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Shadab M, Abbasi AA, Ejaz A, Ben-Mahmoud A, Gupta V, Kim HG, Vona B. Autosomal recessive non-syndromic hearing loss genes in Pakistan during the previous three decades. J Cell Mol Med 2024; 28:e18119. [PMID: 38534090 DOI: 10.1111/jcmm.18119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 11/29/2023] [Accepted: 01/02/2024] [Indexed: 03/28/2024] Open
Abstract
Hearing loss is a clinically and genetically heterogeneous disorder, with over 148 genes and 170 loci associated with its pathogenesis. The spectrum and frequency of causal variants vary across different genetic ancestries and are more prevalent in populations that practice consanguineous marriages. Pakistan has a rich history of autosomal recessive gene discovery related to non-syndromic hearing loss. Since the first linkage analysis with a Pakistani family that led to the mapping of the DFNB1 locus on chromosome 13, 51 genes associated with this disorder have been identified in this population. Among these, 13 of the most prevalent genes, namely CDH23, CIB2, CLDN14, GJB2, HGF, MARVELD2, MYO7A, MYO15A, MSRB3, OTOF, SLC26A4, TMC1 and TMPRSS3, account for more than half of all cases of profound hearing loss, while the prevalence of other genes is less than 2% individually. In this review, we discuss the most common autosomal recessive non-syndromic hearing loss genes in Pakistani individuals as well as the genetic mapping and sequencing approaches used to discover them. Furthermore, we identified enriched gene ontology terms and common pathways involved in these 51 autosomal recessive non-syndromic hearing loss genes to gain a better understanding of the underlying mechanisms. Establishing a molecular understanding of the disorder may aid in reducing its future prevalence by enabling timely diagnostics and genetic counselling, leading to more effective clinical management and treatments of hearing loss.
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Affiliation(s)
- Madiha Shadab
- Department of Zoology, Mirpur University of Science and Technology, Mirpur, Pakistan
| | - Ansar Ahmed Abbasi
- Department of Zoology, Mirpur University of Science and Technology, Mirpur, Pakistan
| | - Ahsan Ejaz
- Department of Physics, University of Kotli Azad Jammu and Kashmir, Kotli, Pakistan
- School of Nuclear Science and Technology, Lanzhou University, Lanzhou, China
| | - Afif Ben-Mahmoud
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Vijay Gupta
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
- College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- Institute for Auditory Neuroscience and Inner Ear Lab, University Medical Center Göttingen, Göttingen, Germany
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2
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Qi J, Tan F, Zhang L, Zhou Y, Zhang Z, Sun Q, Li N, Fang Y, Chen X, Wu Y, Zhong G, Chai R. Critical role of TPRN rings in the stereocilia for hearing. Mol Ther 2024; 32:204-217. [PMID: 37952086 PMCID: PMC10787140 DOI: 10.1016/j.ymthe.2023.11.011] [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: 05/24/2023] [Revised: 09/29/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023] Open
Abstract
Inner ear hair cells detect sound vibration through the deflection of mechanosensory stereocilia. Cytoplasmic protein TPRN has been shown to localize at the taper region of the stereocilia, and mutations in TPRN cause hereditary hearing loss through an unknown mechanism. Here, using biochemistry and dual stimulated emission depletion microscopy imaging, we show that the TPRN, together with its binding proteins CLIC5 and PTPRQ, forms concentric rings in the taper region of stereocilia. The disruption of TPRN rings, triggered by the competitive inhibition of the interaction of TPRN and CLIC5 or exogenous TPRN overexpression, leads to stereocilia degeneration and severe hearing loss. Most importantly, restoration of the TPRN rings can rescue the damaged auditory function of Tprn knockout mice by exogenously expressing TPRN at an appropriate level in HCs via promoter recombinant adeno-associated virus (AAV). In summary, our results reveal highly structured TPRN rings near the taper region of stereocilia that are crucial for stereocilia function and hearing. Also, TPRN ring restoration in stereocilia by AAV-Tprn effectively repairs damaged hearing, which lays the foundation for the clinical application of AAV-mediated gene therapy in patients with TPRN mutation.
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Affiliation(s)
- Jieyu Qi
- State Key Laboratory of Digital Medical Engineering, Department of Otolaryngology Head and Neck Surgery, Zhongda Hospital, School of Life Sciences and Technology, School of Medicine, Advanced Institute for Life and Health, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing 210096, China; Co-Innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China; School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
| | - Fangzhi Tan
- State Key Laboratory of Digital Medical Engineering, Department of Otolaryngology Head and Neck Surgery, Zhongda Hospital, School of Life Sciences and Technology, School of Medicine, Advanced Institute for Life and Health, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing 210096, China.
| | - Liyan Zhang
- State Key Laboratory of Digital Medical Engineering, Department of Otolaryngology Head and Neck Surgery, Zhongda Hospital, School of Life Sciences and Technology, School of Medicine, Advanced Institute for Life and Health, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing 210096, China
| | - Yinyi Zhou
- State Key Laboratory of Digital Medical Engineering, Department of Otolaryngology Head and Neck Surgery, Zhongda Hospital, School of Life Sciences and Technology, School of Medicine, Advanced Institute for Life and Health, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing 210096, China
| | - Ziyu Zhang
- State Key Laboratory of Digital Medical Engineering, Department of Otolaryngology Head and Neck Surgery, Zhongda Hospital, School of Life Sciences and Technology, School of Medicine, Advanced Institute for Life and Health, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing 210096, China
| | - Qiuhan Sun
- State Key Laboratory of Digital Medical Engineering, Department of Otolaryngology Head and Neck Surgery, Zhongda Hospital, School of Life Sciences and Technology, School of Medicine, Advanced Institute for Life and Health, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing 210096, China
| | - Nianci Li
- State Key Laboratory of Digital Medical Engineering, Department of Otolaryngology Head and Neck Surgery, Zhongda Hospital, School of Life Sciences and Technology, School of Medicine, Advanced Institute for Life and Health, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing 210096, China
| | - Yuan Fang
- State Key Laboratory of Digital Medical Engineering, Department of Otolaryngology Head and Neck Surgery, Zhongda Hospital, School of Life Sciences and Technology, School of Medicine, Advanced Institute for Life and Health, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing 210096, China
| | - Xin Chen
- State Key Laboratory of Digital Medical Engineering, Department of Otolaryngology Head and Neck Surgery, Zhongda Hospital, School of Life Sciences and Technology, School of Medicine, Advanced Institute for Life and Health, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing 210096, China
| | - Yunhao Wu
- State Key Laboratory of Digital Medical Engineering, Department of Otolaryngology Head and Neck Surgery, Zhongda Hospital, School of Life Sciences and Technology, School of Medicine, Advanced Institute for Life and Health, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing 210096, China
| | - Guisheng Zhong
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
| | - Renjie Chai
- State Key Laboratory of Digital Medical Engineering, Department of Otolaryngology Head and Neck Surgery, Zhongda Hospital, School of Life Sciences and Technology, School of Medicine, Advanced Institute for Life and Health, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing 210096, China; Co-Innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China; School of Life Science, Beijing Institute of Technology, Beijing 100081, China; Department of Otolaryngology Head and Neck Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China; Southeast University Shenzhen Research Institute, Shenzhen 518063, China.
