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Yun Y, Lee SY. Updates on Genetic Hearing Loss: From Diagnosis to Targeted Therapies. J Audiol Otol 2024; 28:88-92. [PMID: 38695053 PMCID: PMC11065549 DOI: 10.7874/jao.2024.00157] [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: 02/22/2024] [Revised: 03/21/2024] [Accepted: 04/04/2024] [Indexed: 05/05/2024] Open
Abstract
Sensorineural hearing loss (SNHL) is the most common sensory disorder, with a high Mendelian genetic contribution. Considering the genotypic and phenotypic heterogeneity of SNHL, the advent of next-generation sequencing technologies has revolutionized knowledge on its genomic architecture. Nonetheless, the conventional application of panel and exome sequencing in real-world practice is being challenged by the emerging need to explore the diagnostic capability of whole-genome sequencing, which enables the detection of both noncoding and structural variations. Small molecules and gene therapies represent good examples of how breakthroughs in genetic understanding can be translated into targeted therapies for SNHL. For example, targeted small molecules have been used to ameliorate autoinflammatory hearing loss caused by gain-of-function variants of NLRP3 and inner ear proteinopathy with OSBPL2 variants underlying dysfunctional autophagy. Strikingly, the successful outcomes of the first-in-human trial of OTOF gene therapy highlighted its potential in the treatment of various forms of genetic hearing loss. clustered regularly interspaced short palindromic repeats (CRISPR)-based technologies are currently being developed for site-specific genome editing to treat human genetic disorders. These advancements have led to an era of genotype- and mechanism-based precision medicine in SNHL practice.
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Affiliation(s)
- Yejin Yun
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Korea
| | - Sang-Yeon Lee
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Korea
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Korea
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, Korea
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2
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Wu CC. Application of Genetic Information to Cochlear Implantation in Clinical Practice. J Audiol Otol 2024; 28:93-99. [PMID: 38695054 PMCID: PMC11065544 DOI: 10.7874/jao.2024.00080] [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: 01/25/2024] [Accepted: 03/22/2024] [Indexed: 05/05/2024] Open
Abstract
Cochlear implantation is currently the treatment of choice for children with severe-to-profound sensorineural hearing impairment (SNHI). However, the outcomes with cochlear implant (CI) vary significantly among recipients. Genetic diagnosis offers direct clues regarding the pathogenesis of SNHI, which facilitates the development of personalized medicine for potential candidates for CI. In this article, I present a comprehensive overview of the usefulness of genetic information in clinical decision-making for CI. Genetically confirmed diagnosis enables clinicians to: 1) monitor the evolution of SNHI and determine the optimal surgical timing, 2) predict the potential benefits of CI in patients with identified genetic etiology, and 3) select CI devices/electrodes tailored to patients with specific genetic mutations.
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Affiliation(s)
- Chen-Chi Wu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Otolaryngology, National Taiwan University College of Medicine, Taipei, Taiwan
- Hearing and Speech Center, National Taiwan University Hospital, Taipei, Taiwan
- Department of Medical Research, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan
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Lu Y, Hu Y, Wang S, Pan S, An K, Wang T, He Y, Tian C, Lei J. Hereditary Hearing Loss: A Systematic Review of Potential Treatments and Interventions. Am J Audiol 2023; 32:972-989. [PMID: 37889166 DOI: 10.1044/2023_aja-23-00069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023] Open
Abstract
PURPOSE The purpose of this study was to systematically review the research literature with regards to treatments and intervention methods for hereditary hearing loss. Our goal was to provide reference guidelines for the rational use of medication and gene-targeted therapy for patients with hereditary hearing loss and discuss the future development of research in this area. METHOD We searched two core databases, PubMed and Web of Science, for relevant literature relating to potential treatments and interventional methods for hereditary hearing loss. Then, we used Microsoft Excel to perform basic statistical analysis of the data, the R language to perform bibliometric analyses, and VOSviewer and CiteSpace to visualize data. In addition, we clustered and descriptively analyzed the data and identified the relative importance of each approach with regard to precise patient outcomes. RESULTS In this study, we followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) standardized screening process and identified a total of 103 research articles. The average annual growth rate of publications in this area was 12.73%. The country with the highest number of publications and citations was the United States; 80 of these publications (associated with 76.92% of funding) were supported by grants from 16 countries. Potential treatments and interventions were clustered according to the stage of research and showed that 8.74% remain in the research design stage, 59.22% are in the clinical validation stage, and 32.04% are being applied in the clinic. The main research focus in this field is cochlear implants and gene therapy. CONCLUSIONS Hereditary hearing loss is in a critical period of transition from preventive to therapeutic research. Gene-targeted interventions represent one of the most promising and effective treatments. SUPPLEMENTAL MATERIAL https://doi.org/10.23641/asha.24309193.
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Affiliation(s)
- Yang Lu
- College of Medical Technology, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yuanjia Hu
- College of Medical Technology, Zhejiang Chinese Medical University, Hangzhou, China
| | - Shengyue Wang
- College of Medical Technology, Zhejiang Chinese Medical University, Hangzhou, China
| | - Sijia Pan
- College of Medical Technology, Zhejiang Chinese Medical University, Hangzhou, China
| | - Kai An
- Peking University Third Hospital, Beijing, China
- Center for Medical Informatics, Peking University, Beijing, China
| | - Tong Wang
- Department of Medical Informatics, School of Public Health, Jilin University, Changchun, China
| | - Yunfan He
- School of Public Health, Zhejiang University, Hangzhou City, China
| | - Chenghua Tian
- College of Medical Technology, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jianbo Lei
- Center for Medical Informatics, Peking University, Beijing, China
- Institute of Medical Technology, Peking University, Beijing, China
- School of Medical Informatics and Engineering, Southwest Medical University, Luzhou, China
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4
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Zeng B, Xu H, Yu Y, Li S, Tian Y, Li T, Yang Z, Wang H, Wang G, Chang M, Tang W. Increased diagnostic yield in a cohort of hearing loss families using a comprehensive stepwise strategy of molecular testing. Front Genet 2022; 13:1057293. [PMID: 36568381 PMCID: PMC9768221 DOI: 10.3389/fgene.2022.1057293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
Hearing loss is one of the most common sensory disorders in humans. This study proposes a stepwise strategy of deafness gene detection using multiplex PCR combined with high-throughput sequencing, Sanger sequencing, multiplex ligation-dependent probe amplification (MLPA), and whole-exome sequencing (WES) to explore its application in molecular diagnosis of hearing loss families. A total of 152 families with hearing loss were included in this study, the highest overall diagnosis rate was 73% (111/152). The diagnosis rate of multiplex PCR combined with high-throughput sequencing was 52.6% (80/152). One families was diagnosed by Sanger sequencing of GJB2 exon 1. Two families were diagnosed by MLPA analysis of the STRC gene. The diagnosis rate with additional contribution from WES was 18.4% (28/152). We identified 21 novel variants from 15 deafness genes by WES. Combining WES and deep clinical phenotyping, we diagnosed 11 patients with syndromic hearing loss (SHL). This study demonstrated improved diagnostic yield in a cohort of hearing loss families and confirmed the advantages of a stepwise strategy in the molecular diagnosis of hearing loss.
