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Markova TG, Lalayants MR, Alekseeva NN, Ryzhkova OP, Shatokhina OL, Galeeva NM, Bliznetz EA, Weener ME, Belov OA, Chibisova SS, Polyakov AV, Tavartkiladze GA. Early audiological phenotype in patients with mutations in the USH2A gene. Int J Pediatr Otorhinolaryngol 2022; 157:111140. [PMID: 35452909 DOI: 10.1016/j.ijporl.2022.111140] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 03/16/2022] [Accepted: 04/11/2022] [Indexed: 11/27/2022]
Abstract
INTRODUCTION Nowadays, due to universal newborn hearing screening (UNHS) the number of children with mild-to-moderate hearing loss diagnosed in the first year of life has increased significantly. Aside from that, identification of the genetic cause improves the genetic counselling of the families and allows to reveal possible comorbidities which may need a special approach. OBJECTIVE To present the characteristics of the early audiologic phenotype in hearing impaired patients with biallelic mutations in the USH2A gene based on systematic analysis of the audiological data. PATIENTS AND METHODS 13 patients with mutations in the USH2A gene underwent audiological examination. Most of them were found among a large group of infants with bilateral nonsyndromic sensorineural hearing loss (SNHL) examined under 12 months. RESULTS Eight out of eleven children failed UNHS and were initially diagnosed as having bilateral nonsyndromic SNHL. Seven children underwent an audiological assessment before the age of 9 months. The earliest audiological examination was carried out at 1 and 3 months. The children with pathogenic variants in the USH2A gene in our examined group were identified in the first year of life via UNHS. The hearing threshold levels (HTL) for the USH2A group are compactly distributed between 51.25 dB and 66.25 dB, quartiles are 54 dB and 63.4 dB, with a median of 60 dB. The audiological profile of patients with biallelic USH2A mutations differs from audiograms of patients who had STRC-related hearing loss. We have not found any significant elevation in hearing thresholds in the first decade of life. We also estimated the prevalence of the USH2A and STRC mutations among GJB2-negative infants with bilateral nonsyndromic SNHL examined under 12 months, and it was 7.5% and 16.1%, respectively. CONCLUSION According to our results, the early hearing phenotype in pediatric patients with biallelic mutations in the USH2A- gene is characterized by nonsyndromic mild-to-moderate SNHL in the first decade of life. Our results indicate that the presence of mutations in the USH2A or STRC genes can be expected in a child with congenital mild-to-moderate nonsyndromic SNHL. This information is of practical importance for parents, as they have to know the prognosis of hearing loss for their child from the very beginning. Post-screening follow-up should include adequate clinical, genetic, and social support for children and their parents.
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Affiliation(s)
- T G Markova
- National Research Centre for Audiology and Hearing Rehabilitation, Moscow, 117513, Russia; Russian Medical Academy of Continuing Professional Education, Moscow, 125993, Russia
| | - M R Lalayants
- National Research Centre for Audiology and Hearing Rehabilitation, Moscow, 117513, Russia; Russian Medical Academy of Continuing Professional Education, Moscow, 125993, Russia
| | - N N Alekseeva
- National Research Centre for Audiology and Hearing Rehabilitation, Moscow, 117513, Russia; Russian Medical Academy of Continuing Professional Education, Moscow, 125993, Russia
| | - O P Ryzhkova
- Research Centre for Medical Genetics, Moscow, 115478, Russia
| | - O L Shatokhina
- Research Centre for Medical Genetics, Moscow, 115478, Russia
| | - N M Galeeva
- Research Centre for Medical Genetics, Moscow, 115478, Russia
| | - E A Bliznetz
- Research Centre for Medical Genetics, Moscow, 115478, Russia
| | - M E Weener
- CRO LLC «Oftalmic», Moscow, 125167, Russia
| | - O A Belov
- National Research Centre for Audiology and Hearing Rehabilitation, Moscow, 117513, Russia
| | - S S Chibisova
- National Research Centre for Audiology and Hearing Rehabilitation, Moscow, 117513, Russia; Russian Medical Academy of Continuing Professional Education, Moscow, 125993, Russia
| | - A V Polyakov
- Research Centre for Medical Genetics, Moscow, 115478, Russia
| | - G A Tavartkiladze
- National Research Centre for Audiology and Hearing Rehabilitation, Moscow, 117513, Russia; Russian Medical Academy of Continuing Professional Education, Moscow, 125993, Russia.
