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Takahashi S, Homma K. The molecular principles underlying diverse functions of the SLC26 family of proteins. J Biol Chem 2024; 300:107261. [PMID: 38582450 PMCID: PMC11078650 DOI: 10.1016/j.jbc.2024.107261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 03/07/2024] [Accepted: 03/30/2024] [Indexed: 04/08/2024] Open
Abstract
Mammalian SLC26 proteins are membrane-based anion transporters that belong to the large SLC26/SulP family, and many of their variants are associated with hereditary diseases. Recent structural studies revealed a strikingly similar homodimeric molecular architecture for several SLC26 members, implying a shared molecular principle. Now a new question emerges as to how these structurally similar proteins execute diverse physiological functions. In this study, we sought to identify the common versus distinct molecular mechanism among the SLC26 proteins using both naturally occurring and artificial missense changes introduced to SLC26A4, SLC26A5, and SLC26A9. We found: (i) the basic residue at the anion binding site is essential for both anion antiport of SLC26A4 and motor functions of SLC26A5, and its conversion to a nonpolar residue is crucial but not sufficient for the fast uncoupled anion transport in SLC26A9; (ii) the conserved polar residues in the N- and C-terminal cytosolic domains are likely involved in dynamic hydrogen-bonding networks and are essential for anion antiport of SLC26A4 but not for motor (SLC26A5) and uncoupled anion transport (SLC26A9) functions; (iii) the hydrophobic interaction between each protomer's last transmembrane helices, TM14, is not of functional significance in SLC26A9 but crucial for the functions of SLC26A4 and SLC26A5, likely contributing to optimally orient the axis of the relative movements of the core domain with respect to the gate domains within the cell membrane. These findings advance our understanding of the molecular mechanisms underlying the diverse physiological roles of the SLC26 family of proteins.
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Affiliation(s)
- Satoe Takahashi
- Department of Otolaryngology - Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA; Center for Mechanical Excitability, The University of Chicago, Chicago, Illinois, USA
| | - Kazuaki Homma
- Department of Otolaryngology - Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA; Center for Mechanical Excitability, The University of Chicago, Chicago, Illinois, USA; The Hugh Knowles Center for Clinical and Basic Science in Hearing and Its Disorders, Northwestern University, Evanston, Illinois, USA.
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Takahashi S, Kojima T, Wasano K, Homma K. Functional Studies of Deafness-Associated Pendrin and Prestin Variants. Int J Mol Sci 2024; 25:2759. [PMID: 38474007 PMCID: PMC10931795 DOI: 10.3390/ijms25052759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Pendrin and prestin are evolutionary-conserved membrane proteins that are essential for normal hearing. Dysfunction of these proteins results in hearing loss in humans, and numerous deafness-associated pendrin and prestin variants have been identified in patients. However, the pathogenic impacts of many of these variants are ambiguous. Here, we report results from our ongoing efforts to experimentally characterize pendrin and prestin variants using in vitro functional assays. With previously established fluorometric anion transport assays, we determined that many of the pendrin variants identified on transmembrane (TM) 10, which contains the essential anion binding site, and on the neighboring TM9 within the core domain resulted in impaired anion transport activity. We also determined the range of functional impairment in three deafness-associated prestin variants by measuring nonlinear capacitance (NLC), a proxy for motor function. Using the results from our functional analyses, we also evaluated the performance of AlphaMissense (AM), a computational tool for predicting the pathogenicity of missense variants. AM prediction scores correlated well with our experimental results; however, some variants were misclassified, underscoring the necessity of experimentally assessing the effects of variants. Together, our experimental efforts provide invaluable information regarding the pathogenicity of deafness-associated pendrin and prestin variants.
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Affiliation(s)
- Satoe Takahashi
- Department of Otolaryngology—Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Takashi Kojima
- Department of Otolaryngology—Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Department of Otolaryngology, Head and Neck Surgery, National Hospital Organization Tochigi Medical Center, Tochigi 320-0057, Japan
| | - Koichiro Wasano
- Department of Otolaryngology—Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Department of Otolaryngology, Head and Neck Surgery, Tokai University School of Medicine, Isehara 259-1193, Japan
| | - Kazuaki Homma
- Department of Otolaryngology—Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- The Hugh Knowles Center for Clinical and Basic Science in Hearing and Its Disorders, Northwestern University, Evanston, IL 60208, USA
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Wang S, Zhu Y, Xu C, Ding W, Jia H, Bian P, Xu B, Guo Y, Liu X. A novel intronic variant causing aberrant splicing identified in two deaf Chinese siblings with enlarged vestibular aqueducts. Mol Genet Genomic Med 2024; 12:e2361. [PMID: 38348997 PMCID: PMC10863356 DOI: 10.1002/mgg3.2361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 08/13/2023] [Accepted: 12/26/2023] [Indexed: 02/15/2024] Open
Abstract
OBJECTIVE We aimed to evaluate the genotype-phenotype relationship in two Chinese family members with enlarged vestibular aqueduct (EVA). METHODS We collected blood samples and clinical data from each pedigree family member. Genomic DNA was isolated from peripheral leukocytes using standard methods. Targeted next-generation sequencing and Sanger sequencing were performed to find the pathogenic mutation in this family. Minigene assays were used to verify whether the novel intronic mutation SLC26A4c.765+4A>G influenced mRNA splicing. RESULTS Hearing loss in the patients with EVA was diagnosed using auditory tests and imaging examinations. Two pathogenic mutations, c.765+4A>G and c.919-2A>G were detected in SLC26A4. In vitro minigene analysis confirmed that c.765+4A>G variant could cause aberrant splicing, resulting in skipping over exon 6. CONCLUSIONS The SLC26A4c.765+4A>G mutation is the causative variant in the Chinese family with EVA. Particular attention should be paid to intronic variants.
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Affiliation(s)
- Suyang Wang
- Department of Otolaryngology‐Head and Neck SurgeryLanzhou University Second HospitalLanzhouGansuPR China
- Department of Otolaryngology‐Head and Neck SurgeryMaternal and Child Health Hospital of Gansu ProvinceLanzhouGansuChina
| | - Yi‐Ming Zhu
- Department of Otolaryngology‐Head and Neck SurgeryGansu Provincial HospitalLanzhouGansuPR China
| | - ChenYang Xu
- Department of Otolaryngology‐Head and Neck SurgeryLanzhou University Second HospitalLanzhouGansuPR China
| | - Wenjuan Ding
- Department of Otolaryngology‐Head and Neck SurgeryLanzhou University Second HospitalLanzhouGansuPR China
| | - Hui Jia
- Department of Otolaryngology‐Head and Neck SurgeryLanzhou University Second HospitalLanzhouGansuPR China
| | - Panpan Bian
- Department of Otolaryngology‐Head and Neck SurgeryLanzhou University Second HospitalLanzhouGansuPR China
| | - Baicheng Xu
- Department of Otolaryngology‐Head and Neck SurgeryLanzhou University Second HospitalLanzhouGansuPR China
| | - Yufen Guo
- Department of Otolaryngology‐Head and Neck SurgeryLanzhou University Second HospitalLanzhouGansuPR China
- Health Commission of Gansu ProvinceLanzhouGansuPR China
| | - Xiaowen Liu
- Department of Otolaryngology‐Head and Neck SurgeryLanzhou University Second HospitalLanzhouGansuPR China
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Takahashi S, Kojima T, Wasano K, Homma K. Functional studies of deafness-associated pendrin and prestin variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576877. [PMID: 38328051 PMCID: PMC10849616 DOI: 10.1101/2024.01.23.576877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Pendrin and prestin are evolutionary conserved membrane proteins that are essential for normal hearing. Pendrin is an anion transporter required for normal development and maintenance of ion homeostasis in the inner ear, while prestin is a voltage-dependent motor responsible for cochlear amplification essential for high sensitivity and frequency selectivity of mammalian hearing. Dysfunction of these proteins result in hearing loss in humans, and numerous deafness-associated pendrin and prestin variants have been identified in patients. However, the pathogenic impacts of many of these variants are ambiguous. Here we report results from our ongoing efforts in experimentally characterizing pendrin and prestin variants using in vitro functional assays, providing invaluable information regarding their pathogenicity.
