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Mkaouar R, Riahi Z, Marrakchi J, Mezzi N, Romdhane L, Boujemaa M, Dallali H, Sayeb M, Lahbib S, Jaouadi H, Boudabbous H, Zekri L, Chargui M, Messaoud O, Elyounsi M, Kraoua I, Zaouak A, Turki I, Mokni M, Boucher S, Petit C, Giraudet F, Mbarek C, Besbes G, Halayem S, Zainine R, Turki H, Tounsi A, Bonnet C, Mrad R, Abdelhak S, Trabelsi M, Charfeddine C. Current phenotypic and genetic spectrum of syndromic deafness in Tunisia: paving the way for precision auditory health. Front Genet 2024; 15:1384094. [PMID: 38711914 PMCID: PMC11072975 DOI: 10.3389/fgene.2024.1384094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 03/15/2024] [Indexed: 05/08/2024] Open
Abstract
Hearing impairment (HI) is a prevalent neurosensory condition globally, impacting 5% of the population, with over 50% of congenital cases attributed to genetic etiologies. In Tunisia, HI underdiagnosis prevails, primarily due to limited access to comprehensive clinical tools, particularly for syndromic deafness (SD), characterized by clinical and genetic heterogeneity. This study aimed to uncover the SD spectrum through a 14-year investigation of a Tunisian cohort encompassing over 700 patients from four referral centers (2007-2021). Employing Sanger sequencing, Targeted Panel Gene Sequencing, and Whole Exome Sequencing, genetic analysis in 30 SD patients identified diagnoses such as Usher syndrome, Waardenburg syndrome, cranio-facial-hand-deafness syndrome, and H syndrome. This latter is a rare genodermatosis characterized by HI, hyperpigmentation, hypertrichosis, and systemic manifestations. A meta-analysis integrating our findings with existing data revealed that nearly 50% of Tunisian SD cases corresponded to rare inherited metabolic disorders. Distinguishing between non-syndromic and syndromic HI poses a challenge, where the age of onset and progression of features significantly impact accurate diagnoses. Despite advancements in local genetic characterization capabilities, certain ultra-rare forms of SD remain underdiagnosed. This research contributes critical insights to inform molecular diagnosis approaches for SD in Tunisia and the broader North-African region, thereby facilitating informed decision-making in clinical practice.
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Affiliation(s)
- Rahma Mkaouar
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Zied Riahi
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Jihene Marrakchi
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Otorhinolaryngology, District Hospital of Menzel Bourguiba, Bizerte, Tunisia
| | - Nessrine Mezzi
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Biology, Faculty of Sciences of Bizerte, Université Tunis Carthage, Tunis, Tunisia
| | - Lilia Romdhane
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Biology, Faculty of Sciences of Bizerte, Université Tunis Carthage, Tunis, Tunisia
| | - Maroua Boujemaa
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hamza Dallali
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
- Genetic Typing Service, Institut Pasteur of Tunis, Tunis, Tunisia
| | - Marwa Sayeb
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Saida Lahbib
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hager Jaouadi
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
- Marseille Medical Genetics (MMG) U1251, Aix Marseille Université, INSERM, Marseille, France
| | - Hela Boudabbous
- Department of Pediatrics, La Rabta Hospital, Tunis, Tunisia
- Laboratory of Hereditary Diseases of the Metabolism Investigation and Patients Management, Faculty of Medicine in Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Epidemiology and Public Health, Directorate General of Military Health, Faculty of Medicine in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Lotfi Zekri
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
- ICHARA Association (International Research Institute on Sign Language), Tunis, Tunisia
| | - Mariem Chargui
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Olfa Messaoud
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Meriem Elyounsi
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital in Tunis, Tunis, Tunisia
- LR99ES10 Laboratory of Human Genetics, Faculty of Medicine in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Ichraf Kraoua
- Child and Adolescent Neurology Department of Neurology, National Institute of Neurology, Tunis, Tunisia
- LR18SP04 Department of Child Neurology, National Institute Mongi Ben Hmida of Neurology in Tunis. University of Tunis El Manar, Tunis, Tunisia
| | - Anissa Zaouak
- Department of Dermatology, Habib Thameur Hospital, Research Unit Genodermatoses and Cancers LR12SP03, Tunis, Tunisia
| | - Ilhem Turki
- Child and Adolescent Neurology Department of Neurology, National Institute of Neurology, Tunis, Tunisia
- LR18SP04 Department of Child Neurology, National Institute Mongi Ben Hmida of Neurology in Tunis. University of Tunis El Manar, Tunis, Tunisia
| | - Mourad Mokni
- Service de dermatologie, Hôpital La Rabta, Unité de recherche UR 12SP07, Hôpital La Rabta, Tunis, Tunisia
| | - Sophie Boucher
- Service d’ORL et chirurgie cervico-faciale, CHU d’Angers, Angers, France
- Equipe Mitolab, Institut Mitovasc, CNRS UMR6015, UMR Inserm 1083, Université d’Angers, Angers, France
| | - Christine Petit
- Institut Pasteur, Université Paris Cité, Inserm UA06, Institut de l’Audition, Paris, France
- Collège de France, Paris, France
| | - Fabrice Giraudet
- Unité Mixte de Recherche (UMR) 1107, INSERM, Clermont-Ferrand, France
- Centre Auditif SoluSons, Clermont-Ferrand, France
| | - Chiraz Mbarek
- ENT Department, Habib Thameur Hospital, Tunis, Tunisia
| | - Ghazi Besbes
- Department of Otorhinolaryngology and Maxillofacial Surgery - La Rabta Hospital in Tunis, Tunis, Tunisia
| | - Soumeyya Halayem
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
- Service de pédopsychiatrie, Hôpital Razi, Faculté de Médecine de Tunis, Université Tunis el Manar, Tunis, Tunisia
| | - Rim Zainine
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Otorhinolaryngology and Maxillofacial Surgery - La Rabta Hospital in Tunis, Tunis, Tunisia
| | - Hamida Turki
- Dermatology Department Hedi Chaker University Hospital, Sfax University Sfax Tunisia, Tunis, Tunisia
| | | | - Crystel Bonnet
- Institut Pasteur, Université Paris Cité, Inserm UA06, Institut de l’Audition, Paris, France
| | - Ridha Mrad
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital in Tunis, Tunis, Tunisia
- LR99ES10 Laboratory of Human Genetics, Faculty of Medicine in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Mediha Trabelsi
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital in Tunis, Tunis, Tunisia
- LR99ES10 Laboratory of Human Genetics, Faculty of Medicine in Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Cherine Charfeddine
- Laboratory of Biomedical Genomics and Oncogenetics LR16IPT05, Pasteur Institute in Tunis, University of Tunis El Manar, Tunis, Tunisia
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Shadab M, Abbasi AA, Ejaz A, Ben-Mahmoud A, Gupta V, Kim HG, Vona B. Autosomal recessive non-syndromic hearing loss genes in Pakistan during the previous three decades. J Cell Mol Med 2024; 28:e18119. [PMID: 38534090 DOI: 10.1111/jcmm.18119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 11/29/2023] [Accepted: 01/02/2024] [Indexed: 03/28/2024] Open
Abstract
Hearing loss is a clinically and genetically heterogeneous disorder, with over 148 genes and 170 loci associated with its pathogenesis. The spectrum and frequency of causal variants vary across different genetic ancestries and are more prevalent in populations that practice consanguineous marriages. Pakistan has a rich history of autosomal recessive gene discovery related to non-syndromic hearing loss. Since the first linkage analysis with a Pakistani family that led to the mapping of the DFNB1 locus on chromosome 13, 51 genes associated with this disorder have been identified in this population. Among these, 13 of the most prevalent genes, namely CDH23, CIB2, CLDN14, GJB2, HGF, MARVELD2, MYO7A, MYO15A, MSRB3, OTOF, SLC26A4, TMC1 and TMPRSS3, account for more than half of all cases of profound hearing loss, while the prevalence of other genes is less than 2% individually. In this review, we discuss the most common autosomal recessive non-syndromic hearing loss genes in Pakistani individuals as well as the genetic mapping and sequencing approaches used to discover them. Furthermore, we identified enriched gene ontology terms and common pathways involved in these 51 autosomal recessive non-syndromic hearing loss genes to gain a better understanding of the underlying mechanisms. Establishing a molecular understanding of the disorder may aid in reducing its future prevalence by enabling timely diagnostics and genetic counselling, leading to more effective clinical management and treatments of hearing loss.
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Affiliation(s)
- Madiha Shadab
- Department of Zoology, Mirpur University of Science and Technology, Mirpur, Pakistan
| | - Ansar Ahmed Abbasi
- Department of Zoology, Mirpur University of Science and Technology, Mirpur, Pakistan
| | - Ahsan Ejaz
- Department of Physics, University of Kotli Azad Jammu and Kashmir, Kotli, Pakistan
- School of Nuclear Science and Technology, Lanzhou University, Lanzhou, China
| | - Afif Ben-Mahmoud
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Vijay Gupta
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
- College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- Institute for Auditory Neuroscience and Inner Ear Lab, University Medical Center Göttingen, Göttingen, Germany
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Salame M, Bonnet C, Moctar ECM, Brahim SM, Dedy A, Vetah LA, Veten F, Hamed CT, Petit C, Houmeida A. Identification a novel pathogenic LRTOMT mutation in Mauritanian families with nonsyndromic deafness. Eur Arch Otorhinolaryngol 2023; 280:4057-4063. [PMID: 36928321 DOI: 10.1007/s00405-023-07907-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023]
Abstract
PURPOSE Although recessive mutations in GJB2 are the common genetic etiology of sensorineural hearing impairment (SNHI), variants in LRTOMT gene were also identified, mostly in Middle East and North African populations. METHODS Using Sanger sequencing we screened the exon 7 of LRTOMT in a cohort of 128 unrelated Mauritanian children with congenital deafness. RESULTS Only one biallelic missense mutation, predicted as pathogenic (c.179 T > C;p.Leu60Pro) was found at homozygous state in four families. This variant, not reported before, showed a deleterious effect by SIFT (score: 0.01) and a disease-causing effect by Mutation Taster (prob: 1). Exploration of the encoded protein 3D structure revealed a disruption from an organized α helix (in the normal protein structure) into a random conformation. Early fitting of a cochlear implant seemed to improve the audition ability of the mutation carrier. CONCLUSION Further screening using a panel of deafness genes may expose other variants underlying hearing impairment in our population.
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Affiliation(s)
- Malak Salame
- Unité de Recherche sur les Biomarqueurs dans la Population Mauritanienne, UNA-FST, Nouakchott, Mauritania
| | - Crystel Bonnet
- Institut de l'AuditionInstitut Pasteur, Inserm, Paris, France
| | - Ely Cheikh Mohamed Moctar
- Division of Otolaryngology, Department of Surgery, University of California, San Diego, 9500 Gilman Drive, Mail Code 0666, La Jolla, CA, 92093, USA
| | - Selma Mohamed Brahim
- Unité de Recherche sur les Biomarqueurs dans la Population Mauritanienne, UNA-FST, Nouakchott, Mauritania
- Centre National d'Oncologie (CNO), Unité de Recherche et d'Enseignement, Nouakchott, Mauritania
| | - Abdallahi Dedy
- Centre Hospitalier National de Nouakchott (CHN), Nouakchott, Mauritania
| | | | - Fatimetou Veten
- Unité de Recherche sur les Biomarqueurs dans la Population Mauritanienne, UNA-FST, Nouakchott, Mauritania
| | | | - Christine Petit
- Institut de l'AuditionInstitut Pasteur, Inserm, Paris, France
- Collège de France, Paris, France
| | - Ahmed Houmeida
- Unité de Recherche sur les Biomarqueurs dans la Population Mauritanienne, UNA-FST, Nouakchott, Mauritania.