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Affiliation(s)
- Beiping Zeng
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China,National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Henan Institute of Reproduction Health Science and Technology, Zhengzhou, China
| | - Hongen Xu
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China,The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanan Yu
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Siqi Li
- Department of Physiology and Neurobiology, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Yongan Tian
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Tiandong Li
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Zengguang Yang
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Haili Wang
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Henan Institute of Reproduction Health Science and Technology, Zhengzhou, China
| | - Guangke Wang
- Department of Otorhinolaryngology Head and Neck Surgery, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Mingxiu Chang
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Henan Institute of Reproduction Health Science and Technology, Zhengzhou, China,*Correspondence: Mingxiu Chang, ; Wenxue Tang,
| | - Wenxue Tang
- The Research and Application Center of Precision Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China,*Correspondence: Mingxiu Chang, ; Wenxue Tang,
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Zhang S, Xu H, Tian Y, Liu D, Hou X, Zeng B, Chen B, Liu H, Li R, Li X, Zuo B, Tang R, Tang W. High Genetic Heterogeneity in Chinese Patients With Waardenburg Syndrome Revealed by Next-Generation Sequencing. Front Genet 2021; 12:643546. [PMID: 34149797 PMCID: PMC8212959 DOI: 10.3389/fgene.2021.643546] [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: 12/18/2020] [Accepted: 04/23/2021] [Indexed: 01/08/2023] Open
Abstract
Objective This study aimed to explore the genetic causes of probands who were diagnosed with Waardenburg syndrome (WS) or congenital sensorineural hearing loss. Methods A detailed physical and audiological examinations were carried out to make an accurate diagnosis of 14 patients from seven unrelated families. We performed whole-exome sequencing in probands to detect the potential genetic causes and further validated them by Sanger sequencing in the probands and their family members. Results The genetic causes for all 14 patients with WS or congenital sensorineural hearing loss were identified. A total of seven heterozygous variants including c.1459C > T, c.123del, and c.959-409_1173+3402del of PAX3 gene (NM_181459.4), c.198_262del and c.529_556del of SOX10 gene (NM_006941.4), and c.731G > A and c.970dup of MITF gene (NM_000248.3) were found for the first time. Of these mutations, we had confirmed two (c.1459C > T and c.970dup) are de novo by Sanger sequencing of variants in the probands and their parents. Conclusion We revealed a total of seven novel mutations in PAX3, SOX10, and MITF, which underlie the pathogenesis of WS. The clinical and genetic characterization of these families with WS elucidated high heterogeneity in Chinese patients with WS. This study expands the database of PAX3, SOX10, and MITF mutations and improves our understanding of the causes of WS.
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Affiliation(s)
- Sen Zhang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Hongen Xu
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China.,The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yongan Tian
- BGI College, Zhengzhou University, Zhengzhou, China
| | - Danhua Liu
- The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xinyue Hou
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Beiping Zeng
- BGI College, Zhengzhou University, Zhengzhou, China
| | - Bei Chen
- Department of Otology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huanfei Liu
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Ruijun Li
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Xiaohua Li
- Department of Otology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Bin Zuo
- Department of Otology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ryan Tang
- Johns Hopkins University, Maryland, MD, United States
| | - Wenxue Tang
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China.,The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
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Missense Variant of Endoplasmic Reticulum Region of WFS1 Gene Causes Autosomal Dominant Hearing Loss without Syndromic Phenotype. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6624744. [PMID: 34258273 PMCID: PMC8260318 DOI: 10.1155/2021/6624744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/01/2021] [Accepted: 02/14/2021] [Indexed: 12/13/2022]
Abstract
Objective Genetic variants in the WFS1 gene can cause Wolfram syndrome (WS) or autosomal dominant nonsyndromic low-frequency hearing loss (HL). This study is aimed at investigating the molecular basis of HL in an affected Chinese family and the genotype-phenotype correlation of WFS1 variants. Methods The clinical phenotype of the five-generation Chinese family was characterized using audiological examinations and pedigree analysis. Target exome sequencing of 129 known deafness genes and bioinformatics analysis were performed among six patients and four normal subjects to screen suspected pathogenic variants. We built a complete WFS1 protein model to assess the potential effects of the variant on protein structure. Results A novel heterozygous pathogenic variant NM_006005.3 c.2020G>T (p.Gly674Trp) was identified in the WFS1 gene, located in the C-terminal domain of the wolframin protein. We further showed that HL-related WFS1 missense variants were mainly concentrated in the endoplasmic reticulum (ER) domain. In contrast, WS-related missense variants are randomly distributed throughout the protein. Conclusions In this family, we identified a novel variant p.Gly674Trp of WFS1 as the primary pathogenic variant causing the low-frequency sensorineural HL, enriching the mutational spectrum of the WFS1 gene.
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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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Liu WH, Chang PY, Chang SC, Lu JJ, Wu CM. Mutation screening in non-syndromic hearing loss patients with cochlear implantation by massive parallel sequencing in Taiwan. PLoS One 2019; 14:e0211261. [PMID: 30682115 PMCID: PMC6347456 DOI: 10.1371/journal.pone.0211261] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 01/10/2019] [Indexed: 01/05/2023] Open
Abstract
Objectives To explore the molecular epidemiology of rare deafness genes in Taiwanese sensorineural hearing impairment (SNHI) patients with cochlear implantation (CI) by performing massive parallel sequencing (MPS) and correlating genetic factors and CI outcomes. Methods We enrolled 41 Taiwanese non-syndromic deafness patients with CI that lacked known mutations in common deafness genes. All probands were screened by a targeted exon amplification method that used massively parallel sequencing to screen a customized panel that included 40 relatively rare non-syndromic deafness genes. Results Thirteen candidate variants in nine relatively rare deafness genes (MYO15A, TMC1, MYH14, MYO3A, ACTG1, COL11A2, DSPP, GRHL2, and WFS1) were identified in 24.4% (10/41) of the non-syndromic deafness probands with CI. According to the ACMG Standards and Guidelines, five variants in MYO15A and ACTG1 were classified as likely pathogenic variants. Two of three multi-generational pedigrees exhibiting deafness were analyzed for the segregation of the disorder with the possible disease-causing variants. Patients with variants detected in most of the identified variant-bearing genes showed relatively good CI outcomes. Conclusions We successfully identified candidate variants in partially deaf Taiwanese probands who lacked the known mutations in common deafness genes. Comparing the progress of hearing rehabilitation in CI patients with their apparent causative variants and the expression profiles of their altered genes allowed us to speculate on how alterations in specific gene sets may influence outcomes in hearing rehabilitation after CI.
