Department of Otolaryngology, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo, Tokyo, 113-8510 Japan
| | - Ryuhei Okada
- Department of Head and Neck Surgery, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo, Tokyo, 113-8510 Japan
| | - Mitsutaka Sawada
- Department of Otolaryngology, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo, Tokyo, 113-8510 Japan
| | - Kaori Mohri
- Department of Otolaryngology, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo, Tokyo, 113-8510 Japan
| | - Yumiko Tateishi
- Department of Head and Neck Surgery, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo, Tokyo, 113-8510 Japan
| | - Ryosuke Takahashi
- Department of Head and Neck Surgery, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo, Tokyo, 113-8510 Japan
| | - Takahiro Asakage
- Department of Head and Neck Surgery, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo, Tokyo, 113-8510 Japan
| | - Takeshi Tsutsumi
- Department of Otolaryngology, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo, Tokyo, 113-8510 Japan
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Liu Y, Zeng X, Zhang H. An Emerging Approach of Age-Related Hearing Loss Research: Application of Integrated Multi-Omics Analysis. Adv Biol (Weinh) 2024; 8:e2300613. [PMID: 38279573 DOI: 10.1002/adbi.202300613] [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: 11/13/2023] [Revised: 01/03/2024] [Indexed: 01/28/2024]
Abstract
As one of the most common otologic diseases in the elderly, age-related hearing loss (ARHL) usually characterized by hearing loss and cognitive disorders, which have a significant impact on the elderly's physical and mental health and quality of life. However, as a typical disease of aging, it is unclear why aging causes widespread hearing impairment in the elderly. As molecular biological experiments have been conducted for research recently, ARHL is gradually established at various levels with the application and development of integrated multi-omics analysis in the studies of ARHL. Here, the recent progress in the application of multi-omics analysis in the molecular mechanisms of ARHL development and therapeutic regimens, including the combined analysis of different omics, such as transcriptome, proteome, and metabolome, to screen for risk sites, risk genes, and differences in lipid metabolism, etc., is outlined and the integrated histological data further promote the profound understanding of the disease process as well as physiological mechanisms of ARHL. The advantages and disadvantages of multi-omics analysis in disease research are also discussed and the authors speculate on the future prospects and applications of this part-to-whole approach, which may provide more comprehensive guidance for ARHL and aging disease prevention and treatment.
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Affiliation(s)
- Yue Liu
- Department of Otolaryngology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510000, China
- Department of Otolaryngology, Longgang E.N.T. Hospital and Shenzhen Key Laboratory of E.N.T, Institute of E.N.T., Shenzhen, 518172, China
- Department of Graduate and Scientific Research, Zunyi Medical University Zhuhai Campus, Zhuhai, 519041, China
| | - Xianhai Zeng
- Department of Otolaryngology, Longgang E.N.T. Hospital and Shenzhen Key Laboratory of E.N.T, Institute of E.N.T., Shenzhen, 518172, China
- Department of Graduate and Scientific Research, Zunyi Medical University Zhuhai Campus, Zhuhai, 519041, China
| | - Huasong Zhang
- Department of Otolaryngology, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510000, China
- Department of Otolaryngology, Longgang E.N.T. Hospital and Shenzhen Key Laboratory of E.N.T, Institute of E.N.T., Shenzhen, 518172, China
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Jung SH, Lee YC, Shivakumar M, Kim J, Yun JS, Park WY, Won HH, Kim D. Association between genetic risk and adherence to healthy lifestyle for developing age-related hearing loss. BMC Med 2024; 22:141. [PMID: 38532472 DOI: 10.1186/s12916-024-03364-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/18/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND Previous studies have shown that lifestyle/environmental factors could accelerate the development of age-related hearing loss (ARHL). However, there has not yet been a study investigating the joint association among genetics, lifestyle/environmental factors, and adherence to healthy lifestyle for risk of ARHL. We aimed to assess the association between ARHL genetic variants, lifestyle/environmental factors, and adherence to healthy lifestyle as pertains to risk of ARHL. METHODS This case-control study included 376,464 European individuals aged 40 to 69 years, enrolled between 2006 and 2010 in the UK Biobank (UKBB). As a replication set, we also included a total of 26,523 individuals considered of European ancestry and 9834 individuals considered of African-American ancestry through the Penn Medicine Biobank (PMBB). The polygenic risk score (PRS) for ARHL was derived from a sensorineural hearing loss genome-wide association study from the FinnGen Consortium and categorized as low, intermediate, high, and very high. We selected lifestyle/environmental factors that have been previously studied in association with hearing loss. A composite healthy lifestyle score was determined using seven selected lifestyle behaviors and one environmental factor. RESULTS Of the 376,464 participants, 87,066 (23.1%) cases belonged to the ARHL group, and 289,398 (76.9%) individuals comprised the control group in the UKBB. A very high PRS for ARHL had a 49% higher risk of ARHL than those with low PRS (adjusted OR, 1.49; 95% CI, 1.36-1.62; P < .001), which was replicated in the PMBB cohort. A very poor lifestyle was also associated with risk of ARHL (adjusted OR, 3.03; 95% CI, 2.75-3.35; P < .001). These risk factors showed joint effects with the risk of ARHL. Conversely, adherence to healthy lifestyle in relation to hearing mostly attenuated the risk of ARHL even in individuals with very high PRS (adjusted OR, 0.21; 95% CI, 0.09-0.52; P < .001). CONCLUSIONS Our findings of this study demonstrated a significant joint association between genetic and lifestyle factors regarding ARHL. In addition, our analysis suggested that lifestyle adherence in individuals with high genetic risk could reduce the risk of ARHL.
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Affiliation(s)
- Sang-Hyuk Jung
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Young Chan Lee
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, Kyung Hee University, Kyung Hee University Hospital at Gangdong, Seoul, Republic of Korea
| | - Manu Shivakumar
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jaeyoung Kim
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, Republic of Korea
| | - Jae-Seung Yun
- Division of Endocrinology and Metabolism, Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hong-Hee Won
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, Republic of Korea
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Dokyoon Kim
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, USA.
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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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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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Park J, Bird JE. The actin cytoskeleton in hair bundle development and hearing loss. Hear Res 2023; 436:108817. [PMID: 37300948 PMCID: PMC10408727 DOI: 10.1016/j.heares.2023.108817] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/18/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023]
Abstract
Inner ear hair cells assemble mechanosensitive hair bundles on their apical surface that transduce sounds and accelerations. Each hair bundle is comprised of ∼ 100 individual stereocilia that are arranged into rows of increasing height and width; their specific and precise architecture being necessary for mechanoelectrical transduction (MET). The actin cytoskeleton is fundamental to establishing this architecture, not only by forming the structural scaffold shaping each stereocilium, but also by composing rootlets and the cuticular plate that together provide a stable foundation supporting each stereocilium. In concert with the actin cytoskeleton, a large assortment of actin-binding proteins (ABPs) function to cross-link actin filaments into specific topologies, as well as control actin filament growth, severing, and capping. These processes are individually critical for sensory transduction and are all disrupted in hereditary forms of human hearing loss. In this review, we provide an overview of actin-based structures in the hair bundle and the molecules contributing to their assembly and functional properties. We also highlight recent advances in mechanisms driving stereocilia elongation and how these processes are tuned by MET.
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Affiliation(s)
- Jinho Park
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610, United States; Myology Institute, University of Florida, Gainesville, FL 32610, United States
| | - Jonathan E Bird
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610, United States; Myology Institute, University of Florida, Gainesville, FL 32610, United States.
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10
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De Angelis F, Zeleznik OA, Wendt FR, Pathak GA, Tylee DS, De Lillo A, Koller D, Cabrera-Mendoza B, Clifford RE, Maihofer AX, Nievergelt CM, Curhan GC, Curhan SG, Polimanti R. Sex differences in the polygenic architecture of hearing problems in adults. Genome Med 2023; 15:36. [PMID: 37165447 PMCID: PMC10173489 DOI: 10.1186/s13073-023-01186-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/28/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Hearing problems (HP) in adults are common and are associated with several comorbid conditions. Its prevalence increases with age, reflecting the cumulative effect of environmental factors and genetic predisposition. Although several risk loci have been already identified, HP biology and epidemiology are still insufficiently investigated by large-scale genetic studies. METHODS Leveraging the UK Biobank, the Nurses' Health Studies (I and II), the Health Professionals Follow-up Study, and the Million Veteran Program, we conducted a comprehensive genome-wide investigation of HP in 748,668 adult participants (discovery N = 501,825; replication N = 226,043; cross-ancestry replication N = 20,800). We leveraged the GWAS findings to characterize HP polygenic architecture, exploring sex differences, polygenic risk across ancestries, tissue-specific transcriptomic regulation, cause-effect relationships with genetically correlated traits, and gene interactions with HP environmental risk factors. RESULTS We identified 54 risk loci and demonstrated that HP polygenic risk is shared across ancestry groups. Our transcriptomic regulation analysis highlighted the potential role of the central nervous system in HP pathogenesis. The sex-stratified analyses showed several additional associations related to peripheral hormonally regulated tissues reflecting a potential role of estrogen in hearing function. This evidence was supported by the multivariate interaction analysis that showed how genes involved in brain development interact with sex, noise pollution, and tobacco smoking in relation to their HP associations. Additionally, the genetically informed causal inference analysis showed that HP is linked to many physical and mental health outcomes. CONCLUSIONS The results provide many novel insights into the biology and epidemiology of HP in adults. Our sex-specific analyses and transcriptomic associations highlighted molecular pathways that may be targeted for drug development or repurposing. Additionally, the potential causal relationships identified may support novel preventive screening programs to identify individuals at risk.
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Affiliation(s)
- Flavio De Angelis
- Department of Psychiatry, Yale University School of Medicine, 60 Temple, Suite 7A, New Haven, CT, USA
- Veteran Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Oana A Zeleznik
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Frank R Wendt
- Department of Psychiatry, Yale University School of Medicine, 60 Temple, Suite 7A, New Haven, CT, USA
- Veteran Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Gita A Pathak
- Department of Psychiatry, Yale University School of Medicine, 60 Temple, Suite 7A, New Haven, CT, USA
- Veteran Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Daniel S Tylee
- Department of Psychiatry, Yale University School of Medicine, 60 Temple, Suite 7A, New Haven, CT, USA
- Veteran Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Antonella De Lillo
- Department of Psychiatry, Yale University School of Medicine, 60 Temple, Suite 7A, New Haven, CT, USA
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Dora Koller
- Department of Psychiatry, Yale University School of Medicine, 60 Temple, Suite 7A, New Haven, CT, USA
- Veteran Affairs Connecticut Healthcare System, West Haven, CT, USA
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Brenda Cabrera-Mendoza
- Department of Psychiatry, Yale University School of Medicine, 60 Temple, Suite 7A, New Haven, CT, USA
- Veteran Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Royce E Clifford
- Division of Otolaryngology, Department of Surgery, University of California, San Diego, La Jolla, CA, USA
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Adam X Maihofer
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Center of Excellence for Stress and Mental Health, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Caroline M Nievergelt
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Center of Excellence for Stress and Mental Health, Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Gary C Curhan
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sharon G Curhan
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Renato Polimanti
- Department of Psychiatry, Yale University School of Medicine, 60 Temple, Suite 7A, New Haven, CT, USA.
