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Lee J, Jeong H, Won D, Shin S, Lee ST, Choi JR, Byeon SH, Kuht HJ, Thomas MG, Han J. Noncanonical Splice Site and Deep Intronic FRMD7 Variants Activate Cryptic Exons in X-linked Infantile Nystagmus. Transl Vis Sci Technol 2022; 11:25. [PMID: 35762937 PMCID: PMC9251792 DOI: 10.1167/tvst.11.6.25] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Purpose We aim to report noncoding pathogenic variants in patients with FRMD7-related infantile nystagmus (FIN). Methods Genome sequencing (n = 2 families) and reanalysis of targeted panel next generation sequencing (n = 2 families) was performed in genetically unsolved cases of suspected FIN. Previous sequence analysis showed no pathogenic coding variants in genes associated with infantile nystagmus. SpliceAI, SpliceRover, and Alamut consensus programs were used to annotate noncoding variants. Minigene splicing assay was performed to confirm aberrant splicing. In silico analysis of exonic splicing enhancer and silencer was also performed. Results FRMD7 intronic variants were identified based on genome sequencing and targeted next-generation sequencing analysis. These included c.285-12A>G (pedigree 1), c.284+63T>A (pedigrees 2 and 3), and c. 383-1368A>G (pedigree 4). All variants were absent in gnomAD, and the both c.285-12A>G and c.284+63T>A variants were predicted to enhance new splicing acceptor gains with SpliceAI, SpliceRover, and Alamut consensus approaches. However, the c.383-1368 A>G variant only had a significant impact score on the SpliceRover program. The c.383-1368A>G variant was predicted to promote pseudoexon inclusion by binding of exonic splicing enhancer. Aberrant exonizations were validated through minigene constructs, and all variants were segregated in the families. Conclusions Deep learning–based annotation of noncoding variants facilitates the discovery of hidden genetic variations in patients with FIN. This study provides evidence of effectiveness of combined deep learning–based splicing tools to identify hidden pathogenic variants in previously unsolved patients with infantile nystagmus. Translational Relevance These results demonstrate robust analysis using two deep learning splicing predictions and in vitro functional study can lead to finding hidden genetic variations in unsolved patients.
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Affiliation(s)
- Junwon Lee
- Institute of Vision Research, Department of Ophthalmology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Han Jeong
- Brain Korea 21 Project for Medical Science, Yonsei University, Seoul, South Korea.,Institute of Vision Research, Department of Ophthalmology, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Dongju Won
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea.,Dxome Co., Ltd. Seongnam-si, Gyeonggi-do, South Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea.,Dxome Co., Ltd. Seongnam-si, Gyeonggi-do, South Korea
| | - Suk Ho Byeon
- Brain Korea 21 Project for Medical Science, Yonsei University, Seoul, South Korea.,Institute of Vision Research, Department of Ophthalmology, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Helen J Kuht
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, RKCSB, PO Box 65, Leicester LE2 7LX, UK
| | - Mervyn G Thomas
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, RKCSB, PO Box 65, Leicester LE2 7LX, UK
| | - Jinu Han
- Institute of Vision Research, Department of Ophthalmology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
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Liu M, Liang Y, Huang B, Sun J, Chen K. Report of rare and novel mutations in candidate genes in a cohort of hearing-impaired patients. Mol Genet Genomic Med 2022; 10:e1887. [PMID: 35106950 PMCID: PMC9000930 DOI: 10.1002/mgg3.1887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 12/24/2021] [Accepted: 01/14/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Many hearing-impaired patients carry mutations in rare or novel genes undetected in regular genetic hot regions/genes screening. METHODS We collected clinical and genetic data from subjects with hearing loss who visited our department for genetic counseling. Next-generation sequencing was conducted after 154 deafness-related genes were captured using a designed genes panels in 14 unrelated families (37 participants). The results were filtered and assessed with in silico tools, in combination with pedigree mapping. RESULTS Ten mutations in regular deafness genes (GJB2, SLC26A4) and uncommon genes (OTOF, MYO7A, MYO15A, and KARS) were detected, which constituted 57.2% of yielded rate. In particular, two patients with nonsyndromic deafness carried biallelic KARS mutations. In addition, we identified an unreported digenic mutational inheritance in GRP98/USH2A genes in a proband with isolated hearing loss. Functional analyses and molecular modeling suggested the damaging consequence of these variants on encoded proteins. According to the variant pathogenicity guidelines, the 17 identified variants in total were classified as "pathogenic" or "likely pathogenic." CONCLUSION The candidate mutations in deafness genes were suggested to be co-segregated in at least 57.2% of the studied pedigrees. This is the new report of rare/novel mutations causing inherited hearing loss in Chinese.
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Affiliation(s)
- Min Liu
- Department of Otorhinolaryngology, The First Affiliated Hospital, Sun Yat-sen University and Institute of Otorhinolaryngology, Sun Yat-sen University, Guangzhou, China
| | - Yue Liang
- Department of Otorhinolaryngology, The First Affiliated Hospital, Sun Yat-sen University and Institute of Otorhinolaryngology, Sun Yat-sen University, Guangzhou, China
| | - Bixue Huang
- Department of Otorhinolaryngology, The First Affiliated Hospital, Sun Yat-sen University and Institute of Otorhinolaryngology, Sun Yat-sen University, Guangzhou, China
| | - Jincangjian Sun
- Department of Otorhinolaryngology, The First Affiliated Hospital, Sun Yat-sen University and Institute of Otorhinolaryngology, Sun Yat-sen University, Guangzhou, China
| | - Kaitian Chen
- Department of Otorhinolaryngology, The First Affiliated Hospital, Sun Yat-sen University and Institute of Otorhinolaryngology, Sun Yat-sen University, Guangzhou, China
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Fuster-García C, García-Bohórquez B, Rodríguez-Muñoz A, Aller E, Jaijo T, Millán JM, García-García G. Usher Syndrome: Genetics of a Human Ciliopathy. Int J Mol Sci 2021; 22:6723. [PMID: 34201633 PMCID: PMC8268283 DOI: 10.3390/ijms22136723] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 12/21/2022] Open
Abstract
Usher syndrome (USH) is an autosomal recessive syndromic ciliopathy characterized by sensorineural hearing loss, retinitis pigmentosa and, sometimes, vestibular dysfunction. There are three clinical types depending on the severity and age of onset of the symptoms; in addition, ten genes are reported to be causative of USH, and six more related to the disease. These genes encode proteins of a diverse nature, which interact and form a dynamic protein network called the "Usher interactome". In the organ of Corti, the USH proteins are essential for the correct development and maintenance of the structure and cohesion of the stereocilia. In the retina, the USH protein network is principally located in the periciliary region of the photoreceptors, and plays an important role in the maintenance of the periciliary structure and the trafficking of molecules between the inner and the outer segments of photoreceptors. Even though some genes are clearly involved in the syndrome, others are controversial. Moreover, expression of some USH genes has been detected in other tissues, which could explain their involvement in additional mild comorbidities. In this paper, we review the genetics of Usher syndrome and the spectrum of mutations in USH genes. The aim is to identify possible mutation associations with the disease and provide an updated genotype-phenotype correlation.
