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Fernández-Caballero L, Martín-Merida I, Blanco-Kelly F, Avila-Fernandez A, Carreño E, Fernandez-San Jose P, Irigoyen C, Jimenez-Rolando B, Lopez-Grondona F, Mahillo I, Martin-Gutierrez MP, Minguez P, Perea-Romero I, Del Pozo-Valero M, Riveiro-Alvarez R, Rodilla C, Rodriguez-Peña L, Sánchez-Barbero AI, Swafiri ST, Trujillo-Tiebas MJ, Zurita O, García-Sandoval B, Corton M, Ayuso C. PRPH2-Related Retinal Dystrophies: Mutational Spectrum in 103 Families from a Spanish Cohort. Int J Mol Sci 2024; 25:2913. [PMID: 38474159 PMCID: PMC10931554 DOI: 10.3390/ijms25052913] [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: 02/01/2024] [Revised: 02/26/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
PRPH2, one of the most frequently inherited retinal dystrophy (IRD)-causing genes, implies a high phenotypic variability. This study aims to analyze the PRPH2 mutational spectrum in one of the largest cohorts worldwide, and to describe novel pathogenic variants and genotype-phenotype correlations. A study of 220 patients from 103 families recruited from a database of 5000 families. A molecular diagnosis was performed using classical molecular approaches and next-generation sequencing. Common haplotypes were ascertained by analyzing single-nucleotide polymorphisms. We identified 56 variants, including 11 novel variants. Most of them were missense variants (64%) and were located in the D2-loop protein domain (77%). The most frequently occurring variants were p.Gly167Ser, p.Gly208Asp and p.Pro221_Cys222del. Haplotype analysis revealed a shared region in families carrying p.Leu41Pro or p.Pro221_Cys222del. Patients with retinitis pigmentosa presented an earlier disease onset. We describe the largest cohort of IRD families associated with PRPH2 from a single center. Most variants were located in the D2-loop domain, highlighting its importance in interacting with other proteins. Our work suggests a likely founder effect for the variants p.Leu41Pro and p.Pro221_Cys222del in our Spanish cohort. Phenotypes with a primary rod alteration presented more severe affectation. Finally, the high phenotypic variability in PRPH2 hinders the possibility of drawing genotype-phenotype correlations.
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Affiliation(s)
- Lidia Fernández-Caballero
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Inmaculada Martín-Merida
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Fiona Blanco-Kelly
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Almudena Avila-Fernandez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ester Carreño
- Department of Ophthalmology, Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (E.C.); (B.J.-R.); (M.P.M.-G.); (B.G.-S.)
| | - Patricia Fernandez-San Jose
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department of Genetics, Ramón y Cajal University Hospital, 28034 Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
| | - Cristina Irigoyen
- Ophthalmology Service, Donostia University Hospital, 20014 Donostia-San Sebastián, Spain
| | - Belen Jimenez-Rolando
- Department of Ophthalmology, Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (E.C.); (B.J.-R.); (M.P.M.-G.); (B.G.-S.)
| | - Fermina Lopez-Grondona
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ignacio Mahillo
- Department of Statistics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain;
| | - María Pilar Martin-Gutierrez
- Department of Ophthalmology, Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (E.C.); (B.J.-R.); (M.P.M.-G.); (B.G.-S.)
| | - Pablo Minguez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Irene Perea-Romero
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Marta Del Pozo-Valero
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Rosa Riveiro-Alvarez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Cristina Rodilla
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Lidya Rodriguez-Peña
- Sección de Genética Medica, Servicio de Pediatría, HCU Virgen de la Arrixaca, 30120 Murcia, Spain
| | - Ana Isabel Sánchez-Barbero
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Saoud T. Swafiri
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - María José Trujillo-Tiebas
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Olga Zurita
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Blanca García-Sandoval
- Department of Ophthalmology, Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (E.C.); (B.J.-R.); (M.P.M.-G.); (B.G.-S.)