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3
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Liu X, Teng L, Zuo W, Zhong S, Xu Y, Sun J. Deafness gene screening based on a multilevel cascaded BPNN model. BMC Bioinformatics 2023; 24:56. [PMID: 36803022 PMCID: PMC9942297 DOI: 10.1186/s12859-023-05182-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/11/2023] [Indexed: 02/22/2023] Open
Abstract
Sudden sensorineural hearing loss is a common and frequently occurring condition in otolaryngology. Existing studies have shown that sudden sensorineural hearing loss is closely associated with mutations in genes for inherited deafness. To identify these genes associated with deafness, researchers have mostly used biological experiments, which are accurate but time-consuming and laborious. In this paper, we proposed a computational method based on machine learning to predict deafness-associated genes. The model is based on several basic backpropagation neural networks (BPNNs), which were cascaded as multiple-level BPNN models. The cascaded BPNN model showed a stronger ability for screening deafness-associated genes than the conventional BPNN. A total of 211 of 214 deafness-associated genes from the deafness variant database (DVD v9.0) were used as positive data, and 2110 genes extracted from chromosomes were used as negative data to train our model. The test achieved a mean AUC higher than 0.98. Furthermore, to illustrate the predictive performance of the model for suspected deafness-associated genes, we analyzed the remaining 17,711 genes in the human genome and screened the 20 genes with the highest scores as highly suspected deafness-associated genes. Among these 20 predicted genes, three genes were mentioned as deafness-associated genes in the literature. The analysis showed that our approach has the potential to screen out highly suspected deafness-associated genes from a large number of genes, and our predictions could be valuable for future research and discovery of deafness-associated genes.
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Affiliation(s)
- Xiao Liu
- School of Microelectronics and Communication Engineering, Chongqing University, 174 Shapingba District, Chongqing, 400044, China.
| | - Li Teng
- grid.190737.b0000 0001 0154 0904School of Microelectronics and Communication Engineering, Chongqing University, 174 Shapingba District, Chongqing, 400044 China
| | - Wenqi Zuo
- grid.452206.70000 0004 1758 417XDepartment of Otolaryngology, The First Affiliated Hospital of Chongqing Medical University, NO. 1 Youyi Road, Yuzhong District, Chongqing, 400016 China
| | - Shixun Zhong
- grid.452206.70000 0004 1758 417XDepartment of Otolaryngology, The First Affiliated Hospital of Chongqing Medical University, NO. 1 Youyi Road, Yuzhong District, Chongqing, 400016 China
| | - Yuqiao Xu
- grid.190737.b0000 0001 0154 0904School of Microelectronics and Communication Engineering, Chongqing University, 174 Shapingba District, Chongqing, 400044 China
| | - Jing Sun
- grid.190737.b0000 0001 0154 0904School of Microelectronics and Communication Engineering, Chongqing University, 174 Shapingba District, Chongqing, 400044 China
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Li J, Liu C, Müller U, Zhao B. RIPOR2-mediated autophagy dysfunction is critical for aminoglycoside-induced hearing loss. Dev Cell 2022; 57:2204-2220.e6. [PMID: 36113482 PMCID: PMC9529990 DOI: 10.1016/j.devcel.2022.08.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/25/2022] [Accepted: 08/23/2022] [Indexed: 01/18/2023]
Abstract
Aminoglycosides (AGs) are potent antibiotics that are capable of treating a wide variety of life-threatening infections; however, they are ototoxic and cause irreversible damage to cochlear hair cells. Despite substantial progress, little is known about the molecular pathways critical for hair cell function and survival that are affected by AG exposure. We demonstrate here that gentamicin, a representative AG antibiotic, binds to and within minutes triggers translocation of RIPOR2 in murine hair cells from stereocilia to the pericuticular area. Then, by interacting with a central autophagy component, GABARAP, RIPOR2 affects autophagy activation. Reducing the expression of RIPOR2 or GABARAP completely prevents AG-induced hair cell death and subsequent hearing loss in mice. Additionally, abolishing the expression of PINK1 or Parkin, two key mitochondrial autophagy proteins, prevents hair cell death and subsequent hearing loss caused by AG. In summary, our study demonstrates that RIPOR2-mediated autophagic dysfunction is essential for AG-induced hearing loss.
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Affiliation(s)
- Jinan Li
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Chang Liu
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ulrich Müller
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Bo Zhao
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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5
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Liu C, Luo N, Zhao B. Reducing Taperin Expression Restores Hearing in Grxcr2 Mutant Mice. Neuroscience 2022; 498:85-92. [PMID: 35752427 PMCID: PMC9420823 DOI: 10.1016/j.neuroscience.2022.06.030] [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: 02/11/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 11/20/2022]
Abstract
Recessive mutations in GRXCR2 cause deafness in both humans and mice. In Grxcr2 null hair cells, the sensory receptors for sound in the inner ear, stereocilia are disorganized. Reducing the expression of taperin, a protein that interacts with GRXCR2 at the base of stereocilia, corrects the morphological defects of stereocilia and restores hearing in Grxcr2 null mice. To further validate this finding, this study generated two novel taperin mutant mouse lines that exhibit progressive hearing loss. Then Grxcr2 null mice were crossed with one of these taperin mutant mice. The following morphological analysis revealed that reducing taperin expression indeed corrected stereocilia morphological abnormalities in Grxcr2 null mice. Functional analysis further confirmed that reducing taperin expression partially restored hearing in Grxcr2 null mice.
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Affiliation(s)
- Chang Liu
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Na Luo
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Bo Zhao
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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6
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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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7
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Miyoshi T, Belyantseva IA, Kitajiri SI, Miyajima H, Nishio SY, Usami SI, Kim BJ, Choi BY, Omori K, Shroff H, Friedman TB. Human deafness-associated variants alter the dynamics of key molecules in hair cell stereocilia F-actin cores. Hum Genet 2022; 141:363-382. [PMID: 34232383 PMCID: PMC11351816 DOI: 10.1007/s00439-021-02304-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/15/2021] [Indexed: 12/16/2022]
Abstract
Stereocilia protrude up to 100 µm from the apical surface of vertebrate inner ear hair cells and are packed with cross-linked filamentous actin (F-actin). They function as mechanical switches to convert sound vibration into electrochemical neuronal signals transmitted to the brain. Several genes encode molecular components of stereocilia including actin monomers, actin regulatory and bundling proteins, motor proteins and the proteins of the mechanotransduction complex. A stereocilium F-actin core is a dynamic system, which is continuously being remodeled while maintaining an outwardly stable architecture under the regulation of F-actin barbed-end cappers, severing proteins and crosslinkers. The F-actin cores of stereocilia also provide a pathway for motor proteins to transport cargos including components of tip-link densities, scaffolding proteins and actin regulatory proteins. Deficiencies and mutations of stereocilia components that disturb this "dynamic equilibrium" in stereocilia can induce morphological changes and disrupt mechanotransduction causing sensorineural hearing loss, best studied in mouse and zebrafish models. Currently, at least 23 genes, associated with human syndromic and nonsyndromic hearing loss, encode proteins involved in the development and maintenance of stereocilia F-actin cores. However, it is challenging to predict how variants associated with sensorineural hearing loss segregating in families affect protein function. Here, we review the functions of several molecular components of stereocilia F-actin cores and provide new data from our experimental approach to directly evaluate the pathogenicity and functional impact of reported and novel variants of DIAPH1 in autosomal-dominant DFNA1 hearing loss using single-molecule fluorescence microscopy.
