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Trastulli G, Megalizzi D, Calvino G, Andreucci S, Zampatti S, Strafella C, Caltagirone C, Giardina E, Cascella R. RHO Variants and Autosomal Dominant Retinitis Pigmentosa: Insights from the Italian Genetic Landscape. Genes (Basel) 2024; 15:1158. [PMID: 39336749 PMCID: PMC11431160 DOI: 10.3390/genes15091158] [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: 08/01/2024] [Revised: 08/26/2024] [Accepted: 08/30/2024] [Indexed: 09/30/2024] Open
Abstract
Autosomal dominant retinitis pigmentosa (AD-RP) is caused by several genes, among which RHO is one of the most investigated. This article will be focused on RHO and its role in explaining AD-RP cases in the Italian population, taking advantage of the experience of the Genomic Medicine Laboratory UILDM at the Santa Lucia Foundation IRCCS. The retrospective evaluation of the distribution of RHO variants in the Italian patients with a clinical suspicion of RP pointed out eight variants. Of them, four variants (c.632A>T, c.1040C>T, c.1030C>T, c.383_392del) were pathogenic and made it possible to confirm the diagnosis of AD-RP in nine affected patients, highlighting a lower frequency (17%) of RHO variants compared to previous studies (30-40%). In addition, this study identified four variants classified as Variants of Uncertain Significance (VUS). In conclusion, the experience of the Genomic Medicine Laboratory provides an overview of the distribution of RHO variants in the Italian population, highlighting a slightly lower frequency of these variants in our cases series compared to previous reports. However, further studies on RHO variants are essential to characterize peculiar RP phenotypes and extend the spectrum of disease associated with this gene.
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Affiliation(s)
- Giulia Trastulli
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, 00179 Rome, Italy
- Department of Systems Medicine, Tor Vergata University, 00133 Rome, Italy
| | - Domenica Megalizzi
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, 00179 Rome, Italy
- Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy
| | - Giulia Calvino
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, 00179 Rome, Italy
- Department of Science, Roma Tre University, 00146 Rome, Italy
| | - Sarah Andreucci
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, 00179 Rome, Italy
| | - Stefania Zampatti
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, 00179 Rome, Italy
| | - Claudia Strafella
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, 00179 Rome, Italy
| | - Carlo Caltagirone
- Department of Clinical and Behavioral Neurology, IRCCS Fondazione Santa Lucia, 00179 Rome, Italy
| | - Emiliano Giardina
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, 00179 Rome, Italy
- Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy
| | - Raffaella Cascella
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, 00179 Rome, Italy
- Department of Chemical-Toxicological and Pharmacological Evaluation of Drugs, Catholic University Our Lady of Good Counsel, 1010 Tirana, Albania
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2
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Zufiaurre-Seijo M, García-Arumí J, Duarri A. Clinical and Molecular Aspects of C2orf71/PCARE in Retinal Diseases. Int J Mol Sci 2023; 24:10670. [PMID: 37445847 DOI: 10.3390/ijms241310670] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Mutations in the photoreceptor-specific C2orf71 gene (also known as photoreceptor cilium actin regulator protein PCARE) cause autosomal recessive retinitis pigmentosa type 54 and cone-rod dystrophy. No treatments are available for patients with C2orf71 retinal ciliopathies exhibiting a severe clinical phenotype. Our understanding of the disease process and the role of PCARE in the healthy retina significantly limits our capacity to transfer recent technical developments into viable therapy choices. This study summarizes the current understanding of C2orf71-related retinal diseases, including their clinical manifestations and an unclear genotype-phenotype correlation. It discusses molecular and functional studies on the photoreceptor-specific ciliary PCARE, focusing on the photoreceptor cell and its ciliary axoneme. It is proposed that PCARE is an actin-associated protein that interacts with WASF3 to regulate the actin-driven expansion of the ciliary membrane during the development of a new outer segment disk in photoreceptor cells. This review also introduces various cellular and animal models used to model these diseases and provides an overview of potential treatments.
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Affiliation(s)
- Maddalen Zufiaurre-Seijo
- Ophthalmology Research Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, 08035 Barcelona, Spain
| | - José García-Arumí
- Ophthalmology Research Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, 08035 Barcelona, Spain
| | - Anna Duarri
- Ophthalmology Research Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, 08035 Barcelona, Spain
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3
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Cremers FPM, Lee W, Collin RWJ, Allikmets R. Clinical spectrum, genetic complexity and therapeutic approaches for retinal disease caused by ABCA4 mutations. Prog Retin Eye Res 2020; 79:100861. [PMID: 32278709 PMCID: PMC7544654 DOI: 10.1016/j.preteyeres.2020.100861] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/13/2020] [Accepted: 03/18/2020] [Indexed: 12/18/2022]
Abstract
The ABCA4 protein (then called a “rim protein”) was first
identified in 1978 in the rims and incisures of rod photoreceptors. The
corresponding gene, ABCA4, was cloned in 1997, and variants
were identified as the cause of autosomal recessive Stargardt disease (STGD1).
Over the next two decades, variation in ABCA4 has been
attributed to phenotypes other than the classically defined STGD1 or fundus
flavimaculatus, ranging from early onset and fast progressing cone-rod dystrophy
and retinitis pigmentosa-like phenotypes to very late onset cases of mostly mild
disease sometimes resembling, and confused with, age-related macular
degeneration. Similarly, analysis of the ABCA4 locus uncovered
a trove of genetic information, including >1200 disease-causing mutations
of varying severity, and of all types – missense, nonsense, small
deletions/insertions, and splicing affecting variants, of which many are located
deep-intronic. Altogether, this has greatly expanded our understanding of
complexity not only of the diseases caused by ABCA4 mutations,
but of all Mendelian diseases in general. This review provides an in depth
assessment of the cumulative knowledge of ABCA4-associated retinopathy –
clinical manifestations, genetic complexity, pathophysiology as well as current
and proposed therapeutic approaches.
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Affiliation(s)
- Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, PO Box 9104, 6500 HE, Nijmegen, the Netherlands.
| | - Winston Lee
- Department of Ophthalmology, Columbia University, New York, NY, 10032, USA; Department of Genetics & Development, Columbia University, New York, NY, 10032, USA
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, PO Box 9104, 6500 HE, Nijmegen, the Netherlands
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, NY, 10032, USA; Department of Pathology & Cell Biology, Columbia University, New York, NY, 10032, USA.