| | - Marta Corton
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain; (L.F.-C.); (I.M.-M.); (F.B.-K.); (A.A.-F.); (F.L.-G.); (P.M.); (C.R.); (A.I.S.-B.); (S.T.S.); (M.J.T.-T.); (O.Z.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
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Cellular and Molecular Mechanisms of Pathogenesis Underlying Inherited Retinal Dystrophies. Biomolecules 2023; 13:biom13020271. [PMID: 36830640 PMCID: PMC9953031 DOI: 10.3390/biom13020271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/23/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
Inherited retinal dystrophies (IRDs) are congenital retinal degenerative diseases that have various inheritance patterns, including dominant, recessive, X-linked, and mitochondrial. These diseases are most often the result of defects in rod and/or cone photoreceptor and retinal pigment epithelium function, development, or both. The genes associated with these diseases, when mutated, produce altered protein products that have downstream effects in pathways critical to vision, including phototransduction, the visual cycle, photoreceptor development, cellular respiration, and retinal homeostasis. The aim of this manuscript is to provide a comprehensive review of the underlying molecular mechanisms of pathogenesis of IRDs by delving into many of the genes associated with IRD development, their protein products, and the pathways interrupted by genetic mutation.
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Peeters MHCA, Khan M, Rooijakkers AAMB, Mulders T, Haer-Wigman L, Boon CJF, Klaver CCW, van den Born LI, Hoyng CB, Cremers FPM, den Hollander AI, Dhaenens CM, Collin RWJ. PRPH2 mutation update: In silico assessment of 245 reported and 7 novel variants in patients with retinal disease. Hum Mutat 2021; 42:1521-1547. [PMID: 34411390 PMCID: PMC9290825 DOI: 10.1002/humu.24275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/22/2021] [Accepted: 08/16/2021] [Indexed: 01/31/2023]
Abstract
Mutations in PRPH2, encoding peripherin-2, are associated with the development of a wide variety of inherited retinal diseases (IRDs). To determine the causality of the many PRPH2 variants that have been discovered over the last decades, we surveyed all published PRPH2 variants up to July 2020, describing 720 index patients that in total carried 245 unique variants. In addition, we identified seven novel PRPH2 variants in eight additional index patients. The pathogenicity of all variants was determined using the ACMG guidelines. With this, 107 variants were classified as pathogenic, 92 as likely pathogenic, one as benign, and two as likely benign. The remaining 50 variants were classified as variants of uncertain significance. Interestingly, of the total 252 PRPH2 variants, more than half (n = 137) were missense variants. All variants were uploaded into the Leiden Open source Variation and ClinVar databases. Our study underscores the need for experimental assays for variants of unknown significance to improve pathogenicity classification, which would allow us to better understand genotype-phenotype correlations, and in the long-term, hopefully also support the development of therapeutic strategies for patients with PRPH2-associated IRD.
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Affiliation(s)
- Manon H C A Peeters
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics and Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Mubeen Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics and Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | | | - Timo Mulders
- Department of Human Genetics and Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Camiel J F Boon
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands.,Department of Ophthalmology, Amsterdam UMC, Academic Medical Center, Amsterdam, The Netherlands
| | - Caroline C W Klaver
- Department of Human Genetics and Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Ophthalmology, Erasmus University Medical Centre, Rotterdam, The Netherlands.,Institute of Molecular and Clinical Ophthalmology, Basel, Switzerland
| | - L Ingeborgh van den Born
- The Rotterdam Eye Hospital, Rotterdam, The Netherlands.,Rotterdam Ophthalmic Institute, Rotterdam, The Netherlands
| | - Carel B Hoyng
- Department of Human Genetics and Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, 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.,Department of Human Genetics and Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Anneke I den Hollander
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics and Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Claire-Marie Dhaenens
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Biochemistry and Molecular Biology, Univ. Lille, Inserm, CHU Lille, U1172-LilNCog-Lille Neuroscience & Cognition, Lille, France
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics and Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
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Ouyang XL, Chen BY, Xie YF, Wu YD, Guo SJ, Dong XY, Wang GH. Whole transcriptome analysis on blue light-induced eye damage. Int J Ophthalmol 2020; 13:1210-1222. [PMID: 32821674 DOI: 10.18240/ijo.2020.08.06] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/07/2020] [Indexed: 12/20/2022] Open
Abstract
AIM To analyze abnormal gene expressions of mice eyes exposed to blue light using RNA-seq and analyze the related signaling pathways. METHODS Kunming mice were divided into an experimental group that was exposed to blue light and a control group that was exposed to natural light. After 14d, the mice were euthanized and their eyeballs were collected. Whole transcriptome analysis was attempted to analyze the gene expression of the eyeballs using RNA-seq to reconstruct genetic networks. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were used to reveal the related signaling pathways. RESULTS The 737 differentially expressed genes were identified, including 430 up and 307 down regulated genes, by calculating the gene FPKM in each sample and conducting differential gene analysis. GO and KEGG pathway enrichment analysis showed that blue light damage may associated with the visual perception, sensory perception of light stimulus, phototransduction, and JAK-STAT signaling pathways. Differential lncRNA, circRNA and miRNA analysis showed that blue light exposure affected pathways for retinal cone cell development and phototransduction, among others. CONCLUSION Exposure to blue light can cause a certain degree of abnormal gene expression and modulate signaling pathways in the eye.
