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Buckley RM, Ostrander EA. Large-scale genomic analysis of the domestic dog informs biological discovery. Genome Res 2024; 34:811-821. [PMID: 38955465 PMCID: PMC11293549 DOI: 10.1101/gr.278569.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Recent advances in genomics, coupled with a unique population structure and remarkable levels of variation, have propelled the domestic dog to new levels as a system for understanding fundamental principles in mammalian biology. Central to this advance are more than 350 recognized breeds, each a closed population that has undergone selection for unique features. Genetic variation in the domestic dog is particularly well characterized compared with other domestic mammals, with almost 3000 high-coverage genomes publicly available. Importantly, as the number of sequenced genomes increases, new avenues for analysis are becoming available. Herein, we discuss recent discoveries in canine genomics regarding behavior, morphology, and disease susceptibility. We explore the limitations of current data sets for variant interpretation, tradeoffs between sequencing strategies, and the burgeoning role of long-read genomes for capturing structural variants. In addition, we consider how large-scale collections of whole-genome sequence data drive rare variant discovery and assess the geographic distribution of canine diversity, which identifies Asia as a major source of missing variation. Finally, we review recent comparative genomic analyses that will facilitate annotation of the noncoding genome in dogs.
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Affiliation(s)
- Reuben M Buckley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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Bodenbender JP, Bethge L, Stingl K, Mazzola P, Haack T, Biskup S, Wissinger B, Weisschuh N, Kohl S, Kühlewein L. Clinical and Genetic Findings in a Cohort of Patients with PRPF31-Associated Retinal Dystrophy. Am J Ophthalmol 2024; 267:213-229. [PMID: 38909744 DOI: 10.1016/j.ajo.2024.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 06/12/2024] [Accepted: 06/13/2024] [Indexed: 06/25/2024]
Abstract
PURPOSE The purpose of our study was to assess the phenotypic and genotypic spectrum in a large cohort of patients with PRPF31-associated retinal dystrophy. DESIGN Retrospective cohort study. METHODS In this retrospective chart review study, we collected cross-sectional data on the phenotype and genotype of patients with PRPF31-associated retinal dystrophy from the clinics for inherited retinal dystrophies at the University of Tuebingen and the local RetDis database and biobank. Patients underwent thorough ophthalmological examinations and genetic testing. RESULTS Eighty-six patients from 61 families were available for clinical assessment, while genomic DNA was available for 111 individuals (index patients and family members). Fifty-three different disease-associated variants were observed in our cohort. Point mutations were the most common class. All but two patients exhibited features of a typical Retinitis pigmentosa (RP). One patient showed a cone-rod dystrophy pattern. One mutation carrier revealed no signs of a retinal dystrophy. There was a statistically significant better visual acuity for patients with large deletions in the 20-39 age group. Cystoid macular edema was common in those with preserved central retina and showed an association with female sex. CONCLUSION Our study confirms high phenotypic variability in disease onset and age at which legal blindness is reached in PRPF31-associated RP. Non-penetrance is commonly documented in family history, although poorly represented in our study, possibly indicating that true asymptomatic mutation carriers are rare if followed-up over lifetime with thorough ophthalmologic workup.
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Affiliation(s)
- Jan-Philipp Bodenbender
- University Eye Hospital, Center for Ophthalmology, Eberhard Karls University (J.P.B., L.B., K.S., L.K.), Tübingen, Germany
| | - Leon Bethge
- University Eye Hospital, Center for Ophthalmology, Eberhard Karls University (J.P.B., L.B., K.S., L.K.), Tübingen, Germany
| | - Katarina Stingl
- University Eye Hospital, Center for Ophthalmology, Eberhard Karls University (J.P.B., L.B., K.S., L.K.), Tübingen, Germany
| | - Pascale Mazzola
- Institute of Medical Genetics and Applied Genomics, Eberhard Karls University (P.M., T.H.), Tübingen, Germany
| | - Tobias Haack
- Institute of Medical Genetics and Applied Genomics, Eberhard Karls University (P.M., T.H.), Tübingen, Germany; Center for Rare Diseases, Eberhard Karls University (T.H.), Tübingen, Germany
| | | | - Bernd Wissinger
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Center for Ophthalmology, Eberhard Karls University (B.W., N.W., S.K.), Tübingen, Germany
| | - Nicole Weisschuh
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Center for Ophthalmology, Eberhard Karls University (B.W., N.W., S.K.), Tübingen, Germany
| | - Susanne Kohl
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Center for Ophthalmology, Eberhard Karls University (B.W., N.W., S.K.), Tübingen, Germany
| | - Laura Kühlewein
- University Eye Hospital, Center for Ophthalmology, Eberhard Karls University (J.P.B., L.B., K.S., L.K.), Tübingen, Germany; Institute for Ophthalmic Research, Center for Ophthalmology, Eberhard Karls University (L.K.), Tübingen, Germany.
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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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Zheng Y, Chen S. Transcriptional precision in photoreceptor development and diseases - Lessons from 25 years of CRX research. Front Cell Neurosci 2024; 18:1347436. [PMID: 38414750 PMCID: PMC10896975 DOI: 10.3389/fncel.2024.1347436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/19/2024] [Indexed: 02/29/2024] Open
Abstract
The vertebrate retina is made up of six specialized neuronal cell types and one glia that are generated from a common retinal progenitor. The development of these distinct cell types is programmed by transcription factors that regulate the expression of specific genes essential for cell fate specification and differentiation. Because of the complex nature of transcriptional regulation, understanding transcription factor functions in development and disease is challenging. Research on the Cone-rod homeobox transcription factor CRX provides an excellent model to address these challenges. In this review, we reflect on 25 years of mammalian CRX research and discuss recent progress in elucidating the distinct pathogenic mechanisms of four CRX coding variant classes. We highlight how in vitro biochemical studies of CRX protein functions facilitate understanding CRX regulatory principles in animal models. We conclude with a brief discussion of the emerging systems biology approaches that could accelerate precision medicine for CRX-linked diseases and beyond.
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Affiliation(s)
- Yiqiao Zheng
- Molecular Genetics and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Saint Louis, MO, United States
- Department of Ophthalmology and Visual Sciences, Saint Louis, MO, United States
| | - Shiming Chen
- Molecular Genetics and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Saint Louis, MO, United States
- Department of Ophthalmology and Visual Sciences, Saint Louis, MO, United States
- Department of Developmental Biology, Washington University in St. Louis, Saint Louis, MO, United States
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Aweidah H, Xi Z, Sahel JA, Byrne LC. PRPF31-retinitis pigmentosa: Challenges and opportunities for clinical translation. Vision Res 2023; 213:108315. [PMID: 37714045 PMCID: PMC10872823 DOI: 10.1016/j.visres.2023.108315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/17/2023]
Abstract
Mutations in pre-mRNA processing factor 31 cause autosomal dominant retinitis pigmentosa (PRPF31-RP), for which there is currently no efficient treatment, making this disease a prime target for the development of novel therapeutic strategies. PRPF31-RP exhibits incomplete penetrance due to haploinsufficiency, in which reduced levels of gene expression from the mutated allele result in disease. A variety of model systems have been used in the investigation of disease etiology and therapy development. In this review, we discuss recent advances in both in vivo and in vitro model systems, evaluating their advantages and limitations in the context of therapy development for PRPF31-RP. Additionally, we describe the latest approaches for treatment, including AAV-mediated gene augmentation, genome editing, and late-stage therapies such as optogenetics, cell transplantation, and retinal prostheses.
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Affiliation(s)
- Hamzah Aweidah
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhouhuan Xi
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Ophthalmology, Eye Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - José-Alain Sahel
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Leah C Byrne
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA.
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Sakti DH, Cornish EE, Nash BM, Jamieson RV, Grigg JR. IMPDH1-associated autosomal dominant retinitis pigmentosa: natural history of novel variant Lys314Gln and a comprehensive literature search. Ophthalmic Genet 2023; 44:437-455. [PMID: 37259572 DOI: 10.1080/13816810.2023.2215310] [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: 01/27/2023] [Revised: 05/11/2023] [Accepted: 05/14/2023] [Indexed: 06/02/2023]
Abstract
BACKGROUND Inosine monophosphate dehydrogenase (IMPDH) is a key regulatory enzyme in the de novo synthesis of the purine base guanine. Mutations in the inosine monophosphate dehydrogenase 1 gene (IMPDH1) are causative for RP10 autosomal dominant retinitis pigmentosa (adRP). This study reports a novel variant in a family with IMPDH1-associated retinopathy. We also performed a comprehensive review of all reported IMPDH1 disease causing variants with their associated phenotype. MATERIALS AND METHODS Multimodal imaging and functional studies documented the phenotype including best-corrected visual acuity (BCVA), fundus photograph, fundus autofluorescence (FAF), full field electroretinogram (ffERG), optical coherence tomography (OCT) and visual field (VF) data were collected. A literature search was performed in the PubMed and LOVD repositories. RESULTS We report 3 cases from a 2-generation family with a novel heterozygous likely pathogenic variant p. (Lys314Gln) (exon 10). The ophthalmic phenotype showed diffuse outer retinal atrophy with mild pigmentary changes with sparse pigmentary changes. FAF showed early macular involvement with macular hyperautofluorescence (hyperAF) surrounded by hypoAF. Foveal ellipsoid zone island can be found in the youngest patient but not in the older ones. The literature review identified a further 56 heterozygous, 1 compound heterozygous, and 2 homozygous variant. The heterozygous group included 43 missense, 3 in-frame, 1 nonsense, 2 frameshift, 1 synonymous, and 6 intronic variants. Exon 10 was noted as a hotspot harboring 18 variants. CONCLUSIONS We report a novel IMPDH1 variant. IMPDH1-associated retinopathy presents most frequently in the first decade of life with early macular involvement.
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Affiliation(s)
- Dhimas H Sakti
- Save Sight Institute, University of Sydney, Sydney, New South Wales, Australia
- Department of Ophthalmology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Elisa E Cornish
- Save Sight Institute, University of Sydney, Sydney, New South Wales, Australia
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Benjamin M Nash
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Sydney Genome Diagnostics, Western Sydney Genetics Program, Sydney Children's Hospitals Network, Sydney, New South Wales, Australia
| | - Robyn V Jamieson
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - John R Grigg
- Save Sight Institute, University of Sydney, Sydney, New South Wales, Australia
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
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Daich Varela M, Georgiadis A, Michaelides M. Genetic treatment for autosomal dominant inherited retinal dystrophies: approaches, challenges and targeted genotypes. Br J Ophthalmol 2023; 107:1223-1230. [PMID: 36038193 DOI: 10.1136/bjo-2022-321903] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/01/2022] [Indexed: 11/04/2022]
Abstract
Inherited retinal diseases (IRDs) have been in the front line of gene therapy development for the last decade, providing a useful platform to test novel therapeutic approaches. More than 40 clinical trials have been completed or are ongoing, tackling autosomal recessive and X-linked conditions, mostly through adeno-associated viral vector delivery of a normal copy of the disease-causing gene. However, only recently has autosomal dominant (ad) disease been targeted, with the commencement of a trial for rhodopsin (RHO)-associated retinitis pigmentosa (RP), implementing antisense oligonucleotide (AON) therapy, with promising preliminary results (NCT04123626).Autosomal dominant RP represents 15%-25% of all RP, with RHO accounting for 20%-30% of these cases. Autosomal dominant macular and cone-rod dystrophies (MD/CORD) correspond to approximately 7.5% of all IRDs, and approximately 35% of all MD/CORD cases, with the main causative gene being BEST1 Autosomal dominant IRDs are not only less frequent than recessive, but also tend to be less severe and have later onset; for example, an individual with RHO-adRP would typically become severely visually impaired at an age 2-3 times older than in X-linked RPGR-RP.Gain-of-function and dominant negative aetiologies are frequently seen in the prevalent adRP genes RHO, RP1 and PRPF31 among others, which would not be effectively addressed by gene supplementation alone and need creative, novel approaches. Zinc fingers, RNA interference, AON, translational read-through therapy, and gene editing by clustered regularly interspaced short palindromic repeats/Cas are some of the strategies that are currently under investigation and will be discussed here.