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Affiliation(s)
- Wei-Hsiu Liu
- Department of Laboratory Medicine, Chang-Gung Memorial Hospital, Linkou Branch, College of Medicine, Chang-Gung University, Taoyuan, Taiwan
- Department of Otolaryngology—Head and Neck Surgery, Chang-Gung Memorial Hospital, Linkou Branch, College of Medicine, Chang-Gung University, Taoyuan, Taiwan
| | - Pi-Yueh Chang
- Department of Medical Biotechnology and Laboratory Science, Chang-Gung University, Taoyuan, Taiwan
- Department of Medical Research, Chang-Gung Memorial Hospital and Graduate of Institute of Clinical Medical Science, Chang Gung University, Taoyuan, Taiwan
| | - Shih-Cheng Chang
- Department of Medical Biotechnology and Laboratory Science, Chang-Gung University, Taoyuan, Taiwan
- Department of Medical Research, Chang-Gung Memorial Hospital and Graduate of Institute of Clinical Medical Science, Chang Gung University, Taoyuan, Taiwan
| | - Jang-Jih Lu
- Department of Medical Biotechnology and Laboratory Science, Chang-Gung University, Taoyuan, Taiwan
- Department of Medical Research, Chang-Gung Memorial Hospital and Graduate of Institute of Clinical Medical Science, Chang Gung University, Taoyuan, Taiwan
- * E-mail: (CMW); (J-JL)
| | - Che-Ming Wu
- Department of Otolaryngology—Head and Neck Surgery, Chang-Gung Memorial Hospital, Linkou Branch, College of Medicine, Chang-Gung University, Taoyuan, Taiwan
- * E-mail: (CMW); (J-JL)
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Targeted Next-Generation Sequencing Facilitates Genetic Diagnosis and Provides Novel Pathogenetic Insights into Deafness with Enlarged Vestibular Aqueduct. J Mol Diagn 2018; 21:138-148. [PMID: 30268946 DOI: 10.1016/j.jmoldx.2018.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 08/13/2018] [Accepted: 08/30/2018] [Indexed: 12/24/2022] Open
Abstract
Enlarged vestibular aqueduct (EVA) is an inner-ear malformation associated with sensorineural hearing impairment. Most EVAs are associated with Pendred syndrome and nonsyndromic autosomal recessive deafness-4 (DFNB4), two autosomal-recessive disorders caused by mutations in SLC26A4. However, many EVA patients cannot have a confirmed diagnosis by screening common SLC26A4 mutations, constituting an enigma in genetic diagnosis. To enable comprehensive genetic examination and explore the etiologies of EVA, we designed a next-generation sequencing panel targeting the entire length of 3 Pendred syndrome/DFNB4 genes (SLC26A4, FOXI1, and KCNJ10) and exons of 10 other genes related to EVA and performed genetic testing in 50 EVA families without confirmative results on screening for SLC26A4 hotspots (c.919-2A>G and p.H723R). Bi-allelic SLC26A4 mutations were identified in 34 families and EYA1 mutations in two families, yielding a diagnostic rate of 72% (36 of 50). In addition, two variants were identified in KCNJ10 and FOXI1, but findings did not support the previous hypothesis that mutations in these two genes are probable contributors to EVA through recessive inheritance or digenic inheritance with SLC26A4. Of note, a large SLC26A4 deletion was confirmed in one step using our panel. These results show the utility of a next-generation sequencing-based panel to address EVA families by identifying various types of gene mutations with satisfactory diagnostic yields and provide novel insights into the pathogenesis of EVA.
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Ushakov K, Koffler-Brill T, Rom A, Perl K, Ulitsky I, Avraham KB. Genome-wide identification and expression profiling of long non-coding RNAs in auditory and vestibular systems. Sci Rep 2017; 7:8637. [PMID: 28819115 PMCID: PMC5561060 DOI: 10.1038/s41598-017-08320-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/07/2017] [Indexed: 11/09/2022] Open
Abstract
Mammalian genomes encode multiple layers of regulation, including a class of RNA molecules known as long non-coding RNAs (lncRNAs). These are >200 nucleotides in length and similar to mRNAs, they are capped, polyadenylated, and spliced. In contrast to mRNAs, lncRNAs are less abundant and have higher tissue specificity, and have been linked to development, epigenetic processes, and disease. However, little is known about lncRNA function in the auditory and vestibular systems, or how they play a role in deafness and vestibular dysfunction. To help address this need, we performed a whole-genome identification of lncRNAs using RNA-seq at two developmental stages of the mouse inner ear sensory epithelium of the cochlea and vestibule. We identified 3,239 lncRNA genes, most of which were intergenic (lincRNAs) and 721 are novel. We examined temporal and tissue specificity by analyzing the developmental profiles on embryonic day 16.5 and at birth. The spatial and temporal patterns of three lncRNAs, two of which are in proximity to genes associated with hearing and deafness, were explored further. Our findings indicate that lncRNAs are prevalent in the sensory epithelium of the mouse inner ear and are likely to play key roles in regulating critical pathways for hearing and balance.
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Affiliation(s)
- Kathy Ushakov
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Tal Koffler-Brill
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Aviv Rom
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Kobi Perl
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel.,Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel.