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Affiliation(s)
- Xin-Li Ouyang
- Key Laboratory of Biological Medicines in Universities of Shandong Province, Weifang Medical University, Weifang 261053, Shandong Province, China
| | - Bo-Yu Chen
- Shijiazhuang Aier Eye Hospital, Bethune International Peace Hospital of PLA, Shijiazhuang 050082, Hebei Province, China
| | - Yong-Fang Xie
- Key Laboratory of Biological Medicines in Universities of Shandong Province, Weifang Medical University, Weifang 261053, Shandong Province, China
| | - Yi-De Wu
- Key Laboratory of Biological Medicines in Universities of Shandong Province, Weifang Medical University, Weifang 261053, Shandong Province, China
| | - Shao-Jia Guo
- Key Laboratory of Biological Medicines in Universities of Shandong Province, Weifang Medical University, Weifang 261053, Shandong Province, China
| | - Xiao-Yun Dong
- Key Laboratory of Biological Medicines in Universities of Shandong Province, Weifang Medical University, Weifang 261053, Shandong Province, China
| | - Guo-Hui Wang
- Key Laboratory of Biological Medicines in Universities of Shandong Province, Weifang Medical University, Weifang 261053, Shandong Province, China
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Martin-Merida I, Aguilera-Garcia D, Fernandez-San JP, Blanco-Kelly F, Zurita O, Almoguera B, Garcia-Sandoval B, Avila-Fernandez A, Arteche A, Minguez P, Carballo M, Corton M, Ayuso C. Toward the Mutational Landscape of Autosomal Dominant Retinitis Pigmentosa: A Comprehensive Analysis of 258 Spanish Families. Invest Ophthalmol Vis Sci 2019; 59:2345-2354. [PMID: 29847639 DOI: 10.1167/iovs.18-23854] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To provide a comprehensive overview of the molecular basis of autosomal dominant retinitis pigmentosa (adRP) in Spanish families. Thus, we established the molecular characterization rate, gene prevalence, and mutational spectrum in the largest European cohort reported to date. Methods A total of 258 unrelated Spanish families with a clinical diagnosis of RP and suspected autosomal dominant inheritance were included. Clinical diagnosis was based on complete ophthalmologic examination and family history. Retrospective and prospective analysis of Spanish adRP families was carried out using a combined strategy consisting of classic genetic techniques and next-generation sequencing (NGS) for single-nucleotide variants and copy number variation (CNV) screening. Results Overall, 60% of our families were genetically solved. Interestingly, 3.1% of the cohort carried pathogenic CNVs. Disease-causing variants were found in an autosomal dominant gene in 55% of the families; however, X-linked and autosomal recessive forms were also identified in 3% and 2%, respectively. Four genes (RHO, PRPF31, RP1, and PRPH2) explained up to 62% of the solved families. Missense changes were most frequently found in adRP-associated genes; however, CNVs represented a relevant disease cause in PRPF31- and CRX-associated forms. Conclusions Implementation of NGS technologies in the adRP study clearly increased the diagnostic yield compared with classic approaches. Our study outcome expands the spectrum of disease-causing variants, provides accurate data on mutation gene prevalence, and highlights the implication of CNVs as important contributors to adRP etiology.