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5
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Takahashi S, Homma K. The molecular principles underlying diverse functions of the SLC26 family of proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.10.570988. [PMID: 38106153 PMCID: PMC10723444 DOI: 10.1101/2023.12.10.570988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Mammalian SLC26 proteins are membrane-based anion transporters that belong to the large SLC26/SulP family, and many of their variants are associated with hereditary diseases. Recent structural studies revealed a strikingly similar homodimeric molecular architecture for several SLC26 members, implying a shared molecular principle. Now a new question emerges as to how these structurally similar proteins execute diverse physiological functions. In this study we sought to identify the common vs. distinct molecular mechanism among the SLC26 proteins using both naturally occurring and artificial missense changes introduced to SLC26A4, SLC26A5, and SLC26A9. We found: (i) the basic residue at the anion binding site is essential for both anion antiport of SLC26A4 and motor functions of SLC26A5, and its conversion to a nonpolar residue is crucial but not sufficient for the fast uncoupled anion transport in SLC26A9; (ii) the conserved polar residues in the N- and C-terminal cytosolic domains are likely involved in dynamic hydrogen-bonding networks and are essential for anion antiport of SLC26A4 but not for motor (SLC26A5) and uncoupled anion transport (SLC26A9) functions; (iii) the hydrophobic interaction between each protomer's last transmembrane helices, TM14, is not of functional significance in SLC26A9 but crucial for the functions of SLC26A4 and SLC26A5, likely contributing to optimally orient the axis of the relative movements of the core domain with respect to the gate domains within the cell membrane. These findings advance our understanding of the molecular mechanisms underlying the diverse physiological roles of the SLC26 family of proteins.
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6
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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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Wang Q, Hu J, Bian P, Chen C, Wang Y, Cheng S, Guo Y, Xu B. The effect of SLC26A4 gene mutations on long-term rehabilitative outcomes in cochlear implant patients. Acta Otolaryngol 2023; 143:156-162. [PMID: 36780306 DOI: 10.1080/00016489.2023.2174592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
BACKGROUND SLC26A4 gene mutations related to hearing loss patients can obtain good hearing and speech rehabilitation effects after cochlear implantation (CI). OBJECTIVE To explore the long-term rehabilitative outcomes of CI in patients with different SLC26A4 mutation groups. MATERIAL AND METHODS Clinical data of 71 patients with SLC26A4 gene mutations who received CI in the Second Hospital of Lanzhou University from 2012 to 2015 were retrospectively reviewed. According to the genetic test results, use One-way ANOVA analysis to compare the differences in auditory results, categories of auditory performance (CAP) and speech intelligibility rating (SIR) index questionnaire scores and speech recognition rates among different groups in 4-5 years after CI. RESULT Compared with other genotypes of SLC26A4, the patients with homozygous mutation of c.919-2A > G in SLC26A4 had better hearing aid threshold at 500 Hz and better recognition rates of Yangyang words than other monoallelic mutation groups after CI (p < .05). CONCLUSIONS AND SIGNIFICANCE The most common hot spot mutation of SLC26A4 gene is c.919-2A > G. The patients with homozygous mutation of c.919-2A > G in SLC26A4 gene had partly better hearing and speech rehabilitation than other monoallelic mutation groups after CI.
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Affiliation(s)
- Qin Wang
- Department of Otolaryngology-Head & Neck Surgery, Lanzhou University Second Hospital, Lanzhou, China
| | - Jian Hu
- Department of Otorhinolaryngology Head and Neck Surgery, Xijing Hospital, Airforce Military Medical University, Xi'an, Shaanxi Province, China
| | - Panpan Bian
- Department of Otolaryngology-Head & Neck Surgery, Lanzhou University Second Hospital, Lanzhou, China
| | - Chi Chen
- Department of Otolaryngology-Head & Neck Surgery, Lanzhou University Second Hospital, Lanzhou, China
| | - Yanli Wang
- Department of Otolaryngology-Head & Neck Surgery, Lanzhou University Second Hospital, Lanzhou, China
| | - Shihong Cheng
- Department of Otolaryngology-Head & Neck Surgery, Lanzhou University Second Hospital, Lanzhou, China
| | - Yufen Guo
- Department of Otolaryngology-Head & Neck Surgery, Lanzhou University Second Hospital, Lanzhou, China
| | - Baicheng Xu
- Department of Otolaryngology-Head & Neck Surgery, Lanzhou University Second Hospital, Lanzhou, China
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Analysis of SLC26A4, FOXI1, and KCNJ10 Gene Variants in Patients with Incomplete Partition of the Cochlea and Enlarged Vestibular Aqueduct (EVA) Anomalies. Int J Mol Sci 2022; 23:ijms232315372. [PMID: 36499699 PMCID: PMC9740095 DOI: 10.3390/ijms232315372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Pathogenic variants in the SLC26A4, FOXI1, and KCNJ10 genes are associated with hearing loss (HL) and specific inner ear abnormalities (DFNB4). In the present study, phenotype analyses, including clinical data collection, computed tomography (CT), and audiometric examination, were performed on deaf individuals from the Sakha Republic of Russia (Eastern Siberia). In cases with cochleovestibular malformations, molecular genetic analysis of the coding regions of the SLC26A4, FOXI1, and KCNJ10 genes associated with DFNB4 was completed. In six of the 165 patients (3.6%), CT scans revealed an incomplete partition of the cochlea (IP-1 and IP-2), in isolation or combined with an enlarged vestibular aqueduct (EVA) anomaly. Sequencing of the SLC26A4, FOXI1, and KCNJ10 genes was performed in these six patients. In the SLC26A4 gene, we identified four variants, namely c.85G>C p.(Glu29Gln), c.757A>G p.(Ile253Val), c.2027T>A p.(Leu676Gln), and c.2089+1G>A (IVS18+1G>A), which are known as pathogenic, as well as c.441G>A p.(Met147Ile), reported previously as a variant with uncertain significance. Using the AlphaFold algorithm, we found in silico evidence of the pathogenicity of this variant. We did not find any causative variants in the FOXI1 and KCNJ10 genes, nor did we find any evidence of digenic inheritance associated with double heterozygosity for these genes with monoallelic SLC26A4 variants. The contribution of biallelic SLC26A4 variants in patients with IP-1, IP-2, IP-2+EVA, and isolated EVA was 66.7% (DFNB4 in three patients, Pendred syndrome in one patient). Seventy-five percent of SLC26A4-biallelic patients had severe or profound HL. The morphology of the inner ear anomalies demonstrated that, among SLC26A4-biallelic patients, all types of incomplete partition of the cochlea are possible, from IP-1 and IP-2, to a normal cochlea. However, the dominant type of anomaly was IP-2+EVA (50.0%). This finding is very important for cochlear implantation, since the IP-2 anomaly does not have an increased risk of “gushers” and recurrent meningitis.