- Veteran Affairs Connecticut Healthcare System, West Haven, CT, USA.
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11
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Zhang D, Sun Y, Lei M, Wang Y, Cai C. Deciphering the potential ability of RG108 in cisplatin-induced HEI-OC1 ototoxicity: a research based on RNA-seq and molecular biology experiment. Hereditas 2023; 160:18. [PMID: 37088824 PMCID: PMC10124021 DOI: 10.1186/s41065-023-00283-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/11/2023] [Indexed: 04/25/2023] Open
Abstract
BACKGROUND Drug-induced hearing loss (DIHL) is very common, and seriously affects people's happiness in life. RG108 is a small molecule inhibitor. RG108 is protective against DIHL. Our purpose is to probe the incidence of RG108 on cisplatin-induced ototoxicity. MATERIALS AND METHODS In our research, the ototoxicity of RG108 was investigated in HEI-OC1. We observed under the microscope whether RG108 had an effect on cisplatin-induced cochlear hair cells. RNA-seq experiments were further performed to explore possible gene ontology (GO) and pathways. ROS assay was applied to supervisory the effect of RG108 on oxidative harm of auditory cells. In auditory cells, RG108 was tested for its effects on apoptosis-related proteins by Western blotting (WB). RESULTS GO analysis showed that RG108 associated with apoptosis. KEGG analysis shows RG108 may act on PI3K-AKT signaling pathway (PASP) in hearing loss. BIOCARTA analysis showed that RG108 may affect oxidative stress by activating NRF2 pathway. ROS ascerted that RG108 could rescue oxidative harm in HEI-OC1. RG108 rescued cisplatin-induced significant increase in Bax and significant decrease in BCL2. RG108 attenuates cisplatin-induced cochlear apoptosis through upregulated phosphorylated PI3K and phosphorylated AKT and down-regulated caspase3. MTT experiments showed that both PI3K and AKT inhibitors could significantly rescue the damage caused by cisplatin to HEI-OC1. RG108 significantly increases the level of NRF2/HO-1/NQO1 in cisplatin-induced cells. CONCLUSION Overall, these results provide evidence that NRF2/PI3K-AKT axis may mediate RG108 in the treatment of DIHL, which provide a broader outlook on drug-induced deafness treatment.
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Affiliation(s)
- Dongdong Zhang
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, Zhongshan Hospital, Xiamen University, Xiamen, 361003, China
- School of Medicine, Xiamen University, Xiamen, 361003, China
| | - Yixin Sun
- School of Medicine, Xiamen University, Xiamen, 361003, China
- Department of Surgery, The Second People's Hospital of Neijiang Affiliated to Southwest Medical University, Neijiang, 641000, China
- Department of Surgery, The Second People's Hospital of Neijiang, Neijiang, 641000, China
| | - Min Lei
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, Zhongshan Hospital, Xiamen University, Xiamen, 361003, China
- School of Medicine, Xiamen University, Xiamen, 361003, China
| | - Yue Wang
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, Zhongshan Hospital, Xiamen University, Xiamen, 361003, China
| | - Chengfu Cai
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, Zhongshan Hospital, Xiamen University, Xiamen, 361003, China.
- School of Medicine, Xiamen University, Xiamen, 361003, China.
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12
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He YQ, Luo LT, Wang TM, Xue WQ, Yang DW, Li DH, Diao H, Xiao RW, Deng CM, Zhang WL, Liao Y, Wu YX, Wang QL, Zhou T, Li XZ, Zheng XH, Zhang PF, Zhang SD, Hu YZ, Sun Y, Jia WH. Clinical and genome-wide association analysis of chemoradiation-induced hearing loss in nasopharyngeal carcinoma. Hum Genet 2023; 142:759-772. [PMID: 37062025 PMCID: PMC10182145 DOI: 10.1007/s00439-023-02554-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 04/07/2023] [Indexed: 04/17/2023]
Abstract
Chemoradiation-induced hearing loss (CRIHL) is one of the most devasting side effects for nasopharyngeal carcinoma (NPC) patients, which seriously affects survivors' long-term quality of life. However, few studies have comprehensively characterized the risk factors for CRIHL. In this study, we found that age at diagnosis, tumor stage, and concurrent cisplatin dose were positively associated with chemoradiation-induced hearing loss. We performed a genome-wide association study (GWAS) in 777 NPC patients and identified rs1050851 (within the exon 2 of NFKBIA), a variant with a high deleteriousness score, to be significantly associated with hearing loss risk (HR = 5.46, 95% CI 2.93-10.18, P = 9.51 × 10-08). The risk genotype of rs1050851 was associated with higher NFKBIA expression, which was correlated with lower cellular tolerance to cisplatin. According to permutation-based enrichment analysis, the variants mapping to 149 hereditary deafness genes were significantly enriched among GWAS top signals, which indicated the genetic similarity between hereditary deafness and CRIHL. Pathway analysis suggested that synaptic signaling was involved in the development of CRIHL. Additionally, the risk score integrating genetic and clinical factors can predict the risk of hearing loss with a relatively good performance in the test set. Collectively, this study shed new light on the etiology of chemoradiation-induced hearing loss, which facilitates high-risk individuals' identification for personalized prevention and treatment.
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Affiliation(s)
- Yong-Qiao He
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
| | - Lu-Ting Luo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
- School of Public Health, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Tong-Min Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
| | - Wen-Qiong Xue
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
| | - Da-Wei Yang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
- School of Public Health, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Dan-Hua Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
| | - Hua Diao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
- School of Public Health, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Ruo-Wen Xiao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
| | - Chang-Mi Deng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
| | - Wen-Li Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
| | - Ying Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
| | - Yan-Xia Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
| | - Qiao-Ling Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
- School of Public Health, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Ting Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
- Biobank of Sun Yat‑sen University Cancer Center, Guangzhou, People's Republic of China
| | - Xi-Zhao Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
- Biobank of Sun Yat‑sen University Cancer Center, Guangzhou, People's Republic of China
| | - Xiao-Hui Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
- Biobank of Sun Yat‑sen University Cancer Center, Guangzhou, People's Republic of China
| | - Pei-Fen Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
- Biobank of Sun Yat‑sen University Cancer Center, Guangzhou, People's Republic of China
| | - Shao-Dan Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
- Biobank of Sun Yat‑sen University Cancer Center, Guangzhou, People's Republic of China
| | - Ye-Zhu Hu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China
- Biobank of Sun Yat‑sen University Cancer Center, Guangzhou, People's Republic of China
| | - Ying Sun
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, People's Republic of China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, 510060, People's Republic of China.
- School of Public Health, Sun Yat-sen University, Guangzhou, People's Republic of China.
- Biobank of Sun Yat‑sen University Cancer Center, Guangzhou, People's Republic of China.
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13
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Sun G, Zheng Y, Fu X, Zhang W, Ren J, Ma S, Sun S, He X, Wang Q, Ji Z, Cheng F, Yan K, Liu Z, Belmonte JCI, Qu J, Wang S, Chai R, Liu GH. Single-cell transcriptomic atlas of mouse cochlear aging. Protein Cell 2023; 14:180-201. [PMID: 36933008 PMCID: PMC10098046 DOI: 10.1093/procel/pwac058] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 09/16/2022] [Indexed: 11/13/2022] Open
Abstract
Progressive functional deterioration in the cochlea is associated with age-related hearing loss (ARHL). However, the cellular and molecular basis underlying cochlear aging remains largely unknown. Here, we established a dynamic single-cell transcriptomic landscape of mouse cochlear aging, in which we characterized aging-associated transcriptomic changes in 27 different cochlear cell types across five different time points. Overall, our analysis pinpoints loss of proteostasis and elevated apoptosis as the hallmark features of cochlear aging, highlights unexpected age-related transcriptional fluctuations in intermediate cells localized in the stria vascularis (SV) and demonstrates that upregulation of endoplasmic reticulum (ER) chaperon protein HSP90AA1 mitigates ER stress-induced damages associated with aging. Our work suggests that targeting unfolded protein response pathways may help alleviate aging-related SV atrophy and hence delay the progression of ARHL.
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Affiliation(s)
- Guoqiang Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yandong Zheng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolong Fu
- State Key Laboratory of Bioelectronics, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, School of Life Sciences and Technology, Southeast University, Nanjing 211189, China
| | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Jie Ren
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Shuai Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- The Fifth People’s Hospital of Chongqing, Chongqing 400062, China
| | - Shuhui Sun
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Xiaojuan He
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
| | - Qiaoran Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Zhejun Ji
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Fang Cheng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kaowen Yan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Ziyi Liu
- Shandong Provincial Hospital and School of Laboratory Animal Science, Shandong First Medical University, Jinan 250000, China
| | | | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
- The Fifth People’s Hospital of Chongqing, Chongqing 400062, China
| | - Renjie Chai
- State Key Laboratory of Bioelectronics, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, School of Life Sciences and Technology, Southeast University, Nanjing 211189, China
- Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China
- Co-Innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Advanced Innovation Center for Human Brain Protection, National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, CAS, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
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14
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Palmer DS, Zhou W, Abbott L, Wigdor EM, Baya N, Churchhouse C, Seed C, Poterba T, King D, Kanai M, Bloemendal A, Neale BM. Analysis of genetic dominance in the UK Biobank. Science 2023; 379:1341-1348. [PMID: 36996212 PMCID: PMC10345642 DOI: 10.1126/science.abn8455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/15/2023] [Indexed: 04/01/2023]
Abstract
Classical statistical genetics theory defines dominance as any deviation from a purely additive, or dosage, effect of a genotype on a trait, which is known as the dominance deviation. Dominance is well documented in plant and animal breeding. Outside of rare monogenic traits, however, evidence in humans is limited. We systematically examined common genetic variation across 1060 traits in a large population cohort (UK Biobank, N = 361,194 samples analyzed) for evidence of dominance effects. We then developed a computationally efficient method to rapidly assess the aggregate contribution of dominance deviations to heritability. Lastly, observing that dominance associations are inherently less correlated between sites at a genomic locus than their additive counterparts, we explored whether they may be leveraged to identify causal variants more confidently.
