1
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Jackson A, Lin SJ, Jones EA, Chandler KE, Orr D, Moss C, Haider Z, Ryan G, Holden S, Harrison M, Burrows N, Jones WD, Loveless M, Petree C, Stewart H, Low K, Donnelly D, Lovell S, Drosou K, Varshney GK, Banka S. Clinical, genetic, epidemiologic, evolutionary, and functional delineation of TSPEAR-related autosomal recessive ectodermal dysplasia 14. HGG ADVANCES 2023; 4:100186. [PMID: 37009414 PMCID: PMC10064225 DOI: 10.1016/j.xhgg.2023.100186] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/27/2023] [Indexed: 06/11/2023] Open
Abstract
TSPEAR variants cause autosomal recessive ectodermal dysplasia (ARED) 14. The function of TSPEAR is unknown. The clinical features, the mutation spectrum, and the underlying mechanisms of ARED14 are poorly understood. Combining data from new and previously published individuals established that ARED14 is primarily characterized by dental anomalies such as conical tooth cusps and hypodontia, like those seen in individuals with WNT10A-related odontoonychodermal dysplasia. AlphaFold-predicted structure-based analysis showed that most of the pathogenic TSPEAR missense variants likely destabilize the β-propeller of the protein. Analysis of 100000 Genomes Project (100KGP) data revealed multiple founder TSPEAR variants across different populations. Mutational and recombination clock analyses demonstrated that non-Finnish European founder variants likely originated around the end of the last ice age, a period of major climatic transition. Analysis of gnomAD data showed that the non-Finnish European population TSPEAR gene-carrier rate is ∼1/140, making it one of the commonest AREDs. Phylogenetic and AlphaFold structural analyses showed that TSPEAR is an ortholog of drosophila Closca, an extracellular matrix-dependent signaling regulator. We, therefore, hypothesized that TSPEAR could have a role in enamel knot, a structure that coordinates patterning of developing tooth cusps. Analysis of mouse single-cell RNA sequencing (scRNA-seq) data revealed highly restricted expression of Tspear in clusters representing enamel knots. A tspeara -/-;tspearb -/- double-knockout zebrafish model recapitulated the clinical features of ARED14 and fin regeneration abnormalities of wnt10a knockout fish, thus suggesting interaction between tspear and wnt10a. In summary, we provide insights into the role of TSPEAR in ectodermal development and the evolutionary history, epidemiology, mechanisms, and consequences of its loss of function variants.
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Affiliation(s)
- Adam Jackson
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Sheng-Jia Lin
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Elizabeth A. Jones
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Kate E. Chandler
- Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - David Orr
- Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Celia Moss
- Department of Dermatology, Birmingham Children’s Hospital, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, UK
| | - Zahra Haider
- Department of Dermatology, Birmingham Children’s Hospital, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, UK
| | - Gavin Ryan
- West Midlands Regional Genetics Laboratory, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, UK
| | - Simon Holden
- Clinical Genetics, Addenbrooke’s Hospital, Cambridge, UK
| | - Mike Harrison
- Department of Pediatric Dentistry, Guy’s and St Thomas' Dental Institute, London, UK
| | - Nigel Burrows
- Department of Dermatology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Wendy D. Jones
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children, Great Ormond Street NHS Foundation Trust, London, UK
| | - Mary Loveless
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Cassidy Petree
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Karen Low
- Department of Clinical Genetics, St Michael’s Hospital, Bristol, UK
| | - Deirdre Donnelly
- Department of Genetic Medicine, Belfast HSC Trust, Lisburn Road, Belfast, UK
| | - Simon Lovell
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Konstantina Drosou
- Department of Earth and Environmental Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, 99 Oxford Road, Manchester, UK
| | - Gaurav K. Varshney
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Siddharth Banka
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
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Abstract
PURPOSE OF REVIEW Genetic studies in humans and animal models have improved our understanding of the role of numerous genes in the etiology of nonsyndromic tooth agenesis (TA). The purpose of this review is to discuss recently identified genes potentially contributing to TA. RECENT FINDINGS Despite research progress, understanding the genetic factors underlying nonsyndromic TA has been challenging given the genetic heterogeneity, variable expressivity, and incomplete penetrance of putatively pathogenic variants often observed associated with the condition. Next-generation sequencing technologies have provided a platform for novel gene and variant discoveries and informed paradigm-shifting concepts in the etiology of TA. This review summarizes the current knowledge on genes and pathways related to nonsyndromic TA with a focus on recently identified genes/variants. Evidence suggesting possible multi-locus variation in TA is also presented.
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Affiliation(s)
- Ariadne Letra
- Department of Oral and Craniofacial Sciences, and Center for Craniofacial and Dental Genetics, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA, 15219, USA.
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3
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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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4
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Rabie EA, Sayed ISM, Amr K, Ahmed HA, Mostafa MI, Hassib NF, El-Sayed H, Zada SK, El-Kamah G. Confirmation of a Phenotypic Entity for TSPEAR Variants in Egyptian Ectodermal Dysplasia Patients and Role of Ethnicity. Genes (Basel) 2022; 13:1056. [PMID: 35741818 PMCID: PMC9222913 DOI: 10.3390/genes13061056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 02/01/2023] Open
Abstract
Ectodermal dysplasia (ED) are hereditary disorders characterized by the disturbance of the ectodermal development of at least two of four ectodermal tissues: teeth, hair, nails and sweat glands. Clinical classification of ED is challenged by overlapping features, variable expressivity, and low number of patients, hindering full phenotypic spectrum identification. Disease-causing variants in elements of major developmental pathways, e.g., Ectodysplasin/NFκB, Wnt, and Tp63 pathways, have been identified in fewer than half of ED phenotypes. Whole-exome sequencing (WES) was performed for ten Egyptian ED patients presenting with tooth agenesis, normal sweating, scalp hypotrichosis, and sharing characteristic facial features. WES was followed by in silico analysis of the effects of novel detected genetic variants on mRNA and protein structure. The study identified four novel rare pathogenic and likely pathogenic TSPEAR variants, a gene which was recently found to be involved in ectodermal organogenesis. A novel in-frame deletion recurred in eight patients from six unrelated families. Comparing our cohort to previously reported TSPEAR cohorts highlighted the influence of ethnicity on TSPEAR phenotypic affection. Our study expands the clinical and mutational spectrum of the growing TSPEAR associated phenotypes, and pinpoints the influence of WES and in silico tools on identification of rare disease-causing variants.
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Affiliation(s)
- Eman A. Rabie
- Medical Molecular Genetics Department, Human Genetics & Genome Research Division (HGGR), National Research Centre (NRC), Cairo 12622, Egypt;
- Biology Department, School of Sciences and Engineering, The American University in Cairo (AUC), Cairo 11835, Egypt;
| | - Inas S. M. Sayed
- Orodental Genetics Department, Human Genetics & Genome Research Division (HGGR), National Research Centre (NRC), Cairo 12622, Egypt; (I.S.M.S.); (M.I.M.); (N.F.H.)
| | - Khalda Amr
- Medical Molecular Genetics Department, Human Genetics & Genome Research Division (HGGR), National Research Centre (NRC), Cairo 12622, Egypt;
| | - Hoda A. Ahmed
- Medical Molecular Genetics Department, Human Genetics & Genome Research Division (HGGR), National Research Centre (NRC), Cairo 12622, Egypt;
| | - Mostafa I. Mostafa
- Orodental Genetics Department, Human Genetics & Genome Research Division (HGGR), National Research Centre (NRC), Cairo 12622, Egypt; (I.S.M.S.); (M.I.M.); (N.F.H.)
| | - Nehal F. Hassib
- Orodental Genetics Department, Human Genetics & Genome Research Division (HGGR), National Research Centre (NRC), Cairo 12622, Egypt; (I.S.M.S.); (M.I.M.); (N.F.H.)
| | - Heba El-Sayed
- Clinical Genetics Department, Human Genetics & Genome Research Division (HGGR), National Research Centre (NRC), Cairo 12622, Egypt;
| | - Suher K. Zada
- Biology Department, School of Sciences and Engineering, The American University in Cairo (AUC), Cairo 11835, Egypt;
| | - Ghada El-Kamah
- Clinical Genetics Department, Human Genetics & Genome Research Division (HGGR), National Research Centre (NRC), Cairo 12622, Egypt;
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5
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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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6
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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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7
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Pavlenkova Z, Varga L, Borecka S, Karhanek M, Huckova M, Skopkova M, Profant M, Gasperikova D. Comprehensive molecular-genetic analysis of mid-frequency sensorineural hearing loss. Sci Rep 2021; 11:22488. [PMID: 34795337 PMCID: PMC8602250 DOI: 10.1038/s41598-021-01876-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/27/2021] [Indexed: 12/14/2022] Open
Abstract
The genetic heterogeneity of sensorineural hearing loss (SNHL) is a major hurdle to the detection of disease-causing variants. We aimed to identify underlying causal genes associated with mid-frequency hearing loss (HL), which contributes to less than about 1% of SNHL cases, by whole exome sequencing (WES). Thirty families segregating mid-frequency SNHL, in whom biallelic GJB2 mutations had been previously excluded, were selected from among 851 families in our DNA repository of SNHL. DNA samples from the probands were subjected to WES analysis and searched for candidate variants associated with SNHL. We were able to identify the genetic aetiology in six probands (20%). In total, we found three pathogenic and three likely pathogenic variants in four genes (COL4A5, OTOGL, TECTA, TMPRSS3). One more proband was a compound heterozygote for a pathogenic variant and a variant of uncertain significance (VUS) in MYO15A gene. To date, MYO15A and TMPRSS3 have not yet been described in association with mid-frequency SNHL. In eight additional probands, eight candidate VUS variants were detected in five genes (DIAPH1, MYO7A, TECTA, TMC1, TSPEAR). Seven of these 16 variants have not yet been published or mentioned in the available databases. The most prevalent gene was TECTA, identified in 23% of all tested families. Furthermore, we confirmed the hypothesis that a substantive portion of cases with this conspicuous audiogram shape is a consequence of a genetic disorder.