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Affiliation(s)
- Takushi Miyoshi
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, Room 1F-143A, Bethesda, MD, 20892, USA.
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan.
| | - Inna A Belyantseva
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, Room 1F-143A, Bethesda, MD, 20892, USA
| | - Shin-Ichiro Kitajiri
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 390-8621, Matsumoto, Japan
| | - Hiroki Miyajima
- Department of Otolaryngology, Shinshu University School of Medicine, Matsumoto, 390-8621, Japan
- Department of Otolaryngology, Aizawa Hospital, Matsumoto, 390-8510, Japan
| | - Shin-Ya Nishio
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 390-8621, Matsumoto, Japan
| | - Shin-Ichi Usami
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, 390-8621, Matsumoto, Japan
| | - Bong Jik Kim
- Department of Otolaryngology-Head and Neck Surgery, Chungnam National University College of Medicine, Chungnam National University Sejong Hospital, Sejong, 30099, South Korea
- Brain Research Institute, Chungnam National University College of Medicine, Daejeon, 35015, South Korea
| | - Byung Yoon Choi
- Department of Otorhinolaryngology, Seoul National University Bundang Hospital, Seongnam, 13620, South Korea
| | - Koichi Omori
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507, Japan
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, Room 1F-143A, Bethesda, MD, 20892, USA
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8
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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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Azadegan-Dehkordi F, Koohiyan M, Hoseini M. An update on autosomal recessive hearing loss and loci involved in it. INDIAN JOURNAL OF OTOLOGY 2022. [DOI: 10.4103/indianjotol.indianjotol_115_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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10
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Liu C, Zhao B. Murine GRXCR1 Has a Different Function Than GRXCR2 in the Morphogenesis of Stereocilia. Front Cell Neurosci 2021; 15:714070. [PMID: 34366792 PMCID: PMC8333275 DOI: 10.3389/fncel.2021.714070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 06/25/2021] [Indexed: 11/13/2022] Open
Abstract
Mutations in human glutaredoxin domain-containing cysteine-rich protein 1 (GRXCR1) and its paralog GRXCR2 have been linked to hearing loss in humans. Although both GRXCR1 and GRXCR2 are required for the morphogenesis of stereocilia in cochlear hair cells, a fundamental question that remains unclear is whether GRXCR1 and GRXCR2 have similar functions in hair cells. Previously, we found that GRXCR2 is critical for the stereocilia morphogenesis by regulating taperin localization at the base of stereocilia. Reducing taperin expression level rescues the morphological defects of stereocilia and hearing loss in Grxcr2-deficient mice. So far, functions of GRXCR1 in mammalian hair cells are still unclear. Grxcr1-deficient hair cells have very thin stereocilia with less F-actin content inside, which is different from Grxcr2-deficient hair cells. In contrast to GRXCR2, which is concentrated at the base of stereocilia, GRXCR1 is diffusely distributed throughout the stereocilia. Notably, GRXCR1 interacts with GRXCR2. In Grxcr1-deficient hair cells, the expression level of GRXCR2 and taperin is reduced. Remarkably, different from that in Grxcr2-deficient mice, reducing taperin expression level does not rescue the morphological defects of stereocilia or hearing loss in Grxcr1-deficient mice. Thus, our findings suggest that GRXCR1 has different functions than GRXCR2 during the morphogenesis of stereocilia.
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Affiliation(s)
- Chang Liu
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Bo Zhao
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN, United States
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11
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Li J, Liu C, Zhao B. N-Terminus of GRXCR2 Interacts With CLIC5 and Is Essential for Auditory Perception. Front Cell Dev Biol 2021; 9:671364. [PMID: 34026762 PMCID: PMC8131845 DOI: 10.3389/fcell.2021.671364] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/13/2021] [Indexed: 11/17/2022] Open
Abstract
Stereocilia of cochlear hair cells are specialized mechanosensing organelles that convert sound-induced vibration to electrical signals. Glutaredoxin domain-containing cysteine-rich protein 2 (GRXCR2) is localized at the base of stereocilia and is necessary for stereocilia morphogenesis and auditory perception. However, the detailed functions of GRXCR2 in hair cells are still largely unknown. Here, we report that GRXCR2 interacts with chloride intracellular channel protein 5 (CLIC5) which is also localized at the base of stereocilia and required for normal hearing in human and mouse. Immunolocalization analyses suggest that GRXCR2 is not required for the localization of CLIC5 to the stereociliary base during development, or vice versa. Using clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system, we deleted 60 amino acids near the N-terminus of GRXCR2 essential for its interaction with CLIC5. Interestingly, mice harboring this in-frame deletion in Grxcr2 exhibit moderate hearing loss at lower frequencies and severe hearing loss at higher frequencies although the morphogenesis of stereocilia is minimally affected. Thus, our findings reveal that the interaction between GRXCR2 and CLIC5 is crucial for normal hearing.
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Affiliation(s)
- Jinan Li
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Chang Liu
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Bo Zhao
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, IN, United States
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12
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Wonkam A, Lebeko K, Mowla S, Noubiap JJ, Chong M, Pare G. Whole exome sequencing reveals a biallelic frameshift mutation in GRXCR2 in hearing impairment in Cameroon. Mol Genet Genomic Med 2021; 9:e1609. [PMID: 33528103 PMCID: PMC8104159 DOI: 10.1002/mgg3.1609] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/06/2021] [Accepted: 01/11/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Hearing impairment (HI) genes are poorly studied in African populations. METHODS We used whole exome sequencing (WES) to investigate pathogenic and likely pathogenic (PLP) variants in 10 individuals with HI, from four multiplex families from Cameroon, two of which were previously unresolved with a targeted gene enrichment (TGE) panel of 116 genes. In silico protein modelling, western blotting and live imaging of transfected HEK293 cells were performed to study protein structure and functions. RESULTS All PLP variants previously identified with TGE were replicated. In one previously unresolved family, we found a homozygous frameshift PLP variant in GRXCR2 (OMIM: 615762), NM_001080516.1(GRXCR2):c.251delC p.(Ile85SerfsTer33), in two affected siblings; and additionally, in 1/80 unrelated individuals affected with non-syndromic hearing impairment (NSHI). The GRXCR2-c.251delC variant introduced a premature stop codon, leading to truncation and loss of a zinc-finger domain. Fluorescence confocal microscopy tracked the wild-type GRXCR2 protein to the cellular membrane, unlike the mutated GRXCR2 protein. CONCLUSION This study confirms GRXCR2 as a HI-associated gene. GRXCR2 should be included to the currently available TGE panels for HI diagnosis.
