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Tesolin P, Santin A, Morgan A, Lenarduzzi S, Rubinato E, Girotto G, Spedicati B. Which Came First? When Usher Syndrome Type 1 Couples with Neuropsychiatric Disorders. Audiol Res 2023; 13:989-995. [PMID: 38131811 PMCID: PMC10740809 DOI: 10.3390/audiolres13060086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/17/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
Usher syndrome (USH) is an autosomal recessive disorder characterized by sensorineural hearing loss (HL), retinopathy, and vestibular areflexia, with variable severity. Although a high prevalence of behavioural and mental disorders in USH patients has been reported, few studies on these psychiatric and psychological issues have been conducted. This work describes the case of a 16-year-old boy affected by congenital bilateral sensorineural HL, presenting a suddenly altered behaviour concomitant with a decrease in visual acuity. To establish a molecular diagnosis, Whole-Exome Sequencing analysis was performed, detecting a pathogenetic homozygous variant (c. 5985C>A, p.(Tyr1995*)) within the CDH23 gene. CDH23 is a known USH type 1 causative gene, recently associated with schizophrenia-like symptoms and bipolar disorders. To date, no studies have provided evidence of a direct genotype-phenotype correlation between USH patients carrying CDH23 variants and mental/behavioural issues; however, considering the multiple biological functions of CDH23, it can be hypothesised that it could have a pleiotropic effect. Overall, this study highlights the relevance of a continuous clinical evaluation of USH patients, to monitor not only the disease progression, but to early detect any psychological or behavioural alterations, thus allowing a rapid implementation of therapeutic strategies aimed at improving their quality of life and well-being.
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Affiliation(s)
- Paola Tesolin
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy; (P.T.); (G.G.); (B.S.)
| | - Aurora Santin
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy; (P.T.); (G.G.); (B.S.)
| | - Anna Morgan
- Institute for Maternal and Child Health—I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy (S.L.); (E.R.)
| | - Stefania Lenarduzzi
- Institute for Maternal and Child Health—I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy (S.L.); (E.R.)
| | - Elisa Rubinato
- Institute for Maternal and Child Health—I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy (S.L.); (E.R.)
| | - Giorgia Girotto
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy; (P.T.); (G.G.); (B.S.)
- Institute for Maternal and Child Health—I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy (S.L.); (E.R.)
| | - Beatrice Spedicati
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy; (P.T.); (G.G.); (B.S.)
- Institute for Maternal and Child Health—I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy (S.L.); (E.R.)
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2
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Zaw K, Carvalho LS, Aung-Htut MT, Fletcher S, Wilton SD, Chen FK, McLenachan S. Pathogenesis and Treatment of Usher Syndrome Type IIA. Asia Pac J Ophthalmol (Phila) 2022; 11:369-379. [PMID: 36041150 DOI: 10.1097/apo.0000000000000546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/27/2022] [Indexed: 12/16/2022] Open
Abstract
Usher syndrome (USH) is the most common form of deaf-blindness, with an estimated prevalence of 4.4 to 16.6 per 100,000 people worldwide. The most common form of USH is type IIA (USH2A), which is caused by homozygous or compound heterozygous mutations in the USH2A gene and accounts for around half of all USH cases. USH2A patients show moderate to severe hearing loss from birth, with diagnosis of retinitis pigmentosa in the second decade of life and variable vestibular involvement. Although hearing aids or cochlear implants can provide some mitigation of hearing deficits, there are currently no treatments aimed at preventing or restoring vision loss in USH2A patients. In this review, we first provide an overview of the molecular biology of the USH2A gene and its protein isoforms, which include a transmembrane protein (TM usherin) and an extracellular protein (EC usherin). The role of these proteins in the inner ear and retina and their impact on the pathogenesis of USH2A is discussed. We review animal cell-derived and patient cell-derived models currently used in USH2A research and conclude with an overview of potential treatment strategies currently in preclinical development and clinical trials.
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Affiliation(s)
- Khine Zaw
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
- Lions Eye Institute, Nedlands, Western Australia, Australia
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Livia S Carvalho
- Lions Eye Institute, Nedlands, Western Australia, Australia
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Nedlands, Western Australia, Australia
| | - May T Aung-Htut
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
- Perron Institute for Neurological and Translational Science, University of Western Australia, Nedlands, Western Australia, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
- Perron Institute for Neurological and Translational Science, University of Western Australia, Nedlands, Western Australia, Australia
| | - Steve D Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
- Perron Institute for Neurological and Translational Science, University of Western Australia, Nedlands, Western Australia, Australia
| | - Fred K Chen
- Lions Eye Institute, Nedlands, Western Australia, Australia
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Nedlands, Western Australia, Australia
- Department of Ophthalmology, Royal Perth Hospital, Perth, Western Australia, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, Victoria, Australia
| | - Samuel McLenachan
- Lions Eye Institute, Nedlands, Western Australia, Australia
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Nedlands, Western Australia, Australia
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3
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Peng J, Xiang J, Jin X, Meng J, Song N, Chen L, Abou Tayoun A, Peng Z. VIP-HL: Semi-automated ACMG/AMP variant interpretation platform for genetic hearing loss. Hum Mutat 2021; 42:1567-1575. [PMID: 34428318 DOI: 10.1002/humu.24277] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 07/13/2021] [Accepted: 08/20/2021] [Indexed: 12/29/2022]
Abstract
The American College of Medical Genetics and Genomics, and the Association for Molecular Pathology (ACMG/AMP) have proposed a set of evidence-based guidelines to support sequence variant interpretation. The ClinGen hearing loss expert panel (HL-EP) introduced further specifications into the ACMG/AMP framework for genetic hearing loss. This study developed a tool named Variant Interpretation Platform for genetic Hearing Loss (VIP-HL), aiming to semi-automate the HL ACMG/AMP rules. VIP-HL aggregates information from external databases to automate 13 out of 24 ACMG/AMP rules specified by HL-EP, namely PVS1, PS1, PM1, PM2, PM4, PM5, PP3, BA1, BS1, BS2, BP3, BP4, and BP7. We benchmarked VIP-HL using 50 variants in which 82 rules were activated by the ClinGen HL-EP. VIP-HL concordantly activated 93% (76/82) rules, significantly higher than that of by InterVar (48%; 39/82). VIP-HL is an integrated online tool for reliable automated variant classification in hearing loss genes. It assists curators in variant interpretation and provides a platform for users to share classifications with each other. VIP-HL is available with a user-friendly web interface at http://hearing.genetics.bgi.com/.
