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Danilchenko VY, Zytsar MV, Maslova EA, Orishchenko KE, Posukh OL. Insight into the Natural History of Pathogenic Variant c.919-2A>G in the SLC26A4 Gene Involved in Hearing Loss: The Evidence for Its Common Origin in Southern Siberia (Russia). Genes (Basel) 2023; 14:genes14040928. [PMID: 37107686 PMCID: PMC10137394 DOI: 10.3390/genes14040928] [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: 03/19/2023] [Revised: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Pathogenic variants in the SLC26A4 gene leading to nonsyndromic recessive deafness (DFNB4), or Pendred syndrome, are some of the most common causes of hearing loss worldwide. Earlier, we found a high proportion of SLC26A4-related hearing loss with prevailing pathogenic variant c.919-2A>G (69.3% among all mutated SLC26A4 alleles that have been identified) in Tuvinian patients belonging to the indigenous Turkic-speaking Siberian people living in the Tyva Republic (Southern Siberia, Russia), which implies a founder effect in the accumulation of c.919-2A>G in Tuvinians. To evaluate a possible common origin of c.919-2A>G, we genotyped polymorphic STR and SNP markers, intragenic and flanking SLC26A4, in patients homozygous for c.919-2A>G and in healthy controls. The common STR and SNP haplotypes carrying c.919-2A>G were revealed, which convincingly indicates the origin of c.919-2A>G from a single ancestor, supporting a crucial role of the founder effect in the c.919-2A>G prevalence in Tuvinians. Comparison analysis with previously published data revealed the identity of the small SNP haplotype (~4.5 kb) in Tuvinian and Han Chinese carriers of c.919-2A>G, which suggests their common origin from founder chromosomes. We assume that c.919-2A>G could have originated in the geographically close territories of China or Tuva and subsequently spread to other regions of Asia. In addition, the time intervals of the c.919-2A>G occurrence in Tuvinians were roughly estimated.
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Affiliation(s)
- Valeriia Yu Danilchenko
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Marina V Zytsar
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Ekaterina A Maslova
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Konstantin E Orishchenko
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Olga L Posukh
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Novosibirsk State University, 630090 Novosibirsk, Russia
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2
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Sharma N, Kumari D, Panigrahi I, Khetarpal P. A systematic review of the monogenic causes of Non-Syndromic Hearing Loss (NSHL) and discussion of Current Diagnosis and Treatment options. Clin Genet 2023; 103:16-34. [PMID: 36089522 DOI: 10.1111/cge.14228] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 12/13/2022]
Abstract
Hearing impairment is one of the most widespread inheritable sensory disorder affecting at least 1 in every 1000 born. About two-third of hereditary hearing loss (HHL) disorders are non-syndromic. To provide comprehensive update of monogenic causes of non-syndromic hearing loss (NSHL), literature search has been carried out with appropriate keywords in the following databases-PubMed, Google Scholar, Cochrane library, and Science Direct. Out of 2214 papers, 271 papers were shortlisted after applying inclusion and exclusion criterion. Data extracted from selected papers include information about gene name, identified pathogenic variants, ethnicity of the patient, age of onset, gender, title, authors' name, and year of publication. Overall, pathogenic variants in 98 different genes have been associated with NSHL. These genes have important role to play during early embryonic development in ear structure formation and hearing development. Here, we also review briefly the recent information about diagnosis and treatment approaches. Understanding pathogenic genetic variants are helpful in the management of affected and may offer targeted therapies in future.
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Affiliation(s)
- Nandita Sharma
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Divya Kumari
- Department of Pediatrics Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Inusha Panigrahi
- Department of Pediatrics Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Preeti Khetarpal
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
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3
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Lezirovitz K, Mingroni-Netto RC. Genetic etiology of non-syndromic hearing loss in Latin America. Hum Genet 2021; 141:539-581. [PMID: 34652575 DOI: 10.1007/s00439-021-02354-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/23/2021] [Indexed: 12/16/2022]
Abstract
Latin America comprises all countries from South and Central America, in addition to Mexico. It is characterized by a complex mosaic of regions with heterogeneous genetic profiles regarding the geographical origin of the ancestors and proportions of admixture between the Native American, European and African components. In the first years following the findings of the role of the GJB2/GJB6 genes in the etiology of hearing loss, most scientific investigations about the genetics of hearing loss in Latin America focused on assessing the frequencies of pathogenic variants in these genes. More recently, modern techniques allowed researchers in Latin America to make exciting contributions to the finding of new candidate genes, novel mechanisms of inheritance in previously known genes, and characterize a wide diversity of variants, many of them unique to Latin America. This review aimed to provide a general landscape of the genetic studies about non-syndromic hearing loss in Latin America and their main scientific contributions. It allows the conclusion that, although there are similar contributions of some genes, such as GJB2/GJB6, when compared to European and North American countries, Latin American populations revealed some peculiarities that indicate the need for tailored strategies of screening and diagnosis to specific geographic regions.