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Generation and Genetic Correction of USH2A c.2299delG Mutation in Patient-Derived Induced Pluripotent Stem Cells. Genes (Basel) 2021; 12:genes12060805. [PMID: 34070435 PMCID: PMC8227183 DOI: 10.3390/genes12060805] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/15/2021] [Accepted: 05/19/2021] [Indexed: 01/15/2023] Open
Abstract
Usher syndrome (USH) is the leading cause of inherited combined hearing and vision loss. As an autosomal recessive trait, it affects 15,000 people in the United States alone and is responsible for ~21% of inherited blindness and 3 to 6% of early childhood deafness. Approximately 2/3 of the patients with Usher syndrome suffer from USH2, of whom 85% have mutations in the USH2A gene. Patients affected by USH2 suffer from congenital bilateral progressive sensorineural hearing loss and retinitis pigmentosa which leads to progressive loss of vision. To study the molecular mechanisms of this disease and develop a gene therapy strategy, we generated human induced pluripotent stem cells (iPSCs) from peripheral blood mononuclear cells (PBMCs) obtained from a patient carrying compound heterozygous variants of USH2A c.2299delG and c.1256G>T and the patient’s healthy sibling. The pluripotency and stability were confirmed by pluripotency cell specific marker expression and molecular karyotyping. Subsequent CRISPR/Cas9 genome editing using a homology repair template was used to successfully correct the USH2A c.2299delG mutation back to normal c.2299G in the generated patient iPSCs to create an isogenic pair of lines. Importantly, this manuscript describes the first use of the recombinant Cas9 and synthetic gRNA ribonucleoprotein complex approach to correct the USH2A c.2299delG without additional genetic effects in patient-derived iPSCs, an approach that is amenable for therapeutic genome editing. This work lays a solid foundation for future ex vivo and in vivo gene therapy investigations and these patient’s iPSCs also provide an unlimited resource for disease modeling and mechanistic studies.
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Licastro D, Mutarelli M, Peluso I, Neveling K, Wieskamp N, Rispoli R, Vozzi D, Athanasakis E, D'Eustacchio A, Pizzo M, D'Amico F, Ziviello C, Simonelli F, Fabretto A, Scheffer H, Gasparini P, Banfi S, Nigro V. Molecular diagnosis of Usher syndrome: application of two different next generation sequencing-based procedures. PLoS One 2012; 7:e43799. [PMID: 22952768 PMCID: PMC3430670 DOI: 10.1371/journal.pone.0043799] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 07/26/2012] [Indexed: 11/20/2022] Open
Abstract
Usher syndrome (USH) is a clinically and genetically heterogeneous disorder characterized by visual and hearing impairments. Clinically, it is subdivided into three subclasses with nine genes identified so far. In the present study, we investigated whether the currently available Next Generation Sequencing (NGS) technologies are already suitable for molecular diagnostics of USH. We analyzed a total of 12 patients, most of which were negative for previously described mutations in known USH genes upon primer extension-based microarray genotyping. We enriched the NGS template either by whole exome capture or by Long-PCR of the known USH genes. The main NGS sequencing platforms were used: SOLiD for whole exome sequencing, Illumina (Genome Analyzer II) and Roche 454 (GS FLX) for the Long-PCR sequencing. Long-PCR targeting was more efficient with up to 94% of USH gene regions displaying an overall coverage higher than 25×, whereas whole exome sequencing yielded a similar coverage for only 50% of those regions. Overall this integrated analysis led to the identification of 11 novel sequence variations in USH genes (2 homozygous and 9 heterozygous) out of 18 detected. However, at least two cases were not genetically solved. Our result highlights the current limitations in the diagnostic use of NGS for USH patients. The limit for whole exome sequencing is linked to the need of a strong coverage and to the correct interpretation of sequence variations with a non obvious, pathogenic role, whereas the targeted approach suffers from the high genetic heterogeneity of USH that may be also caused by the presence of additional causative genes yet to be identified.