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Affiliation(s)
- Inmaculada Martin-Merida
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Domingo Aguilera-Garcia
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Jose P Fernandez-San
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Fiona Blanco-Kelly
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Olga Zurita
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Berta Almoguera
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Blanca Garcia-Sandoval
- Department of Ophthalmology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Almudena Avila-Fernandez
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Ana Arteche
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Pablo Minguez
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Miguel Carballo
- Molecular Genetics Unit, Hospital de Terrassa, Terrassa, Barcelona, Spain
| | - Marta Corton
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
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Sharon D, Wimberg H, Kinarty Y, Koch KW. Genotype-functional-phenotype correlations in photoreceptor guanylate cyclase (GC-E) encoded by GUCY2D. Prog Retin Eye Res 2018; 63:69-91. [DOI: 10.1016/j.preteyeres.2017.10.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/16/2017] [Accepted: 10/16/2017] [Indexed: 01/09/2023]
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7
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The pros and cons of vertebrate animal models for functional and therapeutic research on inherited retinal dystrophies. Prog Retin Eye Res 2015; 48:137-59. [DOI: 10.1016/j.preteyeres.2015.04.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/12/2015] [Accepted: 04/16/2015] [Indexed: 01/19/2023]
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Application of Whole Exome Sequencing in Six Families with an Initial Diagnosis of Autosomal Dominant Retinitis Pigmentosa: Lessons Learned. PLoS One 2015. [PMID: 26197217 PMCID: PMC4509755 DOI: 10.1371/journal.pone.0133624] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
This study aimed to identify the genetics underlying dominant forms of inherited retinal dystrophies using whole exome sequencing (WES) in six families extensively screened for known mutations or genes. Thirty-eight individuals were subjected to WES. Causative variants were searched among single nucleotide variants (SNVs) and insertion/deletion variants (indels) and whenever no potential candidate emerged, copy number variant (CNV) analysis was performed. Variants or regions harboring a candidate variant were prioritized and segregation of the variant with the disease was further assessed using Sanger sequencing in case of SNVs and indels, and quantitative PCR (qPCR) for CNVs. SNV and indel analysis led to the identification of a previously reported mutation in PRPH2. Two additional mutations linked to different forms of retinal dystrophies were identified in two families: a known frameshift deletion in RPGR, a gene responsible for X-linked retinitis pigmentosa and p.Ser163Arg in C1QTNF5 associated with Late-Onset Retinal Degeneration. A novel heterozygous deletion spanning the entire region of PRPF31 was also identified in the affected members of a fourth family, which was confirmed with qPCR. This study allowed the identification of the genetic cause of the retinal dystrophy and the establishment of a correct diagnosis in four families, including a large heterozygous deletion in PRPF31, typically considered one of the pitfalls of this method. Since all findings in this study are restricted to known genes, we propose that targeted sequencing using gene-panel is an optimal first approach for the genetic screening and that once known genetic causes are ruled out, WES might be used to uncover new genes involved in inherited retinal dystrophies.
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Retinitis Pigmentosa with EYS Mutations Is the Most Prevalent Inherited Retinal Dystrophy in Japanese Populations. J Ophthalmol 2015; 2015:819760. [PMID: 26161267 PMCID: PMC4487330 DOI: 10.1155/2015/819760] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 05/19/2015] [Indexed: 11/18/2022] Open
Abstract
The aim of this study was to gain information about disease prevalence and to identify the responsible genes for inherited retinal dystrophies (IRD) in Japanese populations. Clinical and molecular evaluations were performed on 349 patients with IRD. For segregation analyses, 63 of their family members were employed. Bioinformatics data from 1,208 Japanese individuals were used as controls. Molecular diagnosis was obtained by direct sequencing in a stepwise fashion utilizing one or two panels of 15 and 27 genes for retinitis pigmentosa patients. If a specific clinical diagnosis was suspected, direct sequencing of disease-specific genes, that is, ABCA4 for Stargardt disease, was conducted. Limited availability of intrafamily information and decreasing family size hampered identifying inherited patterns. Differential disease profiles with lower prevalence of Stargardt disease from European and North American populations were obtained. We found 205 sequence variants in 159 of 349 probands with an identification rate of 45.6%. This study found 43 novel sequence variants. In silico analysis suggests that 20 of 25 novel missense variants are pathogenic. EYS mutations had the highest prevalence at 23.5%. c.4957_4958insA and c.8868C>A were the two major EYS mutations identified in this cohort. EYS mutations are the most prevalent among Japanese patients with IRD.