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Jung J, Müller U. Mechanoelectrical transduction-related genetic forms of hearing loss. CURRENT OPINION IN PHYSIOLOGY 2023; 32:100632. [PMID: 36936795 PMCID: PMC10022594 DOI: 10.1016/j.cophys.2023.100632] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Hair cells of the mammalian cochlea are specialized mechanosensory cells that convert mechanical stimuli into electrical signals to initiate the neuronal responses that lead to the perception of sound. The mechanoelectrical transduction (MET) machinery of cochlear hair cells is a multimeric protein complex that consists of the pore forming subunits of the MET channel and several essential accessory subunits that are crucial to regulate channel function and render the channel mechanically sensitive. Mutations have been discovered in the genes that encode all known components of the MET machinery. These mutations cause hearing loss with or without vestibular dysfunction. Some mutations also affect other tissues such as the retina. In this brief review, we will summarize gene mutations that affect the MET machinery of hair cells and how the study of the affected genes has illuminated our understanding of the physiological role of the encoded proteins.
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Affiliation(s)
- Jinsei Jung
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Otorhinolaryngology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Ulrich Müller
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Aliazami F, Gilani S, Farhud D, Naraghi M, Afshari M, Eslami M. Epidemiology, etiology, genetic variants in non- syndromic hearing loss in Iran: A systematic review and meta-analysis. Int J Pediatr Otorhinolaryngol 2023; 168:111512. [PMID: 37086676 DOI: 10.1016/j.ijporl.2023.111512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 02/27/2023] [Accepted: 03/11/2023] [Indexed: 04/24/2023]
Abstract
OBJECTIVES Hearing loss is one of the most common heterogeneous complicated disorders worldwide. We previously analyzed the results of published data on non-syndromic hearing loss in the Iranian population systematically. A broad range of genes is a challenge for molecular screening and clinical diagnosis in our populations on the ground of distinct genetics. The aim of this study was to analyze the role and frequency of the variants accountable for non-syndromic hearing loss (NSHL) in the Iranian population. These were identified with different methods including whole exome sequencing (WES), next-generation sequencing (NGS), targeted genomic enrichment and massively parallel sequencing (TGE + MPS), autozygosity mapping, STR markers, linkage analysis, and direct sequencing. This is the comprehensively study focusing on classifying 13 common NSHL genes according to their frequencies. Previous studies have not studied different regions and the Iranian population, and this is the definitive study on the topic. METHODS We searched Scopus, PubMed, Science Direct databases, and Google Scholar. After a systematic review of the evidence 95 studies were considered then 31 studies were eligible for meta-analysis. In total, 6995 families, 358 variants, and 117 novel variants were included. Statistical analyses were conducted using Stata SE version 11 software. The inverse variance method enjoyed combining data. Heterogeneity of the preliminary results was assessed using Q (Cochrane test), and I square index. Random effects or fixed models were applied to combine the results, relying on the degree of heterogeneity. Point and pooled prevalence of variants acting on different regions were illustrated by forest plots. RESULTS The total prevalence of at least one variant of GJB2 and SLC26A genes was estimated at 26% and 5%, respectively. Variant c.35delG accounted for 18% of the GJB2 variants while 1% of these variants were novel ones. The next most common variants in the GJB2 gene were c.109G>A at 3.5% and c.-23+1G>A at 2.3%. Moreover, the prevalence of GJB2 gene variants varied on average 0.002% from one region to another in Iran (p=0.849). Our meta-analysis also showed that the frequency of at least one variant of MYO15A varied between 1.2% and 12.5%. Corresponding prevalences for the other variants were as follows: ILDR1 (3.5%-3.7%), CDH23 (2%-10%), PJVK (1.4%-33%), TECTA (1.3%-6.7%), MYO6 (2%-4.8%), TMC1 (1.8%-2%), MYO7A (0.7%-5%), MARVELD2 (0.7-5%), OTOF (0.7%-4%), LRTOMT (0.7%-2.5%). Finally, we did not find any relationship between geographic area and the presence of these variants. CONCLUSION GJB2 gene variants were the most common cause of NSHL in Iran. Understanding the prevalence of NSHL gene frequency in Iran may be the foundation for future studies in an Iranian population which may lead to future NSHL therapy.
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Affiliation(s)
- Farnoush Aliazami
- Department of Genetics, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Applied Biotechnology Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Sapideh Gilani
- Department of Surgery, Division of Otolaryngology, University of California, San Diego, 200 West Arbor Drive, MC 8654, San Diego, CA, 92103, United States.
| | - Dariush Farhud
- School of Public Health, Tehran University of Medical Sciences, Tehran, Iran; Department of Basic Sciences, Iranian Academy of Medical Sciences, Valiasr Sq., 22 Keshavarz Blvd, Tehran, 14, Iran.
| | - Mohsen Naraghi
- Department of Otorhinolaryngology-Head and Neck Surgery, TUMS School of Medicine, Rhinology Research Society, Orphans World Wide, 4411 Sunbeam Rd., Jacksonville, FL, 32257, United States.
| | - Mahdi Afshari
- Department of Community Medicine, School of Medicine, Zabol University of Medical Sciences, Rajaee Street, Zabol, Iran.
| | - Maryam Eslami
- Department of Genetics, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Applied Biotechnology Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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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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Kim Y, Han JH, Yoo HS, Choi BY. Molecular aetiology of ski-slope hearing loss and audiological course of cochlear implantees. Eur Arch Otorhinolaryngol 2022; 279:4871-4882. [PMID: 35212774 DOI: 10.1007/s00405-022-07317-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/10/2022] [Indexed: 11/28/2022]
Abstract
PURPOSE A challenge for patients with ski-slope hearing loss is that hearing aids do not adequately amplify the mid-to-high frequencies necessary for speech perception and conversely, cochlear implant (CI) may damage low-frequency hearing. We aimed to describe the clinical profile of patients with ski-slope hearing loss, with a special focus on aetiology of such hearing loss and audiological course of low-frequency hearing after CI. METHODS We recruited hearing-impaired patients who visited a tertiary referral centre and met the criteria for ski-slope hearing loss patients from 2015 to 2021. Genetic testing was performed in all ski-slope hearing loss patients unless refused. Baseline audiograms of patients who continued to use hearing aids or who finally underwent CIs were reviewed. As for CI patients, outcome and hearing preservation rate were rigorously analysed. RESULTS Of 46 recruited patients with ski-slope hearing loss, 45 agreed to undergo genetic testing and causative variants were identified in 17 (37.8%) patients. The TMC1, MYO7A, and TMPRSS3 variants were the most common, while LRTOMT was newly identified as a causative gene. Twenty-five patients eventually received CI, while 13 continued to wear the hearing aid and 8 patients did not ever try hearing aids. CI in ski-slope hearing loss led to immediate and sufficient improvement of sentence recognition by as early as 3 months, however, the duration of hearing loss was inversely correlated with the sentence recognition score. The average hearing preservation rate (using the HEARRING classification) after CI was 53.0% (SD 30.0) and 45.6% (SD 31.1) at 1 year. Seventy-nine percent of implantees maintained functional low-frequency hearing (better than 85 dB at 250 and 500 Hz) eligible for electric-acoustic stimulation (EAS). A trend was found that patients with hair cell stereocilia-associated genetic variants may have a slightly better preservation, albeit with no statistical significance. CONCLUSION Detection rate of a molecular genetic aetiology of ski-slope hearing loss appears to be lower than other type of hearing loss reported in the literature. Especially with short hearing loss duration, CI in ski-slope hearing loss leads to immediate and sufficient speech improvement, while preserving functional low-frequency hearing eligible for EAS as many as in 79%. A certain genetic aetiology might be associated with a trend towards better low-frequency hearing preservation.
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Affiliation(s)
- Yehree Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, 300 Gumi-dong, Bundang-gu, Seongnam, 463-707, Republic of Korea
| | - Jin Hee Han
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, 300 Gumi-dong, Bundang-gu, Seongnam, 463-707, Republic of Korea
| | - Hyo Soon Yoo
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, 300 Gumi-dong, Bundang-gu, Seongnam, 463-707, Republic of Korea
| | - Byung Yoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, 300 Gumi-dong, Bundang-gu, Seongnam, 463-707, Republic of Korea.
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Wang Y, Ma Y, Qin Y, Zeng Z, Zhong Z, Qi Y, Liu Y. Novel Mutations in LRTOMT Associated with Congenital Profound Sensorineural Hearing Loss in a Chinese Patient. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421110144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Mosrati MA, Fadhlaoui-Zid K, Benammar-Elgaaied A, Gibriel AA, Ben Said M, Masmoudi S. Deep analysis of the LRTOMTc.242G>A variant in non-syndromic hearing loss North African patients and the Berber population: Implications for genetic diagnosis and genealogical studies. Mol Genet Genomic Med 2021; 9:e1810. [PMID: 34514748 PMCID: PMC8580077 DOI: 10.1002/mgg3.1810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/15/2021] [Accepted: 08/24/2021] [Indexed: 11/13/2022] Open
Abstract
Autosomal recessive non‐syndromic hearing loss (ARNSHL) is the most common inherited sensory impairment. It is particularly frequent in North African populations who have a high rate of consanguineous marriage. The c.242G>A homozygous variant in LRTOMT gene was previously established as pathogenic and is associated with NSHL in both humans and mice. The aim of this study is to determine the carrier frequency for the LRTOMT c.242G>A variant and also to estimate its age in addition to evaluating its diagnostic potential as a deafness biomarker among various populations and ethnicities in Northern African countries. A total of 179 Tunisian and 34 Libyan unrelated deafness patients were screened for this variant. The homozygous c.242G>A variant was found in 5.02% and 2.94% in Tunisian and Libyan families, respectively. Subsequent screening for this variant in 263 healthy controls of various ethnicities (136 Tunisian Berbers, 32 Andalusian and 95 Tunisian from undefined ethnic origin) revealed higher frequency for the heterozygous state among Tunisians of Berber origin only (19.11%). Genotyping 7 microsatellite markers nearby the variant location in ARNSHL patients who had the homozygous variant revealed the same haplotype suggesting a common founder origin for this variant. The age of this variant was estimated to be between 2025 and 3425 years (this corresponds to 3400 years when the variant rate was set at 10−3 or 2600 years when the variant rate is set at 10−2), spreading along with the Berber population who migrated to North Africa. In conclusion, the LRTOMT c.242G>A homozygous variant could be used as a useful deafness biomarker for North African ARNSHL patients meanwhile the heterozygous variant could be utilized in genealogical studies for tracing those of the Berber ethnic group.