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Affiliation(s)
- Zuzana Pavlenkova
- Department of Otorhinolaryngology-Head and Neck Surgery, Faculty of Medicine and University Hospital, Comenius University, Bratislava, Slovakia.,DIABGENE Laboratory, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lukas Varga
- Department of Otorhinolaryngology-Head and Neck Surgery, Faculty of Medicine and University Hospital, Comenius University, Bratislava, Slovakia. .,DIABGENE Laboratory, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia.
| | - Silvia Borecka
- DIABGENE Laboratory, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Miloslav Karhanek
- Laboratory of Bioinformatics, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Miloslava Huckova
- DIABGENE Laboratory, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Martina Skopkova
- DIABGENE Laboratory, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Milan Profant
- Department of Otorhinolaryngology-Head and Neck Surgery, Faculty of Medicine and University Hospital, Comenius University, Bratislava, Slovakia
| | - Daniela Gasperikova
- DIABGENE Laboratory, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
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8
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Sun H, Wan N. Genotype-Phenotype Analysis of 8q24.3 Duplication and 21q22.3 Deletion in a Chinese Patient and Literature Review. Public Health Genomics 2021; 24:218-228. [PMID: 34265769 DOI: 10.1159/000515547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 02/28/2021] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Copy number variants (CNVs) are responsible for many patients with short stature of unknown etiology. This study aims to analyze clinical phenotypes and identify pathogenic CNVs in a patient with short stature, intellectual disability, craniofacial deformities, and anal imperforation. METHODS G-banded karyotyping and chromosomal microarray analysis (CMA) was used on the patient to identify pathogenic causes. Fluorescence in situ hybridization (FISH) was applied to explore the abnormal genetic origin. Literatures were searched using identified CNVs as keywords in the PubMed database to perform genotype-phenotype analysis. RESULTS Cytogenetic analysis revealed a normal karyotype 46,XY. CMA detected a 6.1 Mb duplication at 8q24.3 and a 3.6 Mb deletion at 21q22.3. FISH confirmed that the abnormal chromosomes were inherited from paternal balanced translocation. We compared phenotypes of our patient with 6 patients with 8q24.3 duplication and 7 cases with 21q22.3 deletion respectively. CONCLUSIONS A novel 8q24.3 duplication and 21q22.3 deletion was identified in a Chinese patient. Genotype-phenotype analysis demonstrated that patients with 8q24.3 duplication and 21q22.3 deletion had specific facial features, intellectual disability, short stature, and multiple malformations.
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Affiliation(s)
- Huihui Sun
- Department of Pediatrics, Beijing Jishuitan Hospital, Beijing, China
| | - Naijun Wan
- Department of Pediatrics, Beijing Jishuitan Hospital, Beijing, China
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9
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Bowles B, Ferrer A, Nishimura CJ, Pinto E Vairo F, Rey T, Leheup B, Sullivan J, Schoch K, Stong N, Agolini E, Cocciadiferro D, Williams A, Cummings A, Loddo S, Genovese S, Roadhouse C, McWalter K, Wentzensen IM, Li C, Babovic-Vuksanovic D, Lanpher BC, Dentici ML, Ankala A, Hamm JA, Dallapiccola B, Radio FC, Shashi V, Gérard B, Bloch-Zupan A, Smith RJ, Klee EW. TSPEAR variants are primarily associated with ectodermal dysplasia and tooth agenesis but not hearing loss: A novel cohort study. Am J Med Genet A 2021; 185:2417-2433. [PMID: 34042254 PMCID: PMC8361973 DOI: 10.1002/ajmg.a.62347] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 04/12/2021] [Accepted: 04/22/2021] [Indexed: 12/30/2022]
Abstract
Biallelic loss‐of‐function variants in the thrombospondin‐type laminin G domain and epilepsy‐associated repeats (TSPEAR) gene have recently been associated with ectodermal dysplasia and hearing loss. The first reports describing a TSPEAR disease association identified this gene is a cause of nonsyndromic hearing loss, but subsequent reports involving additional affected families have questioned this evidence and suggested a stronger association with ectodermal dysplasia. To clarify genotype–phenotype associations for TSPEAR variants, we characterized 13 individuals with biallelic TSPEAR variants. Individuals underwent either exome sequencing or panel‐based genetic testing. Nearly all of these newly reported individuals (11/13) have phenotypes that include tooth agenesis or ectodermal dysplasia, while three newly reported individuals have hearing loss. Of the individuals displaying hearing loss, all have additional variants in other hearing‐loss‐associated genes, specifically TMPRSS3, GJB2, and GJB6, that present competing candidates for their hearing loss phenotype. When presented alongside previous reports, the overall evidence supports the association of TSPEAR variants with ectodermal dysplasia and tooth agenesis features but creates significant doubt as to whether TSPEAR variants are a monogenic cause of hearing loss. Further functional evidence is needed to evaluate this phenotypic association.
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Affiliation(s)
- Bradley Bowles
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Alejandro Ferrer
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Carla J Nishimura
- Molecular Otolaryngology and Renal Research Laboratories, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Filippo Pinto E Vairo
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Tristan Rey
- Faculté de Chirurgie Dentaire, Université de Strasbourg, Strasbourg, France.,Laboratoires de Diagnostic génétique, Pôle de Biologie, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d'Alsace, Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Illkirch, France
| | - Bruno Leheup
- Département de Médecine Infantile, CHRU de Nancy, Nancy, France
| | - Jennifer Sullivan
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Kelly Schoch
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, New York, USA.,Brystol Myers Squibb, New York, New York, USA
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Dario Cocciadiferro
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Abigail Williams
- Department of Pediatrics, East Tennessee Children's Hospital, Knoxville, Tennessee, USA
| | - Alex Cummings
- Department of Pediatrics, East Tennessee Children's Hospital, Knoxville, Tennessee, USA.,University of Wisconsin Hospitals and Clinics, Madison, Wisconsin, USA
| | - Sara Loddo
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Silvia Genovese
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Chelsea Roadhouse
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | | | | | | | - Chumei Li
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Dusica Babovic-Vuksanovic
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Brendan C Lanpher
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Maria Lisa Dentici
- Genetics and Rare Diseases Research Division, Molecular Genetics and Functional Genomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Arun Ankala
- EGL Genetics LLC, Tucker, Georgia, USA.,Emory University School of Medicine, Atlanta, Georgia, USA
| | - J Austin Hamm
- Department of Pediatrics, East Tennessee Children's Hospital, Knoxville, Tennessee, USA
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Molecular Genetics and Functional Genomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Francesca Clementina Radio
- Genetics and Rare Diseases Research Division, Molecular Genetics and Functional Genomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Vandana Shashi
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Benedicte Gérard
- Laboratoires de Diagnostic génétique, Pôle de Biologie, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d'Alsace, Strasbourg, France
| | - Agnes Bloch-Zupan
- Faculté de Chirurgie Dentaire, Université de Strasbourg, Strasbourg, France.,Centre de référence des maladies rares orales et dentaires O-Rares, Filière Santé Maladies rares TETE COU, European Reference Network CRANIO, Pôle de Médecine et Chirurgie Bucco-dentaires, Hôpital Civil, Hôpitaux Universitaires de Strasbourg (HUS), Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Illkirch, France
| | - Richard J Smith
- Molecular Otolaryngology and Renal Research Laboratories, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
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10
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Amalou G, Bonnet C, Riahi Z, Bouzidi A, Elrharchi S, Bousfiha A, Charif M, Kandil M, Lenaers G, Petit C, Barakat A. A homozygous MPZL2 deletion is associated with non syndromic hearing loss in a moroccan family. Int J Pediatr Otorhinolaryngol 2021; 140:110481. [PMID: 33234333 DOI: 10.1016/j.ijporl.2020.110481] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 10/29/2020] [Accepted: 10/29/2020] [Indexed: 12/01/2022]
Abstract
Adhesion glycoproteins are implicated in the pathophysiology of hearing loss, the most frequent inherited sensory disorder, affecting 1 in 1000 new-borns. Exome sequencing of a consanguineous Moroccan patient with mild hearing loss identified for the first time in a North African family a single homozygous mutation c.72delA in MPZL2 gene, encoding the Myelin Protein Zero-Like 2, reported as causing deafness in two other populations. Variable tandem repeat genotyping of this family revealed that the c.72delA MPZL2 allele shared a common haplotype with Turkish and Dutch families. These results confirm the pathogenicity of this MPZL2 mutation in recessive mild to moderate non-syndromic deafness.
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Affiliation(s)
- Ghita Amalou
- Human Molecular Genetics Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco; MitoLab Team, Institut MitoVasc, UMR CNRS 6015, INSERM U1083, Université d'Angers, Angers, France; Team of Anthropogenetics and Biotechnologies, Faculty of Sciences, Chouaib Doukkali University, Eljadida, Morocco
| | - Crystel Bonnet
- Genetics and Physiology of Hearing Laboratory, Institut Pasteur, 75015, Paris, France
| | - Zied Riahi
- Complexité Du Vivant, Sorbonne Universités, 75005, Paris, France
| | - Aymane Bouzidi
- Human Molecular Genetics Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco; MitoLab Team, Institut MitoVasc, UMR CNRS 6015, INSERM U1083, Université d'Angers, Angers, France; Team of Anthropogenetics and Biotechnologies, Faculty of Sciences, Chouaib Doukkali University, Eljadida, Morocco
| | - Soukaina Elrharchi
- Human Molecular Genetics Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Amale Bousfiha
- Human Molecular Genetics Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco; Laboratoire de Physiopathologie et Génétique Moléculaire, Faculté des Sciences Ben M'sik, Université Hassan II, Casablanca, Morocco
| | - Majida Charif
- MitoLab Team, Institut MitoVasc, UMR CNRS 6015, INSERM U1083, Université d'Angers, Angers, France; Genetics, and Immuno-cell Therapy Team, Mohammed First University, Oujda, Morocco
| | - Mostafa Kandil
- Team of Anthropogenetics and Biotechnologies, Faculty of Sciences, Chouaib Doukkali University, Eljadida, Morocco
| | - Guy Lenaers
- MitoLab Team, Institut MitoVasc, UMR CNRS 6015, INSERM U1083, Université d'Angers, Angers, France
| | - Christine Petit
- Genetics and Physiology of Hearing Laboratory, Institut Pasteur, 75015, Paris, France; Institut de L'Audition, 75012, Paris, France; Collège de France, 75005, Paris, France
| | - Abdelhamid Barakat
- Human Molecular Genetics Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco.
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11
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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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12
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Bousfiha A, Riahi Z, Elkhattabi L, Bakhchane A, Charoute H, Snoussi K, Bonnet C, Petit C, Barakat A. Further Evidence for the Implication of the MET Gene in Non-Syndromic Autosomal Recessive Deafness. Hum Hered 2019; 84:109-116. [PMID: 31801140 DOI: 10.1159/000503450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/18/2019] [Indexed: 11/19/2022] Open
Abstract
Mutations in the mesenchymal epithelial transition factor (MET) gene are frequently associated with multiple human cancers but can also lead to human non-syndromic autosomal recessive deafness (DFNB97). In the present study, we identified a novel homozygous missense mutation in the METgene causing a non-syndromic hearing impairment DFNB97 form. Whole-exome sequencing was performed to determine the genetic causes of hearing loss in a Moroccan consanguineous family with an affected daughter. The structural analysis of native and mutant in the SEMA domain of the MET receptor was investigated using a molecular dynamics simulation (MDS) approach. We identified a novel pathogenic homozygous c.948A>G (p.Ile316Met) mutation in the MET gene in one deaf Moroccan young girl carrying a total bilateral non-syndromic hearing impairment. The results of the MDS approach show that an Ile316Met mutation in the SEMA domain leads to protein flexibility loss. This may produce a major impact on the structural conformation of the MET receptor, which also affects the function and binding site of the receptor. This is the first time that a mutation in the MET gene is described in a Moroccan family. Moreover, this study reports the second family in the world associating deafness and mutation in the MET gene.