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Affiliation(s)
- Carla Fuster-García
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain; (C.F.-G.); (B.G.-B.); (A.R.-M.); (E.A.); (T.J.); (G.G.-G.)
- Unidad Mixta de Enfermedades Raras IIS La Fe-Centro de Investigación Príncipe Felipe, 46026 Valencia, Spain
- Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
| | - Belén García-Bohórquez
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain; (C.F.-G.); (B.G.-B.); (A.R.-M.); (E.A.); (T.J.); (G.G.-G.)
- Unidad Mixta de Enfermedades Raras IIS La Fe-Centro de Investigación Príncipe Felipe, 46026 Valencia, Spain
| | - Ana Rodríguez-Muñoz
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain; (C.F.-G.); (B.G.-B.); (A.R.-M.); (E.A.); (T.J.); (G.G.-G.)
- Unidad Mixta de Enfermedades Raras IIS La Fe-Centro de Investigación Príncipe Felipe, 46026 Valencia, Spain
| | - Elena Aller
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain; (C.F.-G.); (B.G.-B.); (A.R.-M.); (E.A.); (T.J.); (G.G.-G.)
- Unidad Mixta de Enfermedades Raras IIS La Fe-Centro de Investigación Príncipe Felipe, 46026 Valencia, Spain
- Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
- Genetics Unit, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
| | - Teresa Jaijo
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain; (C.F.-G.); (B.G.-B.); (A.R.-M.); (E.A.); (T.J.); (G.G.-G.)
- Unidad Mixta de Enfermedades Raras IIS La Fe-Centro de Investigación Príncipe Felipe, 46026 Valencia, Spain
- Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
- Genetics Unit, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
| | - José M. Millán
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain; (C.F.-G.); (B.G.-B.); (A.R.-M.); (E.A.); (T.J.); (G.G.-G.)
- Unidad Mixta de Enfermedades Raras IIS La Fe-Centro de Investigación Príncipe Felipe, 46026 Valencia, Spain
- Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
| | - Gema García-García
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain; (C.F.-G.); (B.G.-B.); (A.R.-M.); (E.A.); (T.J.); (G.G.-G.)
- Unidad Mixta de Enfermedades Raras IIS La Fe-Centro de Investigación Príncipe Felipe, 46026 Valencia, Spain
- Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
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Kortüm F, Kieninger S, Mazzola P, Kohl S, Wissinger B, Prokisch H, Stingl K, Weisschuh N. X-Linked Retinitis Pigmentosa Caused by Non-Canonical Splice Site Variants in RPGR. Int J Mol Sci 2021; 22:ijms22020850. [PMID: 33467000 PMCID: PMC7830253 DOI: 10.3390/ijms22020850] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/14/2021] [Accepted: 01/14/2021] [Indexed: 01/13/2023] Open
Abstract
We aimed to validate the effect of non-canonical splice site variants in the RPGR gene in five patients from four families diagnosed with retinitis pigmentosa. Four variants located in intron 2 (c.154 + 3_154 + 6del), intron 3 (c.247 + 5G>A), intron 7 (c.779-5T>G), and intron 13 (c.1573-12A>G), respectively, were analyzed by means of in vitro splice assays. Splicing analysis revealed different aberrant splicing events, including exon skipping and intronic nucleotide addition, which are predicted to lead either to an in-frame deletion affecting relevant protein domains or to a frameshift of the open reading frame. Our data expand the landscape of pathogenic variants in RPGR, thereby increasing the genetic diagnostic rate in retinitis pigmentosa and allowing patients harboring the analyzed variants to be enrolled in clinical trials.
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Affiliation(s)
- Friederike Kortüm
- Center for Ophthalmology, University Eye Hospital, University of Tübingen, 72076 Tübingen, Germany; (F.K.); (K.S.)
| | - Sinja Kieninger
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, 72076 Tübingen, Germany; (S.K.); (S.K.); (B.W.)
| | - Pascale Mazzola
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany;
| | - Susanne Kohl
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, 72076 Tübingen, Germany; (S.K.); (S.K.); (B.W.)
| | - Bernd Wissinger
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, 72076 Tübingen, Germany; (S.K.); (S.K.); (B.W.)
| | - Holger Prokisch
- Institute of Neurogenomics, Helmholtz Zentrum München, 85764 Neuherberg, Germany;
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany
| | - Katarina Stingl
- Center for Ophthalmology, University Eye Hospital, University of Tübingen, 72076 Tübingen, Germany; (F.K.); (K.S.)
| | - Nicole Weisschuh
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, 72076 Tübingen, Germany; (S.K.); (S.K.); (B.W.)