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Charbel Issa P, Reuter P, Kühlewein L, Birtel J, Gliem M, Tropitzsch A, Whitcroft KL, Bolz HJ, Ishihara K, MacLaren RE, Downes SM, Oishi A, Zrenner E, Kohl S, Hummel T. Olfactory Dysfunction in Patients With CNGB1-Associated Retinitis Pigmentosa. JAMA Ophthalmol 2019; 136:761-769. [PMID: 29800053 DOI: 10.1001/jamaophthalmol.2018.1621] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Importance Co-occurrence of retinitis pigmentosa (RP) and olfactory dysfunction may have a common genetic cause. Objective To report olfactory function and the retinal phenotype in patients with biallelic mutations in CNGB1, a gene coding for a signal transduction channel subunit expressed in rod photoreceptors and olfactory sensory neurons. Design, Setting, and Participants This case series was conducted from August 2015 through July 2017. The setting was a multicenter study involving 4 tertiary referral centers for inherited retinal dystrophies. Participants were 9 patients with CNGB1-associated RP. Main Outcomes and Measures Results of olfactory testing, ocular phenotyping, and molecular genetic testing using targeted next-generation sequencing. Results Nine patients were included in the study, 3 of whom were female. Their ages ranged between 34 and 79 years. All patients had an early onset of night blindness but were usually not diagnosed as having RP before the fourth decade because of slow retinal degeneration. Retinal features were characteristic of a rod-cone dystrophy. Olfactory testing revealed reduced or absent olfactory function, with all except one patient scoring in the lowest quartile in relation to age-related norms. Brain magnetic resonance imaging and electroencephalography measurements in response to olfactory stimulation were available for 1 patient and revealed no visible olfactory bulbs and reduced responses to odor, respectively. Molecular genetic testing identified 5 novel (c.1312C>T, c.2210G>A, c.2492+1G>A, c.2763C>G, and c.3044_3050delGGAAATC) and 5 previously reported mutations in CNGB1. Conclusions and Relevance Mutations in CNGB1 may cause an autosomal recessive RP-olfactory dysfunction syndrome characterized by a slow progression of retinal degeneration and variable anosmia or hyposmia.
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Affiliation(s)
- Peter Charbel Issa
- Oxford Eye Hospital, Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom.,Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom.,Department of Ophthalmology, University of Bonn, Bonn, Germany
| | - Peggy Reuter
- Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Laura Kühlewein
- Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Johannes Birtel
- Department of Ophthalmology, University of Bonn, Bonn, Germany
| | - Martin Gliem
- Oxford Eye Hospital, Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom.,Department of Ophthalmology, University of Bonn, Bonn, Germany
| | - Anke Tropitzsch
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Tübingen, Tübingen, Germany
| | - Katherine L Whitcroft
- University College London (UCL) Ear Institute and Royal National Throat, Nose and Ear Hospital, London, United Kingdom.,Centre for the Study of the Senses, Institute of Philosophy, School of Advanced Study, University of London, London, United Kingdom.,Smell and Taste Clinic, Department of Otorhinolaryngology-Head and Neck Surgery, Technische Universität Dresden, Dresden, Germany
| | - Hanno J Bolz
- Bioscientia Center for Human Genetics, Ingelheim, Germany.,Institute of Human Genetics, University Hospital of Cologne, Cologne, Germany
| | - Kenji Ishihara
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Robert E MacLaren
- Oxford Eye Hospital, Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom.,Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Susan M Downes
- Oxford Eye Hospital, Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom.,Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Akio Oishi
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Eberhart Zrenner
- Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Susanne Kohl
- Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Thomas Hummel
- Smell and Taste Clinic, Department of Otorhinolaryngology-Head and Neck Surgery, Technische Universität Dresden, Dresden, Germany
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5
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Wang H, Tong Z, Li J, Xiao K, Ren F, Xie L. Genetic variants in Forkhead box O1 associated with predisposition to sepsis in a Chinese Han population. BMC Infect Dis 2019; 19:781. [PMID: 31492105 PMCID: PMC6731606 DOI: 10.1186/s12879-019-4330-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 07/29/2019] [Indexed: 12/02/2022] Open
Abstract
Background Genetic variant is one of the causes of sepsis patients’ mortality. Now, many studies have identified several SNPs related to sepsis. However, none of these studies were identified in a genome-wide way. We aimed to detect genetic polymorphisms of sepsis patients. Methods The blood samples of eight normal controls and ten sepsis patients were collected for whole exome sequencing. Then, Single Nucleotide Polymorphisms (SNPs) were selected according to quality score and number of sepsis patients who had this variants. Synonymous mutations were removed. Genes including these remaining variants were used for functional analyses. After analyses, the remaining SNPs and indels were validated in 149 normal controls and 156 sepsis patients. Finally, serum levels of proteins coded by genes including these SNPs were evaluated. Results After whole exome sequencing, 97 SNPs and one indel site were left. Then, functional screening was performed. Only seven SNPs were used for further validation. As a result, the rs2721068 in dominant model and rs17446614 in recessive model were associated with sepsis, and the ORs of these two SNPs were 3.24 (95%CI, 1.25, 8.44) and 0.47 (0.026, 0.88), respectively. These two SNPs were both located in Forkhead box O1 (FOXO1) gene. For rs2721068 (T/T, T/C-C/C) and rs17446614 (A/A-A/G, G/G), serum levels of foxo1 in sepsis patients were both significantly lower in normal controls. Conclusions We firstly reported that the rs2721068 and rs17446614 were correlated to genetic predisposition to sepsis. Electronic supplementary material The online version of this article (10.1186/s12879-019-4330-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Huijuan Wang
- Department of Respiratory Medicine, Chinese PLA General Hospital, 28th Fuxing Road, Beijing, 100853, China.,Department of Respiratory and Critical Care Medicine, Beijing Chao-Yang Hospital, Beijing Institute of Respiratory Medicine, Capital Medical University, Beijing, 100020, China
| | - Zhaohui Tong
- Department of Respiratory and Critical Care Medicine, Beijing Chao-Yang Hospital, Beijing Institute of Respiratory Medicine, Capital Medical University, Beijing, 100020, China
| | - Jia Li
- Department of Nanlou Respiratory Medicine, Chinese PLA General Hospital, 28th Fuxing Road, Beijing, 100853, China
| | - Kun Xiao
- Department of Respiratory Medicine, Chinese PLA General Hospital, 28th Fuxing Road, Beijing, 100853, China
| | - Feifei Ren
- Department of Respiratory Medicine, Chinese PLA General Hospital, 28th Fuxing Road, Beijing, 100853, China
| | - Lixin Xie
- Department of Respiratory Medicine, Chinese PLA General Hospital, 28th Fuxing Road, Beijing, 100853, China.