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Wang HY, Zhao YL, Liu Q, Yuan H, Gao Y, Lan L, Yu L, Wang DY, Guan J, Wang QJ. Identification of Two Disease-causing Genes TJP2 and GJB2 in a Chinese Family with Unconditional Autosomal Dominant Nonsyndromic Hereditary Hearing Impairment. Chin Med J (Engl) 2016; 128:3345-51. [PMID: 26668150 PMCID: PMC4797511 DOI: 10.4103/0366-6999.171440] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background: There are more than 300 genetic loci that have been found to be related to hereditary hearing impairment (HHI), including 92 causative genes for nonsyndromic hearing loss, among which 34 genes are related to autosomal dominant nonsyndromic HHI (ADNSHHI). Traditional linkage analysis and candidate gene sequencing are not effective at detecting the ADNSHHI, especially for the unconditional families that may have more than one pathogenic cause. This study identified two disease-causing genes TJP2 and GJB2 in a Chinese family with unconditional ADNSHHI. Methods: To decipher the genetic code of a Chinese family (family 686) with ADNSHHI, different gene screening techniques have been performed, including linkage analysis, candidate genes screening, high-throughput sequencing and Sanger sequencing. These techniques were done on samples obtained from this family over a period of 10 years. Results: We identified a pathogenic missense mutation, c. 2081G>A (p.G694E), in TJP2, a gene that plays a crucial role in apoptosis and age-related hearing loss (ARHL). The mutation was co-segregated in this pedigree in all, but not in the two patients who presented with different phenotypes from the other affected family members. In one of the two patients, we confirmed that the compound heterozygosity for p. Y136* and p.G45E in the GJB2 gene may account for the phenotype shown in this patient. Conclusions: We identified the co-occurrence of two genetic causes in family 686. The possible disease-causing missense mutation of TJP2 in family 686 presents an opportunity for further investigation into ARHL. It is necessary to combine various genes screening methods, especially for some unconventional cases.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Qiu-Ju Wang
- Department of Otolaryngology-Head and Neck, Chinese People's Liberation Army Institute of Otolaryngology, Chinese People's Liberation Army General Hospital, Beijing 100853, China
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12
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Mutation in the Hair Cell Specific Gene POU4F3 Is a Common Cause for Autosomal Dominant Nonsyndromic Hearing Loss in Chinese Hans. Neural Plast 2016; 2016:9890827. [PMID: 28053790 PMCID: PMC5178374 DOI: 10.1155/2016/9890827] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 10/26/2016] [Accepted: 11/02/2016] [Indexed: 11/17/2022] Open
Abstract
Autosomal dominant nonsyndromic hearing loss (ADNSHL) is extremely heterogeneous. So far the genetic etiological contribution of the gene POU4F3 associated with ADNSHL has been rarely reported. In our previous study, a c.603_604delGG mutation in the hair cell specific gene POU4F3 has been identified as the pathogenic cause in one of the seven Chinese Han ADNSHL families. In the present study, we performed targeted next-generation sequencing of 144 known deafness genes in another nine Chinese Han ADNSHL families and identified two more novel mutations in POU4F3, p.Leu311Pro and c.120+1G>C, as the pathogenic cause. Clinical characterization of the affected individuals in these three families showed that the three POU4F3 mutations may lead to progressive hearing loss with variable ages of onset and degrees of severity. Our results suggested that mutations in POU4F3 are a relatively common cause (3/16) for ADNSHL in Chinese Hans, which should be routinely screened in such cases during genetic testing.
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13
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Minami SB, Mutai H, Namba K, Sakamoto H, Matsunaga T. Clinical characteristics of a Japanese family with hearing loss accompanied by compound heterozygous mutations in LOXHD1. Auris Nasus Larynx 2016; 43:609-13. [PMID: 26973026 DOI: 10.1016/j.anl.2016.02.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 02/09/2016] [Accepted: 02/15/2016] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To report two novel LOXHD1 mutations, including missense mutations and the clinical features of the patients. METHODS We studied a three-generation Japanese family with hearing loss. Targeted next-generation sequencing was used for genetic analysis. Conditional orientation response audiometry and pure tone audiometry were used to assess hearing. SWISS-MODEL was used for molecular modeling of the PLAT domain in LOXHD1 protein. RESULTS The two sisters, who had either mild or severe high-frequency hearing loss, were compound heterozygous for two novel mutations (c.5674G>T [p.V1892F] and c.4212+1G>A) in LOXHD1, which is responsible for autosomal-recessive nonsyndromic hearing loss DFNB77. These cases showed less severe hearing impairment than the previously reported cases carrying LOXHD1 mutations, but their hearing loss appeared to be progressive. Molecular modeling predicted that distorted structure of the PLAT domain in the p.V1892F mutant could lead to decreased affinity of the protein to lipid membrane resulting in hair cell dysfunction. CONCLUSION We report a Japanese family carrying compound heterozygotes of truncating and nontruncating mutations in LOXHD1 identified by targeted NGS analysis. The fact of lower degree of hearing impairment in our cases than previously reported and the molecular modeling of the missense mutant provide insight to the genotype-phenotype correlation of DFNB77.
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Affiliation(s)
- Shujiro B Minami
- National Hospital Organization Tokyo Medical Center, Department of Otolaryngology, 2-5-1 Higashigaoka, Meguroku, Tokyo 152-8901, Japan; National Hospital Organization Tokyo Medical Center, National Institute of Sensory Organs, 2-5-1 Higashigaoka, Meguroku, Tokyo 152-8901, Japan
| | - Hideki Mutai
- National Hospital Organization Tokyo Medical Center, National Institute of Sensory Organs, 2-5-1 Higashigaoka, Meguroku, Tokyo 152-8901, Japan
| | - Kazunori Namba
- National Hospital Organization Tokyo Medical Center, National Institute of Sensory Organs, 2-5-1 Higashigaoka, Meguroku, Tokyo 152-8901, Japan
| | - Hirokazu Sakamoto
- Hyogo Prefectural Kobe Children's Hospital, Department of Otolaryngology, 1-1-1 Takakuradai, Sumaku, Koube, Hyogo 654-0091, Japan
| | - Tatsuo Matsunaga
- National Hospital Organization Tokyo Medical Center, Department of Otolaryngology, 2-5-1 Higashigaoka, Meguroku, Tokyo 152-8901, Japan; National Hospital Organization Tokyo Medical Center, National Institute of Sensory Organs, 2-5-1 Higashigaoka, Meguroku, Tokyo 152-8901, Japan.
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14
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Hu J, Liu F, Xia W, Hao L, Lan J, Zhu Z, Ye J, Ma D, Ma Z. Exome sequencing identifies a mutation in TMC1 as a novel cause of autosomal recessive nonsyndromic hearing loss. J Transl Med 2016; 14:29. [PMID: 26822030 PMCID: PMC4731951 DOI: 10.1186/s12967-016-0780-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 01/12/2016] [Indexed: 12/16/2022] Open
Abstract
Background Autosomal recessive non-syndromic hearing loss (ARNSHL) is highly heterogeneous, and mutations in the gene encoding transmembrane channel-like 1 (TMC1) have been implicated in its development. To date, 35 homozygous mutations in TMC1, identified in over 60 families worldwide, have been shown to be associated with ARNSHL. However, few of these mutations were detected in the Chinese population. In this study, we describe a pathogenic missense mutation located in the T5–T6 domain of TMC1 in a three-generation Chinese family with 14 members. Methods Whole exome sequencing was performed using samples from one unaffected individual and two affected individuals to systematically search for deafness susceptibility genes. Candidate mutations and cosegregation of the phenotype were verified by polymerase chain reaction and Sanger sequencing in all of the family members. Results We identified a novel TMC1 mutation in exon 20, c.1979C>T, p.P660L, which segregated with prelingual autosomal recessive sensorineural hearing loss. Conclusions We found a new missense mutation in the T5–T6 domain of TMC1, which is highly conserved in many species. These data support the potential conserved role of p.P660L in human TMC1 function. Electronic supplementary material The online version of this article (doi:10.1186/s12967-016-0780-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiongjiong Hu
- Department of Otorhinolaryngology, Shanghai East Hospital, Tongji University, Shanghai, 200032, People's Republic of China.
