1
|
Villafuerte-de la Cruz RA, Garza-Garza LA, Garza-Leon M, Rodriguez-De la Torre C, Parra-Bernal C, Vazquez-Camas I, Ramos-Gonzalez D, Rangel-Padilla A, Espino Barros-Palau A, Nava-García J, Castillo-Velazquez J, Castillo-De Leon E, Del Valle-Penella A, Valdez-Garcia JE, Rojas-Martinez A. Spectrum of variants associated with inherited retinal dystrophies in Northeast Mexico. BMC Ophthalmol 2024; 24:60. [PMID: 38347443 PMCID: PMC10860328 DOI: 10.1186/s12886-023-03276-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/26/2023] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Inherited retinal dystrophies are hereditary diseases which have in common the progressive degeneration of photoreceptors. They are a group of diseases with clinical, genetic, and allelic heterogeneity. There is limited information regarding the genetic landscape of inherited retinal diseases in Mexico, therefore, the present study was conducted in the northeast region of the country. METHODS Patients with inherited retinal dystrophies were included. A complete history, full ophthalmological and medical genetics evaluations, and genetic analysis through a targeted NGS panel for inherited retinal dystrophies comprising at least 293 genes were undertaken. RESULTS A total of 126 patients were included. Cases were solved in 74.6% of the study's population. Retinitis pigmentosa accounted for the most found inherited retinal disease. Ninety-nine causal variants were found, being USH2A and ABCA4 the most affected genes (26 and 15 cases, respectively). CONCLUSIONS The present study documents the most prevalent causative genes in IRDs, as USH2A, in northeastern Mexico. This contrasts with previous reports of IRDs in other zones of the country. Further studies, targeting previously unstudied populations in Mexico are important to document the genetic background of inherited retinal dystrophies in the country.
Collapse
Affiliation(s)
- Rocio A Villafuerte-de la Cruz
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de La Salud, Ave. Morones Prieto 3000, Col. Los Doctores, Monterrey, CP 64710, Mexico
- Destellos de Luz, San Pedro Garza García, México
| | | | - Manuel Garza-Leon
- Destellos de Luz, San Pedro Garza García, México
- Clinical Science Department, Health Sciences Division, University of Monterrey, Monterrey, México
| | - Cesar Rodriguez-De la Torre
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de La Salud, Ave. Morones Prieto 3000, Col. Los Doctores, Monterrey, CP 64710, Mexico
| | - Cinthya Parra-Bernal
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de La Salud, Ave. Morones Prieto 3000, Col. Los Doctores, Monterrey, CP 64710, Mexico
| | - Ilse Vazquez-Camas
- Tecnologico de Monterrey, The Institute for Obesity Research, Ave. Morones Prieto 3000, Col. Los Doctores, Monterrey, CP 64710, Mexico
- Tecnologico Nacional de Mexico Campus Tuxtla Gutierrez, Tuxtla Gutierrez, Mexico
| | - David Ramos-Gonzalez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de La Salud, Ave. Morones Prieto 3000, Col. Los Doctores, Monterrey, CP 64710, Mexico
| | - Andrea Rangel-Padilla
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de La Salud, Ave. Morones Prieto 3000, Col. Los Doctores, Monterrey, CP 64710, Mexico
| | - Angelina Espino Barros-Palau
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de La Salud, Ave. Morones Prieto 3000, Col. Los Doctores, Monterrey, CP 64710, Mexico
| | - Jose Nava-García
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de La Salud, Ave. Morones Prieto 3000, Col. Los Doctores, Monterrey, CP 64710, Mexico
| | | | | | | | - Jorge E Valdez-Garcia
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de La Salud, Ave. Morones Prieto 3000, Col. Los Doctores, Monterrey, CP 64710, Mexico
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de La Salud, Ave. Morones Prieto 3000, Col. Los Doctores, Monterrey, CP 64710, Mexico.
- Tecnologico de Monterrey, The Institute for Obesity Research, Ave. Morones Prieto 3000, Col. Los Doctores, Monterrey, CP 64710, Mexico.
| |
Collapse
|
2
|
Alonso‐Luna O, Mercado‐Celis GE, Melendez‐Zajgla J, Barquera R, Zapata‐Tarres M, Juárez‐Villegas LE, Mendoza‐Caamal EC, Rey‐Helo E, Borges‐Yañez SA. Germline mutations in pediatric cancer cohort with mixed-ancestry Mexicans. Mol Genet Genomic Med 2024; 12:e2332. [PMID: 38093606 PMCID: PMC10767611 DOI: 10.1002/mgg3.2332] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/11/2023] [Accepted: 11/28/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND Childhood cancer is one of the primary causes of disease-related death in 5- to 14-year-old children and currently no prevention strategies exist to reduce the incidence of this disease. Childhood cancer has a larger hereditary component compared with cancer in adults. Few genetic studies have been conducted on children with cancer. Additionally, Latin American populations are underrepresented in genomic studies compared with other populations. Therefore, the aim of this study is to analyze germline mutations in a group of mixed-ancestry Mexican pediatric patients with solid and hematological cancers. METHODS We analyzed genetic variants from 40 Mexican childhood cancer patients and their relatives. DNA from saliva or blood samples was used for whole-exome sequencing. All variants were identified following GATK best practices. RESULTS We found that six patients (15%) were carriers of germline mutations in CDKN2A, CHEK2, DICER1, FANCA, MSH6, MUTYH, NF1, and SBDS cancer predisposition genes, and additional new variants predicted to be deleterious by in silico algorithms. A population genetics analysis detected five components consistent with the demographic models assumed for modern mixed-ancestry Mexicans. CONCLUSIONS This report identifies potential genetic risk factors and provides a better understanding of the underlying mechanisms of childhood cancer in this population.
Collapse
Grants
- 365882 Consejo Nacional de Ciencia y Tecnología, CONACyT, Mexico
- 253316 Consejo Nacional de Ciencia y Tecnología, CONACyT, Mexico
- Fundacion Carlos Slim as part of the inaugural phase of Slim Initiative in Genomic Medicine for the Americas, SIGMA
- Broad Institute of MIT and Harvard
- Instituto Nacional de Medicina Genomica (INMEGEN)
- Division de Estudios de Posgrado e Investigacion de la Facultad de Odontologia
- Programa de Maestria y Doctorado en Ciencias Medicas, Odontologicas y de la Salud, UNAM
- "Aqui nadie se rinde, ANSER (I.A.P)
- Max Planck Institute for Evolutionary Anthropology (MPI-EVA)
- Consejo Nacional de Ciencia y Tecnología, CONACyT, Mexico
- Max Planck Institute for Evolutionary Anthropology (MPI‐EVA)
Collapse
Affiliation(s)
- Oscar Alonso‐Luna
- Programa de Maestria y Doctorado en Ciencias Medicas, Odontologicas y de la SaludCiudad Universitaria, Universidad Nacional Autonoma de MexicoMexico CityMexico
| | | | - Jorge Melendez‐Zajgla
- Laboratorio de Genomica Funcional del CancerInstituto Nacional de Medicina GenomicaMexico CityMexico
| | - Rodrigo Barquera
- Department of ArchaeogeneticsMax Plank Institute for Evolutionary Anthropology (MPI‐EVA)LeipzigGermany
| | | | | | | | | | | |
Collapse
|
3
|
Villafuerte-De la Cruz R, Chacon-Camacho OF, Rodriguez-Martinez AC, Xilotl-De Jesus N, Arce-Gonzalez R, Rodriguez-De la Torre C, Valdez-Garcia JE, Rojas-Martinez A, Zenteno JC. Case report: Disease phenotype associated with simultaneous biallelic mutations in ABCA4 and USH2A due to uniparental disomy of chromosome 1. Front Genet 2022; 13:949437. [PMID: 36051698 PMCID: PMC9424670 DOI: 10.3389/fgene.2022.949437] [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: 05/20/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022] Open
Abstract
Inherited retinal diseases (IRDs) represent a spectrum of clinically and genetically heterogeneous disorders. Our study describes an IRD patient carrying ABCA4 and USH2A pathogenic biallelic mutations as a result of paternal uniparental disomy (UPD) in chromosome 1. The proband is a 9-year-old girl born from non-consanguineous parents. Both parents were asymptomatic and denied family history of ocular disease. Clinical history and ophthalmologic examination of the proband were consistent with Stargardt disease. Whispered voice testing disclosed moderate hearing loss. Next-generation sequencing and Sanger sequencing identified pathogenic variants in ABCA4 (c.4926C>G and c.5044_5058del) and USH2A (c.2276G>T). All variants were present homozygously in DNA from the proband and heterozygously in DNA from the father. No variants were found in maternal DNA. Further analysis of single nucleotide polymorphisms confirmed paternal UPD of chromosome 1. This is the first known patient with confirmed UPD for two recessively mutated IRD genes. Our study expands on the genetic heterogeneity of IRDs and highlights the importance of UPD as a mechanism of autosomal recessive disease in non-consanguineous parents. Moreover, a long-term follow-up is essential for the identification of retinal features that may develop as a result of USH2A-related conditions.
Collapse
Affiliation(s)
| | - O. F. Chacon-Camacho
- Carrera Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Genetics Department, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| | - A. C. Rodriguez-Martinez
- Department of Ophthalmology, University Hospital and Faculty of Medicine, Autonomous University of Nuevo Leon (UANL), Monterrey, Mexico
| | - N. Xilotl-De Jesus
- Genetics Department, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| | - R. Arce-Gonzalez
- Genetics Department, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
| | | | - J. E. Valdez-Garcia
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
| | - A. Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
- Institute for Obesity Research, Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
- *Correspondence: A. Rojas-Martinez, ; J. C. Zenteno,
| | - J. C. Zenteno
- Genetics Department, Institute of Ophthalmology “Conde de Valenciana”, Mexico City, Mexico
- Biochemistry Department, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
- *Correspondence: A. Rojas-Martinez, ; J. C. Zenteno,
| |
Collapse
|
4
|
Corradi Z, Salameh M, Khan M, Héon E, Mishra K, Hitti-Malin RJ, AlSwaiti Y, Aslanian A, Banin E, Brooks BP, Zein WM, Hufnagel RB, Roosing S, Dhaenens C, Sharon D, Cremers FPM, AlTalbishi A. ABCA4 c.859-25A>G, a Frequent Palestinian Founder Mutation Affecting the Intron 7 Branchpoint, Is Associated With Early-Onset Stargardt Disease. Invest Ophthalmol Vis Sci 2022; 63:20. [PMID: 35475888 PMCID: PMC9055564 DOI: 10.1167/iovs.63.4.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/02/2022] [Indexed: 11/24/2022] Open
Abstract
Purpose The effect of noncoding variants is often unknown in the absence of functional assays. Here, we characterized an ABCA4 intron 7 variant, c.859-25A>G, identified in Palestinian probands with Stargardt disease (STGD) or cone-rod dystrophy (CRD). We investigated the effect of this variant on the ABCA4 mRNA and retinal phenotype, and its prevalence in Palestine. Methods The ABCA4 gene was sequenced completely or partially in 1998 cases with STGD or CRD. The effect of c.859-25A>G on splicing was investigated in silico using SpliceAI and in vitro using splice assays. Homozygosity mapping was performed for 16 affected individuals homozygous for c.859-25A>G. The clinical phenotype was assessed using functional and structural analyses including visual acuity, full-field electroretinography, and multimodal imaging. Results The smMIPs-based ABCA4 sequencing revealed c.859-25A>G in 10 Palestinian probands from Hebron and Jerusalem. SpliceAI predicted a significant effect of this putative branchpoint-inactivating variant on the nearby intron 7 splice acceptor site. Splice assays revealed exon 8 skipping and two partial inclusions of intron 7, each having a deleterious effect. Additional genotyping revealed another 46 affected homozygous or compound heterozygous individuals carrying variant c.859-25A>G. Homozygotes shared a genomic segment of 59.6 to 87.9 kb and showed severe retinal defects on ophthalmoscopic evaluation. Conclusions The ABCA4 variant c.859-25A>G disrupts a predicted branchpoint, resulting in protein truncation because of different splice defects, and is associated with early-onset STGD1 when present in homozygosity. This variant was found in 25/525 Palestinian inherited retinal dystrophy probands, representing one of the most frequent inherited retinal disease-causing variants in West-Bank Palestine.