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Affiliation(s)
| | - Jiale Xiang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Xiangqian Jin
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Nana Song
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Lisha Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Ahmad Abou Tayoun
- Al Jalila Genomics Center, Al Jalila Children's Specialty Hospital, Dubai, United Arab Emirates.,Center for Genomic Discovery, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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4
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Reurink J, Dockery A, Oziębło D, Farrar GJ, Ołdak M, ten Brink JB, Bergen AA, Rinne T, Yntema HG, Pennings RJE, van den Born LI, Aben M, Oostrik J, Venselaar H, Plomp AS, Khan MI, van Wijk E, Cremers FPM, Roosing S, Kremer H. Molecular Inversion Probe-Based Sequencing of USH2A Exons and Splice Sites as a Cost-Effective Screening Tool in USH2 and arRP Cases. Int J Mol Sci 2021; 22:ijms22126419. [PMID: 34203967 PMCID: PMC8232728 DOI: 10.3390/ijms22126419] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/08/2021] [Accepted: 06/10/2021] [Indexed: 12/19/2022] Open
Abstract
A substantial proportion of subjects with autosomal recessive retinitis pigmentosa (arRP) or Usher syndrome type II (USH2) lacks a genetic diagnosis due to incomplete USH2A screening in the early days of genetic testing. These cases lack eligibility for optimal genetic counseling and future therapy. USH2A defects are the most frequent cause of USH2 and are also causative in individuals with arRP. Therefore, USH2A is an important target for genetic screening. The aim of this study was to assess unscreened or incompletely screened and unexplained USH2 and arRP cases for (likely) pathogenic USH2A variants. Molecular inversion probe (MIP)-based sequencing was performed for the USH2A exons and their flanking regions, as well as published deep-intronic variants. This was done to identify single nucleotide variants (SNVs) and copy number variants (CNVs) in 29 unscreened or partially pre-screened USH2 and 11 partially pre-screened arRP subjects. In 29 out of these 40 cases, two (likely) pathogenic variants were successfully identified. Four of the identified SNVs and one CNV were novel. One previously identified synonymous variant was demonstrated to affect pre-mRNA splicing. In conclusion, genetic diagnoses were obtained for a majority of cases, which confirms that MIP-based sequencing is an effective screening tool for USH2A. Seven unexplained cases were selected for future analysis with whole genome sequencing.
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Affiliation(s)
- Janine Reurink
- Department of Human Genetics, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 Nijmegen, The Netherlands; (J.R.); (T.R.); (H.G.Y.); (M.A.); (M.I.K.); (F.P.M.C.); (S.R.)
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, 6500 Nijmegen, The Netherlands; (R.J.E.P.); (E.v.W.)
| | - Adrian Dockery
- The School of Genetics & Microbiology, Trinity College Dublin, D02 VF25 Dublin, Ireland; (A.D.); (G.J.F.)
| | - Dominika Oziębło
- Department of Genetics, Institute of Physiology and Pathology of Hearing, 02-042 Warsaw/Kajetany, Poland; (D.O.); (M.O.)
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - G. Jane Farrar
- The School of Genetics & Microbiology, Trinity College Dublin, D02 VF25 Dublin, Ireland; (A.D.); (G.J.F.)
| | - Monika Ołdak
- Department of Genetics, Institute of Physiology and Pathology of Hearing, 02-042 Warsaw/Kajetany, Poland; (D.O.); (M.O.)
| | - Jacoline B. ten Brink
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, 1105 Amsterdam, The Netherlands; (J.B.t.B.); (A.A.B.); (A.S.P.)
| | - Arthur A. Bergen
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, 1105 Amsterdam, The Netherlands; (J.B.t.B.); (A.A.B.); (A.S.P.)
- Department of Ophthalmology, Amsterdam UMC, University of Amsterdam, 1105 Amsterdam, The Netherlands
| | - Tuula Rinne
- Department of Human Genetics, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 Nijmegen, The Netherlands; (J.R.); (T.R.); (H.G.Y.); (M.A.); (M.I.K.); (F.P.M.C.); (S.R.)
| | - Helger G. Yntema
- Department of Human Genetics, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 Nijmegen, The Netherlands; (J.R.); (T.R.); (H.G.Y.); (M.A.); (M.I.K.); (F.P.M.C.); (S.R.)
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, 6500 Nijmegen, The Netherlands; (R.J.E.P.); (E.v.W.)
| | - Ronald J. E. Pennings
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, 6500 Nijmegen, The Netherlands; (R.J.E.P.); (E.v.W.)
- Department of Otorhinolaryngology, Radboud University Medical Center, 6500 Nijmegen, The Netherlands;
| | | | - Marco Aben
- Department of Human Genetics, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 Nijmegen, The Netherlands; (J.R.); (T.R.); (H.G.Y.); (M.A.); (M.I.K.); (F.P.M.C.); (S.R.)
| | - Jaap Oostrik
- Department of Otorhinolaryngology, Radboud University Medical Center, 6500 Nijmegen, The Netherlands;
| | - Hanka Venselaar
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 Nijmegen, The Netherlands;
| | - Astrid S. Plomp
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, 1105 Amsterdam, The Netherlands; (J.B.t.B.); (A.A.B.); (A.S.P.)
| | - M. Imran Khan
- Department of Human Genetics, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 Nijmegen, The Netherlands; (J.R.); (T.R.); (H.G.Y.); (M.A.); (M.I.K.); (F.P.M.C.); (S.R.)
| | - Erwin van Wijk
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, 6500 Nijmegen, The Netherlands; (R.J.E.P.); (E.v.W.)