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Affiliation(s)
- Karina Lezirovitz
- Laboratório de Otorrinolaringologia/LIM32, Faculdade de Medicina, Hospital das Clínicas, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Regina Célia Mingroni-Netto
- Departamento de Genética e Biologia Evolutiva, Centro de Pesquisas sobre o Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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Koohiyan M, Hashemzadeh-Chaleshtori M, Tabatabaiefar MA. Molecular diagnosis of SLC26A4-related hereditary hearing loss in a group of patients from two provinces of Iran. Intractable Rare Dis Res 2021; 10:23-30. [PMID: 33614372 PMCID: PMC7882080 DOI: 10.5582/irdr.2020.03090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The SLC26A4 gene has been described as the second gene involved in most cases of autosomal recessive non-syndromic hearing loss (ARNSHL), after GJB2. Over 500 different SLC26A4 mutations have been reported, with each ethnic population having its own distinctive mutations. Here, we aimed to determine the frequency and mutation profile of the SLC26A4 gene from two different provinces (center and west) of Iran. This study included 50 nuclear families with two or more siblings segregating presumed ARNSHL. All affected tested negative for mutations in GJB2 at the DFNB1 locus and were therefore screened for autozygosity by descent using short tandem repeat polymorphisms (STRPs) of DFNB4. Sanger sequencing was performed to screen the 20 exons of the SLC26A4 gene for the families linked to this locus. In silico analyses were also performed using available software tools. Four out of 25 (16%) and 3 of 25 (12%) studied families of Isfahan and Hamedan provinces, respectively. were linked to DFNB4. Sanger sequencing led to the identification of six different mutations, one of which (c.919-2A>G) was recurrent and accounted for 31% of all mutant alleles. One out of 7 (14.3%) families with mutations were confirmed to be Pendred syndrome (PS). The SLC26A4 mutations have a high carrying rate in ARNSHL Iranian patients. The identification of a disease causing mutation can be used to establish a genotypic diagnosis and provide important information to the patients and their families.
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Affiliation(s)
- Mahbobeh Koohiyan
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
- Cancer Research Center, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Morteza Hashemzadeh-Chaleshtori
- Cellular and Molecular Research Center, Basic Health Research Institute, Shahrekord University of Medical Sciences, Shahrekord, 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
- Address correspondence to:Mohammad Amin Tabatabaiefar, Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Hezarjarib St., Isfahan 81746-7346, Iran. E-mail:
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Malesci R, Russo R, Monzillo C, Laria C, Corvino V, Auletta G, Iolascon A, Franzè A. Bimodal strategy for excellent audiological rehabilitation in a subject with a novel nonsense mutation of the SLC26A4 gene: A case report. Int J Pediatr Otorhinolaryngol 2020; 134:110018. [PMID: 32251972 DOI: 10.1016/j.ijporl.2020.110018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 10/24/2022]
Abstract
Sensorineural hearing loss is a heterogeneous disease caused by mutations in many genes. However, in the presence of enlarged vestibular aqueduct, it is frequently associated with mutations in the solute carrier family 26 member 4 (SLC26A4), a gene causative of a syndromic form (Pendred) as well as a non-syndromic form of hearing loss (DFNB4). We describe a clinical case presenting bilateral sensorineural hearing loss and enlarged vestibular aqueduct in which a novel homozygous SLC26A4 mutation was identified. Despite a late diagnosis of hearing loss, a peculiar rehabilitation therapy strategy was identified that provided excellent results.
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Affiliation(s)
- Rita Malesci
- Institute of Audiology, Dept. of Neurosciences, Reproductive and Odontostomatologic Sciences, University of Naples Federico II, Naples, Italy.
| | - Roberta Russo
- Dept. of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Italy; CEINGE- Advanced Biotechnologies, Naples, Italy.
| | - Carmela Monzillo
- Institute of Audiology, Dept. of Neurosciences, Reproductive and Odontostomatologic Sciences, University of Naples Federico II, Naples, Italy.
| | - Carla Laria
- Institute of Audiology, Dept. of Neurosciences, Reproductive and Odontostomatologic Sciences, University of Naples Federico II, Naples, Italy.
| | - Virginia Corvino
- Institute of Audiology, Dept. of Neurosciences, Reproductive and Odontostomatologic Sciences, University of Naples Federico II, Naples, Italy.
| | - Gennaro Auletta
- Institute of Audiology, Dept. of Neurosciences, Reproductive and Odontostomatologic Sciences, University of Naples Federico II, Naples, Italy.
| | - Achille Iolascon
- Dept. of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Italy; CEINGE- Advanced Biotechnologies, Naples, Italy.
| | - Annamaria Franzè
- Institute of Audiology, Dept. of Neurosciences, Reproductive and Odontostomatologic Sciences, University of Naples Federico II, Naples, Italy; CEINGE- Advanced Biotechnologies, Naples, Italy.