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6
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Bauwens M, Garanto A, Sangermano R, Naessens S, Weisschuh N, De Zaeytijd J, Khan M, Sadler F, Balikova I, Van Cauwenbergh C, Rosseel T, Bauwens J, De Leeneer K, De Jaegere S, Van Laethem T, De Vries M, Carss K, Arno G, Fakin A, Webster AR, de Ravel de l'Argentière TJL, Sznajer Y, Vuylsteke M, Kohl S, Wissinger B, Cherry T, Collin RWJ, Cremers FPM, Leroy BP, De Baere E. ABCA4-associated disease as a model for missing heritability in autosomal recessive disorders: novel noncoding splice, cis-regulatory, structural, and recurrent hypomorphic variants. Genet Med 2019; 21:1761-1771. [PMID: 30670881 PMCID: PMC6752479 DOI: 10.1038/s41436-018-0420-y] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 12/17/2018] [Indexed: 12/30/2022] Open
Abstract
Purpose ABCA4-associated disease, a recessive retinal dystrophy, is hallmarked by a large proportion of patients with only one pathogenic ABCA4 variant, suggestive for missing heritability. Methods By locus-specific analysis of ABCA4, combined with extensive functional studies, we aimed to unravel the missing alleles in a cohort of 67 patients (p), with one (p = 64) or no (p = 3) identified coding pathogenic variants of ABCA4. Results We identified eight pathogenic (deep-)intronic ABCA4 splice variants, of which five are novel and six structural variants, four of which are novel, including two duplications. Together, these variants account for the missing alleles in 40.3% of patients. Furthermore, two novel variants with a putative cis-regulatory effect were identified. The common hypomorphic variant c.5603A>T p.(Asn1868Ile) was found as a candidate second allele in 43.3% of patients. Overall, we have elucidated the missing heritability in 83.6% of our cohort. In addition, we successfully rescued three deep-intronic variants using antisense oligonucleotide (AON)-mediated treatment in HEK 293-T cells and in patient-derived fibroblast cells. Conclusion Noncoding pathogenic variants, novel structural variants, and a common hypomorphic allele of the ABCA4 gene explain the majority of unsolved cases with ABCA4-associated disease, rendering this retinopathy a model for missing heritability in autosomal recessive disorders.
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Affiliation(s)
- Miriam Bauwens
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Alejandro Garanto
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Riccardo Sangermano
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sarah Naessens
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Nicole Weisschuh
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Julie De Zaeytijd
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Mubeen Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Françoise Sadler
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Irina Balikova
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Caroline Van Cauwenbergh
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.,Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Toon Rosseel
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Jim Bauwens
- Department of Computer Science, Free University of Brussels, Brussels, Belgium
| | - Kim De Leeneer
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Sarah De Jaegere
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Thalia Van Laethem
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Meindert De Vries
- Department of Ophthalmology, Hôpital des Enfants Reine Fabiola, Brussels, Belgium
| | - Keren Carss
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Cambridge, UK.,UK NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Gavin Arno
- UCL Institute of Ophthalmology, London, UK
| | - Ana Fakin
- UCL Institute of Ophthalmology, London, UK.,Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Andrew R Webster
- UCL Institute of Ophthalmology, London, UK.,Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | | | - Yves Sznajer
- Centre de Génétique Humaine, Cliniques Universitaires St. Luc, Université Catholique de Louvain, Brussels, Belgium
| | | | - Susanne Kohl
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Bernd Wissinger
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Timothy Cherry
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA.,Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA, USA
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bart P Leroy
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.,Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium.,Division of Ophthalmology and Center for Cellular & Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elfride De Baere
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.
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Romdhane K, Vaclavik V, Schorderet DF, Munier FL, Viet Tran H. CRX-linked macular dystrophy with intrafamilial variable expressivity. Ophthalmic Genet 2018; 39:637-641. [PMID: 30067412 DOI: 10.1080/13816810.2018.1502789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND We present a macular dystrophy of differing severity in a single kindred caused by a heterozygous nonsense mutation in CRX. CASE REPORT A 21-year-old Caucasian male from a Swiss family was investigated for decreasing central visual acuity associated with dischromatopsia. Clinical examination revealed posterior pole atrophy, including the maculopapillary bundle. Multimodal imaging, including autofluorescence, showed a hyperautofluorescent paramacular ring in both eyes. Genetic analysis identified a c.313C>T, p.Q105* nonsense mutation in CRX. The same mutation was identified in his father and uncle. Both of them showed signs of the disease, however with different severity. CONCLUSION We describe an intrafamilial variable expressivity of a CRX mutation causing an isolated macular dystrophy.