- Department of Otorhinolaryngology, Radboud University Medical Center, 6500 Nijmegen, The Netherlands;
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 Nijmegen, The Netherlands; (J.R.); (T.R.); (H.G.Y.); (M.A.); (M.I.K.); (F.P.M.C.); (S.R.)
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, 6500 Nijmegen, The Netherlands; (R.J.E.P.); (E.v.W.)
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 Nijmegen, The Netherlands; (J.R.); (T.R.); (H.G.Y.); (M.A.); (M.I.K.); (F.P.M.C.); (S.R.)
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, 6500 Nijmegen, The Netherlands; (R.J.E.P.); (E.v.W.)
| | - Hannie Kremer
- Department of Human Genetics, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 Nijmegen, The Netherlands; (J.R.); (T.R.); (H.G.Y.); (M.A.); (M.I.K.); (F.P.M.C.); (S.R.)
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, 6500 Nijmegen, The Netherlands; (R.J.E.P.); (E.v.W.)
- Department of Otorhinolaryngology, Radboud University Medical Center, 6500 Nijmegen, The Netherlands;
- Correspondence:
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Spectrum of MYO7A Mutations in an Indigenous South African Population Further Elucidates the Nonsyndromic Autosomal Recessive Phenotype of DFNB2 to Include Both Homozygous and Compound Heterozygous Mutations. Genes (Basel) 2021; 12:genes12020274. [PMID: 33671976 PMCID: PMC7919343 DOI: 10.3390/genes12020274] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 11/17/2022] Open
Abstract
MYO7A gene encodes unconventional myosin VIIA, which, when mutated, causes a phenotypic spectrum ranging from recessive hearing loss DFNB2 to deaf-blindness, Usher Type 1B (USH1B). MYO7A mutations are reported in nine DFNB2 families to date, none from sub-Saharan Africa.In DNA, from a cohort of 94 individuals representing 92 families from the Limpopo province of South Africa, eight MYO7A variations were detected among 10 individuals. Family studies identified homozygous and compound heterozygous mutations in 17 individuals out of 32 available family members. Four mutations were novel, p.Gly329Asp, p.Arg373His, p.Tyr1780Ser, and p.Pro2126Leufs*5. Two variations, p.Ser617Pro and p.Thr381Met, previously listed as of uncertain significance (ClinVar), were confirmed to be pathogenic. The identified mutations are predicted to interfere with the conformational properties of myosin VIIA through interruption or abrogation of multiple interactions between the mutant and neighbouring residues. Specifically, p.Pro2126Leufs*5, is predicted to abolish the critical site for the interactions between the tail and the motor domain essential for the autoregulation, leaving a non-functional, unregulated protein that causes hearing loss. We have identified MYO7A as a possible key deafness gene among indigenous sub-Saharan Africans. The spectrum of MYO7A mutations in this South African population points to DFNB2 as a specific entity that may occur in a homozygous or in a compound heterozygous state.
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Panagiotou ES, Papathomas T, Nikopoulos K, Koukoula S, Quinodoz M, Rehman AU, Giannopoulos T, Rivolta C, Konstas AG. Management of Full-Thickness Macular Hole in A Genetically Confirmed Case with Usher Syndrome. Ophthalmol Ther 2020; 9:677-684. [PMID: 32566994 PMCID: PMC7406580 DOI: 10.1007/s40123-020-00276-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Indexed: 11/12/2022] Open
Abstract
INTRODUCTION Full-thickness macular hole (FTMH) formation is rarely seen in patients with retinitis pigmentosa (RP) and can have an adverse impact on their residual visual function. The underlying mechanisms are unknown, and clinical experience is limited regarding surgical outcomes. Here, we describe the surgical management of FTMH in a young patient with genetically confirmed Usher syndrome, the most common form of syndromic RP. CASE REPORT A 28-year-old woman presented with blurred vision in her right eye (RE). She had a history of RP and bilateral hearing impairment since childhood. Fundoscopy and spectral-domain optical coherence tomography revealed a FTMH in the RE along with typical RP features bilaterally. After pars plana vitrectomy (PPV) with internal limiting membrane peel and gas tamponade, the FTMH closed. Six months after PPV the patient underwent cataract surgery in the affected eye, and the visual acuity remained stable compared to baseline. The clinical diagnosis of Usher syndrome was genetically confirmed by whole exome sequencing (WES), which revealed the presence of two pathogenic nucleotide variants in trans (compound heterozygosity) in the gene USH2A. CONCLUSION We report a rare case of successful closure of a FTMH in a patient with Usher syndrome. Surgical treatment of FTMH can help preserve the central vision in RP patients, whose peripheral vision is severely affected.
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Affiliation(s)
- Evangelia S Panagiotou
- 1st Department of Ophthalmology, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki, Greece
| | - Thomas Papathomas
- 1st Department of Ophthalmology, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki, Greece
| | - Konstantinos Nikopoulos
- Laboratory of Oncogenomics, Department of Hematology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | | | - Mathieu Quinodoz
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Atta Ur Rehman
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Theodoros Giannopoulos
- 1st Department of Ophthalmology, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki, Greece
| | - Carlo Rivolta
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Anastasios G Konstas
- 1st Department of Ophthalmology, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki, Greece.
- 3rd Department of Ophthalmology, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki, Greece.