Collapse
Affiliation(s)
- Zelia Corradi
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Manar Salameh
- St John of Jerusalem Eye Hospital Group, East Jerusalem, Palestine
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mubeen Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Elise Héon
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Ontario, Canada
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ketan Mishra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rebekkah J. Hitti-Malin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Yahya AlSwaiti
- St John of Jerusalem Eye Hospital Group, East Jerusalem, Palestine
| | - Alice Aslanian
- St John of Jerusalem Eye Hospital Group, East Jerusalem, Palestine
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Brian P. Brooks
- Ophthalmic Genetics and Visual Function Branch, National Eye Institutes, National Institutes of Health, Bethesda, Maryland, United States
| | - Wadih M. Zein
- Ophthalmic Genetics and Visual Function Branch, National Eye Institutes, National Institutes of Health, Bethesda, Maryland, United States
| | - Robert B. Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institutes, National Institutes of Health, Bethesda, Maryland, United States
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Claire‐Marie Dhaenens
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Univ. Lille, Inserm, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alaa AlTalbishi
- St John of Jerusalem Eye Hospital Group, East Jerusalem, Palestine
| |
Collapse
|
5
|
Molecular analysis of ABCA4 gene in an Iranian cohort with Stargardt disease. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2021.101450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
6
|
Molday RS, Garces FA, Scortecci JF, Molday LL. Structure and function of ABCA4 and its role in the visual cycle and Stargardt macular degeneration. Prog Retin Eye Res 2021; 89:101036. [PMID: 34954332 DOI: 10.1016/j.preteyeres.2021.101036] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/07/2021] [Accepted: 12/13/2021] [Indexed: 12/17/2022]
Abstract
ABCA4 is a member of the superfamily of ATP-binding cassette (ABC) transporters that is preferentially localized along the rim region of rod and cone photoreceptor outer segment disc membranes. It uses the energy from ATP binding and hydrolysis to transport N-retinylidene-phosphatidylethanolamine (N-Ret-PE), the Schiff base adduct of retinal and phosphatidylethanolamine, from the lumen to the cytoplasmic leaflet of disc membranes. This ensures that all-trans-retinal and excess 11-cis-retinal are efficiently cleared from photoreceptor cells thereby preventing the accumulation of toxic retinoid compounds. Loss-of-function mutations in the gene encoding ABCA4 cause autosomal recessive Stargardt macular degeneration, also known as Stargardt disease (STGD1), and related autosomal recessive retinopathies characterized by impaired central vision and an accumulation of lipofuscin and bis-retinoid compounds. High resolution structures of ABCA4 in its substrate and nucleotide free state and containing bound N-Ret-PE or ATP have been determined by cryo-electron microscopy providing insight into the molecular architecture of ABCA4 and mechanisms underlying substrate recognition and conformational changes induced by ATP binding. The expression and functional characterization of a large number of disease-causing missense ABCA4 variants have been determined. These studies have shed light into the molecular mechanisms underlying Stargardt disease and a classification that reliably predicts the effect of a specific missense mutation on the severity of the disease. They also provide a framework for developing rational therapeutic treatments for ABCA4-associated diseases.
Collapse
Affiliation(s)
- Robert S Molday
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, B.C., Canada; Department of Ophthalmology & Visual Sciences, University of British Columbia, Vancouver, B.C., Canada.
| | - Fabian A Garces
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, B.C., Canada
| | | | - Laurie L Molday
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, B.C., Canada
| |
Collapse
|
7
|
Schneider N, Sundaresan Y, Gopalakrishnan P, Beryozkin A, Hanany M, Levanon EY, Banin E, Ben-Aroya S, Sharon D. Inherited retinal diseases: Linking genes, disease-causing variants, and relevant therapeutic modalities. Prog Retin Eye Res 2021; 89:101029. [PMID: 34839010 DOI: 10.1016/j.preteyeres.2021.101029] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/11/2022]
Abstract
Inherited retinal diseases (IRDs) are a clinically complex and heterogenous group of visual impairment phenotypes caused by pathogenic variants in at least 277 nuclear and mitochondrial genes, affecting different retinal regions, and depleting the vision of affected individuals. Genes that cause IRDs when mutated are unique by possessing differing genotype-phenotype correlations, varying inheritance patterns, hypomorphic alleles, and modifier genes thus complicating genetic interpretation. Next-generation sequencing has greatly advanced the identification of novel IRD-related genes and pathogenic variants in the last decade. For this review, we performed an in-depth literature search which allowed for compilation of the Global Retinal Inherited Disease (GRID) dataset containing 4,798 discrete variants and 17,299 alleles published in 31 papers, showing a wide range of frequencies and complexities among the 194 genes reported in GRID, with 65% of pathogenic variants being unique to a single individual. A better understanding of IRD-related gene distribution, gene complexity, and variant types allow for improved genetic testing and therapies. Current genetic therapeutic methods are also quite diverse and rely on variant identification, and range from whole gene replacement to single nucleotide editing at the DNA or RNA levels. IRDs and their suitable therapies thus require a range of effective disease modelling in human cells, granting insight into disease mechanisms and testing of possible treatments. This review summarizes genetic and therapeutic modalities of IRDs, provides new analyses of IRD-related genes (GRID and complexity scores), and provides information to match genetic-based therapies such as gene-specific and variant-specific therapies to the appropriate individuals.
Collapse
Affiliation(s)
- Nina Schneider
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Yogapriya Sundaresan
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Prakadeeswari Gopalakrishnan
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Avigail Beryozkin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Mor Hanany
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Shay Ben-Aroya
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel.
| |
Collapse
|
8
|
Biswas P, Villanueva AL, Soto-Hermida A, Duncan JL, Matsui H, Borooah S, Kurmanov B, Richard G, Khan SY, Branham K, Huang B, Suk J, Bakall B, Goldberg JL, Gabriel L, Khan NW, Raghavendra PB, Zhou J, Devalaraja S, Huynh A, Alapati A, Zawaydeh Q, Weleber RG, Heckenlively JR, Hejtmancik JF, Riazuddin S, Sieving PA, Riazuddin SA, Frazer KA, Ayyagari R. Deciphering the genetic architecture and ethnographic distribution of IRD in three ethnic populations by whole genome sequence analysis. PLoS Genet 2021; 17:e1009848. [PMID: 34662339 PMCID: PMC8589175 DOI: 10.1371/journal.pgen.1009848] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 11/12/2021] [Accepted: 09/29/2021] [Indexed: 12/12/2022] Open
Abstract
Patients with inherited retinal dystrophies (IRDs) were recruited from two understudied populations: Mexico and Pakistan as well as a third well-studied population of European Americans to define the genetic architecture of IRD by performing whole-genome sequencing (WGS). Whole-genome analysis was performed on 409 individuals from 108 unrelated pedigrees with IRDs. All patients underwent an ophthalmic evaluation to establish the retinal phenotype. Although the 108 pedigrees in this study had previously been examined for mutations in known IRD genes using a wide range of methodologies including targeted gene(s) or mutation(s) screening, linkage analysis and exome sequencing, the gene mutations responsible for IRD in these 108 pedigrees were not determined. WGS was performed on these pedigrees using Illumina X10 at a minimum of 30X depth. The sequence reads were mapped against hg19 followed by variant calling using GATK. The genome variants were annotated using SnpEff, PolyPhen2, and CADD score; the structural variants (SVs) were called using GenomeSTRiP and LUMPY. We identified potential causative sequence alterations in 61 pedigrees (57%), including 39 novel and 54 reported variants in IRD genes. For 57 of these pedigrees the observed genotype was consistent with the initial clinical diagnosis, the remaining 4 had the clinical diagnosis reclassified based on our findings. In seven pedigrees (12%) we observed atypical causal variants, i.e. unexpected genotype(s), including 4 pedigrees with causal variants in more than one IRD gene within all affected family members, one pedigree with intrafamilial genetic heterogeneity (different affected family members carrying causal variants in different IRD genes), one pedigree carrying a dominant causative variant present in pseudo-recessive form due to consanguinity and one pedigree with a de-novo variant in the affected family member. Combined atypical and large structural variants contributed to about 20% of cases. Among the novel mutations, 75% were detected in Mexican and 50% found in European American pedigrees and have not been reported in any other population while only 20% were detected in Pakistani pedigrees and were not previously reported. The remaining novel IRD causative variants were listed in gnomAD but were found to be very rare and population specific. Mutations in known IRD associated genes contributed to pathology in 63% Mexican, 60% Pakistani and 45% European American pedigrees analyzed. Overall, contribution of known IRD gene variants to disease pathology in these three populations was similar to that observed in other populations worldwide. This study revealed a spectrum of mutations contributing to IRD in three populations, identified a large proportion of novel potentially causative variants that are specific to the corresponding population or not reported in gnomAD and shed light on the genetic architecture of IRD in these diverse global populations. The study was performed to identify the underlying cause of inherited retinal degeneration (IRD) in 409 individuals from 108 families. Primarily, these families were recruited from three different geographic regions: Mexico, Pakistan and European Americans from the United States. Blood samples were collected from all individuals for genome analysis. This analysis detected causative variants in 61 out of the 108 pedigrees. A total of 93 gene variants were found in the 61 families. Among these, 54 were previously reported as causative variants and the remaining 39 have not been reported in IRD pedigrees. Interestingly, 54% of these novel variants were not listed in gnomAD. In addition to these findings, complex causative genotypes were observed in 20% of pedigrees. Overall, causative variants were detected in 63% Mexican, 60% Pakistani and 45% European American pedigrees. This study revealed the distribution of IRD causative variants in pedigrees with diverse ethnic and geographic backgrounds.