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Affiliation(s)
- Khaled Romdhane
- a Jules-Gonin Eye Hospital, Department of Ophthalmology , University of Lausanne , Lausanne , Switzerland
| | - Veronika Vaclavik
- a Jules-Gonin Eye Hospital, Department of Ophthalmology , University of Lausanne , Lausanne , Switzerland
| | - Daniel F Schorderet
- a Jules-Gonin Eye Hospital, Department of Ophthalmology , University of Lausanne , Lausanne , Switzerland.,b IRO-Institute for Research in Ophthalmology , Sion , Switzerland.,c Faculty of Life Sciences , Ecole Polytechnique Fédérale de Lausanne , Lausanne , Switzerland
| | - Francis L Munier
- a Jules-Gonin Eye Hospital, Department of Ophthalmology , University of Lausanne , Lausanne , Switzerland
| | - H Viet Tran
- a Jules-Gonin Eye Hospital, Department of Ophthalmology , University of Lausanne , Lausanne , Switzerland
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8
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Bojinova RI, Schorderet DF, Valmaggia C, Türksever C, Schoetzau A, Todorova MG. Higher retinal vessel oxygen saturation: investigating its relationship with macular oedema in retinitis pigmentosa patients. Eye (Lond) 2018; 32:1209-1219. [PMID: 29507331 DOI: 10.1038/s41433-018-0043-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 01/20/2018] [Accepted: 01/28/2018] [Indexed: 01/18/2023] Open
Abstract
PURPOSE Primary objective-to investigate the effect of retinal vessel oxygen saturation (SO2) on macular oedema (ME) in retinitis pigmentosa (RP) patients. Secondary objective-to link the presence of ME to metabolic (oxygen saturation of retinal vessels, SO2), functional (multifocal electroretinography, mfERG) and structural (Spectral Domain Optical Coherent Tomography, SD-OCT) alterations in RP. DESIGN Prospective, cross-sectional, non-interventional study. SUBJECTS Patients with typical RP (N = 37) and controls (N = 19), who underwent retinal vessel Oximetry (RO), SD-OCT and mfERG, were included. METHODS A computer-based program of the retinal vessel analyser unit (IMEDOS Systems UG, Jena, Germany) was used to measure SO2. We evaluated the mean SO2, in all major retinal arterioles (oxygen saturation in retinal arterioles, A-SO2, %) and venules (oxygen saturation in retinal venules, V-SO2, %). MfERG responses were averaged in zones (zone 1 (0-3°), zone 2 (3-8°) and zone 3 (8-15°)) and compared to corresponding areas of the OCT. The effect of ME on SO2 was evaluated dividing the RP in two subgroups: with clinical appearance of ME (ME-RP) and without it (no-ME-RP). MAIN OUTCOME MEASURES Parallel recording and juxtaposition of metabolic (SO2) to structural (OCT) and functional-(mfERG) measures. Mean ( ± SD) A-SO2 and V-SO2 were higher in no-ME-RP (96.77% (±6.31) and 59.93% (±7.76)) and even higher in the ME-RP (99.82% (±6.21) and 65.63% (±7.63)), compared to controls (93.15% (±3.76) and 53.77% (±3.70), p ≤ 0.006). RESULTS The subgroup ME-RP differed significantly from the subgroup no-ME-RP by increased A-SO2 and V-SO2, p ≤ 0.026. The presence of ME confirmed a different relationship between the altered SO2 and the vessel diameters, against the functional and structural parameters. CONCLUSION Based on our results, the presence of macular oedema indicates a tendency toward greater alteration of the metabolic function in RP patients.
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Affiliation(s)
- Rossiana I Bojinova
- Department of Ophthalmology, University of Basel, Mittlere Strasse 91, Basel, CH-4031, Switzerland.,University of Montreal, 495 Prince Arthur West, Montreal, H2X1T4, Canada
| | - Daniel F Schorderet
- IRO-Institute for Research in Ophthalmology, Sion, Switzerland.,Department of Ophthalmology, University of Lausanne, Lausanne, Switzerland.,School of Life Sciences, Federal Institute of Technology, Lausanne, Switzerland
| | | | - Cengiz Türksever
- Department of Ophthalmology, University of Basel, Mittlere Strasse 91, Basel, CH-4031, Switzerland.,VISTA Klinik, Binningen, Baselland, Switzerland
| | - Andreas Schoetzau
- Department of Ophthalmology, University of Basel, Mittlere Strasse 91, Basel, CH-4031, Switzerland
| | - Margarita G Todorova
- Department of Ophthalmology, University of Basel, Mittlere Strasse 91, Basel, CH-4031, Switzerland.
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9
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Petersen-Jones SM, Occelli LM, Winkler PA, Lee W, Sparrow JR, Tsukikawa M, Boye SL, Chiodo V, Capasso JE, Becirovic E, Schön C, Seeliger MW, Levin AV, Michalakis S, Hauswirth WW, Tsang SH. Patients and animal models of CNGβ1-deficient retinitis pigmentosa support gene augmentation approach. J Clin Invest 2017; 128:190-206. [PMID: 29202463 PMCID: PMC5749539 DOI: 10.1172/jci95161] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 10/10/2017] [Indexed: 01/07/2023] Open
Abstract
Retinitis pigmentosa (RP) is a major cause of blindness that affects 1.5 million people worldwide. Mutations in cyclic nucleotide-gated channel β 1 (CNGB1) cause approximately 4% of autosomal recessive RP. Gene augmentation therapy shows promise for treating inherited retinal degenerations; however, relevant animal models and biomarkers of progression in patients with RP are needed to assess therapeutic outcomes. Here, we evaluated RP patients with CNGB1 mutations for potential biomarkers of progression and compared human phenotypes with those of mouse and dog models of the disease. Additionally, we used gene augmentation therapy in a CNGβ1-deficient dog model to evaluate potential translation to patients. CNGB1-deficient RP patients and mouse and dog models had a similar phenotype characterized by early loss of rod function and slow rod photoreceptor loss with a secondary decline in cone function. Advanced imaging showed promise for evaluating RP progression in human patients, and gene augmentation using adeno-associated virus vectors robustly sustained the rescue of rod function and preserved retinal structure in the dog model. Together, our results reveal an early loss of rod function in CNGB1-deficient patients and a wide window for therapeutic intervention. Moreover, the identification of potential biomarkers of outcome measures, availability of relevant animal models, and robust functional rescue from gene augmentation therapy support future work to move CNGB1-RP therapies toward clinical trials.