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7
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Vaché C, Puechberty J, Faugère V, Darmaisin F, Liquori A, Baux D, Blanchet C, Garcia-Garcia G, Meunier I, Pellestor F, Koenig M, Roux AF. A 4.6 Mb Inversion Leading to PCDH15- LINC00844 and BICC1- PCDH15 Fusion Transcripts as a New Pathogenic Mechanism Implicated in Usher Syndrome Type 1. Front Genet 2020; 11:623. [PMID: 32714370 PMCID: PMC7343966 DOI: 10.3389/fgene.2020.00623] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 05/22/2020] [Indexed: 01/17/2023] Open
Abstract
Usher type 1 syndrome is a rare autosomal recessive disorder involving congenital severe-to-profound hearing loss, development of vision impairment in the first decade, and severe balance difficulties. The PCDH15 gene, one of the five genes implicated in this disease, is involved in 8–20% of cases. In this study, we aimed to identify and characterize the two causal variants in a French patient with typical Usher syndrome clinical features. Massively parallel sequencing-based gene panel and screening for large rearrangements were used, which detected a single multi-exon deletion in the PCDH15 gene. As the second pathogenic event was likely localized in the unscreened regions of the gene, PCDH15 transcripts from cultured nasal cells were analyzed and revealed a loss of junction between exon 13 and exon 14. This aberration could be explained by the identification of two fusion transcripts, PCDH15-LINC00844 and BICC1-PCDH15, originating from a 4.6 Mb inversion. This complex chromosomal rearrangement could not be detected by our diagnostic approach but was instead characterized by long-read sequencing, which offers the possibility of detecting balanced structural variants (SVs). This finding extends our knowledge of the mutational spectrum of the PCDH15 gene with the first ever identification of a large causal paracentric inversion of chromosome 10 and illustrates the utility of screening balanced SVs in an exhaustive molecular diagnostic approach.
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Affiliation(s)
- Christel Vaché
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Université de Montpellier, Montpellier, France
| | | | - Valérie Faugère
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Université de Montpellier, Montpellier, France
| | - Floriane Darmaisin
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Université de Montpellier, Montpellier, France
| | - Alessandro Liquori
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Université de Montpellier, Montpellier, France
| | - David Baux
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Université de Montpellier, Montpellier, France
| | - Catherine Blanchet
- Service ORL, CHU de Montpellier, Montpellier, France.,Centre de Référence Maladies Sensorielles Génétiques, CHU de Montpellier, Université de Montpellier, Montpellier, France
| | - Gema Garcia-Garcia
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Université de Montpellier, Montpellier, France
| | - Isabelle Meunier
- Centre de Référence Maladies Sensorielles Génétiques, CHU de Montpellier, Université de Montpellier, Montpellier, France
| | - Franck Pellestor
- Laboratoire de Génétique Chromosomique, Plateforme ChromoStem, CHU de Montpellier, Montpellier, France
| | - Michel Koenig
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Université de Montpellier, Montpellier, France
| | - Anne-Françoise Roux
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Université de Montpellier, Montpellier, France
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8
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Yu D, Zou J, Chen Q, Zhu T, Sui R, Yang J. Structural modeling, mutation analysis, and in vitro expression of usherin, a major protein in inherited retinal degeneration and hearing loss. Comput Struct Biotechnol J 2020; 18:1363-1382. [PMID: 32637036 PMCID: PMC7317166 DOI: 10.1016/j.csbj.2020.05.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 11/15/2022] Open
Abstract
Usherin is the most common causative protein associated with autosomal recessive retinitis pigmentosa (RP) and Usher syndrome (USH), which are characterized by retinal degeneration alone and in combination with hearing loss, respectively. Usherin is essential for photoreceptor survival and hair cell bundle integrity. However, the molecular mechanism underlying usherin function in normal and disease conditions is unclear. In this study, we investigated structural models of usherin domains and localization of usherin pathogenic small in-frame mutations, mainly homozygous missense mutations. We found that usherin fibronectin III (FN3) domains and most laminin-related domains have a β-sandwich structure. Some FN3 domains are predicted to interact with each other and with laminin-related domains. The usherin protein may bend at some FN3 linker regions. RP- and USH-associated small in-frame mutations are differentially located in usherin domains. Most of them are located at the periphery of β-sandwiches, with some at the interface between interacting domains. The usherin laminin epidermal growth factor repeats adopt a rod-shaped structure, which is maintained by disulfide bonds. Most missense mutations and deletion of exon 13 in this region disrupt the disulfide bonds and may affect local protein folding. Despite low expression of the recombinant entire protein and protein fragments in mammalian cell culture, usherin FN3 fragments are more robustly expressed and secreted than its laminin-related fragments. Our findings provide new insights into the usherin structure and the disease mechanisms caused by pathogenic small in-frame mutations, which will help inform future experimental research on diagnosis, disease mechanisms, and therapeutic approaches.
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Key Words
- Cell adhesion
- DCC, deleted in colorectal cancer
- FN3, fibronectin III
- GMQE, global quality estimation score
- HGMD, Human Gene Mutation Database
- Hair cell
- I-TASSER, Iterative Threading ASSEmbly Refinement
- LE, laminin EGF
- LG, laminin globular
- LGL, laminin globular-like
- LN, laminin N-terminal
- Membrane protein
- NCBI, National Center for Biotechnology Information
- Photoreceptor
- Protein folding
- QMEAN, qualitative model energy analysis score
- QSQE, Quaternary Structure Quality Estimation
- RMSD, root mean square deviation
- RP, retinitis pigmentosa
- Recombinant protein expression
- Retinitis pigmentosa
- SMTL, SWISS-MODEL template library
- Structural model
- TM-score, template modeling score
- USH, Usher syndrome
- Usher syndrome
- hFc, human Fc fragment
- mFc, mouse Fc fragment
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Affiliation(s)
- Dongmei Yu
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, UT, United States
| | - Junhuang Zou
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, UT, United States
| | - Qian Chen
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, UT, United States
| | - Tian Zhu
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Ruifang Sui
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jun Yang
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah, Salt Lake City, UT, United States
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT, United States
- Division of Otolaryngology, Department of Surgery, University of Utah, Salt Lake City, UT, United States
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9
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Fuster-García C, García-García G, Jaijo T, Blanco-Kelly F, Tian L, Hakonarson H, Ayuso C, Aller E, Millán JM. Expanding the Genetic Landscape of Usher-Like Phenotypes. Invest Ophthalmol Vis Sci 2020; 60:4701-4710. [PMID: 31725169 DOI: 10.1167/iovs.19-27470] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Usher syndrome (USH) is a rare disorder characterized by retinitis pigmentosa (RP) and sensorineural hearing loss. Several genes are responsible for the disease, but not all cases are explained by mutations in any of these, supporting the fact that there remain other unknown genes that have a role in the syndrome. We aimed to find the genetic cause of presumed USH patients lacking pathogenic mutations in the known USH genes. Methods Whole exome sequencing was performed on a priori USH-diagnosed subjects from nine unrelated families, which had shown negative results for an USH-targeted panel in a previous study. Results We identified possible pathogenic variants in six of the studied families. One patient harbored mutations in REEP6 and TECTA, each gene tentatively causative of one of the two main symptoms of the disease, mimicking the syndrome. In three patients, only the retinal degeneration causative mutations were detected (involving EYS, WDR19, and CNGB1 genes). Another family manifested a dementia-linked retinal dystrophy dependent on an allele dosage in the GRN gene. Last, another case presented a homozygous mutation in ASIC5, a gene not yet associated with USH. Conclusions Our findings demonstrate that pending cases should be clinically and genetically carefully assessed, since more patients than expected may be either related phenocopies or affected by a more complex disease encompassing additional symptoms rather than classical USH.