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Different Rates of the SLC26A4-Related Hearing Loss in Two Indigenous Peoples of Southern Siberia (Russia). Diagnostics (Basel) 2021; 11:diagnostics11122378. [PMID: 34943614 PMCID: PMC8699871 DOI: 10.3390/diagnostics11122378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 12/14/2022] Open
Abstract
Hereditary hearing loss (HL) is known to be highly locus/allelic heterogeneous, and the prevalence of different HL forms significantly varies among populations worldwide. Investigation of region-specific landscapes of hereditary HL is important for local healthcare and medical genetic services. Mutations in the SLC26A4 gene leading to nonsyndromic recessive deafness (DFNB4) and Pendred syndrome are common genetic causes of hereditary HL, at least in some Asian populations. We present for the first time the results of a thorough analysis of the SLC26A4 gene by Sanger sequencing in the large cohorts of patients with HL of unknown etiology belonging to two neighboring indigenous Turkic-speaking Siberian peoples (Tuvinians and Altaians). A definite genetic diagnosis based on the presence of biallelic SLC26A4 mutations was established for 28.2% (62/220) of all enrolled Tuvinian patients vs. 4.3% (4/93) of Altaian patients. The rate of the SLC26A4-related HL in Tuvinian patients appeared to be one of the highest among populations worldwide. The SLC26A4 mutational spectrum was characterized by the presence of Asian-specific mutations c.919-2A>G and c.2027T>A (p.Leu676Gln), predominantly found in Tuvinian patients, and c.2168A>G (p.His723Arg), which was only detected in Altaian patients. In addition, a novel pathogenic variant c.1545T>G (p.Phe515Leu) was found with high frequency in Tuvinian patients. Overall, based on the findings of this study and our previous research, we were able to uncover the genetic causes of HL in 50.5% of Tuvinian patients and 34.5% of Altaian patients.
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Roesch S, Rasp G, Sarikas A, Dossena S. Genetic Determinants of Non-Syndromic Enlarged Vestibular Aqueduct: A Review. Audiol Res 2021; 11:423-442. [PMID: 34562878 PMCID: PMC8482117 DOI: 10.3390/audiolres11030040] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/02/2021] [Accepted: 08/24/2021] [Indexed: 12/13/2022] Open
Abstract
Hearing loss is the most common sensorial deficit in humans and one of the most common birth defects. In developed countries, at least 60% of cases of hearing loss are of genetic origin and may arise from pathogenic sequence alterations in one of more than 300 genes known to be involved in the hearing function. Hearing loss of genetic origin is frequently associated with inner ear malformations; of these, the most commonly detected is the enlarged vestibular aqueduct (EVA). EVA may be associated to other cochleovestibular malformations, such as cochlear incomplete partitions, and can be found in syndromic as well as non-syndromic forms of hearing loss. Genes that have been linked to non-syndromic EVA are SLC26A4, GJB2, FOXI1, KCNJ10, and POU3F4. SLC26A4 and FOXI1 are also involved in determining syndromic forms of hearing loss with EVA, which are Pendred syndrome and distal renal tubular acidosis with deafness, respectively. In Caucasian cohorts, approximately 50% of cases of non-syndromic EVA are linked to SLC26A4 and a large fraction of patients remain undiagnosed, thus providing a strong imperative to further explore the etiology of this condition.
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Affiliation(s)
- Sebastian Roesch
- Department of Otorhinolaryngology, Head and Neck Surgery, Paracelsus Medical University, 5020 Salzburg, Austria; (S.R.); (G.R.)
| | - Gerd Rasp
- Department of Otorhinolaryngology, Head and Neck Surgery, Paracelsus Medical University, 5020 Salzburg, Austria; (S.R.); (G.R.)
| | - Antonio Sarikas
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, 5020 Salzburg, Austria;
| | - Silvia Dossena
- Institute of Pharmacology and Toxicology, Paracelsus Medical University, 5020 Salzburg, Austria;
- Correspondence: ; Tel.: +43-(0)662-2420-80564
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11
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Tian Y, Xu H, Liu D, Zhang J, Yang Z, Zhang S, Liu H, Li R, Tian Y, Zeng B, Li T, Lin Q, Wang H, Li X, Lu W, Shi Y, Zhang Y, Zhang H, Jiang C, Xu Y, Chen B, Liu J, Tang W. Increased diagnosis of enlarged vestibular aqueduct by multiplex PCR enrichment and next-generation sequencing of the SLC26A4 gene. Mol Genet Genomic Med 2021; 9:e1734. [PMID: 34170635 PMCID: PMC8404235 DOI: 10.1002/mgg3.1734] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/30/2021] [Accepted: 05/24/2021] [Indexed: 12/11/2022] Open
Abstract
Background The enlarged vestibular aqueduct (EVA) is the commonest malformation of inner ear accompanied by sensorineural hearing loss in children. Three genes SLC26A4, FOXI1, and KCNJ10 have been associated with EVA, among them SLC26A4 being the most common. Yet, hotspot mutation screening can only diagnose a small number of patients. Methods Thus, in this study, we designed a new molecular diagnosis panel for EVA based on multiplex PCR enrichment and next‐generation sequencing of the exon and flanking regions of SLC26A4. A total of 112 hearing loss families with EVA were enrolled and the pathogenicity of the rare variants detected was interpreted according to the American College of Medical Genetics and Genomics (ACMG) guidelines. Results Our results showed that 107/112 (95.54%) families carried SLC26A4 biallelic mutations, 4/112 (3.57%) carried monoallelic variants, and 1/112 (0.89%) had none variant, resulting in a diagnostic rate of 95.54%. A total of 49 different variants were detected in those patients and we classified 30 rare variants as pathogenic/likely pathogenic, of which 13 were not included in the Clinvar database. Conclusion Our diagnostic panel has an increased diagnostic yield with less cost, and the curated list of pathogenic variants in the SLC26A4 gene can be directly used to aid the genetic counseling to patients.