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Koohiyan M. A systematic review of SLC26A4 mutations causing hearing loss in the Iranian population. Int J Pediatr Otorhinolaryngol 2019; 125:1-5. [PMID: 31228605 DOI: 10.1016/j.ijporl.2019.06.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/19/2019] [Accepted: 06/12/2019] [Indexed: 11/16/2022]
Abstract
OBJECTIVES The genetics of sensorineural hearing loss is characterized by a high degree of heterogeneity. In spite of this, mutations in the SLC26A4 gene, have been reported to be the second most common contributor after those of GJB2 in many populations. However, different results have been reported for the frequency of SLC26A4 mutations in Iran, which varies between 0 and 12.3%. Here, we have taken together and reviewed the spectrum and frequency of the reported SLC26A4 mutations to provide a comprehensive collection of data for SLC26A4 mutations and HL in the Iranian population and considered founder mutations. METHODS A systematic literature review of the PubMed, Google Scholar, Web of Science, and Science Direct databases was conducted for articles published before March 2019. The primary data of these studies including the number of samples, mutation frequency and so on were extracted. RESULTS Nine studies involved 827 unrelated families were included and analyzed for the type and prevalence of the SLC26A4 gene mutations. Altogether 39 different genetic mutations were detected. SLC26A4 mutations were found to be 6.39% in the population studied which is significantly lower than that identified in the east Asia. However, c.1334T > G was the most common mutation accounting for 10% of the populations studied. CONCLUSIONS This data gives an overview of the SLC26A4 mutations in Iran, which could be used for screening, diagnostic programs of live births and genetic counseling.
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Affiliation(s)
- Mahbobeh Koohiyan
- Cancer Research Center, Shahrekord University of Medical Sciences, Rahmatieh, Shahrekord, 8813833435, Iran.
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Carvalho SDCES, Grangeiro CHP, Picanço-Albuquerque CG, Dos Anjos TO, De Molfetta GA, Silva WA, Ferraz VEDF. Contribution of SLC26A4 to the molecular diagnosis of nonsyndromic prelingual sensorineural hearing loss in a Brazilian cohort. BMC Res Notes 2018; 11:546. [PMID: 30068397 PMCID: PMC6071330 DOI: 10.1186/s13104-018-3647-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 07/24/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Hereditary hearing loss (HL) is the most common sensorineural disorder in humans. Besides mutations in GJB2 and GJB6 genes, pathogenic variants in the SLC26A4 gene have been reported as a cause of hereditary HL due to its role in the physiology of the inner ear. In this research we wanted to investigate the prevalence of mutations in SLC26A4 in Brazilian patients with nonsyndromic prelingual sensorineural HL. We applied the high-resolution melting technique to screen 88 DNA samples from unrelated deaf individuals that were previously screened for GJB2, GJB6 and MT-RNR1 mutations. RESULTS The frequency of mutations in the SLC26A4 gene was 28.4%. Two novel mutations were found: p.Ile254Val and p.Asn382Lys. The mutation c.-66C>G (rs17154282) in the promoter region of SLC26A4, was the most frequent mutation found and was significantly associated with nonsyndromic prelingual sensorineural HL. After mutations in the GJB2, GJB6 and mitochondrial genes, SLC26A4 mutations are considered the next most common cause of hereditary HL in Brazilian as well as in other populations, which corroborates with our data. Furthermore, we suggest the inclusion of the SCL26A4 gene in the investigation of hereditary HL since there was an increase in the frequency of the mutations found, up to 22.7%.
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Affiliation(s)
| | - Carlos Henrique Paiva Grangeiro
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.,Medical Genetics Service of the University Hospital of the Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Clarissa Gondim Picanço-Albuquerque
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.,Medical Genetics Service of the University Hospital of the Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Thaís Oliveira Dos Anjos
- Center for Medical Genomics at University Hospital of the Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Greice Andreotti De Molfetta
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.,Center for Medical Genomics at University Hospital of the Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Wilson Araujo Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.,Center for Medical Genomics at University Hospital of the Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.,Regional Blood Center of Ribeirão Preto (FUNDHERP) of the Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Victor Evangelista de Faria Ferraz
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil. .,Medical Genetics Service of the University Hospital of the Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil. .,Center for Medical Genomics at University Hospital of the Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.