- Correspondence:
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5
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Splicing mutations in inherited retinal diseases. Prog Retin Eye Res 2021. [DOI: 10.1016/j.preteyeres.2020.100874
expr 921883647 + 833887994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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6
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Genetic Spectrum of Syndromic and Non-Syndromic Hearing Loss in Pakistani Families. Genes (Basel) 2020; 11:genes11111329. [PMID: 33187236 PMCID: PMC7709052 DOI: 10.3390/genes11111329] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/27/2020] [Accepted: 11/09/2020] [Indexed: 12/30/2022] Open
Abstract
The current molecular genetic diagnostic rates for hereditary hearing loss (HL) vary considerably according to the population background. Pakistan and other countries with high rates of consanguineous marriages have served as a unique resource for studying rare and novel forms of recessive HL. A combined exome sequencing, bioinformatics analysis, and gene mapping approach for 21 consanguineous Pakistani families revealed 13 pathogenic or likely pathogenic variants in the genes GJB2, MYO7A, FGF3, CDC14A, SLITRK6, CDH23, and MYO15A, with an overall resolve rate of 61.9%. GJB2 and MYO7A were the most frequently involved genes in this cohort. All the identified variants were either homozygous or compound heterozygous, with two of them not previously described in the literature (15.4%). Overall, seven missense variants (53.8%), three nonsense variants (23.1%), two frameshift variants (15.4%), and one splice-site variant (7.7%) were observed. Syndromic HL was identified in five (23.8%) of the 21 families studied. This study reflects the extreme genetic heterogeneity observed in HL and expands the spectrum of variants in deafness-associated genes.
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7
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Di Scipio M, Tavares E, Deshmukh S, Audo I, Green-Sanderson K, Zubak Y, Zine-Eddine F, Pearson A, Vig A, Tang CY, Mollica A, Karas J, Tumber A, Yu CW, Billingsley G, Wilson MD, Zeitz C, Héon E, Vincent A. Phenotype Driven Analysis of Whole Genome Sequencing Identifies Deep Intronic Variants that Cause Retinal Dystrophies by Aberrant Exonization. Invest Ophthalmol Vis Sci 2020; 61:36. [PMID: 32881472 PMCID: PMC7443117 DOI: 10.1167/iovs.61.10.36] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/16/2020] [Indexed: 02/07/2023] Open
Abstract
Purpose To demonstrate the effectiveness of combining retinal phenotyping and focused variant filtering from genome sequencing (GS) in identifying deep intronic disease causing variants in inherited retinal dystrophies. Methods Affected members from three pedigrees with classical enhanced S-cone syndrome (ESCS; Pedigree 1), congenital stationary night blindness (CSNB; Pedigree 2), and achromatopsia (ACHM; Pedigree 3), respectively, underwent detailed ophthalmologic evaluation, optical coherence tomography, and electroretinography. The probands underwent panel-based genetic testing followed by GS analysis. Minigene constructs (NR2E3, GPR179 and CNGB3) and patient-derived cDNA experiments (NR2E3 and GPR179) were performed to assess the functional effect of the deep intronic variants. Results The electrophysiological findings confirmed the clinical diagnosis of ESCS, CSNB, and ACHM in the respective pedigrees. Panel-based testing revealed heterozygous pathogenic variants in NR2E3 (NM_014249.3; c.119-2A>C; Pedigree 1) and CNGB3 (NM_019098.4; c.1148delC/p.Thr383Ilefs*13; Pedigree 3). The GS revealed heterozygous deep intronic variants in Pedigrees 1 (NR2E3; c.1100+1124G>A) and 3 (CNGB3; c.852+4751A>T), and a homozygous GPR179 variant in Pedigree 2 (NM_001004334.3; c.903+343G>A). The identified variants segregated with the phenotype in all pedigrees. All deep intronic variants were predicted to generate a splice acceptor gain causing aberrant exonization in NR2E3 [89 base pairs (bp)], GPR179 (197 bp), and CNGB3 (73 bp); splicing defects were validated through patient-derived cDNA experiments and/or minigene constructs and rescued by antisense oligonucleotide treatment. Conclusions Deep intronic mutations contribute to missing heritability in retinal dystrophies. Combining results from phenotype-directed gene panel testing, GS, and in silico splice prediction tools can help identify these difficult-to-detect pathogenic deep intronic variants.
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Affiliation(s)
- Matteo Di Scipio
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Erika Tavares
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Shriya Deshmukh
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
- CHNO des Quinze-Vingts, INSERM-DGOS CIC1423, Paris, France
- University College London Institute of Ophthalmology, London, United Kingdom
| | - Kit Green-Sanderson
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Yuliya Zubak
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Fayçal Zine-Eddine
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Alexander Pearson
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Anjali Vig
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Chen Yu Tang
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Antonio Mollica
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Jonathan Karas
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Anupreet Tumber
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Canada
| | - Caberry W. Yu
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Gail Billingsley
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Michael D. Wilson
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Elise Héon
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Canada
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Canada
| | - Ajoy Vincent
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Canada
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Canada
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Novel loss-of-function mutations in COCH cause autosomal recessive nonsyndromic hearing loss. Hum Genet 2020; 139:1565-1574. [PMID: 32562050 DOI: 10.1007/s00439-020-02197-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/12/2020] [Indexed: 12/12/2022]
Abstract
COCH is the most abundantly expressed gene in the cochlea. Unsurprisingly, mutations in COCH underly hearing loss in mice and humans. Two forms of hearing loss are linked to mutations in COCH, the well-established autosomal dominant nonsyndromic hearing loss, with or without vestibular dysfunction (DFNA9) via a gain-of-function/dominant-negative mechanism, and more recently autosomal recessive nonsyndromic hearing loss (DFNB110) via nonsense variants. Using a combination of targeted gene panels, exome sequencing, and functional studies, we identified four novel pathogenic variants (two nonsense variants, one missense, and one inframe deletion) in COCH as the cause of autosomal recessive hearing loss in a multi-ethnic cohort. To investigate whether the non-truncating variants exert their effect via a loss-of-function mechanism, we used minigene splicing assays. Our data showed both the missense and inframe deletion variants altered RNA splicing by creating an exon splicing silencer and abolishing an exon splicing enhancer, respectively. Both variants create frameshifts and are predicted to result in a null allele. This study confirms the involvement of loss-of-function mutations in COCH in autosomal recessive nonsyndromic hearing loss, expands the mutational landscape of DFNB110 to include coding variants that alter RNA splicing, and highlights the need to investigate the effect of coding variants on RNA splicing.
