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Gillesse E, Wade A, Parboosingh JS, Au PYB, Bernier FP, Lamont RE, Innes AM. Genome sequencing identifies biallelic variants in SCLT1 in a patient with syndromic nephronophthisis: Reflections on the SCLT1-related ciliopathy spectrum. Am J Med Genet A 2024:e63789. [PMID: 38924217 DOI: 10.1002/ajmg.a.63789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 05/28/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]
Abstract
Ciliopathies represent a major category of rare multisystem disease. Arriving at a specific diagnosis for a given patient is challenged by the significant genetic and clinical heterogeneity of these conditions. We report the outcome of the diagnostic odyssey of a child with obesity, renal, and retinal disease. Genome sequencing identified biallelic splice site variants in sodium channel and clathrin linker 1 (SCLT1), an emerging ciliopathy gene. We review the literature on all patients reported with biallelic SCLT1 variants highlighting a frequent clinical presentation that overlaps Bardet-Biedl and Senior-Loken syndromes. We also discuss current concepts in syndrome designation in light of these data.
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Affiliation(s)
- E Gillesse
- Alberta Children's Hospital Research Institute, Calgary, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Canada
| | - A Wade
- Alberta Children's Hospital Research Institute, Calgary, Canada
- Department of Pediatrics, University of Calgary, Calgary, Canada
- Department of Cell Biology and Anatomy, University of Calgary, Calgary, Canada
| | - J S Parboosingh
- Alberta Children's Hospital Research Institute, Calgary, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Canada
| | - P Y B Au
- Alberta Children's Hospital Research Institute, Calgary, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Canada
- Department of Pediatrics, University of Calgary, Calgary, Canada
| | - F P Bernier
- Alberta Children's Hospital Research Institute, Calgary, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Canada
- Department of Pediatrics, University of Calgary, Calgary, Canada
| | - R E Lamont
- Alberta Children's Hospital Research Institute, Calgary, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Canada
| | - A M Innes
- Alberta Children's Hospital Research Institute, Calgary, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Canada
- Department of Pediatrics, University of Calgary, Calgary, Canada
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2
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Zhai Y, Ballios BG. Exploring the diverse clinical and variant spectrum of CEP78-associated syndrome: Novel pathogenic variants identified in a case series. Am J Med Genet A 2024:e63720. [PMID: 38780195 DOI: 10.1002/ajmg.a.63720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 04/25/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
Dual sensory impairment, commonly referred to as combined hearing and vision loss, can stem from a diverse spectrum of conditions, each presenting with its unique set of clinical characteristics. Our understanding of dual sensory impairment has expanded significantly in the past decade, broadening the scope of genetic differential diagnoses, including genes such as CEP250, ARSG, TUBB4B, CEP78, and ABHD12. A case series including three patients from two families with genetically diagnosed CEP78-associated cone-rod dystrophy was identified. We collected and reviewed their clinical records, imaging data, and genetic testing results. In addition, a comprehensive literature review was conducted on the phenotype and the genetic testing modality employed in all published CEP78 cases through a PubMed search using the keyword "CEP78." A retinal dystrophy panel detected a novel homozygous CEP78 pathogenic variant (c.1447C>T, p.Arg483*) in siblings-Cases 1 and 2-from Family 1. Both teenagers have a clinical diagnosis of cone-rod dystrophy with presumed normal hearing. Case 3 from Family 2, diagnosed with cone-rod dystrophy and early-onset hearing loss, was found to carry a CEP78 pathogenic variant (c.1206-2A>C) and a likely pathogenic variant (c.856_857del, p.Leu286Glyfs*12) also through panel-based genetic testing. Intriguingly, neither of these variants was reported in an affected sibling's clinical whole-exome sequencing (WES) report when performed in 2015. A review of CEP78-related literature unveiled that the initial report linking CEP78 to cone-rod dystrophy and hearing loss was published in September 2016. Any pathogenic variant found in CEP78 before 2016 would have been categorized as a "clearly disruptive variant in a gene of uncertain significance (GUS)" and might not have been reported in the WES report. It is important to acknowledge that our understanding of genotype-phenotype associations is undergoing rapid expansion. It is also crucial to recognize that repeat genetic testing may represent a fundamentally different approach, given the technological advancements not only in the coverage of the sequencing but also in the more comprehensive understanding of genotype-phenotype associations. This case series also enriches the existing CEP78 literature by providing phenotypic details of the youngest case of CEP78-associated retinopathy reported in the literature (Case 2), which expands our perspective on the natural history of disease in this disorder.
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Affiliation(s)
- Yi Zhai
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Brian G Ballios
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Ontario, Canada
- Department of Ophthalmology, University Health Network, Toronto, Ontario, Canada
- Kensington Vision and Research Centre, Toronto, Ontario, Canada
- Krembil Research Institute, University Health Network, Toronto, Ontario, Canada
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Colombo L, Bonetti G, Maltese PE, Iarossi G, Ziccardi L, Fogagnolo P, De Ruvo V, Murro V, Giorgio D, Falsini B, Placidi G, Martella S, Galantin E, Bertelli M, Rossetti L. Genotypic and Phenotypic Characterization of a Cohort of Patients Affected by Rod Cyclic Nucleotide Channel-Associated Retinitis Pigmentosa. Ophthalmic Res 2024; 67:301-310. [PMID: 38705136 DOI: 10.1159/000538746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/12/2024] [Indexed: 05/07/2024]
Abstract
INTRODUCTION Retinitis pigmentosa (RP), a heterogeneous inherited retinal disorder causing gradual vision loss, affects over 1 million people worldwide. Pathogenic variants in CNGA1 and CNGB1 genes, respectively, accounting for 1% and 4% of cases, impact the cyclic nucleotide-gated channel in rod photoreceptor cells. The aim of this study was to describe and compare genotypic and clinical characteristics of a cohort of patients with CNGA1- or CNGB1-related RP and to explore potential genotype-phenotype correlations. METHODS The following data from patients with CNGA1- or CNGB1-related RP, followed in five Italian inherited retinal degenerations services, were retrospectively collected: genetic variants in CNGA1 and CNGB1, best-corrected visual acuity (BCVA), ellipsoid zone (EZ) width, fundus photographs, and short-wavelength fundus autofluorescence (SW-AF) images. Comparisons and correlation analyses were performed by first dividing the cohort in two groups according to the gene responsible for the disease (CNGA1 and CNGB1 groups). In parallel, the whole cohort of RP patients was divided into two other groups, according to the expected impact of the variants at protein level (low and high group). RESULTS In total, 29 patients were recruited, 11 with CNGA1- and 18 with CNGB1-related RP. In both CNGA1 and CNGB1, 5 novel variants in CNGA1 and 5 in CNGB1 were found. BCVA was comparable between CNGA1 and CNGB1 groups, as well as between low and high groups. CNGA1 group had a larger mean EZ width compared to CNGB1 group, albeit not statistically significant, while EZ width did not differ between low and high groups A statistically significant correlation between EZ width and BCVA as well as between EZ width and age were observed in the whole cohort of RP patients. Fundus photographs of all patients in the cohort showed classic RP pattern, and in SW-AF images an hyperautofluorescent ring was observed in 14/21 patients. CONCLUSION Rod CNG channel-associated RP was demonstrated to be a slowly progressive disease in both CNGA1- and CNGB1-related forms, making it an ideal candidate for gene augmentation therapies.
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Affiliation(s)
- Leonardo Colombo
- Department of Ophthalmology, ASST Santi Paolo e Carlo Hospital, University of Milan, Milan, Italy
| | - Gabriele Bonetti
- MAGI'S LAB S.R.L., Rovereto, Italy
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | | | - Giancarlo Iarossi
- Department of Ophthalmology, Bambino Gesù Children's Hospital, Rome, Italy
| | | | - Paolo Fogagnolo
- Department of Ophthalmology, ASST Santi Paolo e Carlo Hospital, University of Milan, Milan, Italy
| | - Valentino De Ruvo
- Department of Ophthalmology, ASST Santi Paolo e Carlo Hospital, University of Milan, Milan, Italy
| | - Vittoria Murro
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Florence, Italy
| | - Dario Giorgio
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Florence, Italy
| | - Benedetto Falsini
- Department of Ophthalmology, Bambino Gesù Children's Hospital, Rome, Italy
- Ophthalmology Unit, Fondazione Policlinico Universitario "A. Gemelli" IRCCS/Università Cattolica del S. Cuore, Rome, Italy
| | - Giorgio Placidi
- Ophthalmology Unit, Fondazione Policlinico Universitario "A. Gemelli" IRCCS/Università Cattolica del S. Cuore, Rome, Italy
| | - Salvatore Martella
- Department of Ophthalmology, ASST Santi Paolo e Carlo Hospital, University of Milan, Milan, Italy
| | - Eleonora Galantin
- Department of Ophthalmology, ASST Santi Paolo e Carlo Hospital, University of Milan, Milan, Italy
| | - Matteo Bertelli
- MAGI'S LAB S.R.L., Rovereto, Italy
- MAGI EUREGIO, Bolzano, Italy
- MAGISNAT, Atlanta Tech Park, Peachtree Corners, Georgia, USA
| | - Luca Rossetti
- Department of Ophthalmology, ASST Santi Paolo e Carlo Hospital, University of Milan, Milan, Italy
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Azuelos C, Marquis MA, Laberge AM. A systematic review of the assessment of the clinical utility of genomic sequencing: Implications of the lack of standard definitions and measures of clinical utility. Eur J Med Genet 2024; 68:104925. [PMID: 38432472 DOI: 10.1016/j.ejmg.2024.104925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/31/2023] [Accepted: 02/11/2024] [Indexed: 03/05/2024]
Abstract
PURPOSE Exome sequencing (ES) and genome sequencing (GS) are diagnostic tests for rare genetic diseases. Studies report clinical utility of ES/GS. The goal of this systematic review is to establish how clinical utility is defined and measured in studies evaluating the impacts of ES/GS results for pediatric patients. METHODS Relevant articles were identified in PubMed, Medline, Embase, and Web of Science. Eligible studies assessed clinical utility of ES/GS for pediatric patients published before 2021. Other relevant articles were added based on articles' references. Articles were coded to assess definitions and measures of clinical utility. RESULTS Of 1346 articles, 83 articles met eligibility criteria. Clinical utility was not clearly defined in 19% of studies and 92% did not use an explicit measure of clinical utility. When present, definitions of clinical utility diverged from recommended definitions and varied greatly, from narrow (diagnostic yield of ES/GS) to broad (including decisions about withdrawal of care/palliative care and/or impacts on other family members). CONCLUSION Clinical utility is used to guide policy and practice decisions about test use. The lack of a standard definition of clinical utility of ES/GS may lead to under- or overestimations of clinical utility, complicating policymaking and raising ethical issues.
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Affiliation(s)
- Claudia Azuelos
- Medical Genetics, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada.
| | - Marc-Antoine Marquis
- Palliative Care, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada
| | - Anne-Marie Laberge
- Medical Genetics, Dept of Pediatrics, CHU Sainte-Justine and Université de Montréal, Canada.