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Nonose RW, Lezirovitz K, de Mello Auricchio MTB, Batissoco AC, Yamamoto GL, Mingroni-Netto RC. Mutation analysis of SLC26A4 (Pendrin) gene in a Brazilian sample of hearing-impaired subjects. BMC MEDICAL GENETICS 2018; 19:73. [PMID: 29739340 PMCID: PMC5941635 DOI: 10.1186/s12881-018-0585-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 04/19/2018] [Indexed: 12/18/2022]
Abstract
Background Mutations in the SLC26A4 gene are associated with Pendred syndrome and autosomal recessive non-syndromic deafness (DFNB4). Both disorders have similar audiologic characteristics: bilateral hearing loss, often severe or profound, which may be associated with abnormalities of the inner ear, such as dilatation of the vestibular aqueduct or Mondini dysplasia. But, in Pendred syndrome (OMIM #274600), with autosomal recessive inheritance, besides congenital sensorineural deafness, goiter or thyroid dysfunctions are frequently present. The aim of this study was to determine whether mutations in SLC26A4 are a frequent cause of hereditary deafness in Brazilian patients. Methods Microsatellite haplotypes linked to SLC26A4 were investigated in 68 families presenting autosomal recessive non-syndromic deafness. In the probands of the 16 families presenting segregation consistent with linkage to SLC26A4, Sanger sequencing of the 20 coding exons was performed. In an additional sample of 15 individuals with suspected Pendred syndrome, because of the presence of hypothyroidism or cochleovestibular malformations, the SLC26A4 gene coding region was also sequenced. Results In two of the 16 families with indication of linkage to SLC26A4, the probands were found to be compound heterozygotes for probably pathogenic different mutations: three novel (c.1003 T > G (p. F335 V), c.1553G > A (p.W518X), c.2235 + 2 T > C (IVS19 + 2 T > C), and one already described, c.84C > A (p.S28R). Two of the 15 individuals with suspected Pendred syndrome because of hypothyreoidism or cochleovestibular malformations were monoallelic for likely pathogenic mutations: a splice mutation (IVS7 + 2 T > C) and the previously described c.1246A > C (p.T416P). Pathogenic copy number variations were excluded in the monoallelic cases and in those with normal results after Sanger sequencing. Additional mutations in the SLC26A4 gene or other definite molecular cause for deafness were not identified in the monoallelic patients, after exome sequencing. Conclusions Biallelic pathogenic mutations in SLC26A4 explained ~ 3% of cases selected because of autosomal recessive deafness. Monoallelic mutations were present in ~ 13% of isolated cases of deafness with cochleovestibular malformations or suspected Pendred syndrome. These data reinforce the importance of mutation screening of SLC26A4 in Brazilian subjects and highlight the elevated frequency of monoallelic patients.
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Affiliation(s)
- Renata Watanabe Nonose
- Centro de Pesquisas sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Karina Lezirovitz
- Centro de Pesquisas sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.,Laboratório de Investigação Médica/LIM32 do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Maria Teresa Balester de Mello Auricchio
- Centro de Pesquisas sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Ana Carla Batissoco
- Centro de Pesquisas sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Guilherme Lopes Yamamoto
- Centro de Pesquisas sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Regina Célia Mingroni-Netto
- Centro de Pesquisas sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
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Mapping pathogenic mutations suggests an innovative structural model for the pendrin (SLC26A4) transmembrane domain. Biochimie 2016; 132:109-120. [PMID: 27771369 DOI: 10.1016/j.biochi.2016.10.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/03/2016] [Indexed: 12/16/2022]
Abstract
Human pendrin (SLC26A4) is an anion transporter mostly expressed in the inner ear, thyroid and kidney. SLC26A4 gene mutations are associated with a broad phenotypic spectrum, including Pendred Syndrome and non-syndromic hearing loss with enlarged vestibular aqueduct (ns-EVA). No experimental structure of pendrin is currently available, making phenotype-genotype correlations difficult as predictions of transmembrane (TM) segments vary in number. Here, we propose a novel three-dimensional (3D) pendrin transmembrane domain model based on the SLC26Dg transporter. The resulting 14 TM topology was found to include two non-canonical transmembrane segments crucial for pendrin activity. Mutation mapping of 147 clinically validated pathological mutations shows that most affect two previously undescribed TM regions.
