1
|
Guan J, Wu X, Zhang J, Li J, Wang H, Wang Q. Global research landscape on the contribution of de novo mutations to human genetic diseases over the past 20 years: bibliometric analysis. J Neurogenet 2024:1-10. [PMID: 38647210 DOI: 10.1080/01677063.2024.2335171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/21/2024] [Indexed: 04/25/2024]
Abstract
As the contribution of de novo mutations (DNMs) to human genetic diseases has been gradually uncovered, analyzing the global research landscape over the past 20 years is essential. Because of the large and rapidly increasing number of publications in this field, understanding the current landscape of the contribution of DNMs in the human genome to genetic diseases remains a challenge. Bibliometric analysis provides an approach for visualizing these studies using information in published records in a specific field. This study aimed to illustrate the current global research status and explore trends in the field of DNMs underlying genetic diseases. Bibliometric analyses were performed using the Bibliometrix Package based on the R language version 4.1.3 and CiteSpace version 6.1.R2 software for publications from 2000 to 2021 indexed under the Web of Science Core Collection (WoSCC) about DNMs underlying genetic diseases on 17 September 2022. We identified 3435 records, which were published in 731 journals by 26,538 authors from 6052 institutes in 66 countries. There was an upward trend in the number of publications since 2013. The USA, China, and Germany contributed the majority of the records included. The University of Washington, Columbia University, and Baylor College of Medicine were the top-producing institutions. Evan E Eichler of the University of Washington, Stephan J Sanders of the Yale University School of Medicine, and Ingrid E Scheffer of the University of Melbourne were the most high-ranked authors. Keyword co-occurrence analysis suggested that DNMs in neurodevelopmental disorders and intellectual disabilities were research hotspots and trends. In conclusion, our data show that DNMs have a significant effect on human genetic diseases, with a noticeable increase in annual publications over the last 5 years. Furthermore, potential hotspots are shifting toward understanding the causative role and clinical interpretation of newly identified or low-frequency DNMs observed in patients.
Collapse
Affiliation(s)
- Jing Guan
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
| | - Xiaonan Wu
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
| | - Jiao Zhang
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
| | - Jin Li
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
| | - Hongyang Wang
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
| | - Qiuju Wang
- Senior Department of Otolaryngology-Head & Neck Surgery, the Sixth Medical Center of PLA General Hospital, Beijing, PR China
- National Clinical Research Center for Otolaryngologic Diseases, Beijing, PR China
- State Key Laboratory of Hearing and Balance Science, Beijing, PR China
| |
Collapse
|
2
|
Klimara MJ, Nishimura C, Wang D, Kolbe DL, Schaefer AM, Walls WD, Frees KL, Smith RJH, Azaiez H. De novo variants are a common cause of genetic hearing loss. Genet Med 2022; 24:2555-2567. [PMID: 36194208 PMCID: PMC9729384 DOI: 10.1016/j.gim.2022.08.028] [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: 06/29/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/06/2022] Open
Abstract
PURPOSE De novo variants (DNVs) are a well-recognized cause of genetic disorders. The contribution of DNVs to hearing loss (HL) is poorly characterized. We aimed to evaluate the rate of DNVs in HL-associated genes and assess their contribution to HL. METHODS Targeted genomic enrichment and massively parallel sequencing were used for molecular testing of all exons and flanking intronic sequences of known HL-associated genes, with no exclusions on the basis of type of HL or clinical features. Segregation analysis was performed, and previous reports of DNVs in PubMed and ClinVar were reviewed to characterize the rate, distribution, and spectrum of DNVs in HL. RESULTS DNVs were detected in 10% (24/238) of trios for whom segregation analysis was performed. Overall, DNVs were causative in at least ∼1% of probands for whom a genetic diagnosis was resolved, with marked variability based on inheritance mode and phenotype. DNVs of MITF were most common (21% of DNVs), followed by GATA3 (13%), STRC (13%), and ACTG1 (8%). Review of reported DNVs revealed gene-specific variability in contribution of DNV to the mutational spectrum of HL-associated genes. CONCLUSION DNVs are a relatively common cause of genetic HL and must be considered in all cases of sporadic HL.