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Affiliation(s)
- Yongan Tian
- BGI College, Zhengzhou University, Zhengzhou, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Hongen Xu
- The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Danhua Liu
- The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Juanli Zhang
- Henan Province Medical Instrument Testing Institute, Zhengzhou, China
| | | | - Sen Zhang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Huanfei Liu
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Ruijun Li
- Precision Medicine Center, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | | | - Beiping Zeng
- BGI College, Zhengzhou University, Zhengzhou, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Tong Li
- BGI College, Zhengzhou University, Zhengzhou, China.,Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Qianyu Lin
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Haili Wang
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou, China
| | - Xiaohua Li
- Department of Otology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wei Lu
- Department of Otology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Shi
- The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yan Zhang
- The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hui Zhang
- The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chang Jiang
- Department of Otology, Henan Provincial People's Hospital, Zhengzhou, China
| | - Ying Xu
- Zhengzhou Children's Hospital, Zhengzhou, China
| | - Bei Chen
- Department of Otology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jun Liu
- Department of Otology, Henan Provincial People's Hospital, Zhengzhou, China
| | - Wenxue Tang
- The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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12
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Kınoğlu K, Orhan KS, Kara H, Öztürk O, Polat B, Aydoğan H, Çelik M, Ceviz AB, Güldiken Y. Investigation of DFNB4 SLC26A4 mutation in patients with enlarged vestibular aquaduct. Int J Pediatr Otorhinolaryngol 2020; 138:110379. [PMID: 33152970 DOI: 10.1016/j.ijporl.2020.110379] [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: 05/28/2020] [Revised: 08/02/2020] [Accepted: 09/09/2020] [Indexed: 11/30/2022]
Abstract
OBJECTIVES Mutations of the SLC26A4 gene causing enlarged vestibular aqueduct (EVA) syndrome have not yet been fully elucidated. The study aimed to investigate SLC26A4 mutations in patients with EVA syndrome in the Turkish population. Identifying these mutations may play an essential role in determining the prognosis, follow-up, and management options of these patients. METHODS Whole exome sequencing and/or Sanger sequencing of SLC26A4 in 22 patients with sensorineural hearing loss associated with isolated EVA without inner ear anomalies, and 22 controls were performed. RESULTS Twenty-two patients and 22 control subjects were included in the study. The onset of hearing loss was pre-lingual in 15 patients, and post-lingual in 7. The mean (standard deviation) vestibular aqueduct width of the patients was 3.23 mm (1.28). Twenty SLC26A4 variants, 15 of them unique, were identified in 22 patients. Among them, seven variants were heterozygous, and 13 were homozygous. The variants p.E37X (c.109G > T), p.Y27H (c.79T > C), p.C706Y (c.2117G > A) have not been previously reported. CONCLUSION The detection of rare and previously unreported mutations in our study showed that studies with a larger number of patients with EVA might reveal more role of the SLC26A4 gene. Besides, to understand the etiopathogenesis of the disease, other related genes also should be investigated.
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Affiliation(s)
- Kubilay Kınoğlu
- Istanbul University, Aziz Sancar Institute of Experimental Medicine, Turkey
| | - Kadir Serkan Orhan
- Istanbul University, Istanbul Faculty of Medicine, Department of Otorhinolaryngology
| | - Hakan Kara
- Istanbul University, Istanbul Faculty of Medicine, Department of Otorhinolaryngology.
| | - Oğuz Öztürk
- Istanbul University, Aziz Sancar Institute of Experimental Medicine, Turkey
| | - Beldan Polat
- Istanbul University, Istanbul Faculty of Medicine, Department of Otorhinolaryngology
| | - Hülya Aydoğan
- Istanbul University, Aziz Sancar Institute of Experimental Medicine, Turkey
| | - Mehmet Çelik
- Istanbul University, Istanbul Faculty of Medicine, Department of Otorhinolaryngology
| | - Ayşe Begüm Ceviz
- Istanbul University, Aziz Sancar Institute of Experimental Medicine, Turkey
| | - Yahya Güldiken
- Istanbul University, Istanbul Faculty of Medicine, Department of Otorhinolaryngology
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13
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Budde BS, Aly MA, Mohamed MR, Breß A, Altmüller J, Motameny S, Kawalia A, Thiele H, Konrad K, Becker C, Toliat MR, Nürnberg G, Sayed EAF, Mohamed ES, Pfister M, Nürnberg P. Comprehensive molecular analysis of 61 Egyptian families with hereditary nonsyndromic hearing loss. Clin Genet 2020; 98:32-42. [DOI: 10.1111/cge.13754] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/24/2020] [Accepted: 04/06/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Birgit S. Budde
- Cologne Center for Genomics University of Cologne Cologne Germany
| | - Maha Abdelgaber Aly
- Cologne Center for Genomics University of Cologne Cologne Germany
- Audiology Unit, Department of Otolaryngology, Faculty of Medicine Assiut University Egypt
| | - Mostafa R. Mohamed
- Audiology Unit, Department of Otolaryngology, Faculty of Medicine Assiut University Egypt
| | - Andreas Breß
- Department of Otolaryngology University of Tübingen Tübingen Germany
| | - Janine Altmüller
- Cologne Center for Genomics University of Cologne Cologne Germany
| | - Susanne Motameny
- Cologne Center for Genomics University of Cologne Cologne Germany
| | - Amit Kawalia
- Cologne Center for Genomics University of Cologne Cologne Germany
| | - Holger Thiele
- Cologne Center for Genomics University of Cologne Cologne Germany
| | - Kathryn Konrad
- Cologne Center for Genomics University of Cologne Cologne Germany
| | - Christian Becker
- Cologne Center for Genomics University of Cologne Cologne Germany
| | | | - Gudrun Nürnberg
- Cologne Center for Genomics University of Cologne Cologne Germany
| | | | - Enass Sayed Mohamed
- Audiology Unit, Department of Otolaryngology, Faculty of Medicine Assiut University Egypt
| | - Markus Pfister
- Department of Otolaryngology University of Tübingen Tübingen Germany
- HNO Sarnen GmbH & Swisstinnitus AG Sarnen Switzerland
| | - Peter Nürnberg
- Cologne Center for Genomics University of Cologne Cologne Germany
- Center for Molecular Medicine Cologne University of Cologne Cologne Germany
- ATLAS Biolabs GmbH Berlin Germany
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14
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Molecular basis of hearing loss associated with enlarged vestibular aqueduct. JOURNAL OF BIO-X RESEARCH 2019. [DOI: 10.1097/jbr.0000000000000032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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15
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Zhao X, Cheng X, Huang L, Wang X, Wen C, Wang X, Zhao L. Analysis of mutations in the FOXI1 and KCNJ10 genes in infants with a single-allele SLC26A4 mutation. Biosci Trends 2019; 13:261-266. [PMID: 31243244 DOI: 10.5582/bst.2019.01142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The current study investigated how the FOXI1 and KCNJ10 genes were affected in infants with a single-allele mutation in the SLC26A4 gene, and it determined the audiological phenotypes of infants with double heterozygous mutations (DHMs) in the three genes. Subjects were 562 infants with a single-allele SLC26A4 mutation detected during neonatal deafness genetic screening; the infants were seen as outpatients by Otology at Beijing Tongren Hospital. All subjects underwent SLC26A4 sequencing. Twenty infants had a second-allele variant while the remaining 542 had an SLC26A4 single-allele mutation. Infants also underwent FOXI1 and KCNJ10 sequencing. All patients with double heterozygous mutations in the aforementioned genes underwent an audiological evaluation and a limited imaging study; variants and audiological phenotypes were analyzed. Of 562 patients, 20 had SLC26A4 bi-allelic mutations; 8 carried single mutations in both SLC26A4 and KCNJ10. No pathogenic mutations in the FOXI1 gene were found. Four missense mutations in KCNJ10 were detected, including c.812G>A, c.800A>G, c.53G>A, and c.1042C>T. Eight individuals with a DHMs all passed universal newborn hearing screening, and all were found to have normal hearing. These data suggest that individuals with an SLC26A4 single-allele mutation, combined with FOXI1 or KCNJ10 gene mutations, do not suffer hearing loss during infancy, though this finding is worthy of further follow-up and in-depth discussion.