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Affiliation(s)
- Malena Daich Varela
- Moorfields Eye Hospital, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
| | | | - Michel Michaelides
- Moorfields Eye Hospital, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
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Wang Y, Wang J, Jiang Y, Zhu D, Ouyang J, Yi Z, Li S, Jia X, Xiao X, Sun W, Wang P, Zhang Q. New Insight into the Genotype-Phenotype Correlation of PRPH2-Related Diseases Based on a Large Chinese Cohort and Literature Review. Int J Mol Sci 2023; 24:ijms24076728. [PMID: 37047703 PMCID: PMC10095211 DOI: 10.3390/ijms24076728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/21/2023] [Accepted: 03/31/2023] [Indexed: 04/08/2023] Open
Abstract
Variants in PRPH2 are a common cause of inherited retinal dystrophies with high genetic and phenotypic heterogeneity. In this study, variants in PRPH2 were selected from in-house exome sequencing data, and all reported PRPH2 variants were evaluated with the assistance of online prediction tools and the comparative validation of large datasets. All variants were classified based on the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines. Individuals with pathogenic or likely pathogenic variants of PRPH2 were confirmed by Sanger sequencing. Clinical characteristics were summarized. Ten pathogenic or likely pathogenic variants of PRPH2 were identified in 14 families. In our cohort, the most frequent variant was p.G305Afs*19, accounting for 33.3% (5/15) of alleles, in contrast to the literature, where p.R172G (11.6%, 119/1028) was the most common variant. Nine in-house families (63.8%) were diagnosed with retinitis pigmentosa (RP), distinct from the phenotypic spectrum in the literature, which shows that RP accounts for 27.9% (283/1013) and macular degeneration is more common (45.2%, 458/1013). Patients carrying missense variants predicted as damaging by all seven prediction tools and absent in the gnomAD database were more likely to develop RP compared to those carrying missense variants predicted as damaging with fewer tools or with more than one allele number in the gnomAD database (p = 0.001). The population-specific genetic and phenotypic spectra of PRPH2 were explored, and novel insight into the genotype–phenotype correlation of PRPH2 was proposed. These findings demonstrated the importance of assessing PRPH2 variants in distinct populations and the value of providing practical suggestions for the genetic interpretation of PRPH2 variants.
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Affiliation(s)
- Yingwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Junwen Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Yi Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Di Zhu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Jiamin Ouyang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Zhen Yi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Xiaoyun Jia
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Panfeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
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9
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Wawrocka A, Socha M, Walczak-Sztulpa J, Koczyk G, Skorczyk-Werner A, Krawczyński MR. Molecular Re-Diagnosis with Whole-Exome Sequencing Increases the Diagnostic Yield in Patients with Non-Syndromic Retinitis Pigmentosa. Diagnostics (Basel) 2023; 13:diagnostics13040730. [PMID: 36832217 PMCID: PMC9954991 DOI: 10.3390/diagnostics13040730] [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: 01/16/2023] [Revised: 02/08/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
Retinitis pigmentosa (RP) is a clinically and genetically heterogeneous group of disorders with progressive loss of photoreceptor and pigment epithelial function. Nineteen unrelated Polish probands clinically diagnosed with nonsyndromic RP were recruited to this study. We used whole-exome sequencing (WES) to identify potential pathogenic gene variants in molecularly undiagnosed RP patients, as a molecular re-diagnosis after having performed targeted NGS in the past. Targeted NGS allowed for identification of the molecular background in only 5 out of 19 patients. Fourteen patients who remained unsolved despite the targeted NGS were subjected to WES. WES revealed potentially causative variants in RP-related genes in another 12 patients. Together, NGS methods revealed the coexistence of causal variants affecting distinct RP genes in 17 out of 19 RP families, with a very high efficiency of 89%. With the improvement of NGS methods, including higher sequencing depth, broader target enrichment, and better bioinformatic analysis capabilities, the ratio of identified causal gene variants has significantly increased. Therefore, it is important to consider repeating high-throughput sequencing analysis in those patients in whom the previously performed NGS did not reveal any pathogenic variants. The study confirmed the efficiency and clinical utility of re-diagnosis with WES in molecularly undiagnosed RP patients.
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Affiliation(s)
- Anna Wawrocka
- Department of Medical Genetics, Poznan University of Medical Sciences, 60-806 Poznan, Poland
- Correspondence:
| | - Magdalena Socha
- Department of Medical Genetics, Poznan University of Medical Sciences, 60-806 Poznan, Poland
| | - Joanna Walczak-Sztulpa
- Department of Medical Genetics, Poznan University of Medical Sciences, 60-806 Poznan, Poland
| | - Grzegorz Koczyk
- Biometry and Bioinformatics Team, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland
| | - Anna Skorczyk-Werner
- Department of Medical Genetics, Poznan University of Medical Sciences, 60-806 Poznan, Poland
| | - Maciej R. Krawczyński
- Department of Medical Genetics, Poznan University of Medical Sciences, 60-806 Poznan, Poland
- Centers for Medical Genetics GENESIS, 60-529 Poznan, Poland
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10
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The Diagnostic Yield of Next Generation Sequencing in Inherited Retinal Diseases: A Systematic Review and Meta-analysis. Am J Ophthalmol 2022; 249:57-73. [PMID: 36592879 DOI: 10.1016/j.ajo.2022.12.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/16/2022] [Accepted: 12/23/2022] [Indexed: 01/01/2023]
Abstract
PURPOSE Accurate genotyping of individuals with inherited retinal diseases (IRD) is essential for patient management and identifying suitable candidates for gene therapies. This study evaluated the diagnostic yield of next generation sequencing (NGS) in IRDs. DESIGN Systematic review and meta-analysis. METHODS This systematic review was prospectively registered (CRD42021293619). Ovid MEDLINE and Ovid Embase were searched on 6 June 2022. Clinical studies evaluating the diagnostic yield of NGS in individuals with IRDs were eligible for inclusion. Risk of bias assessment was performed. Studies were pooled using a random...effects inverse variance model. Sources of heterogeneity were explored using stratified analysis, meta-regression, and sensitivity analysis. RESULTS This study included 105 publications from 28 countries. Most studies (90 studies) used targeted gene panels. The diagnostic yield of NGS was 61.3% (95% confidence interval: 57.8-64.7%; 51 studies) in mixed IRD phenotypes, 58.2% (51.6-64.6%; 41 studies) in rod-cone dystrophies, 57.7% (46.8-68.3%; eight studies) in macular and cone/cone-rod dystrophies, and 47.6% (95% CI: 41.0-54.3%; four studies) in familial exudative vitreoretinopathy. For mixed IRD phenotypes, a higher diagnostic yield was achieved pooling studies published between 2018-2022 (64.2% [59.5-68.7%]), studies using exome sequencing (73.5% [58.9-86.1%]), and studies using the American College of Medical Genetics variant interpretation standards (65.6% [60.8-70.4%]). CONCLUSION The current diagnostic yield of NGS in IRDs is between 52-74%. The certainty of the evidence was judged as low or very low. A key limitation of the current evidence is the significant heterogeneity between studies. Adoption of standardized reporting guidelines could improve confidence in future meta-analyses.
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11
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Gene augmentation prevents retinal degeneration in a CRISPR/Cas9-based mouse model of PRPF31 retinitis pigmentosa. Nat Commun 2022; 13:7695. [PMID: 36509783 PMCID: PMC9744804 DOI: 10.1038/s41467-022-35361-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
Mutations in PRPF31 cause autosomal dominant retinitis pigmentosa, an untreatable form of blindness. Gene therapy is a promising treatment for PRPF31-retinitis pigmentosa, however, there are currently no suitable animal models in which to develop AAV-mediated gene augmentation. Here we establish Prpf31 mutant mouse models using AAV-mediated CRISPR/Cas9 knockout, and characterize the resulting retinal degeneration phenotype. Mouse models with early-onset morphological and functional impairments like those in patients were established, providing new platforms in which to investigate pathogenetic mechanisms and develop therapeutic methods. AAV-mediated PRPF31 gene augmentation restored the retinal structure and function in a rapidly degenerating mouse model, demonstrating the first in vivo proof-of-concept for AAV-mediated gene therapy to treat PRPF31-retinitis pigmentosa. AAV-CRISPR/Cas9-PRPF31 knockout constructs also mediated efficient PRPF31 knockout in human and non-human primate retinal explants, laying a foundation for establishing non-human primate models using the method developed here.
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12
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Chen Z, Chen J, Gao M, Liu Y, Wu Y, Wang Y, Gong Y, Yu S, Liu W, Wan X, Sun X. Comprehensive analysis of the PRPF31 gene in retinitis pigmentosa patients: Four novel Alu-mediated copy number variations at the PRPF31 locus. Hum Mutat 2022; 43:2279-2294. [PMID: 36317469 DOI: 10.1002/humu.24494] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 10/10/2022] [Accepted: 10/24/2022] [Indexed: 11/11/2022]
Abstract
Retinitis pigmentosa (RP) is a monogenic disease characterized by irreversible degeneration of the retina. PRPF31, the second most common causative gene of autosomal dominant RP, frequently harbors copy number variations (CNVs), but the underlying mechanism is unclear. In this study, we summarized the phenotypic and genotypic characteristics of 18 RP families (F01-F18) with variants in PRPF31. The prevalence of PRPF31 variants in our cohort of Chinese RP families was 1.7% (18/1024). Seventeen different variants in PRPF31 were detected, including eight novel variants. Notably, four novel CNVs encompassing PRPF31, with a proportion of 22.2% (4/18), were validated to harbor gross deletions involving Alu/Alu-mediated rearrangements (AAMRs) in the same orientation. Among a total of 12 CNVs of PRPF31 with breakpoints mapped on nucleotide-resolution, 10 variants (83.3%) were presumably mediated by Alu elements. Furthermore, we described the correlation between the genotypes and phenotypes in PRPF31-related RP. Our findings expand the mutational spectrum of the PRPF31 gene and provide strong evidence that Alu elements of PRPF31 probably contribute to the susceptibility to genomic rearrangement in this locus.