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Affiliation(s)
- Duncan S. Palmer
- Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Wei Zhou
- Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Liam Abbott
- Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Nikolas Baya
- Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Claire Churchhouse
- Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Cotton Seed
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tim Poterba
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel King
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Masahiro Kanai
- Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alex Bloemendal
- Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Benjamin M. Neale
- Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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15
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Imputation of SNPs associated with presbycusis through linkage disequilibrium analysis in the ILDR1 gene. J Genet 2023. [DOI: 10.1007/s12041-022-01416-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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16
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Hui D, Mehrabi S, Quimby AE, Chen T, Chen S, Park J, Li B, Ruckenstein MJ, Rader DJ, Ritchie MD, Brant JA, Epstein DJ, Mathieson I. Gene burden analysis identifies genes associated with increased risk and severity of adult-onset hearing loss in a diverse hospital-based cohort. PLoS Genet 2023; 19:e1010584. [PMID: 36656851 PMCID: PMC9888707 DOI: 10.1371/journal.pgen.1010584] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 01/31/2023] [Accepted: 12/20/2022] [Indexed: 01/20/2023] Open
Abstract
Loss or absence of hearing is common at both extremes of human lifespan, in the forms of congenital deafness and age-related hearing loss. While these are often studied separately, there is increasing evidence that their genetic basis is at least partially overlapping. In particular, both common and rare variants in genes associated with monogenic forms of hearing loss also contribute to the more polygenic basis of age-related hearing loss. Here, we directly test this model in the Penn Medicine BioBank-a healthcare system cohort of around 40,000 individuals with linked genetic and electronic health record data. We show that increased burden of predicted deleterious variants in Mendelian hearing loss genes is associated with increased risk and severity of adult-onset hearing loss. As a specific example, we identify one gene-TCOF1, responsible for a syndromic form of congenital hearing loss-in which deleterious variants are also associated with adult-onset hearing loss. We also identify four additional novel candidate genes (COL5A1, HMMR, RAPGEF3, and NNT) in which rare variant burden may be associated with hearing loss. Our results confirm that rare variants in Mendelian hearing loss genes contribute to polygenic risk of hearing loss, and emphasize the utility of healthcare system cohorts to study common complex traits and diseases.
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Affiliation(s)
- Daniel Hui
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Shadi Mehrabi
- Department of Otolaryngology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Alexandra E. Quimby
- Department of Otolaryngology–Head and Neck Surgery, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Tingfang Chen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sixing Chen
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Joseph Park
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Binglan Li
- Department of Biomedical Data Science, Stanford University, Stanford, California, United States of America
| | | | - Penn Medicine Biobank
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Michael J. Ruckenstein
- Department of Otolaryngology–Head and Neck Surgery, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Daniel J. Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Marylyn D. Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jason A. Brant
- Department of Otolaryngology–Head and Neck Surgery, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Otolaryngology–Head and Neck Surgery, Corporal Michael J. Crescenz VAMC, Philadelphia, Pennsylvania, United States of America
| | - Douglas J. Epstein
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (DJE); (IM)
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (DJE); (IM)
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17
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Naderi E, Cornejo-Sanchez DM, Li G, Schrauwen I, Wang GT, Dewan AT, Leal SM. The genetic contribution of the X chromosome in age-related hearing loss. Front Genet 2023; 14:1106328. [PMID: 36896235 PMCID: PMC9988903 DOI: 10.3389/fgene.2023.1106328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/09/2023] [Indexed: 02/23/2023] Open
Abstract
Age-related (AR) hearing loss (HL) is the most common sensory impairment with heritability of 55%. The aim of this study was to identify genetic variants on chromosome X associated with ARHL through the analysis of data obtained from the UK Biobank. We performed association analysis between self-reported measures of HL and genotyped and imputed variants on chromosome X from ∼460,000 white Europeans. We identified three loci associated with ARHL with a genome-wide significance level (p < 5 × 10-8), ZNF185 (rs186256023, p = 4.9 × 10-10) and MAP7D2 (rs4370706, p = 2.3 × 10-8) in combined analysis of males and females, and LOC101928437 (rs138497700, p = 8.9 × 10-9) in the sex-stratified analysis of males. In-silico mRNA expression analysis showed MAP7D2 and ZNF185 are expressed in mice and adult human inner ear tissues, particularly in the inner hair cells. We estimated that only a small amount of variation of ARHL, 0.4%, is explained by variants on the X chromosome. This study suggests that although there are likely a few genes contributing to ARHL on the X chromosome, the role that the X chromosome plays in the etiology of ARHL may be limited.
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Affiliation(s)
- Elnaz Naderi
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, United States
| | - Diana M Cornejo-Sanchez
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, United States
| | - Guangyou Li
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, United States
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, United States
| | - Gao T Wang
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, United States
| | - Andrew T Dewan
- Department of Chronic Disease Epidemiology and Center for Perinatal, Pediatric and Environmental Epidemiology, Yale School of Public Health, New Haven, CT, United States
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, and the Department of Neurology, Columbia University Medical Center, New York, NY, United States.,Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, United States
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18
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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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19
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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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20
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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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21
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Unbalanced bidirectional radial stiffness gradients within the organ of Corti promoted by TRIOBP. Proc Natl Acad Sci U S A 2022; 119:e2115190119. [PMID: 35737845 PMCID: PMC9245700 DOI: 10.1073/pnas.2115190119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Current understanding of cochlear mechanics assumes that stiffness of the cochlear partition varies only longitudinally along the cochlea. This work examines the stiffness of inner ear epithelium in individual cell types at the nanoscale level. We revealed unrecognized radial stiffness gradients of different magnitudes and opposite orientations within the epithelium. Remarkably, the observed bidirectional stiffness gradients are unbalanced between supporting and sensory cells. Deficiencies in deafness-associated Trio and F-actin binding protein (TRIOBP) caused diverse cytoskeletal ultrastructural remodeling in supporting and sensory cells and significantly diminishes the bidirectional radial stiffness gradients. These results demonstrate the complexity of the mechanical properties within the sensory epithelium and point to a hitherto unrecognized role of these gradients in sensitivity and frequency selectivity of hearing. Hearing depends on intricate morphologies and mechanical properties of diverse inner ear cell types. The individual contributions of various inner ear cell types into mechanical properties of the organ of Corti and the mechanisms of their integration are yet largely unknown. Using sub-100-nm spatial resolution atomic force microscopy (AFM), we mapped the Young’s modulus (stiffness) of the apical surface of the different cells of the freshly dissected P5–P6 cochlear epithelium from wild-type and mice lacking either Trio and F-actin binding protein (TRIOBP) isoforms 4 and 5 or isoform 5 only. Variants of TRIOBP are associated with deafness in human and in Triobp mutant mouse models. Remarkably, nanoscale AFM mapping revealed unrecognized bidirectional radial stiffness gradients of different magnitudes and opposite orientations between rows of wild-type supporting cells and sensory hair cells. Moreover, the observed bidirectional radial stiffness gradients are unbalanced, with sensory cells being stiffer overall compared to neighboring supporting cells. Deafness-associated TRIOBP deficiencies significantly disrupted the magnitude and orientation of these bidirectional radial stiffness gradients. In addition, serial sectioning with focused ion beam and backscatter scanning electron microscopy shows that a TRIOBP deficiency results in ultrastructural changes of supporting cell apical phalangeal microfilaments and bundled cortical F-actin of hair cell cuticular plates, correlating with messenger RNA and protein expression levels and AFM stiffness measurements that exposed a softening of the apical surface of the sensory epithelium in mutant mice. Altogether, this additional complexity in the mechanical properties of the sensory epithelium is hypothesized to be an essential contributor to frequency selectivity and sensitivity of mammalian hearing.
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22
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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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23
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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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24
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Lewis MA, Ingham NJ, Chen J, Pearson S, Di Domenico F, Rekhi S, Allen R, Drake M, Willaert A, Rook V, Pass J, Keane T, Adams DJ, Tucker AS, White JK, Steel KP. Identification and characterisation of spontaneous mutations causing deafness from a targeted knockout programme. BMC Biol 2022; 20:67. [PMID: 35296311 PMCID: PMC8928630 DOI: 10.1186/s12915-022-01257-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 02/17/2022] [Indexed: 11/30/2022] Open
Abstract
Background Mice carrying targeted mutations are important for investigating gene function and the role of genes in disease, but off-target mutagenic effects associated with the processes of generating targeted alleles, for instance using Crispr, and culturing embryonic stem cells, offer opportunities for spontaneous mutations to arise. Identifying spontaneous mutations relies on the detection of phenotypes segregating independently of targeted alleles, and having a broad estimate of the level of mutations generated by intensive breeding programmes is difficult given that many phenotypes are easy to miss if not specifically looked for. Here we present data from a large, targeted knockout programme in which mice were analysed through a phenotyping pipeline. Such spontaneous mutations segregating within mutant lines may confound phenotypic analyses, highlighting the importance of record-keeping and maintaining correct pedigrees. Results Twenty-five lines out of 1311 displayed different deafness phenotypes that did not segregate with the targeted allele. We observed a variety of phenotypes by Auditory Brainstem Response (ABR) and behavioural assessment and isolated eight lines showing early-onset severe progressive hearing loss, later-onset progressive hearing loss, low frequency hearing loss, or complete deafness, with vestibular dysfunction. The causative mutations identified include deletions, insertions, and point mutations, some of which involve new genes not previously associated with deafness while others are new alleles of genes known to underlie hearing loss. Two of the latter show a phenotype much reduced in severity compared to other mutant alleles of the same gene. We investigated the ES cells from which these lines were derived and determined that only one of the 8 mutations could have arisen in the ES cell, and in that case, only after targeting. Instead, most of the non-segregating mutations appear to have occurred during breeding of mutant mice. In one case, the mutation arose within the wildtype colony used for expanding mutant lines. Conclusions Our data show that spontaneous mutations with observable effects on phenotype are a common side effect of intensive breeding programmes, including those underlying targeted mutation programmes. Such spontaneous mutations segregating within mutant lines may confound phenotypic analyses, highlighting the importance of record-keeping and maintaining correct pedigrees. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01257-8.