Collapse
Affiliation(s)
- Pooja Biswas
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
- School of Biotechnology, REVA University, Bengaluru, Karnataka, India
| | - Adda L. Villanueva
- Retina and Genomics Institute, Yucatán, México
- Laboratoire de Diagnostic Moleculaire, Hôpital Maisonneuve Rosemont, Montreal, Quebec, Canada
| | - Angel Soto-Hermida
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Jacque L. Duncan
- Ophthalmology, University of California San Francisco, San Francisco, California, United States of America
| | - Hiroko Matsui
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Shyamanga Borooah
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Berzhan Kurmanov
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | | | - Shahid Y. Khan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Kari Branham
- Ophthalmology & Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan, United States of America
| | - Bonnie Huang
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - John Suk
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Benjamin Bakall
- Ophthalmology, University of Arizona College of Medicine Phoenix, Phoenix, Arizona, United States of America
| | - Jeffrey L. Goldberg
- Byers Eye Institute, Stanford, Palo Alto, California, United States of America
| | - Luis Gabriel
- Genetics and Ophthalmology, Genelabor, Goiânia, Brazil
| | - Naheed W. Khan
- Ophthalmology & Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan, United States of America
| | - Pongali B. Raghavendra
- School of Biotechnology, REVA University, Bengaluru, Karnataka, India
- School of Regenerative Medicine, Manipal University, Bengaluru, Karnataka, India
| | - Jason Zhou
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Sindhu Devalaraja
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Andrew Huynh
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Akhila Alapati
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Qais Zawaydeh
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Richard G. Weleber
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - John R. Heckenlively
- Ophthalmology & Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan, United States of America
| | - J. Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sheikh Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan
| | - Paul A. Sieving
- National Eye Institute, Bethesda, Maryland, United States of America
- Ophthalmology & Vision Science, UC Davis Medical Center, California, United States of America
| | - S. Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (RA); (KAF); (SAR)
| | - Kelly A. Frazer
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, United States of America
- Department of Pediatrics, Rady Children’s Hospital, Division of Genome Information Sciences, San Diego, California, United States of America
- * E-mail: (RA); (KAF); (SAR)
| | - Radha Ayyagari
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
- * E-mail: (RA); (KAF); (SAR)
| |
Collapse
|
9
|
Al-Khuzaei S, Broadgate S, Foster CR, Shah M, Yu J, Downes SM, Halford S. An Overview of the Genetics of ABCA4 Retinopathies, an Evolving Story. Genes (Basel) 2021; 12:1241. [PMID: 34440414 PMCID: PMC8392661 DOI: 10.3390/genes12081241] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 11/16/2022] Open
Abstract
Stargardt disease (STGD1) and ABCA4 retinopathies (ABCA4R) are caused by pathogenic variants in the ABCA4 gene inherited in an autosomal recessive manner. The gene encodes an importer flippase protein that prevents the build-up of vitamin A derivatives that are toxic to the RPE. Diagnosing ABCA4R is complex due to its phenotypic variability and the presence of other inherited retinal dystrophy phenocopies. ABCA4 is a large gene, comprising 50 exons; to date > 2000 variants have been described. These include missense, nonsense, splicing, structural, and deep intronic variants. Missense variants account for the majority of variants in ABCA4. However, in a significant proportion of patients with an ABCA4R phenotype, a second variant in ABCA4 is not identified. This could be due to the presence of yet unknown variants, or hypomorphic alleles being incorrectly classified as benign, or the possibility that the disease is caused by a variant in another gene. This underlines the importance of accurate genetic testing. The pathogenicity of novel variants can be predicted using in silico programs, but these rely on databases that are not ethnically diverse, thus highlighting the need for studies in differing populations. Functional studies in vitro are useful towards assessing protein function but do not directly measure the flippase activity. Obtaining an accurate molecular diagnosis is becoming increasingly more important as targeted therapeutic options become available; these include pharmacological, gene-based, and cell replacement-based therapies. The aim of this review is to provide an update on the current status of genotyping in ABCA4 and the status of the therapeutic approaches being investigated.
Collapse
Affiliation(s)
- Saoud Al-Khuzaei
- Oxford Eye Hospital, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK; (S.A.-K.); (M.S.)
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Level 6 John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (S.B.); (J.Y.)
| | - Suzanne Broadgate
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Level 6 John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (S.B.); (J.Y.)
| | | | - Mital Shah
- Oxford Eye Hospital, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK; (S.A.-K.); (M.S.)
| | - Jing Yu
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Level 6 John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (S.B.); (J.Y.)
| | - Susan M. Downes
- Oxford Eye Hospital, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK; (S.A.-K.); (M.S.)
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Level 6 John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (S.B.); (J.Y.)
| | - Stephanie Halford
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Level 6 John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (S.B.); (J.Y.)
| |
Collapse
|
10
|
Targeted next-generation sequencing identifies ABCA4 mutations in Chinese families with childhood-onset and adult-onset Stargardt disease. Biosci Rep 2021; 41:228645. [PMID: 33988224 PMCID: PMC8173525 DOI: 10.1042/bsr20203497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 11/17/2022] Open
Abstract
Background: Stargardt disease (STGD) is the most common form of juvenile macular dystrophy associated with progressive central vision loss, and is agenetically and clinically heterogeneous disease. Molecular diagnosis is of great significance in aiding the clinical diagnosis, helping to determine the phenotypic severity and visual prognosis. In the present study, we determined the clinical and genetic features of seven childhood-onset and three adult-onset Chinese STGD families. We performed capture next-generation sequencing (NGS) of the probands and searched for potentially disease-causing genetic variants in previously identified retinal or macular dystrophy genes. Methods: In all, ten unrelated Chinese families were enrolled. Panel-based NGS was performed to identify potentially disease-causing genetic variants in previously identified retinal or macular dystrophy genes, including the five known STGD genes (ABCA4, PROM1, PRPH2, VMD2, and ELOVL4). Variant analysis, Sanger validation, and segregation tests were utilized to validate the disease-causing mutations in these families. Results: Using systematic data analysis with an established bioinformatics pipeline and segregation analysis, 17 pathogenic mutations in ABCA4 were identified in the 10 STGD families. Four of these mutations were novel: c.371delG, c.681T > G, c.5509C > T, and EX37del. Childhood-onset STGD was associated with severe visual loss, generalized retinal dysfunction and was due to more severe variants in ABCA4 than those found in adult-onset disease. Conclusions: We expand the existing spectrum of STGD and reveal the genotype–phenotype relationships of the ABCA4 mutations in Chinese patients. Childhood-onset STGD lies at the severe end of the spectrum of ABCA4-associated retinal phenotypes.
Collapse
|
11
|
Camp DA, Gemayel MC, Ciulla TA. Understanding the genetic pathology of Stargardt disease: a review of current findings and challenges. Expert Opin Orphan Drugs 2021. [DOI: 10.1080/21678707.2021.1898373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- David A. Camp
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Michael C. Gemayel
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Thomas A. Ciulla
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN, USA
- Retina Service, Midwest Eye Institute, Indianapolis, IN, USA
| |
Collapse
|
12
|
Mena MD, Moresco AA, Vidal SH, Aguilar-Cortes D, Obregon MG, Fandiño AC, Sendoya JM, Llera AS, Podhajcer OL. Clinical and Genetic Spectrum of Stargardt Disease in Argentinean Patients. Front Genet 2021; 12:646058. [PMID: 33841504 PMCID: PMC8033171 DOI: 10.3389/fgene.2021.646058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/05/2021] [Indexed: 12/11/2022] Open
Abstract
Purpose To describe the clinical and molecular spectrum of Stargardt disease (STGD) in a cohort of Argentinean patients. Methods This retrospective study included 132 subjects comprising 95 probands clinically diagnosed with STGD and relatives from 16 of them. Targeted next-generation sequencing of the coding and splicing regions of ABCA4 and other phenocopying genes (ELOVL4, PROM1, and CNGB3) was performed in 97 STGD patients. Results We found two or more disease-causing variants in the ABCA4 gene in 69/95 (73%) probands, a single ABCA4 variant in 9/95 (9.5%) probands, and no ABCA4 variants in 17/95 (18%) probands. The final analysis identified 173 variants in ABCA4. Seventy-nine ABCA4 variants were unique, of which nine were novel. No significant findings were seen in the other evaluated genes. Conclusion This study describes the phenotypic and genetic features of STGD1 in an Argentinean cohort. The mutations p.(Gly1961Glu) and p.(Arg1129Leu) were the most frequent, representing almost 20% of the mutated alleles. We also expanded the ABCA4 mutational spectrum with nine novel disease-causing variants, of which eight might be associated with South American natives.
Collapse
Affiliation(s)
- Marcela D Mena
- Laboratorio de Terapia Molecular y Celular (Genocan), Fundación Instituto Leloir, CONICET, Buenos Aires, Argentina
| | - Angélica A Moresco
- Servicio de Genética, Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Sofía H Vidal
- Servicio de Oftalmología, Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Diana Aguilar-Cortes
- Laboratorio de Terapia Molecular y Celular (Genocan), Fundación Instituto Leloir, CONICET, Buenos Aires, Argentina
| | - María G Obregon
- Servicio de Genética, Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Adriana C Fandiño
- Servicio de Oftalmología, Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Juan M Sendoya
- Laboratorio de Terapia Molecular y Celular (Genocan), Fundación Instituto Leloir, CONICET, Buenos Aires, Argentina
| | - Andrea S Llera
- Laboratorio de Terapia Molecular y Celular (Genocan), Fundación Instituto Leloir, CONICET, Buenos Aires, Argentina
| | - Osvaldo L Podhajcer
- Laboratorio de Terapia Molecular y Celular (Genocan), Fundación Instituto Leloir, CONICET, Buenos Aires, Argentina
| |
Collapse
|
13
|
Zhu Q, Rui X, Li Y, You Y, Sheng XL, Lei B. Identification of Four Novel Variants and Determination of Genotype-Phenotype Correlations for ABCA4 Variants Associated With Inherited Retinal Degenerations. Front Cell Dev Biol 2021; 9:634843. [PMID: 33732702 PMCID: PMC7957020 DOI: 10.3389/fcell.2021.634843] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 01/26/2021] [Indexed: 12/21/2022] Open
Abstract
Purpose The purpose of the study is to describe the genetic and clinical features of 17 patients with ABCA4-related inherited retinal degenerations (IRDs) and define the phenotype–genotype correlations. Methods In this multicenter retrospective study, 17 patients from 16 families were enrolled, and ABCA4 gene variants were detected using targeted next-generation sequencing using a custom designed panel for IRDs. Sanger sequencing and co-segregation analysis of the suspected pathogenic variants were performed with the family members. The pathogenicities of variants were evaluated according to the American College of Medical Genetics and Genomics guidelines (ACMG). Protein structure modifications mediated by the variants were studied using bioinformatic analyses. Results The probands were diagnosed with Stargardt disease 1 (7), cone-rod dystrophy type 3 (8), cone dystrophy (1), and retinitis pigmentosa 19 (1). Onset of symptoms occurred between 5 and 27 years of age (median age = 12.4 years). A total of 30 unique ABCA4 suspicious pathogenic variations were observed, including 18 missense mutations, seven frameshift mutations, two nonsense mutations, one canonical splice site mutation, one small in-frame deletion, and one insertion. Four novel ABCA4 variants were identified. Two novel frameshift variants, c.1290dupC (p.W431fs), and c.2967dupT (G990fs), were determined to be pathogenic. A novel missense variant c.G5761T (p.V1921L) was likely pathogenic, and another novel missense c.C170G (p.P57R) variant was of undetermined significance. All ABCA4 variants tested in this study inordinately changed the physico-chemical parameters and structure of protein based on in silico analysis. Conclusion ABCA4-related IRD is genetically and clinically highly heterogeneous. Four novel ABCA4 variants were identified. This study will expand the spectrum of disease-causing variants in ABCA4, which will further facilitate genetic counseling.