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Affiliation(s)
- Zhixuan Chen
- Department of Ophthalmology, School of Medicine, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, Shanghai, China.,Department of Ophthalmology, National Clinical Research Center for Eye Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Jieqiong Chen
- Department of Ophthalmology, School of Medicine, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, Shanghai, China.,Department of Ophthalmology, National Clinical Research Center for Eye Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Min Gao
- Department of Ophthalmology, School of Medicine, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, Shanghai, China.,Department of Ophthalmology, National Clinical Research Center for Eye Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Yang Liu
- Department of Ophthalmology, School of Medicine, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, Shanghai, China.,Department of Ophthalmology, National Clinical Research Center for Eye Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Yidong Wu
- Department of Ophthalmology, School of Medicine, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, Shanghai, China.,Department of Ophthalmology, National Clinical Research Center for Eye Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Yafang Wang
- Department of Ophthalmology, School of Medicine, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, Shanghai, China.,Department of Ophthalmology, National Clinical Research Center for Eye Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Yuanyuan Gong
- Department of Ophthalmology, School of Medicine, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, Shanghai, China.,Department of Ophthalmology, National Clinical Research Center for Eye Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Suqin Yu
- Department of Ophthalmology, School of Medicine, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, Shanghai, China.,Department of Ophthalmology, National Clinical Research Center for Eye Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Wenjia Liu
- Department of Ophthalmology, School of Medicine, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, Shanghai, China.,Department of Ophthalmology, National Clinical Research Center for Eye Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Xiaoling Wan
- Department of Ophthalmology, School of Medicine, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, Shanghai, China.,Department of Ophthalmology, National Clinical Research Center for Eye Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Xiaodong Sun
- Department of Ophthalmology, School of Medicine, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, Shanghai, China.,Department of Ophthalmology, National Clinical Research Center for Eye Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
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13
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Developing CIRdb as a catalog of natural genetic variation in the Canary Islanders. Sci Rep 2022; 12:16132. [PMID: 36168029 PMCID: PMC9514705 DOI: 10.1038/s41598-022-20442-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022] Open
Abstract
The current inhabitants of the Canary Islands have a unique genetic makeup in the European diversity landscape due to the existence of African footprints from recent admixture events, especially of North African components (> 20%). The underrepresentation of non-Europeans in genetic studies and the sizable North African ancestry, which is nearly absent from all existing catalogs of worldwide genetic diversity, justify the need to develop CIRdb, a population-specific reference catalog of natural genetic variation in the Canary Islanders. Based on array genotyping of the selected unrelated donors and comparisons against available datasets from European, sub-Saharan, and North African populations, we illustrate the intermediate genetic differentiation of Canary Islanders between Europeans and North Africans and the existence of within-population differences that are likely driven by genetic isolation. Here we describe the overall design and the methods that are being implemented to further develop CIRdb. This resource will help to strengthen the implementation of Precision Medicine in this population by contributing to increase the diversity in genetic studies. Among others, this will translate into improved ability to fine map disease genes and simplify the identification of causal variants and estimate the prevalence of unattended Mendelian diseases.
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14
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Aggregated Genomic Data as Cohort-Specific Allelic Frequencies can Boost Variants and Genes Prioritization in Non-Solved Cases of Inherited Retinal Dystrophies. Int J Mol Sci 2022; 23:ijms23158431. [PMID: 35955564 PMCID: PMC9368980 DOI: 10.3390/ijms23158431] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 02/04/2023] Open
Abstract
The introduction of NGS in genetic diagnosis has increased the repertoire of variants and genes involved and the amount of genomic information produced. We built an allelic-frequency (AF) database for a heterogeneous cohort of genetic diseases to explore the aggregated genomic information and boost diagnosis in inherited retinal dystrophies (IRD). We retrospectively selected 5683 index-cases with clinical exome sequencing tests available, 1766 with IRD and the rest with diverse genetic diseases. We calculated a subcohort’s IRD-specific AF and compared it with suitable pseudocontrols. For non-solved IRD cases, we prioritized variants with a significant increment of frequencies, with eight variants that may help to explain the phenotype, and 10/11 of uncertain significance that were reclassified as probably pathogenic according to ACMG. Moreover, we developed a method to highlight genes with more frequent pathogenic variants in IRD cases than in pseudocontrols weighted by the increment of benign variants in the same comparison. We identified 18 genes for further studies that provided new insights in five cases. This resource can also help one to calculate the carrier frequency in IRD genes. A cohort-specific AF database assists with variants and genes prioritization and operates as an engine that provides a new hypothesis in non-solved cases, augmenting the diagnosis rate.
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15
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Bhardwaj A, Yadav A, Yadav M, Tanwar M. Genetic dissection of non-syndromic retinitis pigmentosa. Indian J Ophthalmol 2022; 70:2355-2385. [PMID: 35791117 PMCID: PMC9426071 DOI: 10.4103/ijo.ijo_46_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Retinitis pigmentosa (RP) belongs to a group of pigmentary retinopathies. It is the most common form of inherited retinal dystrophy, characterized by progressive degradation of photoreceptors that leads to nyctalopia, and ultimately, complete vision loss. RP is distinguished by the continuous retinal degeneration that progresses from the mid-periphery to the central and peripheral retina. RP was first described and named by Franciscus Cornelius Donders in the year 1857. It is one of the leading causes of bilateral blindness in adults, with an incidence of 1 in 3000 people worldwide. In this review, we are going to focus on the genetic heterogeneity of this disease, which is provided by various inheritance patterns, numerosity of variations and inter-/intra-familial variations based upon penetrance and expressivity. Although over 90 genes have been identified in RP patients, the genetic cause of approximately 50% of RP cases remains unknown. Heterogeneity of RP makes it an extremely complicated ocular impairment. It is so complicated that it is known as “fever of unknown origin”. For prognosis and proper management of the disease, it is necessary to understand its genetic heterogeneity so that each phenotype related to the various genetic variations could be treated.
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Affiliation(s)
- Aarti Bhardwaj
- Department of Genetics, M. D. University, Rohtak, Haryana, India
| | - Anshu Yadav
- Department of Genetics, M. D. University, Rohtak, Haryana, India
| | - Manoj Yadav
- Department of Genetics, M. D. University, Rohtak, Haryana, India
| | - Mukesh Tanwar
- Department of Genetics, M. D. University, Rohtak, Haryana, India
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16
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Wang J, Wang Y, Jiang Y, Li X, Xiao X, Li S, Jia X, Sun W, Wang P, Zhang Q. Autosomal Dominant Retinitis Pigmentosa-Associated TOPORS Protein Truncating Variants Are Exclusively Located in the Region of Amino Acid Residues 807 to 867. Invest Ophthalmol Vis Sci 2022; 63:19. [PMID: 35579903 PMCID: PMC9123486 DOI: 10.1167/iovs.63.5.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Heterozygous truncating variants of TOPORS have been reported to cause autosomal dominant retinitis pigmentosa (adRP). The purpose of this study was to investigate whether all heterozygous truncating variants, including copy number variants (CNVs), are pathogenic. Methods TOPORS truncating variants were collected and reviewed through an in-house dataset and existing databases. Individuals with truncating variants underwent ophthalmological evaluation. Results Six truncating variants were detected in seven families. Three N-terminus truncating variants were detected in three families without RP, and the other three were identified in four unrelated families with typical RP. Based on the in-house dataset and published literature, 17 truncating variants were identified in 47 families with RP. All RP-associated truncating alleles, except one, were distributed in the last exon of TOPORS and clustered in amino acid residues 807 to 867 (46/47, 97.9%). Conversely, in the gnomAD database, only one truncating allele (1/27, 3.7%) was in this region, and the others were outside (26/27, 96.3%), suggesting that the pathogenic truncating variants were significantly clustered in residues 807 to 867 (χ2 = 65.6, P = 1.1 × 10–17). Additionally, three CNVs involving the N-terminus of TOPORS were recorded in control populations but were absent in affected patients. Conclusions This study suggests that all pathogenic truncating variants of TOPORS were clustered in residues 807 to 867, whereas the truncating variants outside this region and the CNVs involving the N-terminus were not associated with RP. A dominant-negative effect, rather than haploinsufficiency, is speculated to be the underlying pathogenesis. These findings provide valuable information for interpreting variation in TOPORS and other genes in similar situations, especially for CNVs.
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Affiliation(s)
- Junwen Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yingwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yi Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xueqing Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xiaoyun Jia
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Panfeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
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17
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He K, Zhou Y, Li N. Mutations of TOPORS identified in families with retinitis pigmentosa. Ophthalmic Genet 2022; 43:371-377. [PMID: 35254173 DOI: 10.1080/13816810.2022.2039721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Kaiwen He
- Department of Ophthalmology, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, China 100045
| | - Yunyu Zhou
- Department of Ophthalmology, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, China 100045
| | - Ningdong Li
- Department of Ophthalmology, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, China 100045
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18
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Del Pozo-Valero M, Riveiro-Alvarez R, Martin-Merida I, Blanco-Kelly F, Swafiri S, Lorda-Sanchez I, Trujillo-Tiebas MJ, Carreño E, Jimenez-Rolando B, Garcia-Sandoval B, Corton M, Avila-Fernandez A, Ayuso C. Impact of Next Generation Sequencing in Unraveling the Genetics of 1036 Spanish Families With Inherited Macular Dystrophies. Invest Ophthalmol Vis Sci 2022; 63:11. [PMID: 35119454 PMCID: PMC8819279 DOI: 10.1167/iovs.63.2.11] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Purpose To assess the potential of next-generation sequencing (NGS) technologies to characterize cases diagnosed with autosomal recessive (ar) or sporadic (s) macular dystrophies (ar/sMD) and describe their mutational spectrum. Methods A cohort of 1036 families was classified according to their suspected clinical diagnosis—Stargardt disease (STGD), cone and cone-rod dystrophy (CCRD) or other maculopathies (otherMD). Molecular studies included genotyping microarrays, Sanger sequencing, NGS, and sequencing of intronic regions of the ABCA4 gene. Clinical reclassification was done after the genetic study. Results At the end of the study, 677 patients (65%) had a confirmed genetic diagnosis, representing 78%, 63%, and 38% of STGD, CCRD, and otherMD groups of patients, respectively. ABCA4 is the most mutated gene in all groups, and a second pathogenic variant was found in 76% of STGD patients with one previously identified mutated ABCA4 allele. Autosomal dominant or X-linked mutations were found in 5% of cases together with not-MD genes (CHM, EYS, RHO, RPGR, RLBP1, OPA1, and USH2A among others) leading to their reclassification. Novel variants in the very rare genes PLA2G5 and TTLL5 revealed additional phenotypic associations. Conclusions This study provides for the first time a genetic landscape of 1036 ar/sMD families according to their suspected diagnosis. The analysis of >200 genes associated with retinal dystrophies and the entire locus of ABCA4 increase the rate of characterization, even regardless of available clinical and familiar data. The use of the suspected a priori diagnosis referred by the clinicians, especially in the past, could lead to clinical reclassifications to other inherited retinal dystrophies.
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Affiliation(s)
- Marta Del Pozo-Valero
- 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
| | - Rosa Riveiro-Alvarez
- 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
| | - 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
| | - 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
| | - Saoud Swafiri
- 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
| | - Isabel Lorda-Sanchez
- 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
| | - Maria José Trujillo-Tiebas
- 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
| | - Ester Carreño
- Department of Ophthalmology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Belen Jimenez-Rolando
- Department of Ophthalmology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Blanca Garcia-Sandoval
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain.,Department of Ophthalmology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, 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
| | - 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
| | - 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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19
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Genetic and Phenotypic Landscape of PRPH2-Associated Retinal Dystrophy in Japan. Genes (Basel) 2021; 12:genes12111817. [PMID: 34828423 PMCID: PMC8624169 DOI: 10.3390/genes12111817] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/14/2021] [Accepted: 11/17/2021] [Indexed: 11/29/2022] Open
Abstract
Peripherin-2 (PRPH2) is one of the causative genes of inherited retinal dystrophy. While the gene is relatively common in Caucasians, reports from Asian ethnicities are limited. In the present study, we report 40 Japanese patients from 30 families with PRPH2-associated retinal dystrophy. We identified 17 distinct pathogenic or likely pathogenic variants using next-generation sequencing. Variants p.R142W and p.V200E were relatively common in the cohort. The age of onset was generally in the 40’s; however, some patients had earlier onset (age: 5 years). Visual acuity of the patients ranged from hand motion to 1.5 (Snellen equivalent 20/13). The patients showed variable phenotypes such as retinitis pigmentosa, cone-rod dystrophy, and macular dystrophy. Additionally, intrafamilial phenotypic variability was observed. Choroidal neovascularization was observed in three eyes of two patients with retinitis pigmentosa. The results demonstrate the genotypic and phenotypic variations of the disease in the Asian cohort.