Collapse
Affiliation(s)
- Miles J Klimara
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA
| | - Carla Nishimura
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA
| | - Donghong Wang
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA
| | - Diana L Kolbe
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA
| | - Amanda M Schaefer
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA
| | - William D Walls
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA
| | - Kathy L Frees
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA
| | - Richard J H Smith
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA.
| | - Hela Azaiez
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology-Head and Neck Surgery, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA.
| |
Collapse
|
3
|
Vaché C, Baux D, Bianchi J, Baudoin C, Faugère V, Francannet C, Koenig M, Kalatzis V, Roux AF. Reclassification of a TMC1 synonymous substitution as a variant disrupting splicing regulatory elements associated with recessive hearing loss. Eur J Hum Genet 2022; 30:34-41. [PMID: 34857896 PMCID: PMC8738754 DOI: 10.1038/s41431-021-01010-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 01/03/2023] Open
Abstract
Alterations of the transmembrane channel-like 1 gene (TMC1) are involved in autosomal recessive and dominant nonsyndromic hearing loss (NSHL). To date, up to 117 causal variants including substitutions, insertions and splice variants have been reported in families from different populations. In a patient suffering from severe prelingual NSHL, we identified, in the homozygous state, the previously considered likely benign synonymous c.627C>T; p.(Leu209=) substitution. We used in silico tools predicting variant-induced alterations of splicing regulatory elements (SREs) and pinpointed this transition as a candidate splice-altering variation. Functional splicing analysis, using a minigene assay, confirmed that the variant altered a critical regulatory sequence which is essential for the exon 11 inclusion in the TMC1 transcripts. This result was reinforced by the analysis of orthologous TMC1 mammalian sequences for which the deleterious effect on the mRNA processing of a native thymidine was always counteracted by the presence of a stronger donor splice site or additional enhancer motifs. This study demonstrates, for the first time, the pathogenicity of the c.627C>T alteration leading to its reclassification as a causal variant impacting SREs and highlights the major importance of exhaustive studies to accurately evaluate the pathogenicity of a variant, regardless of the variation type.
Collapse
Affiliation(s)
- Christel Vaché
- grid.157868.50000 0000 9961 060XMolecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France ,grid.121334.60000 0001 2097 0141Institute for Neurosciences of Montpellier, Univ Montpellier, Inserm, Montpellier, France
| | - David Baux
- grid.157868.50000 0000 9961 060XMolecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France ,grid.121334.60000 0001 2097 0141Institute for Neurosciences of Montpellier, Univ Montpellier, Inserm, Montpellier, France
| | - Julie Bianchi
- grid.157868.50000 0000 9961 060XMolecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France
| | - Corinne Baudoin
- grid.157868.50000 0000 9961 060XMolecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France
| | - Valérie Faugère
- grid.157868.50000 0000 9961 060XMolecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France
| | - Christine Francannet
- grid.411163.00000 0004 0639 4151Department of Medical Genetics, Estaing Hospital, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - Michel Koenig
- grid.157868.50000 0000 9961 060XMolecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France
| | - Vasiliki Kalatzis
- grid.121334.60000 0001 2097 0141Institute for Neurosciences of Montpellier, Univ Montpellier, Inserm, Montpellier, France
| | - Anne-Françoise Roux
- grid.157868.50000 0000 9961 060XMolecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France ,grid.121334.60000 0001 2097 0141Institute for Neurosciences of Montpellier, Univ Montpellier, Inserm, Montpellier, France
| |
Collapse
|
4
|
Next-Generation Sequencing Identifies Pathogenic Variants in HGF, POU3F4, TECTA, and MYO7A in Consanguineous Pakistani Deaf Families. Neural Plast 2021; 2021:5528434. [PMID: 33976695 PMCID: PMC8084664 DOI: 10.1155/2021/5528434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/01/2021] [Accepted: 04/11/2021] [Indexed: 01/20/2023] Open
Abstract
Background Approximately 70% of congenital deafness is attributable to genetic causes. Incidence of congenital deafness is known to be higher in families with consanguineous marriage. In this study, we investigated the genetic causes in three consanguineous Pakistani families segregating with prelingual, severe-to-profound deafness. Results Through targeted next-generation sequencing of 414 genes known to be associated with deafness, homozygous variants c.536del (p. Leu180Serfs∗20) in TECTA, c.3719 G>A (p. Arg1240Gln) in MYO7A, and c.482+1986_1988del in HGF were identified as the pathogenic causes of enrolled families. Interestingly, in one large consanguineous family, an additional c.706G>A (p. Glu236Lys) variant in the X-linked POU3F4 gene was also identified in multiple affected family members causing deafness. Genotype-phenotype cosegregation was confirmed in all participating family members by Sanger sequencing. Conclusions Our results showed that the genetic causes of deafness are highly heterogeneous. Even within a single family, the affected members with apparently indistinguishable clinical phenotypes may have different pathogenic variants.