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Affiliation(s)
- Morag A Lewis
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England. .,Wellcome Sanger Institute, Hinxton, CB10 1SA, England.
| | - Neil J Ingham
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England.,Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | - Jing Chen
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England.,Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | | | - Francesca Di Domenico
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Sohinder Rekhi
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Rochelle Allen
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Matthew Drake
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Annelore Willaert
- Research Group of Experimental Oto-Rhino-Laryngology, Department of Neurosciences, KU Leuven - University of Leuven, Leuven, Belgium
| | - Victoria Rook
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Johanna Pass
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England.,Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | - Thomas Keane
- Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | - David J Adams
- Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | - Abigail S Tucker
- Centre for Craniofacial and Regenerative Biology, King's College London, London, SE1 9RT, England
| | | | - Karen P Steel
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England.,Wellcome Sanger Institute, Hinxton, CB10 1SA, England
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25
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Fu Y, Chen W, Guo L, Liu Y. The Inverted-U Relationship Between Dietary Inflammatory Potential and Hearing Loss Among Adults Aged 20 Years and Over in the United States: A Cross-Sectional Study. J Inflamm Res 2021; 14:6671-6683. [PMID: 34916819 PMCID: PMC8669755 DOI: 10.2147/jir.s337737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 11/20/2021] [Indexed: 11/23/2022] Open
Abstract
Purpose The purpose of this study was to examine the relationship between dietary inflammatory index and objective hearing loss (HL). Materials and Methods A cross-sectional analysis of a nationally representative sample of participants was performed based on data in National Health and Nutrition Examination Survey (NHANES) (2009-2016). HL was defined as pure tone averages >25 dB at 500, 1000, and 2000 Hz (low frequency); 3000, 4000, 6000, and 8000 Hz (high frequency) in either ear. The energy-adjusted dietary inflammatory index (E-DII) score was calculated for each participant based on two 24-h dietary recalls to assess diet-associated inflammation. Multivariable logistic regression was used to examine the linear relationship between HL and E-DII score or E-DII quartiles. Restricted cubic spline was applied to identify any non-linear associations of the E-DII score with hearing loss. Subgroup analyses were performed by age and gender to explore the moderating roles of these factors. Akaike's Information Criterion (AIC) values were used to select the better-fitted model among linear and non-linear models. Results An inverted-U shaped relationship with low-frequency hearing loss (LFHL) was identified for the E-DII score (P-nonlinear =0.023) after adjustment for potential confounders. But significant linear or nonlinear association between E-DII score and high-frequency hearing loss (HFHL) was not found. Conclusion E-DII score had inverted-U relationship with LFHL. Both pro-inflammatory diet and anti-inflammatory diet seemed to be associated with a decreased risk of LFHL compared to diet that was neither pro-inflammatory diet nor anti-inflammatory diet.
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Affiliation(s)
- Yanpeng Fu
- Department of Otorhinolaryngology Head and Neck Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Wenyu Chen
- Nursing Department, Second Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Liqing Guo
- Department of Otorhinolaryngology Head and Neck Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
| | - Yuehui Liu
- Department of Otorhinolaryngology Head and Neck Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, People's Republic of China
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Lei M, Zhang D, Sun Y, Zou C, Wang Y, Hong Y, Jiao Y, Cai C. Web-based transcriptome analysis determines a sixteen-gene signature and associated drugs on hearing loss patients: A bioinformatics approach. J Clin Lab Anal 2021; 35:e24065. [PMID: 34758154 PMCID: PMC8649328 DOI: 10.1002/jcla.24065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 12/24/2022] Open
Abstract
Background Hearing loss is becoming more and more general. It may occur at all age and affect the language learning ability of children and trigger serious social problems. Methods The hearing loss differentially expressed genes (HL‐DEGs) were recognized through a comparison with healthy subjects. The Gene Ontology (GO) analysis was executed by DAVID. The reactome analysis of HL‐DEGs was performed by Clue‐GO. Next, we used STRING, an online website, to identify crucial protein‐protein interactions among HL‐DEGs. Cytoscape software was employed to construct a protein‐protein interaction network. MCODE, a plug‐in of the Cytoscape software, was used for module analysis. Finally, we used DGIdb database to ascertain the targeted drugs for MCODE genes. Results Four hundred four HL‐DEGs were identified, among which the most up‐regulated 10 genes were AL008707.1, SDR42E1P5, BX005040.1, AL671883.2, MT1XP1, AC016957.1, U2AF1L5, XIST, DAAM2, and ADAMTS2, and the most down‐regulated 10 genes were ALOX15, PRSS33, IL5RA, SMPD3, IGHV1‐2, IGLV3‐9, RHOXF1P1, CACNG6, MYOM2, and RSAD2. Through STRING database and MCODE analysis, we finally got 16 MCODE genes. These genes can be regarded as hearing loss related genes. Through biological analysis, it is found that these genes are enriched in pathways related to apoptosis such as tumor necrosis factor. Among them, MMP8, LTF, ORM2, FOLR3, and TCN1 have corresponding targeted drugs. Foremost, MCODE genes should be investigated for its usefulness as a new biomarker for diagnosis and treatment. Conclusion In summary, our study produced a sixteen‐gene signature and associated drugs that could be diagnosis and treatment of hearing loss patients.
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Affiliation(s)
- Min Lei
- Department of Otorhinolaryngology - Head and Neck Surgery, School of Medicine, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Dongdong Zhang
- Department of Otorhinolaryngology - Head and Neck Surgery, School of Medicine, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Yixin Sun
- School of Medicine, Xiamen University, Xiamen, China
| | - Cong Zou
- Department of Otorhinolaryngology - Head and Neck Surgery, School of Medicine, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Yue Wang
- Department of Otorhinolaryngology - Head and Neck Surgery, School of Medicine, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Yongjun Hong
- Department of Otorhinolaryngology - Head and Neck Surgery, School of Medicine, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Yanchao Jiao
- Department of Otorhinolaryngology - Head and Neck Surgery, School of Medicine, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Chengfu Cai
- Department of Otorhinolaryngology - Head and Neck Surgery, School of Medicine, Zhongshan Hospital, Xiamen University, Xiamen, China.,Department of Otorhinolaryngology Head and Neck Surgery, Teaching Hospital of Fujian Medical University, Xiamen, China.,Department of Otorhinolaryngology - Head and Neck Surgery, Xiamen University, Xiamen, China
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27
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Xue N, Song L, Song Q, Santos-Sacchi J, Wu H, Navaratnam D. Genes related to SNPs identified by Genome-wide association studies of age-related hearing loss show restriction to specific cell types in the adult mouse cochlea. Hear Res 2021; 410:108347. [PMID: 34536825 DOI: 10.1016/j.heares.2021.108347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/19/2021] [Accepted: 08/28/2021] [Indexed: 01/11/2023]
Abstract
ARHL has been thought to result from disordered hair cell function and their loss. ARHL has a significant genetic component. We sought to determine the expression in the cochlea of genes associated with single nucleotide polymorphisms linked to ARHL. We find widespread and varying expression of genes associated with these SNPs in subtypes of cells in the cochlea identified by single-cell RNA sequencing. Genes associated with SNPs with the highest significance were preferentially expressed highly in hair cells, while genes associated with SNPs with a lower significance were expressed more universally. In addition, we find significant overlap with genesets associated with Alzheimer's disease suggesting shared mechanisms, and genesets enriched for apical cell polarity and vesicle recycling suggesting mechanisms of cell death/ dysfunction with ageing.
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Affiliation(s)
- Na Xue
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China; Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Lei Song
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China; Department of Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Qiang Song
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA; Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Joseph Santos-Sacchi
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA; Department of Cell and Molecular Physiology, Yale School of Medicine, New Haven, CT, USA
| | - Hao Wu
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China.
| | - Dhasakumar Navaratnam
- Department of Surgery, Yale School of Medicine, New Haven, CT, USA; Department of Neurology, Yale School of Medicine, New Haven, CT, USA.
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28
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Højland AT, Tavernier LJM, Schrauwen I, Sommen M, Topsakal V, Schatteman I, Dhooge I, Huber A, Zanetti D, Kunst HPM, Hoischen A, Petersen MB, Van Camp G, Fransen E. A wide range of protective and predisposing variants in aggrecan influence the susceptibility for otosclerosis. Hum Genet 2021; 141:951-963. [PMID: 34410490 DOI: 10.1007/s00439-021-02334-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/04/2021] [Indexed: 12/16/2022]
Abstract
In this study, we investigated the association of ACAN variants with otosclerosis, a frequent cause of hearing loss among young adults. We sequenced the coding, 5'-UTR and 3'-UTR regions of ACAN in 1497 unrelated otosclerosis cases and 1437 matched controls from six different subpopulations. The association between variants in ACAN and the disease risk was tested through single variant and gene-based association tests. After correction for multiple testing, 14 variants were significantly associated with otosclerosis, ten of which represented independent association signals. Eight variants showed a consistent association across all subpopulations. Allelic odds ratios of the variants identified four predisposing and ten protective variants. Gene-based tests showed an association of very rare variants in the 3'-UTR with the phenotype. The associated exonic variants are all located in the CS domain of ACAN and include both protective and predisposing variants with a broad spectrum of effect sizes and population frequencies. This includes variants with strong effect size and low frequency, typical for monogenic diseases, to low effect size variants with high frequency, characteristic for common complex traits. This single-gene allelic spectrum with both protective and predisposing alleles is unique in the field of complex diseases. In conclusion, these findings are a significant advancement to the understanding of the etiology of otosclerosis.
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Affiliation(s)
- Allan Thomas Højland
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Research and Knowledge Center in Sensory Genetics, Department of Clinical Genetics, Aalborg University Hospital, Aalborg, Denmark
| | - Lisse J M Tavernier
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Department of Neurology, Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY, USA
| | - Manou Sommen
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Vedat Topsakal
- Department of ORL and Head and Neck Surgery, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Isabelle Schatteman
- European Institute for ORL, St-Augustinus Hospital Antwerp, Antwerp, Belgium
| | - Ingeborg Dhooge
- Department of Otolaryngology, Ghent University Hospital, Ghent, Belgium
| | - Alex Huber
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Zurich, Zurich, Switzerland
| | - Diego Zanetti
- Department of Clinical Sciences and Community Health, Audiology Unit, University of Milan, I.R.C.C.S. Fondazione "Cà Granda", Osp.Le Maggiore Policlinico, Milano, Italy
| | - Henricus P M Kunst
- Department of Otorhinolaryngology, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands.,Department of Otorhinolaryngology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michael B Petersen
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Research and Knowledge Center in Sensory Genetics, Department of Clinical Genetics, Aalborg University Hospital, Aalborg, Denmark
| | - Guy Van Camp
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium.
| | - Erik Fransen
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium. .,StatUa Center for Statistics, University of Antwerp, Antwerp, Belgium.