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Sangermano R, Gupta P, Price C, Han J, Navarro J, Condroyer C, Place EM, Antonio A, Mukai S, Zanlonghi X, Sahel JA, Duncan JL, Pierce EA, Zeitz C, Audo I, Huckfeldt RM, Bujakowska KM. Coding and non-coding variants in the ciliopathy gene CFAP410 cause early-onset non-syndromic retinal degeneration. RESEARCH SQUARE 2024:rs.3.rs-3871956. [PMID: 38405922 PMCID: PMC10889070 DOI: 10.21203/rs.3.rs-3871956/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Inherited retinal degenerations are blinding genetic disorders characterized by high genetic and phenotypic heterogeneity. The implementation of next-generation sequencing in routine diagnostics, together with advanced clinical phenotyping including multimodal retinal imaging, have contributed to the increase of reports describing novel genotype-phenotype associations and phenotypic expansions. In this study, we describe sixteen families with early-onset non-syndromic retinal degenerations in which affected probands carried rare bi-allelic variants in CFAP410, a ciliary gene previously associated with syndromic recessive Jeune syndrome. The most common retinal phenotypes were cone-rod and rod-cone dystrophies, but the clinical presentations were unified by their early onset as well as the severe impact on central visual function. Twelve variants were detected (three pathogenic, seven likely pathogenic, two of uncertain significance), eight of which were novel. One deep intronic change, c.373+91A>G, led to the creation of a cryptic splice acceptor site in intron four, followed by the inclusion of a 200- base pair pseudoexon and subsequent premature stop codon formation. To our knowledge this is the first likely pathogenic deep-intronic variant identified in this gene. Meta-analysis of all published and novel CFAP410 variants revealed no clear correlation between the severity of the CFAP410-associated phenotypes and the identified causal variants. This is supported by the fact that the frequently encountered missense variant p.(Arg73Pro), often found in syndromic cases, was also associated with non-syndromic retinal degeneration. This study expands the current knowledge of CFAP410-associated ciliopathy by enriching its mutational landscape and supports its association with non-syndromic retinal degeneration.
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Affiliation(s)
- Riccardo Sangermano
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Priya Gupta
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Cherrell Price
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Jinu Han
- Institute of Vision Research, Department of Ophthalmology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Julien Navarro
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | - Emily M. Place
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Aline Antonio
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Shizuo Mukai
- Retina Service, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Xavier Zanlonghi
- Centre de compétence maladies rares, Service d’Ophtalmologie, CHU Rennes, Rennes, France
| | - José-Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, Centre de Référence Maladies Rares REFERET and INSERM-DGOS CIC 1423, Paris, France
- Vision Institute, University of Pittsburgh Medical Center and School of Medicine, Pennsylvania, USA
| | - Jacque L. Duncan
- Department of Ophthalmology, University of California, San Francisco, California, USA
| | - Eric A. Pierce
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, Centre de Référence Maladies Rares REFERET and INSERM-DGOS CIC 1423, Paris, France
| | - Rachel M. Huckfeldt
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Kinga M. Bujakowska
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
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Grudzinska Pechhacker MK, Molnar A, Pekkola Pacheco N, Thonberg H, Querat L, Birkeldh U, Nordgren A, Lindstrand A. Reduced cone photoreceptor function and subtle systemic manifestations in two siblings with loss of SCLT1. Ophthalmic Genet 2024; 45:95-102. [PMID: 37246745 DOI: 10.1080/13816810.2023.2215332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 05/14/2023] [Indexed: 05/30/2023]
Abstract
BACKGROUND The sodium channel and clathrin linker 1 gene (SCLT1) has been involved in the pathogenesis of various ciliopathy disorders such as Bardet-Biedl syndrome, orofaciodigital syndrome type IX, and Senior-Løken syndrome. Detailed exams are warranted to outline all clinical features. Here, we present a family with a milder phenotype of SCLT1-related disease. MATERIAL AND METHODS Comprehensive eye examination including fundus images, OCT, color vision, visual fields and electroretinography were performed. Affected individuals were assessed by a pediatrician and a medical geneticist for systemic features of ciliopathy. Investigations included echocardiography, abdominal ultrasonography, blood work-up for diabetes, liver and kidney function. Genetic testing included NGS retinal dystrophy panel, segregation analysis and transcriptome sequencing. RESULTS Two male children, age 10 and 8 years, were affected with attention deficit hyperactivity disorder (ADHD), obesity and mild photophobia. The ophthalmic exam revealed reduced best-corrected visual acuity (BCVA), strabismus, hyperopia, astigmatism and moderate red-green defects. Milder changes suggesting photoreceptors disease were found on retinal imaging. Electroretinogram confirmed cone photoreceptors dysfunction. Genetic testing revealed a homozygous likely pathogenic, splice-site variant in SCLT1 gene NM_144643.3: c.1439 + 1del in the proband and in the affected brother. The unaffected parents were heterozygous for the SCLT1 variant. Transcriptome sequencing showed retention of intron 16 in the proband. CONCLUSIONS In this report, we highlight the importance of further extensive diagnostics in patients with unexplained reduced vision, strabismus, refractive errors and ADHD spectrum disorders. SCLT1-related retinal degeneration is very rare and isolated reduced function of cone photoreceptors has not previously been observed.
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Affiliation(s)
- Monika K Grudzinska Pechhacker
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Pediatric Ophthalmology, Strabismus and Electrophysiology, St. Erik Eye Hospital, Stockholm, Sweden
| | - Anna Molnar
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Pediatric Ophthalmology, Strabismus and Electrophysiology, St. Erik Eye Hospital, Stockholm, Sweden
| | - Nadja Pekkola Pacheco
- Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Håkan Thonberg
- Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Laurence Querat
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Pediatric Ophthalmology, Strabismus and Electrophysiology, St. Erik Eye Hospital, Stockholm, Sweden
| | - Ulrika Birkeldh
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Pediatric Ophthalmology, Strabismus and Electrophysiology, St. Erik Eye Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Anna Lindstrand
- Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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Yang S, Li Y, Yang L, Guo Q, You Y, Lei B. Pathogenicity and functional analysis of CFAP410 mutations causing cone-rod dystrophy with macular staphyloma. Front Med (Lausanne) 2023; 10:1216427. [PMID: 37901396 PMCID: PMC10601463 DOI: 10.3389/fmed.2023.1216427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023] Open
Abstract
Background Cone-rod dystrophy (CORD) caused by pathogenic variants in CFAP410 is a very rare disease. The mechanisms by which the variants caused the disease remained largely unknown. CFAP410 pathogenic variants were identified in a cone-rod dystrophy with macular staphyloma patient. We explored the pathogenicity and performed functional analysis of two compound heterozygous mutations. Methods A 6-year-old boy complained decreased vision for 1 year, underwent ocular examinations together with systemic X-ray check. Blood sample was taken for targeted next generation sequencing (Tg-NGS). Pathogenicity of identified variants was determined by ACMG guideline. Mutated plasmids were constructed and transferred to HEK293T cells. Cell cycle, protein stability, and protein ubiquitination level was measured. Results The best-corrected visual acuity of proband was 0.20 bilaterally. Fundus showed macular staphyloma and uneven granular pigment disorder in the periphery of the retina. SS-OCT showed thinning and atrophy of the outer retina, residual ellipsoid zone (EZ) in the fovea. Scotopic and photopic ERG responses severe reduced. Two heterozygous missense pathogenic variants, c.319 T > C (p.Tyr107His) and c.347 C > T (p.Pro116Leu) in exon 4 of the CFAP410, were found and were pathogenic by the ACMG guideline. In vitro, pathogenic variants affect cell cycle. Immunofluorescence and western blotting showed that the mutant proteins decreased expression levels protein stability. Meanwhile, co-IP data suggested that ubiquitination level was altered in cells transferred with the mutated plasmids. Conclusion Compound heterozygous pathogenic variants c.319 T > C and c.347 C > T in CFAP410 caused CORD with macular staphyloma. The pathogenic mechanisms may be associated with alternations of protein stability and degradation through the ubiquitin-proteasome pathway.
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Affiliation(s)
- Shaoqing Yang
- Henan University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Ya Li
- Henan Branch of National Clinical Research Center for Ocular Diseases, Henan Eye Institute/Henan Eye Hospital, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Lin Yang
- Henan Branch of National Clinical Research Center for Ocular Diseases, Henan Eye Institute/Henan Eye Hospital, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Qingge Guo
- Henan Branch of National Clinical Research Center for Ocular Diseases, Henan Eye Institute/Henan Eye Hospital, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Ya You
- Henan Branch of National Clinical Research Center for Ocular Diseases, Henan Eye Institute/Henan Eye Hospital, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou, China
| | - Bo Lei
- Henan University People’s Hospital, Henan Provincial People’s Hospital, Zhengzhou, China
- Henan Branch of National Clinical Research Center for Ocular Diseases, Henan Eye Institute/Henan Eye Hospital, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou, China
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Kang M, Kim JA, Song MH, Joo SY, Kim SJ, Jang SH, Lee H, Seong JK, Choi JY, Gee HY, Jung J. Novel Variant in CEP250 Causes Protein Mislocalization and Leads to Nonsyndromic Autosomal Recessive Type of Progressive Hearing Loss. Cells 2023; 12:2328. [PMID: 37759551 PMCID: PMC10528078 DOI: 10.3390/cells12182328] [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: 07/25/2023] [Revised: 09/13/2023] [Accepted: 09/20/2023] [Indexed: 09/29/2023] Open
Abstract
Genetic hearing loss is the most common hereditary sensorial disorder. Though more than 120 genes associated with deafness have been identified, unveiled causative genes and variants of diverse types of hearing loss remain. Herein, we identified a novel nonsense homozygous variant in CEP250 (c.3511C>T; p.Gln1171Ter) among the family members with progressive moderate sensorineural hearing loss in nonsyndromic autosomal recessive type but without retinal degeneration. CEP250 encodes C-Nap1 protein belonging to the CEP protein family, comprising 30 proteins that play roles in centrosome aggregation and cell cycle progression. The nonsense variant in CEP250 led to the early truncating protein of C-Nap1, which hindered centrosome localization; heterologous expression of CEP250 (c.3511C>T) in NIH3T3 cells within cilia expression condition revealed that the truncating C-Nap1 (p.Gln1171Ter) was not localized at the centrosome but was dispersed in the cytosol. In the murine adult cochlea, Cep250 was expressed in the inner and outer hair cells. Knockout mice of Cep250 showed significant hair cell degeneration and progressive hearing loss in auditory brainstem response. In conclusion, a nonsense variant in CEP250 results in a deficit of centrosome localization and hair cell degeneration in the cochlea, which is associated with the progression of hearing loss in humans and mice.
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Affiliation(s)
- Minjin Kang
- Department of Otorhinolaryngology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (M.K.); (J.Y.C.)
- Institute for Lee Won Sang Yonsei Ear Science, Seoul 03722, Republic of Korea (S.Y.J.)
| | - Jung Ah Kim
- Institute for Lee Won Sang Yonsei Ear Science, Seoul 03722, Republic of Korea (S.Y.J.)
- Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Mee Hyun Song
- Department of Otorhinolaryngology Head and Neck Surgery, Myongji Hospital, Hanyang University College of Medicine, Goyang 04763, Republic of Korea
| | - Sun Young Joo
- Institute for Lee Won Sang Yonsei Ear Science, Seoul 03722, Republic of Korea (S.Y.J.)
- Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Se Jin Kim
- Institute for Lee Won Sang Yonsei Ear Science, Seoul 03722, Republic of Korea (S.Y.J.)
- Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Seung Hyun Jang
- Department of Otorhinolaryngology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (M.K.); (J.Y.C.)
- Institute for Lee Won Sang Yonsei Ear Science, Seoul 03722, Republic of Korea (S.Y.J.)
- Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Ho Lee
- Graduate School of Cancer Science and Policy, National Cancer Center, Goyang-si 10408, Republic of Korea;
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, BK21 PLUS Program for Creative Veterinary Science Research, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea;
| | - Jae Young Choi
- Department of Otorhinolaryngology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (M.K.); (J.Y.C.)
- Institute for Lee Won Sang Yonsei Ear Science, Seoul 03722, Republic of Korea (S.Y.J.)
| | - Heon Yung Gee
- Institute for Lee Won Sang Yonsei Ear Science, Seoul 03722, Republic of Korea (S.Y.J.)
- Department of Pharmacology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jinsei Jung
- Department of Otorhinolaryngology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Republic of Korea; (M.K.); (J.Y.C.)
- Institute for Lee Won Sang Yonsei Ear Science, Seoul 03722, Republic of Korea (S.Y.J.)