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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.,CIBER de Enfermedades Raras (CIBERER), Madrid, 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
| | - Fiona Blanco-Kelly
- 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
| | - Lifeng Tian
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Pennsylvania, United States
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Pennsylvania, United States.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - 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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10
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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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11
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McLenachan S, Wong EYM, Zhang X, Leith F, Moon SY, Zhang D, Chen SC, Thompson JA, McLaren T, Lamey T, De Roach JN, Atlas MD, Dilley RJ, Chen FK. Generation of two induced pluripotent stem cell lines from a patient with compound heterozygous mutations in the USH2A gene. Stem Cell Res 2019; 36:101420. [PMID: 30904819 DOI: 10.1016/j.scr.2019.101420] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 03/12/2019] [Indexed: 10/27/2022] Open
Abstract
The human iPSC lines LEIi010-A and LEIi010-B were generated from the dermal fibroblasts of a patient with Usher syndrome using episomal plasmids containing OCT4, SOX2, KLF4, L-MYC, LIN28, mir302/367 microRNA and shRNA for p53. These iPSC lines carry compound heterozygous mutations (c.949C > A and c.1256G > T) in USH2A. LEIi010-A and LEIi010-B expressed pluripotent stem cell markers, had a normal karyotype and could be differentiated into endoderm, mesoderm and ectodermal lineages.
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Affiliation(s)
- Samuel McLenachan
- Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Western Australia, Australia; Lions Eye Institute Australia, Nedlands, Western Australia, Australia
| | - Elaine Y M Wong
- Ear Science Institute Australia, Nedlands, Western Australia, Australia; School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Bentley, Western Australia, Australia; Centre for Neurological & Neuromuscular Diseases, The University of Western Australia, Crawley, Western Australia, Australia
| | - Xiao Zhang
- Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Western Australia, Australia; Lions Eye Institute Australia, Nedlands, Western Australia, Australia
| | - Fiona Leith
- Ear Science Institute Australia, Nedlands, Western Australia, Australia
| | - Sang Yoon Moon
- Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Dan Zhang
- Lions Eye Institute Australia, Nedlands, Western Australia, Australia
| | - Shang-Chih Chen
- Lions Eye Institute Australia, Nedlands, Western Australia, Australia
| | - Jennifer A Thompson
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Terri McLaren
- Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Western Australia, Australia; Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Tina Lamey
- Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Western Australia, Australia; Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - John N De Roach
- Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Western Australia, Australia; Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Marcus D Atlas
- Ear Science Institute Australia, Nedlands, Western Australia, Australia; Ear Sciences Centre, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Rodney J Dilley
- Ear Science Institute Australia, Nedlands, Western Australia, Australia; Centre for Cell Therapy and Regenerative Medicine, The University of Western Australia, Australia; Ear Sciences Centre, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Fred K Chen
- Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Western Australia, Australia; Lions Eye Institute Australia, Nedlands, Western Australia, Australia; Department of Ophthalmology, Royal Perth Hospital, Perth, Western Australia, Australia.
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12
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Liquori A, Vaché C, Baux D, Blanchet C, Hamel C, Malcolm S, Koenig M, Claustres M, Roux AF. Whole USH2A Gene Sequencing Identifies Several New Deep Intronic Mutations. Hum Mutat 2015; 37:184-93. [PMID: 26629787 DOI: 10.1002/humu.22926] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/19/2015] [Indexed: 01/01/2023]
Abstract
Deep intronic mutations leading to pseudoexon (PE) insertions are underestimated and most of these splicing alterations have been identified by transcript analysis, for instance, the first deep intronic mutation in USH2A, the gene most frequently involved in Usher syndrome type II (USH2). Unfortunately, analyzing USH2A transcripts is challenging and for 1.8%-19% of USH2 individuals carrying a single USH2A recessive mutation, a second mutation is yet to be identified. We have developed and validated a DNA next-generation sequencing approach to identify deep intronic variants in USH2A and evaluated their consequences on splicing. Three distinct novel deep intronic mutations have been identified. All were predicted to affect splicing and resulted in the insertion of PEs, as shown by minigene assays. We present a new and attractive strategy to identify deep intronic mutations, when RNA analyses are not possible. Moreover, the bioinformatics pipeline developed is independent of the gene size, implying the possible application of this approach to any disease-linked gene. Finally, an antisense morpholino oligonucleotide tested in vitro for its ability to restore splicing caused by the c.9959-4159A>G mutation provided high inhibition rates, which are indicative of its potential for molecular therapy.