| | - Fei Liu
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, People's Republic of China.
| | - Wenjun Xia
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, People's Republic of China.
| | - Lili Hao
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, People's Republic of China.
| | - Jun Lan
- Department of Otorhinolaryngology, Shanghai East Hospital, Tongji University, Shanghai, 200032, People's Republic of China.
| | - Zhenghua Zhu
- Department of Otorhinolaryngology, Shanghai East Hospital, Tongji University, Shanghai, 200032, People's Republic of China.
| | - Jing Ye
- Department of Otorhinolaryngology, Shanghai East Hospital, Tongji University, Shanghai, 200032, People's Republic of China.
| | - Duan Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, People's Republic of China. .,Institutes of Biomedical Science, Fudan University, Shanghai, 200032, People's Republic of China.
| | - Zhaoxin Ma
- Department of Otorhinolaryngology, Shanghai East Hospital, Tongji University, Shanghai, 200032, People's Republic of China.
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15
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Teeling EC, Jones G, Rossiter SJ. Phylogeny, Genes, and Hearing: Implications for the Evolution of Echolocation in Bats. BAT BIOACOUSTICS 2016. [DOI: 10.1007/978-1-4939-3527-7_2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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16
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Bhonker Y, Abu-Rayyan A, Ushakov K, Amir-Zilberstein L, Shivatzki S, Yizhar-Barnea O, Elkan-Miller T, Tayeb-Fligelman E, Kim SM, Landau M, Kanaan M, Chen P, Matsuzaki F, Sprinzak D, Avraham KB. The GPSM2/LGN GoLoco motifs are essential for hearing. Mamm Genome 2015; 27:29-46. [PMID: 26662512 DOI: 10.1007/s00335-015-9614-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/17/2015] [Indexed: 11/24/2022]
Abstract
The planar cell polarity (PCP) pathway is responsible for polarizing and orienting cochlear hair cells during development through movement of a primary cilium, the kinocilium. GPSM2/LGN, a mitotic spindle-orienting protein associated with deafness in humans, is a PCP effector involved in kinocilium migration. Here, we link human and mouse truncating mutations in the GPSM2/LGN gene, both leading to hearing loss. The human variant, p.(Trp326*), was identified by targeted genomic enrichment of genes associated with deafness, followed by massively parallel sequencing. Lgn (ΔC) mice, with a targeted deletion truncating the C-terminal GoLoco motifs, are profoundly deaf and show misorientation of the hair bundle and severe malformations in stereocilia shape that deteriorates over time. Full-length protein levels are greatly reduced in mutant mice, with upregulated mRNA levels. The truncated Lgn (ΔC) allele is translated in vitro, suggesting that mutant mice may have partially functioning Lgn. Gαi and aPKC, known to function in the same pathway as Lgn, are dependent on Lgn for proper localization. The polarization of core PCP proteins is not affected in Lgn mutants; however, Lgn and Gαi are misoriented in a PCP mutant, supporting the role of Lgn as a PCP effector. The kinocilium, previously shown to be dependent on Lgn for robust localization, is essential for proper localization of Lgn, as well as Gαi and aPKC, suggesting that cilium function plays a role in positioning of apical proteins. Taken together, our data provide a mechanism for the loss of hearing found in human patients with GPSM2/LGN variants.
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Affiliation(s)
- Yoni Bhonker
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Amal Abu-Rayyan
- Department of Biological Sciences, Bethlehem University, Bethlehem, Palestine
| | - Kathy Ushakov
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Liat Amir-Zilberstein
- Department of Biochemistry and Molecular Biology, Weiss Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Shaked Shivatzki
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Ofer Yizhar-Barnea
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Tal Elkan-Miller
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Einav Tayeb-Fligelman
- Department of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Sun Myoung Kim
- Department of Cell Biology, Emory University, Atlanta, GA, 30322, USA
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Moien Kanaan
- Department of Biological Sciences, Bethlehem University, Bethlehem, Palestine
| | - Ping Chen
- Department of Cell Biology, Emory University, Atlanta, GA, 30322, USA
| | - Fumio Matsuzaki
- Laboratory of Cell Asymmetry, Center for Developmental Biology, Riken, Kobe, 650-0047, Japan
| | - David Sprinzak
- Department of Biochemistry and Molecular Biology, Weiss Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel.
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17
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Abstract
Hearing loss (HL) is one of the most common birth defects in developed countries and is a diverse pathologic condition with different classifications. One of these is based on the association with other clinical features, defined as syndromic hearing loss (SHL). Determining the cause of the HL in these patients is extremely beneficial as it enables a personalized approach to caring for the individual. Early screening can further aid in optimal rehabilitation for a child's development and growth. The advancement of high-throughput sequencing technology is facilitating rapid and low-cost diagnostics for patients with SHL.
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Affiliation(s)
- Tal Koffler
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Kathy Ushakov
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel.
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18
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Genetics of non syndromic hearing loss. Med J Armed Forces India 2015; 71:363-8. [PMID: 26663965 DOI: 10.1016/j.mjafi.2015.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 07/03/2015] [Indexed: 11/20/2022] Open
Abstract
Non Syndromic Hearing Loss is an important cause for hearing loss. One in 1000 newborns have some hearing impairment. Over 400 genetic syndromes have been described. Non Syndromic Hearing Loss (NSHL) can be inherited in an Autosomal Dominant, Autosomal Recessive or a Sex Linked fashion. There are several reasons why genetic testing should be done in cases of NSHL, the main reasons being for genetic screening and for planning treatment. This review describes the genes involved in NSHL and the genetic mechanisms involved in the pathogenesis of the disease.