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Affiliation(s)
- Ambroise Wonkam
- Department of Medicine, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Kamogelo Lebeko
- Department of Medicine, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Shaheen Mowla
- Department of Pathology, Division of Haematology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jean Jacques Noubiap
- Centre for Heart Rhythm Disorders, South Australian Health and Medical Research Institute (SAHMRI, University of Adelaide and Royal Adelaide Hospital, Adelaide, Australia
| | - Mike Chong
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
| | - Guillaume Pare
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
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13
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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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14
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Wu D, Huang W, Xu Z, Li S, Zhang J, Chen X, Tang Y, Qiu J, Wang Z, Duan X, Zhang L. Clinical and genetic study of 12 Chinese Han families with nonsyndromic deafness. Mol Genet Genomic Med 2020; 8:e1177. [PMID: 32048449 PMCID: PMC7196461 DOI: 10.1002/mgg3.1177] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/24/2020] [Accepted: 01/30/2020] [Indexed: 12/12/2022] Open
Abstract
Background Nonsyndromic hearing loss is clinically and genetically heterogeneous. In this study, we characterized the clinical features of 12 Chinese Han deaf families in which mutations in common deafness genes GJB2, SLC26A4, and MT‐RNR1 were excluded. Methods Targeted next‐generation sequencing of 147 known deafness genes was performed in probands of 10 families, while whole‐exome sequencing was applied in those of the rest two. Results Pathogenic mutations in a total of 11 rare deafness genes, OTOF, CDH23, PCDH15, PDZD7, ADGRV1, KARS, OTOG, GRXCR2, MYO6, GRHL2, and POU3F4, were identified in all 12 probands, with 16 mutations being novel. Intrafamilial cosegregation of the mutations and the deafness phenotype were confirmed by Sanger sequencing. Conclusion Our results expanded the mutation spectrum and genotype‒phenotype correlation of nonsyndromic hearing loss in Chinese Hans and also emphasized the importance of combining both next‐generation sequencing and detailed auditory evaluation to achieve a more accurate diagnosis for nonsyndromic hearing loss.
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Affiliation(s)
- Di Wu
- Department of Otolaryngology, Affiliated Hospital of Nantong University, Nantong, China
| | - Weiyuan Huang
- Department of Otolaryngology, Affiliated Hospital of Nantong University, Nantong, China
| | - Zhenhang Xu
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, China
| | - Shuo Li
- Department of Otolaryngology, Affiliated Hospital of Nantong University, Nantong, China
| | - Jie Zhang
- Department of Otolaryngology, Affiliated Hospital of Nantong University, Nantong, China
| | - Xiaohua Chen
- Department of Radiology, Affiliated Hospital of Nantong University, Nantong, China
| | - Yan Tang
- Department of Otolaryngology, Affiliated Hospital of Nantong University, Nantong, China
| | - Jinhong Qiu
- Department of Otolaryngology, Affiliated Hospital of Nantong University, Nantong, China
| | - Zhixia Wang
- Department of Otolaryngology, Affiliated Hospital of Nantong University, Nantong, China
| | - Xuchu Duan
- School of Life Science, Nantong University, Nantong, China
| | - Luping Zhang
- Department of Otolaryngology, Affiliated Hospital of Nantong University, Nantong, China
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15
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GRXCR2 Regulates Taperin Localization Critical for Stereocilia Morphology and Hearing. Cell Rep 2019; 25:1268-1280.e4. [PMID: 30380417 PMCID: PMC6317715 DOI: 10.1016/j.celrep.2018.09.063] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/03/2018] [Accepted: 09/19/2018] [Indexed: 12/14/2022] Open
Abstract
Mutations in human GRXCR2, which encodes a protein of undetermined function, cause hearing loss by unknown mechanisms. We found that mouse GRXCR2 localizes to the base of the stereocilia, which are actin-based mechanosensing organelles in cochlear hair cells that convert sound-induced vibrations into electrical signals. The stereocilia base also contains taperin, another protein of unknown function required for human hearing. We show that taperin and GRXCR2 form a complex and that taperin is diffused throughout the stereocilia length in Grxcr2-deficient hair cells. Stereocilia lacking GRXCR2 are longer than normal and disorganized due to the mislocalization of taperin, which could modulate the actin cytoskeleton in stereocilia. Remarkably, reducing taperin expression levels could rescue the morphological defects of stereocilia and restore the hearing of Grxcr2-deficient mice. Thus, our findings suggest that GRXCR2 is critical for the morphogenesis of stereocilia and auditory perception by restricting taperin to the stereocilia base. Liu et al. show that GRXCR2 and taperin form a complex at the base of the stereocilia in cochlear hair cells. Stereocilia lacking GRXCR2 are longer than normal and disorganized due to the mislocalization of taperin, which could modulate the actin cytoskeleton in stereocilia. Reducing taperin expression levels could rescue the morphological defects of stereocilia and restore the hearing of Grxcr2-deficient mice.
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16
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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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17
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Li Y, Liu H, Giffen KP, Chen L, Beisel KW, He DZZ. Transcriptomes of cochlear inner and outer hair cells from adult mice. Sci Data 2018; 5:180199. [PMID: 30277483 PMCID: PMC6167952 DOI: 10.1038/sdata.2018.199] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/02/2018] [Indexed: 01/09/2023] Open
Abstract
Inner hair cells (IHCs) and outer hair cells (OHCs) are the two anatomically and functionally distinct types of mechanosensitive receptor cells in the mammalian cochlea. The molecular mechanisms defining their morphological and functional specializations are largely unclear. As a first step to uncover the underlying mechanisms, we examined the transcriptomes of IHCs and OHCs isolated from adult CBA/J mouse cochleae. One thousand IHCs and OHCs were separately collected using the suction pipette technique. RNA sequencing of IHCs and OHCs was performed and their transcriptomes were analyzed. The results were validated by comparing some IHC and OHC preferentially expressed genes between present study and published microarray-based data as well as by real-time qPCR. Antibody-based immunocytochemistry was used to validate preferential expression of SLC7A14 and DNM3 in IHCs and OHCs. These data are expected to serve as a highly valuable resource for unraveling the molecular mechanisms underlying different biological properties of IHCs and OHCs as well as to provide a road map for future characterization of genes expressed in IHCs and OHCs.
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Affiliation(s)
- Yi Li
- Department of Otorhinolaryngology, Beijing Tongren Hospital, Beijing Capital Medical University, Beijing 100730, China
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska 68170, USA
| | - Huizhan Liu
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska 68170, USA
| | - Kimberlee P. Giffen
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska 68170, USA
| | - Lei Chen
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska 68170, USA
- Chongqing Academy of Animal Science, Chongqing 402460, China
| | - Kirk W. Beisel
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska 68170, USA
| | - David Z. Z. He
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska 68170, USA
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18
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Avenarius MR, Jung JY, Askew C, Jones SM, Hunker KL, Azaiez H, Rehman AU, Schraders M, Najmabadi H, Kremer H, Smith RJH, Géléoc GSG, Dolan DF, Raphael Y, Kohrman DC. Grxcr2 is required for stereocilia morphogenesis in the cochlea. PLoS One 2018; 13:e0201713. [PMID: 30157177 PMCID: PMC6114524 DOI: 10.1371/journal.pone.0201713] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/22/2018] [Indexed: 11/18/2022] Open
Abstract
Hearing and balance depend upon the precise morphogenesis and mechanosensory function of stereocilia, the specialized structures on the apical surface of sensory hair cells in the inner ear. Previous studies of Grxcr1 mutant mice indicated a critical role for this gene in control of stereocilia dimensions during development. In this study, we analyzed expression of the paralog Grxcr2 in the mouse and evaluated auditory and vestibular function of strains carrying targeted mutations of the gene. Peak expression of Grxcr2 occurs during early postnatal development of the inner ear and GRXCR2 is localized to stereocilia in both the cochlea and in vestibular organs. Homozygous Grxcr2 deletion mutants exhibit significant hearing loss by 3 weeks of age that is associated with developmental defects in stereocilia bundle orientation and organization. Despite these bundle defects, the mechanotransduction apparatus assembles in relatively normal fashion as determined by whole cell electrophysiological evaluation and FM1-43 uptake. Although Grxcr2 mutants do not exhibit overt vestibular dysfunction, evaluation of vestibular evoked potentials revealed subtle defects of the mutants in response to linear accelerations. In addition, reduced Grxcr2 expression in a hypomorphic mutant strain is associated with progressive hearing loss and bundle defects. The stereocilia localization of GRXCR2, together with the bundle pathologies observed in the mutants, indicate that GRXCR2 plays an intrinsic role in bundle orientation, organization, and sensory function in the inner ear during development and at maturity.