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20
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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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21
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Kukhtar D, Rubio-Peña K, Serrat X, Cerón J. Mimicking of splicing-related retinitis pigmentosa mutations in C. elegans allow drug screens and identification of disease modifiers. Hum Mol Genet 2021; 29:756-765. [PMID: 31919495 DOI: 10.1093/hmg/ddz315] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/06/2019] [Accepted: 12/20/2019] [Indexed: 12/13/2022] Open
Abstract
CRISPR/Cas and the high conservation of the spliceosome components facilitate the mimicking of human pathological mutations in splicing factors of model organisms. The degenerative retinal disease retinitis pigmentosa (RP) is caused by mutations in distinct types of genes, including missense mutations in splicing factors that provoke RP in an autosomal dominant form (s-adRP). Using CRISPR in Caenorhabditis elegans, we generated mutant strains to mimic s-adRP mutations reported in PRPF8 and SNRNP200. Whereas these inherited mutations are present in heterozygosis in patients, C. elegans allows the maintenance of these mutations as homozygotes, which is advantageous for genetic and drug screens. We found that snrp-200(cer23[V676L]) and prp-8(cer14[H2302del]) display pleiotropic phenotypes, including reduced fertility. However, snrp-200(cer24[S1080L]) and prp-8(cer22[R2303G]) are weak alleles suitable for RNAi screens for identifying genetic interactions, which could uncover potential disease modifiers. We screened a collection of RNAi clones for splicing-related genes and identified three splicing factors: isy-1/ISY1, cyn-15/PPWD1 and mog-2/SNRPA1, whose partial inactivation may modify the course of the disease. Interestingly, these three genes act as modifiers of prp-8(cer22) but not of snrp-200(cer24). Finally, a screen of the strong allele prp-8(cer14) with FDA-approved drugs did not identify molecules capable of alleviating the temperature-sensitive sterility. Instead, we detected drugs, such as dequalinium chloride, which exacerbated the phenotype, and therefore, are potentially harmful to s-adRP patients since they may accelerate the progression of the disease.
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Affiliation(s)
- Dmytro Kukhtar
- Modeling human diseases in C. elegans Group. Genes, Disease and Therapy Program, Institut d'Investigació Biomèdica de Bellvitge-IDIBELL, 08908 Barcelona, Spain
| | - Karinna Rubio-Peña
- Modeling human diseases in C. elegans Group. Genes, Disease and Therapy Program, Institut d'Investigació Biomèdica de Bellvitge-IDIBELL, 08908 Barcelona, Spain
| | - Xènia Serrat
- Modeling human diseases in C. elegans Group. Genes, Disease and Therapy Program, Institut d'Investigació Biomèdica de Bellvitge-IDIBELL, 08908 Barcelona, Spain
| | - Julián Cerón
- Modeling human diseases in C. elegans Group. Genes, Disease and Therapy Program, Institut d'Investigació Biomèdica de Bellvitge-IDIBELL, 08908 Barcelona, Spain
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22
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Iancu IF, Avila-Fernandez A, Arteche A, Trujillo-Tiebas MJ, Riveiro-Alvarez R, Almoguera B, Martin-Merida I, Del Pozo-Valero M, Perea-Romero I, Corton M, Minguez P, Ayuso C. Prioritizing variants of uncertain significance for reclassification using a rule-based algorithm in inherited retinal dystrophies. NPJ Genom Med 2021; 6:18. [PMID: 33623043 PMCID: PMC7902814 DOI: 10.1038/s41525-021-00182-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 01/25/2021] [Indexed: 12/12/2022] Open
Abstract
Inherited retinal dystrophies (IRD) are a highly heterogeneous group of rare diseases with a molecular diagnostic rate of >50%. Reclassification of variants of uncertain significance (VUS) poses a challenge for IRD diagnosis. We collected 668 IRD cases analyzed by our geneticists using two different clinical exome-sequencing tests. We identified 114 unsolved cases pending reclassification of 125 VUS and studied their genomic, functional, and laboratory-specific features, comparing them to pathogenic and likely pathogenic variants from the same cohort (N = 390). While the clinical exome used did not show differences in diagnostic rate, the more IRD-experienced geneticist reported more VUS (p = 4.07e-04). Significantly fewer VUS were reported in recessive cases (p = 2.14e-04) compared to other inheritance patterns, and of all the genes analyzed, ABCA4 and IMPG2 had the lowest and highest VUS frequencies, respectively (p = 3.89e-04, p = 6.93e-03). Moreover, few frameshift and stop-gain variants were found to be informed VUS (p = 6.73e-08 and p = 2.93e-06). Last, we applied five pathogenicity predictors and found there is a significant proof of deleteriousness when all score for pathogenicity in missense variants. Altogether, these results provided input for a set of rules that correctly reclassified ~70% of VUS as pathogenic in validation datasets. Disease- and setting-specific features influence VUS reporting. Comparison with pathogenic and likely pathogenic variants can prioritize VUS more likely to be reclassified as causal.
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Affiliation(s)
- Ionut-Florin Iancu
- 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
| | - 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
| | - Maria Jose Trujillo-Tiebas
- 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
| | - Rosa Riveiro-Alvarez
- 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 Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - 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
| | - Marta Del Pozo-Valero
- 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
| | - Irene Perea-Romero
- 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
| | - 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
| | - Pablo Minguez
- 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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23
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Wang J, Xiao X, Li S, Wang P, Sun W, Zhang Q. Dominant RP in the Middle While Recessive in Both the N- and C-Terminals Due to RP1 Truncations: Confirmation, Refinement, and Questions. Front Cell Dev Biol 2021; 9:634478. [PMID: 33681214 PMCID: PMC7935555 DOI: 10.3389/fcell.2021.634478] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/19/2021] [Indexed: 11/13/2022] Open
Abstract
RP1 truncation variants, including frameshift, nonsense, and splicing, are a common cause of retinitis pigmentosa (RP). RP1 is a unique gene where truncations cause either autosomal dominant RP (adRP) or autosomal recessive RP (arRP) depending on the location of the variants. This study aims to clarify the boundaries between adRP and arRP caused by RP1 truncation variants based on a systemic analysis of 165 RP1 variants from our in-house exome-sequencing data of 7,092 individuals as well as a thorough review of 185 RP1 variants from published literature. In our cohort, potential pathogenic variants were detected in 16 families, including 11 new and five previously described families. Of the 16, seven families with adRP had heterozygous truncations in the middle portion, while nine families with either arRP (eight) or macular degeneration had biallelic variants in the N- and C-terminals, involving 10 known and seven novel variants. In the literature, 147 truncations in RP1 were reported to be responsible for either arRP (85) or adRP (58) or both (four). An overall evaluation of RP1 causative variants suggested three separate regions, i.e., the N-terminal from c.1 (p.1) to c.1837 (p.613), the middle portion from c.1981 (p.661) to c.2749 (p.917), and the C-terminal from c.2816 (p.939) to c.6471 (p.2157), where truncations in the middle portion were associated with adRP, while those in the N- and C-terminals were responsible for arRP. Heterozygous truncations alone in the N- and C- terminals were unlikely pathogenic. However, conflict reports with reverse situation were present for 13 variants, suggesting a complicated pathogenicity awaiting to be further elucidated. In addition, pathogenicity for homozygous truncations around c.5797 and thereafter might also need to be further clarified, so as for missense variants and for truncations located in the two gaps. Our data not only confirmed and refined the boundaries between dominant and recessive RP1 truncations but also revealed unsolved questions valuable for further investigation. These findings remind us that great care is needed in interpreting the results of RP1 variants in clinical gene testing as well as similar features may also be present in some other genes.
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Affiliation(s)
- Junwen Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Panfeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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24
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Zeitz C, Nassisi M, Laurent-Coriat C, Andrieu C, Boyard F, Condroyer C, Démontant V, Antonio A, Lancelot ME, Frederiksen H, Kloeckener-Gruissem B, El-Shamieh S, Zanlonghi X, Meunier I, Roux AF, Mohand-Saïd S, Sahel JA, Audo I. CHM mutation spectrum and disease: An update at the time of human therapeutic trials. Hum Mutat 2021; 42:323-341. [PMID: 33538369 DOI: 10.1002/humu.24174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 12/21/2020] [Accepted: 01/20/2021] [Indexed: 12/15/2022]
Abstract
Choroideremia is an X-linked inherited retinal disorder (IRD) characterized by the degeneration of retinal pigment epithelium, photoreceptors, choriocapillaris and choroid affecting males with variable phenotypes in female carriers. Unlike other IRD, characterized by a large clinical and genetic heterogeneity, choroideremia shows a specific phenotype with causative mutations in only one gene, CHM. Ongoing gene replacement trials raise further interests in this disorder. We describe here the clinical and genetic data from a French cohort of 45 families, 25 of which carry novel variants, in the context of 822 previously reported choroideremia families. Most of the variants represent loss-of-function mutations with eleven families having large (i.e. ≥6 kb) genomic deletions, 18 small insertions, deletions or insertion deletions, six showing nonsense variants, eight splice site variants and two missense variants likely to affect splicing. Similarly, 822 previously published families carry mostly loss-of-function variants. Recurrent variants are observed worldwide, some of which linked to a common ancestor, others arisen independently in specific CHM regions prone to mutations. Since all exons of CHM may harbor variants, Sanger sequencing combined with quantitative polymerase chain reaction or multiplex ligation-dependent probe amplification experiments are efficient to achieve the molecular diagnosis in patients with typical choroideremia features.
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Affiliation(s)
- Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Marco Nassisi
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | - Camille Andrieu
- CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC1423, Paris, France
| | - Fiona Boyard
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | - Vanessa Démontant
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Aline Antonio
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | - Helen Frederiksen
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Barbara Kloeckener-Gruissem
- Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland.,Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Said El-Shamieh
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
| | - Xavier Zanlonghi
- Clinique Pluridisciplinaire Jules Verne, Institut Ophtalmologique de l'Ouest, Nantes, France
| | - Isabelle Meunier
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, Montpellier University Hospital, Montpellier, France.,Institute for Neurosciences of Montpellier (INM), University of Montpellier, INSERM, Montpellier, France
| | - Anne-Françoise Roux
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Université de Montpellier, Montpellier, France
| | - Saddek Mohand-Saïd
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC1423, Paris, France
| | - José-Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC1423, Paris, France.,Fondation Ophtalmologique Adolphe de Rothschild, Paris, France.,Académie des Sciences-Institut de France, Paris, France.,Department of Ophthalmology, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC1423, Paris, France.,Department of Genetics, UCL-Institute of Ophthalmology, London, UK
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25
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Xiao T, Xie Y, Zhang X, Xu K, Zhang X, Jin ZB, Li Y. Variant Profiling of a Large Cohort of 138 Chinese Families With Autosomal Dominant Retinitis Pigmentosa. Front Cell Dev Biol 2021; 8:629994. [PMID: 33598457 PMCID: PMC7882618 DOI: 10.3389/fcell.2020.629994] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
Retinitis pigmentosa (RP) is the most common form of inherited retinal dystrophy, and 15–25% of RP is transmitted as an autosomal dominant (ad) trait. The objectives of this study were to establish the variant profile in a large cohort of adRP families and to elucidate the variant spectrum of each adRP gene in Chinese patients. A total of 138 probands clinically diagnosed with RP as a presumed autosomal dominant trait were recruited. All probands underwent ophthalmic examinations by specialists. A combination of molecular screening methods, including targeted next-generation sequencing, Sanger DNA sequencing, and multiplex ligation probe amplification assay, was used to detect variants. We identified heterozygous variants of 11 adRP genes in 73 probands, hemizygous, or heterozygous variants of X-linked RP genes in six patients, compound heterozygous variants of autosomal recessive RP genes in three pseudodominant families, and one heterozygous variant of one ad cone and rod dystrophy gene in one proband. One proband was found carrying both variants in RPGR and FAM161A. The overall detection rate was 59.4% (82/138). We detected 72 distinct disease-causing variants involving 16 RP genes and one cone-rod dystrophy gene; 33 of these variants have not been reported previously. Disease-causing variants were identified in the adRP genes in 52.9% of the families, followed by 4.3% in the X-linked RP genes, and 2.2% in the autosomal recessive genes. The most frequent mutant genes were RHO, PRPF31, RP1, SNRNP200, and PRPF8, which explained up to 78.0% of the genetically diagnosed families. Most of the variants identified in adRP genes were missense, and copy number variations were common (7/20) in the PRPF31 gene. We established the profile of the mutated genes and the variant spectrum of adRP genes in a large cohort of Chinese patients, providing essential information for genetic counseling and future development of therapeutics for retinal dystrophy inherited as a dominant trait.