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Chen C, Rong Y, Zhuang Y, Tang C, Liu Q, Lin P, Li D, Zhao X, Lu F, Qu J, Liu X. RNA-Seq Analysis Reveals an Essential Role of the cGMP-PKG-MAPK Pathways in Retinal Degeneration Caused by Cep250 Deficiency. Int J Mol Sci 2023; 24:8843. [PMID: 37240188 PMCID: PMC10218315 DOI: 10.3390/ijms24108843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Usher syndrome (USH) is characterised by degenerative vision loss known as retinitis pigmentosa (RP), sensorineural hearing loss, and vestibular dysfunction. RP can cause degeneration and the loss of rod and cone photoreceptors, leading to structural and functional changes in the retina. Cep250 is a candidate gene for atypical Usher syndrome, and this study describes the development of a Cep250 KO mouse model to investigate its pathogenesis. OCT and ERG were applied in Cep250 and WT mice at P90 and P180 to access the general structure and function of the retina. After recording the ERG responses and OCT images at P90 and P180, the cone and rod photoreceptors were visualised using an immunofluorescent stain. TUNEL assays were applied to observe the apoptosis in Cep250 and WT mice retinas. The total RNA was extracted from the retinas and executed for RNA sequencing at P90. Compared with WT mice, the thickness of the ONL, IS/OS, and whole retina of Cep250 mice was significantly reduced. The a-wave and b-wave amplitude of Cep250 mice in scotopic and photopic ERG were lower, especially the a-wave. According to the immunostaining and TUNEL stain results, the photoreceptors in the Cep250 retinas were also reduced. An RNA-seq analysis showed that 149 genes were upregulated and another 149 genes were downregulated in Cep250 KO retinas compared with WT mice retinas. A KEGG enrichment analysis indicated that cGMP-PKG signalling pathways, MAPK signalling pathways, edn2-fgf2 axis pathways, and thyroid hormone synthesis were upregulated, whereas protein processing in the endoplasmic reticulum was downregulated in Cep250 KO eyes. Cep250 KO mice experience a late-stage retinal degeneration that manifests as the atypical USH phenotype. The dysregulation of the cGMP-PKG-MAPK pathways may contribute to the pathogenesis of cilia-related retinal degeneration.
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Affiliation(s)
- Chong Chen
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; (C.C.); (Y.R.); (Y.Z.); (C.T.); (Q.L.); (P.L.); (D.L.); (X.Z.); (F.L.)
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Yu Rong
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; (C.C.); (Y.R.); (Y.Z.); (C.T.); (Q.L.); (P.L.); (D.L.); (X.Z.); (F.L.)
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Youyuan Zhuang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; (C.C.); (Y.R.); (Y.Z.); (C.T.); (Q.L.); (P.L.); (D.L.); (X.Z.); (F.L.)
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Cheng Tang
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; (C.C.); (Y.R.); (Y.Z.); (C.T.); (Q.L.); (P.L.); (D.L.); (X.Z.); (F.L.)
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Qian Liu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; (C.C.); (Y.R.); (Y.Z.); (C.T.); (Q.L.); (P.L.); (D.L.); (X.Z.); (F.L.)
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Peng Lin
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; (C.C.); (Y.R.); (Y.Z.); (C.T.); (Q.L.); (P.L.); (D.L.); (X.Z.); (F.L.)
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Dandan Li
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; (C.C.); (Y.R.); (Y.Z.); (C.T.); (Q.L.); (P.L.); (D.L.); (X.Z.); (F.L.)
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Xinyi Zhao
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; (C.C.); (Y.R.); (Y.Z.); (C.T.); (Q.L.); (P.L.); (D.L.); (X.Z.); (F.L.)
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Fan Lu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; (C.C.); (Y.R.); (Y.Z.); (C.T.); (Q.L.); (P.L.); (D.L.); (X.Z.); (F.L.)
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Jia Qu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; (C.C.); (Y.R.); (Y.Z.); (C.T.); (Q.L.); (P.L.); (D.L.); (X.Z.); (F.L.)
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Xinting Liu
- National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; (C.C.); (Y.R.); (Y.Z.); (C.T.); (Q.L.); (P.L.); (D.L.); (X.Z.); (F.L.)
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
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Abu-Diab A, Gopalakrishnan P, Matsevich C, de Jong M, Obolensky A, Khalaileh A, Salameh M, Ejzenberg A, Gross M, Banin E, Sharon D, Khateb S. Homozygous Knockout of Cep250 Leads to a Relatively Late-Onset Retinal Degeneration and Sensorineural Hearing Loss in Mice. Transl Vis Sci Technol 2023; 12:3. [PMID: 36857066 PMCID: PMC9987170 DOI: 10.1167/tvst.12.3.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
Purpose Usher syndrome (USH) is the most common syndromic inherited retinal disease, causing retinitis pigmentosa and sensorineural hearing loss. We reported previously that a nonsense mutation in the centrosome-associated protein CEP250 gene (encoding C-Nap1) causes atypical USH in patients of Iranian Jewish origin. To better characterize CEP250, we aimed to generate and study a knockout (KO) mouse model for Cep250. Methods Mice heterozygous for a "knockout-first" Cep250 construct were generated and bred with Cre recombinase mice to generate the null allele and produce homozygous Cep250 KO mice. Retinal function was evaluated by full-field electroretinography (ffERG) at variable ages, and retinal structure changes were examined using histological analysis. Hearing thresholds were detected using auditory brainstem response (ABR) at the age of 20 months. Results The Cep250 KO mouse model was generated by activating a construct harboring a deletion of exons 6 and 7. At 6 months, the ffERG was normal, but it decreased gradually with age. For both photopic and scotopic ffERG responses, very low amplitudes were evident at 20 months. Histological analysis confirmed late-onset retinal degeneration. ABR tests illustrated that hearing threshold significantly increased at the age of 20 months. Conclusions Although most USH animal models have normal retinal function and structure, the Cep250 KO mouse model shows both retinal degeneration and hearing loss with a relatively late age of onset. This model may shed more light on CEP250-associated retinal and hearing deficits and represents an efficient platform for the development of treatment modalities for USH. Translational Relevance Our study demonstrates better understanding of Cep250-associated retinal and hearing disease in a mouse model and may help in developing more efficient gene therapy modalities.
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Affiliation(s)
- Alaa Abu-Diab
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Prakadeeswari Gopalakrishnan
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Chen Matsevich
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Marije de Jong
- Department of Otolaryngology, Head and Neck Surgery, Hadassah Hebrew-University Medical Center, Jerusalem, Israel
| | - Alexey Obolensky
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ayat Khalaileh
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Manar Salameh
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ayala Ejzenberg
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Menachem Gross
- Department of Otolaryngology, Head and Neck Surgery, Hadassah Hebrew-University Medical Center, Jerusalem, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Samer Khateb
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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11
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Clinical-genetic findings in a group of subjects with macular dystrophies due to mutations in rare inherited retinopathy genes. Graefes Arch Clin Exp Ophthalmol 2023; 261:353-365. [PMID: 35947183 DOI: 10.1007/s00417-022-05786-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 07/03/2022] [Accepted: 07/22/2022] [Indexed: 01/25/2023] Open
Abstract
PURPOSE To describe the results of clinical and molecular analyses in a group of patients suffering from inherited macular dystrophies, in which next-generation sequencing (NGS) efficiently detected rare causative mutations. METHODS A total of eight unrelated Mexican subjects with a clinical and multimodal imaging diagnosis of macular dystrophy were included. Visual assessment methods included best corrected visual acuity, color fundus photography, Goldmann visual field tests, kinetic perimetry, dark/light adapted chromatic perimetry, full-field electroretinography, autofluorescence imaging, and spectral domain-optical coherence tomography imaging. Genetic screening was performed by means of whole exome sequencing with subsequent Sanger sequencing validation of causal variants. RESULTS All patients exhibited a predominantly macular or cone-dominant disease. Patients' ages ranged from 12 to 60 years. Three cases had mutations in genes associated with autosomal dominant inheritance (UNC119 and PRPH2) while the remaining five cases had mutations in genes associated with autosomal recessive inheritance (CNGA3, POC1B, BEST1, CYP2U1, and PROM1). Of the total of 11 different pathogenic alleles identified, three were previously unreported disease-causing variants. CONCLUSIONS Macular dystrophies can be caused by defects in genes that are not routinely analyzed or not included in NGS gene panels. In this group of patients, whole exome sequencing efficiently detected rare genetic causes of hereditary maculopathies, and our findings contribute to expanding the current knowledge of the clinical and mutational spectrum associated with these disorders.
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12
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The Diagnostic Yield of Next Generation Sequencing in Inherited Retinal Diseases: A Systematic Review and Meta-analysis. Am J Ophthalmol 2022; 249:57-73. [PMID: 36592879 DOI: 10.1016/j.ajo.2022.12.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/16/2022] [Accepted: 12/23/2022] [Indexed: 01/01/2023]
Abstract
PURPOSE Accurate genotyping of individuals with inherited retinal diseases (IRD) is essential for patient management and identifying suitable candidates for gene therapies. This study evaluated the diagnostic yield of next generation sequencing (NGS) in IRDs. DESIGN Systematic review and meta-analysis. METHODS This systematic review was prospectively registered (CRD42021293619). Ovid MEDLINE and Ovid Embase were searched on 6 June 2022. Clinical studies evaluating the diagnostic yield of NGS in individuals with IRDs were eligible for inclusion. Risk of bias assessment was performed. Studies were pooled using a random...effects inverse variance model. Sources of heterogeneity were explored using stratified analysis, meta-regression, and sensitivity analysis. RESULTS This study included 105 publications from 28 countries. Most studies (90 studies) used targeted gene panels. The diagnostic yield of NGS was 61.3% (95% confidence interval: 57.8-64.7%; 51 studies) in mixed IRD phenotypes, 58.2% (51.6-64.6%; 41 studies) in rod-cone dystrophies, 57.7% (46.8-68.3%; eight studies) in macular and cone/cone-rod dystrophies, and 47.6% (95% CI: 41.0-54.3%; four studies) in familial exudative vitreoretinopathy. For mixed IRD phenotypes, a higher diagnostic yield was achieved pooling studies published between 2018-2022 (64.2% [59.5-68.7%]), studies using exome sequencing (73.5% [58.9-86.1%]), and studies using the American College of Medical Genetics variant interpretation standards (65.6% [60.8-70.4%]). CONCLUSION The current diagnostic yield of NGS in IRDs is between 52-74%. The certainty of the evidence was judged as low or very low. A key limitation of the current evidence is the significant heterogeneity between studies. Adoption of standardized reporting guidelines could improve confidence in future meta-analyses.
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13
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Soucy M, Tanaka AJ, Dharmadhikari A. Molecular Genetic Testing Approaches for Retinitis Pigmentosa. Methods Mol Biol 2022; 2560:41-66. [PMID: 36481882 DOI: 10.1007/978-1-0716-2651-1_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Retinitis pigmentosa (RP) affects approximately 1 in 4000 individuals. It has many different genetic etiologies and therefore diagnosis can be challenging. Understanding the different testing methodologies is beneficial for clinicians and researchers in order to select the best testing method, whether it be panel testing, whole exome sequencing, or whole genome sequencing for individuals affected with RP. The Methods section also outlines the steps required to complete a WES assay, which has become a popular method for identifying the molecular diagnosis for individuals with RP.