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Affiliation(s)
- Amale Bousfiha
- Laboratoire de Génomique et Génétique Humaine, Institut Pasteur du Maroc, Casablanca, Morocco.,Laboratoire de Physiopathologie et Génétique Moléculaire, Faculté des Sciences Ben M'Sik, Université Hassan II, Casablanca, Morocco
| | - Zied Riahi
- INSERM UMRS1120, Institut de la Vision, Paris, France.,UPMC-Sorbonnes Universités Paris VI, Paris, France
| | - Lamiae Elkhattabi
- Laboratoire de Génomique et Génétique Humaine, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Amina Bakhchane
- Laboratoire de Génomique et Génétique Humaine, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Hicham Charoute
- Laboratoire de Génomique et Génétique Humaine, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Khalid Snoussi
- Laboratoire de Génomique et Génétique Humaine, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Crystel Bonnet
- INSERM UMRS1120, Institut de la Vision, Paris, France.,UPMC-Sorbonnes Universités Paris VI, Paris, France
| | - Christine Petit
- INSERM UMRS1120, Institut de la Vision, Paris, France.,UPMC-Sorbonnes Universités Paris VI, Paris, France.,Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, Paris, France.,Collège de France, Paris, France
| | - Abdelhamid Barakat
- Laboratoire de Génomique et Génétique Humaine, Institut Pasteur du Maroc, Casablanca, Morocco,
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13
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D'Aguillo C, Bressler S, Yan D, Mittal R, Fifer R, Blanton SH, Liu X. Genetic screening as an adjunct to universal newborn hearing screening: literature review and implications for non-congenital pre-lingual hearing loss. Int J Audiol 2019; 58:834-850. [PMID: 31264897 DOI: 10.1080/14992027.2019.1632499] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Objective: Universal newborn hearing screening (UNHS) uses otoacoustic emissions testing (OAE) and auditory brainstem response testing (ABR) to screen all newborn infants for hearing loss (HL), but may not identify infants with mild HL at birth or delayed onset HL. The purpose of this review is to examine the role of genetic screening to diagnose children with pre-lingual HL that is not detected at birth by determining the rate of children who pass UNHS but have a positive genetic screening. This includes a summary of the current UNHS and its limitations and a review of genetic mutations and screening technologies used to detect patients with an increased risk of undiagnosed pre-lingual HL.Design: Literature review of studies that compare UNHS with concurrent genetic screening.Study sample: Infants and children with HLResults: Sixteen studies were included encompassing 137,895 infants. Pathogenic mutations were detected in 8.66% of patients. In total, 545 patients passed the UNHS but had a positive genetic screening. The average percentage of patients who passed UNHS but had a positive genetic screening was 1.4%.Conclusions: This review demonstrates the positive impact of concurrent genetic screening with UNHS to identify patients with pre-lingual HL.
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Affiliation(s)
- Christine D'Aguillo
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sara Bressler
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Rahul Mittal
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Robert Fifer
- Department of Pediatrics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Susan H Blanton
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA.,Department of Human Genetics, Dr. John T. Macdonald Foundation, Miami, FL, USA.,John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Xuezhong Liu
- Department of Otolaryngology, University of Miami Miller School of Medicine, Miami, FL, USA.,Department of Pediatrics, University of Miami Miller School of Medicine, Miami, FL, USA.,Department of Human Genetics, Dr. John T. Macdonald Foundation, Miami, FL, USA.,John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.,Tsinghua University School of Medicine, Beijing, PR China
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14
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Faridi R, Tona R, Brofferio A, Hoa M, Olszewski R, Schrauwen I, Assir MZ, Bandesha AA, Khan AA, Rehman AU, Brewer C, Ahmed W, Leal SM, Riazuddin S, Boyden SE, Friedman TB. Mutational and phenotypic spectra of KCNE1 deficiency in Jervell and Lange-Nielsen Syndrome and Romano-Ward Syndrome. Hum Mutat 2019; 40:162-176. [PMID: 30461122 PMCID: PMC6328321 DOI: 10.1002/humu.23689] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/01/2018] [Accepted: 11/15/2018] [Indexed: 11/11/2022]
Abstract
KCNE1 encodes a regulatory subunit of the KCNQ1 potassium channel-complex. Both KCNE1 and KCNQ1 are necessary for normal hearing and cardiac ventricular repolarization. Recessive variants in these genes are associated with Jervell and Lange-Nielson syndrome (JLNS1 and JLNS2), a cardio-auditory syndrome characterized by congenital profound sensorineural deafness and a prolonged QT interval that can cause ventricular arrhythmias and sudden cardiac death. Some normal-hearing carriers of heterozygous missense variants of KCNE1 and KCNQ1 have prolonged QT intervals, a dominantly inherited phenotype designated Romano-Ward syndrome (RWS), which is also associated with arrhythmias and elevated risk of sudden death. Coassembly of certain mutant KCNE1 monomers with wild-type KCNQ1 subunits results in RWS by a dominant negative mechanism. This paper reviews variants of KCNE1 and their associated phenotypes, including biallelic truncating null variants of KCNE1 that have not been previously reported. We describe three homozygous nonsense mutations of KCNE1 segregating in families ascertained ostensibly for nonsyndromic deafness: c.50G>A (p.Trp17*), c.51G>A (p.Trp17*), and c.138C>A (p.Tyr46*). Some individuals carrying missense variants of KCNE1 have RWS. However, heterozygotes for loss-of-function variants of KCNE1 may have normal QT intervals while biallelic null alleles are associated with JLNS2, indicating a complex genotype-phenotype spectrum for KCNE1 variants.
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Affiliation(s)
- Rabia Faridi
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 54550, Pakistan
| | - Risa Tona
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alessandra Brofferio
- Cardiology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA
| | - Michael Hoa
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rafal Olszewski
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muhammad Z.K. Assir
- Allama Iqbal Medical Research Centre, Jinnah Hospital Complex, Lahore 54550, Pakistan
| | - Akhtar A. Bandesha
- Cardiology Department, The Pakistan Institute of Medical Sciences, Islamabad, Pakistan
| | - Asma A. Khan
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 54550, Pakistan
| | - Atteeq U. Rehman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Carmen Brewer
- Audiology Unit, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health, Bethesda, MD 20892, USA
| | - Wasim Ahmed
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Suzanne M. Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sheikh Riazuddin
- Allama Iqbal Medical Research Centre, Jinnah Hospital Complex, Lahore 54550, Pakistan
| | - Steven E. Boyden
- Section on Genetics of Communication Disorders, National Institute on Deafness and Other Communication Disorders, 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, Bethesda, MD 20892, USA
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15
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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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16
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Lerat J, Bonnet C, Cartault F, Loundon N, Jacquemont ML, Darcel F, Rouillon I, Mezouaghi K, Guichet A, Litzler J, Gesny R, Gherbi S, Aissa IB, Digeon FSJ, Garabedian EN, Bonnefont JP, Genin E, Denoyelle F, Jonard L, Marlin S. High prevalence of congenital deafness on Reunion Island is due to a founder variant of LHFPL5. Clin Genet 2018; 95:177-181. [PMID: 30298622 DOI: 10.1111/cge.13460] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/02/2018] [Accepted: 10/03/2018] [Indexed: 11/28/2022]
Abstract
Reunion Island is a French oversea department in the Indian Ocean with 1.6/1000, an estimated prevalence of deafness that is almost double as compared to the mainland France. Twelve children having isolated bilateral prelingual profound deafness along with motor delay attributed to vestibular areflexia were enrolled. Their mean walking age was 19 months. Electroretinography and temporal bone CT-scans were normal in all cases. A novel homozygous frameshift lipoma HMGIC fusion partner-like 5 (LHFPL5) variant c.185delT p.(Phe62Serfs*23) was identified using whole-exome sequencing. It was found in seven families. Four patients from two different families from both Reunion Island and mainland France, were compound heterozygous: c.185delT p.(Phe62Serfs*23) and c.472C > T p.(Arg158Trp). The phenotype observed in our patients completely mimics the hurry-scurry (hscy) murine Tmhs knock-out model. The recurrent occurrence of same LHFPL5 variant in Reunion Island is attributed to common ancestor couple born in 1693.
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Affiliation(s)
- Justine Lerat
- INSERM UMR_S1163 IHU Imagine - Institut des Maladies Génétiques - Université Paris Descartes, Paris, France.,Génétique Moléculaire, Necker, AP-HP, Paris, France.,Otorhinolaryngologie, CHU, Limoges, France
| | - Crystel Bonnet
- Institut de la Vision, UMRS 1120 INSERM/UPMC, Paris, France
| | - François Cartault
- Génétique Moléculaire, CHU La Réunion site Felix Guyon, Paris, France
| | - Natalie Loundon
- Centre de Référence Maladies Rares, Surdités Génétiques, Necker, AP-HP, Paris, France.,Otorhinolaryngologie Pédiatrique, Necker, AP-HP, Paris, France
| | | | | | - Isabelle Rouillon
- Centre de Référence Maladies Rares, Surdités Génétiques, Necker, AP-HP, Paris, France.,Otorhinolaryngologie Pédiatrique, Necker, AP-HP, Paris, France
| | - Kheira Mezouaghi
- Centre Régional de Compétences en Surdité Infantile, Sainte-Clothilde, France
| | | | | | | | - Souad Gherbi
- Centre de Référence Maladies Rares, Surdités Génétiques, Necker, AP-HP, Paris, France
| | - Ines Ben Aissa
- Centre de Référence Maladies Rares, Surdités Génétiques, Necker, AP-HP, Paris, France
| | | | - Eréa-Nöel Garabedian
- Centre de Référence Maladies Rares, Surdités Génétiques, Necker, AP-HP, Paris, France.,Otorhinolaryngologie Pédiatrique, Necker, AP-HP, Paris, France
| | | | - Emmanuelle Genin
- UMR1078 Génétique, Génomique Fonctionnelle et Biotechnologies, Inserm, Université de Brest, CHU Brest, France
| | - Françoise Denoyelle
- Centre de Référence Maladies Rares, Surdités Génétiques, Necker, AP-HP, Paris, France.,Otorhinolaryngologie Pédiatrique, Necker, AP-HP, Paris, France
| | - Laurence Jonard
- Génétique Moléculaire, Necker, AP-HP, Paris, France.,Centre de Référence Maladies Rares, Surdités Génétiques, Necker, AP-HP, Paris, France
| | - Sandrine Marlin
- INSERM UMR_S1163 IHU Imagine - Institut des Maladies Génétiques - Université Paris Descartes, Paris, France.,Centre de Référence Maladies Rares, Surdités Génétiques, Necker, AP-HP, Paris, France
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17
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Du R, Dinckan N, Song X, Coban-Akdemir Z, Jhangiani SN, Guven Y, Aktoren O, Kayserili H, Petty LE, Muzny DM, Below JE, Boerwinkle E, Wu N, Gibbs RA, Posey JE, Lupski JR, Letra A, Uyguner ZO. Identification of likely pathogenic and known variants in TSPEAR, LAMB3, BCOR, and WNT10A in four Turkish families with tooth agenesis. Hum Genet 2018; 137:689-703. [PMID: 30046887 PMCID: PMC6165673 DOI: 10.1007/s00439-018-1907-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/10/2018] [Indexed: 10/28/2022]
Abstract
Tooth agenesis (TA), the failure of development of one or more permanent teeth, is a common craniofacial abnormality observed in different world populations. The genetic etiology of TA is heterogeneous; more than a dozen genes have been associated with isolated or nonsyndromic TA, and more than 80 genes with syndromic forms. In this study, we applied whole exome sequencing (WES) to identify candidate genes contributing to TA in four Turkish families. Likely pathogenic variants with a low allele frequency in the general population were identified in four disease-associated genes, including two distinct variants in TSPEAR, associated with syndromic and isolated TA in one family each; a variant in LAMB3 associated with syndromic TA in one family; and a variant in BCOR plus a disease-associated WNT10A variant in one family with syndromic TA. With the notable exception of WNT10A (Tooth agenesis, selective, 4, MIM #150400), the genotype-phenotype relationships described in the present cohort represent an expansion of the clinical spectrum associated with these genes: TSPEAR (Deafness, autosomal recessive 98, MIM #614861), LAMB3 (Amelogenesis imperfecta, type IA, MIM #104530; Epidermolysis bullosa, junctional, MIMs #226700 and #226650), and BCOR (Microphthalmia, syndromic 2, MIM #300166). We provide evidence supporting the candidacy of these genes with TA, and propose TSPEAR as a novel nonsyndromic TA gene. Our data also suggest potential multilocus genomic variation, or mutational burden, in a single family, involving the BCOR and WNT10A loci, underscoring the complexity of the genotype-phenotype relationship in the common complex trait of TA.