Collapse
Affiliation(s)
- Qing Zhu
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China
| | - Xue Rui
- Ningxia Clinical Research Center of Blinding Eye Disease, Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, First Affiliated Hospital of Northwest University for Nationalities, Yinchuan, China
| | - Ya Li
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China.,Henan Branch of National Clinical Research Center for Ocular Diseases, Henan Eye Institute and Henan Eye Hospital, Henan Provincial People's Hospital, Zhengzhou, China
| | - Ya You
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China.,Henan Branch of National Clinical Research Center for Ocular Diseases, Henan Eye Institute and Henan Eye Hospital, Henan Provincial People's Hospital, Zhengzhou, China
| | - Xun-Lun Sheng
- Ningxia Clinical Research Center of Blinding Eye Disease, Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, First Affiliated Hospital of Northwest University for Nationalities, Yinchuan, China
| | - Bo Lei
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China.,Henan Branch of National Clinical Research Center for Ocular Diseases, Henan Eye Institute and Henan Eye Hospital, Henan Provincial People's Hospital, Zhengzhou, China
| |
Collapse
|
14
|
Curtis SB, Molday LL, Garces FA, Molday RS. Functional analysis and classification of homozygous and hypomorphic ABCA4 variants associated with Stargardt macular degeneration. Hum Mutat 2020; 41:1944-1956. [PMID: 32845050 DOI: 10.1002/humu.24100] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/06/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022]
Abstract
Stargardt macular degeneration (Stargardt disease 1 [STGD1]) is caused by mutations in the gene encoding ABCA4, an ATP-binding cassette protein that transports N-retinylidene-phosphatidylethanolamine (N-Ret-PE) across photoreceptor membranes. Reduced ABCA4 activity results in retinoid accumulation leading to photoreceptor degeneration. The disease onset and severity vary from severe loss in visual acuity in the first decade to mild visual impairment late in life. We determined the effect of 22 disease-causing missense mutations on the expression and ATPase activity of ABCA4 in the absence and presence of N-Ret-PE. Three classes were identified that correlated with the disease onset in homozygous STGD1 individuals: Class 1 exhibited reduced ABCA4 expression and ATPase activity that was not stimulated by N-Ret-PE; individuals homozygous for these variants had an early disease onset (≤13 years); Class 2 showed reduced ATPase activity with limited stimulation by N-Ret-PE; these correlated with moderate disease onset (14-40 years); and Class 3 displayed high expression and ATPase activity that was strongly activated by N-Ret-PE; these were associated with late disease onset (>40 years). On the basis of our results, we introduce a functionality index for gauging the effect of missense mutations on STGD1 severity. Our studies support the mild phenotype exhibited by the p.Gly863Ala, p.Asn1868Ile, and p.Gly863Ala/p.Asn1868Ile variants.
Collapse
Affiliation(s)
- Susan B Curtis
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Laurie L Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Fabian A Garces
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert S Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
15
|
Abstract
We report the molecular basis of the largest Tunisian cohort with inherited retinal dystrophies (IRD) reported to date, identify disease-causing pathogenic variants and describe genotype-phenotype correlations. A subset of 26 families from a cohort of 73 families with clinical diagnosis of autosomal recessive IRD (AR-IRD) excluding Usher syndrome was analyzed by whole exome sequencing and autozygosity mapping. Causative pathogenic variants were identified in 50 families (68.4%), 42% of which were novel. The most prevalent pathogenic variants were observed in ABCA4 (14%) and RPE65, CRB1 and CERKL (8% each). 26 variants (8 novel and 18 known) in 19 genes were identified in 26 families (14 missense substitutions, 5 deletions, 4 nonsense pathogenic variants and 3 splice site variants), with further allelic heterogeneity arising from different pathogenic variants in the same gene. The most common phenotype in our cohort is retinitis pigmentosa (23%) and cone rod dystrophy (23%) followed by Leber congenital amaurosis (19.2%). We report the association of new disease phenotypes. This research was carried out in Tunisian patients with IRD in order to delineate the genetic population architecture.
Collapse
|
16
|
Molecular Analysis of the ABCA4 Gene Mutations in Patients with Stargardt Disease Using Human Hair Follicles. Int J Mol Sci 2020; 21:ijms21103430. [PMID: 32413971 PMCID: PMC7279462 DOI: 10.3390/ijms21103430] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/05/2020] [Accepted: 05/10/2020] [Indexed: 12/17/2022] Open
Abstract
ABCA4 gene mutations are the cause of a spectrum of ABCA4 retinopathies, and the most common juvenile macular degeneration is called Stargardt disease. ABCA4 has previously been observed almost exclusively in the retina. Therefore, studying the functional consequences of ABCA4 variants has required advanced molecular analysis techniques. The aim of the present study was to evaluate whether human hair follicles may be used for molecular analysis of the ABCA4 gene splice-site variants in patients with ABCA4 retinopathies. We assessed ABCA4 expression in hair follicles and skin at mRNA and protein levels by means of real-time PCR and Western blot analyses, respectively. We performed cDNA sequencing to reveal the presence of full-length ABCA4 transcripts and analyzed ABCA4 transcripts from three patients with Stargardt disease carrying different splice-site ABCA4 variants: c.5312+1G>A, c.5312+2T>G and c.5836-3C>A. cDNA analysis revealed that c.5312+1G>A, c.5312+2T>G variants led to the skipping of exon 37, and the c.5836-3C>A variant resulted in the insertion of 30 nucleotides into the transcript. Our results strongly argue for the use of hair follicles as a model for the molecular analysis of the pathogenicity of ABCA4 variants in patients with ABCA4 retinopathies.
Collapse
|
17
|
Cremers FPM, Lee W, Collin RWJ, Allikmets R. Clinical spectrum, genetic complexity and therapeutic approaches for retinal disease caused by ABCA4 mutations. Prog Retin Eye Res 2020; 79:100861. [PMID: 32278709 PMCID: PMC7544654 DOI: 10.1016/j.preteyeres.2020.100861] [Citation(s) in RCA: 156] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/13/2020] [Accepted: 03/18/2020] [Indexed: 12/18/2022]
Abstract
The ABCA4 protein (then called a “rim protein”) was first
identified in 1978 in the rims and incisures of rod photoreceptors. The
corresponding gene, ABCA4, was cloned in 1997, and variants
were identified as the cause of autosomal recessive Stargardt disease (STGD1).
Over the next two decades, variation in ABCA4 has been
attributed to phenotypes other than the classically defined STGD1 or fundus
flavimaculatus, ranging from early onset and fast progressing cone-rod dystrophy
and retinitis pigmentosa-like phenotypes to very late onset cases of mostly mild
disease sometimes resembling, and confused with, age-related macular
degeneration. Similarly, analysis of the ABCA4 locus uncovered
a trove of genetic information, including >1200 disease-causing mutations
of varying severity, and of all types – missense, nonsense, small
deletions/insertions, and splicing affecting variants, of which many are located
deep-intronic. Altogether, this has greatly expanded our understanding of
complexity not only of the diseases caused by ABCA4 mutations,
but of all Mendelian diseases in general. This review provides an in depth
assessment of the cumulative knowledge of ABCA4-associated retinopathy –
clinical manifestations, genetic complexity, pathophysiology as well as current
and proposed therapeutic approaches.
Collapse
Affiliation(s)
- Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, PO Box 9104, 6500 HE, Nijmegen, the Netherlands.
| | - Winston Lee
- Department of Ophthalmology, Columbia University, New York, NY, 10032, USA; Department of Genetics & Development, Columbia University, New York, NY, 10032, USA
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, PO Box 9104, 6500 HE, Nijmegen, the Netherlands
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, NY, 10032, USA; Department of Pathology & Cell Biology, Columbia University, New York, NY, 10032, USA.
| |
Collapse
|
18
|
Liu XZ, Tao TC, Qi H, Feng SN, Chen NN, Zhao L, Ma ZZ, Li GL, Yang LP. Simultaneous expression of two pathogenic genes in four Chinese patients affected with inherited retinal dystrophy. Int J Ophthalmol 2020; 13:220-230. [PMID: 32090030 DOI: 10.18240/ijo.2020.02.04] [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] [Received: 11/01/2018] [Accepted: 12/07/2019] [Indexed: 01/14/2023] Open
Abstract
AIM To describe the complex, overlapping phenotype of four Chinese patients with inherited retinal dystrophies (IRDs) who harbored two pathogenic genes simultaneously. METHODS This retrospective study included 4 patients affected with IRDs. Medical and ophthalmic histories were obtained, and clinical examinations were performed. A specific Hereditary Eye Disease Enrichment Panel (HEDEP) based on exome capture technology was used for genetic screening. RESULTS Four patients were identified to harbor disease-causing variants in two different genes. Patient retinitis pigmentosa (RP) 01-II:1 exhibited both classical ABCA4-induced Stargardt disease (STGD) 1 and USH2A-associated RP, patient RP02-III:2 exhibited both classical ABCA4-induced STGD1 and CDH23-associated RP, patient RP03-II:1 exhibited both USH2A-induced autosomal recessive retinitis pigmentosa (arRP) syndrome and SNRNP200-induced autosomal dominant retinitis pigmentosa (adRP), and patient RP04-II:2 exhibited USH2A-induced arRP syndrome and EYS-induced arRP at the same time. CONCLUSION Our study demonstrates that genotype-phenotype correlations and comprehensive genetic screening is crucial for diagnosing IRDs and helping family planning for patients suffering from the disease.