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Affiliation(s)
- Mohamed Ali Mosrati
- Laboratoire de Procédés de Criblages Moléculaire et Cellulaire, Centre de Biotechnologie de Sfax, Université de Sfax, Sfax, Tunisie
| | - Karima Fadhlaoui-Zid
- Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, Tunisia.,Department of Biology, College of Science, Taibah University, Al Madinah Al Munawarah, Saudi Arabia.,Higher Institute of Biotechnology of Beja, University of Jendouba, Beja, Tunisia
| | - Amel Benammar-Elgaaied
- Laboratory of Genetics, Immunology, and Human Pathologies, Faculty of Science of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Abdullah Ahmed Gibriel
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt
| | - Mariem Ben Said
- Laboratoire de Procédés de Criblages Moléculaire et Cellulaire, Centre de Biotechnologie de Sfax, Université de Sfax, Sfax, Tunisie
| | - Saber Masmoudi
- Laboratoire de Procédés de Criblages Moléculaire et Cellulaire, Centre de Biotechnologie de Sfax, Université de Sfax, Sfax, Tunisie
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10
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Souissi A, Gibriel AA, Masmoudi S. Genetics and meta-analysis of recessive non-syndromic hearing impairment and Usher syndrome in Maghreb population: lessons from the past, contemporary actualities and future challenges. Hum Genet 2021; 141:583-593. [PMID: 34268600 DOI: 10.1007/s00439-021-02314-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/08/2021] [Indexed: 11/29/2022]
Abstract
Hereditary hearing impairment (HI) is a heterogeneous condition with over 130 genes associated with genetic non-syndromic HI (NSHI) and Usher syndrome (USH). Approximately 80% of hereditary NSHI cases have autosomal recessive (AR) mode of inheritance. The high rate of consanguinity and endogamy in the Maghreb countries, including Tunisia, Algeria and Morocco, represents a major contributing factor to the development of ARHI. Since the 90s, those populations, with their particular large familiar structure, represented an effective key towards the discovery of the first HI loci and genes. In this study, we performed a deep literature database search to analyze the mutational spectrum and the distribution of pathogenic variants responsible of USH and the NSHI among those populations. To date, 124 pathogenic variants were identified in 32 genes of which over 70% represent population-specific variants. The particular variants' distribution is related to the high rate of consanguinity as well as the multiple shared features such as demographic history of migrations and social behavior that promoted the spreading of several founder mutations within those countries. This is the first study to report lessons from the past and current actualities of HI within the three Maghreb countries. However, despite the great impact placed by such population for the HI genetic studies, only a few next-generation sequencing platforms have so far been implemented with those countries. We, therefore, believe that those countries should be supported to implement this technology that would definitely be of great value in the discovery of additional novel HI genes/variants.
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Affiliation(s)
- Amal Souissi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour road Km 6, BP "1177", 3018, Sfax, Tunisia
| | - Abdullah A Gibriel
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour road Km 6, BP "1177", 3018, Sfax, Tunisia.
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11
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Liu S, Wang S, Zou L, Xiong W. Mechanisms in cochlear hair cell mechano-electrical transduction for acquisition of sound frequency and intensity. Cell Mol Life Sci 2021; 78:5083-5094. [PMID: 33871677 PMCID: PMC11072359 DOI: 10.1007/s00018-021-03840-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 03/30/2021] [Accepted: 04/09/2021] [Indexed: 10/21/2022]
Abstract
Sound signals are acquired and digitized in the cochlea by the hair cells that further transmit the coded information to the central auditory pathways. Any defect in hair cell function may induce problems in the auditory system and hearing-based brain function. In the past 2 decades, our understanding of auditory transduction has been substantially deepened because of advances in molecular, structural, and functional studies. Results from these experiments can be perfectly embedded in the previously established profile from anatomical, histological, genetic, and biophysical research. This review aims to summarize the progress on the molecular and cellular mechanisms of the mechano-electrical transduction (MET) channel in the cochlear hair cells, which is involved in the acquisition of sound frequency and intensity-the two major parameters of an acoustic cue. We also discuss recent studies on TMC1, the molecule likely to form the MET channel pore.
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Affiliation(s)
- Shuang Liu
- School of Life Sciences, Tsinghua University, 1 Qinghuayuan, Beijing, 100084, China
- IDG/McGovern Institute for Brain Research at Tsinghua University, Tsinghua University, 1 Qinghuayuan, Beijing, 100084, China
| | - Shufeng Wang
- School of Life Sciences, Tsinghua University, 1 Qinghuayuan, Beijing, 100084, China
- IDG/McGovern Institute for Brain Research at Tsinghua University, Tsinghua University, 1 Qinghuayuan, Beijing, 100084, China
| | - Linzhi Zou
- School of Life Sciences, Tsinghua University, 1 Qinghuayuan, Beijing, 100084, China
- IDG/McGovern Institute for Brain Research at Tsinghua University, Tsinghua University, 1 Qinghuayuan, Beijing, 100084, China
| | - Wei Xiong
- School of Life Sciences, Tsinghua University, 1 Qinghuayuan, Beijing, 100084, China.
- IDG/McGovern Institute for Brain Research at Tsinghua University, Tsinghua University, 1 Qinghuayuan, Beijing, 100084, China.
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12
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Sarmadi A, Nasrniya S, Soleimani Farsani M, Narrei S, Nouri Z, Sepehrnejad M, Nilforoush MH, Abtahi H, Tabatabaiefar MA. A novel pathogenic variant in the LRTOMT gene causes autosomal recessive non-syndromic hearing loss in an Iranian family. BMC MEDICAL GENETICS 2020; 21:127. [PMID: 32517708 PMCID: PMC7285524 DOI: 10.1186/s12881-020-01061-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 06/02/2020] [Indexed: 02/07/2023]
Abstract
Background Hearing loss (HL) is the most common sensorineural disorder with high phenotypic and genotypic heterogeneity, which negatively affects life quality. Autosomal recessive non-syndromic hearing loss (ARNSHL) constitutes a major share of HL cases. In the present study, Whole exome sequencing (WES) was applied to investigate the underlying etiology of HL in an Iranian patient with ARNSHL. Methods A proband from an Iranian consanguineous family was examined via WES, following GJB2 sequencing. WES was utilized to find possible genetic etiology of the disease. Various Bioinformatics tools were used to assess the pathogenicity of the variants. Co-segregation analysis of the candidate variant was carried out. Interpretation of variants was performed according to the American College of Medical Genetics and Genomics (ACMG) guidelines. Results WES results showed a novel frameshift (16 bp deletion) variant (p.Ala170Alafs*20) in the LRTOMT gene. This variant, which resides in exon 6, was found to be co-segregating in the family. It fulfils the criteria set by the ACMG guidelines of being pathogenic. Conclusion Here, we report successful application of WES to identify the molecular pathogenesis of ARNSHL, which is a genetically heterogeneous disorder, in a patient with ARNSHL.
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Affiliation(s)
- Akram Sarmadi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.,Genetics Department, Erythron Pathobiology and Genetics lab, Isfahan, Iran
| | - Samane Nasrniya
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Maryam Soleimani Farsani
- Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran
| | - Sina Narrei
- Genetics Department, Erythron Pathobiology and Genetics lab, Isfahan, Iran
| | - Zahra Nouri
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahsa Sepehrnejad
- Department of Otolaryngology, Al-Zahra Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Hamidreza Abtahi
- Department of Otolaryngology, Al-Zahra Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Amin Tabatabaiefar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran. .,Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran. .,GenTArget Corp (GTAC), Deputy of Research and Technology, Isfahan University of Medical Sciences, Isfahan, Iran.
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13
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Small fish, big prospects: using zebrafish to unravel the mechanisms of hereditary hearing loss. Hear Res 2020; 397:107906. [PMID: 32063424 DOI: 10.1016/j.heares.2020.107906] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [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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14
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Noman M, Ishaq R, Bukhari SA, Ahmed ZM, Riazuddin S. Delineation of Homozygous Variants Associated with Prelingual Sensorineural Hearing Loss in Pakistani Families. Genes (Basel) 2019; 10:genes10121031. [PMID: 31835641 PMCID: PMC6947215 DOI: 10.3390/genes10121031] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 11/26/2019] [Accepted: 12/03/2019] [Indexed: 12/30/2022] Open
Abstract
Hearing loss is a genetically heterogeneous disorder affecting approximately 360 million people worldwide and is among the most common sensorineural disorders. Here, we report a genetic analysis of seven large consanguineous families segregating prelingual sensorineural hearing loss. Whole-exome sequencing (WES) revealed seven different pathogenic variants segregating with hearing loss in these families, three novel variants (c.1204G>A, c.322G>T, and c.5587C>T) in TMPRSS3, ESRRB, and OTOF, and four previously reported variants (c.208C>T, c.6371G>A, c.226G>A, and c.494C>T) in LRTOMT, MYO15A, KCNE1, and LHFPL5, respectively. All identified variants had very low frequencies in the control databases and were predicted to have pathogenic effects on the encoded proteins. In addition to being familial, we also found intersibship locus heterogeneity in the evaluated families. The known pathogenic c.226C>T variant identified in KCNE1 only segregates with the hearing loss phenotype in a subset of affected members of the family GCNF21. This study further highlights the challenges of identifying disease-causing variants for highly heterogeneous disorders and reports the identification of three novel and four previously reported variants in seven known deafness genes.
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Affiliation(s)
- Muhammad Noman
- Department of Biochemistry, Government College University, Faisalabad 38000, Pakistan
| | - Rafaqat Ishaq
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- University Institute of Biochemistry & Biotechnology, PMAS-Arid Agriculture University, Rawalpindi 46000, Pakistan
| | - Shazia A. Bukhari
- Department of Biochemistry, Government College University, Faisalabad 38000, Pakistan
| | - Zubair M. Ahmed
- Department of Biochemistry, Government College University, Faisalabad 38000, Pakistan
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Correspondence: (Z.M.A); (S.R.)
| | - Saima Riazuddin
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Correspondence: (Z.M.A); (S.R.)
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15
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Corey DP, Akyuz N, Holt JR. Function and Dysfunction of TMC Channels in Inner Ear Hair Cells. Cold Spring Harb Perspect Med 2019; 9:cshperspect.a033506. [PMID: 30291150 DOI: 10.1101/cshperspect.a033506] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The TMC1 channel was identified as a protein essential for hearing in mouse and human, and recognized as one of a family of eight such proteins in mammals. The TMC family is part of a superfamily of seven branches, which includes the TMEM16s. Vertebrate hair cells express both TMC1 and TMC2. They are located at the tips of stereocilia and are required for hair cell mechanotransduction. TMC1 assembles as a dimer and its similarity to the TMEM16s has enabled a predicted tertiary structure with an ion conduction pore in each subunit of the dimer. Cysteine mutagenesis of the pore supports the role of TMC1 and TMC2 as the core channel proteins of a larger mechanotransduction complex that includes PCDH15 and LHFPL5, and perhaps TMIE, CIB2 and others.
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Affiliation(s)
- David P Corey
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts 02115
| | - Nurunisa Akyuz
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts 02115
| | - Jeffrey R Holt
- Departments of Otolaryngology and Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts 02115
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16
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Cunningham CL, Müller U. Molecular Structure of the Hair Cell Mechanoelectrical Transduction Complex. Cold Spring Harb Perspect Med 2019; 9:cshperspect.a033167. [PMID: 30082452 DOI: 10.1101/cshperspect.a033167] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cochlear hair cells employ mechanically gated ion channels located in stereocilia that open in response to sound wave-induced motion of the basilar membrane, converting mechanical stimulation to graded changes in hair cell membrane potential. Membrane potential changes in hair cells cause neurotransmitter release from hair cells that initiate electrical signals in the nerve terminals of afferent fibers from spiral ganglion neurons. These signals are then propagated within the central nervous system (CNS) to mediate the sensation of hearing. Recent studies show that the mechanoelectrical transduction (MET) machinery of hair cells is formed by an ensemble of proteins. Candidate components forming the MET channel have been identified, but none alone fulfills all criteria necessary to define them as pore-forming subunits of the MET channel. We will review here recent findings on the identification and function of proteins that are components of the MET machinery in hair cells and consider remaining open questions.
