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Chen SP, Hsu CL, Chen TH, Pan LLH, Wang YF, Ling YH, Chang HC, Chen YM, Fann CSJ, Wang SJ. A genome-wide association study identifies novel loci of vertigo in an Asian population-based cohort. Commun Biol 2024; 7:1034. [PMID: 39174713 PMCID: PMC11341872 DOI: 10.1038/s42003-024-06603-w] [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: 06/23/2023] [Accepted: 07/18/2024] [Indexed: 08/24/2024] Open
Abstract
The contributing genetic factors of vertigo remain poorly characterized, particularly in individuals of non-European ancestries. Here we show the genetic landscape of vertigo in an Asian population-based cohort. In a two-stage genome-wide association study (Ncase = 6199; Ncontrol = 54,587), we identify vertigo-associated genomic loci in DROSHA and ZNF91/LINC01224, with the latter replicating the findings in European ancestries. Gene-based association testing corroborates these findings. Interestingly, both genes are enriched in cerebellum, a key structure receiving sensory input from the vestibular system. Subjects carrying risk alleles from lead SNPs of DROSHA and ZNF91 incur a 1.74-fold risk of vertigo than those without. Moreover, composite clinical-polygenic risk scores allow differentiation between patients and controls, yielding an area under receiver operating characteristic curve of 0.69. This study identified novel genomic loci for vertigo in an Asian population-based cohort, which may help identifying high risk subjects and provide mechanistic insight in understanding the pathogenesis of vertigo.
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Affiliation(s)
- Shih-Pin Chen
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Division of Translational Research, Department of Medical Research, Taipei Veterans General Hospital, Taipei, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chia-Lin Hsu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Ting-Huei Chen
- Department of Mathematics & Statistics, Laval University, Quebec City, QC, Canada
- Cervo Brain Research Centre, Quebec City, QC, Canada
| | - Li-Ling Hope Pan
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yen-Feng Wang
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yu-Hsiang Ling
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Hsueh-Chen Chang
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yi-Ming Chen
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Division of Translational Research, Department of Medical Research, Taichung Veterans General Hospital, Taipei, Taiwan
| | | | - Shuu-Jiun Wang
- Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan.
- Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan.
- School of Medicine, College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
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Fisch KM, Rosenthal SB, Mark A, Sasik R, Nasamran CA, Clifford R, Derebery MJ, Boussaty E, Jepsen K, Harris J, Friedman RA. The genomic landscape of Ménière's disease: a path to endolymphatic hydrops. BMC Genomics 2024; 25:646. [PMID: 38943082 PMCID: PMC11212243 DOI: 10.1186/s12864-024-10552-3] [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: 02/10/2024] [Accepted: 06/21/2024] [Indexed: 07/01/2024] Open
Abstract
BACKGROUND Ménière's disease (MD) is a disorder of the inner ear that causes episodic bouts of severe dizziness, roaring tinnitus, and fluctuating hearing loss. To date, no targeted therapy exists. As such, we have undertaken a large whole genome sequencing study on carefully phenotyped unilateral MD patients with the goal of gene/pathway discovery and a move towards targeted intervention. This study was a retrospective review of patients with a history of Ménière's disease. Genomic DNA, acquired from saliva samples, was purified and subjected to whole genome sequencing. RESULTS Stringent variant calling, performed on 511 samples passing quality checks, followed by gene-based filtering by recurrence and proximity in molecular interaction networks, led to 481 high priority MD genes. These high priority genes, including MPHOSPH8, MYO18A, TRIOBP, OTOGL, TNC, and MYO6, were previously implicated in hearing loss, balance, and cochlear function, and were significantly enriched in common variant studies of hearing loss. Validation in an independent MD cohort confirmed 82 recurrent genes. Pathway analysis pointed to cell-cell adhesion, extracellular matrix, and cellular energy maintenance as key mediators of MD. Furthermore, the MD-prioritized genes were highly expressed in human inner ear hair cells and dark/vestibular cells, and were differentially expressed in a mouse model of hearing loss. CONCLUSION By enabling the development of model systems that may lead to targeted therapies and MD screening panels, the genes and variants identified in this study will inform diagnosis and treatment of MD.
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Affiliation(s)
- Kathleen M Fisch
- Center for Computational Biology & Bioinformatics, University of California, San Diego, La Jolla, CA, USA.
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA.
| | - Sara Brin Rosenthal
- Center for Computational Biology & Bioinformatics, University of California, San Diego, La Jolla, CA, USA
| | - Adam Mark
- Center for Computational Biology & Bioinformatics, University of California, San Diego, La Jolla, CA, USA
| | - Roman Sasik
- Center for Computational Biology & Bioinformatics, University of California, San Diego, La Jolla, CA, USA
| | - Chanond A Nasamran
- Center for Computational Biology & Bioinformatics, University of California, San Diego, La Jolla, CA, USA
| | - Royce Clifford
- Department of Otolaryngology, Head & Neck Surgery, University of California, San Diego, La Jolla, CA, USA
- Research Department, VA Hospitals, San Diego, CA, USA
| | | | - Ely Boussaty
- Department of Otolaryngology, Head & Neck Surgery, University of California, San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jeffrey Harris
- Department of Otolaryngology, Head & Neck Surgery, University of California, San Diego, La Jolla, CA, USA
| | - Rick A Friedman
- Department of Otolaryngology, Head & Neck Surgery, University of California, San Diego, La Jolla, CA, USA.
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Verdoodt D, van Wijk E, Broekman S, Venselaar H, Aben F, Sels L, De Backer E, Gommeren H, Szewczyk K, Van Camp G, Ponsaerts P, Van Rompaey V, de Vrieze E. Rational design of a genomically humanized mouse model for dominantly inherited hearing loss, DFNA9. Hear Res 2024; 442:108947. [PMID: 38218018 DOI: 10.1016/j.heares.2023.108947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/04/2023] [Accepted: 12/30/2023] [Indexed: 01/15/2024]
Abstract
DFNA9 is a dominantly inherited form of adult-onset progressive hearing impairment caused by mutations in the COCH gene. COCH encodes cochlin, a crucial extracellular matrix protein. We established a genomically humanized mouse model for the Dutch/Belgian c.151C>T founder mutation in COCH. Considering upcoming sequence-specific genetic therapies, we exchanged the genomic murine Coch exons 3-6 for the corresponding human sequence. Introducing human-specific genetic information into mouse exons can be risky. To mitigate unforeseen consequences on cochlin function resulting from the introduction of the human COCH protein-coding sequence, we converted all human-specific amino acids to mouse equivalents. We furthermore optimized the recognition of the human COCH exons by the murine splicing machinery during pre-mRNA splicing. Subsequent observations in mouse embryonic stem cells revealed correct splicing of the hybrid Coch transcript. The inner ear of the established humanized Coch mice displays correctly-spliced wild-type and mutant humanized Coch alleles. For a comprehensive study of auditory function, mice were crossbred with C57BL/6 Cdh23753A>G mice to remove the Cdh23ahl allele from the genetic background of the mice. At 9 months, all humanized Coch genotypes showed hearing thresholds comparable to wild-type C57BL/6 Cdh23753A>G mice. This indicates that both the introduction of human wildtype COCH, and correction of Cdh23ahl in the humanized Coch lines was successful. Overall, our approach proved beneficial in eliminating potential adverse events of genomic humanization of mouse genes, and provides us with a model in which sequence-specific therapies directed against the human mutant COCH alle can be investigated. With the hearing and balance defects anticipated to occur late in the second year of life, a long-term follow-up study is ongoing to fully characterize the humanized Coch mouse model.
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Affiliation(s)
- Dorien Verdoodt
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium; Laboratory of Experimental Hematology, Vaccine and Infectious Disease Institute (Vaxinfectio), University of Antwerp, Antwerp, Belgium
| | - Erwin van Wijk
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Nijmegen, GA 6525, the Netherlands
| | - Sanne Broekman
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Nijmegen, GA 6525, the Netherlands
| | - Hanka Venselaar
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, GA 6525, the Netherlands
| | - Fien Aben
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium; Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Nijmegen, GA 6525, the Netherlands
| | - Lize Sels
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Evi De Backer
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium; Department of Otorhinolaryngology and Head & Neck Surgery, Antwerp University Hospital, Antwerp, Belgium
| | - Hanne Gommeren
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Krystyna Szewczyk
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Guy Van Camp
- Center for Medical Genetics, University of Antwerp, Antwerp 2000, Belgium
| | - Peter Ponsaerts
- Laboratory of Experimental Hematology, Vaccine and Infectious Disease Institute (Vaxinfectio), University of Antwerp, Antwerp, Belgium
| | - Vincent Van Rompaey
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium; Department of Otorhinolaryngology and Head & Neck Surgery, Antwerp University Hospital, Antwerp, Belgium
| | - Erik de Vrieze
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Nijmegen, GA 6525, the Netherlands.
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Pressé MT, Malgrange B, Delacroix L. The cochlear matrisome: Importance in hearing and deafness. Matrix Biol 2024; 125:40-58. [PMID: 38070832 DOI: 10.1016/j.matbio.2023.12.002] [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: 08/25/2023] [Revised: 11/20/2023] [Accepted: 12/06/2023] [Indexed: 02/12/2024]
Abstract
The extracellular matrix (ECM) consists in a complex meshwork of collagens, glycoproteins, and proteoglycans, which serves a scaffolding function and provides viscoelastic properties to the tissues. ECM acts as a biomechanical support, and actively participates in cell signaling to induce tissular changes in response to environmental forces and soluble cues. Given the remarkable complexity of the inner ear architecture, its exquisite structure-function relationship, and the importance of vibration-induced stimulation of its sensory cells, ECM is instrumental to hearing. Many factors of the matrisome are involved in cochlea development, function and maintenance, as evidenced by the variety of ECM proteins associated with hereditary deafness. This review describes the structural and functional ECM components in the auditory organ and how they are modulated over time and following injury.
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Affiliation(s)
- Mary T Pressé
- Developmental Neurobiology Unit, GIGA-Neurosciences, University of Liège, 15 avenue Hippocrate - CHU - B36 (1st floor), Liège B-4000, Belgium
| | - Brigitte Malgrange
- Developmental Neurobiology Unit, GIGA-Neurosciences, University of Liège, 15 avenue Hippocrate - CHU - B36 (1st floor), Liège B-4000, Belgium
| | - Laurence Delacroix
- Developmental Neurobiology Unit, GIGA-Neurosciences, University of Liège, 15 avenue Hippocrate - CHU - B36 (1st floor), Liège B-4000, Belgium.
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Abstract
Orchestration of protein production and degradation and the regulation of protein lifetimes play a central role in many basic biological processes. Nearly all mammalian proteins are replenished by protein turnover in waves of synthesis and degradation. Protein lifetimes in vivo are typically measured in days, but a small number of extremely long-lived proteins (ELLPs) persist for months or even years. ELLPs are rare in all tissues but are enriched in tissues containing terminally differentiated post-mitotic cells and extracellular matrix. Consistently, emerging evidence suggests that the cochlea may be particularly enriched in ELLPs. Damage to ELLPs in specialized cell types, such as crystallin in the lens cells of the eye, causes organ failure such as cataracts. Similarly, damage to cochlear ELLPs is likely to occur with many insults, including acoustic overstimulation, drugs, anoxia, and antibiotics, and may play an underappreciated role in hearing loss. Furthermore, hampered protein degradation may contribute to acquired hearing loss. In this review, I highlight our knowledge of the lifetimes of cochlear proteins with an emphasis on ELLPs and the potential contribution that impaired cochlear protein degradation has on acquired hearing loss and the emerging relevance of ELLPs.
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Affiliation(s)
- Jeffrey N Savas
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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6
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Shi X, Li J, Liu T, Zhao H, Leng H, Sun K, Feng J. Divergence of cochlear transcriptomics between reference‑based and reference‑free transcriptome analyses among Rhinolophus ferrumequinum populations. PLoS One 2023; 18:e0288404. [PMID: 37432940 DOI: 10.1371/journal.pone.0288404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 06/26/2023] [Indexed: 07/13/2023] Open
Abstract
Differences in gene expression within tissues can lead to differences in tissue function. Understanding the transcriptome of a species helps elucidate the molecular mechanisms underlying phenotypic divergence. According to the presence or absence of a reference genome of for a studied species, transcriptome analyses can be divided into reference‑based and reference‑free methods, respectively. Presently, comparisons of complete transcriptome analysis results between those two methods are still rare. In this study, we compared the cochlear transcriptome analysis results of greater horseshoe bats (Rhinolophus ferrumequinum) from three lineages in China with different acoustic phenotypes using reference‑based and reference‑free methods to explore their differences in subsequent analysis. The results gained by reference-based results had lower false-positive rates and were more accurate because differentially expressed genes among the three populations obtained by this method had greater reliability and a higher annotation rate. Some phenotype-related enrichment terms, including those related to inorganic molecules and proton transmembrane channels, were also obtained only by the reference-based method. However, the reference‑based method might have the limitation of incomplete information acquisition. Thus, we believe that a combination of reference‑free and reference‑based methods is ideal for transcriptome analyses. The results of our study provided a reference for the selection of transcriptome analysis methods in the future.