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Affiliation(s)
- Alessandro Liquori
- Laboratoire de Génétique de Maladies Rares EA 7402, Université de Montpellier, Montpellier, France
| | - Christel Vaché
- Laboratoire de Génétique de Maladies Rares EA 7402, Université de Montpellier, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHRU Montpellier, Montpellier, France
| | - David Baux
- Laboratoire de Génétique de Maladies Rares EA 7402, Université de Montpellier, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHRU Montpellier, Montpellier, France
| | - Catherine Blanchet
- Service ORL, CHRU Montpellier, Montpellier, France.,CHU Montpellier, Centre National de Référence Maladies Rares, "Affections Sensorielles Génétiques, France
| | - Christian Hamel
- CHU Montpellier, Centre National de Référence Maladies Rares, "Affections Sensorielles Génétiques, France
| | - Sue Malcolm
- Genetics and Genomic Medicine Programme, Institute of Child Health, UCL, London, UK
| | - Michel Koenig
- Laboratoire de Génétique de Maladies Rares EA 7402, Université de Montpellier, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHRU Montpellier, Montpellier, France
| | - Mireille Claustres
- Laboratoire de Génétique de Maladies Rares EA 7402, Université de Montpellier, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHRU Montpellier, Montpellier, France
| | - Anne-Françoise Roux
- Laboratoire de Génétique de Maladies Rares EA 7402, Université de Montpellier, Montpellier, France.,Laboratoire de Génétique Moléculaire, CHRU Montpellier, Montpellier, France
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13
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Bergougnoux A, Claustres M, De Sario A. Nasal epithelial cells: a tool to study DNA methylation in airway diseases. Epigenomics 2015; 7:119-26. [PMID: 25687471 DOI: 10.2217/epi.14.65] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
A number of chronic airway diseases are characterized by high inflammation and unbalanced activation of the immune response, which lead to tissue damage and progressive reduction of the pulmonary function. Because they are exposed to various environmental stimuli, lung cells are prone to epigenomic changes. Many genes responsible for the immune response and inflammation are tightly regulated by DNA methylation, which suggests that alteration of the epigenome in lung cells may have a considerable impact on the penetrance and/or the severity of airway diseases. A major hurdle in clinical epigenomic studies is to gather appropriate biospecimens. Herein, we show that nasal epithelial cells are suitable to analyze DNA methylation in human diseases primarily affecting the lower airway tract.
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Affiliation(s)
- Anne Bergougnoux
- Laboratory Genetics of Rare Diseases, INSERM U827, Montpellier, France
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14
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Baux D, Blanchet C, Hamel C, Meunier I, Larrieu L, Faugère V, Vaché C, Castorina P, Puech B, Bonneau D, Malcolm S, Claustres M, Roux AF. Enrichment of LOVD-USHbases with 152 USH2A genotypes defines an extensive mutational spectrum and highlights missense hotspots. Hum Mutat 2014; 35:1179-86. [PMID: 24944099 DOI: 10.1002/humu.22608] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 06/09/2014] [Indexed: 12/19/2022]
Abstract
Alterations of USH2A, encoding usherin, are responsible for more than 70% of cases of Usher syndrome type II (USH2), a recessive disorder that combines moderate to severe hearing loss and retinal degeneration. The longest USH2A transcript encodes usherin isoform b, a 5,202-amino-acid transmembrane protein with an exceptionally large extracellular domain consisting notably of a Laminin N-terminal domain and numerous Laminin EGF-like (LE) and Fibronectin type III (FN3) repeats. Mutations of USH2A are scattered throughout the gene and mostly private. Annotating these variants is therefore of major importance to correctly assign pathogenicity. We have extensively genotyped a novel cohort of 152 Usher patients and identified 158 different mutations, of which 93 are newly described. Pooling this new data with the existing pathogenic variants already incorporated in USHbases reveals several previously unappreciated features of the mutational spectrum. We show that parts of the protein are more likely to tolerate single amino acid variations, whereas others constitute pathogenic missense hotspots. We have found, in repeated LE and FN3 domains, a nonequal distribution of the missense mutations that highlights some crucial positions in usherin with possible consequences for the assessment of the pathogenicity of the numerous missense variants identified in USH2A.
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Affiliation(s)
- David Baux
- CHU Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, F-34000, France
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15
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Lenassi E, Saihan Z, Bitner-Glindzicz M, Webster AR. The effect of the common c.2299delG mutation in USH2A on RNA splicing. Exp Eye Res 2014; 122:9-12. [PMID: 24607488 DOI: 10.1016/j.exer.2014.02.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 02/01/2014] [Accepted: 02/20/2014] [Indexed: 10/25/2022]
Abstract
Recessive variants in the USH2A gene are an important cause of both Usher syndrome and nonsyndromic retinitis pigmentosa. A single base-pair deletion in exon 13 (c.2299delG, p.Glu767Serfs*21) is considered the most frequent mutation of USH2A. It is predicted to generate a premature termination codon and is presumed to lead to nonsense mediated decay. However the effect of this variant on RNA has not been formally investigated. It is not uncommon for exonic sequence alterations to cause aberrant splicing and the aim of the present report is to evaluate the effect of c.2299delG on USH2A transcripts. Nasal cells represent the simplest available tissue to study splicing defects in USH2A. Nasal brushing, RNA extraction from nasal epithelial cells and reverse transcription PCR were performed in five Usher syndrome patients who were homozygous for c.2299delG, two unaffected c.2299delG heterozygotes and seven control individuals. Primers to amplify between exons 12 and 15 and exons 10 and 14 were utilised. Significant variability was observed between different RT-PCR experiments. Importantly, in controls, PCR product of the expected size were amplified on all occasions (13/13 experiments); for patients this was true in only 4/14 experiments (Fisher exact test p = 0.0002). Bioinformatics tools predict the c.2299delG change to disrupt an exonic splicing enhancer and to create an exonic splicing silencer within exon 13. Here, we report an effect of the common c.2299delG mutation on splicing of exons 12 and 13 of USH2A. Future studies are expected to provide important insights into the contribution of this effect on the phenotype.