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Affiliation(s)
- Xuelei Zhao
- Beijing Tongren Hospital, Capital Medical University.,Beijing Institute of Otolaryngology.,Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education
| | - Xiaohua Cheng
- Beijing Tongren Hospital, Capital Medical University.,Beijing Institute of Otolaryngology.,Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education
| | - Lihui Huang
- Beijing Tongren Hospital, Capital Medical University.,Beijing Institute of Otolaryngology.,Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education
| | - Xianlei Wang
- Beijing Tongren Hospital, Capital Medical University.,Beijing Institute of Otolaryngology.,Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education
| | - Cheng Wen
- Beijing Tongren Hospital, Capital Medical University.,Beijing Institute of Otolaryngology.,Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education
| | - Xueyao Wang
- Beijing Tongren Hospital, Capital Medical University.,Beijing Institute of Otolaryngology.,Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education
| | - Liping Zhao
- Beijing Tongren Hospital, Capital Medical University.,Beijing Institute of Otolaryngology.,Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education
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16
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Li H, Qiu J, Zhu J, Huang Y. Gene mutation analysis and genetic counseling for patients with non-syndromic hearing loss in Linyi region. Exp Ther Med 2018; 17:413-417. [PMID: 30651814 PMCID: PMC6307381 DOI: 10.3892/etm.2018.6927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 10/25/2018] [Indexed: 11/06/2022] Open
Abstract
Through gene mutation analysis of patients with non-syndromic hearing loss (NSHL) correct genetic counseling for patients with NSHL and their family members were provided. A total of 116 patients suffering from NSHL were selected, and Sanger sequencing was applied to analyze 31 mutation sites in four deafness genes [gap junction β-2 (GJB2), solute carrier family 26, member 4 (SLC26A4), GJB3 and mitochondria 12S ribosomal ribonucleic acid (12SrRNA)]. Based on detection results, for the families with reproductive needs, amniotic fluid was extracted from pregnant women during proper gestational weeks to identify fetal genotypes and predict hearing state. Among 116 patients with NSHL, 51 patients carrying definite pathogenic mutation were found, including 35 patients with GJB2 mutations, 14 patients with SLC26A4 gene mutations and 2 patients with mitochondrial deoxyribonucleic acid 12SrRNA (mtDNA 12SrRNA) mutations. No GJB3 gene mutation site was detected. In addition, prenatal diagnosis to 17 pregnant women who had given birth to babies with deafness was performed, and results suggested that genotypes of 6 fetuses were consistent with those of probands, genotypes of 8 fetuses were consistent with those of their parents, and no mutation was found in the other 3 fetuses. Gene mutation analysis of patients with NSHL can identify the etiology and provide appropriate genetic counseling and birth guiding for patients with NSHL and their family members. In addition, prenatal diagnosis to the families who plan to give birth again can avoid the natality of fetuses with hearing loss.
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Affiliation(s)
- Huafeng Li
- Genetics Laboratory, Women and Children's Health Care Hospital of Linyi, Linyi, Shandong 276014, P.R. China
| | - Jigang Qiu
- Genetics Laboratory, Women and Children's Health Care Hospital of Linyi, Linyi, Shandong 276014, P.R. China
| | - Jinping Zhu
- Genetics Laboratory, Women and Children's Health Care Hospital of Linyi, Linyi, Shandong 276014, P.R. China
| | - Yuqiang Huang
- Genetics Laboratory, Women and Children's Health Care Hospital of Linyi, Linyi, Shandong 276014, P.R. China
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17
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Kuwabara MF, Wasano K, Takahashi S, Bodner J, Komori T, Uemura S, Zheng J, Shima T, Homma K. The extracellular loop of pendrin and prestin modulates their voltage-sensing property. J Biol Chem 2018; 293:9970-9980. [PMID: 29777056 DOI: 10.1074/jbc.ra118.001831] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 04/24/2018] [Indexed: 12/21/2022] Open
Abstract
Pendrin and prestin belong to the solute carrier 26 (SLC26) family of anion transporters. Prestin is unique among the SLC26 family members in that it displays voltage-driven motor activity (electromotility) and concurrent gating currents that manifest as nonlinear cell membrane electrical capacitance (nonlinear capacitance (NLC)). Although the anion transport mechanism of the SLC26 proteins has begun to be elucidated, the molecular mechanism of electromotility, which is thought to have evolved from an ancestral ion transport mechanism, still remains largely elusive. Here, we demonstrate that pendrin also exhibits large NLC and that charged residues present in one of the extracellular loops of pendrin and prestin play significant roles in setting the voltage-operating points of NLC. Our results suggest that the molecular mechanism responsible for sensing voltage is not unique to prestin among the members of the SLC26 family and that this voltage-sensing mechanism works independently of the anion transport mechanism.