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Affiliation(s)
- Matthew R. Avenarius
- Department of Otolaryngology/Kresge Hearing Research Institute, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Jae-Yun Jung
- Department of Otolaryngology/Kresge Hearing Research Institute, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Charles Askew
- Neuroscience Graduate Program, University of Virginia, Charlottesville, Virginia, United States of America
- Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sherri M. Jones
- Department of Communication Sciences and Disorders, East Carolina University, Greenville, North Carolina, United States of America
| | - Kristina L. Hunker
- Department of Otolaryngology/Kresge Hearing Research Institute, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Hela Azaiez
- Molecular Otolaryngology and Renal Research Laboratories, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Atteeq U. Rehman
- Section on Human Genetics, Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Rockville, Maryland, United States of America
| | - Margit Schraders
- Hearing & Genes Division, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hannie Kremer
- Hearing & Genes Division, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Richard J. H. Smith
- Molecular Otolaryngology and Renal Research Laboratories, Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Gwenaëlle S. G. Géléoc
- Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - David F. Dolan
- Department of Otolaryngology/Kresge Hearing Research Institute, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Yehoash Raphael
- Department of Otolaryngology/Kresge Hearing Research Institute, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - David C. Kohrman
- Department of Otolaryngology/Kresge Hearing Research Institute, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
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19
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Genetic Predisposition to Sporadic Congenital Hearing Loss in a Pediatric Population. Sci Rep 2017; 7:45973. [PMID: 28383030 PMCID: PMC5382691 DOI: 10.1038/srep45973] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 03/07/2017] [Indexed: 11/19/2022] Open
Abstract
Discriminating between inherited and non-inherited sporadic hearing loss is challenging. Here, we attempted to delineate genetic inheritance in simplex cases of severe-to-profound congenital hearing loss in Korean children. Variations in SLC26A4 and GJB2 in 28 children with bilateral severe-to-profound non-syndromic hearing loss (NSHL) without familial history were analyzed using Sanger sequencing. Genetic analysis of individuals without mutations in SLC26A4 and GJB2 was performed by whole exome sequencing (WES). Bi-allelic mutations in SLC26A4 and GJB2 were identified in 12 and 3 subjects, respectively. Of the 13 individuals without mutations in SLC26A4 and GJB2, 2 and 1 carried compound heterozygous mutations in MYO15A and CDH23, respectively. Thus, 64.3% (18/28) of individuals with NSHL were determined to be genetically predisposed. Individuals with sporadic severe-to-profound NSHL were found to mostly exhibit an autosomal recessive inheritance pattern. Novel causative candidate genes for NSHL were identified by analysis of WES data of 10 families without mutations in known causative genes. Bi-allelic mutations predisposing to NSHL were identified in 64.3% of subjects with sporadic severe-to-profound NSHL. Given that several causative genes for NSHL are still unidentified, genetic inheritance of sporadic congenital hearing loss could be more common than that indicated by our results.
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20
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Naz S, Imtiaz A, Mujtaba G, Maqsood A, Bashir R, Bukhari I, Khan MR, Ramzan M, Fatima A, Rehman AU, Iqbal M, Chaudhry T, Lund M, Brewer CC, Morell RJ, Friedman TB. Genetic causes of moderate to severe hearing loss point to modifiers. Clin Genet 2016; 91:589-598. [PMID: 27573290 DOI: 10.1111/cge.12856] [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] [Received: 06/30/2016] [Revised: 08/17/2016] [Accepted: 08/22/2016] [Indexed: 11/30/2022]
Abstract
The genetic underpinnings of recessively inherited moderate to severe sensorineural hearing loss are not well understood, despite its higher prevalence in comparison to profound deafness. We recruited 92 consanguineous families segregating stable or progressive, recessively inherited moderate or severe hearing loss. We utilized homozygosity mapping, Sanger sequencing, targeted capture of known deafness genes with massively parallel sequencing and whole exome sequencing to identify the molecular basis of hearing loss in these families. Variants of the known deafness genes were found in 69% of the participating families with the SLC26A4, GJB2, MYO15A, TMC1, TMPRSS3, OTOF, MYO7A and CLDN14 genes together accounting for hearing loss in 54% of the families. We identified 20 reported and 21 novel variants in 21 known deafness genes; 16 of the 20 reported variants, previously associated with stable, profound deafness were associated with moderate to severe or progressive hearing loss in our families. These data point to a prominent role for genetic background, environmental factors or both as modifiers of human hearing loss severity.
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Affiliation(s)
- Sadaf Naz
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Ayesha Imtiaz
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan.,Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, USA 20892
| | - Ghulam Mujtaba
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Azra Maqsood
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Rasheeda Bashir
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Ihtisham Bukhari
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Muhammad R Khan
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Memoona Ramzan
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Amara Fatima
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Atteeq U Rehman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, USA 20892
| | - Muddassar Iqbal
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Taimur Chaudhry
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, USA 20892
| | - Merete Lund
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, USA 20892
| | - Carmen C Brewer
- Audiology Unit, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, USA 20892
| | - Robert J Morell
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, USA 20892.,Genomics and Computational Biology Core, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, USA 20892
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, USA 20892
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21
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Pediatric otolaryngology, molecular diagnosis of hereditary hearing loss: next-generation sequencing approach. Curr Opin Otolaryngol Head Neck Surg 2016; 23:480-4. [PMID: 26488533 DOI: 10.1097/moo.0000000000000208] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Sensorineural hearing loss (SNHL) is the most common sensory birth defect. The purpose of this article is to review the advances in next-generation sequencing (NGS) and molecular diagnosis of hereditary hearing loss. RECENT FINDINGS Early diagnosis and detection of SNHL is critical for the development of appropriate speech and language, as neuroplasticity peaks in the first few years of life. There has been increased accuracy of NGS genetic testing, which has helped created a paradigm shift in the diagnosis of hearing loss. The diagnostic yield of genetic testing now approaches that of radiographic imaging; however, there remains a difference in cost and time delay. With the introduction of comprehensive genetic panels, 23-129 genes can be sequenced from the same blood sample. SUMMARY Diagnostic genetic testing of SNHL in the past has been confined to a few genes through Sanger sequencing. The advent of NGS allows for development of comprehensive genetic panels, which test for up to 129 genes while improving the accuracy and efficiency of testing. This type of testing may become more common as the costs decrease and more genes are discovered.