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Affiliation(s)
- Danilo Licastro
- Cluster in Biomedicine (CBM) scrl - Genomics, Area Science Park, Basovizza, Trieste, Italy
| | | | - Ivana Peluso
- Telethon Institute of Genetics and Medicine (TIGEM), Napoli, Italy
| | - Kornelia Neveling
- Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Nienke Wieskamp
- Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Rossella Rispoli
- Telethon Institute of Genetics and Medicine (TIGEM), Napoli, Italy
| | - Diego Vozzi
- Institute for Maternal and Child Health - IRCCS “Burlo Garofolo”,Trieste, Italy
| | | | - Angela D'Eustacchio
- Institute for Maternal and Child Health - IRCCS “Burlo Garofolo”,Trieste, Italy
| | | | - Francesca D'Amico
- Dipartimento di Patologia Generale, Seconda Università degli Studi di Napoli, Napoli, Italy
| | - Carmela Ziviello
- Telethon Institute of Genetics and Medicine (TIGEM), Napoli, Italy
| | - Francesca Simonelli
- Dipartimento di Oftalmologia, Seconda Università degli Studi di Napoli, Napoli, Italy
| | - Antonella Fabretto
- Institute for Maternal and Child Health - IRCCS “Burlo Garofolo”,Trieste, Italy
| | - Hans Scheffer
- Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Paolo Gasparini
- Institute for Maternal and Child Health - IRCCS “Burlo Garofolo”,Trieste, Italy
- * E-mail: (PG); (SB); (VN)
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine (TIGEM), Napoli, Italy
- Dipartimento di Patologia Generale, Seconda Università degli Studi di Napoli, Napoli, Italy
- * E-mail: (PG); (SB); (VN)
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine (TIGEM), Napoli, Italy
- Dipartimento di Patologia Generale, Seconda Università degli Studi di Napoli, Napoli, Italy
- * E-mail: (PG); (SB); (VN)
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Garcia-Garcia G, Aparisi MJ, Jaijo T, Rodrigo R, Leon AM, Avila-Fernandez A, Blanco-Kelly F, Bernal S, Navarro R, Diaz-Llopis M, Baiget M, Ayuso C, Millan JM, Aller E. Mutational screening of the USH2A gene in Spanish USH patients reveals 23 novel pathogenic mutations. Orphanet J Rare Dis 2011; 6:65. [PMID: 22004887 PMCID: PMC3207874 DOI: 10.1186/1750-1172-6-65] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 10/17/2011] [Indexed: 11/10/2022] Open
Abstract
Background Usher Syndrome type II (USH2) is an autosomal recessive disorder, characterized by moderate to severe hearing impairment and retinitis pigmentosa (RP). Among the three genes implicated, mutations in the USH2A gene account for 74-90% of the USH2 cases. Methods To identify the genetic cause of the disease and determine the frequency of USH2A mutations in a cohort of 88 unrelated USH Spanish patients, we carried out a mutation screening of the 72 coding exons of this gene by direct sequencing. Moreover, we performed functional minigene studies for those changes that were predicted to affect splicing. Results As a result, a total of 144 DNA sequence variants were identified. Based upon previous studies, allele frequencies, segregation analysis, bioinformatics' predictions and in vitro experiments, 37 variants (23 of them novel) were classified as pathogenic mutations. Conclusions This report provide a wide spectrum of USH2A mutations and clinical features, including atypical Usher syndrome phenotypes resembling Usher syndrome type I. Considering only the patients clearly diagnosed with Usher syndrome type II, and results obtained in this and previous studies, we can state that mutations in USH2A are responsible for 76.1% of USH2 disease in patients of Spanish origin.
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Affiliation(s)
- Gema Garcia-Garcia
- Grupo de Investigación en Enfermedades Neurosensoriales, Instituto de Investigación Sanitaria IIS-La Fe, Valencia, Spain
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Vozzi D, Aaspõllu A, Athanasakis E, Berto A, Fabretto A, Licastro D, Külm M, Testa F, Trevisi P, Vahter M, Ziviello C, Martini A, Simonelli F, Banfi S, Gasparini P. Molecular epidemiology of Usher syndrome in Italy. Mol Vis 2011; 17:1662-8. [PMID: 21738395 PMCID: PMC3130723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 06/16/2011] [Indexed: 11/29/2022] Open
Abstract
PURPOSE Usher syndrome is an autosomal recessive disorder characterized by hearing and vision loss. Usher syndrome is divided into three clinical subclasses (type 1, type 2, and type 3), which differ in terms of the severity and progression of hearing loss and the presence or absence of vestibular symptoms. Usher syndrome is defined by significant genetic heterogeneity, with at least 12 distinct loci described and 9 genes identified. This study aims to provide a molecular epidemiology report of Usher syndrome in Italy. METHODS Molecular data have been obtained on 75 unrelated Italian patients using the most up-to date technology available for the screening of Usher syndrome gene mutations, i.e., the genotyping microarray developed by Asper Biotech (Tartu, Estonia), which simultaneously investigates 612 different marker positions using the well established arrayed primer extension methodology (APEX). RESULTS Using this method, we found that 12% of cases (9 out of 75) harbored homozygous or compound heterozygous mutations in the gene positions analyzed, whereas 20% (15 out of 75) of the patients were characterized by the presence of only one mutated allele based on the positions analyzed. One patient was found to be compound heterozygous for mutations in two different genes and this represents an example of possible digenic inheritance in Usher syndrome. A total of 66.6% of cases (50 out of 75) were found to be completely negative for the presence of Usher syndrome gene mutations in the detected positions. Mutations detected by the array were confirmed by direct sequencing. CONCLUSIONS These findings highlight the efficacy of the APEX-based genotyping approach in the molecular assessment of Usher patients, suggesting the presence of alleles not yet identified and/or the involvement of additional putative genes that may account for the pathogenesis of Usher syndrome.