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19
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Nyegaard M, Rendtorff ND, Nielsen MS, Corydon TJ, Demontis D, Starnawska A, Hedemand A, Buniello A, Niola F, Overgaard MT, Leal SM, Ahmad W, Wikman FP, Petersen KB, Crüger DG, Oostrik J, Kremer H, Tommerup N, Frödin M, Steel KP, Tranebjærg L, Børglum AD. A Novel Locus Harbouring a Functional CD164 Nonsense Mutation Identified in a Large Danish Family with Nonsyndromic Hearing Impairment. PLoS Genet 2015. [PMID: 26197441 PMCID: PMC4510537 DOI: 10.1371/journal.pgen.1005386] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Nonsyndromic hearing impairment (NSHI) is a highly heterogeneous condition with more than eighty known causative genes. However, in the clinical setting, a large number of NSHI families have unexplained etiology, suggesting that there are many more genes to be identified. In this study we used SNP-based linkage analysis and follow up microsatellite markers to identify a novel locus (DFNA66) on chromosome 6q15-21 (LOD 5.1) in a large Danish family with dominantly inherited NSHI. By locus specific capture and next-generation sequencing, we identified a c.574C>T heterozygous nonsense mutation (p.R192*) in CD164. This gene encodes a 197 amino acid transmembrane sialomucin (known as endolyn, MUC-24 or CD164), which is widely expressed and involved in cell adhesion and migration. The mutation segregated with the phenotype and was absent in 1200 Danish control individuals and in databases with whole-genome and exome sequence data. The predicted effect of the mutation was a truncation of the last six C-terminal residues of the cytoplasmic tail of CD164, including a highly conserved canonical sorting motif (YXXФ). In whole blood from an affected individual, we found by RT-PCR both the wild-type and the mutated transcript suggesting that the mutant transcript escapes nonsense mediated decay. Functional studies in HEK cells demonstrated that the truncated protein was almost completely retained on the plasma cell membrane in contrast to the wild-type protein, which targeted primarily to the endo-lysosomal compartments, implicating failed endocytosis as a possible disease mechanism. In the mouse ear, we found CD164 expressed in the inner and outer hair cells of the organ of Corti, as well as in other locations in the cochlear duct. In conclusion, we have identified a new DFNA locus located on chromosome 6q15-21 and implicated CD164 as a novel gene for hearing impairment.
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Affiliation(s)
- Mette Nyegaard
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark
- * E-mail:
| | - Nanna D. Rendtorff
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine (ICMM), The Panum Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Otorhinolaryngology, Head & Neck Surgery and Audiology, Bispebjerg Hospital/Rigshospitalet, Copenhagen, Denmark
- Clinical Genetic Clinic, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | | | | | - Ditte Demontis
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark
| | - Anna Starnawska
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark
| | - Anne Hedemand
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark
| | - Annalisa Buniello
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
| | - Francesco Niola
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | | | - Suzanne M. Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Friedrik P. Wikman
- Department of Molecular Medicine, Aarhus University Hospital, Skejby, Aarhus, Denmark
| | | | | | - Jaap Oostrik
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, Nijmegen, Netherlands
| | - Hannie Kremer
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, Nijmegen, Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Nijmegen, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Nijmegen, Netherlands
| | - Niels Tommerup
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine (ICMM), The Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Morten Frödin
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Karen P. Steel
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
| | - Lisbeth Tranebjærg
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine (ICMM), The Panum Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Otorhinolaryngology, Head & Neck Surgery and Audiology, Bispebjerg Hospital/Rigshospitalet, Copenhagen, Denmark
- Clinical Genetic Clinic, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Anders D. Børglum
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Centre for Integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark
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20
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Mizutari K, Mutai H, Namba K, Miyanaga Y, Nakano A, Arimoto Y, Masuda S, Morimoto N, Sakamoto H, Kaga K, Matsunaga T. High prevalence of CDH23 mutations in patients with congenital high-frequency sporadic or recessively inherited hearing loss. Orphanet J Rare Dis 2015; 10:60. [PMID: 25963016 PMCID: PMC4451718 DOI: 10.1186/s13023-015-0276-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/28/2015] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Mutations in CDH23 are responsible for Usher syndrome 1D and recessive non-syndromic hearing loss. In this study, we revealed the prevalence of CDH23 mutations among patients with specific clinical characteristics. METHODS After excluding patients with GJB2 mutations and mitochondrial m.1555A > G and m.3243A > G mutations, subjects for CDH23 mutation analysis were selected according to the following criteria: 1) Sporadic or recessively inherited hearing loss 2) bilateral non-syndromic congenital hearing loss, 3) no cochlear malformation, 4) a poorer hearing level at high frequencies than at low frequencies, and 5) severe or profound hearing loss at higher frequencies. RESULTS Seventy-two subjects were selected from 621 consecutive probands who did not have environmental causes for their hearing loss. After direct sequencing, 13 of the 72 probands (18.1%) had homozygous or compound heterozygous CDH23 mutations. In total, we identified 16 CDH23 mutations, including five novel mutations. The 16 mutations included 12 missense, two frameshift, and two splice-site mutations. CONCLUSIONS These results revealed that CDH23 mutations are highly prevalent in patients with congenital high-frequency sporadic or recessively inherited hearing loss and that the mutation spectrum was diverse, indicating that patients with these clinical features merit genetic analysis.
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Affiliation(s)
- Kunio Mizutari
- Laboratory of Auditory Disorders, National Institute of Sensory Organs, National Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro-ku, Tokyo, 152-8902, Japan. .,Department of Otolaryngology-Head and Neck Surgery, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama, 160-8582, Japan.
| | - Hideki Mutai
- Laboratory of Auditory Disorders, National Institute of Sensory Organs, National Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro-ku, Tokyo, 152-8902, Japan.
| | - Kazunori Namba
- Laboratory of Auditory Disorders, National Institute of Sensory Organs, National Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro-ku, Tokyo, 152-8902, Japan.
| | - Yuko Miyanaga
- Laboratory of Auditory Disorders, National Institute of Sensory Organs, National Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro-ku, Tokyo, 152-8902, Japan.
| | - Atsuko Nakano
- Division of Otorhinolaryngology, Chiba Children's Hospital, 579-1 Hetacho, Midori-ku, Chiba, Chiba, 266-0007, Japan.
| | - Yukiko Arimoto
- Division of Otorhinolaryngology, Chiba Children's Hospital, 579-1 Hetacho, Midori-ku, Chiba, Chiba, 266-0007, Japan.
| | - Sawako Masuda
- Department of Otorhinolaryngology, National Mie Hospital, 357 Osato-Kubota, Tsu, Mie, 514-0125, Japan.
| | - Noriko Morimoto
- Division of Otolaryngology, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan.
| | - Hirokazu Sakamoto
- Department of Otorhinolaryngology, Hyogo Prefectural Kobe Children's Hospital, 1-1-1 Takakuradai, Suma-ku, Kobe, Hyogo, 654-0081, Japan.
| | - Kimitaka Kaga
- National Institute of Sensory Organs, National Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro-ku, Tokyo, 152-8902, Japan.
| | - Tatsuo Matsunaga
- Laboratory of Auditory Disorders, National Institute of Sensory Organs, National Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro-ku, Tokyo, 152-8902, Japan. .,Medical Genetics Center, National Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro-ku, Tokyo, 152-8902, Japan.