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22
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Egilmez OK, Kalcioglu MT. Genetics of Nonsyndromic Congenital Hearing Loss. SCIENTIFICA 2016; 2016:7576064. [PMID: 26989561 PMCID: PMC4775805 DOI: 10.1155/2016/7576064] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 01/19/2016] [Indexed: 06/05/2023]
Abstract
Congenital hearing impairment affects nearly 1 in every 1000 live births and is the most frequent birth defect in developed societies. Hereditary types of hearing loss account for more than 50% of all congenital sensorineural hearing loss cases and are caused by genetic mutations. HL can be either nonsyndromic, which is restricted to the inner ear, or syndromic, a part of multiple anomalies affecting the body. Nonsyndromic HL can be categorised by mode of inheritance, such as autosomal dominant (called DFNA), autosomal recessive (DFNB), mitochondrial, and X-linked (DFN). To date, 125 deafness loci have been reported in the literature: 58 DFNA loci, 63 DFNB loci, and 4 X-linked loci. Mutations in genes that control the adhesion of hair cells, intracellular transport, neurotransmitter release, ionic hemeostasis, and cytoskeleton of hair cells can lead to malfunctions of the cochlea and inner ear. In recent years, with the increase in studies about genes involved in congenital hearing loss, genetic counselling and treatment options have emerged and increased in availability. This paper presents an overview of the currently known genes associated with nonsyndromic congenital hearing loss and mutations in the inner ear.
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Affiliation(s)
- Oguz Kadir Egilmez
- Department of Otorhinolaryngology, Faculty of Medicine, Istanbul Medeniyet University, 34722 Istanbul, Turkey
| | - M. Tayyar Kalcioglu
- Department of Otorhinolaryngology, Faculty of Medicine, Istanbul Medeniyet University, 34722 Istanbul, Turkey
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23
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Oonk AMM, Huygen PLM, Kunst HPM, Kremer H, Pennings RJE. Features of autosomal recessive non-syndromic hearing impairment: a review to serve as a reference. Clin Otolaryngol 2016; 41:487-97. [PMID: 26474130 DOI: 10.1111/coa.12567] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2015] [Indexed: 11/29/2022]
Abstract
OBJECTIVE Non-syndromic sensorineural hearing impairment is inherited in an autosomal recessive fashion in 75-85% of cases. To date, 61 genes with this type of inheritance have been identified as related to hearing impairment, and the genetic heterogeneity is accompanied by a large variety of clinical characteristics. Adequate counselling on a patient's hearing prognosis and rehabilitation is part of the diagnosis on the genetic cause of hearing impairment and, in addition, is important for the psychological well-being of the patient. TYPE OF REVIEW Traditional literature review. DATA SOURCE All articles describing clinical characteristics of the audiovestibular phenotypes of identified genes and related loci have been reviewed. CONCLUSION This review aims to serve as a summary and a reference for counselling purposes when a causative gene has been identified in a patient with a non-syndromic autosomal recessively inherited sensorineural hearing impairment.
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Affiliation(s)
- A M M Oonk
- Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, Nijmegen, The Netherlands. .,Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - P L M Huygen
- Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, Nijmegen, The Netherlands
| | - H P M Kunst
- Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - H Kremer
- Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, Nijmegen, The Netherlands.,Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - R J E Pennings
- Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
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24
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Dahmani M, Ammar-Khodja F, Bonnet C, Lefèvre GM, Hardelin JP, Ibrahim H, Mallek Z, Petit C. EPS8L2 is a new causal gene for childhood onset autosomal recessive progressive hearing loss. Orphanet J Rare Dis 2015; 10:96. [PMID: 26282398 PMCID: PMC4539681 DOI: 10.1186/s13023-015-0316-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 08/03/2015] [Indexed: 12/21/2022] Open
Abstract
Background More than 70 % of the cases of congenital deafness are of genetic origin, of which approximately 80 % are non-syndromic and show autosomal recessive transmission (DFNB forms). To date, 60 DFNB genes have been identified, most of which cause congenital, severe to profound deafness, whereas a few cause delayed progressive deafness in childhood. We report the study of two Algerian siblings born to consanguineous parents, and affected by progressive hearing loss. Method After exclusion of GJB2 (the gene most frequently involved in non-syndromic deafness in Mediterranean countries), we performed whole-exome sequencing in one sibling. Results A frame-shift variant (c.1014delC; p.Ser339Alafs*15) was identified in EPS8L2, encoding Epidermal growth factor receptor Pathway Substrate 8 L2, a protein of hair cells’ stereocilia previously implicated in progressive deafness in the mouse. This variant predicts a truncated, inactive protein, or no protein at all owing to nonsense-mediated mRNA decay. It was detected at the homozygous state in the two clinically affected siblings, and at the heterozygous state in the unaffected parents and one unaffected sibling, whereas it was never found in a control population of 150 Algerians with normal hearing or in the Exome Variant Server database. Conclusion Whole-exome sequencing allowed us to identify a new gene responsible for childhood progressive hearing loss transmitted on the autosomal recessive mode.
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Affiliation(s)
- Malika Dahmani
- Equipe de Génétique, Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumédiène (USTHB), El Alia, Bab-Ezzouar, Algiers, Algeria.
| | - Fatima Ammar-Khodja
- Equipe de Génétique, Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumédiène (USTHB), El Alia, Bab-Ezzouar, Algiers, Algeria.
| | - Crystel Bonnet
- Syndrome de Usher et autres Atteintes Rétino-Cochléaires, Institut de la vision, 75012, Paris, France. .,UMRS 1120, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France. .,Sorbonne Universités, UPMC Université Paris 06, Complexité du Vivant, Paris, 75252 Cedex 05, France.
| | - Gaelle M Lefèvre
- Syndrome de Usher et autres Atteintes Rétino-Cochléaires, Institut de la vision, 75012, Paris, France. .,UMRS 1120, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France. .,Sorbonne Universités, UPMC Université Paris 06, Complexité du Vivant, Paris, 75252 Cedex 05, France.
| | - Jean-Pierre Hardelin
- UMRS 1120, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France. .,Sorbonne Universités, UPMC Université Paris 06, Complexité du Vivant, Paris, 75252 Cedex 05, France. .,Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, 75015, Paris, France.
| | - Hassina Ibrahim
- Service d'otorhinolaryngologie, Centre Hospitalier Universitaire Mustapha Pacha, Algiers, Algeria.
| | - Zahia Mallek
- Service d'otorhinolaryngologie, Centre Hospitalier Universitaire Bab El Oued, Algiers, Algeria.
| | - Christine Petit
- Syndrome de Usher et autres Atteintes Rétino-Cochléaires, Institut de la vision, 75012, Paris, France. .,UMRS 1120, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France. .,Sorbonne Universités, UPMC Université Paris 06, Complexité du Vivant, Paris, 75252 Cedex 05, France. .,Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, 75015, Paris, France. .,Collège de France, 75005, Paris, France.