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9
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Splicing mutations in inherited retinal diseases. Prog Retin Eye Res 2020; 80:100874. [PMID: 32553897 DOI: 10.1016/j.preteyeres.2020.100874] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 05/30/2020] [Accepted: 05/31/2020] [Indexed: 12/15/2022]
Abstract
Mutations which induce aberrant transcript splicing represent a distinct class of disease-causing genetic variants in retinal disease genes. Such mutations may either weaken or erase regular splice sites or create novel splice sites which alter exon recognition. While mutations affecting the canonical GU-AG dinucleotides at the splice donor and splice acceptor site are highly predictive to cause a splicing defect, other variants in the vicinity of the canonical splice sites or those affecting additional cis-acting regulatory sequences within exons or introns are much more difficult to assess or even to recognize and require additional experimental validation. Splicing mutations are unique in that the actual outcome for the transcript (e.g. exon skipping, pseudoexon inclusion, intron retention) and the encoded protein can be quite different depending on the individual mutation. In this article, we present an overview on the current knowledge about and impact of splicing mutations in inherited retinal diseases. We introduce the most common sub-classes of splicing mutations including examples from our own work and others and discuss current strategies for the identification and validation of splicing mutations, as well as therapeutic approaches, open questions, and future perspectives in this field of research.
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10
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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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Role of Targeted Next Generation Sequencing in the Etiological Work-Up of Congenitally Deaf Children. Otol Neurotol 2019; 39:732-738. [PMID: 29889784 DOI: 10.1097/mao.0000000000001847] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
OBJECTIVES The purpose of this study is to report the results of a comprehensive etiological work-up for congenitally deaf children including targeted next generation sequencing. STUDY DESIGN Retrospective case review. SETTING Tertiary referral center. PATIENTS Fifty children with congenital, bilateral profound hearing loss (HL) (>90 dBnHL). INTERVENTIONS Etiological work-up included testing for pathogenic variants in GJB2, a phenotype driven genetic analysis, screening for congenital infections and imaging. When no etiology could be found, comprehensive genetic testing was performed using a HL gene panel including 45 syndromic and 96 non-syndromic HL genes. RESULTS Eleven patients carried bi-allelic pathogenic variants in GJB2. Phenotype driven genetic analysis identified two homozygous KCNQ1 patients (Jervell and Lange Nielsen syndrome) and one heterozygous CHD7 patient (CHARGE syndrome). One patient was diagnosed with achondroplasia and one had a clinical diagnosis of Waardenburg syndrome. A deafness gene panel evaluated 16 patients. In 12 out of 16, we identified a pathogenic (n = 12) or likely pathogenic (n = 2) variant and one variant of unknown significance (VUS). A definite diagnosis of non-syndromic or syndromic HL was made in 18 and seven patients, respectively. Non-genetic causes were congenital cytomegalovirus infection (n = 11), anatomic abnormalities (n = 2), neurological/metabolic/polymalformative conditions (n = 3), meningitis (n = 1), and auditory neuropathy (n = 1). CONCLUSIONS A definite genetic cause was found in 25 (50%) of congenital, bilaterally deaf children. Our data show that implementation of a gene panel improves the diagnostic yield for etiological work-up of congenital profound HL to 86%. Identification of the etiology of congenital HL may contribute to predicting outcomes of cochlear implantation.
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12
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Aberrant Splicing Events Associated to CDH23 Noncanonical Splice Site Mutations in a Proband with Atypical Usher Syndrome 1. Genes (Basel) 2019; 10:genes10100732. [PMID: 31546658 PMCID: PMC6826400 DOI: 10.3390/genes10100732] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/17/2019] [Accepted: 09/19/2019] [Indexed: 12/16/2022] Open
Abstract
Aims: The aim of this study was the genetic diagnosis by next generation sequencing (NGS) of a patient diagnosed with Usher syndrome type 2 and the functional evaluation of the identified genetic variants to establish a phenotype–genotype correlation. Methods: Whole exome sequencing (WES) analysis identified two heterozygous intronic variants in CDH23, a gene responsible of Usher syndrome type 1. Evaluation of the putative splicing effects was performed in vivo, in whole blood samples, and in vitro, by transfection of midigene constructs in HEK293T cells. Results: Two intronic variants were identified in intron 45 of CDH23—one novel, c.6050-15G>A, and the other, c.6050-9G>A, already reported as a noncanonical splice site (NCSS) mutation—with partial functional characterization. In vivo and in vitro analyses showed aberrant transcripts by the addition of 13 and 7 nucleotides to exon 46, respectively. Transcript degradation by nonsense mediated decay (NMD) in blood cells could only be prevented by cycloheximide treatment. Midigene constructs showed that the two variants contributed to exon skipping and generated aberrantly spliced transcripts. Conclusions: A combination of in vivo and in vitro assays provided a comprehensive view of the physiological effects of NCSS variants, which in this case led to a clinical reassignment of the proband as affected with atypical USH1 syndrome.
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13
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Moreau-Le Lan S, Aller E, Calabria I, Gonzalez-Tarancon L, Cardona-Gay C, Martinez-Matilla M, Aparisi MJ, Selles J, Sagath L, Pitarch I, Muelas N, Cervera JV, Millan JM, Pedrola L. New mutations found by Next-Generation Sequencing screening of Spanish patients with Nemaline Myopathy. PLoS One 2018; 13:e0207296. [PMID: 30517146 PMCID: PMC6281284 DOI: 10.1371/journal.pone.0207296] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 10/29/2018] [Indexed: 02/03/2023] Open
Abstract
Nemaline Myopathy (NM) is a rare genetic disorder that encompasses a large spectrum of myopathies characterized by hypotonia and generalized muscle weakness. To date, mutations in thirteen different genes have been associated with NM. The most frequently responsible genes are NEB (50% of cases) and ACTA1 (15–25% of cases). In this report all known NM related genes were screened by Next Generation Sequencing in five Spanish patients in order to genetically confirm the clinical and histological diagnosis of NM. Four mutations in NEB (c.17779_17780delTA, c.11086A>C, c.21076C>T and c.2310+5G>A) and one mutation in ACTA1 (c.871A>T) were found in four patients. Three of the four mutations in NEB were novel. A cDNA sequencing assay of the novel variants c.17779_17780delTA, c.11086A>C and c.2310+5G>A revealed that the intronic variant c.2310+5G>A affected the splicing process. Mutations reported here could help clinicians and geneticists in NM diagnosis.