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Affiliation(s)
- Renqian Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Nuriye Dinckan
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University, Millet Cad., Capa, Fatih, 34093, Istanbul, Turkey
- Center for Craniofacial Research, University of Texas Health Science Center at Houston School of Dentistry, Houston, TX, USA
| | - Xiaofei Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Yeliz Guven
- Department of Pedodontics, Faculty of Dentistry, Istanbul University, Capa, Istanbul, Turkey
| | - Oya Aktoren
- Department of Pedodontics, Faculty of Dentistry, Istanbul University, Capa, Istanbul, Turkey
| | - Hulya Kayserili
- Department of Medical Genetics, Koc University, School of Medicine (KUSOM), Istanbul, Turkey
| | - Lauren E Petty
- Human Genetics Center, University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Below
- Human Genetics Center, University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Human Genetics Center, University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | - Nan Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Beijing, China
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
| | - Ariadne Letra
- Center for Craniofacial Research, University of Texas Health Science Center at Houston School of Dentistry, Houston, TX, USA.
- Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center at Houston School of Dentistry, Houston, TX, USA.
- Pediatric Research Center, University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA.
- Department of Diagnostic and Biomedical Sciences, Center for Craniofacial Research, University of Texas Health Science Center at Houston School of Dentistry, 1941 East Road, BBSB Room 4210, Houston, TX, 77054, USA.
| | - Z Oya Uyguner
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University, Millet Cad., Capa, Fatih, 34093, Istanbul, Turkey.
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18
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Bousfiha A, Bakhchane A, Charoute H, Riahi Z, Snoussi K, Rouba H, Bonnet C, Petit C, Barakat A. A novel PEX1 mutation in a Moroccan family with Zellweger spectrum disorders. Hum Genome Var 2017; 4:17009. [PMID: 28446956 PMCID: PMC5390255 DOI: 10.1038/hgv.2017.9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 02/03/2017] [Accepted: 02/07/2017] [Indexed: 01/18/2023] Open
Abstract
Mutations in the PEX1 gene are usually associated with recessive inherited diseases including Zellweger spectrum disorders. In this work, we identified a new pathogenic missense homozygous PEX1 mutation (p.Leu1026Pro, c.3077T>C) in two Moroccan syndromic deaf siblings from consanguineous parents. This variation is located in the P-loop containing nucleoside triphosphate hydrolase of protein domain and probably causes an alteration in the hydrolysis of ATP.
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Affiliation(s)
- Amale Bousfiha
- Human Molecular Genetics Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Amina Bakhchane
- Human Molecular Genetics Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Hicham Charoute
- Human Molecular Genetics Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Zied Riahi
- INSERM UMRS1120, Institut de la Vision, Paris, France.,UPMC-Sorbonnes Universités Paris VI, Paris, France
| | - Khalid Snoussi
- Human Molecular Genetics Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Hassan Rouba
- Human Molecular Genetics Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Crystel Bonnet
- INSERM UMRS1120, Institut de la Vision, Paris, France.,UPMC-Sorbonnes Universités Paris VI, Paris, France
| | - Christine Petit
- INSERM UMRS1120, Institut de la Vision, Paris, France.,UPMC-Sorbonnes Universités Paris VI, Paris, France.,Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, Paris, France.,Collège de France, Paris, France
| | - Abdelhamid Barakat
- Human Molecular Genetics Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
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19
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Peled A, Sarig O, Samuelov L, Bertolini M, Ziv L, Weissglas-Volkov D, Eskin-Schwartz M, Adase CA, Malchin N, Bochner R, Fainberg G, Goldberg I, Sugawara K, Baniel A, Tsuruta D, Luxenburg C, Adir N, Duverger O, Morasso M, Shalev S, Gallo RL, Shomron N, Paus R, Sprecher E. Mutations in TSPEAR, Encoding a Regulator of Notch Signaling, Affect Tooth and Hair Follicle Morphogenesis. PLoS Genet 2016; 12:e1006369. [PMID: 27736875 PMCID: PMC5065119 DOI: 10.1371/journal.pgen.1006369] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/16/2016] [Indexed: 11/19/2022] Open
Abstract
Despite recent advances in our understanding of the pathogenesis of ectodermal dysplasias (EDs), the molecular basis of many of these disorders remains unknown. In the present study, we aimed at elucidating the genetic basis of a new form of ED featuring facial dysmorphism, scalp hypotrichosis and hypodontia. Using whole exome sequencing, we identified 2 frameshift and 2 missense mutations in TSPEAR segregating with the disease phenotype in 3 families. TSPEAR encodes the thrombospondin-type laminin G domain and EAR repeats (TSPEAR) protein, whose function is poorly understood. TSPEAR knock-down resulted in altered expression of genes known to be regulated by NOTCH and to be involved in murine hair and tooth development. Pathway analysis confirmed that down-regulation of TSPEAR in keratinocytes is likely to affect Notch signaling. Accordingly, using a luciferase-based reporter assay, we showed that TSPEAR knock-down is associated with decreased Notch signaling. In addition, NOTCH1 protein expression was reduced in patient scalp skin. Moreover, TSPEAR silencing in mouse hair follicle organ cultures was found to induce apoptosis in follicular epithelial cells, resulting in decreased hair bulb diameter. Collectively, these observations indicate that TSPEAR plays a critical, previously unrecognized role in human tooth and hair follicle morphogenesis through regulation of the Notch signaling pathway. Ectodermal dysplasias refer to a large group of inherited disorders characterized by developmental defects in tissues of ectodermal origin. The study of these conditions has been instrumental in the discovery of biological pathways involved in the regulation of epithelial tissue morphogenesis. In this report, through the delineation of the molecular basis of a novel form of autosomal recessive ectodermal dysplasia, we identified a new key player in ectodermal development. We detected a number of mutations in TSPEAR co-segregating with abnormal hair and tooth development in three families. TSPEAR encodes the thrombospondin-type laminin G domain and EAR repeats (TSPEAR) protein, whose function is poorly understood. TSPEAR was found to be strongly expressed in murine hair and tooth. Using a reporter assay, we showed that it regulates Notch activity. Accordingly, NOTCH1 expression was altered in patient skin, and NOTCH1, as well as many of its known targets, was down-regulated in TSPEAR deficient keratinocytes. Moreover, Tspear silencing in mouse hair follicle organ cultures was found to induce apoptosis in follicular epithelial cells, resulting in decreased hair bulb diameter. Collectively, these observations indicate that TSPEAR plays a critical, previously unrecognized role in human tooth and hair follicle morphogenesis through regulation of the Notch pathway. As such, these new data are likely to lead to further investigations aimed at characterizing the role of Notch signaling pathway in other forms of ectodermal dysplasias as well as acquired hair and tooth pathologies.
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Affiliation(s)
- Alon Peled
- Department of Dermatology, Tel Aviv Medical Center, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Tel-Aviv University, Tel Aviv, Israel
| | - Ofer Sarig
- Department of Dermatology, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Liat Samuelov
- Department of Dermatology, Tel Aviv Medical Center, Tel Aviv, Israel
- Division of Dermatology, University of California, San Diego, San Diego, California, United States of America
| | - Marta Bertolini
- Department of Dermatology, University of Münster, Münster, Germany
| | - Limor Ziv
- Sheba Medical Center, Ramat Gan, Israel
| | | | - Marina Eskin-Schwartz
- Department of Dermatology, Tel Aviv Medical Center, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Tel-Aviv University, Tel Aviv, Israel
| | - Christopher A. Adase
- Division of Dermatology, University of California, San Diego, San Diego, California, United States of America
| | - Natalia Malchin
- Department of Dermatology, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Ron Bochner
- Department of Dermatology, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Gilad Fainberg
- Department of Dermatology, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Ilan Goldberg
- Department of Dermatology, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Koji Sugawara
- Department of Dermatology, Osaka City University, Osaka, Japan
| | - Avital Baniel
- Department of Dermatology, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Daisuke Tsuruta
- Department of Dermatology, Osaka City University, Osaka, Japan
| | - Chen Luxenburg
- Department of Cell and Developmental Biology, Tel Aviv University, Tel Aviv, Israel
| | - Noam Adir
- Faculty of Chemistry, Technion, Haifa, Israel
| | - Olivier Duverger
- Laboratory of Skin Biology, National Institute of Health, Bethesda, Maryland, United States of America
| | - Maria Morasso
- Laboratory of Skin Biology, National Institute of Health, Bethesda, Maryland, United States of America
| | - Stavit Shalev
- Institute of Human Genetics, Haemek Medical Center, Afula, Israel
- Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Richard L. Gallo
- Division of Dermatology, University of California, San Diego, San Diego, California, United States of America
| | - Noam Shomron
- Department of Cell and Developmental Biology, Tel Aviv University, Tel Aviv, Israel
| | - Ralf Paus
- Department of Dermatology, University of Münster, Münster, Germany
- Centre for Dermatology Research, Institute of Inflammation and Repair, University of Manchester, Manchester, United Kingdom
| | - Eli Sprecher
- Department of Dermatology, Tel Aviv Medical Center, Tel Aviv, Israel
- Department of Human Molecular Genetics and Biochemistry, Tel-Aviv University, Tel Aviv, Israel
- * E-mail:
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A novel biallelic splice site mutation of TECTA causes moderate to severe hearing impairment in an Algerian family. Int J Pediatr Otorhinolaryngol 2016; 87:28-33. [PMID: 27368438 DOI: 10.1016/j.ijporl.2016.04.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 04/25/2016] [Accepted: 04/28/2016] [Indexed: 01/18/2023]
Abstract
Congenital deafness is certainly one of the most common monogenic diseases in humans, but it is also one of the most genetically heterogeneous, which makes molecular diagnosis challenging in most cases. Whole-exome sequencing in two out of three Algerian siblings affected by recessively-inherited, moderate to severe sensorineural deafness allowed us to identify a novel splice donor site mutation (c.5272+1G > A) in the gene encoding α-tectorin, a major component of the cochlear tectorial membrane. The mutation was present at the homozygous state in the three affected siblings, and at the heterozygous state in their unaffected, consanguineous parents. To our knowledge, this is the first reported TECTA mutation leading to the DFNB21 form of hearing impairment among Maghrebian individuals suffering from congenital hearing impairment, which further illustrates the diversity of the genes involved in congenital deafness in the Maghreb.