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Affiliation(s)
- Ting Xiao
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Yue Xie
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Xin Zhang
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Ke Xu
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Xiaohui Zhang
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Zi-Bing Jin
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Yang Li
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
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Perea-Romero I, Gordo G, Iancu IF, Del Pozo-Valero M, Almoguera B, Blanco-Kelly F, Carreño E, Jimenez-Rolando B, Lopez-Rodriguez R, Lorda-Sanchez I, Martin-Merida I, Pérez de Ayala L, Riveiro-Alvarez R, Rodriguez-Pinilla E, Tahsin-Swafiri S, Trujillo-Tiebas MJ, Garcia-Sandoval B, Minguez P, Avila-Fernandez A, Corton M, Ayuso C. Genetic landscape of 6089 inherited retinal dystrophies affected cases in Spain and their therapeutic and extended epidemiological implications. Sci Rep 2021; 11:1526. [PMID: 33452396 PMCID: PMC7810997 DOI: 10.1038/s41598-021-81093-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/31/2020] [Indexed: 02/08/2023] Open
Abstract
Inherited retinal diseases (IRDs), defined by dysfunction or progressive loss of photoreceptors, are disorders characterized by elevated heterogeneity, both at the clinical and genetic levels. Our main goal was to address the genetic landscape of IRD in the largest cohort of Spanish patients reported to date. A retrospective hospital-based cross-sectional study was carried out on 6089 IRD affected individuals (from 4403 unrelated families), referred for genetic testing from all the Spanish autonomous communities. Clinical, demographic and familiar data were collected from each patient, including family pedigree, age of appearance of visual symptoms, presence of any systemic findings and geographical origin. Genetic studies were performed to the 3951 families with available DNA using different molecular techniques. Overall, 53.2% (2100/3951) of the studied families were genetically characterized, and 1549 different likely causative variants in 142 genes were identified. The most common phenotype encountered is retinitis pigmentosa (RP) (55.6% of families, 2447/4403). The most recurrently mutated genes were PRPH2, ABCA4 and RS1 in autosomal dominant (AD), autosomal recessive (AR) and X-linked (XL) NON-RP cases, respectively; RHO, USH2A and RPGR in AD, AR and XL for non-syndromic RP; and USH2A and MYO7A in syndromic IRD. Pathogenic variants c.3386G > T (p.Arg1129Leu) in ABCA4 and c.2276G > T (p.Cys759Phe) in USH2A were the most frequent variants identified. Our study provides the general landscape for IRD in Spain, reporting the largest cohort ever presented. Our results have important implications for genetic diagnosis, counselling and new therapeutic strategies to both the Spanish population and other related populations.
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Affiliation(s)
- Irene Perea-Romero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Gema Gordo
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Ionut F Iancu
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Del Pozo-Valero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Berta Almoguera
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Fiona Blanco-Kelly
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Ester Carreño
- Department of Ophthalmology, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Belen Jimenez-Rolando
- Department of Ophthalmology, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Rosario Lopez-Rodriguez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Isabel Lorda-Sanchez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Inmaculada Martin-Merida
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Lucia Pérez de Ayala
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Rosa Riveiro-Alvarez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Elvira Rodriguez-Pinilla
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Saoud Tahsin-Swafiri
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Maria J Trujillo-Tiebas
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | | | | | | | - Blanca Garcia-Sandoval
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Department of Ophthalmology, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Pablo Minguez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Almudena Avila-Fernandez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Corton
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain. .,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
| | - Carmen Ayuso
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain. .,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
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27
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Del Pozo-Valero M, Riveiro-Alvarez R, Blanco-Kelly F, Aguirre-Lamban J, Martin-Merida I, Iancu IF, Swafiri S, Lorda-Sanchez I, Rodriguez-Pinilla E, Trujillo-Tiebas MJ, Jimenez-Rolando B, Carreño E, Mahillo-Fernandez I, Rivolta C, Corton M, Avila-Fernandez A, Garcia-Sandoval B, Ayuso C. Genotype-Phenotype Correlations in a Spanish Cohort of 506 Families With Biallelic ABCA4 Pathogenic Variants. Am J Ophthalmol 2020; 219:195-204. [PMID: 32619608 DOI: 10.1016/j.ajo.2020.06.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/19/2020] [Accepted: 06/21/2020] [Indexed: 01/28/2023]
Abstract
PURPOSE To define genotype-phenotype correlations in the largest cohort study worldwide of patients with biallelic ABCA4 variants, including 434 patients with Stargardt disease (STGD1) and 72 with cone-rod dystrophy (CRD). DESIGN Cohort study. METHODS We characterized 506 patients with ABCA4 variants using conventional genetic tools and next-generation sequencing technologies. Medical history and ophthalmologic data were obtained from 372 patients. Genotype-phenotype correlation studies were carried out for the following variables: variant type, age at symptom onset (AO), and clinical phenotype. RESULTS A total of 228 different pathogenic variants were identified in 506 ABCA4 patients, 50 of which were novel. Genotype-phenotype correlations showed that most of the patients with biallelic truncating variants presented with CRD and that these cases had a significantly earlier AO than patients with STGD1. Three missense variants are associated with CRD for the first time (c.1804C>T; p.[Arg602Trp], c.3056C>T; p.[Thr1019Met], and c.6320G>C; p.[Arg2107Pro]). Analysis of the most prevalent ABCA4 variant in Spain, c.3386G>T; p.(Arg1129Leu), revealed that is correlated to STGD1, later AO, and foveal sparing. CONCLUSIONS Our study, conducted in the largest ABCA4-associated disease cohort reported to date, updates the genotype-phenotype model established for ABCA4 variants and broadens the mutational spectrum of the gene. According to our observations, patients with ABCA4 presenting with 2 truncating variants may first present features of STGD1 but eventually develop rod dysfunction, and specific missense variants may be associated with a different phenotype, underscoring the importance of an accurate genetic diagnosis. Also, it is a prerequisite for enrollment in clinical trials, and to date, no other treatment has been approved for STGD1.
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Affiliation(s)
- Marta Del Pozo-Valero
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Rosa Riveiro-Alvarez
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Fiona Blanco-Kelly
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Jana Aguirre-Lamban
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain
| | - Inmaculada Martin-Merida
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Ionut-Florin Iancu
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Saoud Swafiri
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Isabel Lorda-Sanchez
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain
| | - Elvira Rodriguez-Pinilla
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain
| | - Maria José Trujillo-Tiebas
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Belen Jimenez-Rolando
- Department of Ophthalmology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ester Carreño
- Department of Ophthalmology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ignacio Mahillo-Fernandez
- Department of Epidemiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Marta Corton
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Almudena Avila-Fernandez
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Blanca Garcia-Sandoval
- Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain; Department of Ophthalmology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain.
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28
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A CRISPR and high-content imaging assay compliant with ACMG/AMP guidelines for clinical variant interpretation in ciliopathies. Hum Genet 2020; 140:593-607. [PMID: 33095315 PMCID: PMC7981318 DOI: 10.1007/s00439-020-02228-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 10/14/2020] [Indexed: 11/04/2022]
Abstract
Ciliopathies are a broad range of inherited developmental and degenerative diseases associated with structural or functional defects in motile or primary non-motile cilia. There are around 200 known ciliopathy disease genes and whilst genetic testing can provide an accurate diagnosis, 24–60% of ciliopathy patients who undergo genetic testing do not receive a genetic diagnosis. This is partly because following current guidelines from the American College of Medical Genetics and the Association for Molecular Pathology, it is difficult to provide a confident clinical diagnosis of disease caused by missense or non-coding variants, which account for more than one-third of cases of disease. Mutations in PRPF31 are the second most common cause of the degenerative retinal ciliopathy autosomal dominant retinitis pigmentosa. Here, we present a high-throughput high-content imaging assay providing quantitative measure of effect of missense variants in PRPF31 which meets the recently published criteria for a baseline standard in vitro test for clinical variant interpretation. This assay utilizes a new PRPF31+/– human retinal cell line generated using CRISPR gene editing to provide a stable cell line with significantly fewer cilia in which novel missense variants are expressed and characterised. We show that high-content imaging of cells expressing missense variants in a ciliopathy gene on a null background can allow characterisation of variants according to the cilia phenotype. We hope that this will be a useful tool for clinical characterisation of PRPF31 variants of uncertain significance, and can be extended to variant classification in other ciliopathies.
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29
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Hernández-Rodríguez EW, Escorcia AM, van der Kamp MW, Montero-Alejo AL, Caballero J. Multi-scale simulation reveals that an amino acid substitution increases photosensitizing reaction inputs in Rhodopsins. J Comput Chem 2020; 41:2278-2295. [PMID: 32757375 DOI: 10.1002/jcc.26392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 06/27/2020] [Accepted: 07/04/2020] [Indexed: 11/11/2022]
Abstract
Evaluating the availability of molecular oxygen (O2 ) and energy of excited states in the retinal binding site of rhodopsin is a crucial challenging first step to understand photosensitizing reactions in wild-type (WT) and mutant rhodopsins by absorbing visible light. In the present work, energies of the ground and excited states related to 11-cis-retinal and the O2 accessibility to the β-ionone ring are evaluated inside WT and human M207R mutant rhodopsins. Putative O2 pathways within rhodopsins are identified by using molecular dynamics simulations, Voronoi-diagram analysis, and implicit ligand sampling while retinal energetic properties are investigated through density functional theory, and quantum mechanical/molecular mechanical methods. Here, the predictions reveal that an amino acid substitution can lead to enough energy and O2 accessibility in the core hosting retinal of mutant rhodopsins to favor the photosensitized singlet oxygen generation, which can be useful in understanding retinal degeneration mechanisms and in designing blue-lighting-absorbing proteic photosensitizers.