Collapse
Affiliation(s)
- Xiao-Zhen Liu
- Department of Ophthalmology, Peking University Third Hospital, Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Beijing 100191, China
| | - Tian-Chang Tao
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing 100730, China
| | - Hong Qi
- Department of Ophthalmology, Peking University Third Hospital, Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Beijing 100191, China
| | - Shan-Na Feng
- Department of Ophthalmology, Peking University Third Hospital, Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Beijing 100191, China
| | - Ning-Ning Chen
- Department of Ophthalmology, Peking University Third Hospital, Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Beijing 100191, China
| | - Lin Zhao
- Department of Ophthalmology, Peking University Third Hospital, Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Beijing 100191, China
| | - Zhi-Zhong Ma
- Department of Ophthalmology, Peking University Third Hospital, Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Beijing 100191, China
| | - Gen-Lin Li
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing 100730, China
| | - Li-Ping Yang
- Department of Ophthalmology, Peking University Third Hospital, Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Beijing 100191, China
| |
Collapse
|
19
|
Chen ZJ, Lin KH, Lee SH, Shen RJ, Feng ZK, Wang XF, Huang XF, Huang ZQ, Jin ZB. Mutation spectrum and genotype-phenotype correlation of inherited retinal dystrophy in Taiwan. Clin Exp Ophthalmol 2020; 48:486-499. [PMID: 31872526 DOI: 10.1111/ceo.13708] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 12/15/2019] [Accepted: 12/15/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND Inherited retinal dystrophy (IRD) is a group of irreversible retinal degenerative disorders with significant genotypic and phenotypic heterogeneity, which cause difficulty in making a precise clinical diagnosis. Furthermore, the mutation spectrum of IRD in Taiwan remains unknown. Therefore, our study focused on investigating the spectrum of mutations among Taiwanese families with IRD using targeted exome sequencing (TES) technology. METHODS We recruited a total of 60 unrelated Taiwanese families with IRD; most of them were retinitis pigmentosa. We employed TES to investigate 284 candidate genes. Bioinformatics analysis, Sanger sequencing-based co-segregation testing, and computational assessment were performed to validate each mutation and its pathogenicity. The genotype-phenotype correlation was analysed in all patients with mutations defined in the guidelines provided by the American College of Medical Genetics. RESULTS We successfully identified genetic causes in 32 families (detection rate of 53.3%). Among them, 16 had a sporadic inheritance (16/36, 44.4%); eight had an autosomal recessive inheritance (8/14, 57.1%); four had an autosomal dominant inheritance (4/5, 80%); four had an X-linked inheritance (4/5, 80%). Among 38 pathological mutations in 19 known genes, 20 mutations are reported here for the first time. Novel mutation spectrum and genotype-phenotype correlations were revealed as well. CONCLUSION Here we achieved a detection rate of 53.3% and elucidated the mutation spectrum in Taiwanese families with IRD for the first time. The results indicated that CYP4V2 and USH2A might be the most common pathogenic genes in IRD patients in Taiwan.
Collapse
Affiliation(s)
- Zhen-Ji Chen
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Wenzhou Medical University, Wenzhou, China.,National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ocular Diseases, Wenzhou Medical University, Wenzhou, China
| | - Keng-Hung Lin
- Department of Ophthalmology, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Shi-Huang Lee
- Department of Ophthalmology, Taichung Tzu Chi Hospital, Taichung, Taiwan
| | - Ren-Juan Shen
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Wenzhou Medical University, Wenzhou, China.,National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ocular Diseases, Wenzhou Medical University, Wenzhou, China
| | - Zhuo-Kun Feng
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Wenzhou Medical University, Wenzhou, China.,National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ocular Diseases, Wenzhou Medical University, Wenzhou, China
| | - Xiao-Fang Wang
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Wenzhou Medical University, Wenzhou, China.,National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ocular Diseases, Wenzhou Medical University, Wenzhou, China
| | - Xiu-Feng Huang
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Wenzhou Medical University, Wenzhou, China.,National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ocular Diseases, Wenzhou Medical University, Wenzhou, China
| | - Zhi-Qin Huang
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Wenzhou Medical University, Wenzhou, China.,National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ocular Diseases, Wenzhou Medical University, Wenzhou, China
| | - Zi-Bing Jin
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Wenzhou Medical University, Wenzhou, China.,National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ocular Diseases, Wenzhou Medical University, Wenzhou, China
| |
Collapse
|
20
|
Hu FY, Li JK, Gao FJ, Qi YH, Xu P, Zhang YJ, Wang DD, Wang LS, Li W, Wang M, Chen F, Shen SM, Xu GZ, Zhang SH, Chang Q, Wu JH. ABCA4 Gene Screening in a Chinese Cohort With Stargardt Disease: Identification of 37 Novel Variants. Front Genet 2019; 10:773. [PMID: 31543898 PMCID: PMC6739639 DOI: 10.3389/fgene.2019.00773] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 07/22/2019] [Indexed: 11/13/2022] Open
Abstract
Purpose: To clarify the mutation spectrum and frequency of ABCA4 in a Chinese cohort with Stargardt disease (STGD1). Methods: A total of 153 subjects, comprising 25 families (25 probands and their family members) and 71 sporadic cases, were recruited for the analysis of ABCA4 variants. All probands with STGD1 underwent a comprehensive ophthalmologic examination. Overall, 792 genes involved in common inherited eye diseases were screened for variants by panel-based next-generation sequencing (NGS). Variants were filtered and analyzed to evaluate possible pathogenicity. Results: The total variant detection rate of at least one ABCA4 mutant allele was 84.3% (129/153): two or three disease-associated variants in 86 subjects (56.2%), one mutant allele in 43 subjects (28.1%), and no variants in 24 subjects (15.7%). Ninety-six variants were identified in the total cohort, which included 62 missense (64%), 15 splicing (16%), 11 frameshift (12%), 6 nonsense (6%), and 2 small insertion or deletion (2%) variants. Thirty-seven novel variants were found, including a de novo variant, c.4561delA. The most prevalent variant was c.101_106delCTTTAT (10.5%), followed by c.2894A > G (6.5%) and c.6563T > C (4.6%), in STGD1 patients from eastern China. Conclusion: Thirty-seven novel variants were detected using panel-based NGS, including one de novo variant, further extending the mutation spectrum of ABCA4. The common variants in a population from eastern China with STGD1 were also identified.
Collapse
Affiliation(s)
- Fang-Yuan Hu
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shanghai, China
| | - Jian-Kang Li
- BGI-Shenzhen, Shenzhen, China.,Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Feng-Juan Gao
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shanghai, China
| | - Yu-He Qi
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shanghai, China
| | - Ping Xu
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shanghai, China
| | - Yong-Jin Zhang
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shanghai, China
| | - Dan-Dan Wang
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shanghai, China
| | - Lu-Sheng Wang
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Wei Li
- BGI-Shenzhen, Shenzhen, China.,BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Min Wang
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shanghai, China
| | - Fang Chen
- BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Shenzhen Engineering Laboratory for Birth Defects Screening, BGI-Shenzhen, Shenzhen, China
| | | | - Ge-Zhi Xu
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shanghai, China
| | - Sheng-Hai Zhang
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shanghai, China
| | - Qing Chang
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shanghai, China
| | - Ji-Hong Wu
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China.,Key Laboratory of Myopia (Fudan University), Chinese Academy of Medical Sciences, National Health Commission, Shanghai, China
| |
Collapse
|
21
|
Garces F, Jiang K, Molday LL, Stöhr H, Weber BH, Lyons CJ, Maberley D, Molday RS. Correlating the Expression and Functional Activity of ABCA4 Disease Variants With the Phenotype of Patients With Stargardt Disease. Invest Ophthalmol Vis Sci 2019; 59:2305-2315. [PMID: 29847635 PMCID: PMC5937799 DOI: 10.1167/iovs.17-23364] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Purpose Stargardt disease (STGD1), the most common early-onset recessive macular degeneration, is caused by mutations in the gene encoding the ATP-binding cassette transporter ABCA4. Although extensive genetic studies have identified more than 1000 mutations that cause STGD1 and related ABCA4-associated diseases, few studies have investigated the extent to which mutations affect the biochemical properties of ABCA4. The purpose of this study was to correlate the expression and functional activities of missense mutations in ABCA4 identified in a cohort of Canadian patients with their clinical phenotype. Methods Eleven patients from British Columbia were diagnosed with STGD1. The exons and exon-intron boundaries were sequenced to identify potential pathologic mutations in ABCA4. Missense mutations were expressed in HEK293T cells and their level of expression, retinoid substrate binding properties, and ATPase activities were measured and correlated with the phenotype of the STGD1 patients. Results Of the 11 STGD1 patients analyzed, 7 patients had two mutations in ABCA4, 3 patients had one detected mutation, and 1 patient had no mutations in the exons and flanking regions. Included in this cohort of patients was a severely affected 11-year-old child who was homozygous for the novel p.Ala1794Pro mutation. Expression and functional analysis of this variant and other disease-associated variants compared favorably with the phenotypes of this cohort of STGD1 patients. Conclusions Although many factors contribute to the phenotype of STGD1 patients, the expression and residual activity of ABCA4 mutants play a major role in determining the disease severity of STGD1 patients.
Collapse
Affiliation(s)
- Fabian Garces
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kailun Jiang
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Laurie L Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Heidi Stöhr
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Bernhard H Weber
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Christopher J Lyons
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - David Maberley
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert S Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
22
|
Sheremet NL, Zhorzholadze NV, Ronzina IA, Grushke IG, Kurbatov SA, Chukhrova AL, Loginova AN, Shcherbakova PO, Tanas AS, Polyakov AV, Strel'nikov VV. [Molecular genetic diagnosis of Stargardt disease]. Vestn Oftalmol 2018; 133:4-11. [PMID: 28980559 DOI: 10.17116/oftalma201713344-11] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
AIM To comparatively evaluate the efficacy of genetic screening in patients with Stargardt disease (SD) by using an express panel of 5 most common ABCA4 mutations and performing massive parallel sequencing of all coding regions of the ABCA4, ELOVL4, PROM1, and CNGB3 genes. MATERIAL AND METHODS MLPA analysis for 5 ABCA4 mutations, namely p.G863A, p.L541P, p.A1038V, p.G1961E, and p.P1380L, was done in 54 patients with SD. In 25 patients, massive parallel sequencing of coding regions (exons) and neighboring introns of the ABCA4, ELOVL4, PROM1, and CNGB3 genes was also performed. RESULTS Gene testing for 5 ABCA4 mutations showed that 50% of patients (27 patients) harbored one mutation and 13% - two mutations. At massive parallel sequencing (25 patients), two pathogenic alleles were found in 21 patients (84%), one mutation - in 23 patients (91.7%). The majority of mutations was accounted for by the ABCA4 gene (83% of all mutation-positive patients). CONCLUSION Sequencing of exons and neighboring introns of the ABCA4, ELOVL4, PROM1, and CNGB3 genes with the new molecular genetic diagnostic system enabled confirmation of the diagnosis of SD in 84% of patients. High prevalence of p.L541P, p.A1038V, and p.G1961E mutations of the ABCA4 gene has been established.