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21
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Imtiaz A, Maqsood A, Rehman AU, Morell RJ, Holt JR, Friedman TB, Naz S. Recessive mutations of TMC1 associated with moderate to severe hearing loss. Neurogenetics 2016; 17:115-123. [PMID: 26879195 PMCID: PMC4795972 DOI: 10.1007/s10048-016-0477-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 02/09/2016] [Indexed: 12/12/2022]
Abstract
TMC1 encodes a protein required for the normal function of mechanically activated channels that enable sensory transduction in auditory and vestibular hair cells. TMC1 protein is localized at the tips of the hair cell stereocilia, the site of conventional mechanotransduction. In many populations, loss-of-function recessive mutations of TMC1 are associated with profound deafness across all frequencies tested. In six families reported here, variable moderate-to-severe or moderate-to-profound hearing loss co-segregated with STR (short tandem repeats) markers at the TMC1 locus DFNB7/11. Massively parallel and Sanger sequencing of genomic DNA revealed each family co-segregating hearing loss with a homozygous TMC1 mutation: two reported mutations (p.R34X and p.R389Q) and three novel mutations (p.S596R, p.N199I, and c.1404 + 1G > T). TMC1 cDNA sequence from affected subjects homozygous for the donor splice site transversion c.1404 + 1G > T revealed skipping of exon 16, deleting 60 amino acids from the TMC1 protein. Since the mutations in our study cause less than profound hearing loss, we speculate that there is hypo-functional TMC1 mechanotransduction channel activity and that other even less damaging variants of TMC1 may be associated with more common mild-to-severe sensorineural hearing loss.
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Affiliation(s)
- Ayesha Imtiaz
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore 54590, Pakistan
- National Institute on Deafness and Other Communication Disorders, National Institutes of Health, USA 20892
| | - Azra Maqsood
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore 54590, Pakistan
| | - Atteeq U. Rehman
- National Institute on Deafness and Other Communication Disorders, National Institutes of Health, USA 20892
| | - Robert J. Morell
- National Institute on Deafness and Other Communication Disorders, National Institutes of Health, USA 20892
| | - Jeffrey R. Holt
- Department of Otolaryngology, F. M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Thomas B. Friedman
- National Institute on Deafness and Other Communication Disorders, National Institutes of Health, USA 20892
| | - Sadaf Naz
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore 54590, Pakistan
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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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Sloan-Heggen CM, Babanejad M, Beheshtian M, Simpson AC, Booth KT, Ardalani F, Frees KL, Mohseni M, Mozafari R, Mehrjoo Z, Jamali L, Vaziri S, Akhtarkhavari T, Bazazzadegan N, Nikzat N, Arzhangi S, Sabbagh F, Otukesh H, Seifati SM, Khodaei H, Taghdiri M, Meyer NC, Daneshi A, Farhadi M, Kahrizi K, Smith RJH, Azaiez H, Najmabadi H. Characterising the spectrum of autosomal recessive hereditary hearing loss in Iran. J Med Genet 2015; 52:823-9. [PMID: 26445815 PMCID: PMC4733363 DOI: 10.1136/jmedgenet-2015-103389] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/14/2015] [Indexed: 11/04/2022]
Abstract
BACKGROUND Countries with culturally accepted consanguinity provide a unique resource for the study of rare recessively inherited genetic diseases. Although hereditary hearing loss (HHL) is not uncommon, it is genetically heterogeneous, with over 85 genes causally implicated in non-syndromic hearing loss (NSHL). This heterogeneity makes many gene-specific types of NSHL exceedingly rare. We sought to define the spectrum of autosomal recessive HHL in Iran by investigating both common and rarely diagnosed deafness-causing genes. DESIGN Using a custom targeted genomic enrichment (TGE) panel, we simultaneously interrogated all known genetic causes of NSHL in a cohort of 302 GJB2-negative Iranian families. RESULTS We established a genetic diagnosis for 67% of probands and their families, with over half of all diagnoses attributable to variants in five genes: SLC26A4, MYO15A, MYO7A, CDH23 and PCDH15. As a reflection of the power of consanguinity mapping, 26 genes were identified as causative for NSHL in the Iranian population for the first time. In total, 179 deafness-causing variants were identified in 40 genes in 201 probands, including 110 novel single nucleotide or small insertion-deletion variants and three novel CNV. Several variants represent founder mutations. CONCLUSION This study attests to the power of TGE and massively parallel sequencing as a diagnostic tool for the evaluation of hearing loss in Iran, and expands on our understanding of the genetics of HHL in this country. Families negative for variants in the genes represented on this panel represent an excellent cohort for novel gene discovery.
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Affiliation(s)
- Christina M Sloan-Heggen
- Molecular Otolaryngology & Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Department of Molecular Physiology & Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Mojgan Babanejad
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Allen C Simpson
- Molecular Otolaryngology & Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Kevin T Booth
- Molecular Otolaryngology & Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Fariba Ardalani
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kathy L Frees
- Molecular Otolaryngology & Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Reza Mozafari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Zohreh Mehrjoo
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Leila Jamali
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Saeideh Vaziri
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Tara Akhtarkhavari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Niloofar Bazazzadegan
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Nooshin Nikzat
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Hasan Otukesh
- Hazrat –e – Ali Asghar Educational & Treatment Center, Iran University of Medical Sciences, Tehran, Iran
| | | | | | | | - Nicole C Meyer
- Molecular Otolaryngology & Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Ahmad Daneshi
- Head and Neck Surgery Department and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Farhadi
- Head and Neck Surgery Department and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Richard JH Smith
- Molecular Otolaryngology & Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Department of Molecular Physiology & Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Interdepartmental PhD Program in Genetics, University of Iowa, Iowa City, IA 52242, USA
| | - Hela Azaiez
- Molecular Otolaryngology & Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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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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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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Abstract
OBJECTIVES This study aimed to characterise feline audiogenic reflex seizures (FARS). METHODS An online questionnaire was developed to capture information from owners with cats suffering from FARS. This was collated with the medical records from the primary veterinarian. Ninety-six cats were included. RESULTS Myoclonic seizures were one of the cardinal signs of this syndrome (90/96), frequently occurring prior to generalised tonic-clonic seizures (GTCSs) in this population. Other features include a late onset (median 15 years) and absence seizures (6/96), with most seizures triggered by high-frequency sounds amid occasional spontaneous seizures (up to 20%). Half the population (48/96) had hearing impairment or were deaf. One-third of cats (35/96) had concurrent diseases, most likely reflecting the age distribution. Birmans were strongly represented (30/96). Levetiracetam gave good seizure control. The course of the epilepsy was non-progressive in the majority (68/96), with an improvement over time in some (23/96). Only 33/96 and 11/90 owners, respectively, felt the GTCSs and myoclonic seizures affected their cat's quality of life (QoL). Despite this, many owners (50/96) reported a slow decline in their cat's health, becoming less responsive (43/50), not jumping (41/50), becoming uncoordinated or weak in the pelvic limbs (24/50) and exhibiting dramatic weight loss (39/50). These signs were exclusively reported in cats experiencing seizures for >2 years, with 42/50 owners stating these signs affected their cat's QoL. CONCLUSIONS AND RELEVANCE In gathering data on audiogenic seizures in cats, we have identified a new epilepsy syndrome named FARS with a geriatric onset. Further studies are warranted to investigate potential genetic predispositions to this condition.
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Affiliation(s)
- Mark Lowrie
- Davies Veterinary Specialists, Hitchin, Hertfordshire, UK
| | | | - Robert J Harvey
- Department of Pharmacology, UCL School of Pharmacy, London, UK
| | | | - Laurent Garosi
- Davies Veterinary Specialists, Hitchin, Hertfordshire, UK
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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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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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Nishio SY, Hattori M, Moteki H, Tsukada K, Miyagawa M, Naito T, Yoshimura H, Iwasa YI, Mori K, Shima Y, Sakuma N, Usami SI. Gene expression profiles of the cochlea and vestibular endorgans: localization and function of genes causing deafness. Ann Otol Rhinol Laryngol 2015; 124 Suppl 1:6S-48S. [PMID: 25814645 DOI: 10.1177/0003489415575549] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
OBJECTIVES We sought to elucidate the gene expression profiles of the causative genes as well as the localization of the encoded proteins involved in hereditary hearing loss. METHODS Relevant articles (as of September 2014) were searched in PubMed databases, and the gene symbols of the genes reported to be associated with deafness were located on the Hereditary Hearing Loss Homepage using localization, expression, and distribution as keywords. RESULTS Our review of the literature allowed us to systematize the gene expression profiles for genetic deafness in the inner ear, clarifying the unique functions and specific expression patterns of these genes in the cochlea and vestibular endorgans. CONCLUSIONS The coordinated actions of various encoded molecules are essential for the normal development and maintenance of auditory and vestibular function.
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Affiliation(s)
- Shin-Ya Nishio
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto, Japan
| | - Mitsuru Hattori
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Hideaki Moteki
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Keita Tsukada
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Maiko Miyagawa
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto, Japan
| | - Takehiko Naito
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Hidekane Yoshimura
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Yoh-Ichiro Iwasa
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Kentaro Mori
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Yutaka Shima
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Naoko Sakuma
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan Department of Otorhinolaryngology and Head and Neck Surgery, Yokohama City University School of Medicine, Yokohama, Japan
| | - Shin-Ichi Usami
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto, Japan
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Riahi Z, Bonnet C, Zainine R, Lahbib S, Bouyacoub Y, Bechraoui R, Marrakchi J, Hardelin JP, Louha M, Largueche L, Ben Yahia S, Kheirallah M, Elmatri L, Besbes G, Abdelhak S, Petit C. Whole exome sequencing identifies mutations in Usher syndrome genes in profoundly deaf Tunisian patients. PLoS One 2015; 10:e0120584. [PMID: 25798947 PMCID: PMC4370767 DOI: 10.1371/journal.pone.0120584] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 01/24/2015] [Indexed: 01/13/2023] Open
Abstract
Usher syndrome (USH) is an autosomal recessive disorder characterized by combined deafness-blindness. It accounts for about 50% of all hereditary deafness blindness cases. Three clinical subtypes (USH1, USH2, and USH3) are described, of which USH1 is the most severe form, characterized by congenital profound deafness, constant vestibular dysfunction, and a prepubertal onset of retinitis pigmentosa. We performed whole exome sequencing in four unrelated Tunisian patients affected by apparently isolated, congenital profound deafness, with reportedly normal ocular fundus examination. Four biallelic mutations were identified in two USH1 genes: a splice acceptor site mutation, c.2283-1G>T, and a novel missense mutation, c.5434G>A (p.Glu1812Lys), in MYO7A, and two previously unreported mutations in USH1G, i.e. a frameshift mutation, c.1195_1196delAG (p.Leu399Alafs*24), and a nonsense mutation, c.52A>T (p.Lys18*). Another ophthalmological examination including optical coherence tomography actually showed the presence of retinitis pigmentosa in all the patients. Our findings provide evidence that USH is under-diagnosed in Tunisian deaf patients. Yet, early diagnosis of USH is of utmost importance because these patients should undergo cochlear implant surgery in early childhood, in anticipation of the visual loss.