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Affiliation(s)
- Xiaoxiao Shi
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, Jilin, China
| | - Jun Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, Jilin, China
| | - Tong Liu
- Department of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Hanbo Zhao
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural, Shenzhen, China
| | - Haixia Leng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, Jilin, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, Jilin, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, Jilin, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, Jilin, China
- Department of Life Science, Jilin Agricultural University, Changchun, Jilin, China
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7
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Liao EN, Taketa E, Mohamad NI, Chan DK. Outcomes of Gene Panel Testing for Sensorineural Hearing Loss in a Diverse Patient Cohort. JAMA Netw Open 2022; 5:e2233441. [PMID: 36166228 PMCID: PMC9516276 DOI: 10.1001/jamanetworkopen.2022.33441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
IMPORTANCE A genetic diagnosis can help elucidate the prognosis of hearing loss, thus significantly affecting management. Previous studies on diagnostic yield of hearing loss genetic tests have been based on largely homogenous study populations. OBJECTIVES To examine the diagnostic yield of genetic testing in a diverse population of children, accounting for sociodemographic and patient characteristics, and assess whether these diagnoses are associated with subsequent changes in clinical management. DESIGN, SETTING, AND PARTICIPANTS This retrospective cohort study included 2075 patients seen at the Children's Communications Clinic, of whom 517 completed hearing loss gene panel testing between January 1, 2015, and November 1, 2021, at the University of California, San Francisco Benioff Children's Hospital system. From those 517 patients, 426 children with at least 2 audiograms were identified and analyzed. Data were gathered from November 2021 to January 2022 and analyzed from January to February 2022. MAIN OUTCOMES AND MEASURES The measures of interest were sociodemographic characteristics (age at testing, gender, race and ethnicity, primary language, and insurance type), hearing loss characteristics, and medical variables. The outcome was genetic testing results. Variables were compared with univariate and multivariable logistic regression. RESULTS Of the 2075 patients seen at the Children's Communications Clinic, 517 (median [range] age, 8 [0-31] years; 264 [51.1%] male; 351 [67.9%] from an underrepresented minority [URM] group) underwent a hearing loss panel genetic test between January 1, 2015, and November 1, 2021. Among those 517 patients, 426 children (median [range] age, 8 [0-18] years; 221 [51.9%] male; 304 [71.4%] from an URM group) with 2 or more audiograms were included in a subsequent analysis. On multivariable logistic regression, age at testing (odds ratio [OR], 0.87; 95% CI, 0.78-0.97), URM group status (OR, 0.29; 95% CI, 0.13-0.66), comorbidities (OR, 0.27; 95% CI, 0.14-0.53), late-identified hearing loss (passed newborn hearing screen; OR, 0.27; 95% CI, 0.08-0.86), and unilateral hearing loss (OR, 0.04; 95% CI, 0.005-0.33) were the only factors associated with genetic diagnosis. No association was found between genetic diagnosis yield and other sociodemographic variables or hearing loss characteristics. Patients in URM and non-URM groups had statistically similar clinical features. A total of 32 of 109 children (29.4%) who received a genetic diagnosis received diagnoses that significantly affected prognosis because of identification of syndromic or progressive sensorineural hearing loss or auditory neuropathy spectrum disorder relating to otoferlin. CONCLUSIONS AND RELEVANCE This cohort study's findings suggest that genetic testing may be broadly useful in improving clinical management of children with hearing loss. More research is warranted to discover and characterize diagnostic genes for those who have been historically underrepresented in research and medicine.
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Affiliation(s)
- Elizabeth N. Liao
- Department of Otolaryngology–Head & Neck Surgery, University of California, San Francisco
| | - Emily Taketa
- Department of Otolaryngology–Head & Neck Surgery, University of California, San Francisco
| | - Noura I. Mohamad
- Department of Otolaryngology–Head & Neck Surgery, University of California, San Francisco
| | - Dylan K. Chan
- Department of Otolaryngology–Head & Neck Surgery, University of California, San Francisco
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8
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Imtiaz A. ARNSHL gene identification: past, present and future. Mol Genet Genomics 2022; 297:1185-1193. [DOI: 10.1007/s00438-022-01926-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 07/05/2022] [Indexed: 10/16/2022]
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Zhang D, Wu J, Yuan Y, Li X, Gao X, Han M, Gao S, Huang S, Dai P. A novel missense variant in CEACAM16 gene causes autosomal dominant nonsyndromic hearing loss. Ann Hum Genet 2022; 86:207-217. [PMID: 35292975 PMCID: PMC9314904 DOI: 10.1111/ahg.12463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 11/27/2022]
Abstract
AbstractAimAutosomal dominant non‐syndromic hearing loss is a common sensorineural disorder with extremely high genetic heterogeneity. CEA antigen‐related cell adhesion molecule 16(CEACAM16)is a secreted glycoprotein encoded by the CEACAM16 gene. Mutations in CEACAM16 lead to autosomal dominant non‐syndromic hearing loss in humans, due defects in the tectorial membrane of the inner ear. Here we reported a novel missense variant in CEACAM16 gene causes autosomal dominant non‐syndromic hearing loss.Material and methodsA four‐generation Chinese family affected by late‐onset and progressive hearing loss was enrolled in this study. The proband was analyzed by targeted next‐generation sequencing and bioinformatic analysis. And in vitro experiments were performed in overexpressed transfected HEK293T cells to investigate the pathogenesis of the mutant protein.ResultsWe identified a novel missense variant in the CEACAM16 gene c.763A>G; (p.Arg255Gly) as causing autosomal dominant non‐syndromic hearing loss in the Chinese family. Using Western blot analysis, ELISA, and immunofluorescence we found increased expression level of the secreted mutant CEACAM16 protein, both intracellularly and extracellularly, compared with wild type CEACAM16 protein.ConclusionOur study showed that the p.Arg255Gly variant leads to increased secretion of mutant CEACAM16 protein, with potential deleterious effect to the function of the protein. Our findings expand the mutation spectrum of CEACAM16, and further the understanding CEACAM16 function and implications in disease.
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Affiliation(s)
- Dejun Zhang
- College of Otolaryngology Head and Neck SurgeryChinese PLA General HospitalBeijingChina
- Department of Otolaryngology Head and Neck SurgeryThe Second Hospital of Jilin UniversityChangchunChina
- State Key Lab of Hearing Science, Ministry of EducationNational Clinical Research Center for Otolaryngologic DiseasesBeijingChina
- Beijing Key Lab of Hearing Impairment for Prevention and TreatmentBeijingChina
| | - Jie Wu
- College of Otolaryngology Head and Neck SurgeryChinese PLA General HospitalBeijingChina
- State Key Lab of Hearing Science, Ministry of EducationNational Clinical Research Center for Otolaryngologic DiseasesBeijingChina
- Beijing Key Lab of Hearing Impairment for Prevention and TreatmentBeijingChina
| | - Yongyi Yuan
- College of Otolaryngology Head and Neck SurgeryChinese PLA General HospitalBeijingChina
- State Key Lab of Hearing Science, Ministry of EducationNational Clinical Research Center for Otolaryngologic DiseasesBeijingChina
- Beijing Key Lab of Hearing Impairment for Prevention and TreatmentBeijingChina
| | - Xiaohong Li
- Department of Otolaryngology, Head and Neck Surgery, National Children's Medical Center/Beijing Children's HospitalCapital Medical UniversityBeijingPR China
| | - Xue Gao
- Department of OtolaryngologyPLA Rocket Force Characteristic Medical CenterBeijingChina
| | - Mingyu Han
- College of Otolaryngology Head and Neck SurgeryChinese PLA General HospitalBeijingChina
- State Key Lab of Hearing Science, Ministry of EducationNational Clinical Research Center for Otolaryngologic DiseasesBeijingChina
- Beijing Key Lab of Hearing Impairment for Prevention and TreatmentBeijingChina
| | - Song Gao
- Department of OtolaryngologySouth‐East Hospital Affiliated to Xiamen UniversityZhangzhouChina
| | - Shasha Huang
- College of Otolaryngology Head and Neck SurgeryChinese PLA General HospitalBeijingChina
- State Key Lab of Hearing Science, Ministry of EducationNational Clinical Research Center for Otolaryngologic DiseasesBeijingChina
- Beijing Key Lab of Hearing Impairment for Prevention and TreatmentBeijingChina
| | - Pu Dai
- College of Otolaryngology Head and Neck SurgeryChinese PLA General HospitalBeijingChina
- State Key Lab of Hearing Science, Ministry of EducationNational Clinical Research Center for Otolaryngologic DiseasesBeijingChina
- Beijing Key Lab of Hearing Impairment for Prevention and TreatmentBeijingChina
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10
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Acharya A, Schrauwen I, Leal SM. Identification of autosomal recessive nonsyndromic hearing impairment genes through the study of consanguineous and non-consanguineous families: past, present, and future. Hum Genet 2022; 141:413-430. [PMID: 34291353 PMCID: PMC10416318 DOI: 10.1007/s00439-021-02309-9] [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: 05/31/2021] [Accepted: 06/24/2021] [Indexed: 10/20/2022]
Abstract
Hearing impairment (HI) is one of the most common sensory disabilities with exceptionally high genetic heterogeneity. Of genetic HI cases, 30% are syndromic and 70% are nonsyndromic. For nonsyndromic (NS) HI, 77% of the cases are due to autosomal recessive (AR) inheritance. ARNSHI is usually congenital/prelingual, severe-to-profound, affects all frequencies and is not progressive. Thus far, 73 ARNSHI genes have been identified. Populations with high rates of consanguinity have been crucial in the identification of ARNSHI genes, and 92% (67/73) of these genes were identified in consanguineous families. Recent changes in genomic technologies and analyses have allowed a shift towards ARNSHI gene discovery in outbred populations. The latter is crucial towards understanding the genetic architecture of ARNSHI in diverse and understudied populations. We present an overview of the 73 ARNSHI genes, the methods used to identify them, including next-generation sequencing which revolutionized the field, and new technologies that show great promise in advancing ARNSHI discoveries.
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Affiliation(s)
- Anushree Acharya
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, New York, NY, USA.
- Department of Neurology, Columbia University Medical Center, New York, NY, USA.
- Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA.
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11
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Pan C, Li J, Wang S, Shi C, Zhang Y, Yu Y. Novel heterozygous mutations in the otogelin-like (OTOGL) gene in a child with bilateral mild nonsyndromic sensorineural hearing loss. Gene 2022; 808:146000. [PMID: 34626719 DOI: 10.1016/j.gene.2021.146000] [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: 08/22/2021] [Revised: 09/22/2021] [Accepted: 10/04/2021] [Indexed: 11/29/2022]
Abstract
Hearing loss is a common disease, of which genetic factors are the main cause. The incidence of mild or moderate postlingual deafness in children is not high, and the impact on life and learning is not as severe as that of prelingual deafness. This leads to insufficient attention to the disorder in the clinic. To date, only a few disease-causing genes have been reported. This report describe a case of novel heterozygous mutations in OTOGL that causes nonsyndromic mild sensorineural hearing loss. Basic information, imaging examinations, audiological examination, and vestibular function tests of the proband were collected. Blood samples of the proband's family were collected and analyzed by whole exome sequencing and Sanger sequencing. A pedigree diagram was drawn and the genetic patterns were analyzed. The proband is a 16-year-old female student with mild sensorineural hearing loss. High-resolution CT of the inner ear and vestibular function tests showed no abnormalities. The age of onset was approximately 4 years old. Except for hearing loss, no lesions were seen in other organs. The parents of the proband were not close relatives and had normal hearing. Two novel heterozygous mutations were found in the OTOGL gene. The c.5038del (p.D1680Ifs*6) variant was inherited from the father, and the c.2770C > T (p.R924X) variant from the mother. They enriched the mutation spectrum of OTOGL, which provides the basis for gene function research and genetic consultation.
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Affiliation(s)
- Chen Pan
- Department of Otolaryngology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Jun Li
- Department of Otolaryngology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Shixin Wang
- Department of Otolaryngology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Chen Shi
- Department of Otolaryngology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Yunmei Zhang
- Department of Otolaryngology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Yafeng Yu
- Department of Otolaryngology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China.
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12
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Crouzier L, Richard EM, Sourbron J, Lagae L, Maurice T, Delprat B. Use of Zebrafish Models to Boost Research in Rare Genetic Diseases. Int J Mol Sci 2021; 22:13356. [PMID: 34948153 PMCID: PMC8706563 DOI: 10.3390/ijms222413356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 02/06/2023] Open
Abstract
Rare genetic diseases are a group of pathologies with often unmet clinical needs. Even if rare by a single genetic disease (from 1/2000 to 1/more than 1,000,000), the total number of patients concerned account for approximatively 400 million peoples worldwide. Finding treatments remains challenging due to the complexity of these diseases, the small number of patients and the challenge in conducting clinical trials. Therefore, innovative preclinical research strategies are required. The zebrafish has emerged as a powerful animal model for investigating rare diseases. Zebrafish combines conserved vertebrate characteristics with high rate of breeding, limited housing requirements and low costs. More than 84% of human genes responsible for diseases present an orthologue, suggesting that the majority of genetic diseases could be modelized in zebrafish. In this review, we emphasize the unique advantages of zebrafish models over other in vivo models, particularly underlining the high throughput phenotypic capacity for therapeutic screening. We briefly introduce how the generation of zebrafish transgenic lines by gene-modulating technologies can be used to model rare genetic diseases. Then, we describe how zebrafish could be phenotyped using state-of-the-art technologies. Two prototypic examples of rare diseases illustrate how zebrafish models could play a critical role in deciphering the underlying mechanisms of rare genetic diseases and their use to identify innovative therapeutic solutions.
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Affiliation(s)
- Lucie Crouzier
- MMDN, University of Montpellier, EPHE, INSERM, 34095 Montpellier, France; (L.C.); (E.M.R.); (T.M.)
| | - Elodie M. Richard
- MMDN, University of Montpellier, EPHE, INSERM, 34095 Montpellier, France; (L.C.); (E.M.R.); (T.M.)
| | - Jo Sourbron
- Department of Development and Regeneration, Section Pediatric Neurology, University Hospital KU Leuven, 3000 Leuven, Belgium; (J.S.); (L.L.)
| | - Lieven Lagae
- Department of Development and Regeneration, Section Pediatric Neurology, University Hospital KU Leuven, 3000 Leuven, Belgium; (J.S.); (L.L.)
| | - Tangui Maurice
- MMDN, University of Montpellier, EPHE, INSERM, 34095 Montpellier, France; (L.C.); (E.M.R.); (T.M.)
| | - Benjamin Delprat
- MMDN, University of Montpellier, EPHE, INSERM, 34095 Montpellier, France; (L.C.); (E.M.R.); (T.M.)