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Affiliation(s)
- Erix W Hernández-Rodríguez
- Laboratorio de Bioinformática y Química Computacional, Escuela de Química y Farmacia, Facultad de Medicina, Universidad Católica del Maule, Talca, Chile
| | - Andrés M Escorcia
- School of Biochemistry, University of Bristol, University Walk, Bristol, UK
| | | | - Ana L Montero-Alejo
- Departamento de Física, Facultad de Ciencias Naturales, Matemática y del Medio Ambiente (FCNMM), Universidad Tecnológica Metropolitana, Santiago, Chile
| | - Julio Caballero
- Departamento de Bioinformática, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Talca, Chile
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30
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Roshandel D, Thompson JA, Charng J, Zhang D, Chelva E, Arunachalam S, Attia MS, Lamey TM, McLaren TL, De Roach JN, Mackey DA, Wilton SD, Fletcher S, McLenachan S, Chen FK. Exploring microperimetry and autofluorescence endpoints for monitoring disease progression in PRPF31-associated retinopathy. Ophthalmic Genet 2020; 42:1-14. [PMID: 32985313 DOI: 10.1080/13816810.2020.1827442] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
BACKGROUND Mutations in the splicing factor pre-messenger RNA processing factor 31 (PRPF31) gene cause autosomal dominant retinitis pigmentosa 11 (RP11) through a haplo-insufficiency mechanism. We describe the phenotype and progression of microperimetry and autofluorescence endpoints in an Indigenous Australian RP11 family. PATIENTS AND METHODS Ophthalmic examination, optical coherence tomography, fundus autofluorescence and microperimetry were performed at baseline and every 6-12 months. Baseline and annual change in best-corrected visual acuity (BCVA), microperimetry mean sensitivity (MS) and number of scotoma loci, residual ellipsoid zone (EZ) span and hyperautofluorescent ring (HAR) area were reported. Next-generation and Sanger sequencing were performed in available members. RESULTS 12 affected members from three generations were examined. Mean (SD, range) age at onset of symptoms was 11 (4.5, 4-19) years. MS declined steadily from the third decade and EZ span and HAR area declined rapidly during the second decade. Serial microperimetry showed negligible change in MS over 2-3 years. However, mean EZ span, near-infrared and short-wavelength HAR area reduction was 203 (6.4%) µm/year, 1.8 (8.7%) mm2/year and 1.1 (8.6%) mm2/year, respectively. Genetic testing was performed on 11 affected and 10 asymptomatic members and PRPF31 c.1205 C > A (p.Ser402Ter) mutation was detected in all affected and two asymptomatic members (non-penetrant carriers). CONCLUSIONS Our findings suggest that in the studied cohort, the optimal window for therapeutic intervention is the second decade of life and residual EZ span and HAR area can be considered as efficacy outcome measures. Further studies on larger samples with different PRPF31 mutations and longer follow-up duration are recommended.
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Affiliation(s)
- Danial Roshandel
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia
| | - Jennifer A Thompson
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia
| | - Jason Charng
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia
| | - Dan Zhang
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia
| | - Enid Chelva
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia
| | - Sukanya Arunachalam
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia
| | - Mary S Attia
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia
| | - Tina M Lamey
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia
| | - Terri L McLaren
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia
| | - John N De Roach
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia
| | - David A Mackey
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia
| | - Steve D Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University , Murdoch, Australia.,The Perron Institute, The University of Western Australia , Nedlands, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University , Murdoch, Australia.,The Perron Institute, The University of Western Australia , Nedlands, Australia
| | - Samuel McLenachan
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia
| | - Fred K Chen
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia.,Department of Ophthalmology, Royal Perth Hospital , Perth, Australia.,Department of Ophthalmology, Perth Children's Hospital , Nedlands, Australia
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31
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Kubota D, Matsumoto K, Hayashi M, Oishi N, Gocho K, Yamaki K, Kobayakawa S, Igarashi T, Takahashi H, Kameya S. High-resolution photoreceptor imaging analysis of patients with autosomal dominant retinitis pigmentosa (adRP) caused by HK1 mutation. Ophthalmic Genet 2020; 41:629-638. [PMID: 32814480 DOI: 10.1080/13816810.2020.1810284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
PURPOSE The hexokinase 1 (HK1) gene encodes one of the four human hexokinases that play essential roles in glucose metabolism. Recently, several cases of E847K mutation in the HK1 gene were reported to cause inherited retinal dystrophy. The purpose of this study was to identify the phenotypical characteristics of patients with a recurrent E847K mutation in the HK1 gene. METHODS Three generations of one family with autosomal dominant retinitis pigmentosa were examined. Whole exome sequencing was performed on the DNA. Fundus imaging by an adaptive optics fundus camera was used to obtain high-resolution photoreceptor images. RESULTS Fundus examination of the proband showed degeneration of the mid-peripheral retina, and SD-OCT images showed an absence of the ellipsoid zone (EZ) and interdigitation zone (IZ) in the parafovea and more peripherally. SD-OCT images of the mother of the proband showed an absence of the EZ and IZ, and fundus autofluorescence images showed hypo-autofluorescence surrounding the macular region. One daughter of the proband had only mild night blindness, however, the density of the cone photoreceptors was reduced in the parafoveal region. Whole exome sequencing identified a heterozygous variant, E847K, in the HK1 gene. This variant was found to co-segregate with the disease in three family members. CONCLUSIONS Although the systemic phenotypes were found to be associated with the HK1 mutations, only the E847K mutation can cause a non-syndromic photoreceptor degeneration. Our study strengthened the hypothesis that the amino acid E847 might play a critical role in the maintenance of the morphology and function of the photoreceptors.
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Affiliation(s)
- Daiki Kubota
- Department of Ophthalmology, Nippon Medical School Chiba Hokusoh Hospital , Inzai, Chiba, Japan
| | - Kaori Matsumoto
- Department of Ophthalmology, Nippon Medical School Chiba Hokusoh Hospital , Inzai, Chiba, Japan.,Department of Ophthalmology, Nippon Medical School , Tokyo, Japan
| | - Mika Hayashi
- Department of Ophthalmology, Nippon Medical School Chiba Hokusoh Hospital , Inzai, Chiba, Japan
| | - Noriko Oishi
- Department of Ophthalmology, Nippon Medical School Chiba Hokusoh Hospital , Inzai, Chiba, Japan
| | - Kiyoko Gocho
- Department of Ophthalmology, Nippon Medical School Chiba Hokusoh Hospital , Inzai, Chiba, Japan.,Clinical Investigation Center 1423, Inserm and Quinze-Vingts National Ophthalmology Hospital , Paris, France
| | - Kunihiko Yamaki
- Department of Ophthalmology, Nippon Medical School Chiba Hokusoh Hospital , Inzai, Chiba, Japan
| | - Shinichiro Kobayakawa
- Department of Ophthalmology, Nippon Medical School Musashikosugi Hospital , Kawasaki-city, Japan
| | - Tsutomu Igarashi
- Department of Ophthalmology, Nippon Medical School , Tokyo, Japan
| | | | - Shuhei Kameya
- Department of Ophthalmology, Nippon Medical School Chiba Hokusoh Hospital , Inzai, Chiba, Japan
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32
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Long Y, Li S, Dai L, Liu X, Yin X, Ren J, Guo H, Liu Y, Meng X, Li S. Nonsyndromic retinitis pigmentosa caused by two novel variants in the HGSNAT gene in a Chinese family. Ophthalmic Genet 2020; 41:390-393. [PMID: 32347150 DOI: 10.1080/13816810.2020.1755986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yanling Long
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University) , Chongqing, China.,Key Lab of Visual Damage and Regeneration & Restoration of Chongqing , Chongqing, China
| | - Sha Li
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University) , Chongqing, China.,Key Lab of Visual Damage and Regeneration & Restoration of Chongqing , Chongqing, China
| | - Limeng Dai
- Department of Medical Genetics, Third Military Medical University (Army Medical University) , Chongqing, China
| | - Xiao Liu
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University) , Chongqing, China.,Key Lab of Visual Damage and Regeneration & Restoration of Chongqing , Chongqing, China
| | - Xin Yin
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University) , Chongqing, China.,Key Lab of Visual Damage and Regeneration & Restoration of Chongqing , Chongqing, China
| | - Jiayun Ren
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University) , Chongqing, China.,Key Lab of Visual Damage and Regeneration & Restoration of Chongqing , Chongqing, China
| | - Hong Guo
- Department of Medical Genetics, Third Military Medical University (Army Medical University) , Chongqing, China
| | - Yong Liu
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University) , Chongqing, China.,Key Lab of Visual Damage and Regeneration & Restoration of Chongqing , Chongqing, China
| | - Xiaohong Meng
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University) , Chongqing, China.,Key Lab of Visual Damage and Regeneration & Restoration of Chongqing , Chongqing, China
| | - Shiying Li
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University) , Chongqing, China.,Key Lab of Visual Damage and Regeneration & Restoration of Chongqing , Chongqing, China
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Rodríguez-Muñoz A, Aller E, Jaijo T, González-García E, Cabrera-Peset A, Gallego-Pinazo R, Udaondo P, Salom D, García-García G, Millán JM. Expanding the Clinical and Molecular Heterogeneity of Nonsyndromic Inherited Retinal Dystrophies. J Mol Diagn 2020; 22:532-543. [PMID: 32036094 DOI: 10.1016/j.jmoldx.2020.01.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/01/2019] [Accepted: 01/12/2020] [Indexed: 12/21/2022] Open
Abstract
A cohort of 172 patients diagnosed clinically with nonsyndromic retinal dystrophies, from 110 families underwent full ophthalmologic examination, including retinal imaging, electrophysiology, and optical coherence tomography, when feasible. Molecular analysis was performed using targeted next-generation sequencing (NGS). Variants were filtered and prioritized according to the minimum allele frequency, and finally classified according to the American College of Medical Genetics and Genomics guidelines. Multiplex ligation-dependent probe amplification and array comparative genomic hybridization were performed to validate copy number variations identified by NGS. The diagnostic yield of this study was 62% of studied families. Thirty novel mutations were identified. The study found phenotypic intra- and interfamilial variability in families with mutations in C1QTNF5, CERKL, and PROM1; biallelic mutations in PDE6B in a unilateral retinitis pigmentosa patient; interocular asymmetry RP in 50% of the symptomatic RPGR-mutated females; the first case with possible digenism between CNGA1 and CNGB1; and a ROM1 duplication in two unrelated retinitis pigmentosa families. Ten unrelated cases were reclassified. This study highlights the clinical utility of targeted NGS for nonsyndromic inherited retinal dystrophy cases and the importance of full ophthalmologic examination, which allows new genotype-phenotype associations and expands the knowledge of this group of disorders. Identifying the cause of disease is essential to improve patient management, provide accurate genetic counseling, and take advantage of gene therapy-based treatments.
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Affiliation(s)
- Ana Rodríguez-Muñoz
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain; Unidad Mixta de Enfermedades raras IIS La Fe-Centro de Investigación Príncipe Felipe, Valencia, Spain; Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Elena Aller
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain; Unidad Mixta de Enfermedades raras IIS La Fe-Centro de Investigación Príncipe Felipe, Valencia, Spain; Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, Valencia, Spain; Genetics Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Teresa Jaijo
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain; Unidad Mixta de Enfermedades raras IIS La Fe-Centro de Investigación Príncipe Felipe, Valencia, Spain; Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, Valencia, Spain; Genetics Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Emilio González-García
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain; Departments of Neurophysiology, Hospital de Manises, Valencia, Spain
| | | | - Roberto Gallego-Pinazo
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain; Macula Unit, Oftalvist Clinic, Valencia, Spain
| | - Patricia Udaondo
- Ophthalmology, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - David Salom
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain; Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, Valencia, Spain; Departments of Ophthalmology, Hospital de Manises, Valencia, Spain
| | - Gema García-García
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain; Unidad Mixta de Enfermedades raras IIS La Fe-Centro de Investigación Príncipe Felipe, Valencia, Spain; Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, Valencia, Spain.
| | - José M Millán
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe, Valencia, Spain; Unidad Mixta de Enfermedades raras IIS La Fe-Centro de Investigación Príncipe Felipe, Valencia, Spain; Biomedical Research Network for Rare Diseases, Hospital Universitario y Politécnico La Fe, Valencia, Spain.