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Affiliation(s)
- Sarah Moreau-Le Lan
- Genomic Unit, Health Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain
| | - Elena Aller
- Genetics Unit, La Fe University Hospital, Valencia, Spain
- Research Group on Molecular, Cellular and Genomic Biomedicine, Instituto de Investigación Sanitaria La Fe, Valencia, Spain
- Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain
| | - Ines Calabria
- Genomic Unit, Health Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain
| | | | - Cristina Cardona-Gay
- Genomic Unit, Health Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain
| | | | - Maria J. Aparisi
- Genomic Unit, Health Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain
| | - Jorge Selles
- Genomic Unit, Health Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain
| | - Lydia Sagath
- The Folkhälsan Institute of Genetics and the Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Finland
| | - Inmaculada Pitarch
- Unit of Rare Neuromuscular Diseases, La Fe University Hospital, Valencia, Spain
| | - Nuria Muelas
- Biomedical Network Research Center in Oncology (CIBERONC), Madrid, Spain
- Neuromuscular Diseases Unit, Neurology Department, La Fe University Hospital, Valencia, Spain, and Neuromuscular & Ataxias Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - Jose V. Cervera
- Genetics Unit, La Fe University Hospital, Valencia, Spain
- Biomedical Network Research Center in Oncology (CIBERONC), Madrid, Spain
| | - Jose M. Millan
- Genomic Unit, Health Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain
- Research Group on Molecular, Cellular and Genomic Biomedicine, Instituto de Investigación Sanitaria La Fe, Valencia, Spain
- Biomedical Network Research Center for Rare Diseases (CIBERER), Madrid, Spain
| | - Laia Pedrola
- Genomic Unit, Health Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain
- * E-mail:
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14
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Fuster-García C, García-García G, Jaijo T, Fornés N, Ayuso C, Fernández-Burriel M, Sánchez-De la Morena A, Aller E, Millán JM. High-throughput sequencing for the molecular diagnosis of Usher syndrome reveals 42 novel mutations and consolidates CEP250 as Usher-like disease causative. Sci Rep 2018; 8:17113. [PMID: 30459346 PMCID: PMC6244211 DOI: 10.1038/s41598-018-35085-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/17/2018] [Indexed: 01/09/2023] Open
Abstract
Usher syndrome is a rare disorder causing retinitis pigmentosa, together with sensorineural hearing loss. Due to the phenotypic and genetic heterogeneity of this disease, the best method to screen the causative mutations is by high-throughput sequencing. In this study, we tested a semiconductor chip based sequencing approach with 77 unrelated patients, as a molecular diagnosis routine. In addition, Multiplex Ligation-dependent Probe Amplification and microarray-based Comparative Genomic Hybridization techniques were applied to detect large rearrangements, and minigene assays were performed to confirm the mRNA processing aberrations caused by splice-site mutations. The designed panel included all the USH causative genes (MYO7A, USH1C, CDH23, PCDH15, USH1G, CIB2, USH2A, ADGRV1, WHRN and CLRN1) as well as four uncertainly associated genes (HARS, PDZD7, CEP250 and C2orf71). The outcome showed an overall mutation detection ratio of 82.8% and allowed the identification of 42 novel putatively pathogenic mutations. Furthermore, we detected two novel nonsense mutations in CEP250 in a patient with a disease mimicking Usher syndrome that associates visual impairment due to cone-rod dystrophy and progressive hearing loss. Therefore, this approach proved reliable results for the molecular diagnosis of the disease and also allowed the consolidation of the CEP250 gene as disease causative for an Usher-like phenotype.
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Affiliation(s)
- Carla Fuster-García
- Grupo de Investigación en Biomedicina Molecular, Celular y Genómica, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Gema García-García
- Grupo de Investigación en Biomedicina Molecular, Celular y Genómica, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain.
- CIBER de Enfermedades Raras (CIBERER), Madrid, Spain.
| | - Teresa Jaijo
- Grupo de Investigación en Biomedicina Molecular, Celular y Genómica, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
- CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
- Unidad de Genética y Diagnóstico Prenatal, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Neus Fornés
- Grupo de Investigación en Biomedicina Molecular, Celular y Genómica, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Carmen Ayuso
- CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
- Servicio de Genética, Fundación Jiménez Díaz, University Hospital, Instituto de Investigación Sanitaria Fundación Jiménez Díaz IIS-FJD, UAM, Madrid, Spain
| | | | | | - Elena Aller
- Grupo de Investigación en Biomedicina Molecular, Celular y Genómica, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
- CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
- Unidad de Genética y Diagnóstico Prenatal, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - José M Millán
- Grupo de Investigación en Biomedicina Molecular, Celular y Genómica, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
- CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
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15
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Neuhaus C, Eisenberger T, Decker C, Nagl S, Blank C, Pfister M, Kennerknecht I, Müller-Hofstede C, Charbel Issa P, Heller R, Beck B, Rüther K, Mitter D, Rohrschneider K, Steinhauer U, Korbmacher HM, Huhle D, Elsayed SM, Taha HM, Baig SM, Stöhr H, Preising M, Markus S, Moeller F, Lorenz B, Nagel-Wolfrum K, Khan AO, Bolz HJ. Next-generation sequencing reveals the mutational landscape of clinically diagnosed Usher syndrome: copy number variations, phenocopies, a predominant target for translational read-through, and PEX26 mutated in Heimler syndrome. Mol Genet Genomic Med 2017; 5:531-552. [PMID: 28944237 PMCID: PMC5606877 DOI: 10.1002/mgg3.312] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 06/06/2017] [Accepted: 06/09/2017] [Indexed: 12/23/2022] Open
Abstract
Background Combined retinal degeneration and sensorineural hearing impairment is mostly due to autosomal recessive Usher syndrome (USH1: congenital deafness, early retinitis pigmentosa (RP); USH2: progressive hearing impairment, RP). Methods Sanger sequencing and NGS of 112 genes (Usher syndrome, nonsyndromic deafness, overlapping conditions), MLPA, and array‐CGH were conducted in 138 patients clinically diagnosed with Usher syndrome. Results A molecular diagnosis was achieved in 97% of both USH1 and USH2 patients, with biallelic mutations in 97% (USH1) and 90% (USH2), respectively. Quantitative readout reliably detected CNVs (confirmed by MLPA or array‐CGH), qualifying targeted NGS as one tool for detecting point mutations and CNVs. CNVs accounted for 10% of identified USH2A alleles, often in trans to seemingly monoallelic point mutations. We demonstrate PTC124‐induced read‐through of the common p.Trp3955* nonsense mutation (13% of detected USH2A alleles), a potential therapy target. Usher gene mutations were found in most patients with atypical Usher syndrome, but the diagnosis was adjusted in case of double homozygosity for mutations in OTOA and NR2E3, genes implicated in isolated deafness and RP. Two patients with additional enamel dysplasia had biallelic PEX26 mutations, for the first time linking this gene to Heimler syndrome. Conclusion Targeted NGS not restricted to Usher genes proved beneficial in uncovering conditions mimicking Usher syndrome.
