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Xiong Y, Chen M, Wang H, Chen L, Huang H, Xu L. Mutation analysis of GJB2, SLC26A4, GJB3 and mtDNA12SrRNA genes in 251 non-syndromic hearing loss patients in Fujian, China. Int J Pediatr Otorhinolaryngol 2024; 176:111777. [PMID: 38029595 DOI: 10.1016/j.ijporl.2023.111777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/23/2023] [Accepted: 11/03/2023] [Indexed: 12/01/2023]
Abstract
OBJECTIVES The molecular etiology of non-syndromic hearing loss (NSHL) in Southeastern China (Fujian) has not been precisely identified. our study selected patients with NSHL and analyzed their causative genes, which helped to improve the accuracy of the diagnosis of hereditary hearing loss (HHL) and its treatment. METHODS 251 unrelated patients who attended the otolaryngology clinic of Fujian Maternal and Child Health Hospital with hearing loss were enrolled to our study. All patients had genetic tests and listening tests, of which 251 were diagnosed with NSHL. In addition, we used whole-exome sequencing (WES) in a patient who has a significant family history of HHL but negative for gene chip testing, as well as in his family members. RESULT Among of 251 patients, Nucleotide changes were found in 63 cases (25.09%), including 34 located in GJB2(13.5%, including 235delC and 299_300delAT), 13 located in SLC26A4(5.18%, including c.919-2G > A and 2168 A > G), 1 located in GJB3(0.4%,538C > T) and 16 located in mtDNA12SrRNA (6.37%,1555 A > G). In addition, we discuss the process of identifying novel PLS1 mutations from 251 patients. CONCLUSION Our results demonstrate the conventional deafness gene mutation in 251 NSHL patients in Fujian, China. Compared with the other area of China, we have a lower detection rate, but GJB2 235delC remains the most common mutation in Fujian. In addition, we discuss the process of discovering novel mutation locus for deafness, which provides an understanding for deafness diagnosis and genetic testing.
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Affiliation(s)
- Yikang Xiong
- The Frist Department of Clinical Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, Fujian Province, China
| | - Meihuan Chen
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, China
| | - Haiwei Wang
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, China
| | - Lingji Chen
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, China.
| | - Liangpu Xu
- The Frist Department of Clinical Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, Fujian Province, China; Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, China.
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Park J, Bird JE. The actin cytoskeleton in hair bundle development and hearing loss. Hear Res 2023; 436:108817. [PMID: 37300948 PMCID: PMC10408727 DOI: 10.1016/j.heares.2023.108817] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/18/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023]
Abstract
Inner ear hair cells assemble mechanosensitive hair bundles on their apical surface that transduce sounds and accelerations. Each hair bundle is comprised of ∼ 100 individual stereocilia that are arranged into rows of increasing height and width; their specific and precise architecture being necessary for mechanoelectrical transduction (MET). The actin cytoskeleton is fundamental to establishing this architecture, not only by forming the structural scaffold shaping each stereocilium, but also by composing rootlets and the cuticular plate that together provide a stable foundation supporting each stereocilium. In concert with the actin cytoskeleton, a large assortment of actin-binding proteins (ABPs) function to cross-link actin filaments into specific topologies, as well as control actin filament growth, severing, and capping. These processes are individually critical for sensory transduction and are all disrupted in hereditary forms of human hearing loss. In this review, we provide an overview of actin-based structures in the hair bundle and the molecules contributing to their assembly and functional properties. We also highlight recent advances in mechanisms driving stereocilia elongation and how these processes are tuned by MET.
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Affiliation(s)
- Jinho Park
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610, United States; Myology Institute, University of Florida, Gainesville, FL 32610, United States
| | - Jonathan E Bird
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610, United States; Myology Institute, University of Florida, Gainesville, FL 32610, United States.
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Yaldiz B, Kucuk E, Hampstead J, Hofste T, Pfundt R, Corominas Galbany J, Rinne T, Yntema HG, Hoischen A, Nelen M, Gilissen C. Twist exome capture allows for lower average sequence coverage in clinical exome sequencing. Hum Genomics 2023; 17:39. [PMID: 37138343 PMCID: PMC10155375 DOI: 10.1186/s40246-023-00485-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/20/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND Exome and genome sequencing are the predominant techniques in the diagnosis and research of genetic disorders. Sufficient, uniform and reproducible/consistent sequence coverage is a main determinant for the sensitivity to detect single-nucleotide (SNVs) and copy number variants (CNVs). Here we compared the ability to obtain comprehensive exome coverage for recent exome capture kits and genome sequencing techniques. RESULTS We compared three different widely used enrichment kits (Agilent SureSelect Human All Exon V5, Agilent SureSelect Human All Exon V7 and Twist Bioscience) as well as short-read and long-read WGS. We show that the Twist exome capture significantly improves complete coverage and coverage uniformity across coding regions compared to other exome capture kits. Twist performance is comparable to that of both short- and long-read whole genome sequencing. Additionally, we show that even at a reduced average coverage of 70× there is only minimal loss in sensitivity for SNV and CNV detection. CONCLUSION We conclude that exome sequencing with Twist represents a significant improvement and could be performed at lower sequence coverage compared to other exome capture techniques.
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Affiliation(s)
- Burcu Yaldiz
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Erdi Kucuk
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Juliet Hampstead
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Tom Hofste
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Jordi Corominas Galbany
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Tuula Rinne
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Marcel Nelen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.