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Affiliation(s)
- Eva Lenassi
- UCL Institute of Ophthalmology, London EC1V 9EL, United Kingdom; Moorfields Eye Hospital, London EC1V 2PD, United Kingdom; Eye Hospital, University Medical Centre, Ljubljana SL 1000, Slovenia
| | - Zubin Saihan
- UCL Institute of Ophthalmology, London EC1V 9EL, United Kingdom; Moorfields Eye Hospital, London EC1V 2PD, United Kingdom
| | - Maria Bitner-Glindzicz
- UCL Institute of Child Health, London WC1N 1EH, United Kingdom; Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, United Kingdom
| | - Andrew R Webster
- UCL Institute of Ophthalmology, London EC1V 9EL, United Kingdom; Moorfields Eye Hospital, London EC1V 2PD, United Kingdom.
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16
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Steele-Stallard HB, Le Quesne Stabej P, Lenassi E, Luxon LM, Claustres M, Roux AF, Webster AR, Bitner-Glindzicz M. Screening for duplications, deletions and a common intronic mutation detects 35% of second mutations in patients with USH2A monoallelic mutations on Sanger sequencing. Orphanet J Rare Dis 2013; 8:122. [PMID: 23924366 PMCID: PMC3751126 DOI: 10.1186/1750-1172-8-122] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 08/04/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Usher Syndrome is the leading cause of inherited deaf-blindness. It is divided into three subtypes, of which the most common is Usher type 2, and the USH2A gene accounts for 75-80% of cases. Despite recent sequencing strategies, in our cohort a significant proportion of individuals with Usher type 2 have just one heterozygous disease-causing mutation in USH2A, or no convincing disease-causing mutations across nine Usher genes. The purpose of this study was to improve the molecular diagnosis in these families by screening USH2A for duplications, heterozygous deletions and a common pathogenic deep intronic variant USH2A: c.7595-2144A>G. METHODS Forty-nine Usher type 2 or atypical Usher families who had missing mutations (mono-allelic USH2A or no mutations following Sanger sequencing of nine Usher genes) were screened for duplications/deletions using the USH2A SALSA MLPA reagent kit (MRC-Holland). Identification of USH2A: c.7595-2144A>G was achieved by Sanger sequencing. Mutations were confirmed by a combination of reverse transcription PCR using RNA extracted from nasal epithelial cells or fibroblasts, and by array comparative genomic hybridisation with sequencing across the genomic breakpoints. RESULTS Eight mutations were identified in 23 Usher type 2 families (35%) with one previously identified heterozygous disease-causing mutation in USH2A. These consisted of five heterozygous deletions, one duplication, and two heterozygous instances of the pathogenic variant USH2A: c.7595-2144A>G. No variants were found in the 15 Usher type 2 families with no previously identified disease-causing mutations. In 11 atypical families, none of whom had any previously identified convincing disease-causing mutations, the mutation USH2A: c.7595-2144A>G was identified in a heterozygous state in one family. All five deletions and the heterozygous duplication we report here are novel. This is the first time that a duplication in USH2A has been reported as a cause of Usher syndrome. CONCLUSIONS We found that 8 of 23 (35%) of 'missing' mutations in Usher type 2 probands with only a single heterozygous USH2A mutation detected with Sanger sequencing could be attributed to deletions, duplications or a pathogenic deep intronic variant. Future mutation detection strategies and genetic counselling will need to take into account the prevalence of these types of mutations in order to provide a more comprehensive diagnostic service.
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17
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Besnard T, García-García G, Baux D, Vaché C, Faugère V, Larrieu L, Léonard S, Millan JM, Malcolm S, Claustres M, Roux AF. Experience of targeted Usher exome sequencing as a clinical test. Mol Genet Genomic Med 2013; 2:30-43. [PMID: 24498627 PMCID: PMC3907913 DOI: 10.1002/mgg3.25] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 06/06/2013] [Indexed: 12/15/2022] Open
Abstract
We show that massively parallel targeted sequencing of 19 genes provides a new and reliable strategy for molecular diagnosis of Usher syndrome (USH) and nonsyndromic deafness, particularly appropriate for these disorders characterized by a high clinical and genetic heterogeneity and a complex structure of several of the genes involved. A series of 71 patients including Usher patients previously screened by Sanger sequencing plus newly referred patients was studied. Ninety-eight percent of the variants previously identified by Sanger sequencing were found by next-generation sequencing (NGS). NGS proved to be efficient as it offers analysis of all relevant genes which is laborious to reach with Sanger sequencing. Among the 13 newly referred Usher patients, both mutations in the same gene were identified in 77% of cases (10 patients) and one candidate pathogenic variant in two additional patients. This work can be considered as pilot for implementing NGS for genetically heterogeneous diseases in clinical service.