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Mutation spectrum of PRPF31, genotype-phenotype correlation in retinitis pigmentosa, and opportunities for therapy. Exp Eye Res 2020; 192:107950. [PMID: 32014492 PMCID: PMC7065041 DOI: 10.1016/j.exer.2020.107950] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/13/2020] [Accepted: 01/27/2020] [Indexed: 12/11/2022]
Abstract
Pathogenic variants in pre-messenger RNA (pre-mRNA) splicing factor 31, PRPF31, are the second most common genetic cause of autosomal dominant retinitis pigmentosa (adRP) in most populations. This remains a completely untreatable and incurable form of blindness, and it can be difficult to predict the clinical course of disease. In order to design appropriate targeted therapies, a thorough understanding of the genetics and molecular mechanism of this disease is required. Here, we present the structure of the PRPF31 gene and PRPF31 protein, current understanding of PRPF31 protein function and the full spectrum of all reported clinically relevant variants in PRPF31. We delineate the correlation between specific PRPF31 genotype and RP phenotype, suggesting that, except in cases of complete gene deletion or large-scale deletions, dominant negative effects contribute to phenotype as well as haploinsufficiency. This has important impacts on design of targeted therapies, particularly the feasibility of gene augmentation as a broad approach for treatment of PRPF31-associated RP. We discuss other opportunities for therapy, including antisense oligonucleotide therapy and gene-independent approaches and offer future perspectives on treatment of this form of RP. PRPF31 is the second most common cause of autosomal dominant retinitis pigmentosa and a potential target for gene therapy. We present all reported pathogenic variants in PRPF31 as a resource for clinicians, diagnostic genetics labs, and researchers. Genotype-phenotype correlations suggest that, dominant negative effects contribute to disease in addition to haploinsufficiency. This finding has important impacts on the suitability of gene augmentation approaches across all mutation types. This finding may aid prognosis of disease in PRPF31-associated RP patients.
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Khan AO, Neri P, Al Teneiji AM. A recurrent arcuate retinopathy in familial cone-rod dystrophy secondary to heterozygous CRX deletion. Ophthalmic Genet 2019; 40:493-499. [PMID: 31743059 DOI: 10.1080/13816810.2019.1688841] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Purpose: To describe an arcuate retinopathy appearance in a familial cone-rod dystrophy and the underlying genetic cause.Methods: Retrospective case series of an affected three-generation family (eight affected members, eight unaffected members)Results: The proband, a 47-year-old male, noted significant visual loss since his early thirties. In addition to central macular atrophic changes, retinal examination was notable for peripapillary atrophy and an arcuate of drusenoid deep yellow lesions in the temporal macula. Spectral-domain optical coherence tomography in the area of the lesions showed regional outer neurosensory retina loss with nasal extension (forming a ring around the central retina) but no drusen. Full-field electroretinography revealed cone-rod dysfunction with an electronegative waveform. Fifteen other available family members were examined, and seven (age range 13-71 years old) showed variable expressivity for similar phenotypic findings, most notably the arcuate lesions in all but the oldest individual who had end-stage atrophy. Exome sequencing of the proband's affected daughter uncovered a heterozygous CRX deletion [NM_000554.4: CRX: c.(100 + 1_101-1)_(c.900 + 1_?)del] that segregated with the disease.Conclusion: An unusual familial cone-rod dystrophy phenotype was associated with heterozygous CRX deletion, a pathogenic variant that had a presumed mechanism of haploinsufficiency. The consistent finding of arcuate temporal macular lesions among affected family members was striking, particularly given the variable expressivity previously associated with CRX-related retinopathy. Additional phenotypic studies are needed to assess how frequently this temporal arcuate retinopathy appearance occurs in individuals harboring a similar deletion who are not from the current family.
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Affiliation(s)
- Arif O Khan
- Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, UAE.,Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine, Cleveland, Ohio, USA
| | - Piergiorgio Neri
- Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, UAE.,Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine, Cleveland, Ohio, USA
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Del Pozo-Valero M, Martin-Merida I, Jimenez-Rolando B, Arteche A, Avila-Fernandez A, Blanco-Kelly F, Riveiro-Alvarez R, Van Cauwenbergh C, De Baere E, Rivolta C, Garcia-Sandoval B, Corton M, Ayuso C. Expanded Phenotypic Spectrum of Retinopathies Associated with Autosomal Recessive and Dominant Mutations in PROM1. Am J Ophthalmol 2019; 207:204-214. [PMID: 31129250 DOI: 10.1016/j.ajo.2019.05.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 05/08/2019] [Accepted: 05/08/2019] [Indexed: 11/28/2022]
Abstract
PURPOSE To describe the genetic and phenotypic characteristics of a cohort of patients with PROM1 variants. DESIGN Case-case study. METHODS We screened a cohort of 2216 families with inherited retinal dystrophies using classical molecular techniques and next-generation sequencing approaches. The clinical histories of 25 patients were reviewed to determine age of onset of symptoms and the results of ophthalmoscopy, best-corrected visual acuity, full-field electroretinography, and visual field studies. Fundus autofluorescence and spectral-domain optical coherence tomography were further assessed in 7 patients. RESULTS PROM1 variants were identified in 32 families. Disease-causing variants were found in 18 autosomal recessive and 4 autosomal dominant families. Monoallelic pathogenic variants or variants of unknown significance were identified in the remaining 10 families. Comprehensive phenotyping of 25 patients from 22 families carrying likely disease-causing variants revealed clinical heterogeneity associated with the PROM1 gene. Most of these patients presented cone-rod dystrophy and some exhibited macular dystrophy or retinitis pigmentosa, while all presented with macular damage. Phenotypic association of a dominant splicing variant with late-onset mild maculopathy was established. This variant is one of the 3 likely founder variants identified in our Spanish cohort. CONCLUSIONS We report the largest cohort of patients with PROM1 variants, describing in detail the phenotype in 25 of them. Interestingly, within the variability of phenotypes related to this gene, macular involvement is a common feature in all patients.
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Affiliation(s)
- Marta Del Pozo-Valero
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain
| | - Inmaculada Martin-Merida
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Belen Jimenez-Rolando
- Department of Ophthalmology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ana Arteche
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain
| | - Almudena Avila-Fernandez
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Fiona Blanco-Kelly
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Rosa Riveiro-Alvarez
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain
| | - 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
| | - Elfride De Baere
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Carlo Rivolta
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Blanca Garcia-Sandoval
- Department of Ophthalmology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain
| | - Marta Corton
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain.
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Yi Z, Xiao X, Li S, Sun W, Zhang Q. Pathogenicity discrimination and genetic test reference for CRX variants based on genotype-phenotype analysis. Exp Eye Res 2019; 189:107846. [PMID: 31626798 DOI: 10.1016/j.exer.2019.107846] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/27/2019] [Accepted: 10/14/2019] [Indexed: 12/22/2022]
Abstract
The cone-rod homeobox (CRX) gene is specifically expressed in developing and mature photoreceptors and is relatively conserved, with limited polymorphisms in coding regions. Rare variants in CRX are usually considered causative for different forms of retinal degeneration, but this might be problematic based on recent data. This study aimed to classify CRX variants based on a genotype-phenotype analysis of our data and the literature. Twenty-four CRX variants, including 14 novel variants, were detected in 37 Chinese families based on exome sequencing data obtained from 4971 Chinese probands with different forms of eye diseases. After detailed phenotypic analysis and cosegregation analysis in families with CRX variants, the 24 variants could be classified into three groups: benign (six), likely benign (six), and pathogenic (12). Somatic mosaicism was identified in a family with unaffected parents (the father had a mutant allele that was detected in approximately 17% of his leukocyte DNA) and two affected sons. Furthermore, a thorough reassessment was systematically performed for all 113 heterozygous variants as well as for their associated phenotypes from our cohort and patients previously reported. Two critical findings on the pathogenicity of CRX variants were obtained based on the genotype-phenotype correlation, family segregation and ensemble predicting methods: 1) approximately half of heterozygous missense variants are likely benign, and 2) heterozygous truncating variants affecting the homeodomain are likely benign. Truncating mutations after the homeodomain are likely associated with a more severe phenotype. Although most heterozygous pathogenic variants in CRX are associated with autosomal dominant retinal degeneration, a homozygous c.268C> T (p.Arg90Trp) substitution and homozygous complete deletion of CRX have been reported to cause Leber congenital amaurosis. In conclusion, many rare missense variants and some truncating variants in CRX are likely benign, although previously, they might have been predicted to be damaging by some online tools. Evaluation of the pathogenicity of a CRX variant should consider both its nature and location. The information obtained in this study is critical in the era of routine clinical genetic test, not only for CRX but also for many other genes with many more variants. Functional studies and additional genotype-phenotype analyses are expected to confirm these associations.
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Affiliation(s)
- Zhen Yi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou, 510060, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou, 510060, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou, 510060, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou, 510060, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou, 510060, China.
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Gao C, Wang X, Mei S, Li D, Duan J, Zhang P, Chen B, Han L, Gao Y, Yang Z, Li B, Yang XA. Diagnostic Yields of Trio-WES Accompanied by CNVseq for Rare Neurodevelopmental Disorders. Front Genet 2019; 10:485. [PMID: 31178897 PMCID: PMC6542989 DOI: 10.3389/fgene.2019.00485] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 05/06/2019] [Indexed: 01/20/2023] Open
Abstract
Objective This study is to investigate the diagnostic yield of the combination of trio whole exome sequencing (Trio-WES) and copy number variation sequencing (CNVseq) for rare neurodevelopmental disorders (NDDs). Methods Clinical data from consecutive pediatric patients who were diagnosed with rare NDDs that were suspected to be monogenic disorders, who were admitted to our hospital from April 2017 to March 2019, and who underwent next generation sequencing (NGS) were extracted from the medical records. Patients for whom Trio-WES and CNVseq data were available were enrolled in this study. Sanger sequencing was applied for the validation of the variants identified by Trio-WES. Sequence alignment and structural modeling were conducted for analyzing the possibility of the variants in the onset of the NDDs. Results In total, 54 patients were enrolled in this study, with the median age of 15 (8–26) months. A total of 242 phenotypic abnormalities belonging to 20 different systems were identified in the cohort. Twenty-four patients were diagnosed by Trio-WES, eight patients were diagnosed by CNVseq, and one case was identified by both WES and CNVseq. Compared with Trio-WES, the diagnosis rate of Trio-WES accompanied by CNVseq was significantly higher (P = 0.016). Trio-WES identified 36 variants in 26 different genes, among which 27 variants were novel. CNVseq detected four duplications and eight deletions, ranging from 310 kb to 23.27 Mb. Our case examples demonstrated the high heterogeneity of NDDs and showed the challenges of rare NDDs for physicians. Conclusion The significantly higher diagnosis rate of Trio-WES accompanied by CNVseq makes this strategy a potential alternative to the most widely used approaches for pediatric children with rare and undiagnosed NDDs.