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Affiliation(s)
- Zied Riahi
- Institut Pasteur de Tunis, LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory, 1002, Tunis, Tunisia
- Faculté des Sciences de Tunis, Université de Tunis El Manar, 2092 El Manar I Tunis, Tunis, Tunisia
| | - Crystel Bonnet
- Institut de la Vision, INSERM UMRS 1120, UPMC- Paris 6, Paris, France
| | - Rim Zainine
- La Rabta Hospital, Otorhinolaryngology Diseases, Tunis, Tunisia
| | - Saida Lahbib
- Institut Pasteur de Tunis, LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory, 1002, Tunis, Tunisia
| | - Yosra Bouyacoub
- Institut Pasteur de Tunis, LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory, 1002, Tunis, Tunisia
- Université de Monastir, Institut Supérieur de Biotechnologie, Monastir, Tunisia
| | - Rym Bechraoui
- La Rabta Hospital, Otorhinolaryngology Diseases, Tunis, Tunisia
| | | | - Jean-Pierre Hardelin
- Institut Pasteur, Unité de Génétique et Physiologie de l’Audition, Paris, France
| | - Malek Louha
- Laboratoire de Biochimie et de Biologie Moléculaire, Hôpital Armand Trousseau, APHP, Paris, France
| | - Leila Largueche
- Department B of Ophthalmology, Hedi Rais Institute of Ophthalmology, Tunis, Tunisia
| | - Salim Ben Yahia
- Universite de Monastir, Faculty of Medicine, Fattouma Bourguiba University Hospital, Department of Ophthalmology, 5000, Monastir, Tunisia
| | - Moncef Kheirallah
- Universite de Monastir, Faculty of Medicine, Fattouma Bourguiba University Hospital, Department of Ophthalmology, 5000, Monastir, Tunisia
| | - Leila Elmatri
- Department B of Ophthalmology, Hedi Rais Institute of Ophthalmology, Tunis, Tunisia
| | - Ghazi Besbes
- La Rabta Hospital, Otorhinolaryngology Diseases, Tunis, Tunisia
| | - Sonia Abdelhak
- Institut Pasteur de Tunis, LR11IPT05, Biomedical Genomics and Oncogenetics Laboratory, 1002, Tunis, Tunisia
- * E-mail:
| | - Christine Petit
- Institut de la Vision, INSERM UMRS 1120, UPMC- Paris 6, Paris, France
- Institut Pasteur, Unité de Génétique et Physiologie de l’Audition, Paris, France
- Collège de France, Paris, France
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Ammar-Khodja F, Bonnet C, Dahmani M, Ouhab S, Lefèvre GM, Ibrahim H, Hardelin JP, Weil D, Louha M, Petit C. Diversity of the causal genes in hearing impaired Algerian individuals identified by whole exome sequencing. Mol Genet Genomic Med 2015; 3:189-96. [PMID: 26029705 PMCID: PMC4444160 DOI: 10.1002/mgg3.131] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Revised: 12/05/2014] [Accepted: 12/06/2014] [Indexed: 11/15/2022] Open
Abstract
The genetic heterogeneity of congenital hearing disorders makes molecular diagnosis expensive and time-consuming using conventional techniques such as Sanger sequencing of DNA. In order to design an appropriate strategy of molecular diagnosis in the Algerian population, we explored the diversity of the involved mutations by studying 65 families affected by autosomal recessive forms of nonsyndromic hearing impairment (DFNB forms), which are the most prevalent early onset forms. We first carried out a systematic screening for mutations in GJB2 and the recurrent p.(Arg34*) mutation in TMC1, which were found in 31 (47.7%) families and 1 (1.5%) family, respectively. We then performed whole exome sequencing in nine of the remaining families, and identified the causative mutations in all the patients analyzed, either in the homozygous state (eight families) or in the compound heterozygous state (one family): (c.709C>T: p.(Arg237*)) and (c.2122C>T: p.(Arg708*)) in OTOF, (c.1334T>G: p.(Leu445Trp)) in SLC26A4, (c.764T>A: p.(Met255Lys)) in GIPC3, (c.518T>A: p.(Cys173Ser)) in LHFPL5, (c.5336T>C: p.(Leu1779Pro)) in MYO15A, (c.1807G>T: p.(Val603Phe)) in OTOA, (c.6080dup: p.(Asn2027Lys*9)) in PTPRQ, and (c.6017del: p.(Gly2006Alafs*13); c.7188_7189ins14: p.(Val2397Leufs*2)) in GPR98. Notably, 7 of these 10 mutations affecting 8 different genes had not been reported previously. These results highlight for the first time the genetic heterogeneity of the early onset forms of nonsyndromic deafness in Algerian families.
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Affiliation(s)
- Fatima Ammar-Khodja
- Equipe de Génétique, Laboratoire de Biologie Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumédiène (USTHB) Alger, Algeria
| | - Crystel Bonnet
- Institut de la Vision, UMRS 1120 INSERM/UPMC/Institut Pasteur Paris, France
| | - Malika Dahmani
- Equipe de Génétique, Laboratoire de Biologie Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumédiène (USTHB) Alger, Algeria
| | - Sofiane Ouhab
- Service d'Otorhinolaryngologie (ORL), Hôpital de Kouba-Bachir Mentouri Alger, Algeria
| | - Gaelle M Lefèvre
- Institut de la Vision, UMRS 1120 INSERM/UPMC/Institut Pasteur Paris, France
| | - Hassina Ibrahim
- Service d'Otorhinolaryngologie (ORL), Hôpital Mustapha Pacha Alger, Algeria
| | - Jean-Pierre Hardelin
- Institut Pasteur, Unité de Génétique et Physiologie de l'Audition UMRS 1120 INSERM/UPMC Paris 6, Paris, France
| | - Dominique Weil
- Institut Pasteur, Unité de Génétique et Physiologie de l'Audition UMRS 1120 INSERM/UPMC Paris 6, Paris, France
| | - Malek Louha
- Service de Biochimie, Hôpital Armand Trousseau UMRS 1120 INSERM, Paris, France
| | - Christine Petit
- Institut de la Vision, UMRS 1120 INSERM/UPMC/Institut Pasteur Paris, France ; Institut Pasteur, Unité de Génétique et Physiologie de l'Audition UMRS 1120 INSERM/UPMC Paris 6, Paris, France ; Collège de France Paris, France
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Lin F, Li D, Wang P, Fan D, De J, Zhu W. Autosomal recessive non-syndromic hearing loss is caused by novel compound heterozygous mutations in TMC1 from a Tibetan Chinese family. Int J Pediatr Otorhinolaryngol 2014; 78:2216-21. [PMID: 25458163 DOI: 10.1016/j.ijporl.2014.10.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 10/07/2014] [Accepted: 10/10/2014] [Indexed: 10/24/2022]
Abstract
OBJECTIVES Hearing loss is the most common sensory disorder worldwide. Biallelic mutations in 42 different genes have been identified as associated with autosomal recessive non-syndromic hearing loss (ARNSHL). One of the common genes responsible for ARNSHL is TMC1. TMC1 mutations have been reported to cause non-syndromic hearing loss in a variety of populations. The current study is designed to investigate mutations prevalent among Chinese ethnic groups with ARNSHL. METHODS Targeted exome sequencing (TES) was employed to study the genetic causes of two siblings with ARNSHL in a Tibetan Chinese family. Variants identified by TES were further confirmed by Sanger sequencing. RESULTS We identified two distinct variants in the TMC1 gene in two deaf siblings of one Tibetan Chinese family using TES. Both siblings inherited a paternal allele containing a deletion of c.1396_1398AAC (p.Asn466del) and a maternal allele containing an insertion of c.2210_2211insCT (p.Glu737HisfsX2). The former disrupts a highly conserved residue in the large intracellular loop domain adjacent to the fourth transmembrane domain, and the latter causes a truncation of a portion of the C-terminal domain. These variants were compound heterzygous and segregated with the hearing impairment in this family. CONCLUSION The novel compound heterozygous mutant alleles of TMC1 identified in this study were responsible for the ARNSHL in this Tibetan Chinese family. Although compound heterozygous mutations in TMC1 occurring in different TMC1 domains have been previously described in Han Chinese; this result suggests that the TMC1 variants contributing to hereditary deafness in Chinese populations may be more complex than initially assumed and that sequence-based diagnostics will be required for a comprehensive evaluation of ARNSHL.
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Affiliation(s)
- Fangzhu Lin
- Department of Otolaryngology-Head and Neck Surgery, First Hospital of Jilin University, Changchun 130021, China
| | - Dejun Li
- Center for Prenatal Diagnosis, First Hospital of Jilin University, Changchun 130021, China
| | - Ping Wang
- Department of Otolaryngology-Head and Neck Surgery, First Hospital of Jilin University, Changchun 130021, China
| | - Dongyan Fan
- School of Medicine, Tibet University, Lhasa 850000, China
| | - Ji De
- School of Medicine, Tibet University, Lhasa 850000, China
| | - Wei Zhu
- Department of Otolaryngology-Head and Neck Surgery, First Hospital of Jilin University, Changchun 130021, China.
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Li J, Zhao X, Xin Q, Shan S, Jiang B, Jin Y, Yuan H, Dai P, Xiao R, Zhang Q, Xiao J, Shao C, Gong Y, Liu Q. Whole-exome sequencing identifies a variant in TMEM132E causing autosomal-recessive nonsyndromic hearing loss DFNB99. Hum Mutat 2014; 36:98-105. [PMID: 25331638 DOI: 10.1002/humu.22712] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 10/06/2014] [Indexed: 11/06/2022]
Abstract
Autosomal-recessive nonsyndromic hearing loss (ARNSHL) features a high degree of genetic heterogeneity. Many genes responsible for ARNSHL have been identified or mapped. We previously mapped an ARNSHL locus at 17q12, herein designated DFNB99, in a consanguineous Chinese family. In this study, whole-exome sequencing revealed a homozygous missense mutation (c.1259G>A, p.Arg420Gln) in the gene-encoding transmembrane protein 132E (TMEM132E) as the causative variant. Immunofluorescence staining of the Organ of Corti showed Tmem132e highly expressed in murine inner hair cells. Furthermore, knockdown of the tmem132e ortholog in zebrafish affected the mechanotransduction of hair cells. Finally, wild-type human TMEM132E mRNA, but not the mRNA carrying the c.1259G>A mutation rescued the Tmem132e knockdown phenotype. We conclude that the variant in TMEM132E is the most likely cause of DFNB99.