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13
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Pavlenkova Z, Varga L, Borecka S, Karhanek M, Huckova M, Skopkova M, Profant M, Gasperikova D. Comprehensive molecular-genetic analysis of mid-frequency sensorineural hearing loss. Sci Rep 2021; 11:22488. [PMID: 34795337 PMCID: PMC8602250 DOI: 10.1038/s41598-021-01876-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/27/2021] [Indexed: 12/14/2022] Open
Abstract
The genetic heterogeneity of sensorineural hearing loss (SNHL) is a major hurdle to the detection of disease-causing variants. We aimed to identify underlying causal genes associated with mid-frequency hearing loss (HL), which contributes to less than about 1% of SNHL cases, by whole exome sequencing (WES). Thirty families segregating mid-frequency SNHL, in whom biallelic GJB2 mutations had been previously excluded, were selected from among 851 families in our DNA repository of SNHL. DNA samples from the probands were subjected to WES analysis and searched for candidate variants associated with SNHL. We were able to identify the genetic aetiology in six probands (20%). In total, we found three pathogenic and three likely pathogenic variants in four genes (COL4A5, OTOGL, TECTA, TMPRSS3). One more proband was a compound heterozygote for a pathogenic variant and a variant of uncertain significance (VUS) in MYO15A gene. To date, MYO15A and TMPRSS3 have not yet been described in association with mid-frequency SNHL. In eight additional probands, eight candidate VUS variants were detected in five genes (DIAPH1, MYO7A, TECTA, TMC1, TSPEAR). Seven of these 16 variants have not yet been published or mentioned in the available databases. The most prevalent gene was TECTA, identified in 23% of all tested families. Furthermore, we confirmed the hypothesis that a substantive portion of cases with this conspicuous audiogram shape is a consequence of a genetic disorder.
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Affiliation(s)
- Zuzana Pavlenkova
- Department of Otorhinolaryngology-Head and Neck Surgery, Faculty of Medicine and University Hospital, Comenius University, Bratislava, Slovakia.,DIABGENE Laboratory, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lukas Varga
- Department of Otorhinolaryngology-Head and Neck Surgery, Faculty of Medicine and University Hospital, Comenius University, Bratislava, Slovakia. .,DIABGENE Laboratory, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia.
| | - Silvia Borecka
- DIABGENE Laboratory, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Miloslav Karhanek
- Laboratory of Bioinformatics, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Miloslava Huckova
- DIABGENE Laboratory, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Martina Skopkova
- DIABGENE Laboratory, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Milan Profant
- Department of Otorhinolaryngology-Head and Neck Surgery, Faculty of Medicine and University Hospital, Comenius University, Bratislava, Slovakia
| | - Daniela Gasperikova
- DIABGENE Laboratory, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
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14
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Skuladottir AT, Bjornsdottir G, Nawaz MS, Petersen H, Rognvaldsson S, Moore KHS, Olafsson PI, Magnusson SH, Bjornsdottir A, Sveinsson OA, Sigurdardottir GR, Saevarsdottir S, Ivarsdottir EV, Stefansdottir L, Gunnarsson B, Muhlestein JB, Knowlton KU, Jones DA, Nadauld LD, Hartmann AM, Rujescu D, Strupp M, Walters GB, Thorgeirsson TE, Jonsdottir I, Holm H, Thorleifsson G, Gudbjartsson DF, Sulem P, Stefansson H, Stefansson K. A genome-wide meta-analysis uncovers six sequence variants conferring risk of vertigo. Commun Biol 2021; 4:1148. [PMID: 34620984 PMCID: PMC8497462 DOI: 10.1038/s42003-021-02673-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 09/09/2021] [Indexed: 11/17/2022] Open
Abstract
Vertigo is the leading symptom of vestibular disorders and a major risk factor for falls. In a genome-wide association study of vertigo (Ncases = 48,072, Ncontrols = 894,541), we uncovered an association with six common sequence variants in individuals of European ancestry, including missense variants in ZNF91, OTOG, OTOGL, and TECTA, and a cis-eQTL for ARMC9. The association of variants in ZNF91, OTOGL, and OTOP1 was driven by an association with benign paroxysmal positional vertigo. Using previous reports of sequence variants associating with age-related hearing impairment and motion sickness, we found eight additional variants that associate with vertigo. Although disorders of the auditory and the vestibular system may co-occur, none of the six genome-wide significant vertigo variants were associated with hearing loss and only one was associated with age-related hearing impairment. Our results uncovered sequence variants associating with vertigo in a genome-wide association study and implicated genes with known roles in inner ear development, maintenance, and disease.
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Affiliation(s)
| | | | - Muhammad Sulaman Nawaz
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Hannes Petersen
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Akureyri Hospital, Akureyri, Iceland
| | | | | | | | | | | | - Olafur A Sveinsson
- Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland
| | | | - Saedis Saevarsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland
| | | | | | | | - Joseph B Muhlestein
- Intermountain Medical Center, Intermountain Heart Institute, Salt Lake City, UT, USA
- University of Utah, School of Medicine, Salt Lake City, UT, USA
| | - Kirk U Knowlton
- Intermountain Medical Center, Intermountain Heart Institute, Salt Lake City, UT, USA
- University of Utah, School of Medicine, Salt Lake City, UT, USA
| | - David A Jones
- Precision Genomics, Intermountain Healthcare, Saint George, UT, USA
| | - Lincoln D Nadauld
- Precision Genomics, Intermountain Healthcare, Saint George, UT, USA
- Stanford University, School of Medicine, Stanford, CA, USA
| | - Annette M Hartmann
- Department of Psychiatry, Psychotherapy and Psychosomatics, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Dan Rujescu
- Department of Psychiatry, Psychotherapy and Psychosomatics, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Michael Strupp
- Department of Neurology and German Center for Vertigo and Balance Disorders, Ludwig Maximilians University, Munich, Germany
| | - G Bragi Walters
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | | | - Ingileif Jonsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Hilma Holm
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
| | | | | | | | | | - Kari Stefansson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland.
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15
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Peusner KD, Bell NM, Hirsch JC, Beraneck M, Popratiloff A. Understanding the Pathophysiology of Congenital Vestibular Disorders: Current Challenges and Future Directions. Front Neurol 2021; 12:708395. [PMID: 34589045 PMCID: PMC8475631 DOI: 10.3389/fneur.2021.708395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/13/2021] [Indexed: 12/13/2022] Open
Abstract
In congenital vestibular disorders (CVDs), children develop an abnormal inner ear before birth and face postnatal challenges to maintain posture, balance, walking, eye-hand coordination, eye tracking, or reading. Only limited information on inner ear pathology is acquired from clinical imaging of the temporal bone or studying histological slides of the temporal bone. A more comprehensive and precise assessment and determination of the underlying mechanisms necessitate analyses of the disorders at the cellular level, which can be achieved using animal models. Two main criteria for a suitable animal model are first, a pathology that mirrors the human disorder, and second, a reproducible experimental outcome leading to statistical power. With over 40 genes that affect inner ear development, the phenotypic abnormalities resulting from congenital vestibular disorders (CVDs) are highly variable. Nonetheless, there is a large subset of CVDs that form a common phenotype of a sac-like inner ear with the semicircular canals missing or dysplastic, and discrete abnormalities in the vestibular sensory organs. We have focused the review on this subset, but to advance research on CVDs we have added other CVDs not forming a sac-like inner ear. We have included examples of animal models used to study these CVDs. Presently, little is known about the central pathology resulting from CVDs at the cellular level in the central vestibular neural network, except for preliminary studies on a chick model that show significant loss of second-order, vestibular reflex projection neurons.
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Affiliation(s)
- Kenna D Peusner
- Department of Neurology, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Nina M Bell
- Department of Neurology, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - June C Hirsch
- Department of Neurology, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Mathieu Beraneck
- Université de Paris, Integrative Neuroscience and Cognition Center, CNRS UMR 8002, Paris, France
| | - Anastas Popratiloff
- The George Washington University Nanofabrication and Imaging Center, Washington, DC, United States
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16
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Mackowetzky K, Yoon KH, Mackowetzky EJ, Waskiewicz AJ. Development and evolution of the vestibular apparatuses of the inner ear. J Anat 2021; 239:801-828. [PMID: 34047378 PMCID: PMC8450482 DOI: 10.1111/joa.13459] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/07/2021] [Accepted: 05/06/2021] [Indexed: 12/16/2022] Open
Abstract
The vertebrate inner ear is a labyrinthine sensory organ responsible for perceiving sound and body motion. While a great deal of research has been invested in understanding the auditory system, a growing body of work has begun to delineate the complex developmental program behind the apparatuses of the inner ear involved with vestibular function. These animal studies have helped identify genes involved in inner ear development and model syndromes known to include vestibular dysfunction, paving the way for generating treatments for people suffering from these disorders. This review will provide an overview of known inner ear anatomy and function and summarize the exciting discoveries behind inner ear development and the evolution of its vestibular apparatuses.
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Affiliation(s)
- Kacey Mackowetzky
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Kevin H. Yoon
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | | | - Andrew J. Waskiewicz
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
- Women & Children’s Health Research InstituteUniversity of AlbertaEdmontonAlbertaCanada
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17
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Smits JJ, de Bruijn SE, Lanting CP, Oostrik J, O'Gorman L, Mantere T, Cremers FPM, Roosing S, Yntema HG, de Vrieze E, Derks R, Hoischen A, Pegge SAH, Neveling K, Pennings RJE, Kremer H. Exploring the missing heritability in subjects with hearing loss, enlarged vestibular aqueducts, and a single or no pathogenic SLC26A4 variant. Hum Genet 2021; 141:465-484. [PMID: 34410491 PMCID: PMC9035008 DOI: 10.1007/s00439-021-02336-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 08/09/2021] [Indexed: 12/11/2022]
Abstract
Pathogenic variants in SLC26A4 have been associated with autosomal recessive hearing loss (arHL) and a unilateral or bilateral enlarged vestibular aqueduct (EVA). SLC26A4 is the second most frequently mutated gene in arHL. Despite the strong genotype–phenotype correlation, a significant part of cases remains genetically unresolved. In this study, we investigated a cohort of 28 Dutch index cases diagnosed with HL in combination with an EVA but without (M0) or with a single (M1) pathogenic variant in SLC26A4. To explore the missing heritability, we first determined the presence of the previously described EVA-associated haplotype (Caucasian EVA (CEVA)), characterized by 12 single nucleotide variants located upstream of SLC26A4. We found this haplotype and a delimited V1-CEVA haplotype to be significantly enriched in our M1 patient cohort (10/16 cases). The CEVA haplotype was also present in two M0 cases (2/12). Short- and long-read whole genome sequencing and optical genome mapping could not prioritize any of the variants present within the CEVA haplotype as the likely pathogenic defect. Short-read whole-genome sequencing of the six M1 cases without this haplotype and the two M0/CEVA cases only revealed previously overlooked or misinterpreted splice-altering SLC26A4 variants in two cases, who are now genetically explained. No deep-intronic or structural variants were identified in any of the M1 subjects. With this study, we have provided important insights that will pave the way for elucidating the missing heritability in M0 and M1 SLC26A4 cases. For pinpointing the pathogenic effect of the CEVA haplotype, additional analyses are required addressing defect(s) at the RNA, protein, or epigenetic level.
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Affiliation(s)
- Jeroen J Smits
- Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Suzanne E de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Cornelis P Lanting
- Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jaap Oostrik
- Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Luke O'Gorman
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Tuomo Mantere
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter Oulu, University of Oulu, Oulu, Finland
| | | | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Erik de Vrieze
- Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronny Derks
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Center for Infectious Diseases (RCI), Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Expertise Center for Immunodeficiency and Autoinflammation and Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sjoert A H Pegge
- Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Ronald J E Pennings
- Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hannie Kremer
- Hearing and Genes, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands. .,Department of Human Genetics, Radboud University Medical Center, Internal Postal Code 855, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands. .,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.
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18
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Li Z, Zhang Y, Zhang X, Cao C, Luo X, Gui Y, Tang Y, Yuan S. OTOGL, a gelforming mucin protein, is nonessential for male germ cell development and spermatogenesis in mice. Reprod Biol Endocrinol 2021; 19:95. [PMID: 34174893 PMCID: PMC8234668 DOI: 10.1186/s12958-021-00779-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/10/2021] [Indexed: 01/05/2023] Open
Abstract
Otogelin-like protein (encoded by Otogl) was highly structural similar to the gelforming mucin proteins. Although human OTOG mutations have been linked to deafness, the biological function of OTOGL in male germ cell development remains enigmatic. In screening 336 patients with non-obstructive azoospermia (NOA), OTOGL displays the high mutant ratio (13.99 %). Then, we examined the expression of OTOGL in developing mouse testes. Otogl mRNA and protein are continually expressed in postnatal developing testes from postnatal day 0 (P0) testes to P21 testes exhibiting a decreased trend with the age growth. We thus generated a global Otogl knockout mouse (KO) model using the CRISPR/Cas9 technology; however, Otogl KO mice displayed normal development and fertility. Further histological analysis of Otogl knockout mouse testes revealed that all types of spermatogenic cells are present in Otogl KO seminiferous tubules. Together, our study suggested that OTOGL is nonessential for male germ cell development and spermatogenesis.