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Affiliation(s)
- Christopher L Cunningham
- The Solomon Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland 21205
| | - Ulrich Müller
- The Solomon Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland 21205
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17
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Gibriel AA, Abou-Elew MH, Masmoudi S. Analysis of p.Gly12Valfs*2, p.Trp24* and p.Trp77Arg mutations in GJB2 and p.Arg81Gln variant in LRTOMT among non syndromic hearing loss Egyptian patients: implications for genetic diagnosis. Mol Biol Rep 2019; 46:2139-2145. [PMID: 30730013 DOI: 10.1007/s11033-019-04667-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/30/2019] [Indexed: 11/28/2022]
Abstract
Hearing loss (HL) is a global sensory disorder that affects children and deprives them from their rights to enjoy standard social and educational levels. Although hundreds of genetic mutations across several genes have been linked to HL, very limited studies are available on Egyptian population which has high rate of consanguinity and HL. The frequency of the p.Gly12Valfs*2, p.Trp24* and p.Trp77Arg mutations in GJB2 along with the p.Arg81Gln variant in LRTOMT gene was investigated in Egyptian patients. 103 non-syndromic HL (NSHL) Egyptian patients and 100 control subjects were recruited in this study. PCR-RFLP and Direct sequencing were performed to screen and confirm presence/absence of those mutations in Egyptian population. The p.Gly12Valfs*2 mutation was found in eight patients (7.8%) (six homozygous and two heterozygous) with an allele frequency of 6.8%. The p.Trp24* and p.Trp77Arg were absent in both HL patients and controls. Another one patient had the heterozygous variant for p.Arg81Gln in LRTOMT gene. This study reports, for the first time, the presence of a heterozygous change for the p.Arg81Gln in LRTOMT gene in one Egyptian patient. The p.Gly12Valfs*2 mutation, but not the p.Trp24* nor the p.Trp77Arg, in GJB2 is the most frequent variant among Egyptian patients and would therefore be recommended for genetic counseling and diagnosis.
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Affiliation(s)
- Abdullah A Gibriel
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, The British University in Egypt (BUE), P.O. Box 259, 11728, Cairo, Egypt.
| | - Maha H Abou-Elew
- Otorhinolaryngology Department, Audio-Vestibular Unit, Faculty of Medicine, Kasr Al-Aini El-Manial University Hospital, Cairo University, Giza, Egypt
| | - Saber Masmoudi
- Laboboratoire Procédés de Criblage Moléculaire et Cellulaire, Centre de Biotechnologie de Sfax, Université de Sfax, Sfax, Tunisia
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18
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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: 20] [Impact Index Per Article: 3.3] [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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19
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Li Y, Liu H, Giffen KP, Chen L, Beisel KW, He DZZ. Transcriptomes of cochlear inner and outer hair cells from adult mice. Sci Data 2018; 5:180199. [PMID: 30277483 PMCID: PMC6167952 DOI: 10.1038/sdata.2018.199] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/02/2018] [Indexed: 01/09/2023] Open
Abstract
Inner hair cells (IHCs) and outer hair cells (OHCs) are the two anatomically and functionally distinct types of mechanosensitive receptor cells in the mammalian cochlea. The molecular mechanisms defining their morphological and functional specializations are largely unclear. As a first step to uncover the underlying mechanisms, we examined the transcriptomes of IHCs and OHCs isolated from adult CBA/J mouse cochleae. One thousand IHCs and OHCs were separately collected using the suction pipette technique. RNA sequencing of IHCs and OHCs was performed and their transcriptomes were analyzed. The results were validated by comparing some IHC and OHC preferentially expressed genes between present study and published microarray-based data as well as by real-time qPCR. Antibody-based immunocytochemistry was used to validate preferential expression of SLC7A14 and DNM3 in IHCs and OHCs. These data are expected to serve as a highly valuable resource for unraveling the molecular mechanisms underlying different biological properties of IHCs and OHCs as well as to provide a road map for future characterization of genes expressed in IHCs and OHCs.
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Affiliation(s)
- Yi Li
- Department of Otorhinolaryngology, Beijing Tongren Hospital, Beijing Capital Medical University, Beijing 100730, China
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska 68170, USA
| | - Huizhan Liu
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska 68170, USA
| | - Kimberlee P. Giffen
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska 68170, USA
| | - Lei Chen
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska 68170, USA
- Chongqing Academy of Animal Science, Chongqing 402460, China
| | - Kirk W. Beisel
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska 68170, USA
| | - David Z. Z. He
- Department of Biomedical Sciences, Creighton University School of Medicine, Omaha, Nebraska 68170, USA
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20
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Elloumi-Zghal H, Chaabouni Bouhamed H. Genetics and genomic medicine in Tunisia. Mol Genet Genomic Med 2018; 6:134-159. [PMID: 29663716 PMCID: PMC5902400 DOI: 10.1002/mgg3.392] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 03/07/2018] [Indexed: 01/19/2023] Open
Abstract
Genetics and genomic medicine in Tunisia.
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21
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DiStefano MT, Hemphill SE, Cushman BJ, Bowser MJ, Hynes E, Grant AR, Siegert RK, Oza AM, Gonzalez MA, Amr SS, Rehm HL, Abou Tayoun AN. Curating Clinically Relevant Transcripts for the Interpretation of Sequence Variants. J Mol Diagn 2018; 20:789-801. [PMID: 30096381 DOI: 10.1016/j.jmoldx.2018.06.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 05/20/2018] [Accepted: 06/19/2018] [Indexed: 10/28/2022] Open
Abstract
Variant interpretation depends on accurate annotations using biologically relevant transcripts. We have developed a systematic strategy for designating primary transcripts and have applied it to 109 hearing loss-associated genes that were divided into three categories. Category 1 genes (n = 38) had a single transcript; category 2 genes (n = 33) had multiple transcripts, but a single transcript was sufficient to represent all exons; and category 3 genes (n = 38) had multiple transcripts with unique exons. Transcripts were curated with respect to gene expression reported in the literature and the Genotype-Tissue Expression Project. In addition, high-frequency loss-of-function variants in the Genome Aggregation Database and disease-causing variants in ClinVar and the Human Gene Mutation Database across the 109 genes were queried. These data were used to classify exons as clinically significant, insignificant, or of uncertain significance. Interestingly, 6% of all exons, containing 124 reportedly disease-causing variants, were of uncertain significance. Finally, we used exon-level next-generation sequencing quality metrics generated at two clinical laboratories and identified a total of 43 technically challenging exons in 20 different genes that had inadequate coverage and/or homology issues that might lead to false-variant calls. We have demonstrated that transcript analysis plays a critical role in accurate clinical variant interpretation.
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Affiliation(s)
- Marina T DiStefano
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Sarah E Hemphill
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Brandon J Cushman
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Mark J Bowser
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Elizabeth Hynes
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Andrew R Grant
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Rebecca K Siegert
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Andrea M Oza
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts
| | - Michael A Gonzalez
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Sami S Amr
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts; Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Heidi L Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; Department of Medical and Population Genetics, The Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Ahmad N Abou Tayoun
- Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania; Genetics Department, Al Jalila Children's Specialty Hospital, Dubai, United Arab Emirates.
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22
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Tu F, Sedzinski J, Ma Y, Marcotte EM, Wallingford JB. Protein localization screening in vivo reveals novel regulators of multiciliated cell development and function. J Cell Sci 2018; 131:jcs.206565. [PMID: 29180514 DOI: 10.1242/jcs.206565] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/20/2017] [Indexed: 12/23/2022] Open
Abstract
Multiciliated cells (MCCs) drive fluid flow in diverse tubular organs and are essential for the development and homeostasis of the vertebrate central nervous system, airway and reproductive tracts. These cells are characterized by dozens or hundreds of motile cilia that beat in a coordinated and polarized manner. In recent years, genomic studies have not only elucidated the transcriptional hierarchy for MCC specification but also identified myriad new proteins that govern MCC ciliogenesis, cilia beating and cilia polarization. Interestingly, this burst of genomic data has also highlighted that proteins with no obvious role in cilia do, in fact, have important ciliary functions. Understanding the function of proteins with little prior history of study presents a special challenge, especially when faced with large numbers of such proteins. Here, we define the subcellular localization in MCCs of ∼200 proteins not previously implicated in cilia biology. Functional analyses arising from the screen provide novel links between actin cytoskeleton and MCC ciliogenesis.
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Affiliation(s)
- Fan Tu
- Dept. of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Jakub Sedzinski
- Dept. of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.,The Danish Stem Cell Centre (DanStem), University of Copenhagen, 2200 Copenhagen, Denmark
| | - Yun Ma
- Dept. of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.,The Otorhinolaryngology Hospital, First Affiliated Hospital of Sun Yat-sen University, SunYat-sen University, Guangzhou, P.R. China
| | - Edward M Marcotte
- Dept. of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - John B Wallingford
- Dept. of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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23
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Ghasemnejad T, Shekari Khaniani M, Zarei F, Farbodnia M, Mansoori Derakhshan S. An update of common autosomal recessive non-syndromic hearing loss genes in Iranian population. Int J Pediatr Otorhinolaryngol 2017; 97:113-126. [PMID: 28483220 DOI: 10.1016/j.ijporl.2017.04.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 04/03/2017] [Accepted: 04/04/2017] [Indexed: 11/16/2022]
Abstract
Autosomal-recessive genes are responsible for about 80% of the hereditary non-syndromic hearing loss (NSHL) cases. In Iran, due to consanguineous marriages, NSHL is the second most frequent disability after intellectual disability, occurring one in 16 individuals. Enormous heterogeneity in the genetic pathology of hearing loss causes a major challenge in identification of responsible genes. In Iran, GJB2 is responsible for the most cases of pre-lingual and non-syndromic hearing loss (with frequency of 16.7%) which followed by other genes with lower frequency. Although several studies have indicated that a large proportion of both syndromic and non-syndromic hearing loss in Iranian populations are caused by defects in just a few genes, new detection strategies such as NGS (Next-generation sequencing) have increased the spectrum of responsible mutations. However, by applying this technique in Iran patients screening, the role of lots of novel related genes have been reported. In this review, we aim to describe function of these genes and their contribution to non-syndromic genetic hearing loss in Iranian population and we classify the genes by their functions.