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Affiliation(s)
- Makoto F Kuwabara
- From the Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Koichiro Wasano
- the Department of Otolaryngology-Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
| | - Satoe Takahashi
- the Department of Otolaryngology-Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
| | | | - Tomotaka Komori
- From the Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Sotaro Uemura
- From the Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Jing Zheng
- the Department of Otolaryngology-Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611.,The Hugh Knowles Center for Clinical and Basic Science in Hearing and Its Disorders, Northwestern University, Evanston, Illinois 60608
| | - Tomohiro Shima
- From the Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan,
| | - Kazuaki Homma
- the Department of Otolaryngology-Head and Neck Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, .,The Hugh Knowles Center for Clinical and Basic Science in Hearing and Its Disorders, Northwestern University, Evanston, Illinois 60608
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18
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Liang Y, Peng Q, Wang K, Zhu P, Wu C, Rao C, Chang J, Li S, Lu X. A novel mutation in the SLC26A4 gene in a Chinese family with non-syndromic hearing loss and enlarged vestibular aqueduct. Int J Pediatr Otorhinolaryngol 2018; 107:97-100. [PMID: 29501320 DOI: 10.1016/j.ijporl.2018.01.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/04/2017] [Accepted: 01/23/2018] [Indexed: 10/18/2022]
Abstract
OBJECTIVES To identity the genetic causes of hearing loss in a Han Chinese family with enlarged vestibular aqueduct syndrome. METHODS Multiplex PCR technology combined with Ion Torrent™ next-generation sequencing technology was used to search for pathogenic mutations. A group of 1500 ethnically-matched normal hearing subjects screened for mutations in deafness-related genes using the same method in previously studied were included as a control. RESULTS The proband and his little sister suffered from typical features of sensorineural hearing loss with enlarged vestibular aqueduct (EVA). Both subjects harbored two compound heterozygous mutations in the SLC26A4 gene. A novel mutation named c.2110 G > C (p.Glu704Gln) in exon 19 and another previously reported mutation c.1673 A > T (p.Asn558Ile) were identified. These mutations were carried in the heterozygous state by the parents and therefore co-segregated with the genetic disease. The c.2110 G > C (p.Glu704Gln) mutation was absent in 1500 healthy newborns. Protein alignment indicated high evolutionary conservation of the p.E704 residue, and this mutation was predicted by online tools to be damaging and deleterious. CONCLUSION This study demonstrates that the novel mutation c.2110 G > C (p.Glu704Gln) in compound heterozygosity with c.1673 A > T (p.Asn558Ile) in the SLC26A4 gene corresponds to the EVA in this family. Our study will provide a foundation for elucidating the SLC26A4-related mechanisms of hearing loss.
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Affiliation(s)
- Yuan Liang
- Department of Neurology, Dongguan Children's Hospital, Dongguan, Guangdong, China; Department of Medical and Molecular Genetics, Dongguan Institute of Pediatrics, Dongguan, Guangdong, China
| | - Qi Peng
- Department of Medical and Molecular Genetics, Dongguan Institute of Pediatrics, Dongguan, Guangdong, China
| | - Kangwei Wang
- Department of Medical and Molecular Genetics, Dongguan Institute of Pediatrics, Dongguan, Guangdong, China
| | - Pengyuan Zhu
- CapitalBio Genomics Co., Ltd, Dongguan, Guangdong, China
| | - Chunqiu Wu
- CapitalBio Genomics Co., Ltd, Dongguan, Guangdong, China
| | - Chunbao Rao
- Department of Medical and Molecular Genetics, Dongguan Institute of Pediatrics, Dongguan, Guangdong, China
| | - Jiang Chang
- Department of Otorhinolaryngology, Dongguan Children's Hospital, Dongguan, Guangdong, China
| | - Siping Li
- Medical Laboratory, Dongguan Children's Hospital, Dongguan, Guangdong, China.
| | - Xiaomei Lu
- Department of Medical and Molecular Genetics, Dongguan Institute of Pediatrics, Dongguan, Guangdong, China.
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19
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A novel missense mutation in the SLC26A4 gene causes nonsyndromic hearing loss and enlarged vestibular aqueduct. Int J Pediatr Otorhinolaryngol 2017; 95:104-108. [PMID: 28576516 DOI: 10.1016/j.ijporl.2017.02.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 02/10/2017] [Accepted: 02/12/2017] [Indexed: 11/20/2022]
Abstract
OBJECTIVES We aimed to investigate the genetic causes of hearing loss in a Chinese proband with nonsyndromic hearing loss and enlarged vestibular aqueduct syndrome. METHODS We conducted clinical and genetic evaluations in a deaf proband and his normal-hearing parents. Multiplex PCR technology combined with Ion Torrent™ next-generation sequencing technology was used to detect the pathogenic mutations. As a control, a group of 1500 previously studied healthy newborns from the same ethnic background were subjected to deafness gene screening using the same method as in our previous study. RESULTS The proband harbored two mutations in the SLC26A4 gene in the form of compound heterozygosity. He was found to be heterozygous for a novel mutation named c.1742 G > T (p.Arg581Met) in exon 13 and for the known mutation c.589 G > A (p.Gly197Arg). These variants were carried in the heterozygous state by the parents and therefore co-segregated with the genetic disease. The c.1742 G > T (p.Arg581Met) mutation was absent in 1500 healthy newborns. Protein alignment indicated high evolutionary conservation of the p.R581 residue, and this mutation was predicted by PolyPhen-2 and other online tools to be damaging. CONCLUSION This study demonstrates that the novel mutation c.1742 G > T (p.Arg581Met) in compound heterozygosity with c.589 G > A in the SLC26A4 gene is the main cause of deafness in a family clinically diagnosed with enlarged vestibular aqueduct (EVA). Our study will provide a basic foundation for further investigations to elucidate the SLC26A4-related mechanisms of hearing loss.
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20
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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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21
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Sagong B, Baek JI, Lee KY, Kim UK. A Novel Frameshift Mutation of SLC26A4 in a Korean Family With Nonsyndromic Hearing Loss and Enlarged Vestibular Aqueduct. Clin Exp Otorhinolaryngol 2016; 10:50-55. [PMID: 27384033 PMCID: PMC5327591 DOI: 10.21053/ceo.2016.00430] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 05/22/2016] [Accepted: 05/26/2016] [Indexed: 11/23/2022] Open
Abstract
Objectives We aimed to identify the causative mutation for siblings in a Korean family with nonsyndromic hearing loss (HL) and enlarged vestibular aqueduct (EVA). The siblings were a 19-year-old female with bilateral profound HL and an 11-year-old male with bilateral moderately severe HL. Methods We extracted genomic DNA from blood samples of the siblings with HL, their parents, and 100 controls. We performed mutation analysis for SLC26A4 using direct sequencing. Results The two siblings were compound heterozygotes with the novel mutation p.I713LfsX8 and the previously described mutation p.H723R. Their parents had heterozygous mono-allelic mutations. Father had p.I713LfsX8 mutation as heterozygous, and mother had p.H723R mutation as heterozygous. However, novel mutation p.I713LfsX8 was not detected in 100 unrelated controls. Conclusion Both mutations identified in this study were located in the sulfate transporter and anti-sigma factor antagonist domain, the core region for membrane targeting of SulP/SLC26 anion transporters, which strongly suggests that failure in membrane trafficking by SLC26A4 is a direct cause of HL in this family. Our study could therefore provide a foundation for further investigations elucidating the SLC26A4-related mechanisms of HL.