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25
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Shen J, Scheffer DI, Kwan KY, Corey DP. SHIELD: an integrative gene expression database for inner ear research. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015. [PMID: 26209310 PMCID: PMC4513695 DOI: 10.1093/database/bav071] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The inner ear is a highly specialized mechanosensitive organ responsible for hearing and balance. Its small size and difficulty in harvesting sufficient tissue has hindered the progress of molecular studies. The protein components of mechanotransduction, the molecular biology of inner ear development and the genetic causes of many hereditary hearing and balance disorders remain largely unknown. Inner-ear gene expression data will help illuminate each of these areas. For over a decade, our laboratories and others have generated extensive sets of gene expression data for different cell types in the inner ear using various sample preparation methods and high-throughput genome-wide approaches. To facilitate the study of genes in the inner ear by efficient presentation of the accumulated data and to foster collaboration among investigators, we have developed the Shared Harvard Inner Ear Laboratory Database (SHIELD), an integrated resource that seeks to compile, organize and analyse the genomic, transcriptomic and proteomic knowledge of the inner ear. Five datasets are currently available. These datasets are combined in a relational database that integrates experimental data and annotations relevant to the inner ear. The SHIELD has a searchable web interface with two data retrieval options: viewing the gene pages online or downloading individual datasets as data tables. Each retrieved gene page shows the gene expression data and detailed gene information with hyperlinks to other online databases with up-to-date annotations. Downloadable data tables, for more convenient offline data analysis, are derived from publications and are current as of the time of publication. The SHIELD has made published and some unpublished data freely available to the public with the hope and expectation of accelerating discovery in the molecular biology of balance, hearing and deafness. Database URL:https://shield.hms.harvard.edu
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Affiliation(s)
- Jun Shen
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School Center for Hereditary Deafness,
| | | | - Kelvin Y Kwan
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA and
| | - David P Corey
- Harvard Medical School Center for Hereditary Deafness, Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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26
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Abstract
Hair cells of the inner ear are essential for hearing and balance. As a consequence, pathogenic variants in genes specifically expressed in hair cells often cause hereditary deafness. Hair cells are few in number and not easily isolated from the adjacent supporting cells, so the biochemistry and molecular biology of hair cells can be difficult to study. To study gene expression in hair cells, we developed a protocol for hair cell isolation by FACS. With nearly pure hair cells and surrounding cells, from cochlea and utricle and from E16 to P7, we performed a comprehensive cell type-specific RNA-Seq study of gene expression during mouse inner ear development. Expression profiling revealed new hair cell genes with distinct expression patterns: some are specific for vestibular hair cells, others for cochlear hair cells, and some are expressed just before or after maturation of mechanosensitivity. We found that many of the known hereditary deafness genes are much more highly expressed in hair cells than surrounding cells, suggesting that genes preferentially expressed in hair cells are good candidates for unknown deafness genes.
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27
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Gao X, Huang SS, Yuan YY, Wang GJ, Xu JC, Ji YB, Han MY, Yu F, Kang DY, Lin X, Dai P. Targeted gene capture and massively parallel sequencing identify TMC1 as the causative gene in a six-generation Chinese family with autosomal dominant hearing loss. Am J Med Genet A 2015; 167A:2357-65. [PMID: 26079994 DOI: 10.1002/ajmg.a.37206] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 05/25/2015] [Indexed: 12/26/2022]
Abstract
Hereditary nonsyndromic hearing loss is extremely heterogeneous. Mutations in the transmembrane channel-like gene1 (TMC1) are known to cause autosomal dominant and recessive forms of nonsyndromic hearing loss linked to the loci of DFNA36 and DFNB7/11, respectively. We characterized a six-generation Chinese family (5315) with progressive, postlingual autosomal dominant nonsyndromic hearing loss (ADNSHL). By combining targeted capture of 82 known deafness genes, next-generation sequencing and bioinformatic analysis, we identified TMC1 c.1714G>A (p. D572N) as the disease-causing mutation. This mutation co-segregated with hearing loss in other family members and was not detected in 308 normal controls. In order to determine the prevalence of TMC1 c.1714G>A in Chinese ADNSHL families, we used DNA samples from 67 ADNSHL families with sloping audiogram and identified two families carry this mutation. To determine whether it arose from a common ancestor, we analyzed nine STR markers. Our results indicated that TMC1 c.1714G>A (p.D572N) account for about 4.4% (3/68) of ADNSHL in the Chinese population.
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Affiliation(s)
- Xue Gao
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China.,Department of Otolaryngology, Hainan Branch of PLA General Hospital, Sanya, P. R. China.,Department of Otorhinolaryngology, Second Artillery General Hospital, Beijing, P. R. China
| | - Sha-Sha Huang
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
| | - Yong-Yi Yuan
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
| | - Guo-Jian Wang
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China.,Department of Otolaryngology, Hainan Branch of PLA General Hospital, Sanya, P. R. China
| | - Jin-Cao Xu
- Department of Otorhinolaryngology, Second Artillery General Hospital, Beijing, P. R. China
| | - Yu-Bin Ji
- Department of Otorhinolaryngology, Second Artillery General Hospital, Beijing, P. R. China
| | - Ming-Yu Han
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China.,Department of Otolaryngology, Hainan Branch of PLA General Hospital, Sanya, P. R. China
| | - Fei Yu
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
| | - Dong-Yang Kang
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
| | - Xi Lin
- Department of Otolaryngology, Emory University School of Medicine, Atlanta, GA
| | - Pu Dai
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China.,Department of Otolaryngology, Hainan Branch of PLA General Hospital, Sanya, P. R. China
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28
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Characterization of the transcriptome of nascent hair cells and identification of direct targets of the Atoh1 transcription factor. J Neurosci 2015; 35:5870-83. [PMID: 25855195 DOI: 10.1523/jneurosci.5083-14.2015] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Hair cells are sensory receptors for the auditory and vestibular system in vertebrates. The transcription factor Atoh1 is both necessary and sufficient for the differentiation of hair cells, and is strongly upregulated during hair-cell regeneration in nonmammalian vertebrates. To identify genes involved in hair cell development and function, we performed RNA-seq profiling of purified Atoh1-expressing hair cells from the neonatal mouse cochlea. We identified >600 enriched transcripts in cochlear hair cells, of which 90% have not been previously shown to be expressed in hair cells. We identified 233 of these hair cell genes as candidates to be directly regulated by Atoh1 based on the presence of Atoh1 binding sites in their regulatory regions and by analyzing Atoh1 ChIP-seq datasets from the cerebellum and small intestine. We confirmed 10 of these genes as being direct Atoh1 targets in the cochlea by ChIP-PCR. The identification of candidate Atoh1 target genes is a first step in identifying gene regulatory networks for hair-cell development and may inform future studies on the potential role of Atoh1 in mammalian hair cell regeneration.