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GUCY2D- or GUCA1A-related autosomal dominant cone-rod dystrophy: is there a phenotypic difference? Retina 2014; 34:1576-87. [PMID: 24875811 DOI: 10.1097/iae.0000000000000129] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
PURPOSE To compare the phenotype of patients with heterozygous mutation in GUCY2D or GUCA1A causing autosomal dominant cone or cone-rod dystrophies. METHODS Five patients from one family with GUCA1A and nine patients from four families with GUCY2D mutations were included. Psychophysical and electrophysiological examinations were performed to study retinal function. Fundus autofluorescence imaging and spectral domain optical coherence tomography were performed for morphologic characterization. RESULTS Genetic analysis revealed the mutation c.451C>T (p.L151F) in the GUCA1A family. In the GUCY2D group, c.2512C>T (p.R838C) was the most frequent (2 families), c.2512C>G (p.R838G) and c.2513G>A (p.R838H) were found in one family each. Visual acuity was reduced to 0.04 to 0.7 in GUCA1A and to 0.014 to 0.5 in patients with GUCY2D. Dark adaptation showed elevated thresholds in the GUCY2D group. Scotopic electroretinography revealed a tendency to a more affected rod function in the GUCY2D group. Photopic electroretinography showed residual or absent responses in both groups. Fundus alterations were confined to the macula in both groups. CONCLUSION GUCA1A and GUCY2D mutations are both accompanied by similar pattern of generalized cone dysfunction with a tendency to less involvement of the rod photoreceptors and a less severe phenotype in patients with GUCA1A.
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Roosing S, Thiadens AAHJ, Hoyng CB, Klaver CCW, den Hollander AI, Cremers FPM. Causes and consequences of inherited cone disorders. Prog Retin Eye Res 2014; 42:1-26. [PMID: 24857951 DOI: 10.1016/j.preteyeres.2014.05.001] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 04/29/2014] [Accepted: 05/06/2014] [Indexed: 11/18/2022]
Abstract
Hereditary cone disorders (CDs) are characterized by defects of the cone photoreceptors or retinal pigment epithelium underlying the macula, and include achromatopsia (ACHM), cone dystrophy (COD), cone-rod dystrophy (CRD), color vision impairment, Stargardt disease (STGD) and other maculopathies. Forty-two genes have been implicated in non-syndromic inherited CDs. Mutations in the 5 genes implicated in ACHM explain ∼93% of the cases. On the contrary, only 21% of CRDs (17 genes) and 25% of CODs (8 genes) have been elucidated. The fact that the large majority of COD and CRD-associated genes are yet to be discovered hints towards the existence of unknown cone-specific or cone-sensitive processes. The ACHM-associated genes encode proteins that fulfill crucial roles in the cone phototransduction cascade, which is the most frequently compromised (10 genes) process in CDs. Another 7 CD-associated proteins are required for transport processes towards or through the connecting cilium. The remaining CD-associated proteins are involved in cell membrane morphogenesis and maintenance, synaptic transduction, and the retinoid cycle. Further novel genes are likely to be identified in the near future by combining large-scale DNA sequencing and transcriptomics technologies. For 31 of 42 CD-associated genes, mammalian models are available, 14 of which have successfully been used for gene augmentation studies. However, gene augmentation for CDs should ideally be developed in large mammalian models with cone-rich areas, which are currently available for only 11 CD genes. Future research will aim to elucidate the remaining causative genes, identify the molecular mechanisms of CD, and develop novel therapies aimed at preventing vision loss in individuals with CD in the future.
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Affiliation(s)
- Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | | | - Carel B Hoyng
- Department of Ophthalmology, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Caroline C W Klaver
- Department of Ophthalmology Erasmus Medical Centre, 3000 CA, Rotterdam, The Netherlands; Department of Epidemiology, Erasmus Medical Centre, 3000 CA, Rotterdam, The Netherlands
| | - Anneke I den Hollander
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, PO Box 9101, 6500 HB, Nijmegen, The Netherlands; Department of Ophthalmology, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.
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