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Affiliation(s)
- Simon M Petersen-Jones
- Department of Small Animal Clinical Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Laurence M Occelli
- Department of Small Animal Clinical Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Paige A Winkler
- Department of Small Animal Clinical Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Winston Lee
- Department of Ophthalmology Pathology & Cell Biology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Janet R Sparrow
- Department of Ophthalmology Pathology & Cell Biology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Mai Tsukikawa
- Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Sanford L Boye
- Department of Ophthalmology, University of Florida, Gainesville, Florida, USA
| | - Vince Chiodo
- Department of Ophthalmology, University of Florida, Gainesville, Florida, USA
| | - Jenina E Capasso
- Ocular Genetics, Wills Eye Hospital (WEH), Philadelphia, Pennsylvania, USA
| | - Elvir Becirovic
- Center for Integrated Protein Science Munich (CIPSM), Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Christian Schön
- Center for Integrated Protein Science Munich (CIPSM), Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Mathias W Seeliger
- Division of Ocular Neurodegeneration, Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Alex V Levin
- Thomas Jefferson University, Philadelphia, Pennsylvania, USA.,Ocular Genetics, Wills Eye Hospital (WEH), Philadelphia, Pennsylvania, USA
| | - Stylianos Michalakis
- Center for Integrated Protein Science Munich (CIPSM), Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - William W Hauswirth
- Department of Ophthalmology, University of Florida, Gainesville, Florida, USA
| | - Stephen H Tsang
- Department of Ophthalmology Pathology & Cell Biology, College of Physicians and Surgeons, Columbia University, New York, New York, USA.,Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, New York, USA.,Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University Medical Center (CUMC), Edward S. Harkness Eye Institute, New York, New York, USA
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10
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Yang Z, Sun G. High-frequency, low-coverage "false positives" mutations may be true in GS Junior sequencing studies. Sci Rep 2017; 7:13751. [PMID: 29062110 PMCID: PMC5653793 DOI: 10.1038/s41598-017-13116-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 09/19/2017] [Indexed: 12/29/2022] Open
Abstract
The GS Junior sequencer provides simplified procedures for library preparation and data processing. Errors in pyrosequencing generate some biases during library construction and emulsion PCR amplification. False-positive mutations are identified by related characteristics described in the manufacturer’s manual, and some detected mutations may have ‘borderline’ characteristics when they are detected in few reads or at low frequency. Among these mutations, however, some may be true positives. This study aimed to improve the accuracy of identifying true positives among mutations with borderline false-positive characteristics detected with GS Junior sequencing. Mutations with the borderline features were tested for validity with Sanger sequencing. We examined 10 mutations detected in coverages <20-fold at frequencies >30% (group A) and 16 mutations detected in coverages >20-fold at frequencies < 30% (group B). In group A, two mutations were not confirmed, and two mutations with 100% frequency were confirmed as heterozygous alleles. No mutation in group B was confirmed. The two groups had significantly different false-positive prevalences (p = 0.001). These results suggest that mutations detected at frequencies less than 30% can be confidently identified as false-positives but that mutations detected at frequencies over 30%, despite coverages less than 20-fold, should be verified with Sanger sequencing.
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Affiliation(s)
- Zhiliang Yang
- Department of Pediatrics, the First Hospital of China Medical University, Shenyang, 110001, China.
| | - Guilian Sun
- Department of Pediatrics, the First Hospital of China Medical University, Shenyang, 110001, China
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11
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Habibi I, Chebil A, Falfoul Y, Allaman-Pillet N, Kort F, Schorderet DF, El Matri L. Identifying mutations in Tunisian families with retinal dystrophy. Sci Rep 2016; 6:37455. [PMID: 27874104 PMCID: PMC5118704 DOI: 10.1038/srep37455] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/26/2016] [Indexed: 02/08/2023] Open
Abstract
Retinal dystrophies (RD) are a rare genetic disorder with high genetic heterogeneity. This study aimed at identifying disease-causing variants in fifteen consanguineous Tunisian families. Full ophthalmic examination was performed. Index patients were subjected to IROme analysis or whole exome sequencing followed by homozygosity mapping. All detected variations were confirmed by direct Sanger sequencing. Mutation analysis in our patients revealed two compound heterozygous mutations p.(R91W);(V172D) in RPE65, and five novel homozygous mutations: p.R765C in CNGB1, p.H337R in PDE6B, splice site variant c.1129-2A > G and c.678_681delGAAG in FAM161A and c.1133 + 3_1133 + 6delAAGT in CERKL. The latter mutation impacts pre-mRNA splicing of CERKL. The other changes detected were six previously reported mutations in CNGB3 (p.R203*), ABCA4 (p.W782*), NR2E3 (p.R311Q), RPE65 (p.H182Y), PROM1 (c.1354dupT) and EYS (c.5928-2A > G). Segregation analysis in each family showed that all affected individuals were homozygotes and unaffected individuals were either heterozygote carriers or homozygous wild type allele. These results confirm the involvement of a large number of genes in RD in the Tunisian population.