Collapse
|
5
|
Identification and Characterization of a Cryptic Genomic Deletion-Insertion in EYA1 Associated with Branchio-Otic Syndrome. Neural Plast 2021; 2021:5524381. [PMID: 33880118 PMCID: PMC8046558 DOI: 10.1155/2021/5524381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 03/19/2021] [Indexed: 11/17/2022] Open
Abstract
Branchio-oto-renal spectrum disorder (BORSD) is characterized by hearing loss accompanied by ear malformations, branchial cysts, and fistulae, with (branchio-oto-renal syndrome (BORS)) or without renal abnormalities (BOS (branchio-otic syndrome)). As the most common causative gene for BORSD, dominant mutations in EYA1 are responsible for approximately 40% of the cases. In a sporadic deaf patient diagnosed as BOS, we identified an apparent heterozygous genomic deletion spanning the first four coding exons and one 5′ noncoding exon of EYA1 by targeted next-generation sequencing of 406 known deafness genes. Real-time PCR at multiple regions of EYA1 confirmed the existence of this genomic deletion and extended its 5′ boundary beyond the 5′-UTR. Whole genome sequencing subsequently located the 5′ and 3′ breakpoints to 19268 bp upstream to the ATG initiation codon and 3180 bp downstream to exon 5. PCR amplification across the breakpoints in both the patient and his parents showed that the genomic alteration occurred de novo. Sanger sequencing of this PCR product revealed that it is in fact a GRCh38/hg38:chr8:g.71318554_71374171delinsTGCC genomic deletion-insertion. Our results showed that the genomic variant is responsible for the hearing loss associated with BOS and provided an example for deciphering such cryptic genomic alterations following pipelines of comprehensive exome/genome sequencing and designed verification.
Collapse
|
6
|
Compound Heterozygous Mutations in TMC1 and MYO15A Are Associated with Autosomal Recessive Nonsyndromic Hearing Loss in Two Chinese Han Families. Neural Plast 2020; 2020:8872185. [PMID: 32802042 PMCID: PMC7416276 DOI: 10.1155/2020/8872185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/12/2020] [Accepted: 07/06/2020] [Indexed: 12/19/2022] Open
Abstract
Genetic hearing loss is a common sensory disorder, and its cause is highly heterogeneous. In this study, by targeted next-generation sequencing of 414 known deafness genes, we identified compound heterozygous mutations p.R34X/p.M413T in TMC1 and p.S3417del/p.R1407T in MYO15A in two recessive Chinese Han deaf families. Intrafamilial cosegregation of the mutations with the hearing phenotype was confirmed in both families by the Sanger sequencing. Auditory features of the affected individuals are consistent with that previously reported for recessive mutations in TMC1 and MYO15A. The two novel mutations identified in this study, p.M413T in TMC1 and p.R1407T in MYO15A, are classified as likely pathogenic according to the guidelines of ACMG. Our study expanded the mutation spectrums of TMC1 and MYO15A and illustrated that genotype-phenotype correlation in combination with next-generation sequencing may improve the accuracy for genetic diagnosis of deafness.
Collapse
|
7
|
Wu D, Huang W, Xu Z, Li S, Zhang J, Chen X, Tang Y, Qiu J, Wang Z, Duan X, Zhang L. Clinical and genetic study of 12 Chinese Han families with nonsyndromic deafness. Mol Genet Genomic Med 2020; 8:e1177. [PMID: 32048449 PMCID: PMC7196461 DOI: 10.1002/mgg3.1177] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/24/2020] [Accepted: 01/30/2020] [Indexed: 12/12/2022] Open
Abstract
Background Nonsyndromic hearing loss is clinically and genetically heterogeneous. In this study, we characterized the clinical features of 12 Chinese Han deaf families in which mutations in common deafness genes GJB2, SLC26A4, and MT‐RNR1 were excluded. Methods Targeted next‐generation sequencing of 147 known deafness genes was performed in probands of 10 families, while whole‐exome sequencing was applied in those of the rest two. Results Pathogenic mutations in a total of 11 rare deafness genes, OTOF, CDH23, PCDH15, PDZD7, ADGRV1, KARS, OTOG, GRXCR2, MYO6, GRHL2, and POU3F4, were identified in all 12 probands, with 16 mutations being novel. Intrafamilial cosegregation of the mutations and the deafness phenotype were confirmed by Sanger sequencing. Conclusion Our results expanded the mutation spectrum and genotype‒phenotype correlation of nonsyndromic hearing loss in Chinese Hans and also emphasized the importance of combining both next‐generation sequencing and detailed auditory evaluation to achieve a more accurate diagnosis for nonsyndromic hearing loss.