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29
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Ahmadmehrabi S, Li B, Hui D, Park J, Ritchie M, Rader DJ, Ruckenstein MJ, Epstein DJ, Brant J. A Genome-First Approach to Rare Variants in Dominant Postlingual Hearing Loss Genes in a Large Adult Population. Otolaryngol Head Neck Surg 2021; 166:746-752. [PMID: 34281439 DOI: 10.1177/01945998211029544] [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] [Indexed: 11/15/2022]
Abstract
OBJECTIVE To investigate the importance of rare variants in adult-onset hearing loss. STUDY DESIGN Genomic association study. SETTING Large biobank from tertiary care center. METHODS We investigated rare variants (minor allele frequency <5%) in 42 autosomal dominant (DFNA) postlingual hearing loss (HL) genes in 16,657 unselected individuals in the Penn Medicine Biobank. We determined the prevalence of known pathogenic and predicted deleterious variants in subjects with audiometric-proven sensorineural hearing loss. We scanned across known postlingual DFNA HL genes to determine those most significantly contributing to the phenotype. We replicated findings in an independent cohort (UK Biobank). RESULTS While rare individually, when considering the accumulation of variants in all postlingual DFNA genes, more than 90% of participants carried at least 1 rare variant. Rare variants predicted to be deleterious were enriched in adults with audiometric-proven hearing loss (pure-tone average >25 dB; P = .015). Patients with a rare predicted deleterious variant had an odds ratio of 1.27 for HL compared with genotypic controls (P = .029). Gene burden in DIABLO, PTPRQ, TJP2, and POU4F3 were independently associated with sensorineural hearing loss. CONCLUSION Although prior reports have focused on common variants, we find that rare predicted deleterious variants in DFNA postlingual HL genes are enriched in patients with adult-onset HL in a large health care system population. We show the value of investigating rare variants to uncover hearing loss phenotypes related to implicated genes.
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Affiliation(s)
- Shadi Ahmadmehrabi
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Binglan Li
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Daniel Hui
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Joseph Park
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marylyn Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael J Ruckenstein
- Department of Otorhinolaryngology Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Douglas J Epstein
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jason Brant
- Department of Otorhinolaryngology Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, Pennsylvania, USA
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30
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A Genome-Wide Association Study of Age-Related Hearing Impairment in Middle- and Old-Aged Chinese Twins. BIOMED RESEARCH INTERNATIONAL 2021; 2021:3629624. [PMID: 34337005 PMCID: PMC8314043 DOI: 10.1155/2021/3629624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 06/17/2021] [Accepted: 07/03/2021] [Indexed: 11/17/2022]
Abstract
Background Age-related hearing impairment (ARHI) is considered an unpreventable disorder. We aimed to detect specific genetic variants that are potentially related to ARHI via genome-wide association study (GWAS). Methods A sample of 131 dizygotic twins was genotyped for single-nucleotide polymorphism- (SNP-) based GWAS. Gene-based test was performed using VEGAS2. Pathway enrichment analysis was conducted by PASCAL. Results The twins are with a median age of 49 years, of which 128 were females and 134 were males. rs6633657 was the only SNP that reached the genome-wide significance level for better ear hearing level (BEHL) at 2.0 kHz (P = 1.19 × 10-8). Totally, 9, 10, 42, 7, 17, and 5 SNPs were suggestive evidence level for (P < 1 × 10-5) BEHLs at 0.5, 1.0, 2.0, 4.0, and 8.0 kHz and pure tone average (PTA), respectively. Several promising genetic regions in chromosomes (near the C20orf196, AQPEP, UBQLN3, OR51B5, OR51I2, OR52D1, GLTP, GIT2, and PARK2) nominally associated with ARHI were identified. Gene-based analysis revealed 165, 173, 77, 178, 170, and 145 genes nominally associated with BEHLs at 0.5, 1.0, 2.0, 4.0, and 8.0 kHz and PTA, respectively (P < 0.05). For BEHLs at 0.5, 1.0, and 2.0 kHz, the main enriched pathways were phosphatidylinositol signaling system, regulation of ornithine decarboxylase, eukaryotic translation initiation factor (EIF) pathway, amine compound solute carrier (SLC) transporters, synthesis of phosphoinositides (PIPS) at the plasma membrane, and phosphatidylinositols (PI) metabolism. Conclusions The genetic variations reported herein are significantly involved in functional genes and regulatory domains that mediate ARHI pathogenesis. These findings provide clues for the further unraveling of the molecular physiology of hearing functions and identifying novel diagnostic biomarkers and therapeutic targets of ARHI.
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31
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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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32
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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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33
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Ahmadmehrabi S, Li B, Park J, Devkota B, Vujkovic M, Ko YA, Van Wagoner D, Tang WHW, Krantz I, Ritchie M, Brant J, Ruckenstein MJ, Epstein DJ, Rader DJ. Genome-first approach to rare EYA4 variants and cardio-auditory phenotypes in adults. Hum Genet 2021; 140:957-967. [PMID: 33745059 DOI: 10.1007/s00439-021-02263-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/02/2021] [Indexed: 12/20/2022]
Abstract
While newborns and children with hearing loss are routinely offered genetic testing, adults are rarely clinically tested for a genetic etiology. One clinically actionable result from genetic testing in children is the discovery of variants in syndromic hearing loss genes. EYA4 is a known hearing loss gene which is also involved in important pathways in cardiac tissue. The pleiotropic effects of rare EYA4 variants are poorly understood and their prevalence in a large cohort has not been previously reported. We investigated cardio-auditory phenotypes in 11,451 individuals in a large biobank using a rare variant, genome-first approach to EYA4. We filtered 256 EYA4 variants carried by 6737 participants to 26 rare and predicted deleterious variants carried by 42 heterozygotes. We aggregated predicted deleterious EYA4 gene variants into a combined variable (i.e. "gene burden") and performed association studies across phenotypes compared to wildtype controls. We validated findings with replication in three independent cohorts and human tissue expression data. EYA4 gene burden was significantly associated with audiometric-proven HL (p = [Formula: see text], Mobitz Type II AV block (p = [Formula: see text]) and the syndromic presentation of HL and primary cardiomyopathy (p = 0.0194). Analyses on audiogram, echocardiogram, and electrocardiogram data validated these associations. Prior reports have focused on identifying variants in families with severe or syndromic phenotypes. In contrast, we found, using a genotype-first approach, that gene burden in EYA4 is associated with more subtle cardio-auditory phenotypes in an adult medical biobank population, including cardiac conduction disorders which have not been previously reported. We show the value of using a focused approach to uncover human disease related to pleiotropic gene variants and suggest a role for genetic testing in adults presenting with hearing loss.
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Affiliation(s)
- Shadi Ahmadmehrabi
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Binglan Li
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph Park
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Batsal Devkota
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marijana Vujkovic
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Yi-An Ko
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David Van Wagoner
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - W H Wilson Tang
- Cleveland Clinic, Heart and Vascular Institute, Cleveland, OH, USA
| | - Ian Krantz
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marylyn Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jason Brant
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Otorhinolaryngology Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael J Ruckenstein
- Department of Otorhinolaryngology Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Douglas J Epstein
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Medicine, Division of Translational Medicine and Human Genetics, Perelman School of Medicine at the University of Pennsylvania, 11-125 Smilow Center for Translational Research, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA.
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Ahmadmehrabi S, Li B, Epstein DJ, Ruckenstein MJ, Brant JA. How Does the "Cookie-Bite" Audiogram Shape Perform in Discriminating Genetic Hearing Loss in Adults? Otolaryngol Head Neck Surg 2021; 166:537-539. [PMID: 34058916 DOI: 10.1177/01945998211015181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
"Cookie-bite" or U-shaped audiograms-specifically, those showing midfrequency sensorineural hearing loss (HL)-are traditionally taught to be associated with genetic HL; however, their utility as a screening tool has not been reported. We aim to determine the performance of a cookie-bite audiogram shape in stratifying patients carrying putative loss-of-function variants in known HL genes from wild-type controls. We merged audiometric and exome sequencing data from adults enrolled in a large biobank at a tertiary care center. Of 321 patients, 50 carried a putative loss-of-function variant in an HL gene. The cookie-bite shape was present in 9 of those patients, resulting in low sensitivity (18%) and positive predictive value (15%) in stratifying genetic carrier status; 84% of patients with a cookie-bite audiogram did not carry a genetic variant. A cookie-bite audiogram should not be used to screen adults for possible genetic testing.
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Affiliation(s)
- Shadi Ahmadmehrabi
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Binglan Li
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Douglas J Epstein
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael J Ruckenstein
- Department of Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jason A Brant
- Department of Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Corporal Michael J. Crescenz VA Medical Center, Philadelphia, Pennsylvania, USA
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Eckert MA, Harris KC, Lang H, Lewis MA, Schmiedt RA, Schulte BA, Steel KP, Vaden KI, Dubno JR. Translational and interdisciplinary insights into presbyacusis: A multidimensional disease. Hear Res 2021; 402:108109. [PMID: 33189490 PMCID: PMC7927149 DOI: 10.1016/j.heares.2020.108109] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 10/19/2020] [Accepted: 10/25/2020] [Indexed: 12/18/2022]
Abstract
There are multiple etiologies and phenotypes of age-related hearing loss or presbyacusis. In this review we summarize findings from animal and human studies of presbyacusis, including those that provide the theoretical framework for distinct metabolic, sensory, and neural presbyacusis phenotypes. A key finding in quiet-aged animals is a decline in the endocochlear potential (EP) that results in elevated pure-tone thresholds across frequencies with greater losses at higher frequencies. In contrast, sensory presbyacusis appears to derive, in part, from acute and cumulative effects on hair cells of a lifetime of environmental exposures (e.g., noise), which often result in pronounced high frequency hearing loss. These patterns of hearing loss in animals are recognizable in the human audiogram and can be classified into metabolic and sensory presbyacusis phenotypes, as well as a mixed metabolic+sensory phenotype. However, the audiogram does not fully characterize age-related changes in auditory function. Along with the effects of peripheral auditory system declines on the auditory nerve, primary degeneration in the spiral ganglion also appears to contribute to central auditory system aging. These inner ear alterations often correlate with structural and functional changes throughout the central nervous system and may explain suprathreshold speech communication difficulties in older adults with hearing loss. Throughout this review we highlight potential methods and research directions, with the goal of advancing our understanding, prevention, diagnosis, and treatment of presbyacusis.