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de Moraes VCS, Bernardinelli E, Zocal N, Fernandez JA, Nofziger C, Castilho AM, Sartorato EL, Paulmichl M, Dossena S. Reduction of Cellular Expression Levels Is a Common Feature of Functionally Affected Pendrin (SLC26A4) Protein Variants. Mol Med 2016; 22:41-53. [PMID: 26752218 DOI: 10.2119/molmed.2015.00226] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 01/04/2016] [Indexed: 11/06/2022] Open
Abstract
Sequence alterations in the pendrin gene (SLC26A4) leading to functionally affected protein variants are frequently involved in the pathogenesis of syndromic and nonsyndromic deafness. Considering the high number of SLC26A4 sequence alterations reported to date, discriminating between functionally affected and unaffected pendrin protein variants is essential in contributing to determine the genetic cause of deafness in a given patient. In addition, identifying molecular features common to the functionally affected protein variants can be extremely useful to design future molecule-directed therapeutic approaches. Here we show the functional and molecular characterization of six previously uncharacterized pendrin protein variants found in a cohort of 58 Brazilian deaf patients. Two variants (p.T193I and p.L445W) were undetectable in the plasma membrane, completely retained in the endoplasmic reticulum and showed no transport function; four (p.P142L, p.G149R, p.C282Y and p.Q413R) showed reduced function and significant, although heterogeneous, expression levels in the plasma membrane. Importantly, total expression levels of all of the functionally affected protein variants were significantly reduced with respect to the wild-type and a fully functional variant (p.R776C), regardless of their subcellular localization. Interestingly, reduction of expression may also reduce the transport activity of variants with an intrinsic gain of function (p.Q413R). As reduction of overall cellular abundance was identified as a common molecular feature of pendrin variants with affected function, the identification of strategies to prevent reduction in expression levels may represent a crucial step of potential future therapeutic interventions aimed at restoring the transport activity of dysfunctional pendrin variants.
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Affiliation(s)
- Vanessa C S de Moraes
- Center of Molecular Biology and Genetic Engineering (CBMEG), Molecular Biology Laboratory, State University of Campinas, UNICAMP, Campinas/São Paulo, Brazil
| | - Emanuele Bernardinelli
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, Salzburg, Austria
| | - Nathalia Zocal
- Center of Molecular Biology and Genetic Engineering (CBMEG), Molecular Biology Laboratory, State University of Campinas, UNICAMP, Campinas/São Paulo, Brazil
| | - Jhonathan A Fernandez
- Center of Molecular Biology and Genetic Engineering (CBMEG), Molecular Biology Laboratory, State University of Campinas, UNICAMP, Campinas/São Paulo, Brazil
| | - Charity Nofziger
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, Salzburg, Austria
| | - Arthur M Castilho
- Otology, Audiology and Implantable Ear Prostheses, State University of Campinas, UNICAMP, Campinas/São Paulo, Brazil
| | - Edi L Sartorato
- Center of Molecular Biology and Genetic Engineering (CBMEG), Molecular Biology Laboratory, State University of Campinas, UNICAMP, Campinas/São Paulo, Brazil
| | - Markus Paulmichl
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, Salzburg, Austria
| | - Silvia Dossena
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, Salzburg, Austria
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Sloan-Heggen CM, Babanejad M, Beheshtian M, Simpson AC, Booth KT, Ardalani F, Frees KL, Mohseni M, Mozafari R, Mehrjoo Z, Jamali L, Vaziri S, Akhtarkhavari T, Bazazzadegan N, Nikzat N, Arzhangi S, Sabbagh F, Otukesh H, Seifati SM, Khodaei H, Taghdiri M, Meyer NC, Daneshi A, Farhadi M, Kahrizi K, Smith RJH, Azaiez H, Najmabadi H. Characterising the spectrum of autosomal recessive hereditary hearing loss in Iran. J Med Genet 2015; 52:823-9. [PMID: 26445815 PMCID: PMC4733363 DOI: 10.1136/jmedgenet-2015-103389] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 09/14/2015] [Indexed: 11/04/2022]
Abstract
BACKGROUND Countries with culturally accepted consanguinity provide a unique resource for the study of rare recessively inherited genetic diseases. Although hereditary hearing loss (HHL) is not uncommon, it is genetically heterogeneous, with over 85 genes causally implicated in non-syndromic hearing loss (NSHL). This heterogeneity makes many gene-specific types of NSHL exceedingly rare. We sought to define the spectrum of autosomal recessive HHL in Iran by investigating both common and rarely diagnosed deafness-causing genes. DESIGN Using a custom targeted genomic enrichment (TGE) panel, we simultaneously interrogated all known genetic causes of NSHL in a cohort of 302 GJB2-negative Iranian families. RESULTS We established a genetic diagnosis for 67% of probands and their families, with over half of all diagnoses attributable to variants in five genes: SLC26A4, MYO15A, MYO7A, CDH23 and PCDH15. As a reflection of the power of consanguinity mapping, 26 genes were identified as causative for NSHL in the Iranian population for the first time. In total, 179 deafness-causing variants were identified in 40 genes in 201 probands, including 110 novel single nucleotide or small insertion-deletion variants and three novel CNV. Several variants represent founder mutations. CONCLUSION This study attests to the power of TGE and massively parallel sequencing as a diagnostic tool for the evaluation of hearing loss in Iran, and expands on our understanding of the genetics of HHL in this country. Families negative for variants in the genes represented on this panel represent an excellent cohort for novel gene discovery.