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Affiliation(s)
- Diego Vozzi
- Medical Genetics, Department of Reproductive Sciences, Development and Public Health, IRCCS-Burlo Garofolo Children Hospital, University of Trieste, Trieste, 34100 Italy
| | - Anu Aaspõllu
- Asper Biotech, Vaksali 17a, 50410 Tartu, Estonia
| | - Emmanouil Athanasakis
- Medical Genetics, Department of Reproductive Sciences, Development and Public Health, IRCCS-Burlo Garofolo Children Hospital, University of Trieste, Trieste, 34100 Italy
| | | | - Antonella Fabretto
- Medical Genetics, Department of Reproductive Sciences, Development and Public Health, IRCCS-Burlo Garofolo Children Hospital, University of Trieste, Trieste, 34100 Italy
| | - Danilo Licastro
- CBM scrl - Genomics, Area Science Park, Basovizza, Trieste, Italy
| | - Maigi Külm
- Asper Biotech, Vaksali 17a, 50410 Tartu, Estonia
| | - Francesco Testa
- Department of Ophthalmology, Second University of Naples, Napoli, Italy
| | | | - Marju Vahter
- Asper Biotech, Vaksali 17a, 50410 Tartu, Estonia
| | - Carmela Ziviello
- Medical Genetics, Department of General Pathology, Second University of Naples, Naples, Italy
| | | | | | - Sandro Banfi
- Medical Genetics, Department of General Pathology, Second University of Naples, Naples, Italy
| | - Paolo Gasparini
- Medical Genetics, Department of Reproductive Sciences, Development and Public Health, IRCCS-Burlo Garofolo Children Hospital, University of Trieste, Trieste, 34100 Italy
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Pieke-Dahl S, Möller CG, Kelley PM, Astuto LM, Cremers CW, Gorin MB, Kimberling WJ. Genetic heterogeneity of Usher syndrome type II: localisation to chromosome 5q. J Med Genet 2000; 37:256-62. [PMID: 10745043 PMCID: PMC1734554 DOI: 10.1136/jmg.37.4.256] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Usher syndrome is a group of autosomal recessive disorders that includes retinitis pigmentosa (RP) with hearing loss. Usher syndrome type II is defined as moderate to severe hearing loss with RP. The USH2A gene at 1q41 has been isolated and characterised. In 1993, a large Usher II family affected with a mild form of RP was found to be unlinked to 1q41 markers. Subsequent linkage studies of families in our Usher series identified several type II families unlinked to USH2A and USH3 on 3q25. After a second unlinked family with many affected members and a mild retinal phenotype was discovered, a genome search using these two large families showed another Usher II locus on 5q (two point lod = 3.1 at D5S484). To date, we have identified nine unrelated 5q linked families (maximum combined multipoint lod = 5.86) as well as three Usher II families that show no significant linkage to any known Usher loci. Haplotype analysis of 5q markers indicates that the new locus is flanked by D5S428 and D5S433. Review of ophthalmological data suggests that RP symptoms are milder in 5q linked families; the RP is often not diagnosed until patients near their third decade. Enamel hypoplasia and severe, very early onset RP were observed in two of the three unlinked families; dental anomalies have not been previously described as a feature of Usher type II.
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Affiliation(s)
- S Pieke-Dahl
- Genetics Department, Boys Town National Research Hospital, 555 N 30th Street, Omaha, NE 68131 USA
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Bessant DA, Payne AM, Plant C, Bird AC, Bhattacharya SS. Further refinement of the Usher 2A locus at 1q41. J Med Genet 1998; 35:773-4. [PMID: 9733039 PMCID: PMC1051433 DOI: 10.1136/jmg.35.9.773] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Usher syndrome (USH) is characterised by congenital sensorineural hearing loss and progressive pigmentary retinopathy. All three subtypes (USH1, USH2, and USH3) are inherited as recessive traits. People with Usher type 2 (USH2) have normal vestibular responses and moderate to severe hearing loss. These syndromes have been found to be genetically heterogeneous, with a single locus for USH2 at 1q41 (USH2A), six loci for USH1, and one for USH3. Some USH2 families have been excluded from the 1q41 locus suggesting that a second, as yet unidentified, locus (USH2B) must exist. Linkage studies suggest that around 90% of USH2 families are USH2A. Four USH2 families were analysed for linkage to markers flanking the USH2A locus. In one of these families a recombination event was observed in an affected subject which excludes the USH2A gene from proximal to the marker AFM143XF10 and defines this as the new centromeric flanking marker for the USH2A locus. A further recombination event in another patient from this family confirmed AFM144XF2 as the telomeric flanking marker. The interval between these polymorphic markers is estimated to be 400 kb. This region is completely contained in each of three YACs from the CEPH library: 867g9, 919h3, and 848b9. This refinement more than halves the critical genetic interval and will greatly facilitate positional cloning of the USH2A gene.
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Affiliation(s)
- D A Bessant
- Department of Molecular Genetics, Institute of Ophthalmology, University College London, UK
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