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Affiliation(s)
- Zhiming Li
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, Hubei, China
| | - Yan Zhang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, Hubei, China
| | - Xinzong Zhang
- NHC Key Laboratory of Male Reproduction and Genetics, Family Planning Research Institute of Guangdong Province, Guangzhou, China
| | - Congcong Cao
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, Hubei, China
| | - Xiaomin Luo
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen Peking University- Hong Kong University of Science and Technology Medical Center, 518036, Shenzhen, China
| | - Yaoting Gui
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen Peking University- Hong Kong University of Science and Technology Medical Center, 518036, Shenzhen, China
| | - Yunge Tang
- NHC Key Laboratory of Male Reproduction and Genetics, Family Planning Research Institute of Guangdong Province, Guangzhou, China.
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, Hubei, China.
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, Guangdong, China.
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19
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Sheets L, Holmgren M, Kindt KS. How Zebrafish Can Drive the Future of Genetic-based Hearing and Balance Research. J Assoc Res Otolaryngol 2021; 22:215-235. [PMID: 33909162 PMCID: PMC8110678 DOI: 10.1007/s10162-021-00798-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/23/2021] [Indexed: 02/06/2023] Open
Abstract
Over the last several decades, studies in humans and animal models have successfully identified numerous molecules required for hearing and balance. Many of these studies relied on unbiased forward genetic screens based on behavior or morphology to identify these molecules. Alongside forward genetic screens, reverse genetics has further driven the exploration of candidate molecules. This review provides an overview of the genetic studies that have established zebrafish as a genetic model for hearing and balance research. Further, we discuss how the unique advantages of zebrafish can be leveraged in future genetic studies. We explore strategies to design novel forward genetic screens based on morphological alterations using transgenic lines or behavioral changes following mechanical or acoustic damage. We also outline how recent advances in CRISPR-Cas9 can be applied to perform reverse genetic screens to validate large sequencing datasets. Overall, this review describes how future genetic studies in zebrafish can continue to advance our understanding of inherited and acquired hearing and balance disorders.
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Affiliation(s)
- Lavinia Sheets
- Department of Otolaryngology-Head & Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Melanie Holmgren
- Department of Otolaryngology-Head & Neck Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Katie S Kindt
- Section On Sensory Cell Development and Function, National Institutes On Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, USA.
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20
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Jedrychowska J, Gasanov EV, Korzh V. Kcnb1 plays a role in development of the inner ear. Dev Biol 2020; 471:65-75. [PMID: 33316259 DOI: 10.1016/j.ydbio.2020.12.007] [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: 04/05/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 10/22/2022]
Abstract
The function of the inner ear depends on the maintenance of high concentrations of K+ ions. The slow-inactivating delayed rectifier Kv2.1/KCNB1 channel works in the inner ear in mammals. The kcnb1 gene is expressed in the otic vesicle of developing zebrafish, suggesting its role in development of the inner ear. In the present study, we found that a Kcnb1 loss-of-function mutation affected development of the inner ear at multiple levels, including otic vesicle expansion, otolith formation, and the proliferation and differentiation of mechanosensory cells. This resulted in defects of kinocilia and stereocilia and abnormal function of the inner ear detected by behavioral assays. The quantitative transcriptional analysis of 75 genes demonstrated that the kcnb1 mutation affected the transcription of genes that are involved in K+ metabolism, cell proliferation, cilia development, and intracellular protein trafficking. These results demonstrate a role for Kv2.1/Kcnb1 channels in development of the inner ear in zebrafish.
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Affiliation(s)
- Justyna Jedrychowska
- International Institute of Molecular and Cell Biology in Warsaw, Poland; Postgraduate School of Molecular Medicine, Warsaw Medical University, Warsaw, Poland
| | - Eugene V Gasanov
- International Institute of Molecular and Cell Biology in Warsaw, Poland
| | - Vladimir Korzh
- International Institute of Molecular and Cell Biology in Warsaw, Poland.
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21
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Vona B, Doll J, Hofrichter MAH, Haaf T, Varshney GK. Small fish, big prospects: using zebrafish to unravel the mechanisms of hereditary hearing loss. Hear Res 2020; 397:107906. [PMID: 32063424 PMCID: PMC7415493 DOI: 10.1016/j.heares.2020.107906] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/13/2020] [Accepted: 01/29/2020] [Indexed: 12/16/2022]
Abstract
Over the past decade, advancements in high-throughput sequencing have greatly enhanced our knowledge of the mutational signatures responsible for hereditary hearing loss. In its present state, the field has a largely uncensored view of protein coding changes in a growing number of genes that have been associated with hereditary hearing loss, and many more that have been proposed as candidate genes. Sequencing data can now be generated using methods that have become widespread and affordable. The greatest hurdles facing the field concern functional validation of uncharacterized genes and rapid application to human diseases, including hearing and balance disorders. To date, over 30 hearing-related disease models exist in zebrafish. New genome editing technologies, including CRISPR/Cas9 will accelerate the functional validation of hearing loss genes and variants in zebrafish. Here, we discuss current progress in the field and recent advances in genome editing approaches.
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Affiliation(s)
- Barbara Vona
- Department of Otolaryngology--Head & Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, Tübingen, Germany.
| | - Julia Doll
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | | | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Gaurav K Varshney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States.
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22
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Su X, Feng Y, Rahman SA, Wu S, Li G, Rüschendorf F, Zhao L, Cui H, Liang J, Fang L, Hu H, Froehler S, Yu Y, Patone G, Hummel O, Chen Q, Raile K, Luft FC, Bähring S, Hussain K, Chen W, Zhang J, Gong M. Phosphatidylinositol 4-kinase β mutations cause nonsyndromic sensorineural deafness and inner ear malformation. J Genet Genomics 2020; 47:618-626. [PMID: 33358777 DOI: 10.1016/j.jgg.2020.07.008] [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: 03/05/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 10/23/2022]
Abstract
Congenital hearing loss is a common disorder worldwide. Heterogeneous gene variation accounts for approximately 20-25% of such patients. We investigated a five-generation Chinese family with autosomal-dominant nonsyndromic sensorineural hearing loss (SNHL). No wave was detected in the pure-tone audiometry, and the auditory brainstem response was absent in all patients. Computed tomography of the patients, as well as of two sporadic SNHL cases, showed bilateral inner ear anomaly, cochlear maldevelopment, absence of the osseous spiral lamina, and an enlarged vestibular aqueduct. Such findings were absent in nonaffected persons. We used linkage analysis and exome sequencing and uncovered a heterozygous missense mutation in the PI4KB gene (p.Gln121Arg) encoding phosphatidylinositol 4-kinase β (PI4KB) from the patients in this family. In addition, 3 missense PI4KB (p.Val434Gly, p.Glu667Lys, and p.Met739Arg) mutations were identified in five patients with nonsyndromic SNHL from 57 sporadic cases. No such mutations were present within 600 Chinese controls, the 1000 genome project, gnomAD, or similar databases. Depleting pi4kb mRNA expression in zebrafish caused inner ear abnormalities and audiosensory impairment, mimicking the patient phenotypes. Moreover, overexpression of 4 human missense PI4KB mutant mRNAs in zebrafish embryos resulted in impaired hearing function, suggesting dominant-negative effects. Taken together, our results reveal that PI4KB mutations can cause SNHL and inner ear malformation. PI4KB should be included in neonatal deafness screening.
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Affiliation(s)
- Xiulan Su
- Clinical Medicine Research Center, Affiliated Hospital of Inner Mongolia Medical University, Huhhot, 010050, China
| | - Yufei Feng
- Affiliated Hospital of Guangdong Medical University & Key Laboratory of Zebrafish Model for Development and Disease of Guangdong Medical University, Zhanjiang, 524001, China; Marine Medical Research Institute of Guangdong Zhanjiang, Zhanjiang, 524023, China
| | - Sofia A Rahman
- Genomic Medicine Programme, UCL Institute of Child Health and Great Ormond Street Hospital for Children, 30 Guilford Street, London, WC1N 1EH, UK
| | - Shuilong Wu
- Affiliated Hospital of Guangdong Medical University & Key Laboratory of Zebrafish Model for Development and Disease of Guangdong Medical University, Zhanjiang, 524001, China; Marine Medical Research Institute of Guangdong Zhanjiang, Zhanjiang, 524023, China
| | - Guoan Li
- Affiliated Hospital of Guangdong Medical University & Key Laboratory of Zebrafish Model for Development and Disease of Guangdong Medical University, Zhanjiang, 524001, China; Marine Medical Research Institute of Guangdong Zhanjiang, Zhanjiang, 524023, China
| | - Franz Rüschendorf
- Max-Delbrueck-Center for Molecular Medicine (MDC), Robert-Roessle-Str.10, Berlin, 13125, Germany
| | - Lei Zhao
- Department of Radiology, Affiliated Hospital of Inner Mongolia Medical University, Huhhot, 010050, China
| | - Hongwei Cui
- Clinical Medicine Research Center, Affiliated Hospital of Inner Mongolia Medical University, Huhhot, 010050, China
| | - Junqing Liang
- Affiliated People Hospital of Inner Mongolia Medical University, Huhhot, 010050, China
| | - Liang Fang
- Max-Delbrueck-Center for Molecular Medicine (MDC), Robert-Roessle-Str.10, Berlin, 13125, Germany; Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Hao Hu
- Guangzhou Women and Children's Medical Center, Guangzhou, 510623, China
| | - Sebastian Froehler
- Max-Delbrueck-Center for Molecular Medicine (MDC), Robert-Roessle-Str.10, Berlin, 13125, Germany
| | - Yong Yu
- Max-Delbrueck-Center for Molecular Medicine (MDC), Robert-Roessle-Str.10, Berlin, 13125, Germany
| | - Giannino Patone
- Max-Delbrueck-Center for Molecular Medicine (MDC), Robert-Roessle-Str.10, Berlin, 13125, Germany
| | - Oliver Hummel
- Max-Delbrueck-Center for Molecular Medicine (MDC), Robert-Roessle-Str.10, Berlin, 13125, Germany
| | - Qinghua Chen
- Department of Radiology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
| | - Klemens Raile
- Experimental and Clinical Research Center (ECRC), A Joint Cooperation Between the Charité Medical Faculty and the Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Lindenberger Weg.80, Berlin, 13125, Germany
| | - Friedrich C Luft
- Experimental and Clinical Research Center (ECRC), A Joint Cooperation Between the Charité Medical Faculty and the Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Lindenberger Weg.80, Berlin, 13125, Germany
| | - Sylvia Bähring
- Experimental and Clinical Research Center (ECRC), A Joint Cooperation Between the Charité Medical Faculty and the Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Lindenberger Weg.80, Berlin, 13125, Germany
| | - Khalid Hussain
- Department of Paediatric Medicine Division of Endocrinology, Sidra Medical & Research Center, OPC, Doha, C6-337, Qatar
| | - Wei Chen
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China; Medi-X Institute, SUSTec Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jingjing Zhang
- Affiliated Hospital of Guangdong Medical University & Key Laboratory of Zebrafish Model for Development and Disease of Guangdong Medical University, Zhanjiang, 524001, China; Marine Medical Research Institute of Guangdong Zhanjiang, Zhanjiang, 524023, China.
| | - Maolian Gong
- Experimental and Clinical Research Center (ECRC), A Joint Cooperation Between the Charité Medical Faculty and the Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Lindenberger Weg.80, Berlin, 13125, Germany.
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23
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Akil O. Dual and triple AAV delivery of large therapeutic gene sequences into the inner ear. Hear Res 2020; 394:107912. [DOI: 10.1016/j.heares.2020.107912] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 02/04/2020] [Accepted: 02/07/2020] [Indexed: 12/17/2022]
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24
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Zhao T, Liu X, Sun Z, Zhang J, Zhang X, Wang C, Geng R, Zheng T, Li B, Zheng QY. RNA-seq analysis of potential lncRNAs for age-related hearing loss in a mouse model. Aging (Albany NY) 2020; 12:7491-7510. [PMID: 32335544 PMCID: PMC7202524 DOI: 10.18632/aging.103103] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 03/02/2020] [Indexed: 12/13/2022]
Abstract
Age-related hearing loss (AHL) is an important health problem in the elderly population. Its molecular mechanisms have not been fully elucidated. In this study, we analyzed the differential expression of lncRNAs and mRNAs in the cochleae of six-week-old and one-year-old C57BL/6J mice through RNA-seq analysis. We found 738 and 2033 differentially expressed lncRNAs and mRNAs, respectively, in these two groups (corrected P < 0.05). We focused on the intersection of known genes associated with hearing loss and differentially expressed mRNAs in RNA-seq. There are 34 mRNAs in this intersection, which include all 29 mRNAs enriched in the sensory perception of sound (GO: 0007605). We selected 11 lncRNAs that are predicted to regulate the 34 mRNAs to validate their expression levels in animal and cellular models of AHL by qRT-PCR. Among these lncRNAs, four were significantly different in both animal and cellular models of AHL, and the lncRNA NONMMUT010961.2 was the most markedly different. Knocking down lncRNA NONMMUT010961.2, we found the expression of oxidative stress and apoptosis-related gene Ar and hearing loss-related gene Hgf is significantly reduced in HEI-OC1 cells. Our results suggest that lncRNAs NONMMUT010961.2 may be associated with AHL and may thus lead to a new treatment for AHL.