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Affiliation(s)
- Jiangxia Li
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, Shandong University School of Medicine, Jinan, Shandong, 250012, China
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Park JH, Kim NKD, Kim AR, Rhee J, Oh SH, Koo JW, Nam JY, Park WY, Choi BY. Exploration of molecular genetic etiology for Korean cochlear implantees with severe to profound hearing loss and its implication. Orphanet J Rare Dis 2014; 9:167. [PMID: 25373420 PMCID: PMC4243193 DOI: 10.1186/s13023-014-0167-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 10/17/2014] [Indexed: 02/01/2023] Open
Abstract
Background Severe to profound sensorineural hearing loss (SNHL) requires cochlear implantation (CI) for auditory rehabilitation. Etiologic diagnoses can contribute to candidacy selection and decision-making regarding the timing of successful CI. However, few studies have been performed to address the etiologic spectrum of severe SNHL in the population where there is no consanguineous marriage and the majority of SNHL cases are sporadic in small sized families. The authors sought to comprehensively understand the etiologies of Korean cochlear implantees by incorporating the targeted resequencing of 204 candidate deafness genes (TRS-204) and a phenotype-driven candidate gene approach. Methods Ninety-three that consented to molecular genetic testing and underwent at least one molecular genetic test were included. Patients with a characteristic Phenotypic marker were subject to Sanger sequencing to detect variants in corresponding candidate genes. The rest of patients without any prominent phenotype were tested on GJB2. Next, TRS-204 was applied in GJB2-negative cases without any phenotypic marker. In addition, the sibling recurrence-risk of SNHL among families with non-diagnostic genotypes after TRS-204 was performed to gain insight of etiologies in non-diagnostic cases. Results Overall, we could find causative variants in 51 (54.8%) of the 93 cochlear implantees. Thirty (32.3%) probands could be diagnosed by direct Sanger sequencing of candidate genes selected by their phenotypes. GJB2 sequencing added 10 subjects to the group with a diagnostic genotype. TRS-204 could detect a causative variant from additional 11 cases (11.8%). We could not detect any pathogenic deletion or duplication on 204 target genes. The sibling recurrence-risk of SNHL among 42 genetically undiagnosed families with 0.03 (1/38) was significantly lower than among genetically diagnosed recessive families with 0.19 (7/37). Conclusion Despite that the majority of severe or more degree of SNHL occurs sporadically in Koreans, at least 54.8% of such cases that were willing to join the genetic study in the Korean population are monogenic Mendelian disorders with convincing causative variants. This study also indicates that a substantial portion of unsolved cases after applying our current protocol are predicted to have non-genetic or complex etiology rather than a Mendelian genetic disorder involving new genes beyond the 204 target genes. Electronic supplementary material The online version of this article (doi:10.1186/s13023-014-0167-8) contains supplementary material, which is available to authorized users.
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Pepermans E, Michel V, Goodyear R, Bonnet C, Abdi S, Dupont T, Gherbi S, Holder M, Makrelouf M, Hardelin JP, Marlin S, Zenati A, Richardson G, Avan P, Bahloul A, Petit C. The CD2 isoform of protocadherin-15 is an essential component of the tip-link complex in mature auditory hair cells. EMBO Mol Med 2014; 6:984-92. [PMID: 24940003 PMCID: PMC4119359 DOI: 10.15252/emmm.201403976] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/02/2014] [Accepted: 05/08/2014] [Indexed: 11/09/2022] Open
Abstract
Protocadherin-15 (Pcdh15) is a component of the tip-links, the extracellular filaments that gate hair cell mechano-electrical transduction channels in the inner ear. There are three Pcdh15 splice isoforms (CD1, CD2 and CD3), which only differ by their cytoplasmic domains; they are thought to function redundantly in mechano-electrical transduction during hair-bundle development, but whether any of these isoforms composes the tip-link in mature hair cells remains unknown. By immunolabelling and both morphological and electrophysiological analyses of post-natal hair cell-specific conditional knockout mice (Pcdh15ex38-fl/ex38-fl Myo15-cre+/-) that lose only this isoform after normal hair-bundle development, we show that Pcdh15-CD2 is an essential component of tip-links in mature auditory hair cells. The finding, in the homozygous or compound heterozygous state, of a PCDH15 frameshift mutation (p.P1515Tfs*4) that affects only Pcdh15-CD2, in profoundly deaf children from two unrelated families, extends this conclusion to humans. These results provide key information for identification of new components of the mature auditory mechano-electrical transduction machinery. This will also serve as a basis for the development of gene therapy for deafness caused by PCDH15 defects.
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Affiliation(s)
- Elise Pepermans
- Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, Paris, France UMRS 1120, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France Université Pierre et Marie Curie (Paris VI), Paris, France
| | - Vincent Michel
- Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, Paris, France UMRS 1120, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France Université Pierre et Marie Curie (Paris VI), Paris, France
| | | | - Crystel Bonnet
- UMRS 1120, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France Université Pierre et Marie Curie (Paris VI), Paris, France Syndrome de Usher et autres Atteintes Rétino-Cochléaires, Institut de la vision, Paris, France
| | - Samia Abdi
- Centre Hospitalier universitaire de Blida, Université Saad Dahleb, Blida, Algérie
| | - Typhaine Dupont
- Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, Paris, France UMRS 1120, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France Université Pierre et Marie Curie (Paris VI), Paris, France
| | - Souad Gherbi
- Centre de référence des Surdités Génétiques, Hôpital Necker, Paris, France
| | - Muriel Holder
- Service de Génétique Clinique, Hôpital Jeanne-de-Flandre, Lille, France
| | - Mohamed Makrelouf
- Laboratoire de Biochimie Génétique, Université d'Alger 1, Alger, Algérie
| | - Jean-Pierre Hardelin
- Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, Paris, France UMRS 1120, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France Université Pierre et Marie Curie (Paris VI), Paris, France
| | - Sandrine Marlin
- Centre de référence des Surdités Génétiques, Hôpital Necker, Paris, France
| | - Akila Zenati
- Laboratoire de Biochimie Génétique, Université d'Alger 1, Alger, Algérie
| | - Guy Richardson
- School of Life Sciences, University of Sussex, Brighton, UK
| | - Paul Avan
- Laboratoire de Biophysique Sensorielle, Université d'Auvergne, Clermont-Ferrand, France UMR 1107, Institut National de la Santé et de la Recherche Médicale (INSERM), Clermont-Ferrand, France Centre Jean Perrin, Clermont-Ferrand Cedex 01, France
| | - Amel Bahloul
- Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, Paris, France UMRS 1120, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France Université Pierre et Marie Curie (Paris VI), Paris, France
| | - Christine Petit
- Unité de Génétique et Physiologie de l'Audition, Institut Pasteur, Paris, France UMRS 1120, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France Université Pierre et Marie Curie (Paris VI), Paris, France Syndrome de Usher et autres Atteintes Rétino-Cochléaires, Institut de la vision, Paris, France Collège de France, Paris, France
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Riahi Z, Bonnet C, Zainine R, Louha M, Bouyacoub Y, Laroussi N, Chargui M, Kefi R, Jonard L, Dorboz I, Hardelin JP, Salah SB, Levilliers J, Weil D, McElreavey K, Boespflug OT, Besbes G, Abdelhak S, Petit C. Whole exome sequencing identifies new causative mutations in Tunisian families with non-syndromic deafness. PLoS One 2014; 9:e99797. [PMID: 24926664 PMCID: PMC4057390 DOI: 10.1371/journal.pone.0099797] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 05/17/2014] [Indexed: 11/29/2022] Open
Abstract
Identification of the causative mutations in patients affected by autosomal recessive non syndromic deafness (DFNB forms), is demanding due to genetic heterogeneity. After the exclusion of GJB2 mutations and other mutations previously reported in Tunisian deaf patients, we performed whole exome sequencing in patients affected with severe to profound deafness, from four unrelated consanguineous Tunisian families. Four biallelic non previously reported mutations were identified in three different genes: a nonsense mutation, c.208C>T (p.R70X), in LRTOMT, a missense mutation, c.5417T>C (p.L1806P), in MYO15A and two splice site mutations, c.7395+3G>A, and c.2260+2T>A, in MYO15A and TMC1 respectively. We thereby provide evidence that whole exome sequencing is a powerful, cost-effective screening tool to identify mutations causing recessive deafness in consanguineous families.
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Affiliation(s)
- Zied Riahi
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Tunis, Tunisia
- Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | | | - Rim Zainine
- Service d'ORL et de Chirurgie Maxillo-faciale, CHU La Rabta, Tunis, Tunisia
| | - Malek Louha
- Centre de Référence des Surdités Génétiques, Hôpital Trousseau- APHP, Paris, France
| | - Yosra Bouyacoub
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Nadia Laroussi
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Tunis, Tunisia
- Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Mariem Chargui
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Rym Kefi
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Laurence Jonard
- Centre de Référence des Surdités Génétiques, Hôpital Trousseau- APHP, Paris, France
| | | | - Jean-Pierre Hardelin
- Unité de Génétique et Physiologie de l'Audition, Institut Pasteur de Paris, Paris, France
| | - Sihem Belhaj Salah
- Service d'ORL et de Chirurgie Maxillo-faciale, CHU La Rabta, Tunis, Tunisia
| | - Jacqueline Levilliers
- Unité de Génétique et Physiologie de l'Audition, Institut Pasteur de Paris, Paris, France
| | - Dominique Weil
- Unité de Génétique et Physiologie de l'Audition, Institut Pasteur de Paris, Paris, France
| | - Kenneth McElreavey
- Unité de Génétique du Développement Humain, Institut Pasteur de Paris, Paris, France
| | | | - Ghazi Besbes
- Service d'ORL et de Chirurgie Maxillo-faciale, CHU La Rabta, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Tunis, Tunisia
- Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisia
- * E-mail:
| | - Christine Petit
- INSERM UMRS 1120, Institut de la Vision, Paris, France
- Unité de Génétique et Physiologie de l'Audition, Institut Pasteur de Paris, Paris, France
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Choi BY, Kim J, Chung J, Kim AR, Mun SJ, Kang SI, Lee SH, Kim N, Oh SH. Whole-exome sequencing identifies a novel genotype-phenotype correlation in the entactin domain of the known deafness gene TECTA. PLoS One 2014; 9:e97040. [PMID: 24816743 PMCID: PMC4016231 DOI: 10.1371/journal.pone.0097040] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 04/14/2014] [Indexed: 12/18/2022] Open
Abstract
Postlingual progressive hearing loss, affecting primarily the high frequencies, is the clinical finding in most cases of autosomal dominant nonsyndromic hearing loss (ADNSHL). The molecular genetic etiology of ADNSHL is extremely heterogeneous. We applied whole-exome sequencing to reveal the genetic etiology of high-frequency hearing loss in a mid-sized Korean family without any prior linkage data. Whole-exome sequencing of four family members (two affected and two unaffected), together with our filtering strategy based on comprehensive bioinformatics analyses, identified 21 potential pathogenic candidates. Sanger validation of an additional five family members excluded 20 variants, leaving only one novel variant, TECTA c.710C>T (p.T237I), as the strongest candidate. This variant resides in the entactin (ENT) domain and co-segregated perfectly with non-progressive high-frequency hearing loss in the family. It was absent among 700 ethnically matched control chromosomes, and the T237 residue is conserved among species, which supports its pathogenicity. Interestingly, this finding contrasted with a previously proposed genotype-phenotype correlation in which variants of the ENT domain of TECTA were associated with mid-frequency hearing loss. Based upon what we observed, we propose a novel “genotype to phenotype” correlation in the ENT domain of TECTA. Our results shed light on another important application of whole-exome sequencing: the establishment of a novel genotype-phenotype in the molecular genetic diagnosis of autosomal dominant hearing loss.