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Affiliation(s)
- Mark A Eckert
- Medical University of South Carolina, Department of Otolaryngology - Head and Neck Surgery, Charleston, SC 29425, USA.
| | - Kelly C Harris
- Medical University of South Carolina, Department of Otolaryngology - Head and Neck Surgery, Charleston, SC 29425, USA
| | - Hainan Lang
- Medical University of South Carolina, Department of Pathology and Laboratory Medicine, Charleston, SC 29425, USA
| | - Morag A Lewis
- King's College London, Wolfson Centre for Age-Related Diseases, London SE1 1UL, United Kingdom
| | - Richard A Schmiedt
- Medical University of South Carolina, Department of Otolaryngology - Head and Neck Surgery, Charleston, SC 29425, USA
| | - Bradley A Schulte
- Medical University of South Carolina, Department of Pathology and Laboratory Medicine, Charleston, SC 29425, USA; Medical University of South Carolina, Department of Otolaryngology - Head and Neck Surgery, Charleston, SC 29425, USA
| | - Karen P Steel
- King's College London, Wolfson Centre for Age-Related Diseases, London SE1 1UL, United Kingdom
| | - Kenneth I Vaden
- Medical University of South Carolina, Department of Otolaryngology - Head and Neck Surgery, Charleston, SC 29425, USA
| | - Judy R Dubno
- Medical University of South Carolina, Department of Otolaryngology - Head and Neck Surgery, Charleston, SC 29425, USA; Medical University of South Carolina, Department of Pathology and Laboratory Medicine, Charleston, SC 29425, USA
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Stojkovic M, Han D, Jeong M, Stojkovic P, Stankovic KM. Human induced pluripotent stem cells and CRISPR/Cas-mediated targeted genome editing: Platforms to tackle sensorineural hearing loss. STEM CELLS (DAYTON, OHIO) 2021; 39:673-696. [PMID: 33586253 DOI: 10.1002/stem.3353] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/13/2020] [Indexed: 11/09/2022]
Abstract
Hearing loss (HL) is a major global health problem of pandemic proportions. The most common type of HL is sensorineural hearing loss (SNHL) which typically occurs when cells within the inner ear are damaged. Human induced pluripotent stem cells (hiPSCs) can be generated from any individual including those who suffer from different types of HL. The development of new differentiation protocols to obtain cells of the inner ear including hair cells (HCs) and spiral ganglion neurons (SGNs) promises to expedite cell-based therapy and screening of potential pharmacologic and genetic therapies using human models. Considering age-related, acoustic, ototoxic, and genetic insults which are the most frequent causes of irreversible damage of HCs and SGNs, new methods of genome editing (GE), especially the CRISPR/Cas9 technology, could bring additional opportunities to understand the pathogenesis of human SNHL and identify novel therapies. However, important challenges associated with both hiPSCs and GE need to be overcome before scientific discoveries are correctly translated to effective and patient-safe applications. The purpose of the present review is (a) to summarize the findings from published reports utilizing hiPSCs for studies of SNHL, hence complementing recent reviews focused on animal studies, and (b) to outline promising future directions for deciphering SNHL using disruptive molecular and genomic technologies.
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Affiliation(s)
- Miodrag Stojkovic
- Eaton Peabody Laboratories, Department of Otolaryngology Head and Neck Surgery, Massachusetts Eye and Ear, Boston, Massachusetts, USA.,Department of Otolaryngology Head and Neck Surgery, Harvard Medical School, Boston, Massachusetts, USA
| | - Dongjun Han
- Eaton Peabody Laboratories, Department of Otolaryngology Head and Neck Surgery, Massachusetts Eye and Ear, Boston, Massachusetts, USA.,Department of Otolaryngology Head and Neck Surgery, Harvard Medical School, Boston, Massachusetts, USA
| | - Minjin Jeong
- Eaton Peabody Laboratories, Department of Otolaryngology Head and Neck Surgery, Massachusetts Eye and Ear, Boston, Massachusetts, USA.,Department of Otolaryngology Head and Neck Surgery, Harvard Medical School, Boston, Massachusetts, USA
| | - Petra Stojkovic
- Eaton Peabody Laboratories, Department of Otolaryngology Head and Neck Surgery, Massachusetts Eye and Ear, Boston, Massachusetts, USA.,Department of Otolaryngology Head and Neck Surgery, Harvard Medical School, Boston, Massachusetts, USA
| | - Konstantina M Stankovic
- Eaton Peabody Laboratories, Department of Otolaryngology Head and Neck Surgery, Massachusetts Eye and Ear, Boston, Massachusetts, USA.,Department of Otolaryngology Head and Neck Surgery, Harvard Medical School, Boston, Massachusetts, USA.,Program in Speech and Hearing Bioscience and Technology, Harvard University, Cambridge, Massachusetts, USA.,Harvard Program in Therapeutic Science, Harvard Medical School, Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts, USA
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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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Clifford RE, Maihofer AX, Stein MB, Ryan AF, Nievergelt CM. Novel Risk Loci in Tinnitus and Causal Inference With Neuropsychiatric Disorders Among Adults of European Ancestry. JAMA Otolaryngol Head Neck Surg 2020; 146:1015-1025. [PMID: 32970095 PMCID: PMC7516809 DOI: 10.1001/jamaoto.2020.2920] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 07/27/2020] [Indexed: 02/06/2023]
Abstract
Importance Tinnitus affects at least 16 million US adults, but its pathophysiology is complicated, and treatment options remain limited. A heritable component has been identified in family and twin studies; however, no large-scale genome-wide association studies (GWAS) have been accomplished. Objective To identify genetic risk loci associated with tinnitus, determine genetic correlations, and infer possible relationships of tinnitus with hearing loss and neuropsychiatric disorders and traits. Design, Setting, and Participants A GWAS of self-reported tinnitus was performed in the UK Biobank (UKB) cohort using a linear mixed-model method implemented in BOLT-LMM (linear mixed model). Replication of significant findings was sought in the nonoverlapping US Million Veteran Program (MVP) cohort. A total of 172 995 UKB (discovery) and 260 832 MVP (replication) participants of European ancestry with self-report regarding tinnitus and hearing loss underwent genomic analysis. Linkage-disequilibrium score regression and mendelian randomization were performed between tinnitus and hearing loss and neuropsychiatric disorders. Data from the UKB were acquired and analyzed from September 24, 2018, to December 13, 2019. Data acquisition for the MVP cohort was completed July 22, 2019. Data analysis for both cohorts was completed on February 11, 2020. Main Outcomes and Measures Estimates of single nucleotide variation (SNV)-based heritability for tinnitus, identification of genetic risk loci and genes, functional mapping, and replication were performed. Genetic association and inferred causality of tinnitus compared with hearing loss and neuropsychiatric disorders and traits were analyzed. Results Of 172 995 UKB participants (53.7% female; mean [SD], 58.0 [8.2] years), 155 395 unrelated participants underwent SNV-based heritability analyses across a range of tinnitus phenotype definitions that explained approximately 6% of the heritability. The GWAS based on the most heritable model in the full UKB cohort identified 6 genome-wide significant loci and 27 genes in gene-based analyses, with replication of 3 of 6 loci and 8 of 27 genes in 260 832 MVP cohort participants (92.8% men; mean [SD] age, 63.8 [13.2] years). Mendelian randomization indicated that major depressive disorder had a permissive effect (β = 0.133; P = .003) and years of education had a protective effect (β = -0.322, P = <.001) on tinnitus, whereas tinnitus and hearing loss inferred a bidirectional association (β = 0.072, P = .001 and β = 1.546, P = <.001, respectively). Conclusions and Relevance This large GWAS characterizes the genetic architecture of tinnitus, demonstrating modest but significant heritability and a polygenic profile with multiple significant risk loci and genes. Genetic correlation and inferred causation between tinnitus and major depressive disorder, educational level, and hearing impairment were identified, consistent with clinical and neuroimaging evidence. These findings may guide gene-based diagnostic and therapeutic approaches to this pervasive disorder.
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Affiliation(s)
- Royce E Clifford
- Division of Otolaryngology, Department of Surgery, University of California, San Diego, La Jolla
- Harvard School of Public Health, Boston, Massachusetts
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Adam X Maihofer
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, California
- Department of Psychiatry, University of California, San Diego, La Jolla
| | - Murray B Stein
- Department of Psychiatry, University of California, San Diego, La Jolla
- Psychiatry Service, Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Allen F Ryan
- Division of Otolaryngology, Department of Surgery, University of California, San Diego, La Jolla
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Caroline M Nievergelt
- Research Service, Veterans Affairs San Diego Healthcare System, San Diego, California
- Department of Psychiatry, University of California, San Diego, La Jolla
- Center of Excellence for Stress and Mental Health, Veterans Affairs San Diego Healthcare System, San Diego, California
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Zaharija B, Samardžija B, Bradshaw NJ. The TRIOBP Isoforms and Their Distinct Roles in Actin Stabilization, Deafness, Mental Illness, and Cancer. Molecules 2020; 25:molecules25214967. [PMID: 33121024 PMCID: PMC7663296 DOI: 10.3390/molecules25214967] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/22/2020] [Accepted: 10/26/2020] [Indexed: 12/16/2022] Open
Abstract
The TRIOBP (TRIO and F-actin Binding Protein) gene encodes multiple proteins, which together play crucial roles in modulating the assembly of the actin cytoskeleton. Splicing of the TRIOBP gene is complex, with the two most studied TRIOBP protein isoforms sharing no overlapping amino acid sequence with each other. TRIOBP-1 (also known as TARA or TAP68) is a mainly structured protein that is ubiquitously expressed and binds to F-actin, preventing its depolymerization. It has been shown to be important for many processes including in the cell cycle, adhesion junctions, and neuronal differentiation. TRIOBP-1 has been implicated in schizophrenia through the formation of protein aggregates in the brain. In contrast, TRIOBP-4 is an entirely disordered protein with a highly specialized expression pattern. It is known to be crucial for the bundling of actin in the stereocilia of the inner ear, with mutations in it causing severe or profound hearing loss. Both of these isoforms are implicated in cancer. Additional longer isoforms of TRIOBP exist, which overlap with both TRIOBP-1 and 4. These appear to participate in the functions of both shorter isoforms, while also possessing unique functions in the inner ear. In this review, the structures and functions of all of these isoforms are discussed, with a view to understanding how they operate, both alone and in combination, to modulate actin and their consequences for human illness.