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29
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Gao X, Su Y, Chen YL, Han MY, Yuan YY, Xu JC, Xin F, Zhang MG, Huang SS, Wang GJ, Kang DY, Guan LP, Zhang JG, Dai P. Identification of Two Novel Compound Heterozygous PTPRQ Mutations Associated with Autosomal Recessive Hearing Loss in a Chinese Family. PLoS One 2015; 10:e0124757. [PMID: 25919374 PMCID: PMC4412678 DOI: 10.1371/journal.pone.0124757] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 03/05/2015] [Indexed: 11/25/2022] Open
Abstract
Mutations in PTPRQ are associated with deafness in humans due to defects of stereocilia in hair cells. Using whole exome sequencing, we identified responsible gene of family 1572 with autosomal recessively non-syndromic hearing loss (ARNSHL). We also used DNA from 74 familial patients with ARNSHL and 656 ethnically matched control chromosomes to perform extended variant analysis. We identified two novel compound heterozygous missense mutations, c. 3125 A>G p.D1042G (maternal allele) and c.5981 A>G p.E1994G (paternal allele), in the PTPRQ gene, as the cause of recessively inherited sensorineural hearing loss in family 1572. Both variants co-segregated with hearing loss phenotype in family 1572, but were absent in 74 familial patients. Heterozygosity for c. 3125 A>G was identified in two samples from unaffected Chinese individuals (656 chromosomes). Therefore, the hearing loss in this family was caused by two novel compound heterozygous mutations in PTPRQ.
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Affiliation(s)
- Xue Gao
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
- Department of Otolaryngology, Hainan Branch of PLA General Hospital, Sanya, P. R. China
- Department of Otorhinolaryngology, the Second Artillery General Hospital, Beijing, P. R. China
| | - Yu Su
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
- Department of Otolaryngology, Hainan Branch of PLA General Hospital, Sanya, P. R. China
| | | | - Ming-Yu Han
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
| | - Yong-Yi Yuan
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
- Department of Otolaryngology, Hainan Branch of PLA General Hospital, Sanya, P. R. China
| | - Jin-Cao Xu
- Department of Otorhinolaryngology, the Second Artillery General Hospital, Beijing, P. R. China
| | - Feng Xin
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
| | - Mei-Guang Zhang
- Department of Otorhinolaryngology, the Second Artillery General Hospital, Beijing, P. R. China
| | - Sha-Sha Huang
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
| | - Guo-Jian Wang
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
| | - Dong-Yang Kang
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
| | | | | | - Pu Dai
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
- Department of Otolaryngology, Hainan Branch of PLA General Hospital, Sanya, P. R. China
- * E-mail:
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30
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Vona B, Nanda I, Hofrichter MAH, Shehata-Dieler W, Haaf T. Non-syndromic hearing loss gene identification: A brief history and glimpse into the future. Mol Cell Probes 2015; 29:260-70. [PMID: 25845345 DOI: 10.1016/j.mcp.2015.03.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 03/19/2015] [Accepted: 03/23/2015] [Indexed: 11/27/2022]
Abstract
From the first identified non-syndromic hearing loss gene in 1995, to those discovered in present day, the field of human genetics has witnessed an unparalleled revolution that includes the completion of the Human Genome Project in 2003 to the $1000 genome in 2014. This review highlights the classical and cutting-edge strategies for non-syndromic hearing loss gene identification that have been used throughout the twenty year history with a special emphasis on how the innovative breakthroughs in next generation sequencing technology have forever changed candidate gene approaches. The simplified approach afforded by next generation sequencing technology provides a second chance for the many linked loci in large and well characterized families that have been identified by linkage analysis but have presently failed to identify a causative gene. It also discusses some complexities that may restrict eventual candidate gene discovery and calls for novel approaches to answer some of the questions that make this simple Mendelian disorder so intriguing.
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Affiliation(s)
- Barbara Vona
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany.
| | - Indrajit Nanda
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | | | - Wafaa Shehata-Dieler
- Comprehensive Hearing Center, Department of Otorhinolaryngology, Plastic, Aesthetic and Reconstructive Surgery, University Hospital, Würzburg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
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31
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Abstract
Next-generation sequencing (NGS) technologies have played a central role in the genetic revolution. These technologies, especially whole-exome sequencing, have become the primary tool of geneticists to identify the causative DNA variants in Mendelian disorders, including hereditary deafness. Current research estimates that 1% of all human genes have a function in hearing. To date, mutations in over 80 genes have been reported to cause nonsyndromic hearing loss (NSHL). Strikingly, more than a quarter of all known genes related to NSHL were discovered in the past 5 years via NGS technologies. In this article, we review recent developments in the usage of NGS for hereditary deafness, with an emphasis on whole-exome sequencing.
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32
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Holzerová E, Prokisch H. Mitochondria: Much ado about nothing? How dangerous is reactive oxygen species production? Int J Biochem Cell Biol 2015; 63:16-20. [PMID: 25666559 PMCID: PMC4444525 DOI: 10.1016/j.biocel.2015.01.021] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/20/2015] [Accepted: 01/29/2015] [Indexed: 01/12/2023]
Abstract
For more than 50 years, reactive oxygen species have been considered as harmful agents, which can attack proteins, lipids or nucleic acids. In order to deal with reactive oxygen species, there is a sophisticated system developed in mitochondria to prevent possible damage. Indeed, increased reactive oxygen species levels contribute to pathomechanisms in several human diseases, either by its impaired defense system or increased production of reactive oxygen species. However, in the last two decades, the importance of reactive oxygen species in many cellular signaling pathways has been unraveled. Homeostatic levels were shown to be necessary for correct differentiation during embryonic expansion of stem cells. Although the mechanism is still not fully understood, we cannot only regard reactive oxygen species as a toxic by-product of mitochondrial respiration anymore. This article is part of a Directed Issue entitled: Energy Metabolism Disorders and Therapies.
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Affiliation(s)
- Eliška Holzerová
- Institute of Human Genetics, Technische Universität München, Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Technische Universität München, Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.
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33
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Gao X, Dai P. Impact of next-generation sequencing on molecular diagnosis of inherited non-syndromic hearing loss. J Otol 2014. [DOI: 10.1016/j.joto.2014.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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Identification of OSBPL2 as a novel candidate gene for progressive nonsyndromic hearing loss by whole-exome sequencing. Genet Med 2014; 17:210-8. [PMID: 25077649 DOI: 10.1038/gim.2014.90] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 06/11/2014] [Indexed: 01/10/2023] Open
Abstract
PURPOSE Various forms of hearing loss have genetic causes, but many of the responsible genes have not yet been identified. Here, we describe a large seven-generation Chinese family with autosomal dominant nonsyndromic hearing loss that has been excluded as being caused by known deafness gene mutations associated with autosomal dominant nonsyndromic hearing loss with the aim of identifying a novel causative gene involved in deafness. METHODS Whole-exome sequencing was conducted in three affected family members, and cosegregation analysis was performed on other members of the family. RESULTS Whole-exome sequencing and subsequent segregation analysis identified a heterozygous frameshift mutation (c.153_154delCT, p.Gln53Argfs*100) in the oxysterol binding protein-like 2 (OSBPL2) gene in 25 affected family members. The deletion mutation is predicted to lead to premature truncation of the OSBPL2 protein. Modeling and structure-based analysis support the theory that this gene deletion is functionally deleterious. Our finding was further confirmed by the detection of another missense mutation, a c.583C>A transversion (p.Leu195Met) in exon 7 of OSBPL2, in an additional sporadic case of deafness. CONCLUSION Based on this study, OSBPL2 was identified as an excellent novel candidate gene for autosomal dominant nonsyndromic hearing loss; this study is the first to implicate OSBPL2 mutations in autosomal dominant nonsyndromic hearing loss.
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