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Affiliation(s)
- Borum Sagong
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, Korea
| | - Jeong-In Baek
- Department of Aroma Applied Industry, College of Herbal Bio-Industry, Daegu Haany University, Gyeongsan, Korea
| | - Kyu-Yup Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Kyungpook National University School of Medicine, Daegu, Korea
| | - Un-Kyung Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, Korea.,School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, Korea
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22
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Jung J, Suh MJ, Kim SH. Discrepancies between video head impulse and caloric tests in patients with enlarged vestibular aqueduct. Laryngoscope 2016; 127:921-926. [DOI: 10.1002/lary.26122] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 05/04/2016] [Accepted: 05/06/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Jinsei Jung
- Department of Otorhinolaryngology; Yonsei University College of Medicine; Seoul Republic of Korea
| | - Michelle J. Suh
- Department of Otorhinolaryngology; Yonsei University College of Medicine; Seoul Republic of Korea
| | - Sung Huhn Kim
- Department of Otorhinolaryngology; Yonsei University College of Medicine; Seoul Republic of Korea
- The Airway Mucus Institute; Yonsei University College of Medicine; Seoul Republic of Korea
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23
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The R130S mutation significantly affects the function of prestin, the outer hair cell motor protein. J Mol Med (Berl) 2016; 94:1053-62. [PMID: 27041369 DOI: 10.1007/s00109-016-1410-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 02/01/2016] [Accepted: 02/29/2016] [Indexed: 01/29/2023]
Abstract
UNLABELLED A missense mutation, R130S, was recently found in the prestin gene, SLC26A5, of patients with moderate to severe hearing loss (DFNB61). In order to define the pathology of hearing loss associated with this missense mutation, a recombinant prestin construct harboring the R130S mutation (R130S-prestin) was generated, and its functional consequences examined in a heterologous expression system. We found that R130S-prestin targets the plasma membrane but less efficiently compared to wild-type. The voltage operating point and voltage sensitivity of the motor function of R130S-prestin were similar to wild-type prestin. However, the motor activity of R130S-prestin is greatly reduced at higher voltage stimulus frequencies, indicating a reduction in motor kinetics. Our study thus provides experimental evidence that supports a causal relationship between the R130S mutation in the prestin gene and hearing loss found in patients with this missense mutation. KEY MESSAGE Membrane targeting of prestin is impaired by the R130S missense mutation. The fast motor kinetics of prestin is impaired by the R130S missense mutation. Our study strongly suggests that the prestin R130S missense mutation is pathogenic.
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24
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Pang X, Chai Y, He L, Chen P, Wang X, Li L, Jia H, Wu H, Yang T. A 7666-bp genomic deletion is frequent in Chinese Han deaf patients with non-syndromic enlarged vestibular aqueduct but without bi-allelic SLC26A4 mutations. Int J Pediatr Otorhinolaryngol 2015; 79:2248-52. [PMID: 26549381 DOI: 10.1016/j.ijporl.2015.10.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 10/12/2015] [Accepted: 10/13/2015] [Indexed: 11/30/2022]
Abstract
OBJECTIVES To investigate the genetic cause of the patients with non-syndromic enlarged vestibular aqueduct (EVA) but without bi-allelic SLC26A4 mutations. METHODS Presence of a homozygous genomic deletion was detected in a Chinese Han deaf patient (D1467-1) who failed to amplify the first three exons of SLC26A4. The breakpoints of the deletion were fine-mapped and revealed by PCR amplification and sequencing. This deletion was subsequently screened in 22 Chinese Han EVA probands with mono-allelic SLC26A4 mutations. The possible founder effect of the newly identified genomic deletion was evaluated by haplotype analysis. RESULTS A homozygous c.-2071_307+3801del7666 deletion of SLC26A4 was identified in patient D1467-1. This novel genomic deletion was subsequently identified in 18% (4/22) of the Chinese Han EVA probands with mono-allelic SLC26A4 mutations. Haplotype analysis showed that this genomic deletion is likely a founder mutation in Chinese Hans. CONCLUSION Our results suggested that the cryptic c.-2071_307+3801del7666 deletion of SLC26A4 is relatively frequent in Chinese Han non-syndromic EVA patients without bi-allelic SLC26A4 mutations. Screening of this genomic deletion should be incorporated into the routine DNA testing of SLC26A4 in Chinese Hans.
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Affiliation(s)
- Xiuhong Pang
- Department of Otorhinolaryngology-Head and Neck Surgery, Taizhou People's Hospital, Jiangsu Province, China; Department of Otolaryngology-Head and Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Yongchuan Chai
- Department of Otorhinolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China; Department of Otolaryngology-Head and Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Longxia He
- Department of Otolaryngology-Head and Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Penghui Chen
- Department of Otolaryngology-Head and Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Xiaowen Wang
- Department of Otolaryngology-Head and Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Lei Li
- Department of Otolaryngology-Head and Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Huan Jia
- Department of Otolaryngology-Head and Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Hao Wu
- Department of Otolaryngology-Head and Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China.
| | - Tao Yang
- Department of Otolaryngology-Head and Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China.
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Lu YJ, Yao J, Wei QJ, Xing GQ, Cao X. Diagnostic Value of SLC26A4 Mutation Status in Hereditary Hearing Loss With EVA: A PRISMA-Compliant Meta-Analysis. Medicine (Baltimore) 2015; 94:e2248. [PMID: 26683941 PMCID: PMC5058913 DOI: 10.1097/md.0000000000002248] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Many SLC26A4 mutations have been identified in patients with nonsyndromic enlarged vestibular aqueduct (EVA). However, the roles of SLC26A4 genotypes and phenotypes in hereditary deafness remain unexplained. This study aims to perform a meta-analysis based on the PRISMA statement to evaluate the diagnostic value of SLC26A4 mutant alleles and their correlations with multiethnic hearing phenotypes in EVA patients. The systematic literature search of the PubMed, Wiley Online Library, EMBASE, Web of Science, and Science Direct databases was conducted in English for articles published before July 15, 2015. Two investigators independently reviewed retrieved literature and evaluated eligibility. Discrepancy was resolved by discussion and a third investigator. Quality of included studies was evaluated using Newcastle-Ottawa Quality Assessment Scale. Data were synthesized using random-effect or fixed-effect models. The effect sizes were estimated by measuring odds ratios (ORs) with 95% confidence interval (CI). Twenty-five eligible studies involved 2294 cases with EVA data. A total of 272 SLC26A4 variations were found in deafness with EVA and 26 mutations of SCL26A4 had higher frequency. The overall OR was 646.71 (95% CI: 383.30-1091.15, P = 0.000). A total of 22 mutants were considered statistically significant in all ethnicities (ORs >1, P < 0.05). In particular, 8 mutants were specificity of EVA phenotypes in mutations of SLC26A4 for Asia deafness populations (ORs >1, P < 0.05), 4 mutants for Europe and North America (ORs >1, P < 0.05), and the IVS7-2A>G mutations in SLC26A4 were found to have the highest frequency in deafness individuals with EVA phenotype (62.42%). Moreover, subgroups for studies limited to cases with EVA phenotype, 11 mutants relevant risks (RRs) were P < 0.05, especially for IVS7-2A>G bi-allelic mutants assayed in a deafness population (RR = 0.880, P = 0.000). Diagnostic accuracy of SLC26A4 mutation results also identified the significant association of IVS7-2A>G (AUC = 0.99, 95% CI: 0.97-0.99) and p.H723R (AUC = 0.99, 95% CI: 0.98-1.00) detecting deafness with EVA. To conclude, the IVS7-2A>G and H723R in SLC26A4 present a significant predicting value and discriminatory ability for clinical use on diagnosis of EVA within a deafness population.