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Affiliation(s)
- Tong Zhao
- Hearing and Speech Rehabilitation Institute, Binzhou Medical University, Yantai, China
| | - Xiuzhen Liu
- Clinical Medicine Laboratory, Binzhou Medical University Hospital, Binzhou, China
| | - Zehua Sun
- Hearing and Speech Rehabilitation Institute, Binzhou Medical University, Yantai, China
| | - Jinjin Zhang
- Hearing and Speech Rehabilitation Institute, Binzhou Medical University, Yantai, China
| | - Xiaolin Zhang
- Department of Otolaryngology-Head and Neck Surgery, Binzhou Medical University Hospital, Binzhou, China
| | - Chaoyun Wang
- Hearing and Speech Rehabilitation Institute, Binzhou Medical University, Yantai, China
| | - Ruishuang Geng
- Hearing and Speech Rehabilitation Institute, Binzhou Medical University, Yantai, China
| | - Tihua Zheng
- Hearing and Speech Rehabilitation Institute, Binzhou Medical University, Yantai, China
| | - Bo Li
- Hearing and Speech Rehabilitation Institute, Binzhou Medical University, Yantai, China
| | - Qing Yin Zheng
- Department of Otolaryngology- Head and Neck Surgery, Case Western Reserve University, Cleveland, USA
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25
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Lee S, Dondzillo A, Gubbels SP, Raphael Y. Practical aspects of inner ear gene delivery for research and clinical applications. Hear Res 2020; 394:107934. [PMID: 32204962 DOI: 10.1016/j.heares.2020.107934] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/26/2020] [Accepted: 02/28/2020] [Indexed: 12/24/2022]
Abstract
The application of gene therapy is widely expanding in research and continuously improving in preparation for clinical applications. The inner ear is an attractive target for gene therapy for treating environmental and genetic diseases in both the auditory and vestibular systems. With the lack of spontaneous cochlear hair cell replacement, hair cell regeneration in adult mammals is among the most important goals of gene therapy. In addition, correcting gene defects can open up a new era for treating inner ear diseases. The relative isolation and small size of the inner ear dictate local administration routes and carefully calculated small volumes of reagents. In the current review, we will cover effective timing, injection routes and types of vectors for successful gene delivery to specific target cells within the inner ear. Differences between research purposes and clinical applications are also discussed.
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Affiliation(s)
- Sungsu Lee
- Kresge Hearing Research Institute, Department of Otolaryngology, Head and Neck Surgery, Michigan Medicine, Ann Arbor, MI, USA
| | - Anna Dondzillo
- Department of Otolaryngology, Head and Neck Surgery, University of Colorado School of Medicine, Aurora, CO, USA
| | - Samuel P Gubbels
- Department of Otolaryngology, Head and Neck Surgery, University of Colorado School of Medicine, Aurora, CO, USA
| | - Yehoash Raphael
- Kresge Hearing Research Institute, Department of Otolaryngology, Head and Neck Surgery, Michigan Medicine, Ann Arbor, MI, USA.
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26
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Yao Q, Wang L, Mittal R, Yan D, Richmond MT, Denyer S, Requena T, Liu K, Varshney GK, Lu Z, Liu XZ. Transcriptomic Analyses of Inner Ear Sensory Epithelia in Zebrafish. Anat Rec (Hoboken) 2019; 303:527-543. [PMID: 31883312 DOI: 10.1002/ar.24331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 08/01/2019] [Accepted: 11/18/2019] [Indexed: 12/25/2022]
Abstract
Analysis of gene expression has the potential to assist in the understanding of multiple cellular processes including proliferation, cell-fate specification, senesence, and activity in both healthy and disease states. Zebrafish model has been increasingly used to understand the process of hearing and the development of the vertebrate auditory system. Within the zebrafish inner ear, there are three otolith organs, each containing a sensory macula of hair cells. The saccular macula is primarily involved in hearing, the utricular macula is primarily involved in balance and the function of the lagenar macula is not completely understood. The goal of this study is to understand the transcriptional differences in the sensory macula associated with different otolith organs with the intention of understanding the genetic mechanisms responsible for the distinct role each organ plays in sensory perception. The sensory maculae of the saccule, utricle, and lagena were dissected out of adult Et(krt4:GFP)sqet4 zebrafish expressing green fluorescent protein in hair cells for transcriptional analysis. The total RNAs of the maculae were isolated and analyzed by RNA GeneChip microarray. Several of the differentially expressed genes are known to be involved in deafness, otolith development and balance. Gene expression among these otolith organs was very well conserved with less than 10% of genes showing differential expression. Data from this study will help to elucidate which genes are involved in hearing and balance. Furthermore, the findings of this study will assist in the development of the zebrafish model for human hearing and balance disorders. Anat Rec, 303:527-543, 2020. © 2019 American Association for Anatomy.
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Affiliation(s)
- Qi Yao
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, Florida.,Department of Biology, University of Miami, Miami, Florida
| | - Lingyu Wang
- Department of Biology, University of Miami, Miami, Florida
| | - Rahul Mittal
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, Florida
| | - Denise Yan
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, Florida
| | | | - Steven Denyer
- Department of Biology, University of Miami, Miami, Florida
| | - Teresa Requena
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - Kaili Liu
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - Gaurav K Varshney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - Zhongmin Lu
- Department of Biology, University of Miami, Miami, Florida
| | - Xue Zhong Liu
- Department of Otolaryngology, Miller School of Medicine, University of Miami, Miami, Florida.,Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China
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27
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Otogelin, otogelin-like, and stereocilin form links connecting outer hair cell stereocilia to each other and the tectorial membrane. Proc Natl Acad Sci U S A 2019; 116:25948-25957. [PMID: 31776257 DOI: 10.1073/pnas.1902781116] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The function of outer hair cells (OHCs), the mechanical actuators of the cochlea, involves the anchoring of their tallest stereocilia in the tectorial membrane (TM), an acellular structure overlying the sensory epithelium. Otogelin and otogelin-like are TM proteins related to secreted epithelial mucins. Defects in either cause the DFNB18B and DFNB84B genetic forms of deafness, respectively, both characterized by congenital mild-to-moderate hearing impairment. We show here that mutant mice lacking otogelin or otogelin-like have a marked OHC dysfunction, with almost no acoustic distortion products despite the persistence of some mechanoelectrical transduction. In both mutants, these cells lack the horizontal top connectors, which are fibrous links joining adjacent stereocilia, and the TM-attachment crowns coupling the tallest stereocilia to the TM. These defects are consistent with the previously unrecognized presence of otogelin and otogelin-like in the OHC hair bundle. The defective hair bundle cohesiveness and the absence of stereociliary imprints in the TM observed in these mice have also been observed in mutant mice lacking stereocilin, a model of the DFNB16 genetic form of deafness, also characterized by congenital mild-to-moderate hearing impairment. We show that the localizations of stereocilin, otogelin, and otogelin-like in the hair bundle are interdependent, indicating that these proteins interact to form the horizontal top connectors and the TM-attachment crowns. We therefore suggest that these 2 OHC-specific structures have shared mechanical properties mediating reaction forces to sound-induced shearing motion and contributing to the coordinated displacement of stereocilia.
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28
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Zhao H, Wang H, Liu T, Liu S, Jin L, Huang X, Dai W, Sun K, Feng J. Gene expression vs. sequence divergence: comparative transcriptome sequencing among natural Rhinolophus ferrumequinum populations with different acoustic phenotypes. Front Zool 2019; 16:37. [PMID: 31528181 PMCID: PMC6743130 DOI: 10.1186/s12983-019-0336-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/04/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Although the sensory drive hypothesis can explain the geographic variation in echolocation frequencies of some bat species, the molecular mechanisms underlying this phenomenon are still unclear. The three lineages of greater horseshoe bat (Rhinolophus ferrumequinum) in China (northeast, central-east, and southwest) have significant geographic variation in resting frequencies (RF) of echolocation calls. Because their cochleae have an acoustic fovea that is highly sensitive to a narrow range of frequencies, we reported the transcriptomes of cochleae collected from three genetic lineages of R. ferrumequinum, which is an ideal organism for studying geographic variation in echolocation signals, and tried to understand the mechanisms behind this bat phenomenon by analyzing gene expression and sequence variation. RESULTS A total of 8190 differentially expressed genes (DEGs) were identified. We identified five modules from all DEGs that were significantly related to RF or forearm length (FL). DEGs in the RF-related modules were significantly enriched in the gene categories involved in neural activity, learning, and response to sound. DEGs in the FL-related modules were significantly enriched in the pathways related to muscle and actin functions. Using 21,945 single nucleotide polymorphisms, we identified 18 candidate unigenes associated with hearing, five of which were differentially expressed among the three populations. Additionally, the gene ERBB4, which regulates diverse cellular processes in the inner ear such as cell proliferation and differentiation, was in the largest module. We also found 49 unigenes that were under positive selection from 4105 one-to-one orthologous gene pairs between the three R. ferrumequinum lineages and three other Chiroptera species. CONCLUSIONS The variability of gene expression and sequence divergence at the molecular level might provide evidence that can help elucidate the genetic basis of geographic variation in echolocation signals of greater horseshoe bats.
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Affiliation(s)
- Hanbo Zhao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Hui Wang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Tong Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Sen Liu
- Institute of Resources & Environment, Henan Polytechnic University, Jiaozuo, 454000 China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Xiaobin Huang
- Vector Laboratory, Institute of Pathogens and Vectors, Branch of Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali University, Dali, 671003 China
| | - Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117 China
- College of Life Science, Jilin Agricultural University, Changchun, 130118 China
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29
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DeSmidt AA, Zou B, Grati M, Yan D, Mittal R, Yao Q, Richmond MT, Denyer S, Liu XZ, Lu Z. Zebrafish Model for Nonsyndromic X-Linked Sensorineural Deafness, DFNX1. Anat Rec (Hoboken) 2019; 303:544-555. [PMID: 30874365 DOI: 10.1002/ar.24115] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 08/23/2018] [Accepted: 09/05/2018] [Indexed: 11/08/2022]
Abstract
Hereditary deafness is often a neurosensory disorder and affects the quality of life of humans. Only three X-linked genes (POU class 3 homeobox 4 (POU3F4), phosphoribosyl pyrophosphate synthetase 1 (PRPS1), and small muscle protein X-linked (SMPX)) are known to be involved in nonsyndromic hearing loss. Four PRPS1 missense mutations have been found to associate with X-linked nonsyndromic sensorineural deafness (DFNX1/DFN2) in humans. However, a causative relationship between PRPS1 mutations and hearing loss in humans has not been well studied in any animal model. Phosphoribosyl pyrophosphate synthetase 1 (PRS-I) is highly conserved in vertebrate taxa. In this study, we used the zebrafish as a model to investigate the auditory role of zebrafish orthologs (prps1a and prps1b) of the human PRPS1 gene with whole mount in situ hybridization, reverse transcription polymerase chain reaction, phenotypic screening, confocal imaging, and electrophysiological methods. We found that both prps1a and prps1b genes were expressed in the inner ear of zebrafish. Splice-blocking antisense morpholino oligonucleotides (MO1 and MO2) caused exon-2 skip and intron-2 retention of prps1a and exon-2 skip and intron-1 retention of prps1b to knock down functions of the genes, respectively. MO1 and MO2 morphants had smaller otic vesicles and otoliths, fewer inner ear hair cells, and lower microphonic response amplitude and sensitivity than control zebrafish. Therefore, knockdown of either prps1a or prps1b resulted in significant sensorineural hearing loss in zebrafish. We conclude that the prps1 genes are essential for hearing in zebrafish, which has the potential to help us understand the biology of human deafness DFNX1/DFN2. Anat Rec, 303:544-555, 2020. © 2019 American Association for Anatomy.
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Affiliation(s)
| | - Bing Zou
- Department of Biology, University of Miami, Coral Gables, Florida.,Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - M'hamed Grati
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Rahul Mittal
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | - Qi Yao
- Department of Biology, University of Miami, Coral Gables, Florida.,Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida
| | | | - Steven Denyer
- Department of Biology, University of Miami, Coral Gables, Florida
| | - Xue Zhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida.,Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Zhongmin Lu
- Department of Biology, University of Miami, Coral Gables, Florida.,Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida.,Neuroscience Program, University of Miami, Miami, Florida.,International Center for Marine Studies, Shanghai Ocean University, Shanghai, People's Republic of China
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30
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Kalka M, Markiewicz N, Ptak M, Sone ED, Ożyhar A, Dobryszycki P, Wojtas M. In vivo and in vitro analysis of starmaker activity in zebrafish otolith biomineralization. FASEB J 2019; 33:6877-6886. [PMID: 30840836 DOI: 10.1096/fj.201802268r] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Otoliths are one of the biominerals whose formation is highly controlled by proteins. The first protein discovered to be involved in otolith biomineralization in zebrafish was starmaker (Stm). Previously, Stm was shown to be responsible for the preferential formation of aragonite, a polymorph of calcium carbonate, in otoliths. In this work, proteomic analysis of adult zebrafish otoliths was performed. Stm is the only highly phosphorylated protein found in our studies. Besides previously studied otolith proteins, we discovered several dozens of unknown proteins that reveal the likely mechanism of biomineralization. A comparison of aragonite and vaterite otoliths showed similarities in protein composition. We observed the presence of Stm in both types of otoliths. In vitro studies of 2 characteristic Stm fragments indicated that the DS-rich region has a special biomineralization activity, especially after phosphorylation.-Kalka, M., Markiewicz, N., Ptak, M., Sone, E. D., Ożyhar, A., Dobryszycki, P., Wojtas, M. In vivo and in vitro analysis of starmaker activity in zebrafish otolith biomineralization.