Collapse
Affiliation(s)
- N L Sheremet
- Research Institute of Eye Diseases, 11 A, B, Rossolimo St., Moscow, Russia, 119021
| | - N V Zhorzholadze
- Research Institute of Eye Diseases, 11 A, B, Rossolimo St., Moscow, Russia, 119021
| | - I A Ronzina
- Research Institute of Eye Diseases, 11 A, B, Rossolimo St., Moscow, Russia, 119021
| | - I G Grushke
- Research Institute of Eye Diseases, 11 A, B, Rossolimo St., Moscow, Russia, 119021
| | - S A Kurbatov
- Voronezh Regional Clinical Consultative and Diagnostic Center, 5a Lenina Sq., Voronezh, Russia, 394018
| | - A L Chukhrova
- Research Centre of Medical Genetics, 1 Moskvorech'e St., Moscow, Russia, 115478
| | - A N Loginova
- Research Centre of Medical Genetics, 1 Moskvorech'e St., Moscow, Russia, 115478
| | - P O Shcherbakova
- Pirogov Russian National Research Medical University, 1 Ostrovityanova St., Moscow, Russia, 117997
| | - A S Tanas
- Research Centre of Medical Genetics, 1 Moskvorech'e St., Moscow, Russia, 115478
| | - A V Polyakov
- Research Centre of Medical Genetics, 1 Moskvorech'e St., Moscow, Russia, 115478
| | - V V Strel'nikov
- Research Centre of Medical Genetics, 1 Moskvorech'e St., Moscow, Russia, 115478
| |
Collapse
|
23
|
Peripheral Pigmented Retinal Lesions in Stargardt Disease. Am J Ophthalmol 2018; 188:104-110. [PMID: 29288030 DOI: 10.1016/j.ajo.2017.12.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 12/16/2017] [Accepted: 12/18/2017] [Indexed: 11/24/2022]
Abstract
PURPOSE To investigate the prevalence of peripheral pigmented retinal lesions and associated clinical findings in patients with Stargardt disease. DESIGN Retrospective case series. METHODS Records at a single academic institution were reviewed for patients with genetically confirmed Stargardt disease with peripheral pigmented retinal lesions on wide-field retinal imaging. For this cohort we described demographics, clinical features, and pathogenic variants. RESULTS Out of 62 patients with Stargardt disease and wide-field retinal imaging, 14 had peripheral pigmented retinal lesions. These flat, subretinal lesions were located in the mid or far periphery and had well-defined borders, resembling congenital hypertrophy of retinal pigment epithelium (CHRPE) lesions. For this group of 14 patients, median age at initial diagnosis of Stargardt disease was 9.5 years, and the median duration of disease was 21.5 years. Median Snellen visual acuity was 20/200, and median central scotoma size was 20.0 degrees. All 14 patients had electroretinographic abnormalities. Four out of 14 patients developed new lesions during clinical follow-up. CONCLUSIONS Wide-field retinal imaging revealed the presence of peripheral pigmented retinal lesions resembling CHRPE lesions in a subset of patients with genetically confirmed Stargardt disease. Presence of these lesions may be associated with severe phenotypes of the disease.
Collapse
|
24
|
Villanueva A, Biswas P, Kishaba K, Suk J, Tadimeti K, Raghavendra PB, Nadeau K, Lamontagne B, Busque L, Geoffroy S, Mongrain I, Asselin G, Provost S, Dubé MP, Nudleman E, Ayyagari R. Identification of the genetic determinants responsible for retinal degeneration in families of Mexican descent. Ophthalmic Genet 2017; 39:73-79. [PMID: 28945494 DOI: 10.1080/13816810.2017.1373830] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
PURPOSE To investigate the clinical characteristics and genetic basis of inherited retinal degeneration (IRD) in six unrelated pedigrees from Mexico. METHODS A complete ophthalmic evaluation including measurement of visual acuities, Goldman kinetic or Humphrey dynamic perimetry, Amsler test, fundus photography, and color vision testing was performed. Family history and blood samples were collected from available family members. DNA from members of two pedigrees was examined for known mutations using the APEX ARRP genotyping microarray and one pedigree using the APEX LCA genotyping microarray. The remaining three pedigrees were analyzed using a custom-designed targeted capture array covering the exons of 233 known retinal degeneration genes. Sequencing was performed on Illumina HiSeq. Reads were mapped against hg19, and variants were annotated using GATK and filtered by exomeSuite. Segregation and ethnicity-matched control sample analyses were performed by dideoxy sequencing. RESULTS Six pedigrees with IRD were analyzed. Nine rare or novel, potentially pathogenic variants segregating with the phenotype were detected in IMPDH1, USH2A, RPE65, ABCA4, and FAM161A genes. Among these, six were known mutations while the remaining three changes in USH2A, RPE65, and FAM161A genes have not been previously reported to be associated with IRD. Analysis of 100 ethnicity-matched controls did not detect the presence of these three novel variants indicating, these are rare variants in the Mexican population. CONCLUSIONS Screening patients diagnosed with IRD from Mexico identified six known mutations and three rare or novel potentially damaging variants in IMPDH1, USH2A, RPE65, ABCA4, and FAM161A genes that segregated with disease.
Collapse
Affiliation(s)
- Adda Villanueva
- a Retina Department Genomics Institute, Mejora Vision MD/Virtual Eye Care MD , Mérida , Yucatán , México.,b Laboratoire de Diagnostic Moleculaire , Hôpital Maisonneuve Rosemont , Montreal , Quebec , Canada
| | - Pooja Biswas
- c School of Biotechnology , REVA University , Bengaluru , India.,d Shiley Eye Institute, University of California San Diego , La Jolla , CA , USA
| | - Kameron Kishaba
- d Shiley Eye Institute, University of California San Diego , La Jolla , CA , USA
| | - John Suk
- d Shiley Eye Institute, University of California San Diego , La Jolla , CA , USA
| | - Keerti Tadimeti
- d Shiley Eye Institute, University of California San Diego , La Jolla , CA , USA
| | | | - Karine Nadeau
- a Retina Department Genomics Institute, Mejora Vision MD/Virtual Eye Care MD , Mérida , Yucatán , México.,b Laboratoire de Diagnostic Moleculaire , Hôpital Maisonneuve Rosemont , Montreal , Quebec , Canada
| | - Bruno Lamontagne
- a Retina Department Genomics Institute, Mejora Vision MD/Virtual Eye Care MD , Mérida , Yucatán , México.,b Laboratoire de Diagnostic Moleculaire , Hôpital Maisonneuve Rosemont , Montreal , Quebec , Canada
| | - Lambert Busque
- a Retina Department Genomics Institute, Mejora Vision MD/Virtual Eye Care MD , Mérida , Yucatán , México.,b Laboratoire de Diagnostic Moleculaire , Hôpital Maisonneuve Rosemont , Montreal , Quebec , Canada
| | - Steve Geoffroy
- e Montreal Heart Institute, Université de Montréal , Montreal , Canada.,f Université de Montréal Beaulieu-Saucier Pharmacogenomics Center, Montreal Heart Institute, Université de Montréal , Montreal , Canada
| | - Ian Mongrain
- e Montreal Heart Institute, Université de Montréal , Montreal , Canada.,f Université de Montréal Beaulieu-Saucier Pharmacogenomics Center, Montreal Heart Institute, Université de Montréal , Montreal , Canada
| | - Géraldine Asselin
- e Montreal Heart Institute, Université de Montréal , Montreal , Canada.,f Université de Montréal Beaulieu-Saucier Pharmacogenomics Center, Montreal Heart Institute, Université de Montréal , Montreal , Canada
| | - Sylvie Provost
- e Montreal Heart Institute, Université de Montréal , Montreal , Canada.,f Université de Montréal Beaulieu-Saucier Pharmacogenomics Center, Montreal Heart Institute, Université de Montréal , Montreal , Canada
| | - Marie-Pierre Dubé
- e Montreal Heart Institute, Université de Montréal , Montreal , Canada.,f Université de Montréal Beaulieu-Saucier Pharmacogenomics Center, Montreal Heart Institute, Université de Montréal , Montreal , Canada.,g Department of Medicine, Université de Montréal , Montreal , Canada
| | - Eric Nudleman
- d Shiley Eye Institute, University of California San Diego , La Jolla , CA , USA
| | - Radha Ayyagari
- d Shiley Eye Institute, University of California San Diego , La Jolla , CA , USA
| |
Collapse
|
25
|
Schulz HL, Grassmann F, Kellner U, Spital G, Rüther K, Jägle H, Hufendiek K, Rating P, Huchzermeyer C, Baier MJ, Weber BHF, Stöhr H. Mutation Spectrum of the ABCA4 Gene in 335 Stargardt Disease Patients From a Multicenter German Cohort-Impact of Selected Deep Intronic Variants and Common SNPs. Invest Ophthalmol Vis Sci 2017; 58:394-403. [PMID: 28118664 PMCID: PMC5270621 DOI: 10.1167/iovs.16-19936] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Purpose Stargardt disease (STGD1) is an autosomal recessive retinopathy, caused by mutations in the retina-specific ATP-binding cassette transporter (ABCA4) gene. To establish the mutational spectrum and to assess effects of selected deep intronic and common genetic variants on disease, we performed a comprehensive sequence analysis in a large cohort of German STGD1 patients. Methods DNA samples of 335 STGD1 patients were analyzed for ABCA4 mutations in its 50 coding exons and adjacent intronic sequences by resequencing array technology or next generation sequencing (NGS). Parts of intron 30 and 36 were screened by Sanger chain-terminating dideoxynucleotide sequencing. An in vitro splicing assay was used to test selected variants for their splicing behavior. By logistic regression analysis we assessed the association of common ABCA4 alleles while a multivariate logistic regression model calculated a genetic risk score (GRS). Results Our analysis identified 148 pathogenic or likely pathogenic mutations, of which 48 constitute so far unpublished ABCA4-associated disease alleles. Four rare deep intronic variants were found once in 472 alleles analyzed. In addition, we identified six risk-modulating common variants. Genetic risk score estimates suggest that defined common ABCA4 variants influence disease risk in carriers of a single pathogenic ABCA4 allele. Conclusions Our study adds to the mutational spectrum of the ABCA4 gene. Moreover, in our cohort, deep intronic variants in intron 30 and 36 likely play no or only a minor role in disease pathology. Of note, our findings demonstrate a possible modifying effect of common sequence variants on ABCA4-associated disease.
Collapse
Affiliation(s)
- Heidi L Schulz
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Felix Grassmann
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Ulrich Kellner
- Rare Retinal Disease Center, AugenZentrum Siegburg, MVZ ADTC Siegburg GmbH, Siegburg, Germany 3RetinaScience, Bonn, Germany
| | - Georg Spital
- Department of Ophthalmology, St. Franziskus-Hospital, Münster, Germany
| | | | - Herbert Jägle
- Department of Ophthalmology, University Hospital Regensburg, Regensburg, Germany
| | | | - Philipp Rating
- Department of Ophthalmology, University Hospital Essen, Essen, Germany
| | - Cord Huchzermeyer
- Department of Ophthalmology, University Hospital Erlangen, Erlangen, Germany
| | - Maria J Baier
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Bernhard H F Weber
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Heidi Stöhr
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| |
Collapse
|
26
|
Lee W, Schuerch K, Xie Y, Zernant J, Tsang SH, Sparrow JR, Allikmets R. Simultaneous Expression of ABCA4 and GPR143 Mutations: A Complex Phenotypic Manifestation. Invest Ophthalmol Vis Sci 2017; 57:3409-15. [PMID: 27367509 PMCID: PMC4961055 DOI: 10.1167/iovs.16-19621] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Purpose To describe the complex, overlapping phenotype expressed in a two generation family harboring pathogenic mutations in the ABCA4 and GPR143 genes. Methods Clinical evaluation of a two generation family included quantitative autofluorescence imaging (qAF, 488-nm excitation) using a modified confocal scanning laser ophthalmoscope equipped with an internal fluorescent reference to account for varying laser power detector sensitivity, spectral-domain optical coherence tomography, and full-field ERG testing. Complete sequencing of the ABCA4 and GPR143 genes was carried out in each individual. Results Affected individuals presented with bull's eye lesions and qAF levels above the 95% confidence interval for healthy eyes; full-field ERG revealed no generalized rod dysfunction but mild implicit time delays in cone responses. Complete sequencing of the ABCA4 gene revealed two disease-causing mutations, p.L541P and p.G1961E; and mutational phase was confirmed in each unaffected parent. Further examination in the affected patients revealed a peripheral “mud-splattered” pattern of hypopigmented RPE after which sequencing of GPR143 revealed a novel missense variant, p.Y157C. The GPR143 variant segregated from the father who did not exhibit any indications of retinal disease with the exception of an abnormal near-infrared autofluorescence (NIR-AF) signal distribution in the macula. Conclusions An individual carrying both ABCA4 and GPR143 disease-causing mutations can express a complex, overlapping phenotype associated with both Stargardt disease and X-linked ocular albinism (OA1). The absence of OA1-related disease changes (with the exception of NIR-AF changes associated with melanin distribution) in the father may be indicative of mild expressivity or variable gene penetrance.