Collapse
Affiliation(s)
- Di Wu
- Department of Otolaryngology, Affiliated Hospital of Nantong University, Nantong, China
| | - Weiyuan Huang
- Department of Otolaryngology, Affiliated Hospital of Nantong University, Nantong, China
| | - Zhenhang Xu
- Department of Otolaryngology, Xiangya Hospital, Central South University, Changsha, China
| | - Shuo Li
- Department of Otolaryngology, Affiliated Hospital of Nantong University, Nantong, China
| | - Jie Zhang
- Department of Otolaryngology, Affiliated Hospital of Nantong University, Nantong, China
| | - Xiaohua Chen
- Department of Radiology, Affiliated Hospital of Nantong University, Nantong, China
| | - Yan Tang
- Department of Otolaryngology, Affiliated Hospital of Nantong University, Nantong, China
| | - Jinhong Qiu
- Department of Otolaryngology, Affiliated Hospital of Nantong University, Nantong, China
| | - Zhixia Wang
- Department of Otolaryngology, Affiliated Hospital of Nantong University, Nantong, China
| | - Xuchu Duan
- School of Life Science, Nantong University, Nantong, China
| | - Luping Zhang
- Department of Otolaryngology, Affiliated Hospital of Nantong University, Nantong, China
| |
Collapse
|
8
|
Mid-Frequency Hearing Loss Is Characteristic Clinical Feature of OTOA-Associated Hearing Loss. Genes (Basel) 2019; 10:genes10090715. [PMID: 31527525 PMCID: PMC6770988 DOI: 10.3390/genes10090715] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/09/2019] [Accepted: 09/12/2019] [Indexed: 12/03/2022] Open
Abstract
The OTOA gene (Locus: DFNB22) is reported to be one of the causative genes for non-syndromic autosomal recessive hearing loss. The copy number variations (CNVs) identified in this gene are also known to cause hearing loss, but have not been identified in Japanese patients with hearing loss. Furthermore, the clinical features of OTOA-associated hearing loss have not yet been clarified. In this study, we performed CNV analyses of a large Japanese hearing loss cohort, and identified CNVs in 234 of 2262 (10.3%, 234/2262) patients with autosomal recessive hearing loss. Among the identified CNVs, OTOA gene-related CNVs were the second most frequent (0.6%, 14/2262). Among the 14 cases, 2 individuals carried OTOA homozygous deletions, 4 carried heterozygous deletions with single nucleotide variants (SNVs) in another allele. Additionally, 1 individual with homozygous SNVs in the OTOA gene was also identified. Finally, we identified 7 probands with OTOA-associated hearing loss, so that its prevalence in Japanese patients with autosomal recessive hearing loss was calculated to be 0.3% (7/2262). As novel clinical features identified in this study, the audiometric configurations of patients with OTOA-associated hearing loss were found to be mid-frequency. This is the first study focused on the detailed clinical features of hearing loss caused by this gene mutation and/or gene deletion.