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40
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Brenowitz WD, Filshtein TJ, Yaffe K, Walter S, Ackley SF, Hoffmann TJ, Jorgenson E, Whitmer RA, Glymour MM. Association of genetic risk for Alzheimer disease and hearing impairment. Neurology 2020; 95:e2225-e2234. [PMID: 32878991 PMCID: PMC7713783 DOI: 10.1212/wnl.0000000000010709] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 05/12/2020] [Indexed: 01/09/2023] Open
Abstract
OBJECTIVE To test the hypothesis that incipient Alzheimer disease (AD) may adversely affect hearing and that hearing loss may adversely affect cognition, we evaluated whether genetic variants that increase AD risk also increase problem hearing and genetic variants that increase hearing impairment risk do not influence cognition. METHODS UK Biobank participants without dementia ≥56 years of age with Caucasian genetic ancestry completed a Digit Triplets Test of speech-in-noise hearing (n = 80,074), self-reported problem hearing and hearing with background noise (n = 244,915), and completed brief cognitive assessments. A genetic risk score for AD (AD-GRS) was calculated as a weighted sum of 23 previously identified AD-related polymorphisms. A genetic risk score for hearing (hearing-GRS) was calculated using 3 previously identified polymorphisms related to hearing impairment. Using age-, sex-, and genetic ancestry-adjusted logistic and linear regression models, we evaluated whether the AD-GRS predicted poor hearing and whether the hearing-GRS predicted worse cognition. RESULTS Poor speech-in-noise hearing (>-5.5-dB speech reception threshold; prevalence 14%) was associated with lower cognitive scores (ß = -1.28; 95% confidence interval [CI] -1.54 to -1.03). Higher AD-GRS was significantly associated with poor speech-in-noise hearing (odds ratio [OR] 1.06; 95% CI 1.01-1.11) and self-reported problems hearing with background noise (OR 1.03; 95% CI 1.00-1.05). Hearing-GRS was not significantly associated with cognitive scores (ß = -0.05; 95% CI -0.17 to 0.07). CONCLUSIONS Genetic risk for AD also influences speech-in-noise hearing. We failed to find evidence that genetic risk for hearing impairment affects cognition. AD disease processes or a that shared etiology may cause speech-in-noise difficulty before dementia onset.
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Affiliation(s)
- Willa D Brenowitz
- From the Department of Psychiatry and Behavioral Sciences (W.D.B., K.Y.), Department of Epidemiology and Biostatistics (K.Y., S.F.A., T.J.H., M.M.G.), Department of Neurology (K.Y.), and Institute for Human Genetics (T.J.H.), University of California, San Francisco; 23andMe (T.J.F.), Mountain View; San Francisco VA Health Care System (K.Y.), CA; Department of Medicine and Public Health (S.W.), Rey Juan Carlos University, Madrid, Spain; Kaiser Permanente Northern California Division of Research (E.J.), Oakland; and Public Health Sciences (R.A.W.), Division of Epidemiology, Alzheimer's Disease Research Center, UC Davis School of Medicine, CA.
| | - Teresa J Filshtein
- From the Department of Psychiatry and Behavioral Sciences (W.D.B., K.Y.), Department of Epidemiology and Biostatistics (K.Y., S.F.A., T.J.H., M.M.G.), Department of Neurology (K.Y.), and Institute for Human Genetics (T.J.H.), University of California, San Francisco; 23andMe (T.J.F.), Mountain View; San Francisco VA Health Care System (K.Y.), CA; Department of Medicine and Public Health (S.W.), Rey Juan Carlos University, Madrid, Spain; Kaiser Permanente Northern California Division of Research (E.J.), Oakland; and Public Health Sciences (R.A.W.), Division of Epidemiology, Alzheimer's Disease Research Center, UC Davis School of Medicine, CA
| | - Kristine Yaffe
- From the Department of Psychiatry and Behavioral Sciences (W.D.B., K.Y.), Department of Epidemiology and Biostatistics (K.Y., S.F.A., T.J.H., M.M.G.), Department of Neurology (K.Y.), and Institute for Human Genetics (T.J.H.), University of California, San Francisco; 23andMe (T.J.F.), Mountain View; San Francisco VA Health Care System (K.Y.), CA; Department of Medicine and Public Health (S.W.), Rey Juan Carlos University, Madrid, Spain; Kaiser Permanente Northern California Division of Research (E.J.), Oakland; and Public Health Sciences (R.A.W.), Division of Epidemiology, Alzheimer's Disease Research Center, UC Davis School of Medicine, CA
| | - Stefan Walter
- From the Department of Psychiatry and Behavioral Sciences (W.D.B., K.Y.), Department of Epidemiology and Biostatistics (K.Y., S.F.A., T.J.H., M.M.G.), Department of Neurology (K.Y.), and Institute for Human Genetics (T.J.H.), University of California, San Francisco; 23andMe (T.J.F.), Mountain View; San Francisco VA Health Care System (K.Y.), CA; Department of Medicine and Public Health (S.W.), Rey Juan Carlos University, Madrid, Spain; Kaiser Permanente Northern California Division of Research (E.J.), Oakland; and Public Health Sciences (R.A.W.), Division of Epidemiology, Alzheimer's Disease Research Center, UC Davis School of Medicine, CA
| | - Sarah F Ackley
- From the Department of Psychiatry and Behavioral Sciences (W.D.B., K.Y.), Department of Epidemiology and Biostatistics (K.Y., S.F.A., T.J.H., M.M.G.), Department of Neurology (K.Y.), and Institute for Human Genetics (T.J.H.), University of California, San Francisco; 23andMe (T.J.F.), Mountain View; San Francisco VA Health Care System (K.Y.), CA; Department of Medicine and Public Health (S.W.), Rey Juan Carlos University, Madrid, Spain; Kaiser Permanente Northern California Division of Research (E.J.), Oakland; and Public Health Sciences (R.A.W.), Division of Epidemiology, Alzheimer's Disease Research Center, UC Davis School of Medicine, CA
| | - Thomas J Hoffmann
- From the Department of Psychiatry and Behavioral Sciences (W.D.B., K.Y.), Department of Epidemiology and Biostatistics (K.Y., S.F.A., T.J.H., M.M.G.), Department of Neurology (K.Y.), and Institute for Human Genetics (T.J.H.), University of California, San Francisco; 23andMe (T.J.F.), Mountain View; San Francisco VA Health Care System (K.Y.), CA; Department of Medicine and Public Health (S.W.), Rey Juan Carlos University, Madrid, Spain; Kaiser Permanente Northern California Division of Research (E.J.), Oakland; and Public Health Sciences (R.A.W.), Division of Epidemiology, Alzheimer's Disease Research Center, UC Davis School of Medicine, CA
| | - Eric Jorgenson
- From the Department of Psychiatry and Behavioral Sciences (W.D.B., K.Y.), Department of Epidemiology and Biostatistics (K.Y., S.F.A., T.J.H., M.M.G.), Department of Neurology (K.Y.), and Institute for Human Genetics (T.J.H.), University of California, San Francisco; 23andMe (T.J.F.), Mountain View; San Francisco VA Health Care System (K.Y.), CA; Department of Medicine and Public Health (S.W.), Rey Juan Carlos University, Madrid, Spain; Kaiser Permanente Northern California Division of Research (E.J.), Oakland; and Public Health Sciences (R.A.W.), Division of Epidemiology, Alzheimer's Disease Research Center, UC Davis School of Medicine, CA
| | - Rachel A Whitmer
- From the Department of Psychiatry and Behavioral Sciences (W.D.B., K.Y.), Department of Epidemiology and Biostatistics (K.Y., S.F.A., T.J.H., M.M.G.), Department of Neurology (K.Y.), and Institute for Human Genetics (T.J.H.), University of California, San Francisco; 23andMe (T.J.F.), Mountain View; San Francisco VA Health Care System (K.Y.), CA; Department of Medicine and Public Health (S.W.), Rey Juan Carlos University, Madrid, Spain; Kaiser Permanente Northern California Division of Research (E.J.), Oakland; and Public Health Sciences (R.A.W.), Division of Epidemiology, Alzheimer's Disease Research Center, UC Davis School of Medicine, CA
| | - M Maria Glymour
- From the Department of Psychiatry and Behavioral Sciences (W.D.B., K.Y.), Department of Epidemiology and Biostatistics (K.Y., S.F.A., T.J.H., M.M.G.), Department of Neurology (K.Y.), and Institute for Human Genetics (T.J.H.), University of California, San Francisco; 23andMe (T.J.F.), Mountain View; San Francisco VA Health Care System (K.Y.), CA; Department of Medicine and Public Health (S.W.), Rey Juan Carlos University, Madrid, Spain; Kaiser Permanente Northern California Division of Research (E.J.), Oakland; and Public Health Sciences (R.A.W.), Division of Epidemiology, Alzheimer's Disease Research Center, UC Davis School of Medicine, CA
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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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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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Jimenez JE, Nourbakhsh A, Colbert B, Mittal R, Yan D, Green CL, Nisenbaum E, Liu G, Bencie N, Rudman J, Blanton SH, Zhong Liu X. Diagnostic and therapeutic applications of genomic medicine in progressive, late-onset, nonsyndromic sensorineural hearing loss. Gene 2020; 747:144677. [PMID: 32304785 PMCID: PMC7244213 DOI: 10.1016/j.gene.2020.144677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/12/2020] [Accepted: 04/14/2020] [Indexed: 02/06/2023]
Abstract
The progressive, late-onset, nonsyndromic, sensorineural hearing loss (PNSHL) is the most common cause of sensory impairment globally, with presbycusis affecting greater than a third of individuals over the age of 65. The etiology underlying PNSHL include presbycusis, noise-induced hearing loss, drug ototoxicity, and delayed-onset autosomal dominant hearing loss (AD PNSHL). The objective of this article is to discuss the potential diagnostic and therapeutic applications of genomic medicine in PNSHL. Genomic factors contribute greatly to PNSHL. The heritability of presbycusis ranges from 25 to 75%. Current therapies for PNSHL range from sound amplification to cochlear implantation (CI). PNSHL is an excellent candidate for genomic medicine approaches as it is common, has well-described pathophysiology, has a wide time window for treatment, and is amenable to local gene therapy by currently utilized procedural approaches. AD PNSHL is especially suited to genomic medicine approaches that can disrupt the expression of an aberrant protein product. Gene therapy is emerging as a potential therapeutic strategy for the treatment of PNSHL. Viral gene delivery approaches have demonstrated promising results in human clinical trials for two inherited causes of blindness and are being used for PNSHL in animal models and a human trial. Non-viral gene therapy approaches are useful in situations where a transient biologic effect is needed or for delivery of genome editing reagents (such as CRISPR/Cas9) into the inner ear. Many gene therapy modalities that have proven efficacious in animal trials have potential to delay or prevent PNSHL in humans. The development of new treatment modalities for PNSHL will lead to improved quality of life of many affected individuals and their families.