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Affiliation(s)
- Christina M Sloan-Heggen
- Molecular Otolaryngology & Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Department of Molecular Physiology & Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Mojgan Babanejad
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Allen C Simpson
- Molecular Otolaryngology & Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Kevin T Booth
- Molecular Otolaryngology & Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Fariba Ardalani
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kathy L Frees
- Molecular Otolaryngology & Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Reza Mozafari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Zohreh Mehrjoo
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Leila Jamali
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Saeideh Vaziri
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Tara Akhtarkhavari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Niloofar Bazazzadegan
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Nooshin Nikzat
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Hasan Otukesh
- Hazrat –e – Ali Asghar Educational & Treatment Center, Iran University of Medical Sciences, Tehran, Iran
| | | | | | | | - Nicole C Meyer
- Molecular Otolaryngology & Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Ahmad Daneshi
- Head and Neck Surgery Department and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Farhadi
- Head and Neck Surgery Department and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Richard JH Smith
- Molecular Otolaryngology & Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Department of Molecular Physiology & Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Interdepartmental PhD Program in Genetics, University of Iowa, Iowa City, IA 52242, USA
| | - Hela Azaiez
- Molecular Otolaryngology & Renal Research Labs, Department of Otolaryngology-Head and Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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Svidnicki MCCM, Silva-Costa SM, Ramos PZ, dos Santos NZP, Martins FTA, Castilho AM, Sartorato EL. Screening of genetic alterations related to non-syndromic hearing loss using MassARRAY iPLEX® technology. BMC MEDICAL GENETICS 2015; 16:85. [PMID: 26399936 PMCID: PMC4581412 DOI: 10.1186/s12881-015-0232-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 09/15/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND Recent advances in molecular genetics have enabled to determine the genetic causes of non-syndromic hearing loss, and more than 100 genes have been related to the phenotype. Due to this extraordinary genetic heterogeneity, a large percentage of patients remain without any molecular diagnosis. This condition imply the need for new methodological strategies in order to detect a greater number of mutations in multiple genes. In this work, we optimized and tested a panel of 86 mutations in 17 different genes screened using a high-throughput genotyping technology to determine the molecular etiology of hearing loss. METHODS The technology used in this work was the MassARRAY iPLEX® platform. This technology uses silicon chips and DNA amplification products for accurate genotyping by mass spectrometry of previous reported mutations. The generated results were validated using conventional techniques, as direct sequencing, multiplex PCR and RFLP-PCR. RESULTS An initial genotyping of control subjects, showed failures in 20 % of the selected alterations. To optimize these results, the failed tests were re-designed and new primers were synthesized. Then, the specificity and sensitivity of the panel demonstrated values above 97 %. Additionally, a group of 180 individuals with NSHL without a molecular diagnosis was screened to test the diagnostic value of our panel, and mutations were identified in 30 % of the cases. In 20 % of the individuals, it was possible to explain the etiology of the HL. Mutations in GJB2 gene were the most prevalent, followed by other mutations in in SLC26A4, CDH23, MT-RNR1, MYO15A, and OTOF genes. CONCLUSIONS The MassARRAY technology has the potential for high-throughput identification of genetic variations. However, we demonstrated that optimization is required to increase the genotyping success and accuracy. The developed panel proved to be efficient and cost-effective, being suitable for applications involving the molecular diagnosis of hearing loss.
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Affiliation(s)
- Maria Carolina Costa Melo Svidnicki
- Human Molecular Genetics Laboratory, Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Sueli Matilde Silva-Costa
- Human Molecular Genetics Laboratory, Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Priscila Zonzini Ramos
- Human Molecular Genetics Laboratory, Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Nathalia Zocal Pereira dos Santos
- Human Molecular Genetics Laboratory, Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Fábio Tadeu Arrojo Martins
- Human Molecular Genetics Laboratory, Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Arthur Menino Castilho
- ENT Department, Faculty of Medical Sciences, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
| | - Edi Lúcia Sartorato
- Human Molecular Genetics Laboratory, Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
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Tsukada K, Nishio SY, Hattori M, Usami SI. Ethnic-specific spectrum of GJB2 and SLC26A4 mutations: their origin and a literature review. Ann Otol Rhinol Laryngol 2015; 124 Suppl 1:61S-76S. [PMID: 25999548 DOI: 10.1177/0003489415575060] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE The mutation spectrum of the GJB2 and SLC26A4 genes, the 2 most common genes causing deafness, are known to be ethnic specific. In this study, the spectrum of the reported GJB2 and SLC26A4 mutations in different populations are reviewed and considered from a human migration perspective. METHODS Fifty-two and 17 articles on GJB2 and SLC26A4 mutations, respectively, were reviewed through the PubMed database from April 1996 to September 2014. The 4 most prevalent mutations were selected and compared. A cluster analysis was subsequently performed for these selected mutations. RESULTS The present review of frequent mutations shows the ethnic-specific GJB2 and SLC26A4 gene mutation spectrum. A cluster analysis of the GJB2 and SLC26A4 genes revealed similarities between ethnic populations. CONCLUSION The mutation spectrum reviewed in this study clearly indicated that the frequent mutations in the GJB2 and SLC26A4 genes are consistent with the founder mutation hypothesis. A comparison with the Y-chromosome phylogenetic tree indicated that these mutations may have occurred during human migration.