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21
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Behlouli A, Bonnet C, Abdi S, Bouaita A, Lelli A, Hardelin JP, Schietroma C, Rous Y, Louha M, Cheknane A, Lebdi H, Boudjelida K, Makrelouf M, Zenati A, Petit C. EPS8, encoding an actin-binding protein of cochlear hair cell stereocilia, is a new causal gene for autosomal recessive profound deafness. Orphanet J Rare Dis 2014; 9:55. [PMID: 24741995 PMCID: PMC4022326 DOI: 10.1186/1750-1172-9-55] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 04/08/2014] [Indexed: 11/10/2022] Open
Abstract
Background Almost 90% of all cases of congenital, non-syndromic, severe to profound inherited deafness display an autosomal recessive mode of transmission (DFNB forms). To date, 47 causal DFNB genes have been identified, but many others remain to be discovered. We report the study of two siblings born to consanguineous Algerian parents and affected by isolated, profound congenital deafness. Method Whole-exome sequencing was carried out on these patients after a failure to identify mutations in the DFNB genes frequently involved. Results A biallelic nonsense mutation, c.88C > T (p.Gln30*), was identified in EPS8 that encodes epidermal growth factor receptor pathway substrate 8, a 822 amino-acid protein involved in actin dynamics. This mutation predicts a truncated inactive protein or no protein at all. The mutation was also present, in the heterozygous state, in one clinically unaffected sibling and in both unaffected parents, and was absent from the other two unaffected siblings. It was not found in 120 Algerian normal hearing control individuals or in the Exome Variant Server database. EPS8 is an F-actin capping and bundling protein. Mutant mice lacking EPS8 (Eps8−/− mice), which is present in the hair bundle, the sensory antenna of the auditory sensory cells that operate the mechano-electrical transduction, are also profoundly deaf and have abnormally short hair bundle stereocilia. Conclusion This new DFNB form is likely to arise from abnormal hair bundles resulting in compromised detection of physiological sound pressures.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Christine Petit
- INSERM UMRS1120, UPMC, Institut de la Vision, Paris, France.
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22
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Isakov O, Perrone M, Shomron N. Exome sequencing analysis: a guide to disease variant detection. Methods Mol Biol 2014; 1038:137-58. [PMID: 23872973 DOI: 10.1007/978-1-62703-514-9_8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Whole exome sequencing presents a powerful tool to study rare genetic disorders. The most challenging part of using exome sequencing for the purpose of disease-causing variant detection is analyzing, interpreting, and filtering the large number of detected variants. In this chapter we provide a comprehensive description of the various steps required for such an analysis. We address strategies in selecting samples to sequence, and technical considerations involved in exome sequencing. We then discuss how to identify variants, and methods for first annotating detected variants using characteristics such as allele frequency, location in the genome, and predicted severity, and then classifying and prioritizing the detected variants based on those annotations. Finally, we review possible gene annotations that may help to establish a relationship between genes carrying high-priority variants and the phenotype in question, in order to identify the most likely causative mutations.
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Affiliation(s)
- Ofer Isakov
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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23
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Mutai H, Suzuki N, Shimizu A, Torii C, Namba K, Morimoto N, Kudoh J, Kaga K, Kosaki K, Matsunaga T. Diverse spectrum of rare deafness genes underlies early-childhood hearing loss in Japanese patients: a cross-sectional, multi-center next-generation sequencing study. Orphanet J Rare Dis 2013; 8:172. [PMID: 24164807 PMCID: PMC4231469 DOI: 10.1186/1750-1172-8-172] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 10/05/2013] [Indexed: 11/16/2022] Open
Abstract
Background Genetic tests for hereditary hearing loss inform clinical management of patients and can provide the first step in the development of therapeutics. However, comprehensive genetic tests for deafness genes by Sanger sequencing is extremely expensive and time-consuming. Next-generation sequencing (NGS) technology is advantageous for genetic diagnosis of heterogeneous diseases that involve numerous causative genes. Methods Genomic DNA samples from 58 subjects with hearing loss from 15 unrelated Japanese families were subjected to NGS to identify the genetic causes of hearing loss. Subjects did not have pathogenic GJB2 mutations (the gene most often associated with inherited hearing loss), mitochondrial m.1555A>G or 3243A>G mutations, enlarged vestibular aqueduct, or auditory neuropathy. Clinical features of subjects were obtained from medical records. Genomic DNA was subjected to a custom-designed SureSelect Target Enrichment System to capture coding exons and proximal flanking intronic sequences of 84 genes responsible for nonsyndromic or syndromic hearing loss, and DNA was sequenced by Illumina GAIIx (paired-end read). The sequences were mapped and quality-checked using the programs BWA, Novoalign, Picard, and GATK, and analyzed by Avadis NGS. Results Candidate genes were identified in 7 of the 15 families. These genes were ACTG1, DFNA5, POU4F3, SLC26A5, SIX1, MYO7A, CDH23, PCDH15, and USH2A, suggesting that a variety of genes underlie early-childhood hearing loss in Japanese patients. Mutations in Usher syndrome-related genes were detected in three families, including one double heterozygous mutation of CDH23 and PCDH15. Conclusion Targeted NGS analysis revealed a diverse spectrum of rare deafness genes in Japanese subjects and underscores implications for efficient genetic testing.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Tatsuo Matsunaga
- Laboratory of Auditory Disorders, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro, Tokyo 152-8902, Japan.
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24
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Gao X, Su Y, Guan LP, Yuan YY, Huang SS, Lu Y, Wang GJ, Han MY, Yu F, Song YS, Zhu QY, Wu J, Dai P. Novel compound heterozygous TMC1 mutations associated with autosomal recessive hearing loss in a Chinese family. PLoS One 2013; 8:e63026. [PMID: 23690975 PMCID: PMC3653921 DOI: 10.1371/journal.pone.0063026] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 03/27/2013] [Indexed: 11/19/2022] Open
Abstract
Hereditary nonsyndromic hearing loss is highly heterogeneous and most patients with a presumed genetic etiology lack a specific diagnosis. It has been estimated that several hundred genes may be associated with this sensory deficit in humans. Here, we identified compound heterozygous mutations in the TMC1 gene as the cause of recessively inherited sensorineural hearing loss by using whole-exome sequencing in a family with two deaf siblings. Sanger sequencing confirmed that both siblings inherited a missense mutation, c.589G>A p.G197R (maternal allele), and a nonsense mutation, c.1171C>T p.Q391X (paternal allele), in TMC1. We also used DNA from 50 Chinese familial patients with ARNSHL and 208 ethnicity-matched negative samples to perform extended variants analysis. Both variants co-segregated in family 1953, which had the hearing loss phenotype, but were absent in 50 patients and 208 ethnicity-matched controls. Therefore, we concluded that the hearing loss in this family was caused by novel compound heterozygous mutations in TMC1.