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Affiliation(s)
- Joaquin E Jimenez
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Aida Nourbakhsh
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Brett Colbert
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Human Genetics and John P. Hussman Institute of Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA; Medical Scientist Training Program, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Rahul Mittal
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Carlos L Green
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Eric Nisenbaum
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - George Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Nicole Bencie
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jason Rudman
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Susan H Blanton
- Department of Human Genetics and John P. Hussman Institute of Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Xue Zhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Human Genetics and John P. Hussman Institute of Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.
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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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Wu H, Sun H, He Z, Chen X, Li Y, Zhao X, Kong W, Kong W. The effect and mechanism of 19S proteasome PSMD11/Rpn6 subunit in D-Galactose induced mimetic aging models. Exp Cell Res 2020; 394:112093. [PMID: 32450067 DOI: 10.1016/j.yexcr.2020.112093] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/14/2020] [Accepted: 05/16/2020] [Indexed: 11/30/2022]
Abstract
Regulating proteasome activity is a potent therapeutic aspect of age-related hearing loss, which has been proven to protect neurons from age-related damaging. PSMD11, subunit of the 19S proteasome regulatory particle, is known to mainly up-regulate proteasome activity and prolong aging. However, the mechanism of PSMD11 in age-related hearing loss has not been deeply explored. In the present study, we explore the function and mechanism of PSMD11 protecting neurons in d-Galactose (D-Gal) mimetic aging models. Age-related pathologies were detected by Taq-PCR, ABR, Transmission electron microscopy, toluidine blue and β-galactosidase staining. The relative expressions of the proteins were explored by Western blotting, oxyblot, immunoprecipitation and immunofluorescence. Flow cytometry was used to manifest the oxidative state. We discovered that proteasome activity was impaired with aging, and that ROS and toxic protein accumulated in D-Gal induced aging models. PSMD11 changed with aging, and was associated with the metabolism of proteasome activity in the D-Gal treated models. Moreover, the knockdown or overexpression of PSMD11 was sufficient to change the oxidative state caused by D-Gal. Our results also demonstrated that PSMD11 could bond to AMPKα1/2 in the auditory cortex and PC12 cells, and AMPKα2 but not AMPKα1 was efficient to regulate the function of PSMD11. Deeper insights into the mechanisms of regulating PSMD11 for the anti-aging process are needed, and may offer novel therapeutic methods for central presbycusis.
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Affiliation(s)
- Han Wu
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Haiying Sun
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Zuhong He
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Xi Chen
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Yongqin Li
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Xueyan Zhao
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Wen Kong
- Departments of Endocrinology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430022, China.
| | - Weijia Kong
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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Data-driven segmentation of audiometric phenotypes across a large clinical cohort. Sci Rep 2020; 10:6704. [PMID: 32317648 PMCID: PMC7174357 DOI: 10.1038/s41598-020-63515-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/30/2020] [Indexed: 12/21/2022] Open
Abstract
Pure tone audiograms are used to assess the degree and underlying source of hearing loss. Audiograms are typically categorized into a few canonical types, each thought to reflect distinct pathologies of the ear. Here, we analyzed 116,400 patient records from our clinic collected over a 24-year period and found that standard categorization left 46% of patient records unclassified. To better account for the full spectrum of hearing loss profiles, we used a Gaussian Mixture Model (GMM) to segment audiograms without any assumptions about frequency relationships, interaural symmetry or etiology. The GMM converged on ten types, featuring varying degrees of high-frequency hearing loss, flat loss, mixed loss, and notched profiles, with predictable relationships to patient age and sex. A separate GMM clustering of 15,380 audiograms from the National Health and Nutrition Examination Survey (NHANES) identified six similar types, that only lacked the more extreme hearing loss configurations observed in our patient cohort. Whereas traditional approaches distill hearing loss configurations down to a few canonical types by disregarding much of the underlying variability, an objective probabilistic model that accounted for all of the data identified an organized, but more heterogenous set of audiogram types that was consistent across two large clinical databases.
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47
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Ahmadmehrabi S, Brant J, Epstein DJ, Ruckenstein MJ, Rader DJ. Genetics of Postlingual Sensorineural Hearing Loss. Laryngoscope 2020; 131:401-409. [PMID: 32243624 DOI: 10.1002/lary.28646] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/19/2020] [Accepted: 02/28/2020] [Indexed: 12/11/2022]
Abstract
Literature and clinical practice around adult-onset hearing loss (HL) has traditionally focused on environmental risk factors, including noise exposure, ototoxic drug exposure, and cardiovascular disease. The most common diagnosis in adult-onset HL is presbycusis. However, the age of onset of presbycusis varies, and patients often describe family history of HL as well as individual variation in progression and severity. In recent years, there has been accumulating evidence of gene-environment interactions underlying adult cases of HL. Susceptibility loci for age-related HL have been identified, and genes related to postlingual nonsyndromic HL continue to be discovered through individual reports and genome-wide association studies. This review will outline main concepts in genetics as related to HL, identify implicated genes, and discuss clinical implications. Laryngoscope, 131:401-409, 2021.
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Affiliation(s)
- Shadi Ahmadmehrabi
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jason Brant
- Department of Otorhinolaryngology Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Douglas J Epstein
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael J Ruckenstein
- Department of Otorhinolaryngology Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel J Rader
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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48
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Self-reported hearing loss questions provide a good measure for genetic studies: a polygenic risk score analysis from UK Biobank. Eur J Hum Genet 2020; 28:1056-1065. [PMID: 32203203 PMCID: PMC7382483 DOI: 10.1038/s41431-020-0603-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 01/20/2020] [Accepted: 02/18/2020] [Indexed: 02/07/2023] Open
Abstract
Age-related hearing impairment (ARHI) is very common in older adults and has major impact on quality of life. The heritability of ARHI has been estimated to be around 50%. The present study aimed to estimate heritability and environmental contributions to liability of ARHI and the extent to which a polygenic risk score (PRS) derived from a recent genome-wide association study of questionnaire items regarding hearing loss using the UK Biobank is predictive of hearing loss in other samples. We examined (1) a sample from TwinsUK who have had hearing ability measured by pure-tone audiogram and the speech-to-noise ratio test as well as questionnaire measures that are comparable with the UK Biobank questionnaire items and (2) European and non-European samples from the UK Biobank which were not part of the original GWAS. Results indicated that the questionnaire items were over 50% heritable in TwinsUK and comparable with the objective hearing measures. In addition, we found very high genetic correlation (0.30-0.84) between the questionnaire responses and objective hearing measures in the TwinsUK sample. Finally, PRS computed from weighted UK Biobank GWAS results were predictive of both questionnaire and objective measures of hearing loss in the TwinsUK sample, as well as questionnaire-measured hearing loss in Europeans but not non-European subpopulations. These results demonstrate the utility of questionnaire-based methods in genetic association studies of hearing loss in adults and highlight the differences in genetic predisposition to ARHI by ethnic background.
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Stavber L, Hovnik T, Kotnik P, Lovrečić L, Kovač J, Tesovnik T, Bertok S, Dovč K, Debeljak M, Battelino T, Avbelj Stefanija M. High frequency of pathogenic ACAN variants including an intragenic deletion in selected individuals with short stature. Eur J Endocrinol 2020; 182:243-253. [PMID: 31841439 PMCID: PMC7087498 DOI: 10.1530/eje-19-0771] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/13/2019] [Indexed: 12/30/2022]
Abstract
CONTEXT Defining the underlying etiology of idiopathic short stature (ISS) improves the overall management of an individual. OBJECTIVE To assess the frequency of pathogenic ACAN variants in selected individuals. DESIGN The single-center cohort study was conducted at a tertiary university children's hospital. From 51 unrelated patients with ISS, the 16 probands aged between 3 and 18 years (12 females) with advanced bone age and/or autosomal dominant inheritance pattern of short stature were selected for the study. Fifteen family members of ACAN-positive probands were included. Exome sequencing was performed in all probands, and additional copy number variation (CNV) detection was applied in selected probands with a distinct ACAN-associated phenotype. RESULTS Systematic phenotyping of the study cohort yielded 37.5% (6/16) ACAN-positive probands, with all novel pathogenic variants, including a 6.082 kb large intragenic deletion, detected by array comparative genomic hybridization (array CGH) and exome data analysis. All variants were co-segregated with short stature phenotype, except in one family member with the intragenic deletion who had an unexpected growth pattern within the normal range (-0.5 SDS). One patient presented with otosclerosis, a sign not previously associated with aggrecanopathy. CONCLUSIONS ACAN pathogenic variants presented a common cause of familial ISS. The selection criteria used in our study were suggested for a personalized approach to genetic testing of the ACAN gene in clinical practice. Our results expanded the number of pathogenic ACAN variants, including the first intragenic deletion, and suggested CNV evaluation in patients with typical clinical features of aggrecanopathy as reasonable. Intra-familial phenotypic variability in growth patterns should be considered.
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Affiliation(s)
- L Stavber
- Unit for Special Laboratory Diagnostics, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre, Ljubljana, Slovenia
| | - T Hovnik
- Unit for Special Laboratory Diagnostics, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre, Ljubljana, Slovenia
| | - P Kotnik
- Department of Pediatric Endocrinology, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre, Ljubljana, Slovenia
| | - L Lovrečić
- Clinical Institute of Medical Genetics, University Medical Centre, Ljubljana, Slovenia
| | - J Kovač
- Unit for Special Laboratory Diagnostics, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre, Ljubljana, Slovenia
| | - T Tesovnik
- Unit for Special Laboratory Diagnostics, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre, Ljubljana, Slovenia
| | - S Bertok
- Department of Pediatric Endocrinology, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre, Ljubljana, Slovenia
| | - K Dovč
- Department of Pediatric Endocrinology, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - M Debeljak
- Unit for Special Laboratory Diagnostics, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre, Ljubljana, Slovenia
| | - T Battelino
- Department of Pediatric Endocrinology, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - M Avbelj Stefanija
- Department of Pediatric Endocrinology, Diabetes and Metabolic Diseases, University Children’s Hospital, University Medical Centre, Ljubljana, Slovenia
- Correspondence should be addressed to M Avbelj Stefanija;
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50
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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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