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Xu L, Wang X, Li J, Chen L, Wang H, Xu S, Zhang Y, Li W, Yao P, Tan M, Zhou S, Chen M, Pan Y, Chen X, Chen X, Liu Y, Lin N, Huang H, Cao H. A novel PLS1 c.981+1G>A variant causes autosomal-dominant hereditary hearing loss in a family. Clin Genet 2023; 103:413-423. [PMID: 36537221 DOI: 10.1111/cge.14283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/03/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
The fimbrin protein family contains a variety of proteins, among which Plastin1 (PLS1) is an important member. According to recent studies, variations in the coding region of the PLS1 gene are associated with the development of deafness. However, the molecular mechanism of deafness caused by PLS1 gene variants remains unknown. Whole-exome sequencing was performed on hearing-impaired family members and hearing family members to identify pathogenic variants, followed by Sanger sequencing. A minigene assay was conducted to investigate the effect of the variant on PLS1 mRNA splicing. The pathogenicity of the variant was further investigated in zebrafish. RNA-sequencing (RNA-seq) was performed to analyze the dysregulation of downstream signaling pathways caused by knockdown of PLS1 expression. We identified a novel variant, PLS1 c.981+1G>A, in a large Chinese family with hearing loss and showed that the variant is responsible for the occurrence of hearing loss by inducing exon 8 skipping. The variant caused abnormal inner ear phenotypes, characterized by decreases in the mean otolith distance, anterior otolith diameter, posterior otolith diameter, cochlear diameter, and swimming speed and distance in zebrafish. Furthermore, silencing PLS1 expression significantly upregulated the expression of genes in the PI3K-Akt signaling pathway, including Col6a3, Spp1, Itgb3 and hepatocyte growth factor (Hgf). PLS1 c.981+1G>A is a novel pathogenic variant causing hearing loss by inducing exon 8 skipping. Upregulation of the expression of genes in the PI3K-Akt signaling pathway plays an important role in the pathogenesis caused by variants in the PLS1 gene.
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Affiliation(s)
- Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xinrui Wang
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primates, Fujian Maternity and Child Health Hospital, Fuzhou, China
| | - Jia Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Shijiazhuang BGI Genomics Co., Ltd., Shijiazhuang, China
| | - Lingji Chen
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Haiwei Wang
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
| | - Shiyi Xu
- The First Clinical Medical College, Guangxi Medical University, Nanning, China
| | - Yanhong Zhang
- Department of Laboratory Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Wei Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Meihua Tan
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Si Zhou
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Hebei Industrial Technology Research Institute of Genomics in Maternal & Child Health, Shijiazhuang BGI Genomics Co., Ltd., Shijiazhuang, China
- College of Life Sciences, University of Chinese Academy of Sciences, China
| | - Meihuan Chen
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Yali Pan
- Department of Laboratory Medicine, Medical Technology and Engineering College of Fujian Medical University, Fuzhou, China
| | - Xuemei Chen
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xiaolan Chen
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Yunliang Liu
- Otolaryngological Department of Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Hua Cao
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primates, Fujian Maternity and Child Health Hospital, Fuzhou, China
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Rajan S, Kudryashov DS, Reisler E. Actin Bundles Dynamics and Architecture. Biomolecules 2023; 13:450. [PMID: 36979385 PMCID: PMC10046292 DOI: 10.3390/biom13030450] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/04/2023] Open
Abstract
Cells use the actin cytoskeleton for many of their functions, including their division, adhesion, mechanosensing, endo- and phagocytosis, migration, and invasion. Actin bundles are the main constituent of actin-rich structures involved in these processes. An ever-increasing number of proteins that crosslink actin into bundles or regulate their morphology is being identified in cells. With recent advances in high-resolution microscopy and imaging techniques, the complex process of bundles formation and the multiple forms of physiological bundles are beginning to be better understood. Here, we review the physiochemical and biological properties of four families of highly conserved and abundant actin-bundling proteins, namely, α-actinin, fimbrin/plastin, fascin, and espin. We describe the similarities and differences between these proteins, their role in the formation of physiological actin bundles, and their properties-both related and unrelated to their bundling abilities. We also review some aspects of the general mechanism of actin bundles formation, which are known from the available information on the activity of the key actin partners involved in this process.
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Affiliation(s)
- Sudeepa Rajan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Dmitri S. Kudryashov
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Emil Reisler
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
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Allosteric regulation controls actin-bundling properties of human plastins. Nat Struct Mol Biol 2022; 29:519-528. [PMID: 35589838 DOI: 10.1038/s41594-022-00771-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 04/05/2022] [Indexed: 11/08/2022]
Abstract
Plastins/fimbrins are conserved actin-bundling proteins contributing to motility, cytokinesis and other cellular processes by organizing strikingly different actin assemblies as in aligned bundles and branched networks. We propose that this ability of human plastins stems from an allosteric communication between their actin-binding domains (ABD1/2) engaged in a tight spatial association. Here we show that ABD2 can bind actin three orders of magnitude stronger than ABD1, unless the domains are involved in an equally strong inhibitory engagement. A mutation mimicking physiologically relevant phosphorylation at the ABD1-ABD2 interface greatly weakened their association, dramatically potentiating actin cross-linking. Cryo-EM reconstruction revealed the ABD1-actin interface and enabled modeling of the plastin bridge and domain separation in parallel bundles. We predict that a strong and tunable allosteric inhibition between the domains allows plastins to modulate the cross-linking strength, contributing to remodeling of actin assemblies of different morphologies defining the unique place of plastins in actin organization.
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