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Affiliation(s)
- Xue Gao
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
- Department of Otorhinolaryngology, 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
| | - Li-Ping Guan
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, P. R. China
| | - Yong-Yi Yuan
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
| | - Sha-Sha Huang
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
| | - Yu Lu
- 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
| | - Ming-Yu Han
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
- Department of Otorhinolaryngology, 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
| | - Yue-Shuai Song
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
- Department of Otorhinolaryngology, Hainan Branch of PLA General Hospital, Sanya, P. R. China
| | - Qing-Yan Zhu
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, P. R. China
| | - Jing Wu
- BGI-Tianjin, Tianjin, P. R. China
| | - Pu Dai
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, Beijing, P. R. China
- Department of Otorhinolaryngology, Hainan Branch of PLA General Hospital, Sanya, P. R. China
- * E-mail:
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25
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Parzefall T, Shivatzki S, Lenz DR, Rathkolb B, Ushakov K, Karfunkel D, Shapira Y, Wolf M, Mohr M, Wolf E, Sabrautzki S, de Angelis MH, Frydman M, Brownstein Z, Avraham KB. Cytoplasmic mislocalization of POU3F4 due to novel mutations leads to deafness in humans and mice. Hum Mutat 2013; 34:1102-10. [PMID: 23606368 DOI: 10.1002/humu.22339] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 04/08/2013] [Indexed: 11/12/2022]
Abstract
POU3F4 is a POU domain transcription factor that is required for hearing. In the ear, POU3F4 is essential for mesenchymal remodeling of the bony labyrinth and is the causative gene for DFNX2 human nonsyndromic deafness. Ear abnormalities underlie this form of deafness, characterized previously in multiple spontaneous, radiation-induced and transgenic mouse mutants. Here, we report three novel mutations in the POU3F4 gene that result in profound hearing loss in both humans and mice. A p.Gln79* mutation was identified in a child from an Israeli family, revealed by massively parallel sequencing (MPS). This strategy demonstrates the strength of MPS for diagnosis with only one affected individual. A second mutation, p.Ile285Argfs*43, was identified by Sanger sequencing. A p.Cys300* mutation was found in an ENU-induced mutant mouse, schwindel (sdl), by positional cloning. The mutation leads to a predicted truncated protein, similar to the human mutations, providing a relevant mouse model. The p.Ile285Argfs*43 and p.Cys300* mutations lead to a shift of Pou3f4 nuclear localization to the cytoplasm, demonstrated in cellular localization studies and in the inner ears of the mutant mice. The discovery of these mutations facilitates a deeper comprehension of the molecular basis of inner ear defects due to mutations in the POU3F4 transcription factor.
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Affiliation(s)
- Thomas Parzefall
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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26
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Wu CC, Lin YH, Lu YC, Chen PJ, Yang WS, Hsu CJ, Chen PL. Application of massively parallel sequencing to genetic diagnosis in multiplex families with idiopathic sensorineural hearing impairment. PLoS One 2013; 8:e57369. [PMID: 23451214 PMCID: PMC3579845 DOI: 10.1371/journal.pone.0057369] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 01/21/2013] [Indexed: 11/18/2022] Open
Abstract
Despite the clinical utility of genetic diagnosis to address idiopathic sensorineural hearing impairment (SNHI), the current strategy for screening mutations via Sanger sequencing suffers from the limitation that only a limited number of DNA fragments associated with common deafness mutations can be genotyped. Consequently, a definitive genetic diagnosis cannot be achieved in many families with discernible family history. To investigate the diagnostic utility of massively parallel sequencing (MPS), we applied the MPS technique to 12 multiplex families with idiopathic SNHI in which common deafness mutations had previously been ruled out. NimbleGen sequence capture array was designed to target all protein coding sequences (CDSs) and 100 bp of the flanking sequence of 80 common deafness genes. We performed MPS on the Illumina HiSeq2000, and applied BWA, SAMtools, Picard, GATK, Variant Tools, ANNOVAR, and IGV for bioinformatics analyses. Initial data filtering with allele frequencies (<5% in the 1000 Genomes Project and 5400 NHLBI exomes) and PolyPhen2/SIFT scores (>0.95) prioritized 5 indels (insertions/deletions) and 36 missense variants in the 12 multiplex families. After further validation by Sanger sequencing, segregation pattern, and evolutionary conservation of amino acid residues, we identified 4 variants in 4 different genes, which might lead to SNHI in 4 families compatible with autosomal dominant inheritance. These included GJB2 p.R75Q, MYO7A p.T381M, KCNQ4 p.S680F, and MYH9 p.E1256K. Among them, KCNQ4 p.S680F and MYH9 p.E1256K were novel. In conclusion, MPS allows genetic diagnosis in multiplex families with idiopathic SNHI by detecting mutations in relatively uncommon deafness genes.
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Affiliation(s)
- Chen-Chi Wu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Yin-Hung Lin
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Molecular Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ying-Chang Lu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Pei-Jer Chen
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Wei-Shiung Yang
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
| | - Chuan-Jen Hsu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
- * E-mail: (CJH); (PLC)
| | - Pei-Lung Chen
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan
- * E-mail: (CJH); (PLC)
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27
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Horn HF, Brownstein Z, Lenz DR, Shivatzki S, Dror AA, Dagan-Rosenfeld O, Friedman LM, Roux KJ, Kozlov S, Jeang KT, Frydman M, Burke B, Stewart CL, Avraham KB. The LINC complex is essential for hearing. J Clin Invest 2013; 123:740-50. [PMID: 23348741 DOI: 10.1172/jci66911] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 11/29/2012] [Indexed: 01/08/2023] Open
Abstract
Hereditary hearing loss is the most common sensory deficit. We determined that progressive high-frequency hearing loss in 2 families of Iraqi Jewish ancestry was due to homozygosity for the protein truncating mutation SYNE4 c.228delAT. SYNE4, a gene not previously associated with hearing loss, encodes nesprin-4 (NESP4), an outer nuclear membrane (ONM) protein expressed in the hair cells of the inner ear. The truncated NESP4 encoded by the families' mutation did not localize to the ONM. NESP4 and SUN domain-containing protein 1 (SUN1), which localizes to the inner nuclear membrane (INM), are part of the linker of nucleoskeleton and cytoskeleton (LINC) complex in the nuclear envelope. Mice lacking either Nesp4 or Sun1 were evaluated for hair cell defects and hearing loss. In both Nesp4-/- and Sun1-/- mice, OHCs formed normally, but degenerated as hearing matured, leading to progressive hearing loss. The nuclei of OHCs from mutant mice failed to maintain their basal localization, potentially affecting cell motility and hence the response to sound. These results demonstrate that the LINC complex is essential for viability and normal morphology of OHCs and suggest that the position of the nucleus in sensory epithelial cells is critical for maintenance of normal hearing.
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