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Affiliation(s)
- Keita Tsukada
- 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
| | - Mitsuru Hattori
- Department of Otorhinolaryngology, 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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Yazdanpanahi N, Tabatabaiefar MA, Bagheri N, Azadegan Dehkordi F, Farrokhi E, Hashemzadeh Chaleshtori M. The role and spectrum of SLC26A4 mutations in Iranian patients with autosomal recessive hereditary deafness. Int J Audiol 2014; 54:124-30. [PMID: 25290043 DOI: 10.3109/14992027.2014.944276] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVE To determine the prevalence and types of SLC26A4 mutations and the relevant phenotypes in a series of Iranian deaf patients. DESIGN A descriptive laboratory study. STUDY SAMPLE One hundred and twenty-one families including 60 unrelated patients and 61 unrelated multiplex families with autosomal recessive deafness were included. In the 61 multiplex families, linkage was conducted for short tandem repeats (STRs) of the DFNB4. Selected individuals from the linked families and all of the 60 deaf individuals were subjected to sequencing of SLC26A4. RESULTS Seven out of the 61 (11.5%) families were linked to the locus which upon further inquiry led to identification of eight different mutations. Also, five out of the 60 (8.3%) patients were positive for the mutations. The SLC26A4 mutations clarified in 9.1% (12 families) of total investigated alleles included: c.2106delG, c.65-66insT, c.881-882delAC, c.863-864insT, c.1226G> A, c.1238A> G, c.1334T> G, c.1790T> C, c.1489G> A, c.919-2A> G (IVS7-2A> G), c.1412delT, and c.1197delT. Six out of 12 (50%) families with mutations were confirmed to be Pendred syndrome (PS). CONCLUSIONS The results probably suggest a high prevalence and specificity of SLC26A4 mutations among Iranian deaf patients. Molecular study of SLC26A4 may lead to elucidation of the population-specific mutation profile which is of importance in diagnostics of deafness.
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Affiliation(s)
- Nasrin Yazdanpanahi
- * Department of Biochemistry, Falavarjan Branch, Islamic Azad University , Isfahan , Iran
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15
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JIANG HUA, CHEN JIA, SHAN XINJI, LI YING, HE JIANGUO, YANG BEIBEI. Prevalence and range of GJB2 and SLC26A4 mutations in patients with autosomal recessive non-syndromic hearing loss. Mol Med Rep 2014; 10:379-86. [DOI: 10.3892/mmr.2014.2148] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 03/13/2014] [Indexed: 11/05/2022] Open
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Kopp P. Mutations in the Pendred Syndrome (PDS/SLC26A) gene: an increasingly complex phenotypic spectrum from goiter to thyroid hypoplasia. J Clin Endocrinol Metab 2014; 99:67-9. [PMID: 24384016 DOI: 10.1210/jc.2013-4319] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Peter Kopp
- Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
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Kühnen P, Turan S, Fröhler S, Güran T, Abali S, Biebermann H, Bereket A, Grüters A, Chen W, Krude H. Identification of PENDRIN (SLC26A4) mutations in patients with congenital hypothyroidism and "apparent" thyroid dysgenesis. J Clin Endocrinol Metab 2014; 99:E169-76. [PMID: 24248179 DOI: 10.1210/jc.2013-2619] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
CONTEXT Congenital hypothyroidism, the most frequent endocrine congenital disease, can occur either based on a thyroid hormone biosynthesis defect or can predominantly be due to thyroid dysgenesis. However, a genetic cause could so far only be identified in less than 10% of patients with a thyroid dysgenesis. OBJECTIVES Exome sequencing was used for the first time to find additional genetic defects in thyroid dysgenesis. PATIENTS AND METHODS In a consanguineous family with thyroid dysgenesis, exome sequencing was applied, and findings were further validated by Sanger sequencing in a cohort of 94 patients with thyroid dysgenesis. RESULTS By exome sequencing we identified a homozygous missense mutation (p.Leu597Ser) in the SLC26A4 gene of a patient with hypoplastic thyroid tissue, who was otherwise healthy. In the cohort of patients with thyroid dysgenesis, we observed a second case with a homozygous missense mutation (p.Gln413Arg) in the SLC26A4 gene, who was additionally affected by severe hearing problems. Both mutations were previously described as loss-of-function mutations in patients with Pendred syndrome and nonsyndromic enlarged vestibular aqueduct. CONCLUSION We unexpectedly identified SLC26A4 mutations that were hitherto diagnosed in thyroid dyshormonogenesis patients, now for the first time in patients with structural thyroid defects. This result resembles the historic description of thyroid atrophy in patients with the so-called myxedematous form of cretinism after severe iodine deficiency. Most likely the thyroid defect of the two homozygous SLC26A4 gene mutation carriers represents a kind of secondary thyroid atrophy, rather than a primary defect of thyroid development in the sense of thyroid agenesis. Our study extends the variable clinical spectrum of patients with SLC26A4 mutations and points out the necessity to analyze the SLC26A4 gene in patients with apparent thyroid dysgenesis in addition to the known candidate genes TSHR, PAX8, NKX2.1, NKX2.5, and FOXE1.