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Affiliation(s)
- Tohid Ghasemnejad
- Neurosciences Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Medical Genetic, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Fatemeh Zarei
- Department of Stem Cells and Developmental Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mina Farbodnia
- Department of Cellular and Molecular Biology, Faculty of Sciences, Saba University, Urmia, Iran
| | - Sima Mansoori Derakhshan
- Neurosciences Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Medical Genetic, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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24
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Erickson T, Morgan CP, Olt J, Hardy K, Busch-Nentwich E, Maeda R, Clemens R, Krey JF, Nechiporuk A, Barr-Gillespie PG, Marcotti W, Nicolson T. Integration of Tmc1/2 into the mechanotransduction complex in zebrafish hair cells is regulated by Transmembrane O-methyltransferase (Tomt). eLife 2017; 6. [PMID: 28534737 PMCID: PMC5462536 DOI: 10.7554/elife.28474] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 05/20/2017] [Indexed: 01/18/2023] Open
Abstract
Transmembrane O-methyltransferase (TOMT/LRTOMT) is responsible for non-syndromic deafness DFNB63. However, the specific defects that lead to hearing loss have not been described. Using a zebrafish model of DFNB63, we show that the auditory and vestibular phenotypes are due to a lack of mechanotransduction (MET) in Tomt-deficient hair cells. GFP-tagged Tomt is enriched in the Golgi of hair cells, suggesting that Tomt might regulate the trafficking of other MET components to the hair bundle. We found that Tmc1/2 proteins are specifically excluded from the hair bundle in tomt mutants, whereas other MET complex proteins can still localize to the bundle. Furthermore, mouse TOMT and TMC1 can directly interact in HEK 293 cells, and this interaction is modulated by His183 in TOMT. Thus, we propose a model of MET complex assembly where Tomt and the Tmcs interact within the secretory pathway to traffic Tmc proteins to the hair bundle. DOI:http://dx.doi.org/10.7554/eLife.28474.001
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Affiliation(s)
- Timothy Erickson
- Oregon Hearing Research Center and the Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Clive P Morgan
- Oregon Hearing Research Center and the Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Jennifer Olt
- Department of Biomedical Science, University of Sheffield, Sheffield, United States
| | - Katherine Hardy
- Department of Biomedical Science, University of Sheffield, Sheffield, United States
| | | | - Reo Maeda
- Oregon Hearing Research Center and the Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Rachel Clemens
- Oregon Hearing Research Center and the Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Jocelyn F Krey
- Oregon Hearing Research Center and the Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Alex Nechiporuk
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, United States
| | - Peter G Barr-Gillespie
- Oregon Hearing Research Center and the Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Walter Marcotti
- Department of Biomedical Science, University of Sheffield, Sheffield, United States
| | - Teresa Nicolson
- Oregon Hearing Research Center and the Vollum Institute, Oregon Health and Science University, Portland, United States
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25
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Cunningham CL, Wu Z, Jafari A, Zhao B, Schrode K, Harkins-Perry S, Lauer A, Müller U. The murine catecholamine methyltransferase mTOMT is essential for mechanotransduction by cochlear hair cells. eLife 2017; 6. [PMID: 28504928 PMCID: PMC5462538 DOI: 10.7554/elife.24318] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 05/14/2017] [Indexed: 12/26/2022] Open
Abstract
Hair cells of the cochlea are mechanosensors for the perception of sound. Mutations in the LRTOMT gene, which encodes a protein with homology to the catecholamine methyltransferase COMT that is linked to schizophrenia, cause deafness. Here, we show that Tomt/Comt2, the murine ortholog of LRTOMT, has an unexpected function in the regulation of mechanotransduction by hair cells. The role of mTOMT in hair cells is independent of mTOMT methyltransferase function and mCOMT cannot substitute for mTOMT function. Instead, mTOMT binds to putative components of the mechanotransduction channel in hair cells and is essential for the transport of some of these components into the mechanically sensitive stereocilia of hair cells. Our studies thus suggest functional diversification between mCOMT and mTOMT, where mTOMT is critical for the assembly of the mechanotransduction machinery of hair cells. Defects in this process are likely mechanistically linked to deafness caused by mutations in LRTOMT/Tomt. DOI:http://dx.doi.org/10.7554/eLife.24318.001
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Affiliation(s)
- Christopher L Cunningham
- The Solomon Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, United States
| | - Zizhen Wu
- The Solomon Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, United States
| | - Aria Jafari
- Department of Surgery, University of California, San Diego, San Diego, United States
| | - Bo Zhao
- Department of Otolaryngology Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, United States
| | - Kat Schrode
- Department of Otolaryngology, Johns Hopkins University, Baltimore, United States
| | - Sarah Harkins-Perry
- Department of Molecular and Cellular Biology, The Scripps Research Institute, La Jolla, United States
| | - Amanda Lauer
- Department of Otolaryngology, Johns Hopkins University, Baltimore, United States
| | - Ulrich Müller
- The Solomon Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, United States
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26
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Yan D, Tekin D, Bademci G, Foster J, Cengiz FB, Kannan-Sundhari A, Guo S, Mittal R, Zou B, Grati M, Kabahuma RI, Kameswaran M, Lasisi TJ, Adedeji WA, Lasisi AO, Menendez I, Herrera M, Carranza C, Maroofian R, Crosby AH, Bensaid M, Masmoudi S, Behnam M, Mojarrad M, Feng Y, Duman D, Mawla AM, Nord AS, Blanton SH, Liu XZ, Tekin M. Spectrum of DNA variants for non-syndromic deafness in a large cohort from multiple continents. Hum Genet 2016; 135:953-61. [PMID: 27344577 PMCID: PMC5497215 DOI: 10.1007/s00439-016-1697-z] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/11/2016] [Indexed: 12/21/2022]
Abstract
Hearing loss is the most common sensory deficit in humans with causative variants in over 140 genes. With few exceptions, however, the population-specific distribution for many of the identified variants/genes is unclear. Until recently, the extensive genetic and clinical heterogeneity of deafness precluded comprehensive genetic analysis. Here, using a custom capture panel (MiamiOtoGenes), we undertook a targeted sequencing of 180 genes in a multi-ethnic cohort of 342 GJB2 mutation-negative deaf probands from South Africa, Nigeria, Tunisia, Turkey, Iran, India, Guatemala, and the United States (South Florida). We detected causative DNA variants in 25 % of multiplex and 7 % of simplex families. The detection rate varied between 0 and 57 % based on ethnicity, with Guatemala and Iran at the lower and higher end of the spectrum, respectively. We detected causative variants within 27 genes without predominant recurring pathogenic variants. The most commonly implicated genes include MYO15A, SLC26A4, USH2A, MYO7A, MYO6, and TRIOBP. Overall, our study highlights the importance of family history and generation of databases for multiple ethnically discrete populations to improve our ability to detect and accurately interpret genetic variants for pathogenicity.
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Affiliation(s)
- Denise Yan
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA
| | - Demet Tekin
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA
| | - Guney Bademci
- Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - Joseph Foster
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA.,Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - F Basak Cengiz
- Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - Abhiraami Kannan-Sundhari
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA
| | - Shengru Guo
- Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - Rahul Mittal
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA
| | - Bing Zou
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA
| | - Mhamed Grati
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA
| | - Rosemary I Kabahuma
- Department of Otorhinolaryngology, Steve Biko Academic Hospital, University of Pretoria, Cnr Malan and Steve Biko Road, Gezina, Pretoria, South Africa
| | - Mohan Kameswaran
- Madras ENT Research Foundation (MERF), No-1, 1st Cross Street, Off. II Main Road, Raja Annamalai Puram, Chennai, 600028, Tamil Nadu, India
| | - Taye J Lasisi
- Department of Otorhinolaryngology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Waheed A Adedeji
- Department of Otorhinolaryngology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Akeem O Lasisi
- Department of Otorhinolaryngology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Ibis Menendez
- Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA
| | - Marianna Herrera
- Institute for Research on Genetic and Metabolic Diseases, INVEGEM, Guatemala City, Guatemala
| | - Claudia Carranza
- Institute for Research on Genetic and Metabolic Diseases, INVEGEM, Guatemala City, Guatemala
| | - Reza Maroofian
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Wellcome Wolfson Centre, Exeter, UK
| | - Andrew H Crosby
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Wellcome Wolfson Centre, Exeter, UK
| | - Mariem Bensaid
- Laboratoire Procédés de Criblage Moléculaire et Cellulaire, Centre de Biotechnologie de Sfax, Université de Sfax, Sfax, Tunisia
| | - Saber Masmoudi
- Laboratoire Procédés de Criblage Moléculaire et Cellulaire, Centre de Biotechnologie de Sfax, Université de Sfax, Sfax, Tunisia
| | | | - Majid Mojarrad
- Department of Medical Genetics, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Yong Feng
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Duygu Duman
- Division of Genetics, Department of Pediatrics, Ankara University School of Medicine, Ankara, Turkey
| | - Alex M Mawla
- Department of Neurobiology, Physiology, and Behavior, Center for Neuroscience, UC Davis, Davis, CA, 95616, USA.,Department of Psychiatry and Behavioral Sciences, Center for Neuroscience, UC Davis, Davis, CA, 95616, USA
| | - Alex S Nord
- Department of Neurobiology, Physiology, and Behavior, Center for Neuroscience, UC Davis, Davis, CA, 95616, USA.,Department of Psychiatry and Behavioral Sciences, Center for Neuroscience, UC Davis, Davis, CA, 95616, USA
| | - Susan H Blanton
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA.,Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA.,Dr. John T. Macdonald Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Xue Z Liu
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA. .,Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA. .,Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Mustafa Tekin
- Department of Otolaryngology (D-48), University of Miami Miller School of Medicine, 1666 NW 12th Avenue, Miami, FL, 33136, USA. .,Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami, 1501 NW 10th Avenue, BRB-610 (M-860), Miami, FL, 33136, USA. .,Dr. John T. Macdonald Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
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27
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Elkon R, Milon B, Morrison L, Shah M, Vijayakumar S, Racherla M, Leitch CC, Silipino L, Hadi S, Weiss-Gayet M, Barras E, Schmid CD, Ait-Lounis A, Barnes A, Song Y, Eisenman DJ, Eliyahu E, Frolenkov GI, Strome SE, Durand B, Zaghloul NA, Jones SM, Reith W, Hertzano R. RFX transcription factors are essential for hearing in mice. Nat Commun 2015; 6:8549. [PMID: 26469318 PMCID: PMC4634137 DOI: 10.1038/ncomms9549] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 09/04/2015] [Indexed: 01/23/2023] Open
Abstract
Sensorineural hearing loss is a common and currently irreversible disorder, because mammalian hair cells (HCs) do not regenerate and current stem cell and gene delivery protocols result only in immature HC-like cells. Importantly, although the transcriptional regulators of embryonic HC development have been described, little is known about the postnatal regulators of maturating HCs. Here we apply a cell type-specific functional genomic analysis to the transcriptomes of auditory and vestibular sensory epithelia from early postnatal mice. We identify RFX transcription factors as essential and evolutionarily conserved regulators of the HC-specific transcriptomes, and detect Rfx1,2,3,5 and 7 in the developing HCs. To understand the role of RFX in hearing, we generate Rfx1/3 conditional knockout mice. We show that these mice are deaf secondary to rapid loss of initially well-formed outer HCs. These data identify an essential role for RFX in hearing and survival of the terminally differentiating outer HCs.
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Affiliation(s)
- Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Beatrice Milon
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA
| | - Laura Morrison
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA
| | - Manan Shah
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA
| | - Sarath Vijayakumar
- Department of Special Education and Communication Disorders, University of Nebraska Lincoln, Lincoln, Nebraska 68583-0738, USA
| | - Manoj Racherla
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA
| | - Carmen C. Leitch
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, School of Medicine, University of Maryland Baltimore, Baltimore, Maryland 21201, USA
| | - Lorna Silipino
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA
| | - Shadan Hadi
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, Kentucky 40536-0298, USA
| | - Michèle Weiss-Gayet
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR 5534, Université Claude Bernard Lyon-1, 69622 Villeurbanne, France
| | - Emmanuèle Barras
- Department of Pathology and Immunology, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Christoph D. Schmid
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, and University of Basel, 4051 Basel, Switzerland
| | - Aouatef Ait-Lounis
- Department of Pathology and Immunology, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Ashley Barnes
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA
| | - Yang Song
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - David J. Eisenman
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA
| | - Efrat Eliyahu
- Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Gregory I. Frolenkov
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, Kentucky 40536-0298, USA
| | - Scott E. Strome
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA
| | - Bénédicte Durand
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR 5534, Université Claude Bernard Lyon-1, 69622 Villeurbanne, France
| | - Norann A. Zaghloul
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, School of Medicine, University of Maryland Baltimore, Baltimore, Maryland 21201, USA
| | - Sherri M. Jones
- Department of Special Education and Communication Disorders, University of Nebraska Lincoln, Lincoln, Nebraska 68583-0738, USA
| | - Walter Reith
- Department of Pathology and Immunology, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Ronna Hertzano
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA,
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28
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Yan D, Kannan-Sundhari A, Vishwanath S, Qing J, Mittal R, Kameswaran M, Liu XZ. The Genetic Basis of Nonsyndromic Hearing Loss in Indian and Pakistani Populations. Genet Test Mol Biomarkers 2015; 19:512-27. [PMID: 26186295 DOI: 10.1089/gtmb.2015.0023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Deafness encompasses a series of etiologically heterogeneous disorders with mutations in more than 400 independent genes. However, several studies indicate that a large proportion of both syndromic and nonsyndromic forms of deafness in the racially diverse Indian and Pakistani populations are caused by defects in just a few genes. In these countries, there is a strong cultural preference for consanguineous marriage and an associated relatively high prevalence of genetic disorders. The current Indian population is approximately 1.2 billion and it is estimated that 30,000 infants are born with congenital sensorineural hearing loss (HL) each year. The estimated rate of profound bilateral HL is 1.6 per 1000 in Pakistan and 70% of this HL arises in consanguineous families. Knowledge of the genetic cause of deafness within a distinct population is important for accurate genetic counseling and early diagnosis for timely intervention and treatment options. Many sources and technologies are now available for the testing of hearing efficiency. Population-based screening has been proposed as one of the major strategies for translating genetic and genomic advances into population health gains. This review of the genetics of deafness in Indian and Pakistani populations deals with the major causes of deafness in these countries and prospectives for reducing the incidence of inherited deafness.