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Affiliation(s)
- Megan Soucy
- Columbia University Irving Medical Center, New York, NY, USA.
| | - Akemi Joy Tanaka
- Genetics and Genomics, Columbia University Irving Medical Center, New York, NY, USA
| | - Avinash Dharmadhikari
- Clinical Genomics, Department of Clinical Pathology, Children's Hospital Los Angeles, Los Angeles, CA, USA
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14
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A Novel Autosomal Recessive Variant of the NRL Gene Causing Enhanced S-Cone Syndrome: A Morpho-Functional Analysis of Two Unrelated Pediatric Patients. Diagnostics (Basel) 2022; 12:diagnostics12092183. [PMID: 36140584 PMCID: PMC9497687 DOI: 10.3390/diagnostics12092183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Enhanced S-cone syndrome (ESCS) is a rare autosomal recessive retinal degeneration mainly associated with pathogenic variations in the NR2E3 gene. Only a few pathogenic variations in the NRL gene associated with ESCS have been reported to date. Here, we describe the clinical and genetic findings of two unrelated pediatric patients with a novel frameshift homozygous variant in the NRL gene. Fundus examinations showed signs of peripheral degeneration in both patients, more severe in Proband 2, with relative sparing of the macular area. Spectral domain optical coherence tomography (SD-OCT) revealed a significant macular involvement with cysts in Proband 1, and minimal foveal alteration with peripheral retina involvement in Proband 2. Visual acuity was abnormal in both patients, but more severely affected in Proband 1 than Proband 2. The electroretinogram recordings showed reduced scotopic, mixed and single flash cone responses, with a typical supernormal S-cone response, meeting the criteria for a clinical diagnosis of ESCS in both patients. The present report expands the clinical and genetic spectrum of NRL-associated ESCS, and confirms the age-independent variability of phenotypic presentation already described in the NR2E3-associated ESCS.
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15
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The genetic and phenotypic landscapes of Usher syndrome: from disease mechanisms to a new classification. Hum Genet 2022; 141:709-735. [PMID: 35353227 PMCID: PMC9034986 DOI: 10.1007/s00439-022-02448-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 03/04/2022] [Indexed: 12/16/2022]
Abstract
Usher syndrome (USH) is the most common cause of deaf–blindness in humans, with a prevalence of about 1/10,000 (~ 400,000 people worldwide). Cochlear implants are currently used to reduce the burden of hearing loss in severe-to-profoundly deaf patients, but many promising treatments including gene, cell, and drug therapies to restore the native function of the inner ear and retinal sensory cells are under investigation. The traditional clinical classification of Usher syndrome defines three major subtypes—USH1, 2 and 3—according to hearing loss severity and onset, the presence or absence of vestibular dysfunction, and age at onset of retinitis pigmentosa. Pathogenic variants of nine USH genes have been initially reported: MYO7A, USH1C, PCDH15, CDH23, and USH1G for USH1, USH2A, ADGRV1, and WHRN for USH2, and CLRN1 for USH3. Based on the co-occurrence of hearing and vision deficits, the list of USH genes has been extended to few other genes, but with limited supporting information. A consensus on combined criteria for Usher syndrome is crucial for the development of accurate diagnosis and to improve patient management. In recent years, a wealth of information has been obtained concerning the properties of the Usher proteins, related molecular networks, potential genotype–phenotype correlations, and the pathogenic mechanisms underlying the impairment or loss of hearing, balance and vision. The advent of precision medicine calls for a clear and more precise diagnosis of Usher syndrome, exploiting all the existing data to develop a combined clinical/genetic/network/functional classification for Usher syndrome.
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16
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Lähteenoja L, Häkli S, Tuupanen S, Kuismin O, Palosaari T, Rahikkala E, Falck A. A novel frameshift variant in CEP78 associated with nonsyndromic retinitis pigmentosa, and a review of CEP78-related phenotypes. Ophthalmic Genet 2022; 43:152-158. [PMID: 35240912 DOI: 10.1080/13816810.2022.2045511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND Pathogenic variants in the CEP78 gene can present as atypical Usher syndrome or as retinitis pigmentosa. Here, we present a review of all reported cases of CEP78 variants in the literature to date and present a novel variant of CEP78, c.1261_1262delinsA, in a consanguineous northern Finnish family with two individuals. MATERIALS AND METHODS Our patients were first discovered in a registry-based study. Later, they gave their written consent for this study. In order to describe the genotype and phenotype, their historic clinical patient data and genetic data were gathered, and a clinical ophthalmic examination and an audiogram were performed. For this review, a PubMed search using the keyword CEP78 was carried out. The first article on CEP78 was published in the year 2007, and the publications from the years 2007-2021 were included. RESULTS A large gene panel identified a homozygous CEP78 c.1261_1262delinsA variant in two affected siblings. In addition to the classical signs of retinitis pigmentosa, both siblings had large round atrophic spots in the mid periphery, and hyperautofluorescence of the macula. Patient 1 had age-related hearing impairment; patient 2 had normal hearing. In total, 20 articles have been published about CEP78. Eight of these papers report patient data with the affected individuals typically having retinal dystrophy combined with sensorineural hearing impairment, classified as atypical Usher syndrome. CONCLUSIONS Here, we present a comprehensive review of CEP78 and expand the knowledge of pathogenic CEP78 variants and the phenotypic variety.
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Affiliation(s)
- Laura Lähteenoja
- Pedego Research Unit and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland.,Department of Clinical Genetics, Oulu University Hospital, Oulu, Finland.,Department of Ophthalmology, Oulu University Hospital, Oulu, Finland
| | - Sanna Häkli
- Pedego Research Unit and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland.,Department of Otorhinolaryngology, Oulu University Hospital, Oulu, Finland
| | | | - Outi Kuismin
- Pedego Research Unit and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland.,Department of Clinical Genetics, Oulu University Hospital, Oulu, Finland
| | - Tapani Palosaari
- Pedego Research Unit and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland.,Department of Ophthalmology, Oulu University Hospital, Oulu, Finland
| | - Elisa Rahikkala
- Pedego Research Unit and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland.,Department of Clinical Genetics, Oulu University Hospital, Oulu, Finland
| | - Aura Falck
- Pedego Research Unit and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland.,Department of Ophthalmology, Oulu University Hospital, Oulu, Finland
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Abstract
To gain a holistic understanding of cellular function, we must understand not just the role of individual organelles, but also how multiple macromolecular assemblies function collectively. Centrioles produce fundamental cellular processes through their ability to organise cytoskeletal fibres. In addition to nucleating microtubules, centrioles form lesser-known polymers, termed rootlets. Rootlets were identified over a 100 years ago and have been documented morphologically since by electron microscopy in different eukaryotic organisms. Rootlet-knockout animals have been created in various systems, providing insight into their physiological functions. However, the precise structure and function of rootlets is still enigmatic. Here, I consider common themes of rootlet function and assembly across diverse cellular systems. I suggest that the capability of rootlets to form physical links from centrioles to other cellular structures is a general principle unifying their functions in diverse cells and serves as an example of how cellular function arises from collective organellar activity. Summary: This Review discusses the structure and function of enigmatic cytoskeletal fibres termed centriolar rootlets, suggesting that they form physical links between subcellular structures to allow collective organelle function.
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Affiliation(s)
- Robert Mahen
- The Medical Research Council Cancer Unit, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK
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18
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Gonçalves AB, Hasselbalch SK, Joensen BB, Patzke S, Martens P, Ohlsen SK, Quinodoz M, Nikopoulos K, Suleiman R, Damsø Jeppesen MP, Weiss C, Christensen ST, Rivolta C, Andersen JS, Farinelli P, Pedersen LB. CEP78 functions downstream of CEP350 to control biogenesis of primary cilia by negatively regulating CP110 levels. eLife 2021; 10:63731. [PMID: 34259627 PMCID: PMC8354638 DOI: 10.7554/elife.63731] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 07/13/2021] [Indexed: 12/12/2022] Open
Abstract
CEP78 is a centrosomal protein implicated in ciliogenesis and ciliary length control, and mutations in the CEP78 gene cause retinal cone-rod dystrophy associated with hearing loss. However, the mechanism by which CEP78 affects cilia formation is unknown. Based on a recently discovered disease-causing CEP78 p.L150S mutation, we identified the disease-relevant interactome of CEP78. We confirmed that CEP78 interacts with the EDD1-DYRK2-DDB1VPRBP E3 ubiquitin ligase complex, which is involved in CP110 ubiquitination and degradation, and identified a novel interaction between CEP78 and CEP350 that is weakened by the CEP78L150S mutation. We show that CEP350 promotes centrosomal recruitment and stability of CEP78, which in turn leads to centrosomal recruitment of EDD1. Consistently, cells lacking CEP78 display significantly increased cellular and centrosomal levels of CP110, and depletion of CP110 in CEP78-deficient cells restored ciliation frequency to normal. We propose that CEP78 functions downstream of CEP350 to promote ciliogenesis by negatively regulating CP110 levels via an EDD1-dependent mechanism.
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Affiliation(s)
- André Brás Gonçalves
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Sarah Kirstine Hasselbalch
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Beinta Biskopstø Joensen
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Sebastian Patzke
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Pernille Martens
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Signe Krogh Ohlsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | | | - Reem Suleiman
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Magnus Per Damsø Jeppesen
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Catja Weiss
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Søren Tvorup Christensen
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Jens S Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Pietro Farinelli
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Lotte Bang Pedersen
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
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19
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Nassisi M, Smirnov VM, Solis Hernandez C, Mohand‐Saïd S, Condroyer C, Antonio A, Kühlewein L, Kempf M, Kohl S, Wissinger B, Nasser F, Ragi SD, Wang N, Sparrow JR, Greenstein VC, Michalakis S, Mahroo OA, Ba‐Abbad R, Michaelides M, Webster AR, Degli Esposti S, Saffren B, Capasso J, Levin A, Hauswirth WW, Dhaenens C, Defoort‐Dhellemmes S, Tsang SH, Zrenner E, Sahel J, Petersen‐Jones SM, Zeitz C, Audo I. CNGB1-related rod-cone dystrophy: A mutation review and update. Hum Mutat 2021; 42:641-666. [PMID: 33847019 PMCID: PMC8218941 DOI: 10.1002/humu.24205] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/26/2021] [Accepted: 04/08/2021] [Indexed: 12/29/2022]
Abstract
Cyclic nucleotide-gated channel β1 (CNGB1) encodes the 240-kDa β subunit of the rod photoreceptor cyclic nucleotide-gated ion channel. Disease-causing sequence variants in CNGB1 lead to autosomal recessive rod-cone dystrophy/retinitis pigmentosa (RP). We herein present a comprehensive review and analysis of all previously reported CNGB1 sequence variants, and add 22 novel variants, thereby enlarging the spectrum to 84 variants in total, including 24 missense variants (two of which may also affect splicing), 21 nonsense, 19 splicing defects (7 at noncanonical positions), 10 small deletions, 1 small insertion, 1 small insertion-deletion, 7 small duplications, and 1 gross deletion. According to the American College of Medical Genetics and Genomics classification criteria, 59 variants were considered pathogenic or likely pathogenic and 25 were variants of uncertain significance. In addition, we provide further phenotypic data from 34 CNGB1-related RP cases, which, overall, are in line with previous findings suggesting that this form of RP has long-term retention of useful central vision despite the early onset of night blindness, which is valuable for patient counseling, but also has implications for it being considered a priority target for gene therapy trials.