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Affiliation(s)
| | | | | | - Sandra Nagl
- Bioscientia Center for Human GeneticsIngelheimGermany
| | | | - Markus Pfister
- HNO-Praxis SarnenSarnenSwitzerland.,Molecular Genetics, THRCDepartment of OtolaryngologyUniversity of TübingenTübingenGermany
| | - Ingo Kennerknecht
- Institute of Human GeneticsWestfälische Wilhelms-UniversitätMünsterGermany
| | | | - Peter Charbel Issa
- Department of OphthalmologyUniversity of BonnBonnGermany.,Center for Rare Diseases Bonn (ZSEB)University of BonnBonnGermany.,Oxford Eye HospitalUniversity of OxfordOxfordUK
| | - Raoul Heller
- Institute of Human GeneticsUniversity Hospital of CologneCologneGermany
| | - Bodo Beck
- Institute of Human GeneticsUniversity Hospital of CologneCologneGermany
| | | | - Diana Mitter
- Institute of Human GeneticsUniversity of Leipzig Hospitals and ClinicsLeipzigGermany
| | | | | | - Heike M Korbmacher
- Department of OrthodonticsGiessen and Marburg University Hospital, Marburg CampusMarburgGermany
| | | | - Solaf M Elsayed
- Medical Genetics CenterCairoEgypt.,Children's HospitalAin Shams UniversityCairoEgypt
| | | | - Shahid M Baig
- Human Molecular Genetics LaboratoryHealth Biotechnology DivisionNational Institute for Biotechnology and Genetic Engineering (NIBGE)FaisalabadPakistan
| | - Heidi Stöhr
- Department of Human GeneticsUniversity Medical Center RegensburgRegensburgGermany
| | - Markus Preising
- Department of OphthalmologyJustus-Liebig-University GiessenGiessenGermany
| | | | - Fabian Moeller
- Department of Cell and Matrix BiologyInstitute of Zoology, Johannes GutenbergUniversity of MainzMainzGermany
| | - Birgit Lorenz
- Department of OphthalmologyJustus-Liebig-University GiessenGiessenGermany
| | - Kerstin Nagel-Wolfrum
- Department of Cell and Matrix BiologyInstitute of Zoology, Johannes GutenbergUniversity of MainzMainzGermany
| | - Arif O Khan
- Division of Pediatric OphthalmologyKing Khaled Eye Specialist HospitalRiyadhSaudi Arabia.,Eye InstituteCleveland ClinicAbu DhabiUAE
| | - Hanno J Bolz
- Bioscientia Center for Human GeneticsIngelheimGermany.,Institute of Human GeneticsUniversity Hospital of CologneCologneGermany
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16
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Pousada G, Lupo V, Cástro-Sánchez S, Álvarez-Satta M, Sánchez-Monteagudo A, Baloira A, Espinós C, Valverde D. Molecular and functional characterization of the BMPR2 gene in Pulmonary Arterial Hypertension. Sci Rep 2017; 7:1923. [PMID: 28507310 PMCID: PMC5432510 DOI: 10.1038/s41598-017-02074-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 04/05/2017] [Indexed: 11/09/2022] Open
Abstract
Pulmonary arterial hypertension is a progressive disease that causes the obstruction of precapillary pulmonary arteries and a sustained increase in pulmonary vascular resistance. The aim was to analyze functionally the variants found in the BMPR2 gene and to establish a genotype-phenotype correlation. mRNA expression studies were performed using pSPL3 vector, studies of subcellular localization were performed using pEGFP-N1 vector and luciferase assays were performed using pGL3-Basic vector. We have identified 30 variants in the BMPR2 gene in 27 of 55 patients. In 16 patients we detected pathogenic mutations. Minigene assays revealed that 6 variants (synonymous, missense) result in splicing defect. By immunofluorescence assay, we observed that 4 mutations affect the protein localization. Finally, 4 mutations located in the 5'UTR region showed a decreased transcriptional activity in luciferase assays. Genotype-phenotype correlation, revealed that patients with pathogenic mutations have a more severe phenotype (sPaP p = 0.042, 6MWT p = 0.041), a lower age at diagnosis (p = 0.040) and seemed to have worse response to phosphodiesterase-5-inhibitors (p = 0.010). Our study confirms that in vitro expression analysis is a suitable approach in order to investigate the phenotypic consequences of the nucleotide variants, especially in cases where the involved genes have a pattern of expression in tissues of difficult access.