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Affiliation(s)
- Denise Yan
- 1 Departments of Otolaryngology-Head and Neck Surgery, Leonard M. Miller School of Medicine, University of Miami , Miami, Florida
| | - Abhiraami Kannan-Sundhari
- 1 Departments of Otolaryngology-Head and Neck Surgery, Leonard M. Miller School of Medicine, University of Miami , Miami, Florida.,2 SRM University , SRM Nagar, Chennai, India
| | - Subramanian Vishwanath
- 1 Departments of Otolaryngology-Head and Neck Surgery, Leonard M. Miller School of Medicine, University of Miami , Miami, Florida.,2 SRM University , SRM Nagar, Chennai, India
| | - Jie Qing
- 1 Departments of Otolaryngology-Head and Neck Surgery, Leonard M. Miller School of Medicine, University of Miami , Miami, Florida
| | - Rahul Mittal
- 1 Departments of Otolaryngology-Head and Neck Surgery, Leonard M. Miller School of Medicine, University of Miami , Miami, Florida
| | | | - Xue Zhong Liu
- 1 Departments of Otolaryngology-Head and Neck Surgery, Leonard M. Miller School of Medicine, University of Miami , Miami, Florida
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29
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Wu CC, Lin YH, Liu TC, Lin KN, Yang WS, Hsu CJ, Chen PL, Wu CM. Identifying Children With Poor Cochlear Implantation Outcomes Using Massively Parallel Sequencing. Medicine (Baltimore) 2015; 94:e1073. [PMID: 26166082 PMCID: PMC4504554 DOI: 10.1097/md.0000000000001073] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cochlear implantation is currently the treatment of choice for children with severe to profound hearing impairment. However, the outcomes with cochlear implants (CIs) vary significantly among recipients. The purpose of the present study is to identify the genetic determinants of poor CI outcomes. Twelve children with poor CI outcomes (the "cases") and 30 "matched controls" with good CI outcomes were subjected to comprehensive genetic analyses using massively parallel sequencing, which targeted 129 known deafness genes. Audiological features, imaging findings, and auditory/speech performance with CIs were then correlated to the genetic diagnoses. We identified genetic variants which are associated with poor CI outcomes in 7 (58%) of the 12 cases; 4 cases had bi-allelic PCDH15 pathogenic mutations and 3 cases were homozygous for the DFNB59 p.G292R variant. Mutations in the WFS1, GJB3, ESRRB, LRTOMT, MYO3A, and POU3F4 genes were detected in 7 (23%) of the 30 matched controls. The allele frequencies of PCDH15 and DFNB59 variants were significantly higher in the cases than in the matched controls (both P < 0.001). In the 7 CI recipients with PCDH15 or DFNB59 variants, otoacoustic emissions were absent in both ears, and imaging findings were normal in all 7 implanted ears. PCDH15 or DFNB59 variants are associated with poor CI performance, yet children with PCDH15 or DFNB59 variants might show clinical features indistinguishable from those of other typical pediatric CI recipients. Accordingly, genetic examination is indicated in all CI candidates before operation.
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Affiliation(s)
- Chen-Chi Wu
- From Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan (C-CW, Y-HL, T-CL, K-NL, C-JH); Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan (C-CW, W-SY, P-LC); Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan (Y-HL, P-LC); Department of Otolaryngology, Cardinal Tien Hospital, New Taipei, Taiwan (K-NL); Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan (W-SY, P-LC); Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan (W-SY, P-LC); Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan (W-SY, P-LC); Department of Otolaryngology, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung, Taiwan (C-JH); and Department of Otolaryngology, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan, Taiwan (C-MW)
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30
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Characterization of the transcriptome of nascent hair cells and identification of direct targets of the Atoh1 transcription factor. J Neurosci 2015; 35:5870-83. [PMID: 25855195 DOI: 10.1523/jneurosci.5083-14.2015] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Hair cells are sensory receptors for the auditory and vestibular system in vertebrates. The transcription factor Atoh1 is both necessary and sufficient for the differentiation of hair cells, and is strongly upregulated during hair-cell regeneration in nonmammalian vertebrates. To identify genes involved in hair cell development and function, we performed RNA-seq profiling of purified Atoh1-expressing hair cells from the neonatal mouse cochlea. We identified >600 enriched transcripts in cochlear hair cells, of which 90% have not been previously shown to be expressed in hair cells. We identified 233 of these hair cell genes as candidates to be directly regulated by Atoh1 based on the presence of Atoh1 binding sites in their regulatory regions and by analyzing Atoh1 ChIP-seq datasets from the cerebellum and small intestine. We confirmed 10 of these genes as being direct Atoh1 targets in the cochlea by ChIP-PCR. The identification of candidate Atoh1 target genes is a first step in identifying gene regulatory networks for hair-cell development and may inform future studies on the potential role of Atoh1 in mammalian hair cell regeneration.
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31
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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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Ichinose A, Moteki H, Hattori M, Nishio SY, Usami SI. Novel mutations in LRTOMT associated with moderate progressive hearing loss in autosomal recessive inheritance. Ann Otol Rhinol Laryngol 2015; 124 Suppl 1:142S-7S. [PMID: 25788562 DOI: 10.1177/0003489415575043] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE We present a patient who was identified with novel mutations in the LRTOMT gene and describe the clinical features of the phenotype including serial audiological findings. METHODS One hundred six Japanese patients with mild to moderate sensorineural hearing loss from unrelated and nonconsanguineous families were enrolled in the study. Targeted genomic enrichment and massively parallel sequencing of all known nonsyndromic hearing loss genes were performed to identify the genetic cause of hearing loss. RESULTS Compound heterozygotes with a novel frame-shift mutation and a missense mutation were identified in the LRTOMT gene. The mutated residues were segregated in both alleles of LRTOMT, present within the LRTOMT2 protein coding region. The patient had moderate sloping hearing loss at high frequencies, which progressed at 1000 Hz and higher frequencies over a period of 6 years. CONCLUSION Hearing loss caused by mutations in the LRTOMT gene is extremely rare. This is the first case report of a compound heterozygous mutation in a nonconsanguineous family.
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Affiliation(s)
- Aya Ichinose
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Hideaki Moteki
- 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
| | - 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
| | - 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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Abstract
Hearing loss is the most common form of sensory impairment in humans and affects more than 40 million people in the United States alone. No drug-based therapy has been approved by the Food and Drug Administration, and treatment mostly relies on devices such as hearing aids and cochlear implants. Over recent years, more than 100 genetic loci have been linked to hearing loss and many of the affected genes have been identified. This understanding of the genetic pathways that regulate auditory function has revealed new targets for pharmacological treatment of the disease. Moreover, approaches that are based on stem cells and gene therapy, which may have the potential to restore or maintain auditory function, are beginning to emerge.
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Affiliation(s)
- Ulrich Müller
- Department of Molecular and Cellular Neuroscience, Dorris Neuroscience Center, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, San Diego, California 92037, USA
| | - Peter G Barr-Gillespie
- Oregon Hearing Research Center, Vollum Institute, Oregon Health &Science University, 3181 South West Sam Jackson Park Road, Portland, Oregon 97239, USA
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Chakchouk I, Ben Said M, Jbeli F, Benmarzoug R, Loukil S, Smeti I, Chakroun A, Gibriel AA, Ghorbel A, Hadjkacem H, Masmoudi S. NADf chip, a two-color microarray for simultaneous screening of multigene mutations associated with hearing impairment in North African Mediterranean countries. J Mol Diagn 2015; 17:155-61. [PMID: 25560255 DOI: 10.1016/j.jmoldx.2014.11.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 10/10/2014] [Accepted: 11/18/2014] [Indexed: 11/20/2022] Open
Abstract
Hearing impairment (HI) is the most frequent sensory defect. Genetic causes are involved in two thirds of prelingual cases. Moreover, the autosomal recessive HI frequency is increased in countries where there is a high rate of consanguinity, such as in North African Mediterranean countries. This population shares several features, including history and social behavior, that promote the spread of founder mutations. HI is characterized by tremendous heterogeneity in both the genetic and clinical aspects. The identification of the causal mutation is important for early diagnosis, clinical follow-up, and genetic counseling. Addressing the extreme genetic heterogeneity of HI using classic molecular methods would be expensive and time-consuming. We designed a cost-effective North African Deafness chip for rapid and simultaneous analysis of 58 mutations using multiplex PCR coupled with dual-color arrayed primer extension. These mutations are found in North African HI patients and are distributed over 31 exons and five introns in 21 distinct genes. Assay specificity was initially optimized using 103 archived DNA samples of known genotypes. Blind validation of HI-unrelated patients revealed mutant alleles in 13 samples, and these mutations were confirmed by Sanger sequencing. The North African Deafness chip allows for simultaneous genotyping of eight different samples, at a minimal cost and in a single day, and is therefore amenable to large-scale molecular screening of HI in North Africa.
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Affiliation(s)
- Imen Chakchouk
- Processes Laboratory of Molecular and Cellular Screening, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Mariem Ben Said
- Processes Laboratory of Molecular and Cellular Screening, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Fida Jbeli
- Processes Laboratory of Molecular and Cellular Screening, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Riadh Benmarzoug
- Processes Laboratory of Molecular and Cellular Screening, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Salma Loukil
- Processes Laboratory of Molecular and Cellular Screening, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Ibtihel Smeti
- Processes Laboratory of Molecular and Cellular Screening, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Amine Chakroun
- Otorhinolaryngology Service, Habib Bourguiba University Hospital Sfax, Sfax, Tunisia
| | - Abdullah Ahmed Gibriel
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Ahram Canadian University, Giza, Egypt; Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, British University in Egypt, Cairo, Egypt
| | - Abdelmonem Ghorbel
- Otorhinolaryngology Service, Habib Bourguiba University Hospital Sfax, Sfax, Tunisia
| | - Hassen Hadjkacem
- Processes Laboratory of Molecular and Cellular Screening, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Saber Masmoudi
- Processes Laboratory of Molecular and Cellular Screening, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia.