Collapse
Affiliation(s)
- Winston Lee
- Department of Ophthalmology, Columbia University, New York, New York, United States
| | - Kaspar Schuerch
- Department of Ophthalmology, Columbia University, New York, New York, United States
| | - Yajing Xie
- Department of Ophthalmology, Columbia University, New York, New York, United States
| | - Jana Zernant
- Department of Ophthalmology, Columbia University, New York, New York, United States
| | - Stephen H Tsang
- Department of Ophthalmology, Columbia University, New York, New York, United States 2Department of Pathology & Cell Biology, Columbia University, New York, New York, United States
| | - Janet R Sparrow
- Department of Ophthalmology, Columbia University, New York, New York, United States 2Department of Pathology & Cell Biology, Columbia University, New York, New York, United States
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, New York, United States 2Department of Pathology & Cell Biology, Columbia University, New York, New York, United States
| |
Collapse
|
27
|
Lee W, Schuerch K, Zernant J, Collison FT, Bearelly S, Fishman GA, Tsang SH, Sparrow JR, Allikmets R. Genotypic spectrum and phenotype correlations of ABCA4-associated disease in patients of south Asian descent. Eur J Hum Genet 2017; 25:735-743. [PMID: 28327576 DOI: 10.1038/ejhg.2017.13] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/12/2016] [Accepted: 01/11/2017] [Indexed: 11/09/2022] Open
Abstract
Variants in the ABCA4 gene are the most common cause of juvenile-onset blindness affecting close to 1 in 10 000 people worldwide. Disease severity varies largely according to genotype, which can be specific to ethnic and racial groups. Here we investigate the spectrum of ABCA4 variation and its phenotypic expression in 38 patients of South Asian descent, notably from India, Pakistan, Bangladesh and Sri Lanka. Sequencing of all exons and flanking intronic sequences of ABCA4 revealed disease-causing variants in all patients: 3 in 2.6%, 2 in 81.6% and 1 in 15.8%. Altogether, 36 distinct variants were identified, including 9 previously not described. The most frequent variant c.5882G>A, p.(G1961E) was found in half the patients, the highest ever reported in a single study cohort. The South Asian founder variant c.859-9T>C was identified along with other founder variants ascribed to Danish, Chinese, Mexican and African patients. Patients carrying c.5882G>A, p.(G1961E) exhibited a consistently confined disease phenotype, normal quantitative autofluorescence (qAF) levels and preserved full-field ERG (ffERG) while c.859-9T>C resulted in widespread disease, significantly elevated qAF and reduced to non-detectable ffERG. South Asian patients present with a relatively unique ABCA4 profile comprised of various ethnic founder variants resulting in two or three major retinal phenotypes.
Collapse
Affiliation(s)
- Winston Lee
- Department of Ophthalmology, Columbia University, New York, NY, USA
| | - Kaspar Schuerch
- Department of Ophthalmology, Columbia University, New York, NY, USA
| | - Jana Zernant
- Department of Ophthalmology, Columbia University, New York, NY, USA
| | - Frederick T Collison
- The Pangere Center for Inherited Retinal Diseases, The Chicago Lighthouse, Chicago, IL, USA
| | | | - Gerald A Fishman
- The Pangere Center for Inherited Retinal Diseases, The Chicago Lighthouse, Chicago, IL, USA
| | - Stephen H Tsang
- Department of Ophthalmology, Columbia University, New York, NY, USA.,Department of Pathology & Cell Biology, Columbia University, New York, NY, USA
| | - Janet R Sparrow
- Department of Ophthalmology, Columbia University, New York, NY, USA.,Department of Pathology & Cell Biology, Columbia University, New York, NY, USA
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, NY, USA.,Department of Pathology & Cell Biology, Columbia University, New York, NY, USA
| |
Collapse
|
28
|
Zolnikova IV, Strelnikov VV, Skvortsova NA, Tanas AS, Barh D, Rogatina EV, Egorova IV, Levina DV, Demenkova ON, Prikaziuk EG, Ivanova ME. Stargardt disease-associated mutation spectrum of a Russian Federation cohort. Eur J Med Genet 2016; 60:140-147. [PMID: 27939946 DOI: 10.1016/j.ejmg.2016.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 11/26/2016] [Accepted: 12/01/2016] [Indexed: 12/24/2022]
Abstract
ABCA4-associated mutation screening is extensively performed in European, African, American and several other populations for various retinopathies. However, it has not been well studied in a Russian cohort. Using next-generation (325 genes inherited disease panel) and Sanger sequencing technologies for the first time we documented the spectrum of genetic variations in a Russian retinopathy cohort of 51 patients from 10 ethnic groups. We found ABCA4 variations in 70.5% cases and one case with BEST1 variation. Multiple ABCA4 variations, ABCA4 + RDH12, and ABCA4 + BEST1 variations are also observed and the disease severity is found proportionate to the variation burden. Ten novel ABCA4 variations are detected of which 8 belongs to non-Slavonian population. Most of the detected known variations are found in European and American Stargardt disease populations. No retinopathy causing variation is detected in 14 (27%) cases suggesting that in this Russian retinopathies cohort the causal variants could be in genes that are not covered by our 325 gene panel. Therefore, whole genome/exome analysis is required to identify novel retinopathy associated genes and provide better disease management for this heterogeneous cohort.
Collapse
Affiliation(s)
- Inna V Zolnikova
- Moscow Helmholtz Research Institute of Eye Diseases, Sadovaya Chernogryazskaya Str. 14/19, Moscow 105062, Russia
| | | | - Natalia A Skvortsova
- Posterior Eye Segment Diagnostics and Surgery Centre, 2nd Vladimirskaya Str. b.2, 4th Floor, Moscow 111123, Russia
| | - Alexander S Tanas
- Research Centre for Medical Genetics, Moskvorechie Str. 1, Moscow 15478, Russia
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB 721172, India; Xcode Life Sciences, 3D Eldorado, 112 Nungambakkam High Road, Nungambakkam, Chennai, Tamil Nadu 600034, India.
| | - Elena V Rogatina
- Moscow Helmholtz Research Institute of Eye Diseases, Sadovaya Chernogryazskaya Str. 14/19, Moscow 105062, Russia
| | - Irina V Egorova
- Moscow Helmholtz Research Institute of Eye Diseases, Sadovaya Chernogryazskaya Str. 14/19, Moscow 105062, Russia
| | - Darja V Levina
- Moscow Helmholtz Research Institute of Eye Diseases, Sadovaya Chernogryazskaya Str. 14/19, Moscow 105062, Russia
| | - Olga N Demenkova
- Moscow Helmholtz Research Institute of Eye Diseases, Sadovaya Chernogryazskaya Str. 14/19, Moscow 105062, Russia
| | - Egor G Prikaziuk
- Bioinformatics Institute, Kantemirovskaya Str. b.2a, Saint Petersburg 197342, Russia
| | | |
Collapse
|
29
|
Genomic screening of ABCA4 and array CGH analysis underline the genetic variability of Greek patients with inherited retinal diseases. Meta Gene 2016; 8:37-43. [PMID: 27014590 PMCID: PMC4792891 DOI: 10.1016/j.mgene.2016.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 01/12/2016] [Accepted: 02/10/2016] [Indexed: 11/22/2022] Open
Abstract
Background Retinal dystrophies are a clinically and genetically heterogeneous group of disorders which affect more than two million people worldwide. The present study focused on the role of the ABCA4 gene in the pathogenesis of hereditary retinal dystrophies (autosomal recessive Stargardt disease, autosomal recessive cone-rod dystrophy, and autosomal recessive retinitis pigmentosa) in patients of Greek origin. Materials and methods Our cohort included 26 unrelated patients and their first degree healthy relatives. The ABCA4 mutation screening involved Sanger sequencing of all exons and flanking regions. Evaluation of novel variants included sequencing of control samples, family segregation analysis and characterization by in silico prediction tools. Twenty five patients were also screened for copy number variations by array-comparative genomic hybridization. Results Excluding known disease-causing mutations and polymorphisms, two novel variants were identified in coding and non-coding regions of ABCA4. Array-CGH analysis revealed two partial deletions of USH2A and MYO3A in two patients with nonsyndromic autosomal recessive retinitis pigmentosa. Conclusions The ABCA4 mutation spectrum in Greek patients differs from other populations. Bioinformatic tools, segregation analysis along with clinical data from the patients seemed to be crucial for the evaluation of genetic variants and particularly for the discrimination between causative and non-causative variants. Sixteen known pathological genetic variants were identified in ABCA4 gene in Greek patients with retinal dystrophies. Two novel variants were found in patients with Stargardt’s disease and cone-rod dystrophy respectively. Two reported mutations in Stargardt's patients were identified in retinitis pigmentosa and cone-rod dystrophy patients. The mutations p.Gly1961Glu and p.Ala1038Val, which are common in other populations, where also found in our cohort consisted of 26 Greek patients. Array-comparative genome hybridization revealed large deletions in two out of the 25 cases studied.
Collapse
|
30
|
Ścieżyńska A, Oziębło D, Ambroziak AM, Korwin M, Szulborski K, Krawczyński M, Stawiński P, Szaflik J, Szaflik JP, Płoski R, Ołdak M. Next-generation sequencing of ABCA4: High frequency of complex alleles and novel mutations in patients with retinal dystrophies from Central Europe. Exp Eye Res 2015; 145:93-99. [PMID: 26593885 DOI: 10.1016/j.exer.2015.11.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 09/04/2015] [Accepted: 11/11/2015] [Indexed: 10/22/2022]
Abstract
Variation in the ABCA4 locus has emerged as the most prevalent cause of monogenic retinal diseases. The study aimed to discover causative ABCA4 mutations in a large but not previously investigated cohort with ABCA4-related diseases originating from Central Europe and to refine the genetic relevance of all identified variants based on population evidence. Comprehensive clinical studies were performed to identify patients with Stargardt disease (STGD, n = 76) and cone-rod dystrophy (CRD, n = 16). Next-generation sequencing targeting ABCA4 was applied for a widespread screening of the gene. The results were analyzed in the context of exome data from a corresponding population (n = 594) and other large genomic databases. Our data disprove the pathogenic status of p.V552I and provide more evidence against a causal role of four further ABCA4 variants as drivers of the phenotype under a recessive paradigm. The study identifies 12 novel potentially pathogenic mutations (four of them recurrent) and a novel complex allele p.[(R152*; V2050L)]. In one third (31/92) of our cohort we detected the p.[(L541P; A1038V)] complex allele, which represents an unusually high level of genetic homogeneity for ABCA4-related diseases. Causative ABCA4 mutations account for 79% of STGD and 31% of CRD cases. A combination of p.[(L541P; A1038V)] and/or a truncating ABCA4 mutation always resulted in an early disease onset. Identification of ABCA4 retinopathies provides a specific molecular diagnosis and justifies a prompt introduction of simple precautions that may slow disease progression. The comprehensive, population-specific study expands our knowledge on the genetic landscape of retinal diseases.