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Affiliation(s)
- Byung Yoon Choi
- Department of Otorhinolaryngology, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Jiwoong Kim
- Korean Bioinformation center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Juyong Chung
- Department of Otolaryngology, Ajou University School of Medicine, Suwon, South Korea
| | - Ah Reum Kim
- Department of Otorhinolaryngology, Seoul national University College of Medicine, Seoul, South Korea
| | - Sue Jean Mun
- Department of Otorhinolaryngology, Seoul national University College of Medicine, Seoul, South Korea
| | - Seong Il Kang
- Department of Otorhinolaryngology, Seoul national University College of Medicine, Seoul, South Korea
| | - Sang-Heon Lee
- Korean Bioinformation center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
- Department of Bioinformatics, University of Science and Technology, Daejeon, South Korea
| | - Namshin Kim
- Korean Bioinformation center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
- Department of Bioinformatics, University of Science and Technology, Daejeon, South Korea
- * E-mail: (NSK); (SHO)
| | - Seung-Ha Oh
- Department of Otorhinolaryngology, Seoul national University College of Medicine, Seoul, South Korea
- * E-mail: (NSK); (SHO)
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38
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Seco CZ, Oonk AMM, Domínguez-Ruiz M, Draaisma JMT, Gandía M, Oostrik J, Neveling K, Kunst HPM, Hoefsloot LH, del Castillo I, Pennings RJE, Kremer H, Admiraal RJC, Schraders M. Progressive hearing loss and vestibular dysfunction caused by a homozygous nonsense mutation in CLIC5. Eur J Hum Genet 2014; 23:189-94. [PMID: 24781754 DOI: 10.1038/ejhg.2014.83] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 03/20/2014] [Accepted: 04/04/2014] [Indexed: 11/10/2022] Open
Abstract
In a consanguineous Turkish family diagnosed with autosomal recessive nonsyndromic hearing impairment (arNSHI), a homozygous region of 47.4 Mb was shared by the two affected siblings on chromosome 6p21.1-q15. This region contains 247 genes including the known deafness gene MYO6. No pathogenic variants were found in MYO6, neither with sequence analysis of the coding region and splice sites nor with mRNA analysis. Subsequent candidate gene evaluation revealed CLIC5 as an excellent candidate gene. The orthologous mouse gene is mutated in the jitterbug mutant that exhibits progressive hearing impairment and vestibular dysfunction. Mutation analysis of CLIC5 revealed a homozygous nonsense mutation c.96T>A (p.(Cys32Ter)) that segregated with the hearing loss. Further analysis of CLIC5 in 213 arNSHI patients from mostly Dutch and Spanish origin did not reveal any additional pathogenic variants. CLIC5 mutations are thus not a common cause of arNSHI in these populations. The hearing loss in the present family had an onset in early childhood and progressed from mild to severe or even profound before the second decade. Impaired hearing is accompanied by vestibular areflexia and in one of the patients with mild renal dysfunction. Although we demonstrate that CLIC5 is expressed in many other human tissues, no additional symptoms were observed in these patients. In conclusion, our results show that CLIC5 is a novel arNSHI gene involved in progressive hearing impairment, vestibular and possibly mild renal dysfunction in a family of Turkish origin.
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Affiliation(s)
- Celia Zazo Seco
- 1] Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, Nijmegen, The Netherlands [2] Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands [3] Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anne M M Oonk
- 1] Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, Nijmegen, The Netherlands [2] Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - María Domínguez-Ruiz
- 1] Servicio de Genética, Hospital Universitario Ramon y Cajal, IRYCIS, Madrid, Spain [2] Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Jos M T Draaisma
- Department of Pediatrics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marta Gandía
- 1] Servicio de Genética, Hospital Universitario Ramon y Cajal, IRYCIS, Madrid, Spain [2] Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Jaap Oostrik
- 1] Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, Nijmegen, The Netherlands [2] Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands [3] Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kornelia Neveling
- 1] Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands [2] Institute for Genetic and Metabolic Disease, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Henricus P M Kunst
- 1] Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, Nijmegen, The Netherlands [2] Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lies H Hoefsloot
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ignacio del Castillo
- Servicio de Genética, Hospital Universitario Ramon y Cajal, IRYCIS, Madrid, Spain
| | - Ronald J E Pennings
- 1] Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, Nijmegen, The Netherlands [2] Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hannie Kremer
- 1] Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, Nijmegen, The Netherlands [2] Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands [3] Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands [4] Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ronald J C Admiraal
- 1] Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, Nijmegen, The Netherlands [2] Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Margit Schraders
- 1] Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, Nijmegen, The Netherlands [2] Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands [3] Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
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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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Gao X, Zhu QY, Song YS, Wang GJ, Yuan YY, Xin F, Huang SS, Kang DY, Han MY, Guan LP, Zhang JG, Dai P. Novel compound heterozygous mutations in the MYO15A gene in autosomal recessive hearing loss identified by whole-exome sequencing. J Transl Med 2013; 11:284. [PMID: 24206587 PMCID: PMC3828584 DOI: 10.1186/1479-5876-11-284] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 11/06/2013] [Indexed: 11/25/2022] Open
Abstract
Background Inherited genetic defects play an important role in congenital hearing loss, contributing to about 60% of deafness occurring in infants. Hereditary nonsyndromic hearing loss is highly heterogeneous, and most patients with a presumed genetic etiology lack a specific molecular diagnosis. Methods By whole exome sequencing, we identified responsible gene of family 4794 with autosomal recessively nonsyndromic hearing loss (ARNSHL). We also used DNA from 56 Chinese familial patients with ARNSHL (autosomal recessive nonsyndromic hearing loss) and 108 ethnicity-matched negative samples to perform extended variants analysis. Results We identified MYO15A c.IVS25 + 3G > A and c.8375 T > C (p.V2792A) as the disease-causing mutations. Both mutations co-segregated with hearing loss in family 4794, but were absent in the 56 index patients and 108 ethnicity-matched controls. Conclusions Our results demonstrated that the hearing loss of family 4794 was caused by novel compound heterozygous mutations in MYO15A.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Pu Dai
- Department of Otorhinolaryngology, Head and Neck Surgery, PLA General Hospital, 28# Fuxing Road, Beijing 100853, P, R, China.
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41
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The promise of whole-exome sequencing in medical genetics. J Hum Genet 2013; 59:5-15. [DOI: 10.1038/jhg.2013.114] [Citation(s) in RCA: 312] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Revised: 09/29/2013] [Accepted: 10/11/2013] [Indexed: 12/14/2022]
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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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43
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Biallelic nonsense mutations in the otogelin-like gene (OTOGL) in a child affected by mild to moderate hearing impairment. Gene 2013; 527:537-40. [DOI: 10.1016/j.gene.2013.06.044] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 06/06/2013] [Accepted: 06/08/2013] [Indexed: 12/17/2022]
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44
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Handel AE, Disanto G, Ramagopalan SV. Next-generation sequencing in understanding complex neurological disease. Expert Rev Neurother 2013; 13:215-27. [PMID: 23368808 DOI: 10.1586/ern.12.165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Next-generation sequencing techniques have made vast quantities of data on human genomes and transcriptomes available to researchers. Huge progress has been made towards understanding the basis of many Mendelian neurological conditions, but progress has been considerably slower in complex neurological diseases (multiple sclerosis, migraine, Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and so on). The authors review current next-generation sequencing methodologies and present selected studies illustrating how these have been used to cast light on the genetic etiology of complex neurological diseases with specific focus on multiple sclerosis. The authors highlight particular pitfalls in next-generation sequencing experiments and speculate on both clinical and research applications of these sequencing platforms for complex neurological disorders in the future.
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Affiliation(s)
- Adam E Handel
- Department of Physiology, Anatomy and Genetics, University of Oxford, UK
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45
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The application of next-generation sequencing in the autozygosity mapping of human recessive diseases. Hum Genet 2013; 132:1197-211. [PMID: 23907654 DOI: 10.1007/s00439-013-1344-x] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 07/20/2013] [Indexed: 02/08/2023]
Abstract
Autozygosity, or the inheritance of two copies of an ancestral allele, has the potential to not only reveal phenotypes caused by biallelic mutations in autosomal recessive genes, but to also facilitate the mapping of such mutations by flagging the surrounding haplotypes as tractable runs of homozygosity (ROH), a process known as autozygosity mapping. Since SNPs replaced microsatellites as markers for the purpose of genomewide identification of ROH, autozygosity mapping of Mendelian genes has witnessed a significant acceleration. Historically, successful mapping traditionally required favorable family structure that permits the identification of an autozygous interval that is amenable to candidate gene selection and confirmation by Sanger sequencing. This requirement presented a major bottleneck that hindered the utilization of simplex cases and many multiplex families with autosomal recessive phenotypes. However, the advent of next-generation sequencing that enables massively parallel sequencing of DNA has largely bypassed this bottleneck and thus ushered in an era of unprecedented pace of Mendelian disease gene discovery. The ability to identify a single causal mutation among a massive number of variants that are uncovered by next-generation sequencing can be challenging, but applying autozygosity as a filter can greatly enhance the enrichment process and its throughput. This review will discuss the power of combining the best of both techniques in the mapping of recessive disease genes and offer some tips to troubleshoot potential limitations.
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Abstract
The development and function of the vertebrate nervous system depend on specific interactions between different cell types. Two examples of such interactions are synaptic transmission and myelination. LGI1-4 (leucine-rich glioma inactivated proteins) play important roles in these processes. They are secreted proteins consisting of an LRR (leucine-rich repeat) domain and a so-called epilepsy-associated or EPTP (epitempin) domain. Both domains are thought to function in protein–protein interactions. The first LGI gene to be identified, LGI1, was found at a chromosomal translocation breakpoint in a glioma cell line. It was subsequently found mutated in ADLTE (autosomal dominant lateral temporal (lobe) epilepsy) also referred to as ADPEAF (autosomal dominant partial epilepsy with auditory features). LGI1 protein appears to act at synapses and antibodies against LGI1 may cause the autoimmune disorder limbic encephalitis. A similar function in synaptic remodelling has been suggested for LGI2, which is mutated in canine Benign Familial Juvenile Epilepsy. LGI4 is required for proliferation of glia in the peripheral nervous system and binds to a neuronal receptor, ADAM22, to foster ensheathment and myelination of axons by Schwann cells. Thus, LGI proteins play crucial roles in nervous system development and function and their study is highly important, both to understand their biological functions and for their therapeutic potential. Here, we review our current knowledge about this important family of proteins, and the progress made towards understanding their functions.
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47
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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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48
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Abstract
The very large G protein coupled receptor (Vlgr1) is a member of adhesion receptors or large N-terminal family B-7 transmembrane helixes (LNB7TM) receptors within the seven trans-membrane receptor superfamily. Vlgr1 is the largest GPCR identified to date; its mRNA spans 19 kb and encodes 6,300 amino acids. Vlgr1 is a core component of ankle-link complex in inner ear hair cells. Knock-out and mutation mouse models show that loss of Vlgr1 function leads to abnormal stereociliary development and hearing loss, indicating crucial roles of Vlgr1 in hearing transduction or auditory system development. Over the past 10 or so years, human genetics data suggested that Vlgr1 mutations cause Usher syndromes and seizures. Although significant progresses have been made, the details of Vlgr1's function in hair cells, its signaling cascade, and the mechanisms underlying causative effects of Vlgr1 mutations in human diseases remain elusive and ask for further investigation.
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