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Affiliation(s)
- Marta Kalka
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Natalia Markiewicz
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Maciej Ptak
- Division of Optical Spectroscopy, Institute of Low Temperature and Structure Research, Polish Academy of Sciences, Wrocław, Poland; and
| | - Eli D Sone
- Department of Materials Science and Engineering, Institute of Biomaterials and Biomedical Engineering, and.,Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
| | - Andrzej Ożyhar
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Piotr Dobryszycki
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Magdalena Wojtas
- Department of Biochemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland.,Department of Materials Science and Engineering, Institute of Biomaterials and Biomedical Engineering, and.,Faculty of Dentistry, University of Toronto, Toronto, Ontario, Canada
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31
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Sun Y, Yuan J, Wu L, Li M, Cui X, Yan C, Du L, Mao L, Man J, Li W, Kristiansen K, Wu X, Pan W, Yang Y. Panel-based NGS reveals disease-causing mutations in hearing loss patients using BGISEQ-500 platform. Medicine (Baltimore) 2019; 98:e14860. [PMID: 30896630 PMCID: PMC6709004 DOI: 10.1097/md.0000000000014860] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Hearing loss is a highly heterogeneous disease presented with various phenotypes. Genetic testing of disease-causing mutations plays an important role in precise diagnosis and fertility guidance of heredity hearing loss. Here we reported an effective method employing target enrichment and BGISEQ-500 platform to detect clinically relevant alterations for heredity hearing patients in a single assay.In this study, we designed an array based chip, containing 127 genes related to hearing loss. Then we conducted targeted next-generation sequencing toward 58 patients to make a precise diagnosis using BGISEQ-500 platform.We successfully detected disease-causing mutations in 77.59% (45/58) of the patients with hearing loss. Finally, a total of 62 disease-causing mutations were identified, including 31 missense, 17 Indel, 11 splicing, 2 synonymous, and 1 copy number variant. 58.06% (36/62) of which has never been reported before.To our knowledge, this is the first report using BGISEQ-500 platform to investigate both syndromic and nonsyndromic hearing loss in the Chinese population. The results showed that this method can greatly assist and enhance hearing loss diagnosis and improve molecular diagnostics outcome.
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Affiliation(s)
- Yan Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
- BGI-Wuhan, BGI-Shenzhen, Wuhan, China
| | - Jing Yuan
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Anhui Province Key Laboratory of Reproductive Health and Genetics, Biopreservation and Artificial Organs, Anhui Provincial Engineering Research Center, Anhui Medical University
| | - Limin Wu
- Center for Reproductive Medicine and Prenatal Diagnosis, Anhui Provincial Hospital, The First Affiliated Hospital of University of Science and Technology of China, Hefei
| | - Min Li
- Prenatal Diagnosis Center, Yancheng Maternity and Child Health Care Hospital, Yancheng, Jiangsu Province
| | - Xiaoli Cui
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Lique Du
- BGI-Wuhan, BGI-Shenzhen, Wuhan, China
| | - Liangwei Mao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, Hubei University, Wuhan
| | | | - Wei Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Xuan Wu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Weijun Pan
- The Center for Reproductive Medicine, Ma’anshan Maternal and Child Health Hospital, Ma’anshan, China
| | - Yun Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- BGI-Wuhan, BGI-Shenzhen, Wuhan, China
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32
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Andrew SC, Taylor MP, Lundregan S, Lien S, Jensen H, Griffith SC. Signs of adaptation to trace metal contamination in a common urban bird. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 650:679-686. [PMID: 30212697 DOI: 10.1016/j.scitotenv.2018.09.052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 09/03/2018] [Accepted: 09/04/2018] [Indexed: 06/08/2023]
Abstract
Metals and metalloids at elevated concentrations can be toxic to both humans and wildlife. In particular, lead exposure can act as a stressor to wildlife and cause negative effects on fitness. Any ability to adapt to stress caused by the negative effects of trace metal exposure would be beneficial for species living in contaminated environments. However, mechanisms for responding adaptively to metal contamination are not fully understood in free-living organisms. The Australian populations of the house sparrow (Passer domesticus) provides an excellent opportunity to study potential adaptation to environmental lead contamination because they have a commensal relationship with humans and are distributed broadly across Australian settlements including many long-term mining and smelting communities. To examine the potential for an evolutionary response to long-term lead exposure, we collected genomic SNP data using the house sparrow 200 K SNP array, from 11 localities across the Australian distribution including two mining sites (Broken Hill and Mount Isa, which are two genetically independent populations) that have well-established elevated levels of lead contamination as well as trace metals and metalloids. We contrast these known contaminated locations to other lesser-contaminated environments. Using an ecological association genome scan method to identify genomic differentiation associated with estimates of lead contamination we identified 60 outlier loci across three tests. A total of 39 genes were found to be physically linked (within 20 kbps) of all outliers in the house sparrow reference genome. The linked candidate genes included 12 genes relevant to lead exposure, such as two metal transporters that can transport metals including lead and zinc across cell membranes. These candidate genes provide targets for follow up experiments comparing resilience to lead exposure between populations exposed to varied levels of lead contamination.
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Affiliation(s)
- Samuel C Andrew
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Mark Patrick Taylor
- Department of Environmental Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Sarah Lundregan
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, NO-1432 Ås, Norway
| | - Henrik Jensen
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Simon C Griffith
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
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33
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Pickett SB, Raible DW. Water Waves to Sound Waves: Using Zebrafish to Explore Hair Cell Biology. J Assoc Res Otolaryngol 2019; 20:1-19. [PMID: 30635804 DOI: 10.1007/s10162-018-00711-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/19/2018] [Indexed: 01/09/2023] Open
Abstract
Although perhaps best known for their use in developmental studies, over the last couple of decades, zebrafish have become increasingly popular model organisms for investigating auditory system function and disease. Like mammals, zebrafish possess inner ear mechanosensory hair cells required for hearing, as well as superficial hair cells of the lateral line sensory system, which mediate detection of directional water flow. Complementing mammalian studies, zebrafish have been used to gain significant insights into many facets of hair cell biology, including mechanotransduction and synaptic physiology as well as mechanisms of both hereditary and acquired hair cell dysfunction. Here, we provide an overview of this literature, highlighting some of the particular advantages of using zebrafish to investigate hearing and hearing loss.
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Affiliation(s)
- Sarah B Pickett
- Department of Biological Structure, University of Washington, Health Sciences Building H-501, 1959 NE Pacific Street, Box 357420, Seattle, WA, 98195-7420, USA
- Graduate Program in Neuroscience, University of Washington, 1959 NE Pacific Street, Box 357270, Seattle, WA, 98195-7270, USA
| | - David W Raible
- Department of Biological Structure, University of Washington, Health Sciences Building H-501, 1959 NE Pacific Street, Box 357420, Seattle, WA, 98195-7420, USA.
- Graduate Program in Neuroscience, University of Washington, 1959 NE Pacific Street, Box 357270, Seattle, WA, 98195-7270, USA.
- Virginia Merrill Bloedel Hearing Research Center, University of Washington, 1701 NE Columbia Rd, Box 357923, Seattle, WA, 98195-7923, USA.
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34
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Carpena NT, Lee MY. Genetic Hearing Loss and Gene Therapy. Genomics Inform 2018; 16:e20. [PMID: 30602081 PMCID: PMC6440668 DOI: 10.5808/gi.2018.16.4.e20] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 12/04/2018] [Indexed: 12/15/2022] Open
Abstract
Genetic hearing loss crosses almost all the categories of hearing loss which includes the following: conductive, sensory, and neural; syndromic and nonsyndromic; congenital, progressive, and adult onset; high-frequency, low-frequency, or mixed frequency; mild or profound; and recessive, dominant, or sex-linked. Genes play a role in almost half of all cases of hearing loss but effective treatment options are very limited. Genetic hearing loss is considered to be extremely genetically heterogeneous. The advancements in genomics have been instrumental to the identification of more than 6,000 causative variants in more than 150 genes causing hearing loss. Identification of genes for hearing impairment provides an increased insight into the normal development and function of cells in the auditory system. These defective genes will ultimately be important therapeutic targets. However, the auditory system is extremely complex which requires tremendous advances in gene therapy including gene vectors, routes of administration, and therapeutic approaches. This review summarizes and discusses recent advances in elucidating the genomics of genetic hearing loss and technologies aimed at developing a gene therapy that may become a treatment option for in the near future.
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Affiliation(s)
- Nathanial T Carpena
- Department of Otolaryngology-Head and Neck Surgery, Dankook University College of Medicine, Cheonan 31116, Korea
| | - Min Young Lee
- Department of Otolaryngology-Head and Neck Surgery, Dankook University College of Medicine, Cheonan 31116, Korea.,Beckman Laser Institute Korea, Dankook University, Cheonan 31116, Korea
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35
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Schulz-Mirbach T, Ladich F, Plath M, Heß M. Enigmatic ear stones: what we know about the functional role and evolution of fish otoliths. Biol Rev Camb Philos Soc 2018; 94:457-482. [DOI: 10.1111/brv.12463] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 08/16/2018] [Accepted: 08/20/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Tanja Schulz-Mirbach
- Department Biology II, Zoology; Ludwig-Maximilians-University; Großhaderner Strasse 2, 82152 Planegg-Martinsried Germany
| | - Friedrich Ladich
- Department of Behavioural Biology; University of Vienna; Althanstrasse 14, 1090 Vienna Austria
| | - Martin Plath
- College of Animal Science & Technology; Northwest A&F University; 22 Xinong Road, Yangling Shaanxi China
| | - Martin Heß
- Department Biology II, Zoology; Ludwig-Maximilians-University; Großhaderner Strasse 2, 82152 Planegg-Martinsried Germany
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36
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Bademci G, Abad C, Incesulu A, Rad A, Alper O, Kolb SM, Cengiz FB, Diaz-Horta O, Silan F, Mihci E, Ocak E, Najafi M, Maroofian R, Yilmaz E, Nur BG, Duman D, Guo S, Sant DW, Wang G, Monje PV, Haaf T, Blanton SH, Vona B, Walz K, Tekin M. MPZL2 is a novel gene associated with autosomal recessive nonsyndromic moderate hearing loss. Hum Genet 2018; 137:479-486. [PMID: 29982980 DOI: 10.1007/s00439-018-1901-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 07/02/2018] [Indexed: 02/07/2023]
Abstract
While recent studies have revealed a substantial portion of the genes underlying human hearing loss, the extensive genetic landscape has not been completely explored. Here, we report a loss-of-function variant (c.72delA) in MPZL2 in three unrelated multiplex families from Turkey and Iran with autosomal recessive nonsyndromic hearing loss. The variant co-segregates with moderate sensorineural hearing loss in all three families. We show a shared haplotype flanking the variant in our families implicating a single founder. While rare in other populations, the allele frequency of the variant is ~ 0.004 in Ashkenazi Jews, suggesting that it may be an important cause of moderate hearing loss in that population. We show that Mpzl2 is expressed in mouse inner ear, and the protein localizes in the auditory inner and outer hair cells, with an asymmetric subcellular localization. We thus present MPZL2 as a novel gene associated with sensorineural hearing loss.
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Affiliation(s)
- Guney Bademci
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - Clemer Abad
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - Armagan Incesulu
- Department of Otorhinolaryngology, Faculty of Medicine, Eskisehir Osmangazi University, 26040, Eskisehir, Turkey
| | - Abolfazl Rad
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, 009851, Iran
| | - Ozgul Alper
- Department of Medical Biology and Genetics, Faculty of Medicine, Akdeniz University, 07070, Antalya, Turkey
| | - Susanne M Kolb
- Institute of Human Genetics, Julius Maximilians University Würzburg, 97074, Würzburg, Germany
| | - Filiz B Cengiz
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - Oscar Diaz-Horta
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - Fatma Silan
- Department of Medical Genetics, Canakkale Onsekiz Mart University School of Medicine, 17100, Canakkale, Turkey
| | - Ercan Mihci
- Department of Pediatric Genetics, Akdeniz University School of Medicine, 07070, Antalya, Turkey
| | - Emre Ocak
- Department of Otolaryngology, Ankara University School of Medicine, 06260, Ankara, Turkey
| | - Maryam Najafi
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 KL, Nijmegen, The Netherlands
| | - Reza Maroofian
- Genetics and Molecular Cell Sciences Research Centre, St George's, University of London, Cranmer Terrace, London, SW17 0RE, UK
| | - Elanur Yilmaz
- Department of Medical Biology and Genetics, Faculty of Medicine, Akdeniz University, 07070, Antalya, Turkey
| | - Banu G Nur
- Department of Pediatric Genetics, Akdeniz University School of Medicine, 07070, Antalya, Turkey
| | - Duygu Duman
- Division of Genetics, Department of Pediatrics, Ankara University School of Medicine, 06260, Ankara, Turkey
| | - Shengru Guo
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - David W Sant
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - Gaofeng Wang
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Paula V Monje
- The Miami Project to Cure Paralysis and the Department of Neurological Surgery, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University Würzburg, 97074, Würzburg, Germany
| | - Susan H Blanton
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA.,Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.,Dr. John T. Macdonald Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Barbara Vona
- Institute of Human Genetics, Julius Maximilians University Würzburg, 97074, Würzburg, Germany.,Department of Otorhinolaryngology, Head and Neck Surgery, Tübingen Hearing Research Centre (THRC), Eberhard Karls University Tübingen, 72076, Tübingen, Germany
| | - Katherina Walz
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA.,Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Mustafa Tekin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA. .,Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA. .,Dr. John T. Macdonald Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
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37
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Goodyear RJ, Richardson GP. Structure, Function, and Development of the Tectorial Membrane: An Extracellular Matrix Essential for Hearing. Curr Top Dev Biol 2018; 130:217-244. [PMID: 29853178 DOI: 10.1016/bs.ctdb.2018.02.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The tectorial membrane is an extracellular matrix that lies over the apical surface of the auditory epithelia in the inner ears of reptiles, birds, and mammals. Recent studies have shown it is composed of a small set of proteins, some of which are only produced at high levels in the ear and many of which are the products of genes that, when mutated, cause nonsyndromic forms of human hereditary deafness. Quite how the proteins of the tectorial membrane are assembled within the lumen of the inner ear to form a structure that is precisely regulated in its size and physical properties along the length of a tonotopically organized hearing organ is a question that remains to be fully answered. In this brief review we will summarize what is known thus far about the structure, protein composition, and function of the tectorial membrane in birds and mammals, describe how the tectorial membrane develops, and discuss major events that have occurred during the evolution of this extracellular matrix.