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Affiliation(s)
- Marco Nassisi
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
- Centre Hospitalier National d'Ophtalmologie des Quinze‐Vingts, INSERM‐DGOS CIC1423ParisFrance
- Department of Clinical Sciences and Community HealthUniversity of MilanMilanItaly
- Ophthalmological Unit, Fondazione IRCCS Ca' GrandaOspedale Maggiore PoliclinicoMilanItaly
| | - Vasily M. Smirnov
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
- Exploration de la vision et Neuro‐Ophthalmologie, CHU de LilleLilleFrance
- Faculté de MédecineUniversité de LilleLilleFrance
| | - Cyntia Solis Hernandez
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
| | - Saddek Mohand‐Saïd
- Centre Hospitalier National d'Ophtalmologie des Quinze‐Vingts, INSERM‐DGOS CIC1423ParisFrance
| | - Christel Condroyer
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
| | - Aline Antonio
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
| | - Laura Kühlewein
- University Eye Hospital, Centre for OphthalmologyUniversity of TübingenTübingenGermany
- Institute for Ophthalmic Research, Centre for OphthalmologyUniversity of TübingenTübingenGermany
| | - Melanie Kempf
- University Eye Hospital, Centre for OphthalmologyUniversity of TübingenTübingenGermany
| | - Susanne Kohl
- Institute for Ophthalmic Research, Centre for OphthalmologyUniversity of TübingenTübingenGermany
| | - Bernd Wissinger
- Institute for Ophthalmic Research, Centre for OphthalmologyUniversity of TübingenTübingenGermany
| | - Fadi Nasser
- University Eye Hospital, Centre for OphthalmologyUniversity of TübingenTübingenGermany
| | - Sara D. Ragi
- Department of OphthalmologyColumbia University, New YorkNew YorkUSA
| | - Nan‐Kai Wang
- Department of OphthalmologyColumbia University, New YorkNew YorkUSA
- College of MedicineChang Gung UniversityTaoyuanTaiwan
- Department of Ophthalmology, Chang Gung Memorial HospitalLinkou Medical CenterTaoyuanTaiwan
| | - Janet R. Sparrow
- Department of OphthalmologyColumbia University, New YorkNew YorkUSA
| | | | | | - Omar A. Mahroo
- Moorfields Eye HospitalLondonUK
- UCL Institute of Ophthalmology, University College LondonLondonUK
| | - Rola Ba‐Abbad
- Moorfields Eye HospitalLondonUK
- UCL Institute of Ophthalmology, University College LondonLondonUK
| | - Michel Michaelides
- Moorfields Eye HospitalLondonUK
- UCL Institute of Ophthalmology, University College LondonLondonUK
| | - Andrew R. Webster
- Moorfields Eye HospitalLondonUK
- UCL Institute of Ophthalmology, University College LondonLondonUK
| | - Simona Degli Esposti
- Moorfields Eye HospitalLondonUK
- UCL Institute of Ophthalmology, University College LondonLondonUK
| | - Brooke Saffren
- Philadelphia College of Osteopathic MedicinePhiladelphiaPennsylvaniaUSA
| | | | - Alex Levin
- Pediatric Ophthalmology and Ocular Genetics, Flaum Eye Institute, Pediatric Genetics, Golisano Children's HospitalUniversity of RochesterRochesterNew YorkUSA
| | | | - Claire‐Marie Dhaenens
- Univ. Lille, Inserm, CHU Lille, U1172‐LilNCog‐Lille Neuroscience & CognitionLilleFrance
| | | | - Stephen H. Tsang
- Department of OphthalmologyColumbia University, New YorkNew YorkUSA
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma LaboratoryNew YorkNew YorkUSA
- Department of Pathology and Cell BiologyColumbia UniversityNew YorkNew YorkUSA
- Stem Cell Initiative (CSCI), Institute of Human Nutrition, Vagelos College of Physicians and SurgeonsNew YorkNew YorkUSA
| | - Eberhart Zrenner
- University Eye Hospital, Centre for OphthalmologyUniversity of TübingenTübingenGermany
| | - Jose‐Alain Sahel
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
- Department of OphthalmologyThe University of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Fondation Ophtalmologique Adolphe de RothschildParisFrance
| | - Simon M. Petersen‐Jones
- Department of Small Animal Clinical SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Christina Zeitz
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
| | - Isabelle Audo
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
- Centre Hospitalier National d'Ophtalmologie des Quinze‐Vingts, INSERM‐DGOS CIC1423ParisFrance
- University College London Institute of OphthalmologyLondonUK
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20
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Next-Generation Sequencing Applications for Inherited Retinal Diseases. Int J Mol Sci 2021; 22:ijms22115684. [PMID: 34073611 PMCID: PMC8198572 DOI: 10.3390/ijms22115684] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 12/12/2022] Open
Abstract
Inherited retinal diseases (IRDs) represent a collection of phenotypically and genetically diverse conditions. IRDs phenotype(s) can be isolated to the eye or can involve multiple tissues. These conditions are associated with diverse forms of inheritance, and variants within the same gene often can be associated with multiple distinct phenotypes. Such aspects of the IRDs highlight the difficulty met when establishing a genetic diagnosis in patients. Here we provide an overview of cutting-edge next-generation sequencing techniques and strategies currently in use to maximise the effectivity of IRD gene screening. These techniques have helped researchers globally to find elusive causes of IRDs, including copy number variants, structural variants, new IRD genes and deep intronic variants, among others. Resolving a genetic diagnosis with thorough testing enables a more accurate diagnosis and more informed prognosis and should also provide information on inheritance patterns which may be of particular interest to patients of a child-bearing age. Given that IRDs are heritable conditions, genetic counselling may be offered to help inform family planning, carrier testing and prenatal screening. Additionally, a verified genetic diagnosis may enable access to appropriate clinical trials or approved medications that may be available for the condition.
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21
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Ascari G, Rendtorff ND, De Bruyne M, De Zaeytijd J, Van Lint M, Bauwens M, Van Heetvelde M, Arno G, Jacob J, Creytens D, Van Dorpe J, Van Laethem T, Rosseel T, De Pooter T, De Rijk P, De Coster W, Menten B, Rey AD, Strazisar M, Bertelsen M, Tranebjaerg L, De Baere E. Long-Read Sequencing to Unravel Complex Structural Variants of CEP78 Leading to Cone-Rod Dystrophy and Hearing Loss. Front Cell Dev Biol 2021; 9:664317. [PMID: 33968938 PMCID: PMC8097100 DOI: 10.3389/fcell.2021.664317] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/08/2021] [Indexed: 11/13/2022] Open
Abstract
Inactivating variants as well as a missense variant in the centrosomal CEP78 gene have been identified in autosomal recessive cone-rod dystrophy with hearing loss (CRDHL), a rare syndromic inherited retinal disease distinct from Usher syndrome. Apart from this, a complex structural variant (SV) implicating CEP78 has been reported in CRDHL. Here we aimed to expand the genetic architecture of typical CRDHL by the identification of complex SVs of the CEP78 region and characterization of their underlying mechanisms. Approaches used for the identification of the SVs are shallow whole-genome sequencing (sWGS) combined with quantitative polymerase chain reaction (PCR) and long-range PCR, or ExomeDepth analysis on whole-exome sequencing (WES) data. Targeted or whole-genome nanopore long-read sequencing (LRS) was used to delineate breakpoint junctions at the nucleotide level. For all SVs cases, the effect of the SVs on CEP78 expression was assessed using quantitative PCR on patient-derived RNA. Apart from two novel canonical CEP78 splice variants and a frameshifting single-nucleotide variant (SNV), two SVs affecting CEP78 were identified in three unrelated individuals with CRDHL: a heterozygous total gene deletion of 235 kb and a partial gene deletion of 15 kb in a heterozygous and homozygous state, respectively. Assessment of the molecular consequences of the SVs on patient's materials displayed a loss-of-function effect. Delineation and characterization of the 15-kb deletion using targeted LRS revealed the previously described complex CEP78 SV, suggestive of a recurrent genomic rearrangement. A founder haplotype was demonstrated for the latter SV in cases of Belgian and British origin, respectively. The novel 235-kb deletion was delineated using whole-genome LRS. Breakpoint analysis showed microhomology and pointed to a replication-based underlying mechanism. Moreover, data mining of bulk and single-cell human and mouse transcriptional datasets, together with CEP78 immunostaining on human retina, linked the CEP78 expression domain with its phenotypic manifestations. Overall, this study supports that the CEP78 locus is prone to distinct SVs and that SV analysis should be considered in a genetic workup of CRDHL. Finally, it demonstrated the power of sWGS and both targeted and whole-genome LRS in identifying and characterizing complex SVs in patients with ocular diseases.
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Affiliation(s)
- Giulia Ascari
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Nanna D Rendtorff
- The Kennedy Center, Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Marieke De Bruyne
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Julie De Zaeytijd
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
| | - Michel Van Lint
- Department of Ophthalmology, Antwerp University Hospital, Antwerp, Belgium
| | - Miriam Bauwens
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Mattias Van Heetvelde
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Gavin Arno
- Great Ormond Street Hospital, London, United Kingdom.,Moorfields Eye Hospital, London, United Kingdom.,UCL Institute of Ophthalmology, London, United Kingdom
| | - Julie Jacob
- Department of Ophthalmology, University Hospitals Leuven, Leuven, Belgium
| | - David Creytens
- Department of Pathology, Ghent University Hospital, Ghent, Belgium.,Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital, Ghent, Belgium.,Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Thalia Van Laethem
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Toon Rosseel
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Tim De Pooter
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Neuromics Support Facility, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Peter De Rijk
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Neuromics Support Facility, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Wouter De Coster
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Applied and Translational Neurogenomics Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Björn Menten
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Alfredo Dueñas Rey
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Mojca Strazisar
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Neuromics Support Facility, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Mette Bertelsen
- The Kennedy Center, Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Ophthalmology, Rigshospitalet-Glostrup, University of Copenhagen, Glostrup, Denmark
| | - Lisbeth Tranebjaerg
- The Kennedy Center, Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Elfride De Baere
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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22
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Duong Phu M, Bross S, Burkhalter MD, Philipp M. Limitations and opportunities in the pharmacotherapy of ciliopathies. Pharmacol Ther 2021; 225:107841. [PMID: 33771583 DOI: 10.1016/j.pharmthera.2021.107841] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/11/2021] [Indexed: 01/10/2023]
Abstract
Ciliopathies are a family of rather diverse conditions, which have been grouped based on the finding of altered or dysfunctional cilia, potentially motile, small cellular antennae extending from the surface of postmitotic cells. Cilia-related disorders include embryonically arising conditions such as Joubert, Usher or Kartagener syndrome, but also afflictions with a postnatal or even adult onset phenotype, i.e. autosomal dominant polycystic kidney disease. The majority of ciliopathies are syndromic rather than affecting only a single organ due to cilia being found on almost any cell in the human body. Overall ciliopathies are considered rare diseases. Despite that, pharmacological research and the strive to help these patients has led to enormous therapeutic advances in the last decade. In this review we discuss new treatment options for certain ciliopathies, give an outlook on promising future therapeutic strategies, but also highlight the limitations in the development of therapeutic approaches of ciliopathies.
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Affiliation(s)
- Max Duong Phu
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Section of Pharmacogenomics, Eberhard-Karls-University of Tübingen, 72074 Tübingen, Germany
| | - Stefan Bross
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Section of Pharmacogenomics, Eberhard-Karls-University of Tübingen, 72074 Tübingen, Germany
| | - Martin D Burkhalter
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Section of Pharmacogenomics, Eberhard-Karls-University of Tübingen, 72074 Tübingen, Germany
| | - Melanie Philipp
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Section of Pharmacogenomics, Eberhard-Karls-University of Tübingen, 72074 Tübingen, Germany.
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23
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Sánchez-Bellver L, Toulis V, Marfany G. On the Wrong Track: Alterations of Ciliary Transport in Inherited Retinal Dystrophies. Front Cell Dev Biol 2021; 9:623734. [PMID: 33748110 PMCID: PMC7973215 DOI: 10.3389/fcell.2021.623734] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/09/2021] [Indexed: 01/14/2023] Open
Abstract
Ciliopathies are a group of heterogeneous inherited disorders associated with dysfunction of the cilium, a ubiquitous microtubule-based organelle involved in a broad range of cellular functions. Most ciliopathies are syndromic, since several organs whose cells produce a cilium, such as the retina, cochlea or kidney, are affected by mutations in ciliary-related genes. In the retina, photoreceptor cells present a highly specialized neurosensory cilium, the outer segment, stacked with membranous disks where photoreception and phototransduction occurs. The daily renewal of the more distal disks is a unique characteristic of photoreceptor outer segments, resulting in an elevated protein demand. All components necessary for outer segment formation, maintenance and function have to be transported from the photoreceptor inner segment, where synthesis occurs, to the cilium. Therefore, efficient transport of selected proteins is critical for photoreceptor ciliogenesis and function, and any alteration in either cargo delivery to the cilium or intraciliary trafficking compromises photoreceptor survival and leads to retinal degeneration. To date, mutations in more than 100 ciliary genes have been associated with retinal dystrophies, accounting for almost 25% of these inherited rare diseases. Interestingly, not all mutations in ciliary genes that cause retinal degeneration are also involved in pleiotropic pathologies in other ciliated organs. Depending on the mutation, the same gene can cause syndromic or non-syndromic retinopathies, thus emphasizing the highly refined specialization of the photoreceptor neurosensory cilia, and raising the possibility of photoreceptor-specific molecular mechanisms underlying common ciliary functions such as ciliary transport. In this review, we will focus on ciliary transport in photoreceptor cells and discuss the molecular complexity underpinning retinal ciliopathies, with a special emphasis on ciliary genes that, when mutated, cause either syndromic or non-syndromic retinal ciliopathies.