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Affiliation(s)
- Guillermo Pousada
- Dep. Biochemistry, Genetics and Immunology. Faculty of Biology, University of Vigo, As Lagoas Marcosende S/N, 36310, Vigo, Spain.,Grupo de Investigación Enfermedades Raras y Medicina Pediátrica, Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Vincenzo Lupo
- Unit of Genetics and Genomics of Neuromuscular and Neurodegenerative Disorders, Centro de Investigación Príncipe Felipe (CIPF), 46012, Valencia, Spain
| | - Sheila Cástro-Sánchez
- Dep. Biochemistry, Genetics and Immunology. Faculty of Biology, University of Vigo, As Lagoas Marcosende S/N, 36310, Vigo, Spain.,Grupo de Investigación Enfermedades Raras y Medicina Pediátrica, Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - María Álvarez-Satta
- Dep. Biochemistry, Genetics and Immunology. Faculty of Biology, University of Vigo, As Lagoas Marcosende S/N, 36310, Vigo, Spain.,Grupo de Investigación Enfermedades Raras y Medicina Pediátrica, Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Ana Sánchez-Monteagudo
- Unit of Genetics and Genomics of Neuromuscular and Neurodegenerative Disorders, Centro de Investigación Príncipe Felipe (CIPF), 46012, Valencia, Spain
| | - Adolfo Baloira
- Neumology Service, Complexo Hospitalario Universitario de Pontevedra, 36071, Pontevedra, Spain
| | - Carmen Espinós
- Unit of Genetics and Genomics of Neuromuscular and Neurodegenerative Disorders, Centro de Investigación Príncipe Felipe (CIPF), 46012, Valencia, Spain
| | - Diana Valverde
- Dep. Biochemistry, Genetics and Immunology. Faculty of Biology, University of Vigo, As Lagoas Marcosende S/N, 36310, Vigo, Spain. .,Grupo de Investigación Enfermedades Raras y Medicina Pediátrica, Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain.
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17
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Álvarez-Satta M, Castro-Sánchez S, Pousada G, Valverde D. Functional analysis by minigene assay of putative splicing variants found in Bardet-Biedl syndrome patients. J Cell Mol Med 2017; 21:2268-2275. [PMID: 28502102 PMCID: PMC5618670 DOI: 10.1111/jcmm.13147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/30/2017] [Indexed: 01/05/2023] Open
Abstract
Bardet–Biedl syndrome (BBS) and Alström syndrome (ALMS) are rare diseases belonging to the group of ciliopathies. Although mutational screening studies of BBS/ALMS cohorts have been extensively reported, little is known about the functional effect of those changes. Thus, splicing variants are estimated to represent 15% of disease‐causing mutations, and there is growing evidence that many exonic changes are really splicing variants misclassified. In this study, we aimed to analyse for the first time several variants in BBS2,ARL6/BBS3,BBS4 and ALMS1 genes predicted to produce aberrant splicing by minigene assay. We found discordance between bioinformatics analysis and experimental data when comparing wild‐type and mutant constructs. Remarkably, we identified nonsense variants presumably resistant to nonsense‐mediated decay, even when a premature termination codon would be introduced in the second amino acid (p.(G2*) mutation in ARL6/BBS3 gene). As a whole, we report one of the first functional studies of BBS/ALMS1 variants using minigene assay, trying to elucidate their role in disease. Functional studies of variants identified in BBS and ALMS patients are essential for their proper classification and subsequent genetic counselling and could also be the start point for new therapeutic approaches, currently based only on symptomatic treatment.
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Affiliation(s)
- María Álvarez-Satta
- Grupo de Biomarcadores Moleculares (BB1), Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, Spain.,Instituto de Investigación Sanitaria Galicia Sur (IISGS), Vigo, Spain
| | - Sheila Castro-Sánchez
- Grupo de Biomarcadores Moleculares (BB1), Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, Spain.,Instituto de Investigación Sanitaria Galicia Sur (IISGS), Vigo, Spain
| | - Guillermo Pousada
- Grupo de Biomarcadores Moleculares (BB1), Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, Spain.,Instituto de Investigación Sanitaria Galicia Sur (IISGS), Vigo, Spain
| | - Diana Valverde
- Grupo de Biomarcadores Moleculares (BB1), Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Vigo, Spain.,Instituto de Investigación Sanitaria Galicia Sur (IISGS), Vigo, Spain
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18
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Zong L, Chen K, Wu X, Liu M, Jiang H. Compound heterozygous MYO7A mutations segregating Usher syndrome type 2 in a Han family. Int J Pediatr Otorhinolaryngol 2016; 90:150-155. [PMID: 27729122 DOI: 10.1016/j.ijporl.2016.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/10/2016] [Accepted: 09/11/2016] [Indexed: 12/01/2022]
Abstract
OBJECTIVE Identification of rare deafness genes for inherited congenital sensorineural hearing impairment remains difficult, because a large variety of genes are implicated. In this study we applied targeted capture and next-generation sequencing to uncover the underlying gene in a three-generation Han family segregating recessive inherited hearing loss and retinitis pigmentosa. METHODS After excluding mutations in common deafness genes GJB2, SLC26A4 and the mitochondrial gene, genomic DNA of the proband of a Han family was subjected to targeted next-generation sequencing. The candidate mutations were confirmed by Sanger sequencing and subsequently analyzed with in silico tools. RESULTS An unreported splice site mutation c.3924+1G > C compound with c.6028G > A in the MYO7A gene were detected to cosegregate with the phenotype in this pedigree. Both mutations, located in the evolutionarily conserved FERM domain in myosin VIIA, were predicted to be pathogenic. In this family, profound sensorineural hearing impairment and retinitis pigmentosa without vestibular disorder, constituted the typical Usher syndrome type 2. CONCLUSION Identification of novel mutation in compound heterozygosity in MYO7A gene revealed the genetic origin of Usher syndrome type 2 in this Han family.
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Affiliation(s)
- Ling Zong
- Department of Otorhinolaryngology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, PR China; Department of Otorhinolaryngology, The First Affiliated Hospital, Sun Yat-sen University and Institute of Otorhinolaryngology, Sun Yat-sen University, Guangzhou, 510080, PR China
| | - Kaitian Chen
- Department of Otorhinolaryngology, The First Affiliated Hospital, Sun Yat-sen University and Institute of Otorhinolaryngology, Sun Yat-sen University, Guangzhou, 510080, PR China
| | - Xuan Wu
- Department of Otorhinolaryngology, The First Affiliated Hospital, Sun Yat-sen University and Institute of Otorhinolaryngology, Sun Yat-sen University, Guangzhou, 510080, PR China
| | - Min Liu
- Department of Otorhinolaryngology, The First Affiliated Hospital, Sun Yat-sen University and Institute of Otorhinolaryngology, Sun Yat-sen University, Guangzhou, 510080, PR China
| | - Hongyan Jiang
- Department of Otorhinolaryngology, The First Affiliated Hospital, Sun Yat-sen University and Institute of Otorhinolaryngology, Sun Yat-sen University, Guangzhou, 510080, PR China; Department of Otorhinolaryngology, Hainan General Hospital, Haikou, 570311, PR China.