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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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Rehman AU, Santos-Cortez RLP, Morell RJ, Drummond MC, Ito T, Lee K, Khan AA, Basra MAR, Wasif N, Ayub M, Ali RA, Raza SI, Nickerson DA, Shendure J, Bamshad M, Riazuddin S, Billington N, Khan SN, Friedman PL, Griffith AJ, Ahmad W, Riazuddin S, Leal SM, Friedman TB. Mutations in TBC1D24, a gene associated with epilepsy, also cause nonsyndromic deafness DFNB86. Am J Hum Genet 2014; 94:144-52. [PMID: 24387994 DOI: 10.1016/j.ajhg.2013.12.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 12/06/2013] [Indexed: 01/12/2023] Open
Abstract
Inherited deafness is clinically and genetically heterogeneous. We recently mapped DFNB86, a locus associated with nonsyndromic deafness, to chromosome 16p. In this study, whole-exome sequencing was performed with genomic DNA from affected individuals from three large consanguineous families in which markers linked to DFNB86 segregate with profound deafness. Analyses of these data revealed homozygous mutation c.208G>T (p.Asp70Tyr) or c.878G>C (p.Arg293Pro) in TBC1D24 as the underlying cause of deafness in the three families. Sanger sequence analysis of TBC1D24 in an additional large family in which deafness segregates with DFNB86 identified the c.208G>T (p.Asp70Tyr) substitution. These mutations affect TBC1D24 amino acid residues that are conserved in orthologs ranging from fruit fly to human. Neither variant was observed in databases of single-nucleotide variants or in 634 chromosomes from ethnically matched control subjects. TBC1D24 in the mouse inner ear was immunolocalized predominantly to spiral ganglion neurons, indicating that DFNB86 deafness might be an auditory neuropathy spectrum disorder. Previously, six recessive mutations in TBC1D24 were reported to cause seizures (hearing loss was not reported) ranging in severity from epilepsy with otherwise normal development to epileptic encephalopathy resulting in childhood death. Two of our four families in which deafness segregates with mutant alleles of TBC1D24 were available for neurological examination. Cosegregation of epilepsy and deafness was not observed in these two families. Although the causal relationship between genotype and phenotype is not presently understood, our findings, combined with published data, indicate that recessive alleles of TBC1D24 can cause either epilepsy or nonsyndromic deafness.
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Affiliation(s)
- Atteeq U Rehman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Rockville, MD 20850, USA
| | - Regie Lyn P Santos-Cortez
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Robert J Morell
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Rockville, MD 20850, USA
| | - Meghan C Drummond
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Rockville, MD 20850, USA
| | - Taku Ito
- Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Rockville, MD 20850, USA
| | - Kwanghyuk Lee
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Asma A Khan
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 54500, Pakistan
| | - Muhammad Asim R Basra
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 54500, Pakistan
| | - Naveed Wasif
- Center for Research in Molecular Medicine, Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore 54000, Pakistan
| | - Muhammad Ayub
- Institute of Biochemistry, University of Baluchistan, Quetta 87300, Pakistan
| | - Rana A Ali
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 54500, Pakistan
| | - Syed I Raza
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad 45320, Pakistan
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Michael Bamshad
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Saima Riazuddin
- Division of Pediatric Otolaryngology - Head and Neck Surgery, Cincinnati Children's Research Foundation, Cincinnati, OH 45229 USA; Department of Otolaryngology - Head and Neck Surgery, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Neil Billington
- Laboratory of Molecular Physiology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shaheen N Khan
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 54500, Pakistan
| | | | - Andrew J Griffith
- Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Rockville, MD 20850, USA
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad 45320, Pakistan
| | - Sheikh Riazuddin
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 54500, Pakistan; Allama Iqbal Medical College and Jinnah Hospital Complex, University of Health Sciences, Lahore 54550, Pakistan
| | - Suzanne M Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Rockville, MD 20850, USA.
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Taghizadeh SH, Kazeminezhad SR, Sefidgar SAA, Yazdanpanahi N, Tabatabaeifar MA, Yousefi A, Lesani SM, Abolhasani M, Hashemzadeh Chaleshtori M. Investigation of LRTOMT gene (locus DFNB63) mutations in Iranian patients with autosomal recessive non-syndromic hearing loss. INTERNATIONAL JOURNAL OF MOLECULAR AND CELLULAR MEDICINE 2013; 2:41-5. [PMID: 24551789 PMCID: PMC3920523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Accepted: 03/03/2013] [Indexed: 11/12/2022]
Abstract
Hearing loss (HL) is the most frequent sensory defect affecting 1 in 1000 neonates. This can occur due to genetic or environmental causes or both. The genetic causes are very heterogenous and over 100 loci have been identified to cause autosomal recessive non - syndromic hearing loss (ARNSHL). The aim of this study was to determine the contribution of the LRTOMT gene mutations in causing ARNSHL. One hundred fifty seven pupils affected with ARNSHL from Azarbaijan Sharghi, Kordestan, Gilan and Golestan provinces, north and west of Iran, were ascertained. In this descriptive - laboratory study, the presence of LRTOMT mutations were initially checked using PCR - Single - strand conformation polymorphism (SSCP) and heteroduplex analysis (HA) strategy. Samples with shifted bands on the gel were confirmed by DNA sequencing method. The PCR-SSCP/HA and the subsequent direct DNA sequencing showed no mutation in the population studied. We conclude that LRTOMT mutations have no role in causing sporadic deafness in the studied population. Further studies on other populations and samples could clarify the exact role of LRTOMT mutations.
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Affiliation(s)
| | | | - Seyyed Ali Asghar Sefidgar
- Cellular and Molecular Biology Research Center (CMBRC), Babol University of Medical Sciences, Babol, Iran.
| | - Nasrin Yazdanpanahi
- Department of Biochemistry and Genetics, Falavarjan Branch, Islamic Azad University, Isfahan, Iran.
| | | | - Ahmad Yousefi
- Department of Basic Sciences, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran.
| | | | - Marziyeh Abolhasani
- Cellular and Molecular Research Center, Shahrekord University of Medical Sciences, Shahrekord, Iran.
| | - Morteza Hashemzadeh Chaleshtori
- Cellular and Molecular Research Center, Shahrekord University of Medical Sciences, Shahrekord, Iran.,Corresponding author: Cellular and Molecular Research Center, Shahrekord University of Medical Sciences, Shahrekord, Iran.
E-mail: .
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Charif M, Bounaceur S, Abidi O, Nahili H, Rouba H, Kandil M, Boulouiz R, Barakat A. The c.242G>A mutation in LRTOMT gene is responsible for a high prevalence of deafness in the Moroccan population. Mol Biol Rep 2012; 39:11011-6. [PMID: 23053991 DOI: 10.1007/s11033-012-2003-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 10/01/2012] [Indexed: 10/27/2022]
Abstract
Congenital hearing impairment (HI) affects one in 1,000 newborns and has a genetic cause in 50 % of the cases. Autosomal recessive non-syndromic hearing impairment is responsible for 70-80 % of all hereditary cases of HI. Recently, it has been demonstrated that, mutations of LRTOMT are associated with profound nonsyndromic hearing impairment at the DFNB63 locus. The objective of this study is to evaluate the carrier frequency of c.242G>A mutation in LRTOMT gene and define the contribution of this gene in the etiology of deafness in Moroccan population. We screened 105 unrelated Moroccan families with non-syndromic HI and 120 control individuals for mutation in the exon 8 of the LRTOMT gene, by sequencing and PCR-RFLP. The Homozygous c.242G>A mutation was found in 8.75 % of the families tested and in 4.16 % of control in the heterozygous state. Our results show that after the GJB2 gene mutation in LRTOMT gene is the second cause of congenital hearing impairment in Moroccan patients. This finding should facilitate diagnosis of congenital deafness of the affected subjects in Morocco.
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Affiliation(s)
- Majida Charif
- Laboratoire de Génétique Moléculaire et Humaine, Département de Recherche Scientifique, Institut Pasteur, 1, Place Louis Pasteur, C.P 20360, Casablanca, Morocco
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Jaworek TJ, Bhatti R, Latief N, Khan SN, Riazuddin S, Ahmed ZM. USH1K, a novel locus for type I Usher syndrome, maps to chromosome 10p11.21-q21.1. J Hum Genet 2012; 57:633-7. [PMID: 22718019 PMCID: PMC3596105 DOI: 10.1038/jhg.2012.79] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We ascertained two large Pakistani consanguineous families (PKDF231 and PKDF608) segregating profound hearing loss, vestibular dysfunction, and retinitis pigmentosa; the defining features of Usher syndrome type 1 (USH1). To date, seven USH1 loci have been reported. Here, we map a novel locus, USH1K, on chromosome 10p11.21-q21.1. In family PKDF231, we performed a genome-wide linkage screen and found a region of homozygosity shared among the affected individuals at chromosome 10p11.21-q21.1. Meiotic recombination events in family PKDF231 define a critical interval of 11.74 cM (20.20 Mb) bounded by markers D10S1780 (63.83 cM) and D10S546 (75.57 cM). Affected individuals of family PKDF608 were also homozygous for chromosome 10p11.21-q21.1-linked STR markers. Of the 85 genes within the linkage interval, PCDH15, GJD4, FZD4, RET and LRRC18 were sequenced in both families, but no potential pathogenic mutation was identified. The USH1K locus overlaps the non-syndromic deafness locus DFNB33 raising the possibility that the two disorders may be caused by allelic mutations.
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Affiliation(s)
- Thomas J Jaworek
- Division of Pediatric Ophthalmology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
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Lin MF, Kheradpour P, Washietl S, Parker BJ, Pedersen JS, Kellis M. Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes. Genome Res 2011; 21:1916-28. [PMID: 21994248 DOI: 10.1101/gr.108753.110] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The degeneracy of the genetic code allows protein-coding DNA and RNA sequences to simultaneously encode additional, overlapping functional elements. A sequence in which both protein-coding and additional overlapping functions have evolved under purifying selection should show increased evolutionary conservation compared to typical protein-coding genes--especially at synonymous sites. In this study, we use genome alignments of 29 placental mammals to systematically locate short regions within human ORFs that show conspicuously low estimated rates of synonymous substitution across these species. The 29-species alignment provides statistical power to locate more than 10,000 such regions with resolution down to nine-codon windows, which are found within more than a quarter of all human protein-coding genes and contain ∼2% of their synonymous sites. We collect numerous lines of evidence that the observed synonymous constraint in these regions reflects selection on overlapping functional elements including splicing regulatory elements, dual-coding genes, RNA secondary structures, microRNA target sites, and developmental enhancers. Our results show that overlapping functional elements are common in mammalian genes, despite the vast genomic landscape.
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Affiliation(s)
- Michael F Lin
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Tabatabaiefar MA, Alasti F, Shariati L, Farrokhi E, Fransen E, Nooridaloii MR, Chaleshtori MH, Van Camp G. DFNB93, a novel locus for autosomal recessive moderate-to-severe hearing impairment. Clin Genet 2011; 79:594-8. [PMID: 21542834 DOI: 10.1111/j.1399-0004.2010.01593.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Vanwesemael M, Schrauwen I, Ceuppens R, Alasti F, Jorssen E, Farrokhi E, Chaleshtori MH, Van Camp G. A 1 bp deletion in the dual reading frame deafness gene LRTOMT causes a frameshift from the first into the second reading frame. Am J Med Genet A 2011; 155A:2021-3. [PMID: 21739586 DOI: 10.1002/ajmg.a.34096] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 02/04/2011] [Accepted: 04/12/2011] [Indexed: 11/05/2022]
Affiliation(s)
- Maarten Vanwesemael
- Department of Medical Genetics, University of Antwerp, 2610, Wilrijk, Belgium
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Abstract
Cisplatin ototoxicity affects different individuals in a widely variable manner. These variations are likely to be explained by genetic differences among those affected. It would be highly advantageous to identify genetic variants that predispose to cisplatin ototoxicity in order to minimize the risk to susceptible subgroups. Although this area of research is very important, only a few studies have rigorously examined the genetic basis for cisplatin-induced susceptibility to hearing loss. This article addresses recent progress in clarifying the incidence of cisplatin ototoxicity and the risk factors and controversies regarding the identification of genetic variants associated with cisplatin-induced hearing loss.