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Affiliation(s)
- Chao Gao
- Department of Pediatric Rehabilitation Medicine, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China.,Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Xiaona Wang
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Shiyue Mei
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Dongxiao Li
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Jiali Duan
- Department of Pediatric Rehabilitation Medicine, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Pei Zhang
- Department of Pediatric Neurology and Rehabilitation, First People's Hospital of Shangqiu, Shangqiu, China
| | - Baiyun Chen
- Department of Pediatric Rehabilitation Medicine, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Liang Han
- Department of Pediatric Rehabilitation Medicine, Children's Hospital Affiliated to Zhengzhou University/Henan Children's Hospital/Zhengzhou Children's Hospital, Zhengzhou, China
| | - Yang Gao
- Graduate School of Zhengzhou University, Zhengzhou, China
| | - Zhenhua Yang
- Third People's Hospital of Qingdao West Coast New District, Qingdao, China
| | - Bing Li
- Central Laboratory, Jinshan Hospital Affiliated to Fudan University, Shanghai, China
| | - Xiu-An Yang
- School of Basic Medical Science, Chengde Medical University, Chengde, China
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Genome Editing as a Treatment for the Most Prevalent Causative Genes of Autosomal Dominant Retinitis Pigmentosa. Int J Mol Sci 2019; 20:ijms20102542. [PMID: 31126147 PMCID: PMC6567127 DOI: 10.3390/ijms20102542] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/15/2019] [Accepted: 05/22/2019] [Indexed: 02/07/2023] Open
Abstract
: Inherited retinal dystrophies (IRDs) are a clinically and genetically heterogeneous group of diseases with more than 250 causative genes. The most common form is retinitis pigmentosa. IRDs lead to vision impairment for which there is no universal cure. Encouragingly, a first gene supplementation therapy has been approved for an autosomal recessive IRD. However, for autosomal dominant IRDs, gene supplementation therapy is not always pertinent because haploinsufficiency is not the only cause. Disease-causing mechanisms are often gain-of-function or dominant-negative, which usually require alternative therapeutic approaches. In such cases, genome-editing technology has raised hopes for treatment. Genome editing could be used to i) invalidate both alleles, followed by supplementation of the wild type gene, ii) specifically invalidate the mutant allele, with or without gene supplementation, or iii) to correct the mutant allele. We review here the most prevalent genes causing autosomal dominant retinitis pigmentosa and the most appropriate genome-editing strategy that could be used to target their different causative mutations.
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Birtel J, Gliem M, Oishi A, Müller PL, Herrmann P, Holz FG, Mangold E, Knapp M, Bolz HJ, Charbel Issa P. Genetic testing in patients with retinitis pigmentosa: Features of unsolved cases. Clin Exp Ophthalmol 2019; 47:779-786. [PMID: 30977268 DOI: 10.1111/ceo.13516] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 03/18/2019] [Accepted: 04/02/2019] [Indexed: 01/15/2023]
Abstract
IMPORTANCE Uncommon characteristics in genetically unsolved retinitis pigmentosa (RP) patients may indicate an incorrect clinical diagnosis or as yet unknown genetic causes resulting in specific retinal phenotypes. The diagnostic yield of targeted next-generation sequencing may be increased by a reasonable preselection of RP-patients. BACKGROUND To systematically evaluate and compare features of genetically solved and unsolved RP-patients. DESIGN Retrospective, observational study. PARTICIPANTS One-hundred and twelve consecutive RP-patients who underwent extensive molecular genetic analysis. METHODS Characterization of patients based on multimodal imaging and medical history. MAIN OUTCOME MEASURES Differences between genetically solved and unsolved RP-patients. RESULTS Compared to genetically solved patients (n = 77), genetically unsolved patients (n = 35) more frequently had an age of disease-onset above 30 years (60% vs 8%; P < 0.0001), showed atypical fundus features (49% vs 8%; P < 0. 0001) and indicators for phenocopies (eg, autoimmune diseases) (17% vs 0%; P < 0. 001). Evidence for a particular inheritance pattern was less common (20% vs 49%; P < 0. 01). The diagnostic yield was 84% (71/85) in patients with first symptoms below 30 years-of-age, compared to 69% (77/112) in the overall cohort. The other selection criteria alone or in combination resulted in limited further increase of the diagnostic yield (up to 89%) while excluding considerably more patients (up to 56%) from genetic testing. CONCLUSIONS AND RELEVANCE The medical history and retinal phenotype differ between genetically solved and a subgroup of unsolved RP-patients, which may reflect undetected genotypes or retinal conditions mimicking RP. Patient stratification may inform on the individual likelihood of identifying disease-causing mutations and may impact patient counselling.
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Affiliation(s)
- Johannes Birtel
- Department of Ophthalmology, University of Bonn, Bonn, Germany.,Center for Rare Diseases Bonn (ZSEB), University of Bonn, Bonn, Germany
| | - Martin Gliem
- Department of Ophthalmology, University of Bonn, Bonn, Germany.,Center for Rare Diseases Bonn (ZSEB), University of Bonn, Bonn, Germany.,Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, and Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Akio Oishi
- Department of Ophthalmology, University of Bonn, Bonn, Germany.,Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Philipp L Müller
- Department of Ophthalmology, University of Bonn, Bonn, Germany.,Center for Rare Diseases Bonn (ZSEB), University of Bonn, Bonn, Germany
| | - Philipp Herrmann
- Department of Ophthalmology, University of Bonn, Bonn, Germany.,Center for Rare Diseases Bonn (ZSEB), University of Bonn, Bonn, Germany
| | - Frank G Holz
- Department of Ophthalmology, University of Bonn, Bonn, Germany.,Center for Rare Diseases Bonn (ZSEB), University of Bonn, Bonn, Germany
| | | | - Michael Knapp
- Institute of Medical Biometry, Informatics, and Epidemiology, University of Bonn, Bonn, Germany
| | - Hanno J Bolz
- Institute of Human Genetics, University Hospital of Cologne, Cologne, Germany.,Bioscientia Center for Human Genetics, Ingelheim, Germany
| | - Peter Charbel Issa
- Department of Ophthalmology, University of Bonn, Bonn, Germany.,Center for Rare Diseases Bonn (ZSEB), University of Bonn, Bonn, Germany.,Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, and Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford, UK
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41
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Natural models for retinitis pigmentosa: progressive retinal atrophy in dog breeds. Hum Genet 2019; 138:441-453. [PMID: 30904946 DOI: 10.1007/s00439-019-01999-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/14/2019] [Indexed: 01/24/2023]
Abstract
Retinitis pigmentosa (RP) is a heterogeneous group of inherited retinal disorders eventually leading to blindness with different ages of onset, progression and severity. Human RP, first characterized by the progressive degeneration of rod photoreceptor cells, shows high genetic heterogeneity with more than 90 genes identified. However, about one-third of patients have no known genetic causes. Interestingly, dogs are also severely affected by similar diseases, called progressive retinal atrophy (PRA). Indeed, RP and PRA have comparable clinical signs, physiopathology and outcomes, similar diagnosis methods and most often, orthologous genes are involved. The many different dog PRAs often segregate in specific breeds. Indeed, undesired alleles have been selected and amplified through drastic selection and excessive use of inbreeding. Out of the 400 breeds, nearly 100 have an inherited form of PRA, which are natural animal models that can be used to investigate the genetics, disease progression and therapies in dogs for the benefit of both dogs and humans. Recent knowledge on the canine genome and access to new genotyping and sequencing technologies now efficiently allows the identification of mutations involved in canine genetic diseases. To date, PRA genes identified in dog breeds correspond to the same genes in humans and represent relevant RP models, and new genes found in dogs represent good candidate for still unknown human RP. We present here a review of the main advantages of the dog models for human RP with the genes already identified and an X-linked PRA in the Border collie as a model for orphan X-linked RPs in human.
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Wheway G, Nazlamova L, Meshad N, Hunt S, Jackson N, Churchill A. A Combined in silico, in vitro and Clinical Approach to Characterize Novel Pathogenic Missense Variants in PRPF31 in Retinitis Pigmentosa. Front Genet 2019; 10:248. [PMID: 30967900 PMCID: PMC6438860 DOI: 10.3389/fgene.2019.00248] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 03/05/2019] [Indexed: 11/30/2022] Open
Abstract
At least six different proteins of the spliceosome, including PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, and SNRNP200, are mutated in autosomal dominant retinitis pigmentosa (adRP). These proteins have recently been shown to localize to the base of the connecting cilium of the retinal photoreceptor cells, elucidating this form of RP as a retinal ciliopathy. In the case of loss-of-function variants in these genes, pathogenicity can easily be ascribed. In the case of missense variants, this is more challenging. Furthermore, the exact molecular mechanism of disease in this form of RP remains poorly understood. In this paper we take advantage of the recently published cryo EM-resolved structure of the entire human spliceosome, to predict the effect of a novel missense variant in one component of the spliceosome; PRPF31, found in a patient attending the genetics eye clinic at Bristol Eye Hospital. Monoallelic variants in PRPF31 are a common cause of autosomal dominant retinitis pigmentosa (adRP) with incomplete penetrance. We use in vitro studies to confirm pathogenicity of this novel variant PRPF31 c.341T > A, p.Ile114Asn. This work demonstrates how in silico modeling of structural effects of missense variants on cryo-EM resolved protein complexes can contribute to predicting pathogenicity of novel variants, in combination with in vitro and clinical studies. It is currently a considerable challenge to assign pathogenic status to missense variants in these proteins.
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Affiliation(s)
- Gabrielle Wheway
- Centre for Research in Biosciences, University of the West of England, Bristol, United Kingdom
| | - Liliya Nazlamova
- Centre for Research in Biosciences, University of the West of England, Bristol, United Kingdom
| | - Nervine Meshad
- Bristol Eye Hospital, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Samantha Hunt
- Bristol Eye Hospital, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Nicola Jackson
- Clinical Genetics Service, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Amanda Churchill
- Bristol Eye Hospital, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
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Martin-Merida I, Avila-Fernandez A, Del Pozo-Valero M, Blanco-Kelly F, Zurita O, Perez-Carro R, Aguilera-Garcia D, Riveiro-Alvarez R, Arteche A, Trujillo-Tiebas MJ, Tahsin-Swafiri S, Rodriguez-Pinilla E, Lorda-Sanchez I, Garcia-Sandoval B, Corton M, Ayuso C. Genomic Landscape of Sporadic Retinitis Pigmentosa: Findings from 877 Spanish Cases. Ophthalmology 2019; 126:1181-1188. [PMID: 30902645 DOI: 10.1016/j.ophtha.2019.03.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 03/11/2019] [Accepted: 03/12/2019] [Indexed: 10/27/2022] Open
Abstract
PURPOSE We aimed to unravel the molecular basis of sporadic retinitis pigmentosa (sRP) in the largest cohort reported to date. DESIGN Case series. PARTICIPANTS A cohort of 877 unrelated Spanish sporadic cases with a clinical diagnosis of retinitis pigmentosa (RP) and negative family history. METHODS The cohort was studied by classic genotyping or targeted next-generation sequencing (NGS). Multiplex ligation-dependent probe amplification (MLPA) and array-based comparative genomic hybridization were performed to confirm copy number variations detected by NGS. Quantitative fluorescent polymerase chain reaction was assessed in sRP cases carrying de novo variants to confirm paternity. MAIN OUTCOME MEASURES The study of the sRP cohort showed a high proportion of causal autosomal dominant (AD) and X-linked (XL) variants, most of them being de novo. RESULTS Causative variants were identified in 38% of the patients studied, segregating recessively in 84.5% of the solved cases. Biallelic variants detected in only 6 different autosomal recessive genes explained 50% of the cases characterized. Causal AD and XL variants were found in 7.6% and 7.9% of cases, respectively. Remarkably, 20 de novo variants were confirmed after trio analysis, explaining 6% of the cases. In addition, 17% of the solved sRP cases were reclassified to a different retinopathy phenotype. CONCLUSIONS This study highlights the clinical utility of NGS testing for sRP cases, expands the mutational spectrum, and provides accurate prevalence of mutated genes. Our findings evidence the underestimated role of de novo variants in the etiology of RP, emphasizing the importance of segregation analysis as well as comprehensive screening of genes carrying XL and AD variants in sporadic cases. Such in-depth study is essential for accurate family counseling and future enrollment in gene therapy-based treatments.
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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
| | - 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
| | - Marta Del Pozo-Valero
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), 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
| | - Raquel Perez-Carro
- 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
| | - Rosa Riveiro-Alvarez
- 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
| | - Maria Jose Trujillo-Tiebas
- 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
| | - Saoud Tahsin-Swafiri
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Elvira Rodriguez-Pinilla
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Isabel Lorda-Sanchez
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Blanca Garcia-Sandoval
- Department of Ophthalmology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, 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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