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19
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Ribeiro JC, Oliveiros B, Pereira P, António N, Hummel T, Paiva A, Silva ED. Accelerated age-related olfactory decline among type 1 Usher patients. Sci Rep 2016; 6:28309. [PMID: 27329700 PMCID: PMC4916436 DOI: 10.1038/srep28309] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 06/02/2016] [Indexed: 12/22/2022] Open
Abstract
Usher Syndrome (USH) is a rare disease with hearing loss, retinitis pigmentosa and, sometimes, vestibular dysfunction. A phenotype heterogeneity is reported. Recent evidence indicates that USH is likely to belong to an emerging class of sensory ciliopathies. Olfaction has recently been implicated in ciliopathies, but the scarce literature about olfaction in USH show conflicting results. We aim to evaluate olfactory impairment as a possible clinical manifestation of USH. Prospective clinical study that included 65 patients with USH and 65 normal age-gender-smoking-habits pair matched subjects. A cross culturally validated version of the Sniffin’ Sticks olfaction test was used. Young patients with USH have significantly better olfactory scores than healthy controls. We observe that USH type 1 have a faster ageing olfactory decrease than what happens in healthy subjects, leading to significantly lower olfactory scores in older USH1 patients. Moreover, USH type 1 patients showed significantly higher olfactory scores than USH type 2, what can help distinguishing them. Olfaction represents an attractive tool for USH type classification and pre diagnostic screening due to the low cost and non-invasive nature of the testing. Olfactory dysfunction should be considered among the spectrum of clinical manifestations of Usher syndrome.
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Affiliation(s)
- João Carlos Ribeiro
- Department of Otorhinolaryngology, Coimbra University Hospitals, Portugal.,Faculty of Medicine, University of Coimbra, Portugal.,Centre of Ophthalmology and Vision Sciences, IBILI, Faculty of Medicine, University of Coimbra, Portugal
| | - Bárbara Oliveiros
- Faculty of Medicine, University of Coimbra, Portugal.,Centre of Ophthalmology and Vision Sciences, IBILI, Faculty of Medicine, University of Coimbra, Portugal
| | - Paulo Pereira
- Faculty of Medicine, University of Coimbra, Portugal.,Centre of Ophthalmology and Vision Sciences, IBILI, Faculty of Medicine, University of Coimbra, Portugal
| | | | - Thomas Hummel
- Department of Otorhinolaryngology, TU Dresden, Dresden, Germany
| | - António Paiva
- Department of Otorhinolaryngology, Coimbra University Hospitals, Portugal.,Faculty of Medicine, University of Coimbra, Portugal
| | - Eduardo D Silva
- Faculty of Medicine, University of Coimbra, Portugal.,Centre of Ophthalmology and Vision Sciences, IBILI, Faculty of Medicine, University of Coimbra, Portugal
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Pousada G, Baloira A, Fontán D, Núñez M, Valverde D. Mutational and clinical analysis of the ENG gene in patients with pulmonary arterial hypertension. BMC Genet 2016; 17:72. [PMID: 27260700 PMCID: PMC4893224 DOI: 10.1186/s12863-016-0384-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/25/2016] [Indexed: 02/03/2023] Open
Abstract
Background Pulmonary arterial hypertension (PAH) is a rare vascular disorder characterized by a capillary wedge pressure ≤ 15 mmHg and a mean pulmonary arterial pressure ≥ 25 mmHg at rest. PAH can be idiopathic, heritable or associated with other conditions. The aim of this study was to analyze the Endoglin (ENG) gene and assess the influence of the c.572G > A (p.G191D) mutation in patients with idiopathic or associated PAH. The correlation between the pathogenic mutations and clinical and functional parameters was further analyzed. Results Sixteen different changes in the ENG gene were found in 44 out of 57 patients. After in silico analysis, we classified eight mutations as pathogenic in 16 of patients. The c.572G>A (p.G191D) variation was observed in ten patients, and the analysis for the splicing process using hybrid minigenes, with pSPL3 vector to assess splicing alterations, do not generate a new transcript. Age at diagnosis (p = 0.049) and the 6-min walking test (p = 0.041) exhibited statistically significant differences between carriers and non-carriers of pathogenic mutations. Patients with pathogenic mutations exhibited disease symptoms 8 years before non-carriers. Five patients with pathogenic mutations were carriers of another mutation in the BMPR2 or ACVRL1 genes. Conclusions We present a series of PAH patients with mutations in the ENG gene, some of them not previously described, exhibiting clinical and hemodynamic alterations suggesting that the presence of these mutations may be associated with the severity of the disease. Moreover, genetic analysis in patients with PAH may be of clinical relevance and indicates the complexity of the genetic background.
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Affiliation(s)
- Guillermo Pousada
- Department Biochemistry, Genetics and Immunology, Faculty of Biology, University of Vigo, As Lagoas Marcosende S/N, 36310, Vigo, Spain.,Instituto de Investigación Biomédica de Vigo (IBIV), Vigo, Spain
| | - Adolfo Baloira
- Complexo Hospitalario Universitario de Pontevedra, Servicio de neumología, Pontevedra, Spain
| | - Diego Fontán
- Department Biochemistry, Genetics and Immunology, Faculty of Biology, University of Vigo, As Lagoas Marcosende S/N, 36310, Vigo, Spain
| | - Marta Núñez
- Complexo Hospitalario Universitario de Pontevedra, Servicio de neumología, Pontevedra, Spain
| | - Diana Valverde
- Department Biochemistry, Genetics and Immunology, Faculty of Biology, University of Vigo, As Lagoas Marcosende S/N, 36310, Vigo, Spain. .,Instituto de Investigación Biomédica de Vigo (IBIV), Vigo, Spain.
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Toms M, Bitner-Glindzicz M, Webster A, Moosajee M. Usher syndrome: a review of the clinical phenotype, genes and therapeutic strategies. EXPERT REVIEW OF OPHTHALMOLOGY 2015. [DOI: 10.1586/17469899.2015.1033403] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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