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Affiliation(s)
- Laura Sánchez-Bellver
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
- Institute of Biomedicine (IBUB-IRSJD), Universitat de Barcelona, Barcelona, Spain
| | - Vasileios Toulis
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
- CIBERER, ISCIII, Universitat de Barcelona, Barcelona, Spain
| | - Gemma Marfany
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
- Institute of Biomedicine (IBUB-IRSJD), Universitat de Barcelona, Barcelona, Spain
- CIBERER, ISCIII, Universitat de Barcelona, Barcelona, Spain
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24
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Genetic and Clinical Findings in an Ethnically Diverse Cohort with Retinitis Pigmentosa Associated with Pathogenic Variants in CERKL. Genes (Basel) 2020; 11:genes11121497. [PMID: 33322828 PMCID: PMC7763961 DOI: 10.3390/genes11121497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 01/06/2023] Open
Abstract
Autosomal recessive retinitis pigmentosa is caused by mutations in over 40 genes, one of which is the ceramide kinase-like gene (CERKL). We present a case series of six patients from six unrelated families diagnosed with inherited retinal dystrophies (IRD) and with two variants in CERKL recruited from a multi-ethnic British population. A retrospective review of clinical data in these patients was performed and included colour fundus photography, fundus autofluorescence (AF) imaging, spectral domain–optical coherence tomography (SD–OCT), visual fields and electroretinogram (ERG) assessment where available. Three female and three male patients were included. Age at onset ranged from 7 years old to 45 years, with three presenting in their 20s and two presenting in their 40s. All but one had central visual loss as one of their main presenting symptoms. Four patients had features of retinitis pigmentosa with significant variation in severity and extent of disease, and two patients had no pigment deposition with only macular involvement clinically. Seven variants in CERKL were identified, of which three are novel. The inherited retinopathies associated with the CERKL gene vary in age at presentation and in degree of severity, but generally are characterised by a central visual impairment early on.
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25
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Alexander SP, Armstrong JF, Davenport AP, Davies JA, Faccenda E, Harding SD, Levi‐Schaffer F, Maguire JJ, Pawson AJ, Southan C, Spedding M. A rational roadmap for SARS-CoV-2/COVID-19 pharmacotherapeutic research and development: IUPHAR Review 29. Br J Pharmacol 2020; 177:4942-4966. [PMID: 32358833 PMCID: PMC7267163 DOI: 10.1111/bph.15094] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 12/13/2022] Open
Abstract
In this review, we identify opportunities for drug discovery in the treatment of COVID-19 and, in so doing, provide a rational roadmap whereby pharmacology and pharmacologists can mitigate against the global pandemic. We assess the scope for targeting key host and viral targets in the mid-term, by first screening these targets against drugs already licensed, an agenda for drug repurposing, which should allow rapid translation to clinical trials. A simultaneous, multi-pronged approach using conventional drug discovery methods aimed at discovering novel chemical and biological means of targeting a short list of host and viral entities which should extend the arsenal of anti-SARS-CoV-2 agents. This longer term strategy would provide a deeper pool of drug choices for future-proofing against acquired drug resistance. Second, there will be further viral threats, which will inevitably evade existing vaccines. This will require a coherent therapeutic strategy which pharmacology and pharmacologists are best placed to provide. LINKED ARTICLES: This article is part of a themed issue on The Pharmacology of COVID-19. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v177.21/issuetoc.
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Affiliation(s)
- Steve P.H. Alexander
- Chair, Nomenclature and Standards Committee of the International Union of Basic and Clinical Pharmacology (NC‐IUPHAR), School of Life SciencesUniversity of NottinghamNottinghamUK
| | - Jane F. Armstrong
- Curator, Guide to PHARMACOLOGY (GtoPdb), Deanery of Biomedical SciencesUniversity of EdinburghEdinburghUK
| | | | - Jamie A. Davies
- Principal Investigator, Guide to PHARMACOLOGY (GtoPdb), Executive Committee, NC‐IUPHAR, Deanery of Biomedical SciencesUniversity of EdinburghEdinburghUK
| | - Elena Faccenda
- Curator, Guide to PHARMACOLOGY (GtoPdb), Deanery of Biomedical SciencesUniversity of EdinburghEdinburghUK
| | - Simon D. Harding
- Database Developer, Guide to PHARMACOLOGY (GtoPdb), Deanery of Biomedical SciencesUniversity of EdinburghEdinburghUK
| | - Francesca Levi‐Schaffer
- First Vice‐President and Chair of Immunopharmacology Section, International Union of Basic and Clinical Pharmacology (IUPHAR)Hebrew University of JerusalemJerusalemIsrael
| | | | - Adam J. Pawson
- Senior Curator, Guide to PHARMACOLOGY (GtoPdb), Executive Committee, NC‐IUPHAR, Deanery of Biomedical SciencesUniversity of EdinburghEdinburghUK
| | - Christopher Southan
- Deanery of Biomedical SciencesUniversity of EdinburghEdinburghUK
- TW2Informatics LtdGothenburgSweden
| | - Michael Spedding
- Secretary‐General, International Union of Basic and Clinical Pharmacology (IUPHAR) and Spedding Research Solutions SASLe VesinetFrance
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26
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Nolen RM, Hufnagel RB, Friedman TB, Turriff AE, Brewer CC, Zalewski CK, King KA, Wafa TT, Griffith AJ, Brooks BP, Zein WM. Atypical and ultra-rare Usher syndrome: a review. Ophthalmic Genet 2020; 41:401-412. [PMID: 32372680 DOI: 10.1080/13816810.2020.1747090] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Usher syndrome has classically been described as a combination of hearing loss and rod-cone dystrophy; vestibular dysfunction is present in many patients. Three distinct clinical subtypes were documented in the late 1970s. Genotyping efforts have led to the identification of several genes associated with the disease. Recent literature has seen multiple publications referring to "atypical" Usher syndrome presentations. This manuscript reviews the molecular etiology of Usher syndrome, highlighting rare presentations and molecular causes. Reports of "atypical" disease are summarized noting the wide discrepancy in the spectrum of phenotypic deviations from the classical presentation. Guidelines for establishing a clear nomenclature system are suggested.
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Affiliation(s)
- Rosalie M Nolen
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health , Bethesda, MD, USA
| | - Robert B Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health , Bethesda, MD, USA
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health , Bethesda, MD, USA
| | - Amy E Turriff
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health , Bethesda, MD, USA
| | - Carmen C Brewer
- Otolaryngology Branch, National Institute of Deafness and Other Communication Disorders, National Institutes of Health , Bethesda, MD, USA
| | - Christopher K Zalewski
- Otolaryngology Branch, National Institute of Deafness and Other Communication Disorders, National Institutes of Health , Bethesda, MD, USA
| | - Kelly A King
- Otolaryngology Branch, National Institute of Deafness and Other Communication Disorders, National Institutes of Health , Bethesda, MD, USA
| | - Talah T Wafa
- Otolaryngology Branch, National Institute of Deafness and Other Communication Disorders, National Institutes of Health , Bethesda, MD, USA
| | - Andrew J Griffith
- Otolaryngology Branch, National Institute of Deafness and Other Communication Disorders, National Institutes of Health , Bethesda, MD, USA
| | - Brian P Brooks
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health , Bethesda, MD, USA
| | - Wadih M Zein
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health , Bethesda, MD, USA
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27
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Ascari G, Peelman F, Farinelli P, Rosseel T, Lambrechts N, Wunderlich KA, Wagner M, Nikopoulos K, Martens P, Balikova I, Derycke L, Holtappels G, Krysko O, Van Laethem T, De Jaegere S, Guillemyn B, De Rycke R, De Bleecker J, Creytens D, Van Dorpe J, Gerris J, Bachert C, Neuhofer C, Walraedt S, Bischoff A, Pedersen LB, Klopstock T, Rivolta C, Leroy BP, De Baere E, Coppieters F. Functional characterization of the first missense variant in CEP78, a founder allele associated with cone-rod dystrophy, hearing loss, and reduced male fertility. Hum Mutat 2020; 41:998-1011. [PMID: 31999394 PMCID: PMC7187288 DOI: 10.1002/humu.23993] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 12/27/2019] [Accepted: 01/16/2020] [Indexed: 12/19/2022]
Abstract
Inactivating variants in the centrosomal CEP78 gene have been found in cone-rod dystrophy with hearing loss (CRDHL), a particular phenotype distinct from Usher syndrome. Here, we identified and functionally characterized the first CEP78 missense variant c.449T>C, p.(Leu150Ser) in three CRDHL families. The variant was found in a biallelic state in two Belgian families and in a compound heterozygous state-in trans with c.1462-1G>T-in a third German family. Haplotype reconstruction showed a founder effect. Homology modeling revealed a detrimental effect of p.(Leu150Ser) on protein stability, which was corroborated in patients' fibroblasts. Elongated primary cilia without clear ultrastructural abnormalities in sperm or nasal brushes suggest impaired cilia assembly. Two affected males from different families displayed sperm abnormalities causing infertility. One of these is a heterozygous carrier of a complex allele in SPAG17, a ciliary gene previously associated with autosomal recessive male infertility. Taken together, our data indicate that a missense founder allele in CEP78 underlies the same sensorineural CRDHL phenotype previously associated with inactivating variants. Interestingly, the CEP78 phenotype has been possibly expanded with male infertility. Finally, CEP78 loss-of-function variants may have an underestimated role in misdiagnosed Usher syndrome, with or without sperm abnormalities.