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Affiliation(s)
- Debashree Mukherjea
- Department of Surgery, Division of Otolaryngology, Southern Illinois University, School of Medicine, Springfield, IL, USA.
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Riazuddin S, Ahmed ZM, Hegde RS, Khan SN, Nasir I, Shaukat U, Riazuddin S, Butman JA, Griffith AJ, Friedman TB, Choi BY. Variable expressivity of FGF3 mutations associated with deafness and LAMM syndrome. BMC MEDICAL GENETICS 2011; 12:21. [PMID: 21306635 PMCID: PMC3042908 DOI: 10.1186/1471-2350-12-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Accepted: 02/09/2011] [Indexed: 12/18/2022]
Abstract
Background Recessive mutations of fibroblast growth factor 3 (FGF3) can cause LAMM syndrome (OMIM 610706), characterized by fully penetrant complete labyrinthine aplasia, microtia and microdontia. Methods We performed a prospective molecular genetic and clinical study of families segregating hearing loss linked to FGF3 mutations. Ten affected individuals from three large Pakistani families segregating FGF3 mutations were imaged with CT, MRI, or both to detect inner ear abnormalities. We also modeled the three dimensional structure of FGF3 to better understand the structural consequences of the three missense mutations. Results Two families segregated reported mutations (p.R104X and p.R95W) and one family segregated a novel mutation (p.R132GfsX26) of FGF3. All individuals homozygous for p.R104X or p.R132GfsX26 had fully penetrant features of LAMM syndrome. However, recessive p.R95W mutations were associated with nearly normal looking auricles and variable inner ear structural phenotypes, similar to that reported for a Somali family also segregating p.R95W. This suggests that the mild phenotype is not entirely due to genetic background. Molecular modeling result suggests a less drastic effect of p.R95W on FGF3 function compared with known missense mutations detected in fully penetrant LAMM syndrome. Since we detected significant intrafamilial variability of the inner ear structural phenotype in the family segregating p.R95W, we also sequenced FGF10 as a likely candidate for a modifier. However, we did not find any sequence variation, pointing out that a larger sample size will be needed to map and identify a modifier. We also observed a mild to moderate bilateral conductive hearing loss in three carriers of p.R95W, suggesting either a semi-dominant effect of this mutant allele of FGF3, otitis media, or a consequence of genetic background in these three family members. Conclusions We noted a less prominent dental and external ear phenotype in association with the homozygous p.R95W. Therefore, we conclude that the manifestations of recessive FGF3 mutations range from fully penetrant LAMM syndrome to deafness with residual inner ear structures and, by extension, with minimal syndromic features, an observation with implications for cochlear implantation candidacy.
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Affiliation(s)
- Saima Riazuddin
- Laboratory of Molecular Genetics, Division of Pediatric Otolaryngology Head & Neck Surgery, Cincinnati Children's Hospital Research Foundation, and University of Cincinnati, College of Medicine, Cincinnati, OH, USA
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Duman D, Sirmaci A, Cengiz FB, Ozdag H, Tekin M. Screening of 38 genes identifies mutations in 62% of families with nonsyndromic deafness in Turkey. Genet Test Mol Biomarkers 2010; 15:29-33. [PMID: 21117948 DOI: 10.1089/gtmb.2010.0120] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
More than 60% of prelingual deafness is genetic in origin, and of these up to 95% are monogenic autosomal recessive traits. Causal mutations have been identified in 1 of 38 different genes in a subset of patients with nonsyndromic autosomal recessive deafness. In this study, we screened 49 unrelated Turkish families with at least three affected children born to consanguineous parents. Probands from all families were negative for mutations in the GJB2 gene, two large deletions in the GJB6 gene, and the 1555A>G substitution in the mitochondrial DNA MTRNR1 gene. Each family was subsequently screened via autozygosity mapping with genomewide single-nucleotide polymorphism arrays. If the phenotype cosegregated with a haplotype flanking one of the 38 genes, mutation analysis of the gene was performed. We identified 22 different autozygous mutations in 11 genes, other than GJB2, in 26 of 49 families, which overall explains deafness in 62% of families. Relative frequencies of genes following GJB2 were MYO15A (9.9%), TMIE (6.6%), TMC1 (6.6%), OTOF (5.0%), CDH23 (3.3%), MYO7A (3.3%), SLC26A4 (1.7%), PCDH15 (1.7%), LRTOMT (1.7%), SERPINB6 (1.7%), and TMPRSS3 (1.7%). Nineteen of 22 mutations are reported for the first time in this study. Unknown rare genes for deafness appear to be present in the remaining 23 families.
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Affiliation(s)
- Duygu Duman
- Division of Genetics, Department of Pediatrics, Ankara University School of Medicine, Dikimevi, Ankara, Turkey
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Finding new genes for non-syndromic hearing loss through an in silico prioritization study. PLoS One 2010; 5. [PMID: 20927407 PMCID: PMC2946934 DOI: 10.1371/journal.pone.0012742] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 08/17/2010] [Indexed: 11/19/2022] Open
Abstract
At present, 51 genes are already known to be responsible for Non-Syndromic hereditary Hearing Loss (NSHL), but the knowledge of 121 NSHL-linked chromosomal regions brings to the hypothesis that a number of disease genes have still to be uncovered. To help scientists to find new NSHL genes, we built a gene-scoring system, integrating Gene Ontology, NCBI Gene and Map Viewer databases, which prioritizes the candidate genes according to their probability to cause NSHL. We defined a set of candidates and measured their functional similarity with respect to the disease gene set, computing a score () that relies on the assumption that functionally related genes might contribute to the same (disease) phenotype. A Kolmogorov-Smirnov test, comparing the pair-wise distribution on the disease gene set with the distribution on the remaining human genes, provided a statistical assessment of this assumption. We found at a p-value that the former pair-wise is greater than the latter, justifying a prioritization strategy based on the functional similarity of candidate genes respect to the disease gene set. A cross-validation test measured to what extent the ranking for NSHL is different from a random ordering: adding 15% of the disease genes to the candidate gene set, the ranking of the disease genes in the first eight positions resulted statistically different from a hypergeometric distribution with a p-value and a power. The twenty top-scored genes were finally examined to evaluate their possible involvement in NSHL. We found that half of them are known to be expressed in human inner ear or cochlea and are mainly involved in remodeling and organization of actin formation and maintenance of the cilia and the endocochlear potential. These findings strongly indicate that our metric was able to suggest excellent NSHL candidates to be screened in patients and controls for causative mutations.
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Rehman AU, Morell RJ, Belyantseva IA, Khan SY, Boger ET, Shahzad M, Ahmed ZM, Riazuddin S, Khan SN, Riazuddin S, Friedman TB. Targeted capture and next-generation sequencing identifies C9orf75, encoding taperin, as the mutated gene in nonsyndromic deafness DFNB79. Am J Hum Genet 2010; 86:378-88. [PMID: 20170899 DOI: 10.1016/j.ajhg.2010.01.030] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2009] [Revised: 01/22/2010] [Accepted: 01/25/2010] [Indexed: 10/19/2022] Open
Abstract
Targeted genome capture combined with next-generation sequencing was used to analyze 2.9 Mb of the DFNB79 interval on chromosome 9q34.3, which includes 108 candidate genes. Genomic DNA from an affected member of a consanguineous family segregating recessive, nonsyndromic hearing loss was used to make a library of fragments covering the DFNB79 linkage interval defined by genetic analyses of four pedigrees. Homozygosity for eight previously unreported variants in transcribed sequences was detected by evaluating a library of 402,554 sequencing reads and was later confirmed by Sanger sequencing. Of these variants, six were determined to be polymorphisms in the Pakistani population, and one was in a noncoding gene that was subsequently excluded genetically from the DFNB79 linkage interval. The remaining variant was a nonsense mutation in a predicted gene, C9orf75, renamed TPRN. Evaluation of the other three DFNB79-linked families identified three additional frameshift mutations, for a total of four truncating alleles of this gene. Although TPRN is expressed in many tissues, immunolocalization of the protein product in the mouse cochlea shows prominent expression in the taper region of hair cell stereocilia. Consequently, we named the protein taperin.
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Ross CJD, Katzov-Eckert H, Dubé MP, Brooks B, Rassekh SR, Barhdadi A, Feroz-Zada Y, Visscher H, Brown AMK, Rieder MJ, Rogers PC, Phillips MS, Carleton BC, Hayden MR. Genetic variants in TPMT and COMT are associated with hearing loss in children receiving cisplatin chemotherapy. Nat Genet 2009; 41:1345-9. [PMID: 19898482 DOI: 10.1038/ng.478] [Citation(s) in RCA: 248] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Accepted: 10/01/2009] [Indexed: 11/09/2022]
Abstract
Cisplatin is a widely used and effective chemotherapeutic agent, although its use is restricted by the high incidence of irreversible ototoxicity associated with it. In children, cisplatin ototoxicity is a serious and pervasive problem, affecting more than 60% of those receiving cisplatin and compromising language and cognitive development. Candidate gene studies have previously reported associations of cisplatin ototoxicity with genetic variants in the genes encoding glutathione S-transferases and megalin. We report association analyses for 220 drug-metabolism genes in genetic susceptibility to cisplatin-induced hearing loss in children. We genotyped 1,949 SNPs in these candidate genes in an initial cohort of 54 children treated in pediatric oncology units, with replication in a second cohort of 112 children recruited through a national surveillance network for adverse drug reactions in Canada. We identified genetic variants in TPMT (rs12201199, P value = 0.00022, OR = 17.0, 95% CI 2.3-125.9) and COMT (rs9332377, P value = 0.00018, OR = 5.5, 95% CI 1.9-15.9) associated with cisplatin-induced hearing loss in children.
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Affiliation(s)
- Colin J D Ross
- Department of Medical Genetics, University of British Columbia, Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
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MicroRNAs and epigenetic regulation in the mammalian inner ear: implications for deafness. Mamm Genome 2009; 20:581-603. [PMID: 19876605 DOI: 10.1007/s00335-009-9230-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Accepted: 09/30/2009] [Indexed: 01/19/2023]
Abstract
Sensorineural hearing loss is the most common sensory disorder in humans and derives, in most cases, from inner-ear defects or degeneration of the cochlear sensory neuroepithelial hair cells. Genetic factors make a significant contribution to hearing impairment. While mutations in 51 genes have been associated with hereditary sensorineural nonsyndromic hearing loss (NSHL) in humans, the responsible mutations in many other chromosomal loci linked with NSHL have not been identified yet. Recently, mutations in a noncoding microRNA (miRNA) gene, MIR96, which is expressed specifically in the inner-ear hair cells, were linked with progressive hearing loss in humans and mice. Furthermore, additional miRNAs were found to have essential roles in the development and survival of inner-ear hair cells. Epigenetic mechanisms, in particular, DNA methylation and histone modifications, have also been implicated in human deafness, suggesting that several layers of noncoding genes that have never been studied systematically in the inner-ear sensory epithelia are required for normal hearing. This review aims to summarize the current knowledge about the roles of miRNAs and epigenetic regulatory mechanisms in the development, survival, and function of the inner ear, specifically in the sensory epithelia, tectorial membrane, and innervation, and their contribution to hearing.
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