Collapse
|
9
|
Zou S, Mei X, Yang W, Zhu R, Yang T, Hu H. Whole-exome sequencing identifies rare pathogenic and candidate variants in sporadic Chinese Han deaf patients. Clin Genet 2019; 97:352-356. [PMID: 31486067 DOI: 10.1111/cge.13638] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 08/29/2019] [Accepted: 09/01/2019] [Indexed: 12/21/2022]
Abstract
Genetic causes of hearing loss are highly heterogeneous and often ethnically specific. In recent years, a variety of next-generation sequencing (NGS) panels have been developed to target deafness-causative genes. Whole-exome sequencing (WES), on the other hand, was rarely used for genetic testing for deafness. In this study, we performed WES in 38 sporadic Chinese Han deaf patients who have been pre-excluded for mutations in common deafness genes GJB2, SLC26A4 and MT-RNR1. Non-synonymous variants have been filtered based on their minor allele frequencies in public databases and ethnically matched controls. Bi-allelic pathogenic mutations in eight deafness genes, OTOF, TRIOBP, ESPN, HARS2, CDH23, MYO7A, USH1C and TJP2, were identified in 10 patients, with 17 mutations identified in this study not being associated with deafness previously. For the rest 28 patients, possibly bi-allelic rare non-synonymous variants in an averaged 4.7 genes per patient were identified as candidate pathogenic causes for future analysis. Our study showed that WES may provide a unified platform for genetic testing of deafness and enables retro-analyzing when new causative genes are revealed.
Collapse
Affiliation(s)
- Songfeng Zou
- Department of Otorhinolaryngology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Xueshuang Mei
- Department of Otorhinolaryngology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Weiqiang Yang
- Department of Otorhinolaryngology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Rvfei Zhu
- Department of Otorhinolaryngology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Tao Yang
- Department of Otorhinolaryngology-Head and Neck Surgery, Ninth People's 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
| | - Hongyi Hu
- Department of Otorhinolaryngology, Peking University Shenzhen Hospital, Shenzhen, China
| |
Collapse
|
10
|
Kim BJ, Kim DK, Han JH, Oh J, Kim AR, Lee C, Kim NK, Park HR, Kim MY, Lee S, Lee S, Oh DY, Park WY, Park S, Choi BY. Clarification of glycosylphosphatidylinositol anchorage of OTOANCORIN and human OTOA variants associated with deafness. Hum Mutat 2019; 40:525-531. [PMID: 30740825 DOI: 10.1002/humu.23719] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 01/23/2019] [Accepted: 02/06/2019] [Indexed: 12/22/2022]
Abstract
Otoancorin (OTOA), encoded by OTOA, is required for the development of the tectorial membrane in the inner ear. Mutations in this gene cause nonsyndromic hearing loss (DFNB22). The molecular mechanisms underlying most DFNB22 remain poorly understood. Disruption of glycosylphosphatidylinositol (GPI) anchorage has been assumed to be the pathophysiology mandating experimental validation. From a Korean deaf family, we identified two trans OTOA variants (c.1320 + 5 G > C and p.Gln589ArgfsX55 [NM_144672.3]) . The pathogenic potential of c.1320 + 5 G > C was confirmed by a minigene splicing assay. To experimentally determine the GPI anchorage, wild-type (WT) and mutant OTOA harboring p.Gln589ArgfsX55 were expressed in HEK293T cells. The mutant OTOA with p.Gln589ArgfsX55 resulted in an uncontrolled release of OTOA into the medium in contrast with phosphatidylinositol-specific phospholipase C-induced controlled release of WT OTOA from the cell surface. Together, the results of this reverse translational study confirmed GPI-anchorage of OTOA and showed that downstream sequences from the 589th amino acid are critical for GPI-anchorage.
Collapse
Affiliation(s)
- Bong Jik Kim
- Department of Otolaryngology - Head and Neck Surgery, Chungnam National University College of Medicine, Daejeon, South Korea.,Department of Otorhinolaryngology - Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Dong-Kyu Kim
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, Utah
| | - Jin Hee Han
- Department of Otorhinolaryngology - Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Jayoung Oh
- Department of Otorhinolaryngology - Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Ah Reum Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Chung Lee
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Nayoung Kd Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea
| | - Hye-Rim Park
- Department of Otorhinolaryngology - Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Min Young Kim
- Precision Medicine Center, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Sejoon Lee
- Department of Otorhinolaryngology - Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Seungmin Lee
- Department of Otorhinolaryngology - Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Doo Yi Oh
- Department of Otorhinolaryngology - Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, South Korea.,Department of Molecular Cell Biology, School of Medicine, Sungkyunkwan University, Seoul, South Korea
| | - Sungjin Park
- Department of Neurobiology and Anatomy, University of Utah School of Medicine, Salt Lake City, Utah
| | - Byung Yoon Choi
- Department of Otorhinolaryngology - Head and Neck Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| |
Collapse
|