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Affiliation(s)
- Imen Habibi
- Institute for Research in Ophthalmology (IRO), Sion, Switzerland.,Research Laboratory of Oculogenetic (LR14SP01), Department B of Ophthalmology, Hedi Rais Institute of Ophthalmology, Tunis, Tunisia.,Research Laboratory of renal Transplantation and Immunopathology (LR03SP01), University Tunis El Manar, Immunology Laboratory, Tunis, Tunisia.,Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Ahmed Chebil
- Research Laboratory of Oculogenetic (LR14SP01), Department B of Ophthalmology, Hedi Rais Institute of Ophthalmology, Tunis, Tunisia.,Faculty of medicine, University Tunis El Manar, Tunisia
| | - Yosra Falfoul
- Research Laboratory of Oculogenetic (LR14SP01), Department B of Ophthalmology, Hedi Rais Institute of Ophthalmology, Tunis, Tunisia.,Faculty of medicine, University Tunis El Manar, Tunisia
| | | | - Fedra Kort
- Research Laboratory of Oculogenetic (LR14SP01), Department B of Ophthalmology, Hedi Rais Institute of Ophthalmology, Tunis, Tunisia.,Faculty of medicine, University Tunis El Manar, Tunisia
| | - Daniel F Schorderet
- Institute for Research in Ophthalmology (IRO), Sion, Switzerland.,Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Jules-Gonin Eye Hospital, Faculty of biology and medicine, University of Lausanne, Switzerland
| | - Leila El Matri
- Research Laboratory of Oculogenetic (LR14SP01), Department B of Ophthalmology, Hedi Rais Institute of Ophthalmology, Tunis, Tunisia.,Faculty of medicine, University Tunis El Manar, Tunisia
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12
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Chakraborty D, Conley SM, Pittler SJ, Naash MI. Role of RDS and Rhodopsin in Cngb1-Related Retinal Degeneration. Invest Ophthalmol Vis Sci 2016; 57:787-97. [PMID: 26934134 PMCID: PMC4777275 DOI: 10.1167/iovs.15-18516] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Rod photoreceptor outer segment (OS) morphogenesis, structural integrity, and proper signal transduction rely on critical proteins found in the different OS membrane domains (e.g., plasma, disc, and disc rim membrane). Among these key elements are retinal degeneration slow (RDS, also known as peripherin-2), rhodopsin, and the beta subunit of the cyclic nucleotide gated channel (CNGB1a), which have been found to interact in a complex. The purpose of this study was to evaluate the potential interplay between these three proteins by examining retinal disease phenotypes in animal models expressing varying amounts of CNGB1a, rhodopsin, and RDS. Methods Outer segment trafficking, retinal function, and photoreceptor structure were evaluated using knockout mouse lines. Results Eliminating Cngb1 and reducing RDS leads to additive defects in RDS expression levels and rod electroretinogram (ERG) function, (e.g., Cngb1−/−/rds+/− versus rds+/− or Cngb1−/−) but not to additive defects in rod ultrastructure. These additive effects also manifested in cone function: Photopic ERG responses were significantly lower in the Cngb1−/−/rds+/− versus rds+/− or Cngb1−/−, suggesting that eliminating Cngb1 can accelerate the cone degeneration that usually presents later in the rds+/−. This was not the case with rhodopsin; reducing rhodopsin levels in concert with eliminating CNGB1a did not lead to phenotypes more severe than those observed in the Cngb1 knockout alone. Conclusions These data support a role for RDS as the core component of a multiprotein plasma membrane-rim-disc complex that has both a structural role in photoreceptor OS formation and maintenance and a functional role in orienting proteins for optimal signal transduction.
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Affiliation(s)
- Dibyendu Chakraborty
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States
| | - Shannon M Conley
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States
| | - Steven J Pittler
- Department of Vision Sciences, School of Optometry, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Muna I Naash
- Department of Biomedical Engineering, University of Houston, Houston, Texas, United States
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13
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Barandika O, Irigoyen C, Anasagasti A, Egiguren G, Ezquerra-Inchausti M, López de Munain A, Ruiz-Ederra J. A Cost-Effective Mutation Screening Strategy for Inherited Retinal Dystrophies. Ophthalmic Res 2016; 56:123-31. [PMID: 27160245 DOI: 10.1159/000445690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/21/2016] [Indexed: 11/19/2022]
Abstract
OBJECTIVE We developed a simple, time- and cost-effective Excel-based genetic screening strategy for the diagnosis of inherited retinal dystrophies (IRD). DESIGN 76 patients diagnosed with IRD and 112 nonaffected family members, from 55 unrelated families, were included. DNA samples were analyzed using Axiom Exome Genotyping Array Plates (Affymetrix) that contain over 300,000 genetic variants, including more than 5,000 variants present in 181 genes involved in IRD. We used a simple Excel-based data mining strategy in order to screen IRD variants likely involved in the development of IRD. RESULTS A total of 5 relevant genetic variants were found in 5 IRD genes. Four variants were reported either as pathogenic or with a prediction of probably damaging, and 1 variant was reported to affect a regulatory region. These variants were present in 14 patients and in 11 carriers, in 10 unrelated families. CONCLUSION Using our Excel-based data screening strategy, we were able to assign likely genetic diagnoses in a fast and cost-effective manner to over 18% of patients analyzed, with a comparable ratio of genetic findings to that reported with retina-specific arrays for about 1/5 of the cost. Our approach proved efficient in reducing costs and time for IRD diagnosis as a first tier genetic screening method.
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Affiliation(s)
- Olatz Barandika
- Division of Neurosciences, Instituto Biodonostia, Donostia-San Sebastián, Spain
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14
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Fradin M, Colin E, Hannouche-Bared D, Audo I, Sahel JA, Biskup S, Carré W, Ziegler A, Wilhelm C, Guichet A, Odent S, Bonneau D. Run of homozygosity analysis reveals a novel nonsense variant of the CNGB1 gene involved in retinitis pigmentosa 45. Ophthalmic Genet 2016; 37:357-9. [PMID: 26901671 DOI: 10.3109/13816810.2015.1087578] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Mélanie Fradin
- a Service de Génétique Clinique, Centre de référence CLAD-Ouest, CHU Rennes , Rennes , France
| | - Estelle Colin
- b Service de Génétique, CLAD-Ouest, CHU d'Angers , Angers , France
| | | | - Isabelle Audo
- d INSERM U968, CNRS UMR_7210, Université Pierre et Marie Curie, Paris 06, UMR_S 968, Département de Génétique, Institut de la Vision , Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, INSERM-DHOSCIC 503 , Paris , France
| | - Jose Alain Sahel
- d INSERM U968, CNRS UMR_7210, Université Pierre et Marie Curie, Paris 06, UMR_S 968, Département de Génétique, Institut de la Vision , Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, INSERM-DHOSCIC 503 , Paris , France
| | | | - Wilfried Carré
- f Laboratoire de Génétique Moléculaire et Génomique, CHU Pontchaillou , Rennes , France