Collapse
Affiliation(s)
- Aneta Ścieżyńska
- Department of Histology and Embryology, Medical University of Warsaw, Warsaw, Poland
| | - Dominika Oziębło
- Department of Genetics, Institute of Physiology and Pathology of Hearing, Warsaw/Kajetany, Poland
| | - Anna M Ambroziak
- Department of Ophthalmology, Medical University of Warsaw, Warsaw, Poland; Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Magdalena Korwin
- Department of Ophthalmology, Medical University of Warsaw, Warsaw, Poland
| | - Kamil Szulborski
- Department of Ophthalmology, Medical University of Warsaw, Warsaw, Poland
| | - Maciej Krawczyński
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland; Center for Medical Genetics GENESIS, Poznan, Poland
| | - Piotr Stawiński
- Department of Genetics, Institute of Physiology and Pathology of Hearing, Warsaw/Kajetany, Poland
| | - Jerzy Szaflik
- Department of Ophthalmology, Medical University of Warsaw, Warsaw, Poland
| | - Jacek P Szaflik
- Department of Ophthalmology, Medical University of Warsaw, Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland.
| | - Monika Ołdak
- Department of Histology and Embryology, Medical University of Warsaw, Warsaw, Poland; Department of Genetics, Institute of Physiology and Pathology of Hearing, Warsaw/Kajetany, Poland.
| |
Collapse
|
31
|
Xin W, Xiao X, Li S, Jia X, Guo X, Zhang Q. Identification of Genetic Defects in 33 Probands with Stargardt Disease by WES-Based Bioinformatics Gene Panel Analysis. PLoS One 2015; 10:e0132635. [PMID: 26161775 PMCID: PMC4498695 DOI: 10.1371/journal.pone.0132635] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 06/16/2015] [Indexed: 11/19/2022] Open
Abstract
Stargardt disease (STGD) is the most common hereditary macular degeneration in juveniles, with loss of central vision occurring in the first or second decade of life. The aim of this study is to identify the genetic defects in 33 probands with Stargardt disease. Clinical data and genomic DNA were collected from 33 probands from unrelated families with STGD. Variants in coding genes were initially screened by whole exome sequencing. Candidate variants were selected from all known genes associated with hereditary retinal dystrophy and then confirmed by Sanger sequencing. Putative pathogenic variants were further validated in available family members and controls. Potential pathogenic mutations were identified in 19 of the 33 probands (57.6%). These mutations were all present in ABCA4, but not in the other four STGD-associated genes or in genes responsible for other retinal dystrophies. Of the 19 probands, ABCA4 mutations were homozygous in one proband and compound heterozygous in 18 probands, involving 28 variants (13 novel and 15 known). Analysis of normal controls and available family members in 12 of the 19 families further support the pathogenicity of these variants. Clinical manifestation of all probands met the diagnostic criteria of STGD. This study provides an overview of a genetic basis for STGD in Chinese patients. Mutations in ABCA4 are the most common cause of STGD in this cohort. Genetic defects in approximately 42.4% of STGD patients await identification in future studies.
Collapse
Affiliation(s)
- Wei Xin
- 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
| | - Xiaoyun Jia
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiangming Guo
- 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
- * E-mail:
| |
Collapse
|
32
|
Zernant J, Collison FT, Lee W, Fishman GA, Noupuu K, Yuan B, Cai C, Lupski JR, Yannuzzi LA, Tsang SH, Allikmets R. Genetic and clinical analysis of ABCA4-associated disease in African American patients. Hum Mutat 2015; 35:1187-94. [PMID: 25066811 PMCID: PMC4283973 DOI: 10.1002/humu.22626] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 06/25/2014] [Indexed: 12/30/2022]
Abstract
Autosomal recessive Stargardt disease (STGD1) is caused by hundreds of mutations in the ABCA4 gene, which are often specific to racial and ethnic groups. Here, we investigated the ABCA4 variation and their phenotypic expression in a cohort of 44 patients of African American descent, a previously under-characterized racial group. Patients were screened for mutations in ABCA4 by next-generation sequencing and array-comparative genomic hybridization (aCGH), followed by analyses for pathogenicity by in silico programs. Thorough ophthalmic examination was performed on all patients. At least two (expected) disease-causing alleles in the ABCA4 gene were identified in 27 (61.4%) patients, one allele in 11 (25%) patients, and no ABCA4 mutations were found in six (13.6%) patients. Altogether, 39 different disease-causing ABCA4 variants, including seven new, were identified on 65 (74%) chromosomes, most of which were unique for this racial group. The most frequent ABCA4 mutation in this cohort was c.6320G>A (p.(R2107H)), representing 19.3% of all disease-associated alleles. No large copy number variants were identified in any patient. Most patients reported later onset of symptoms. In summary, the ABCA4 mutation spectrum in patients of West African descent differs significantly from that in patients of European descent, resulting in a later onset and "milder" disease.
Collapse
Affiliation(s)
- Jana Zernant
- Department of Ophthalmology, Columbia University, New York, New York
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Zernant J, Xie YA, Ayuso C, Riveiro-Alvarez R, Lopez-Martinez MA, Simonelli F, Testa F, Gorin MB, Strom SP, Bertelsen M, Rosenberg T, Boone PM, Yuan B, Ayyagari R, Nagy PL, Tsang SH, Gouras P, Collison FT, Lupski JR, Fishman GA, Allikmets R. Analysis of the ABCA4 genomic locus in Stargardt disease. Hum Mol Genet 2014; 23:6797-806. [PMID: 25082829 DOI: 10.1093/hmg/ddu396] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Autosomal recessive Stargardt disease (STGD1, MIM 248200) is caused by mutations in the ABCA4 gene. Complete sequencing of ABCA4 in STGD patients identifies compound heterozygous or homozygous disease-associated alleles in 65-70% of patients and only one mutation in 15-20% of patients. This study was designed to find the missing disease-causing ABCA4 variation by a combination of next-generation sequencing (NGS), array-Comparative Genome Hybridization (aCGH) screening, familial segregation and in silico analyses. The entire 140 kb ABCA4 genomic locus was sequenced in 114 STGD patients with one known ABCA4 exonic mutation revealing, on average, 200 intronic variants per sample. Filtering of these data resulted in 141 candidates for new mutations. Two variants were detected in four samples, two in three samples, and 20 variants in two samples, the remaining 117 new variants were detected only once. Multimodal analysis suggested 12 new likely pathogenic intronic ABCA4 variants, some of which were specific to (isolated) ethnic groups. No copy number variation (large deletions and insertions) was detected in any patient suggesting that it is a very rare event in the ABCA4 locus. Many variants were excluded since they were not conserved in non-human primates, were frequent in African populations and, therefore, represented ancestral, and not disease-associated, variants. The sequence variability in the ABCA4 locus is extensive and the non-coding sequences do not harbor frequent mutations in STGD patients of European-American descent. Defining disease-associated alleles in the ABCA4 locus requires exceptionally well characterized large cohorts and extensive analyses by a combination of various approaches.
Collapse
Affiliation(s)
| | | | - Carmen Ayuso
- Department of Genetics, Instituto de Investigacion Sanitaria-University Hospital Fundacion Jimenez Diaz, UAM (IIS-FJD), Madrid, Spain Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Rosa Riveiro-Alvarez
- Department of Genetics, Instituto de Investigacion Sanitaria-University Hospital Fundacion Jimenez Diaz, UAM (IIS-FJD), Madrid, Spain Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Miguel-Angel Lopez-Martinez
- Department of Genetics, Instituto de Investigacion Sanitaria-University Hospital Fundacion Jimenez Diaz, UAM (IIS-FJD), Madrid, Spain Centro de Investigacion Biomedica en Red (CIBER) de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Second University of Naples, Naples, Italy
| | - Francesco Testa
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Second University of Naples, Naples, Italy
| | - Michael B Gorin
- Department of Ophthalmology Department of Human Genetics, Jules Stein Eye Institute and
| | - Samuel P Strom
- Department of Ophthalmology Department of Human Genetics, Jules Stein Eye Institute and Department of Pathology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Mette Bertelsen
- Kennedy Center Eye Clinic, Glostrup Hospital, Glostrup, Denmark
| | | | - Philip M Boone
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Radha Ayyagari
- Department of Ophthalmology, University of California San Diego, La Jolla, CA, USA and
| | - Peter L Nagy
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Stephen H Tsang
- Department of Ophthalmology and Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | | | - Frederick T Collison
- The Pangere Center for Hereditary Retinal Diseases, The Chicago Lighthouse for People Who are Blind or Visually Impaired, Chicago, IL, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Gerald A Fishman
- The Pangere Center for Hereditary Retinal Diseases, The Chicago Lighthouse for People Who are Blind or Visually Impaired, Chicago, IL, USA
| | - Rando Allikmets
- Department of Ophthalmology and Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| |
Collapse
|
34
|
Zhang X, Ge X, Shi W, Huang P, Min Q, Li M, Yu X, Wu Y, Zhao G, Tong Y, Jin ZB, Qu J, Gu F. Molecular diagnosis of putative Stargardt disease by capture next generation sequencing. PLoS One 2014; 9:e95528. [PMID: 24763286 PMCID: PMC3999032 DOI: 10.1371/journal.pone.0095528] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Accepted: 03/27/2014] [Indexed: 01/01/2023] Open
Abstract
Stargardt Disease (STGD) is the commonest genetic form of juvenile or early adult onset macular degeneration, which is a genetically heterogeneous disease. Molecular diagnosis of STGD remains a challenge in a significant proportion of cases. To address this, seven patients from five putative STGD families were recruited. We performed capture next generation sequencing (CNGS) of the probands and searched for potentially disease-causing genetic variants in previously identified retinal or macular dystrophy genes. Seven disease-causing mutations in ABCA4 and two in PROM1 were identified by CNGS, which provides a confident genetic diagnosis in these five families. We also provided a genetic basis to explain the differences among putative STGD due to various mutations in different genes. Meanwhile, we show for the first time that compound heterozygous mutations in PROM1 gene could cause cone-rod dystrophy. Our findings support the enormous potential of CNGS in putative STGD molecular diagnosis.
Collapse
Affiliation(s)
- Xiao Zhang
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang, China
| | - Xianglian Ge
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang, China
| | - Wei Shi
- Department of Ophthalmology, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Ping Huang
- Department of Development and Planning, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qingjie Min
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Minghan Li
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang, China
| | - Xinping Yu
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang, China
| | - Yaming Wu
- Department of Ophthalmology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | | | - Yi Tong
- Fuzhou Southeastern Eye Hospital, Fuzhou, China
| | - Zi-Bing Jin
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang, China
| | - Jia Qu
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang, China
| | - Feng Gu
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, State Key Laboratory Cultivation Base and Key Laboratory of Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou, Zhejiang, China
- * E-mail:
| |
Collapse
|