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Affiliation(s)
- Thomas Besnard
- U827, Inserm Montpellier, F-34000, France ; Univ, Montpellier I Montpellier, F-34000, France
| | - Gema García-García
- U827, Inserm Montpellier, F-34000, France ; Grupo de Investigación en Enfermedades Neurosensoriales, Instituto de Investigación Sanitaria IIS-La Fe and CIBERER Valencia, Spain
| | - David Baux
- Laboratoire de Génétique Moléculaire, CHU Montpellier Montpellier, F-34000, France
| | - Christel Vaché
- Laboratoire de Génétique Moléculaire, CHU Montpellier Montpellier, F-34000, France
| | - Valérie Faugère
- Laboratoire de Génétique Moléculaire, CHU Montpellier Montpellier, F-34000, France
| | - Lise Larrieu
- Laboratoire de Génétique Moléculaire, CHU Montpellier Montpellier, F-34000, France
| | - Susana Léonard
- Laboratoire de Génétique Moléculaire, CHU Montpellier Montpellier, F-34000, France
| | - Jose M Millan
- Grupo de Investigación en Enfermedades Neurosensoriales, Instituto de Investigación Sanitaria IIS-La Fe and CIBERER Valencia, Spain
| | - Sue Malcolm
- Clinical and Molecular Genetics, Institute of Child Health, University College London London, United Kingdom
| | - Mireille Claustres
- U827, Inserm Montpellier, F-34000, France ; Univ, Montpellier I Montpellier, F-34000, France ; Laboratoire de Génétique Moléculaire, CHU Montpellier Montpellier, F-34000, France
| | - Anne-Françoise Roux
- U827, Inserm Montpellier, F-34000, France ; Laboratoire de Génétique Moléculaire, CHU Montpellier Montpellier, F-34000, France
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18
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Aparisi MJ, García-García G, Aller E, Sequedo MD, Martínez-Fernández de la Cámara C, Rodrigo R, Armengot M, Cortijo J, Milara J, Díaz-LLopis M, Jaijo T, Millán JM. Study of USH1 splicing variants through minigenes and transcript analysis from nasal epithelial cells. PLoS One 2013; 8:e57506. [PMID: 23451239 PMCID: PMC3581446 DOI: 10.1371/journal.pone.0057506] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 01/22/2013] [Indexed: 11/18/2022] Open
Abstract
Usher syndrome type I (USH1) is an autosomal recessive disorder characterized by congenital profound deafness, vestibular areflexia and prepubertal retinitis pigmentosa. The first purpose of this study was to determine the pathologic nature of eighteen USH1 putative splicing variants found in our series and their effect in the splicing process by minigene assays. These variants were selected according to bioinformatic analysis. The second aim was to analyze the USH1 transcripts, obtained from nasal epithelial cells samples of our patients, in order to corroborate the observed effect of mutations by minigenes in patient’s tissues. The last objective was to evaluate the nasal ciliary beat frequency in patients with USH1 and compare it with control subjects. In silico analysis were performed using four bioinformatic programs: NNSplice, Human Splicing Finder, NetGene2 and Spliceview. Afterward, minigenes based on the pSPL3 vector were used to investigate the implication of selected changes in the mRNA processing. To observe the effect of mutations in the patient’s tissues, RNA was extracted from nasal epithelial cells and RT-PCR analyses were performed. Four MYO7A (c.470G>A, c.1342_1343delAG, c.5856G>A and c.3652G>A), three CDH23 (c.2289+1G>A, c.6049G>A and c.8722+1delG) and one PCDH15 (c.3717+2dupTT) variants were observed to affect the splicing process by minigene assays and/or transcripts analysis obtained from nasal cells. Based on our results, minigenes are a good approach to determine the implication of identified variants in the mRNA processing, and the analysis of RNA obtained from nasal epithelial cells is an alternative method to discriminate neutral Usher variants from those with a pathogenic effect on the splicing process. In addition, we could observe that the nasal ciliated epithelium of USH1 patients shows a lower ciliary beat frequency than control subjects.
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Affiliation(s)
- María José Aparisi
- Research Group on Sensorineural Diseases, Instituto de Investigación Sanitaria - La Fe, Valencia, Spain
| | - Gema García-García
- Research Group on Sensorineural Diseases, Instituto de Investigación Sanitaria - La Fe, Valencia, Spain
| | - Elena Aller
- Research Group on Sensorineural Diseases, Instituto de Investigación Sanitaria - La Fe, Valencia, Spain
- Biomedical Network Research Center for Rare Diseases, Valencia, Spain
| | - María Dolores Sequedo
- Research Group on Sensorineural Diseases, Instituto de Investigación Sanitaria - La Fe, Valencia, Spain
| | | | - Regina Rodrigo
- Research Group on Sensorineural Diseases, Instituto de Investigación Sanitaria - La Fe, Valencia, Spain
| | - Miguel Armengot
- Rhinology Unit, General and University Hospital, Medical School, Valencia University, Valencia, Spain
| | - Julio Cortijo
- Research Foundation of the University General Hospital of Valencia, Valencia, Spain
- Biomedical Network Research Center for Respiratory Diseases, Valencia, Spain
- University of Valencia, Valencia, Spain
| | - Javier Milara
- Biomedical Network Research Center for Respiratory Diseases, Valencia, Spain
- Clinical Pharmacology Unit, University Clinic Hospital, Valencia, Spain
- Research Unit, University General Hospital Consortium, Valencia, Spain
| | - Manuel Díaz-LLopis
- Department of Ophthalmology, La Fe University Hospital, Medical School, Valencia University, Valencia, Spain
| | - Teresa Jaijo
- Research Group on Sensorineural Diseases, Instituto de Investigación Sanitaria - La Fe, Valencia, Spain
- Biomedical Network Research Center for Rare Diseases, Valencia, Spain
- * E-mail:
| | - José María Millán
- Research Group on Sensorineural Diseases, Instituto de Investigación Sanitaria - La Fe, Valencia, Spain
- Biomedical Network Research Center for Rare Diseases, Valencia, Spain
- Genetics Unit, La Fe University Hospital, Valencia, Spain
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Vaché C, Besnard T, le Berre P, García-García G, Baux D, Larrieu L, Abadie C, Blanchet C, Bolz HJ, Millan J, Hamel C, Malcolm S, Claustres M, Roux AF. Usher syndrome type 2 caused by activation of an USH2A pseudoexon: implications for diagnosis and therapy. Hum Mutat 2011; 33:104-8. [PMID: 22009552 DOI: 10.1002/humu.21634] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 10/07/2011] [Indexed: 11/09/2022]
Abstract
USH2A sequencing in three affected members of a large family, referred for the recessive USH2 syndrome, identified a single pathogenic alteration in one of them and a different mutation in the two affected nieces. As the patients carried a common USH2A haplotype, they likely shared a mutation not found by standard sequencing techniques. Analysis of RNA from nasal cells in one affected individual identified an additional pseudoexon (PE) resulting from a deep intronic mutation. This was confirmed by minigene assay. This is the first example in Usher syndrome (USH) with a mutation causing activation of a PE. The finding of this alteration in eight other individuals of mixed European origin emphasizes the importance of including RNA analysis in a comprehensive diagnostic service. Finally, this mutation, which would not have been found by whole-exome sequencing, could offer, for the first time in USH, the possibility of therapeutic correction by antisense oligonucleotides (AONs).
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Affiliation(s)
- Christel Vaché
- CHU Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France
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