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Affiliation(s)
- Richard J Goodyear
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Guy P Richardson
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom.
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38
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Rudman JR, Mei C, Bressler SE, Blanton SH, Liu XZ. Precision medicine in hearing loss. J Genet Genomics 2018; 45:99-109. [PMID: 29500086 DOI: 10.1016/j.jgg.2018.02.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 02/12/2018] [Accepted: 02/12/2018] [Indexed: 11/26/2022]
Abstract
Precision medicine (PM) proposes customized medical care based on a patient's unique genome, biomarkers, environment and behaviors. Hearing loss (HL) is the most common sensorineural disorder worldwide and is frequently caused by a single genetic mutation. With recent advances in PM tools such as genetic sequencing and data analysis, the field of HL is ideally positioned to adopt the strategies of PM. Here, we review current and future applications of PM in HL as they relate to the four core qualities of PM (P4): predictive, personalized, patient-centered, and participatory. We then introduce a strategy for effective incorporation of HL PM into the design of future research studies, electronic medical records, and clinical practice to improve diagnostics, prognostics, and, ultimately, individualized patient treatment. Finally, specific anticipated ethical and economic concerns in this growing era of genomics-based HL treatment are discussed. By integrating PM principles into translational HL research and clinical practice, hearing specialists are uniquely positioned to effectively treat the heterogeneous causes and manifestations of HL on an individualized basis.
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Affiliation(s)
- Jason R Rudman
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Christine Mei
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Sara E Bressler
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Susan H Blanton
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA; John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Xue-Zhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA; John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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39
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Astuti GDN, van den Born LI, Khan MI, Hamel CP, Bocquet B, Manes G, Quinodoz M, Ali M, Toomes C, McKibbin M, El-Asrag ME, Haer-Wigman L, Inglehearn CF, Black GCM, Hoyng CB, Cremers FPM, Roosing S. Identification of Inherited Retinal Disease-Associated Genetic Variants in 11 Candidate Genes. Genes (Basel) 2018; 9:genes9010021. [PMID: 29320387 PMCID: PMC5793174 DOI: 10.3390/genes9010021] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 12/31/2017] [Accepted: 01/03/2018] [Indexed: 01/09/2023] Open
Abstract
Inherited retinal diseases (IRDs) display an enormous genetic heterogeneity. Whole exome sequencing (WES) recently identified genes that were mutated in a small proportion of IRD cases. Consequently, finding a second case or family carrying pathogenic variants in the same candidate gene often is challenging. In this study, we searched for novel candidate IRD gene-associated variants in isolated IRD families, assessed their causality, and searched for novel genotype-phenotype correlations. Whole exome sequencing was performed in 11 probands affected with IRDs. Homozygosity mapping data was available for five cases. Variants with minor allele frequencies ≤ 0.5% in public databases were selected as candidate disease-causing variants. These variants were ranked based on their: (a) presence in a gene that was previously implicated in IRD; (b) minor allele frequency in the Exome Aggregation Consortium database (ExAC); (c) in silico pathogenicity assessment using the combined annotation dependent depletion (CADD) score; and (d) interaction of the corresponding protein with known IRD-associated proteins. Twelve unique variants were found in 11 different genes in 11 IRD probands. Novel autosomal recessive and dominant inheritance patterns were found for variants in Small Nuclear Ribonucleoprotein U5 Subunit 200 (SNRNP200) and Zinc Finger Protein 513 (ZNF513), respectively. Using our pathogenicity assessment, a variant in DEAH-Box Helicase 32 (DHX32) was the top ranked novel candidate gene to be associated with IRDs, followed by eight medium and lower ranked candidate genes. The identification of candidate disease-associated sequence variants in 11 single families underscores the notion that the previously identified IRD-associated genes collectively carry > 90% of the defects implicated in IRDs. To identify multiple patients or families with variants in the same gene and thereby provide extra proof for pathogenicity, worldwide data sharing is needed.
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Affiliation(s)
- Galuh D. N. Astuti
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (G.D.N.A.); (M.I.K.); (L.H.-W.); (F.P.M.C.)
- Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands
| | | | - M. Imran Khan
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (G.D.N.A.); (M.I.K.); (L.H.-W.); (F.P.M.C.)
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, 6525 EN Nijmegen, The Netherlands
| | - Christian P. Hamel
- Institut National de la Santé et de la Recherche Médicale, Institute for Neurosciences of Montpellier, 34080 Montpellier, France; (B.B.); (G.M.)
- University of Montpellier, 34090 Montpellier, France
- CHRU, Genetics of Sensory Diseases, 34295 Montpellier, France
| | - Béatrice Bocquet
- Institut National de la Santé et de la Recherche Médicale, Institute for Neurosciences of Montpellier, 34080 Montpellier, France; (B.B.); (G.M.)
- University of Montpellier, 34090 Montpellier, France
- CHRU, Genetics of Sensory Diseases, 34295 Montpellier, France
| | - Gaël Manes
- Institut National de la Santé et de la Recherche Médicale, Institute for Neurosciences of Montpellier, 34080 Montpellier, France; (B.B.); (G.M.)
- University of Montpellier, 34090 Montpellier, France
| | - Mathieu Quinodoz
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, 1015 Lausanne, Switzerland;
| | - Manir Ali
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, St. James’s University Hospital, LS9 7TF Leeds, UK; (M.A.); (C.T.); (M.E.E.-A.); (C.F.I.)
| | - Carmel Toomes
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, St. James’s University Hospital, LS9 7TF Leeds, UK; (M.A.); (C.T.); (M.E.E.-A.); (C.F.I.)
| | - Martin McKibbin
- Department of Ophthalmology, St. James’s University Hospital, LS9 7TF Leeds, UK;
| | - Mohammed E. El-Asrag
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, St. James’s University Hospital, LS9 7TF Leeds, UK; (M.A.); (C.T.); (M.E.E.-A.); (C.F.I.)
- Department of Zoology, Faculty of Science, Benha University, 13511 Benha, Egypt
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (G.D.N.A.); (M.I.K.); (L.H.-W.); (F.P.M.C.)
| | - Chris F. Inglehearn
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, St. James’s University Hospital, LS9 7TF Leeds, UK; (M.A.); (C.T.); (M.E.E.-A.); (C.F.I.)
| | - Graeme C. M. Black
- Centre for Genomic Medicine, St. Mary’s Hospital, Manchester Academic Health Science Centre, University of Manchester, M13 9PL Manchester, UK;
| | - Carel B. Hoyng
- Department of Ophthalmology, Radboud University Medical Center, 6525 EX Nijmegen, The Netherlands;
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (G.D.N.A.); (M.I.K.); (L.H.-W.); (F.P.M.C.)
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, 6525 EN Nijmegen, The Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (G.D.N.A.); (M.I.K.); (L.H.-W.); (F.P.M.C.)
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, 6525 EN Nijmegen, The Netherlands
- Correspondence: ; Tel.: +31-(0)24-365-5266
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Kim SY, Kim AR, Kim NKD, Lee C, Han JH, Kim MY, Jeon EH, Park WY, Mittal R, Yan D, Liu XZ, Choi BY. Functional characterization of a novel loss-of-function mutation of PRPS1 related to early-onset progressive nonsyndromic hearing loss in Koreans (DFNX1): Potential implications on future therapeutic intervention. J Gene Med 2017; 18:353-358. [PMID: 27886419 DOI: 10.1002/jgm.2935] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 11/22/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The symptoms of phosphoribosyl pyrophosphate synthetase 1 (PRPS1) deficiency diseases have been reported to be alleviated by medication. In the present study, we report biochemical data that favor PRPS1 deficiency-related hearing loss as a potential target for pharmaceutical treatment. METHODS We recruited 42 probands from subjects aged less than 15 years with a moderate degree of nonsyndromic autosomal-recessive or sporadic sensorineural hearing loss (SNHL) in at least one side. Molecular genetic testing, including targeted exome sequencing (TES) of 129 genes for deafness, and in silico prediction were performed. RESULTS A strong candidate variant (p.A82P) of PRPS1 is co-segregated with SNHL in X-linked recessive inheritance from one Korean multiplex SNHL family. Subsequent measurement of in vitro enzymatic activities of PRPS1 from erythrocytes of affected and unaffected family members, as well as unrelated normal controls, confirmed a pathogenic role of this variant. In detail, compared to normal hearing controls (0.23-0.26 nmol/ml/h), the proband, the affected sibling and their normal hearing mother demonstrated a significantly decreased PRPS1 enzymatic activity (0.07, 0.03 and 0.11 nmol/ml/h, respectively). This novel loss-of-function mutation of PRPS1 (p.A82P) is the ninth and sixth most reported mutation in the world and in Asia, respectively. CONCLUSIONS DFNX1 was found to account for approximately 2.4% (1/42) of moderate SNHL in a Korean pediatric population. Confirmation of PRPS1 activity deficiency and an audiologic phenotype that initially begins in a milder form of SNHL, as in our family, should indicate the need for rigorous genetic screening as early as possible.
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Affiliation(s)
- So Young Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, CHA Bundang Medical Center, CHA University, Seongnam, South Korea
| | - Ah Reum Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Nayoung K D Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Chung Lee
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea.,Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Suwon, South Korea
| | - Jin Hee Han
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Min Young Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Eun-Hee Jeon
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea.,Department of Molecular Cell Biology, School of Medicine, Sungkyunkwan University, Seoul, South Korea
| | - Rahul Mittal
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Xue Zhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Byung Yoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea.,Wide River Institute of Immunology, Seoul National University College of Medicine, Hongcheon, South Korea
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Goodyear RJ, Lu X, Deans MR, Richardson GP. A tectorin-based matrix and planar cell polarity genes are required for normal collagen-fibril orientation in the developing tectorial membrane. Development 2017; 144:3978-3989. [PMID: 28935705 PMCID: PMC5702074 DOI: 10.1242/dev.151696] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 09/08/2017] [Indexed: 12/20/2022]
Abstract
The tectorial membrane is an extracellular structure of the cochlea. It develops on the surface of the auditory epithelium and contains collagen fibrils embedded in a tectorin-based matrix. The collagen fibrils are oriented radially with an apically directed slant - a feature considered crucial for hearing. To determine how this pattern is generated, collagen-fibril formation was examined in mice lacking a tectorin-based matrix, epithelial cilia or the planar cell polarity genes Vangl2 and Ptk7 In wild-type mice, collagen-fibril bundles appear within a tectorin-based matrix at E15.5 and, as fibril number rapidly increases, become co-aligned and correctly oriented. Epithelial width measurements and data from Kif3acKO mice suggest, respectively, that radial stretch and cilia play little, if any, role in determining normal collagen-fibril orientation; however, evidence from tectorin-knockout mice indicates that confinement is important. PRICKLE2 distribution reveals the planar cell polarity axis in the underlying epithelium is organised along the length of the cochlea and, in mice in which this polarity is disrupted, the apically directed collagen offset is no longer observed. These results highlight the importance of the tectorin-based matrix and epithelial signals for precise collagen organisation in the tectorial membrane.
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Affiliation(s)
- Richard J Goodyear
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
| | - Xiaowei Lu
- Department of Cell Biology, University of Virginia Health System, Charlottesville, VA 22098, USA
| | - Michael R Deans
- Department of Surgery, Division of Otolaryngology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Guy P Richardson
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
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Ma Z, Xia W, Liu F, Ma J, Sun S, Zhang J, Jiang N, Wang X, Hu J, Ma D. SLC44A4 mutation causes autosomal dominant hereditary postlingual non-syndromic mid-frequency hearing loss. Hum Mol Genet 2017; 26:383-394. [PMID: 28013291 DOI: 10.1093/hmg/ddw394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/11/2016] [Indexed: 01/28/2023] Open
Abstract
Clinical, genetic, and functional investigations were performed to identify the causative mutation in a distinctive Chinese family with postlingual non-syndromic mid-frequency sensorineural hearing loss. Whole-exome sequencing revealed SLC44A4, which encodes the choline transport protein, as the pathogenic gene in this family. In the zebrafish model, downregulation of slc44a4 using morpholinos led to significant abnormalities in the zebrafish inner ear and lateral line neuromasts and contributed, to some extent, to disabilities in hearing and balance. SH-SY5Y cells transfected with SLC44A4 showed higher choline uptake and acetylcholine release than that of cells transfected with mutant SLC44A4. We concluded that mutation of SLC44A4 may cause defects in the Choline- acetylcholine system, which is crucial to the efferent innervation of hair cells in the olivocochlear bundle for the maintenance of physiological function of outer hair cells and the protection of hair cells from acoustic injury, leading to hearing loss.