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Affiliation(s)
- Ya-Jie Lu
- From the Department of Biotechnology, School of Basic Medical Science, Nanjing Medical University (Y-JL, JY, Q-JW, XC,); Department of Otolaryngology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, P.R. China (G-Q X)
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Chai Y, Pang X, Chen D, Li L, Chen Y, Sun L, Wang X, Wu H, Yang T. Molecular etiology of non-dominant, non-syndromic, mild-to-moderate childhood hearing impairment in Chinese Hans. Am J Med Genet A 2014; 164A:3115-9. [PMID: 25251670 DOI: 10.1002/ajmg.a.36785] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 08/21/2014] [Indexed: 11/07/2022]
Abstract
Childhood hearing impairment (HI) is genetically heterogeneous. Compared with the severe-to-profound HI, the molecular etiology of mild-to-moderate HI in children has been less well characterized, especially for those not inherited in the dominant mode. In this study, we recruited 114 probands with non-dominant, non-syndromic, mild-to-moderate childhood HI. Sequencing of GJB2, SLC26A4, and MTRNR1 identified causative mutations in 30.7% (35/114), 4.4% (5/114), and 4.4% (5/114) of subjects, respectively. A majority (62.9%) of bi-allelic GJB2 mutations have non-truncating mutations in at least one allele. In 10 multiplex probands with no GJB2, SLC26A4, and MTRNR1 mutations identified, targeted next-generation sequencing (NGS) of 79 known deafness genes did not identify any additional causes. Our data showed that the molecular etiology of mild-to-moderate childhood HI is considerably different from what reported for severe-to-profound HI and far from complete for those inherited in non-dominant modes.
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Affiliation(s)
- Yongchuan Chai
- Department of Otorhinolaryngology-Head and Neck Surgery, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China; Ear Institute, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Du W, Cheng J, Ding H, Jiang Z, Guo Y, Yuan H. A rapid method for simultaneous multi-gene mutation screening in children with nonsyndromic hearing loss. Genomics 2014; 104:264-70. [PMID: 25149764 DOI: 10.1016/j.ygeno.2014.07.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 06/30/2014] [Accepted: 07/17/2014] [Indexed: 11/19/2022]
Abstract
Hearing loss (HL) is a common genetically heterogeneous sensory disorder, occurring in 1 to 3 per 1000 live births. In spite of the extraordinary genetic heterogeneity, variants in GJB2, MT-RNR1, and SLC26A4 genes have been considered as the main reasons of nonsyndromic hearing loss in Chinese population. We developed a rapid multiplex genetic screening system called the SNPscan assay technique which could detect the 115 mutations of the above three genes. This technique is a high-throughput and cost-saving SNP genotyping method. We found that the carrier rate of mutations in the GJB2 gene, MT-RNR1 gene, and SLC26A4 gene was 26.21%, 1.86%, and 25.46% of the patients with nonsyndromic hearing loss, respectively. Using this method, up to 50% of the patients in our study were identified to have hereditary HL caused by mutations in the three genes. It is applicable to not only genetic diagnosis of HL, but also molecular screening of other inherited diseases.
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Affiliation(s)
- Wan Du
- Department of Otolaryngology-Head and Neck Surgery, the Second Hospital of Lanzhou University, Lanzhou, Gansu, People's Republic of China; Department of Otolaryngology-Head and Neck Surgery, Chinese People's Liberation Army Institute of Otolaryngology, Chinese People's Liberation Army General Hospital, Beijing, People's Republic of China
| | - Jing Cheng
- Department of Otolaryngology-Head and Neck Surgery, Chinese People's Liberation Army Institute of Otolaryngology, Chinese People's Liberation Army General Hospital, Beijing, People's Republic of China
| | - Hui Ding
- Department of Urology, the Second Hospital of Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Zhengwen Jiang
- Center for Human Genetics Research, Genesky Biotechnologies Inc., Shanghai, People's Republic of China
| | - Yufen Guo
- Department of Otolaryngology-Head and Neck Surgery, the Second Hospital of Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Huijun Yuan
- Department of Otolaryngology-Head and Neck Surgery, Chinese People's Liberation Army Institute of Otolaryngology, Chinese People's Liberation Army General Hospital, Beijing, People's Republic of China
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Pique LM, Brennan ML, Davidson CJ, Schaefer F, Greinwald J, Schrijver I. Mutation analysis of the SLC26A4, FOXI1 and KCNJ10 genes in individuals with congenital hearing loss. PeerJ 2014; 2:e384. [PMID: 24860705 PMCID: PMC4017815 DOI: 10.7717/peerj.384] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 04/25/2014] [Indexed: 01/05/2023] Open
Abstract
Pendred syndrome (PDS) and DFNB4 comprise a phenotypic spectrum of sensorineural hearing loss disorders that typically result from biallelic mutations of the SLC26A4 gene. Although PDS and DFNB4 are recessively inherited, sequencing of the coding regions and splice sites of SLC26A4 in individuals suspected to be affected with these conditions often fails to identify two mutations. We investigated the potential contribution of large SLC26A4 deletions and duplications to sensorineural hearing loss (SNHL) by screening 107 probands with one known SLC26A4 mutation by Multiplex Ligation-dependent Probe Amplification (MLPA). A heterozygous deletion, spanning exons 4-6, was detected in only one individual, accounting for approximately 1% of the missing mutations in our cohort. This low frequency is consistent with previously published MLPA results. We also examined the potential involvement of digenic inheritance in PDS/DFNB4 by sequencing the coding regions of FOXI1 and KCNJ10. Of the 29 probands who were sequenced, three carried nonsynonymous variants including one novel sequence change in FOXI1 and two polymorphisms in KCNJ10. We performed a review of prior studies and, in conjunction with our current data, conclude that the frequency of FOXI1 (1.4%) and KCNJ10 (3.6%) variants in PDS/DFNB4 individuals is low. Our results, in combination with previously published reports, indicate that large SLC26A4 deletions and duplications as well as mutations of FOXI1 and KCNJ10 play limited roles in the pathogenesis of SNHL and suggest that other genetic factors likely contribute to the phenotype.
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Affiliation(s)
- Lynn M Pique
- Department of Pathology, Stanford University Medical Center , Stanford, CA , USA
| | - Marie-Luise Brennan
- Department of Pediatrics, Stanford University Medical Center , Stanford, CA , USA
| | | | - Frederick Schaefer
- Molecular Genetics, Center for Genetic Testing at Saint Francis Hospital , Tulsa, OK , USA
| | - John Greinwald
- Divisions of Human Genetics and Otolaryngology, Cincinnati Children's Hospital Medical Center , Cincinnati, OH , USA
| | - Iris Schrijver
- Department of Pathology, Stanford University Medical Center , Stanford, CA , USA ; Department of Pediatrics, Stanford University Medical Center , Stanford, CA , USA
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