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Affiliation(s)
- Peter Kühnen
- Institute of Experimental Pediatric Endocrinology (P.K., H.B., A.G., H.K.), Charité Universitätsmedizin Berlin, 13353 Berlin, Germany; Department of Pediatric Endocrinology and Diabetes (S.T., T.G., S.A., A.B.), Marmara University Hospital, 34722 Istanbul, Turkey; and Max-Delbrück Center for Molecular Medicine (S.F., W.C.), 13092 Berlin-Buch, Germany
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Martins FTA, Ramos PZ, Svidnicki MCCM, Castilho AM, Sartorato EL. Optimization of simultaneous screening of the main mutations involved in non-syndromic deafness using the TaqMan® OpenArray™ Genotyping platform. BMC MEDICAL GENETICS 2013; 14:112. [PMID: 24156272 PMCID: PMC4015212 DOI: 10.1186/1471-2350-14-112] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 10/14/2013] [Indexed: 11/23/2022]
Abstract
Background Hearing loss is the most common sensory deficit in humans, affecting approximately 10% of the global population. In developed countries, one in every 500 individuals suffers from severe to profound bilateral sensorineural hearing loss. For those up to 5 years old, the proportion is higher, at 2.7 in 1000 individuals, and for adolescents the average is 3.5 in 1000. Among the causes of hearing loss, more than 50% are related to genetic factors. To date, nearly 150 loci and 64 genes have been associated with hearing loss. Mutations in the GJB2 gene, which encodes connexin 26, constitute the main genetic cause. So far, more than 300 variations have been described in this gene. As a response to the clinical and genetic heterogeneity of hearing loss and the importance of correct molecular diagnosis of individuals with hereditary hearing loss, this study worked in the optimization for a diagnostic protocol employing a high-throughput genotyping technology. Methods For this work, was used the TaqMan® OpenArray™ Genotyping platform. This is a high performance, high-throughput technology based on real-time PCR, which enables the evaluation of up to 3072 SNPs (Single Nucleotide Polymorphisms), point mutations, small deletions, and insertions, using a single genotyping plate. For the study, were selected the layout allowing to analyze 32 alterations in 96 individuals simultaneously. In the end, the generated results were validated by conventional techniques, as direct sequencing, Multiplex PCR and RFLP-PCR. Results A total of 376 individuals were analyzed, of which 94 were healthy controls, totaling 4 plates in duplicate. All 31 of the changes analyzed were present in the nuclear genes GJB2, GJB6, CRYL1, TMC1, SLC26A4, miR-96, and OTOF, and in the mitochondrial genes MT-RNR1 and MT-TS1. The reactions were subsequently validated by established techniques (direct sequencing, multiplex PCR, and RFLP-PCR) that had previously been used to perform molecular screening of hearing loss at the Human Genetics Laboratory of the Center for Molecular Biology and Genetic Engineering (CBMEG), at the State University of Campinas (UNICAMP). In total, 11,656 genotyping reactions were performed. Of these, only 351 reactions failed, representing approximately 3.01% of the total. The average accuracy of genotyping using the OpenArray™ plates was 96.99%. Conclusions The results demonstrated the accuracy, low cost, and good reproducibility of the technique, indicating that the TaqMan® OpenArray™ Genotyping Platform is a useful and reliable tool for application in molecular diagnostic testing of hearing loss.
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Affiliation(s)
- Fábio Tadeu Arrojo Martins
- Human Molecular Genetics Laboratory, Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas - UNICAMP, Campinas, SP, Brazil.
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