| | - Alban Ziegler
- b Service de Génétique, CLAD-Ouest, CHU d'Angers , Angers , France
| | | | - Agnès Guichet
- b Service de Génétique, CLAD-Ouest, CHU d'Angers , Angers , France
| | - Sylvie Odent
- a Service de Génétique Clinique, Centre de référence CLAD-Ouest, CHU Rennes , Rennes , France.,g Université de Rennes 1 , CNRS UMR 6290, Rennes , France
| | - Dominique Bonneau
- b Service de Génétique, CLAD-Ouest, CHU d'Angers , Angers , France.,h UMR CNRS 6214 - INSERM 1083, Université d'Angers , Angers , France
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15
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Méndez-Vidal C, Bravo-Gil N, González-Del Pozo M, Vela-Boza A, Dopazo J, Borrego S, Antiñolo G. Novel RP1 mutations and a recurrent BBS1 variant explain the co-existence of two distinct retinal phenotypes in the same pedigree. BMC Genet 2014; 15:143. [PMID: 25494902 PMCID: PMC4271491 DOI: 10.1186/s12863-014-0143-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 12/03/2014] [Indexed: 12/30/2022] Open
Abstract
Background Molecular diagnosis of Inherited Retinal Dystrophies (IRD) has long been challenging due to the extensive clinical and genetic heterogeneity present in this group of disorders. Here, we describe the clinical application of an integrated next-generation sequencing approach to determine the underlying genetic defects in a Spanish family with a provisional clinical diagnosis of autosomal recessive Retinitis Pigmentosa (arRP). Results Exome sequencing of the index patient resulted in the identification of the homozygous BBS1 p.M390R mutation. Sanger sequencing of additional members of the family showed lack of co-segregation of the p.M390R variant in some individuals. Clinical reanalysis indicated co-ocurrence of two different phenotypes in the same family: Bardet-Biedl syndrome in the individual harboring the BBS1 mutation and non-syndromic arRP in extended family members. To identify possible causative mutations underlying arRP, we conducted disease-targeted gene sequencing using a panel of 26 IRD genes. The in-house custom panel was validated using 18 DNA samples known to harbor mutations in relevant genes. All variants were redetected, indicating a high mutation detection rate. This approach allowed the identification of two novel heterozygous null mutations in RP1 (c.4582_4585delATCA; p.I1528Vfs*10 and c.5962dupA; p.I1988Nfs*3) which co-segregated with the disease in arRP patients. Additionally, a mutational screening in 96 patients of our cohort with genetically unresolved IRD revealed the presence of the c.5962dupA mutation in one unrelated family. Conclusions The combination of molecular findings for RP1 and BBS1 genes through exome and gene panel sequencing enabled us to explain the co-existence of two different retinal phenotypes in a family. The identification of two novel variants in RP1 suggests that the use of panels containing the prevalent genes of a particular population, together with an optimized data analysis pipeline, is an efficient and cost-effective approach that can be reliably implemented into the routine diagnostic process of diverse inherited retinal disorders. Moreover, the identification of these novel variants in two unrelated families supports the relatively high prevalence of RP1 mutations in Spanish population and the role of private mutations for commonly mutated genes, while extending the mutational spectrum of RP1. Electronic supplementary material The online version of this article (doi:10.1186/s12863-014-0143-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cristina Méndez-Vidal
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Avenida Manuel Siurot s/n, 41013, Seville, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain.
| | - Nereida Bravo-Gil
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Avenida Manuel Siurot s/n, 41013, Seville, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain.
| | - María González-Del Pozo
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Avenida Manuel Siurot s/n, 41013, Seville, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain.
| | - Alicia Vela-Boza
- Genomics and Bioinformatics Platform of Andalusia (GBPA), Seville, Spain.
| | - Joaquín Dopazo
- Genomics and Bioinformatics Platform of Andalusia (GBPA), Seville, Spain. .,Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.
| | - Salud Borrego
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Avenida Manuel Siurot s/n, 41013, Seville, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain.
| | - Guillermo Antiñolo
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Avenida Manuel Siurot s/n, 41013, Seville, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain. .,Genomics and Bioinformatics Platform of Andalusia (GBPA), Seville, Spain.
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16
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El-Haig WM, Jakobsson C, Favez T, Schorderet DF, Abouzeid H. Novel ADAM9 homozygous mutation in a consanguineous Egyptian family with severe cone-rod dystrophy and cataract. Br J Ophthalmol 2014; 98:1718-23. [PMID: 25091951 DOI: 10.1136/bjophthalmol-2014-305231] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVE To genetically and phenotypically describe a new ADAM9 homozygous mutation in a consanguineous family from Egypt with autosomal recessive cone-rod dystrophy (arCRD), anterior polar and posterior subcapsular cataract. DESIGN, SETTING AND PARTICIPANTS The parents and their six children were included. They underwent a complete ophthalmic examination with fundus photography and optical coherence tomography (OCT). INTERVENTION DNA was extracted from peripheral blood from all family members. Screening for mutations in genes known to be implicated in retinal disorders was done with the IROme, an in-solution enrichment array, followed by high-throughput sequencing. Validation of the results was done by bidirectional Sanger sequencing of ADAM9 exon 14, including exon-intron junctions. Screening of normal controls was done by denaturing high-performance liquid chromatography. RESULTS arCRD was diagnosed in the mother and two of her children. Bilateral anterior polar and posterior subcapsular cataract was observed in the mother and bilateral dot cataract was diagnosed in three of the four children not affected with arCRD, one of whom also had glaucoma. The characteristics of the arCRD were childhood-onset visual impairment, reorganisation of the retinal pigment epithelium with mid-periphery greyish-white discolouration, attenuated retinal vasculatur and optic disc pallor. A coloboma-like macular lesion was observed in one of the arCRD-affected children. IROme analysis identified a c.1396-2A>G homozygous mutation in the splice acceptor site of intron 13 of ADAM9. This mutation was homozygous in the two children affected by arCRD and in their affected mother. This mutation was heterozygous in the unaffected father and the four unaffected children. CONCLUSIONS AND RELEVANCE We identified a novel autosomal recessive ADAM9 mutation causing arCRD in a consanguineous Egyptian family. The percentage of arCRD cases caused by mutation in ADAM9 remains to be determined. Few families are reported in the literature to date; hence extensive clinical descriptions of families with ADAM9 mutations are of significant importance.