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Affiliation(s)
- Giulia Ascari
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Frank Peelman
- Department of Medical Protein Research, Faculty of Medicine and Health Sciences, Flanders Institute for Biotechnology (VIB), Ghent University, Ghent, Belgium
| | - Pietro Farinelli
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Toon Rosseel
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Nina Lambrechts
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Kirsten A Wunderlich
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland.,Department of Physiological Genomics, BMC, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Matias Wagner
- Institute of Human Genetics, Faculty of Medicine, Technical University of Munich, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.,Institut für Neurogenomik, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Konstantinos Nikopoulos
- Oncogenomics laboratory, Department of Hematology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Pernille Martens
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Irina Balikova
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium.,Department of Ophthalmology, University Hospital Leuven, Leuven, Belgium
| | - Lara Derycke
- Upper Airways Research Laboratory, Department Otorhinolaryngology, Ghent University Hospital, Ghent, Belgium
| | - Gabriële Holtappels
- Upper Airways Research Laboratory, Department Otorhinolaryngology, Ghent University Hospital, Ghent, Belgium
| | - Olga Krysko
- Upper Airways Research Laboratory, Department Otorhinolaryngology, Ghent University Hospital, Ghent, Belgium
| | - Thalia Van Laethem
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Sarah De Jaegere
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Brecht Guillemyn
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Riet De Rycke
- Department of Biomedical Molecular Biology and Expertise Centre for Transmission Electron Microscopy, Ghent University, Ghent, Belgium.,VIB Center for Inflammation Research and BioImaging Core, VIB, Ghent, Belgium
| | - Jan De Bleecker
- Department of Neurology, Ghent University Hospital, Ghent, Belgium
| | - David Creytens
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Jan Gerris
- Department of Human Structure and Repair, Ghent University Hospital, Ghent, Belgium
| | - Claus Bachert
- Upper Airways Research Laboratory, Department Otorhinolaryngology, Ghent University Hospital, Ghent, Belgium
| | - Christiane Neuhofer
- Institute of Human Genetics, University Medical Center Göttingen (UMG), Göttingen, Germany
| | - Sophie Walraedt
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
| | - Almut Bischoff
- Department of Neurology, Friedrich-Baur-Institute, Ludwig-Maximilians-University, Munich, Germany
| | - Lotte B Pedersen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institute, Ludwig-Maximilians-University, Munich, Germany.,German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Carlo Rivolta
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland.,Clinical Research Center, Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University Hospital Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Bart P Leroy
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium.,Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium.,Division of Ophthalmology and Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Elfride De Baere
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Frauke Coppieters
- Department of Biomolecular Medicine, Center for Medical Genetics Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
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Yohe S, Sivasankar M, Ghosh A, Ghosh A, Holle J, Murugan S, Gupta R, Schimmenti LA, Vedam R, Thyagarajan B. Prevalence of mutations in inherited retinal diseases: A comparison between the United States and India. Mol Genet Genomic Med 2019; 8:e1081. [PMID: 31816670 PMCID: PMC7005662 DOI: 10.1002/mgg3.1081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 10/14/2019] [Accepted: 10/30/2019] [Indexed: 11/26/2022] Open
Abstract
Background Studies evaluating next‐generation sequencing (NGS) for retinal disorders may not reflect clinical practice. We report results of retrospective analysis of patients referred for clinical testing at two institutions (US and India). Methods This retrospective study of 131 patients who underwent clinically validated targeted NGS or exome sequencing for a wide variety of clinical phenotypes categorized results into a definitive, indeterminate, or negative molecular diagnosis. Results A definitive molecular diagnosis (52%) was more common in the India cohort (62% vs. 39%, p = .009), while an indeterminate molecular diagnosis occurred only in the US cohort (12%). In the US cohort, a lower diagnostic rate in Hispanic, non‐Caucasians (23%) was seen compared to Caucasians (57%). The India cohort had a high rate of homozygous variants (61%) and different frequency of genes involved compared to the US cohort. Conclusion Despite inherent limitations in clinical testing, the diagnostic rate across the two cohorts (52%) was similar to the 50%–65% diagnostic rate in the literature. However, the diagnostic rate was lower in the US cohort and appears partly explained by racial background. The high rate of consanguinity in the Indian population is reflected in the high rate of homozygosity for pathogenic mutations and may have implications for population level screening and genetic counseling. Clinical laboratories may note diagnostic rates that differ from the literature, due to factors such as heterogeneity in racial background or consanguinity rates in the populations being tested. This information may be useful for post‐test counseling.
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Affiliation(s)
- Sophia Yohe
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | | | | | | | - Jennifer Holle
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | | | | | - Lisa A Schimmenti
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | | | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
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29
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Zenteno JC, García-Montaño LA, Cruz-Aguilar M, Ronquillo J, Rodas-Serrano A, Aguilar-Castul L, Matsui R, Vencedor-Meraz CI, Arce-González R, Graue-Wiechers F, Gutiérrez-Paz M, Urrea-Victoria T, de Dios Cuadras U, Chacón-Camacho OF. Extensive genic and allelic heterogeneity underlying inherited retinal dystrophies in Mexican patients molecularly analyzed by next-generation sequencing. Mol Genet Genomic Med 2019; 8. [PMID: 31736247 PMCID: PMC6978239 DOI: 10.1002/mgg3.1044] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 10/23/2019] [Indexed: 12/27/2022] Open
Abstract
Background Retinal dystrophies (RDs) are one of the most genetically heterogeneous monogenic disorders with ~270 associated loci identified by early 2019. The recent application of next‐generation sequencing (NGS) has greatly improved the molecular diagnosis of RD patients. Genetic characterization of RD cohorts from different ethnic groups is justified, as it would improve the knowledge of molecular basis of the disease. Here, we present the results of genetic analysis in a large cohort of 143 unrelated Mexican subjects with a variety of RDs. Methods A targeted NGS approach covering 199 RD genes was employed for molecular screening of 143 unrelated patients. In addition to probands, 258 relatives were genotyped by Sanger sequencing for familial segregation of pathogenic variants. Results A solving rate of 66% (95/143) was achieved, with evidence of extensive loci (44 genes) and allelic (110 pathogenic variants) heterogeneity. Forty‐eight percent of the identified pathogenic variants were novel while ABCA4, CRB1, USH2A, and RPE65 carried the greatest number of alterations. Novel deleterious variants in IDH3B and ARL6 were identified, supporting their involvement in RD. Familial segregation of causal variants allowed the recognition of 124 autosomal or X‐linked carriers. Conclusion Our results illustrate the utility of NGS for genetic diagnosis of RDs of different populations for a better knowledge of the mutational landscape associated with the disease.
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Affiliation(s)
- Juan C Zenteno
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico.,Department of Biochemistry, Faculty of Medicine, UNAM, Mexico City, Mexico
| | | | - Marisa Cruz-Aguilar
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | - Josué Ronquillo
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | - Agustín Rodas-Serrano
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | | | - Rodrigo Matsui
- Department of Retina, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | | | - Rocío Arce-González
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | | | - Mario Gutiérrez-Paz
- Department of Retina, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | - Tatiana Urrea-Victoria
- Department of Retina, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | - Ulises de Dios Cuadras
- Department of Retina, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
| | - Oscar F Chacón-Camacho
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Mexico City, Mexico
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30
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Olson RJ, Hopp K, Wells H, Smith JM, Furtado J, Constans MM, Escobar DL, Geurts AM, Torres VE, Harris PC. Synergistic Genetic Interactions between Pkhd1 and Pkd1 Result in an ARPKD-Like Phenotype in Murine Models. J Am Soc Nephrol 2019; 30:2113-2127. [PMID: 31427367 PMCID: PMC6830782 DOI: 10.1681/asn.2019020150] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 07/12/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Autosomal recessive polycystic kidney disease (ARPKD) and autosomal dominant polycystic kidney disease (ADPKD) are genetically distinct, with ADPKD usually caused by the genes PKD1 or PKD2 (encoding polycystin-1 and polycystin-2, respectively) and ARPKD caused by PKHD1 (encoding fibrocystin/polyductin [FPC]). Primary cilia have been considered central to PKD pathogenesis due to protein localization and common cystic phenotypes in syndromic ciliopathies, but their relevance is questioned in the simple PKDs. ARPKD's mild phenotype in murine models versus in humans has hampered investigating its pathogenesis. METHODS To study the interaction between Pkhd1 and Pkd1, including dosage effects on the phenotype, we generated digenic mouse and rat models and characterized and compared digenic, monogenic, and wild-type phenotypes. RESULTS The genetic interaction was synergistic in both species, with digenic animals exhibiting phenotypes of rapidly progressive PKD and early lethality resembling classic ARPKD. Genetic interaction between Pkhd1 and Pkd1 depended on dosage in the digenic murine models, with no significant enhancement of the monogenic phenotype until a threshold of reduced expression at the second locus was breached. Pkhd1 loss did not alter expression, maturation, or localization of the ADPKD polycystin proteins, with no interaction detected between the ARPKD FPC protein and polycystins. RNA-seq analysis in the digenic and monogenic mouse models highlighted the ciliary compartment as a common dysregulated target, with enhanced ciliary expression and length changes in the digenic models. CONCLUSIONS These data indicate that FPC and the polycystins work independently, with separate disease-causing thresholds; however, a combined protein threshold triggers the synergistic, cystogenic response because of enhanced dysregulation of primary cilia. These insights into pathogenesis highlight possible common therapeutic targets.
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Affiliation(s)
- Rory J Olson
- Department of Biochemistry and Molecular Biology, Mayo Graduate School of Biomedical Sciences, Rochester, Minnesota
| | - Katharina Hopp
- Division of Renal Diseases and Hypertension, University of Colorado, Denver, Colorado
| | - Harrison Wells
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Jessica M Smith
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Jessica Furtado
- Department of Biochemistry and Molecular Biology, Mayo Graduate School of Biomedical Sciences, Rochester, Minnesota
- Biological and Biomedical Sciences Program, Yale University School of Medicine, New Haven, Connecticut; and
| | - Megan M Constans
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Diana L Escobar
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Aron M Geurts
- Gene Editing Rat Resource Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Vicente E Torres
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Peter C Harris
- Department of Biochemistry and Molecular Biology, Mayo Graduate School of Biomedical Sciences, Rochester, Minnesota;
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
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31
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Huang XF, Xiang L, Fang XL, Liu WQ, Zhuang YY, Chen ZJ, Shen RJ, Cheng W, Han RY, Zheng SS, Chen XJ, Liu X, Jin ZB. Functional characterization of CEP250 variant identified in nonsyndromic retinitis pigmentosa. Hum Mutat 2019; 40:1039-1045. [PMID: 30998843 DOI: 10.1002/humu.23759] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 03/16/2019] [Accepted: 04/02/2019] [Indexed: 12/29/2022]
Abstract
Retinitis pigmentosa (RP) is the most common manifestation of inherited retinal diseases with high degree of genetic, allelic, and phenotypic heterogeneity. CEP250 encodes the C-Nap1 protein and has been associated with various retinal phenotypes. Here, we report the identification of a mutation (c.562C>T, p.R188*) in the CEP250 in a consanguineous family with nonsyndromic RP. To gain insights into the molecular pathomechanism underlying CEP250 defects and the functional relevance of CEP250 variants in humans, we conducted a functional characterization of CEP250 variant using a novel Cep250 knockin mouse line. Remarkably, the disruption of Cep250 resulted in severe impairment of retinal function and significant retinal morphological alterations. The homozygous knockin mice showed significantly reduced retinal thickness and ERG responses. This study not only broadens the spectrum of phenotypes associated with CEP250 mutations, but also, for the first time, elucidates the function of CEP250 in photoreceptors using a newly established animal model.
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Affiliation(s)
- Xiu-Feng Huang
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Lue Xiang
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Xiao-Long Fang
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Wei-Qin Liu
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - You-Yuan Zhuang
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Zhen-Ji Chen
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Ren-Juan Shen
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Wan Cheng
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Ru-Yi Han
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Si-Si Zheng
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Xue-Jiao Chen
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Xiaoling Liu
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
- Department of Medical Retina, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Zi-Bing Jin
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Vision Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
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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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33
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Compound heterozygous splice site variants in the SCLT1 gene highlight an additional candidate locus for Senior-Løken syndrome. Sci Rep 2018; 8:16733. [PMID: 30425282 PMCID: PMC6233217 DOI: 10.1038/s41598-018-35152-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/29/2018] [Indexed: 12/19/2022] Open
Abstract
Senior Løken syndrome (SLS) is a heterogeneous disorder characterized by severe retinal degenerations and juvenile-onset nephronophthisis. Genetic variants in ten different genes have been reported as the causes of SLS. Clinical evaluation of a patient with SLS and her unaffected parents revealed that the patient had infantile-onset retinal dystrophy and juvenile-onset nephronophthisis. Other systemic abnormalities included hepatic dysfunction, megacystis, mild learning disability, autism, obesity, and hyperinsulinemia. Whole-exome sequencing identified compound heterozygous SCLT1 variants (c.1218 + 3insT and c.1631A > G) in the patient. The unaffected parents were heterozygous for each variant. Transcript analysis using reverse transcription PCR demonstrated that the c.1218 + 3insT variant leads to exon 14 skipping (p.V383_M406del), while the other variant (c.1631A > G) primarily leads to exon 17 skipping (p.D480EfsX11) as well as minor amounts of two transcripts (6 bps deletion in the last of exon 17 [p.V543_K544del] and exons 17 and 18 skipping [p.D480E, S481_K610del]). Immunohistochemical analysis demonstrated that the Sclt1 protein was localized to the distal appendage of the photoreceptor basal body, indicating a ciliary protein. In conclusion, we identified compound heterozygous splice site variants of SCLT1 in a patient with a new form of ciliopathies that exhibits clinical features of SLS.