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Affiliation(s)
- Zhaoxin Ma
- Department of Otorhinolaryngology, Shanghai East Hospital, Tongji University, Shanghai, 200120, People's Republic of China
| | - Wenjun Xia
- Institute of Biomedical Science, Fudan University, Shanghai, 200032, People's Republic of China
| | - Fei Liu
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, Collaborative Innovation Center of Genetics and Development, School of Basic Medical Sciences, Fudan University, Shanghai, People's Republic of China and
| | - Jing Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, Collaborative Innovation Center of Genetics and Development, School of Basic Medical Sciences, Fudan University, Shanghai, People's Republic of China and
| | - Shaoyang Sun
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, Collaborative Innovation Center of Genetics and Development, School of Basic Medical Sciences, Fudan University, Shanghai, People's Republic of China and
| | - Jin Zhang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, Collaborative Innovation Center of Genetics and Development, School of Basic Medical Sciences, Fudan University, Shanghai, People's Republic of China and
| | - Nan Jiang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, Collaborative Innovation Center of Genetics and Development, School of Basic Medical Sciences, Fudan University, Shanghai, People's Republic of China and
| | - Xu Wang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, Collaborative Innovation Center of Genetics and Development, School of Basic Medical Sciences, Fudan University, Shanghai, People's Republic of China and
| | - Jiongjiong Hu
- Department of Otorhinolaryngology, Shanghai East Hospital, Tongji University, Shanghai, 200120, People's Republic of China
| | - Duan Ma
- Institute of Biomedical Science, Fudan University, Shanghai, 200032, People's Republic of China.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, Collaborative Innovation Center of Genetics and Development, School of Basic Medical Sciences, Fudan University, Shanghai, People's Republic of China and.,Children's Hospital, Fudan University, 200032, People's Republic of China
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Barake R, Abou-Rizk S, Nemer G, Bassim M. The OTOGL p.Arg925* Variant is Associated with Moderate Hearing Loss in a Syrian Nonconsanguineous Family. Genet Test Mol Biomarkers 2017; 21:445-449. [PMID: 28426234 DOI: 10.1089/gtmb.2016.0406] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
AIM To screen for the genetic basis of congenital hearing loss in a Syrian family. METHODS A Syrian patient living in Lebanon presented with moderate congenital hearing loss. The patient's large nonconsanguineous family was recruited. DNA was extracted from blood samples and sent for whole-exome sequencing. A detailed clinical examination along with audiograms was obtained for all subjects. RESULTS Hearing loss was noted to be mild to moderate in the low and mid frequencies, sloping to moderate to severe in the high frequencies for all affected members. Results of DNA analysis showed the presence of a previously described p.Arg925* mutation in the OTOGL gene on both alleles in affected family members, whereas nonaffected members either had the wild type or one copy of the mutated allele. DISCUSSION Mutations affecting the OTOGL gene have been recently connected with nonsyndromic sensorineural hearing loss. Seven such mutations have already been described. The p.Arg925* reported in this study has been found once in a French family. The current report is the first to describe this mutation in a Middle Eastern family.
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Affiliation(s)
- Rana Barake
- 1 Department of Otolaryngology - Head & Neck Surgery, American University of Beirut , Beirut, Lebanon
| | - Samer Abou-Rizk
- 1 Department of Otolaryngology - Head & Neck Surgery, American University of Beirut , Beirut, Lebanon
| | - Georges Nemer
- 2 Department of Biochemistry and Molecular Genetics Faculty of Medicine, American University of Beirut , Beirut, Lebanon
| | - Marc Bassim
- 1 Department of Otolaryngology - Head & Neck Surgery, American University of Beirut , Beirut, Lebanon
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Delayed Otolith Development Does Not Impair Vestibular Circuit Formation in Zebrafish. J Assoc Res Otolaryngol 2017; 18:415-425. [PMID: 28332011 DOI: 10.1007/s10162-017-0617-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/21/2017] [Indexed: 10/19/2022] Open
Abstract
What is the role of normally patterned sensory signaling in development of vestibular circuits? For technical reasons, including the difficulty in depriving animals of vestibular inputs, this has been a challenging question to address. Here we take advantage of a vestibular-deficient zebrafish mutant, rock solo AN66 , in order to examine whether normal sensory input is required for formation of vestibular-driven postural circuitry. We show that the rock solo AN66 mutant is a splice site mutation in the secreted glycoprotein otogelin (otog), which we confirm through both whole genome sequencing and complementation with an otog early termination mutant. Using confocal microscopy, we find that elements of postural circuits are anatomically normal in rock solo AN66 mutants, including hair cells, vestibular ganglion neurons, and vestibulospinal neurons. Surprisingly, the balance and postural deficits that are readily apparent in younger larvae disappear around 2 weeks of age. We demonstrate that this behavioral recovery follows the delayed development of the anterior (utricular) otolith, which appears around 14 days post-fertilization (dpf), compared to 1 dpf in WT. These findings indicate that utricular signaling is not required for normal structural development of the inner ear and vestibular nucleus neurons. Furthermore, despite the otolith's developmental delay until well after postural behaviors normally appear, downstream circuits can drive righting reflexes within ∼1-2 days of its arrival, indicating that vestibular circuit wiring is not impaired by a delay in patterned activity. The functional recovery of postural behaviors may shed light on why humans with mutations in otog exhibit only subclinical vestibular deficits.
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Zamora LY, Miguel KC, Lu Z. The alcohol-sensitive period during early octavolateral organ development in zebrafish (Danio rerio). J Neurosci Res 2017; 95:1194-1203. [PMID: 28105691 DOI: 10.1002/jnr.24017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 11/30/2016] [Accepted: 12/19/2016] [Indexed: 12/15/2022]
Abstract
Fetal alcohol exposure can cause Fetal Alcohol Spectrum Disorders (FASD), completely preventable developmental disabilities characterized by permanent birth defects. However, specific gestational timing when developing organs are most sensitive to alcohol exposure is unclear. In this study, we examined the temporal effects of embryonic alcohol exposure on octavolateral organs in zebrafish (Danio rerio), including inner ears and lateral line neuromasts that function in hearing, balance, and hydrodynamic detection, respectively. To determine an alcohol-sensitive period in the first 24 hours post fertilization (hpf), Et(krt4:EGFP)sqet4 zebrafish that express green fluorescent protein in sensory hair cells were treated in 2% alcohol for 2, 3, and 5-hours. Octavolateral organs of control and alcohol-exposed larvae were examined at 3, 5, and 7 days post fertilization (dpf). Using confocal and light microscopy, we found that alcohol-exposed larvae had significantly smaller otic vesicles and saccular otoliths than control larvae at 3 dpf. Only alcohol-exposed larvae from 12-17 hpf had smaller otic vesicles at 5 dpf, smaller saccular otoliths at 7 dpf and fewer saccular hair cells, neuromasts and hair cells per neuromast at 3 dpf. In addition, auditory function was assessed by microphonic potential recordings from inner ear hair cells in response to 200-Hz stimulation. Hearing sensitivity was reduced for alcohol-exposed larvae from 7-12 and 12-17 hpf. Our results show that 12-17 hpf is an alcohol-sensitive time window when morphology and function of zebrafish octavolateral organs are most vulnerable to alcohol exposure. This study implies that embryonic alcohol exposure timing during early development can influence severity of hearing deficits. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Lilliann Y Zamora
- University of Miami, Department of Biology, Coral Gables, Florida.,University of Miami, Neuroscience Program, Miami, Florida
| | - Kayla C Miguel
- University of Miami, Neuroscience Program, Miami, Florida
| | - Zhongmin Lu
- University of Miami, Department of Biology, Coral Gables, Florida.,University of Miami, Neuroscience Program, Miami, Florida.,International Center for Marine Studies, Shanghai Ocean University, Shanghai, China
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46
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Korver AMH, Smith RJH, Van Camp G, Schleiss MR, Bitner-Glindzicz MAK, Lustig LR, Usami SI, Boudewyns AN. Congenital hearing loss. Nat Rev Dis Primers 2017; 3:16094. [PMID: 28079113 PMCID: PMC5675031 DOI: 10.1038/nrdp.2016.94] [Citation(s) in RCA: 287] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Congenital hearing loss (hearing loss that is present at birth) is one of the most prevalent chronic conditions in children. In the majority of developed countries, neonatal hearing screening programmes enable early detection; early intervention will prevent delays in speech and language development and has long-lasting beneficial effects on social and emotional development and quality of life. A diagnosis of hearing loss is usually followed by a search for an underlying aetiology. Congenital hearing loss might be attributed to environmental and prenatal factors, which prevail in low-income settings; congenital infections, particularly cytomegalovirus infection, are also a common risk factor for hearing loss. Genetic causes probably account for the majority of cases in developed countries; mutations can affect any component of the hearing pathway, in particular, inner ear homeostasis (endolymph production and maintenance) and mechano-electrical transduction (the conversion of a mechanical stimulus into electrochemical activity). Once the underlying cause of hearing loss is established, it might direct therapeutic decision making and guide prevention and (genetic) counselling. Management options include specific antimicrobial therapies, surgical treatment of craniofacial abnormalities and implantable or non-implantable hearing devices. An improved understanding of the pathophysiology and molecular mechanisms that underlie hearing loss and increased awareness of recent advances in genetic testing will promote the development of new treatment and screening strategies.
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Affiliation(s)
- Anna M H Korver
- Department of Pediatrics, St Antonius Hospital, PO BOX 2500, 3430 EM Nieuwegein, The Netherlands
| | - Richard J H Smith
- Molecular Otolaryngology and Renal Research Laboratories and the Genetics PhD Program, University of Iowa, Iowa City, Iowa, USA
| | - Guy Van Camp
- Department of Medical Genetics, Antwerp University Hospital, University of Antwerp, Antwerp, Belgium
| | - Mark R Schleiss
- Division of Pediatric Infectious Diseases and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Maria A K Bitner-Glindzicz
- Genetics and Genomic Medicine Programme, University College London Great Ormond Street Institute of Child Health, London, UK
| | - Lawrence R Lustig
- Department of Otolaryngology-Head and Neck Surgery, Columbia University Medical Center, New York, New York, USA
| | - Shin-Ichi Usami
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - An N Boudewyns
- Department of Otorhinolaryngology, Head and Neck Surgery, Antwerp University Hospital, University of Antwerp, Antwerp, Belgium
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The diagnostic yield of whole-exome sequencing targeting a gene panel for hearing impairment in The Netherlands. Eur J Hum Genet 2016; 25:308-314. [PMID: 28000701 DOI: 10.1038/ejhg.2016.182] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 10/19/2016] [Accepted: 11/22/2016] [Indexed: 12/12/2022] Open
Abstract
Hearing impairment (HI) is genetically heterogeneous which hampers genetic counseling and molecular diagnosis. Testing of several single HI-related genes is laborious and expensive. In this study, we evaluate the diagnostic utility of whole-exome sequencing (WES) targeting a panel of HI-related genes. Two hundred index patients, mostly of Dutch origin, with presumed hereditary HI underwent WES followed by targeted analysis of an HI gene panel of 120 genes. We found causative variants underlying the HI in 67 of 200 patients (33.5%). Eight of these patients have a large homozygous deletion involving STRC, OTOA or USH2A, which could only be identified by copy number variation detection. Variants of uncertain significance were found in 10 patients (5.0%). In the remaining 123 cases, no potentially causative variants were detected (61.5%). In our patient cohort, causative variants in GJB2, USH2A, MYO15A and STRC, and in MYO6 were the leading causes for autosomal recessive and dominant HI, respectively. Segregation analysis and functional analyses of variants of uncertain significance will probably further increase the diagnostic yield of WES.
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Abstract
PURPOSE OF REVIEW In the age of targeted genomic enrichment and massively parallel sequencing, there is no more efficient genetic testing method for the diagnosis of hereditary hearing loss. More clinical tests are on the market, which can make choosing good tests difficult. RECENT FINDINGS More and larger comprehensive genetic studies in patients with hearing loss have been published recently. They remind us of the importance of looking for both single nucleotide variation and copy number variation in all genes implicated in nonsyndromic hearing loss. They also inform us of how a patient's history and phenotype provide essential information in the interpretation of genetic data. SUMMARY Choosing the most comprehensive genetic test improves the chances of a genetic diagnosis and thereby impacts clinical care.
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Blanco-Sánchez B, Clément A, Phillips JB, Westerfield M. Zebrafish models of human eye and inner ear diseases. Methods Cell Biol 2016; 138:415-467. [PMID: 28129854 DOI: 10.1016/bs.mcb.2016.10.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Eye and inner ear diseases are the most common sensory impairments that greatly impact quality of life. Zebrafish have been intensively employed to understand the fundamental mechanisms underlying eye and inner ear development. The zebrafish visual and vestibulo-acoustic systems are very similar to these in humans, and although not yet mature, they are functional by 5days post-fertilization (dpf). In this chapter, we show how the zebrafish has significantly contributed to the field of biomedical research and how researchers, by establishing disease models and meticulously characterizing their phenotypes, have taken the first steps toward therapies. We review here models for (1) eye diseases, (2) ear diseases, and (3) syndromes affecting eye and/or ear. The use of new genome editing technologies and high-throughput screening systems should increase considerably the speed at which knowledge from zebrafish disease models is acquired, opening avenues for better diagnostics, treatments, and therapies.
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Affiliation(s)
| | - A Clément
- University of Oregon, Eugene, OR, United States
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Antisense Oligonucleotide-based Splice Correction for USH2A-associated Retinal Degeneration Caused by a Frequent Deep-intronic Mutation. MOLECULAR THERAPY. NUCLEIC ACIDS 2016; 5:e381. [PMID: 27802265 DOI: 10.1038/mtna.2016.89] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 09/07/2016] [Indexed: 12/21/2022]
Abstract
Usher syndrome (USH) is the most common cause of combined deaf-blindness in man. The hearing loss can be partly compensated by providing patients with hearing aids or cochlear implants, but the loss of vision is currently untreatable. In general, mutations in the USH2A gene are the most frequent cause of USH explaining up to 50% of all patients worldwide. The first deep-intronic mutation in the USH2A gene (c.7595-2144A>G) was reported in 2012, leading to the insertion of a pseudoexon (PE40) into the mature USH2A transcript. When translated, this PE40-containing transcript is predicted to result in a truncated non-functional USH2A protein. In this study, we explored the potential of antisense oligonucleotides (AONs) to prevent aberrant splicing of USH2A pre-mRNA as a consequence of the c.7595-2144A>G mutation. Engineered 2'-O-methylphosphorothioate AONs targeting the PE40 splice acceptor site and/or exonic splice enhancer regions displayed significant splice correction potential in both patient derived fibroblasts and a minigene splice assay for USH2A c.7595-2144A>G, whereas a non-binding sense oligonucleotide had no effect on splicing. Altogether, AON-based splice correction could be a promising approach for the development of a future treatment for USH2A-associated retinitis pigmentosa caused by the deep-intronic c.7595-2144A>G mutation.
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