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Affiliation(s)
- Wael M El-Haig
- Department of Ophthalmology, Zagazig University, Zagazig, Egypt
| | - Cecilia Jakobsson
- IRO-Institute for Research in Ophthalmology, Sion, Switzerland Department of Ophthalmology, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, University of Lausanne, Lausanne, Switzerland
| | - Tatiana Favez
- IRO-Institute for Research in Ophthalmology, Sion, Switzerland
| | - Daniel F Schorderet
- IRO-Institute for Research in Ophthalmology, Sion, Switzerland Department of Ophthalmology, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, University of Lausanne, Lausanne, Switzerland EPFL-Faculté des Sciences du Vivant, Ecole polytechnique fédérale de Lausanne, Lausanne, Switzerland
| | - Hana Abouzeid
- IRO-Institute for Research in Ophthalmology, Sion, Switzerland Department of Ophthalmology, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, University of Lausanne, Lausanne, Switzerland
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17
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Siemiatkowska AM, Collin RWJ, den Hollander AI, Cremers FPM. Genomic approaches for the discovery of genes mutated in inherited retinal degeneration. Cold Spring Harb Perspect Med 2014; 4:a017137. [PMID: 24939053 PMCID: PMC4109577 DOI: 10.1101/cshperspect.a017137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In view of their high degree of genetic heterogeneity, inherited retinal diseases (IRDs) pose a significant challenge for identifying novel genetic causes. Thus far, more than 200 genes have been found to be mutated in IRDs, which together contain causal variants in >80% of the cases. Accurate genetic diagnostics is particularly important for isolated cases, in which X-linked and de novo autosomal dominant variants are not uncommon. In addition, new gene- or mutation-specific therapies are emerging, underlining the importance of identifying causative mutations in each individual. Sanger sequencing of selected genes followed by cost-effective targeted next-generation sequencing (NGS) can identify defects in known IRD-associated genes in the majority of the cases. Exome NGS in combination with genetic linkage or homozygosity mapping studies can aid the identification of the remaining causal genes. As these are thought to be mutated in <1% of the cases, validation through functional modeling in, for example, zebrafish and/or replication through the genotyping of large patient cohorts is required. In the near future, whole genome NGS in combination with transcriptome NGS may reveal mutations that are currently hidden in the noncoding regions of the human genome.
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Affiliation(s)
- Anna M Siemiatkowska
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anneke I den Hollander
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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18
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Application of Massively Parallel Sequencing in the Clinical Diagnostic Testing of Inherited Cardiac Conditions. Med Sci (Basel) 2014. [DOI: 10.3390/medsci2020098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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19
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Jin X, Qu LH, Meng XH, Xu HW, Yin ZQ. Detecting genetic variations in hereditary retinal dystrophies with next-generation sequencing technology. Mol Vis 2014; 20:553-60. [PMID: 24791140 PMCID: PMC4000715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 04/24/2014] [Indexed: 11/27/2022] Open
Abstract
PURPOSE To identify pathogenic mutations responsible for retinal dystrophies (RDs) in three unrelated Chinese families. METHODS Three probands from unrelated families with RDs were recruited. Genomic DNA prepared from leukocytes was analyzed using gene chip-based next-generation sequencing (NGS) to capture and sequence all of the exons of 100 known RD-associated genes. Candidate variants were validated with PCR and Sanger sequencing in the respective families. Thorough ophthalmic examinations including best-corrected visual acuity, funduscopic examination, and full-field electroretinograms were performed in the affected individuals. RESULTS We successfully identified causative mutations in patients from the Chinese families with RDS: the known mutation IMPDH1 c.942_944delGAA in a family with retinitis pigmentosa, the novel mutation ABCA4 c.1924T>A in a family with Stargardt disease, and the novel mutation NMNAT1 c.272A>G and known mutation NMNAT1 c.196C>T in a family with Leber congenital amaurosis. All variations segregated with the disease phenotypes in the respective families and were absent from ethnically matched control chromosomes. Prediction analysis demonstrated the two novel missense mutations might be damaging. CONCLUSIONS The results strongly suggested these mutations were responsible for different RD phenotypes in the Chinese families. NGS technology provides an accurate and economic method for identifying causative genes for RDs.
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Affiliation(s)
- Xin Jin
- Southwest Hospital, Southwest Eye Hospital, Third Military Medical University, Chongqing, China,Department of Ophthalmology, Chinese PLA General Hospital, Beijing, China,Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Ling Hui Qu
- Southwest Hospital, Southwest Eye Hospital, Third Military Medical University, Chongqing, China,Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Xiao Hong Meng
- Southwest Hospital, Southwest Eye Hospital, Third Military Medical University, Chongqing, China,Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Hai Wei Xu
- Southwest Hospital, Southwest Eye Hospital, Third Military Medical University, Chongqing, China,Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
| | - Zheng Qin Yin
- Southwest Hospital, Southwest Eye Hospital, Third Military Medical University, Chongqing, China,Department of Ophthalmology, Chinese PLA General Hospital, Beijing, China,Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China
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Schorderet DF, Bernasconi M, Tiab L, Favez T, Escher P. IROme, a new high-throughput molecular tool for the diagnosis of inherited retinal dystrophies-a price comparison with Sanger sequencing. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 801:171-6. [PMID: 24664695 DOI: 10.1007/978-1-4614-3209-8_22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The molecular diagnosis of retinal dystrophies (RD) is difficult because of genetic and clinical heterogeneity. Previously, the molecular screening of genes was done one by one, sometimes in a scheme based on the frequency of sequence variants and the number of exons/length of the candidate genes. Payment for these procedures was complicated and the sequential billing of several genes created endless paperwork. We therefore evaluated the costs of generating and sequencing a hybridization-based DNA library enriched for the 64 most frequently mutated genes in RD, called IROme, and compared them to the costs of amplifying and sequencing these genes by the Sanger method. The production cost generated by the high-throughput (HT) sequencing of IROme was established at CHF 2,875.75 per case. Sanger sequencing of the same exons cost CHF 69,399.02. Turnaround time of the analysis was 3 days for IROme. For Sanger sequencing, it could only be estimated, as we never sequenced all 64 genes in one single patient. Sale cost for IROme calculated on the basis of the sale cost of one exon by Sanger sequencing is CHF 8,445.88, which corresponds to the sale price of 40 exons. In conclusion, IROme is cheaper and faster than Sanger sequencing and therefore represents a sound approach for the diagnosis of RD, both scientifically and economically. As a drop in the costs of HT sequencing is anticipated, target resequencing might become the new gold standard in the molecular diagnosis of RD.
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Affiliation(s)
- Daniel F Schorderet
- IRO, Institute for Research in Ophthalmology, 64 Avenue du Grand-Champsec, 1950, Sion, Switzerland,
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