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34
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Hearn T. ALMS1 and Alström syndrome: a recessive form of metabolic, neurosensory and cardiac deficits. J Mol Med (Berl) 2018; 97:1-17. [PMID: 30421101 PMCID: PMC6327082 DOI: 10.1007/s00109-018-1714-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/25/2018] [Accepted: 10/30/2018] [Indexed: 12/12/2022]
Abstract
Alström syndrome (AS) is characterised by metabolic deficits, retinal dystrophy, sensorineural hearing loss, dilated cardiomyopathy and multi-organ fibrosis. Elucidating the function of the mutated gene, ALMS1, is critical for the development of specific treatments and may uncover pathways relevant to a range of other disorders including common forms of obesity and type 2 diabetes. Interest in ALMS1 is heightened by the recent discovery of its involvement in neonatal cardiomyocyte cell cycle arrest, a process with potential relevance to regenerative medicine. ALMS1 encodes a ~ 0.5 megadalton protein that localises to the base of centrioles. Some studies have suggested a role for this protein in maintaining centriole-nucleated sensory organelles termed primary cilia, and AS is now considered to belong to the growing class of human genetic disorders linked to ciliary dysfunction (ciliopathies). However, mechanistic details are lacking, and recent studies have implicated ALMS1 in several processes including endosomal trafficking, actin organisation, maintenance of centrosome cohesion and transcription. In line with a more complex picture, multiple isoforms of the protein likely exist and non-centrosomal sites of localisation have been reported. This review outlines the evidence for both ciliary and extra-ciliary functions of ALMS1.
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Affiliation(s)
- Tom Hearn
- Institute of Life Science, Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK.
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Kubota D, Gocho K, Kikuchi S, Akeo K, Miura M, Yamaki K, Takahashi H, Kameya S. CEP250 mutations associated with mild cone-rod dystrophy and sensorineural hearing loss in a Japanese family. Ophthalmic Genet 2018; 39:500-507. [PMID: 29718797 DOI: 10.1080/13816810.2018.1466338] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 04/13/2018] [Accepted: 04/15/2018] [Indexed: 10/17/2022]
Abstract
BACKGROUND CEP250 encodes the C-Nap1 protein which belongs to the CEP family of proteins. C-Nap1 has been reported to be expressed in the photoreceptor cilia and is known to interact with other ciliary proteins. Mutations of CEP250 cause atypical Usher syndrome which is characterized by early-onset sensorineural hearing loss (SNHL) and a relatively mild retinitis pigmentosa. This study tested the hypothesis that the mild cone-rod dystrophy (CRD) and SNHL in a non-consanguineous Japanese family was caused by CEP250 mutations. METHODS Detailed ophthalmic and auditory examinations were performed on the proband and her family members. Whole exome sequencing (WES) was used on the DNA obtained from the proband. RESULTS Electrophysiological analysis revealed a mild CRD in two family members. Adaptive optics (AO) imaging showed reduced cone density around the fovea. Auditory examinations showed a slight SNHL in both patients. WES of the proband identified compound heterozygous variants c.361C>T, p.R121*, and c.562C>T, p.R188* in CEP250. The variants were found to co-segregate with the disease in five members of the family. CONCLUSIONS The variants of CEP250 are both null variants and according to American College of Medical Genetics and Genomics (ACMG) standards and guideline, these variants are classified into the very strong category (PVS1). The criteria for both alleles will be pathogenic. Our data indicate that mutations of CEP250 can cause mild CRD and SNHL in Japanese patients. Because the ophthalmological phenotypes were very mild, high-resolution retinal imaging analysis, such as AO, will be helpful in diagnosing CEP250-associated disease.
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Affiliation(s)
- Daiki Kubota
- a Department of Ophthalmology , Nippon Medical School Chiba Hokusoh Hospital , Inzai , Japan
| | - Kiyoko Gocho
- a Department of Ophthalmology , Nippon Medical School Chiba Hokusoh Hospital , Inzai , Japan
| | - Sachiko Kikuchi
- a Department of Ophthalmology , Nippon Medical School Chiba Hokusoh Hospital , Inzai , Japan
| | - Keiichiro Akeo
- a Department of Ophthalmology , Nippon Medical School Chiba Hokusoh Hospital , Inzai , Japan
| | - Masahiro Miura
- b Department of Ophthalmology , Tokyo Medical University, Ibaraki Medical Center , Ibaraki , Japan
| | - Kunihiko Yamaki
- a Department of Ophthalmology , Nippon Medical School Chiba Hokusoh Hospital , Inzai , Japan
| | - Hiroshi Takahashi
- c Department of Ophthalmology , Nippon Medical School , Bunkyo-ku , Japan
| | - Shuhei Kameya
- a Department of Ophthalmology , Nippon Medical School Chiba Hokusoh Hospital , Inzai , Japan
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Aradhya S, Nussbaum RL. Genetics in mainstream medicine: Finally within grasp to influence healthcare globally. Mol Genet Genomic Med 2018; 6:473-480. [PMID: 29807392 PMCID: PMC6081234 DOI: 10.1002/mgg3.415] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 04/24/2018] [Indexed: 01/02/2023] Open
Abstract
A modern genomics ecosystem has emerged. This commentary describes recent trends in clinical genomics that enable its successful integration in mainstream medicine. The rapid expansion of clinical genomics will have a positive impact on the healthcare of individuals worldwide.
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Affiliation(s)
- Swaroop Aradhya
- InvitaeSan FranciscoCalifornia
- Adjunct clinical associate professorStanford University School of MedicineStanfordCalifornia
| | - Robert L. Nussbaum
- InvitaeSan FranciscoCalifornia
- Volunteer facultyUniversity of California San FranciscoSan FranciscoCalifornia
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de Castro-Miró M, Tonda R, Marfany G, Casaroli-Marano RP, Gonzàlez-Duarte R. Novel mutation in the choroideremia gene and multi-Mendelian phenotypes in Spanish families. Br J Ophthalmol 2018; 102:1378-1386. [DOI: 10.1136/bjophthalmol-2017-311427] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 12/20/2017] [Accepted: 12/30/2017] [Indexed: 11/04/2022]
Abstract
AimsWe aimed to accurately diagnose several retinitis pigmentosa (RP) patients with complex ocular phenotypes by combining massive sequencing genetic diagnosis and powerful clinical imaging techniques.MethodsWhole-exome sequencing (WES) of selected patients from two RP families was undertaken. The variants identified were validated by Sanger sequencing and cosegregation analysis. Accurate clinical re-evaluation was performed using electrophysiological and visual field records as well as non-invasive imaging techniques, such as swept-source optical coherence tomography and fundus autofluorescence.ResultsThe WES results highlighted one novel and one reported causative mutations in the X-linked choroideremia gene (CHM), which challenged the initial RP diagnosis. Subsequent clinical re-evaluation confirmed the choroideremia diagnosis. Carrier females showed different degrees of affectation, even between twin sisters, probably due to lyonization. A severe multi-Mendelian phenotype was associated with coincidental dominant pathogenic mutations in two additional genes: PAX6 and PDE6B.ConclusionsGenetic diagnosis via massive sequencing is instrumental in identifying causative mutations in retinal dystrophies and additional genetic variants with an impact on the phenotype. Multi-Mendelian phenotypes previously ascribed to rare syndromes can thus be dissected and molecularly diagnosed. Overall, the combination of powerful genetic diagnosis and clinical non-invasive imaging techniques enables efficient management of patients and their prioritisation for gene-specific therapies.
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Farrar GJ, Carrigan M, Dockery A, Millington-Ward S, Palfi A, Chadderton N, Humphries M, Kiang AS, Kenna PF, Humphries P. Toward an elucidation of the molecular genetics of inherited retinal degenerations. Hum Mol Genet 2017; 26:R2-R11. [PMID: 28510639 PMCID: PMC5886474 DOI: 10.1093/hmg/ddx185] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 05/08/2017] [Indexed: 02/06/2023] Open
Abstract
While individually classed as rare diseases, hereditary retinal degenerations (IRDs) are the major cause of registered visual handicap in the developed world. Given their hereditary nature, some degree of intergenic heterogeneity was expected, with genes segregating in autosomal dominant, recessive, X-linked recessive, and more rarely in digenic or mitochondrial modes. Today, it is recognized that IRDs, as a group, represent one of the most genetically diverse of hereditary conditions - at least 260 genes having been implicated, with 70 genes identified in the most common IRD, retinitis pigmentosa (RP). However, targeted sequencing studies of exons from known IRD genes have resulted in the identification of candidate mutations in only approximately 60% of IRD cases. Given recent advances in the development of gene-based medicines, characterization of IRD patient cohorts for known IRD genes and elucidation of the molecular pathologies of disease in those remaining unresolved cases has become an endeavor of the highest priority. Here, we provide an outline of progress in this area.
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Affiliation(s)
- G Jane Farrar
- Institute of Genetics, School of Genetics and Microbiology, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Matthew Carrigan
- Institute of Genetics, School of Genetics and Microbiology, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Adrian Dockery
- Institute of Genetics, School of Genetics and Microbiology, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Sophia Millington-Ward
- Institute of Genetics, School of Genetics and Microbiology, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Arpad Palfi
- Institute of Genetics, School of Genetics and Microbiology, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Naomi Chadderton
- Institute of Genetics, School of Genetics and Microbiology, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Marian Humphries
- Institute of Genetics, School of Genetics and Microbiology, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Anna Sophia Kiang
- Institute of Genetics, School of Genetics and Microbiology, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Paul F Kenna
- Research Foundation, Royal Victoria Eye and Ear Hospital, Dublin 2, Ireland
| | - Pete Humphries
- Institute of Genetics, School of Genetics and Microbiology, University of Dublin, Trinity College, Dublin 2, Ireland
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Target 5000: Target Capture Sequencing for Inherited Retinal Degenerations. Genes (Basel) 2017; 8:genes8110304. [PMID: 29099798 PMCID: PMC5704217 DOI: 10.3390/genes8110304] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 10/23/2017] [Accepted: 10/27/2017] [Indexed: 01/02/2023] Open
Abstract
There are an estimated 5000 people in Ireland who currently have an inherited retinal degeneration (IRD). It is the goal of this study, through genetic diagnosis, to better enable these 5000 individuals to obtain a clearer understanding of their condition and improved access to potentially applicable therapies. Here we show the current findings of a target capture next-generation sequencing study of over 750 patients from over 520 pedigrees currently situated in Ireland. We also demonstrate how processes can be implemented to retrospectively analyse patient datasets for the detection of structural variants in previously obtained sequencing reads. Pathogenic or likely pathogenic mutations were detected in 68% of pedigrees tested. We report nearly 30 novel mutations including three large structural variants. The population statistics related to our findings are presented by condition and credited to their respective candidate gene mutations. Rediagnosis rates of clinical phenotypes after genotyping are discussed. Possible causes of failure to detect a candidate mutation are evaluated. Future elements of this project, with a specific emphasis on structural variants and non-coding pathogenic variants, are expected to increase detection rates further and thereby produce an even more comprehensive representation of the genetic landscape of IRDs in Ireland.
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Chacón-Camacho OF, García-Montaño LA, Zenteno JC. The clinical implications of molecular monitoring and analyses of inherited retinal diseases. Expert Rev Mol Diagn 2017; 17:1009-1021. [DOI: 10.1080/14737159.2017.1384314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Oscar F. Chacón-Camacho
- Genetics Department-research Unit, Institute of Ophthalmology ‘Conde de Valenciana’, Mexico City, Mexico
| | - Leopoldo A. García-Montaño
- Genetics Department-research Unit, Institute of Ophthalmology ‘Conde de Valenciana’, Mexico City, Mexico
| | - Juan C Zenteno
- Genetics Department-research Unit, Institute of Ophthalmology ‘Conde de Valenciana’, Mexico City, Mexico
- Biochemistry Department, Faculty of Medicine, UNAM, Mexico City, Mexico
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