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Kayani S, Edgar VB, Lowden A, Nettesheim ER, Dahshi H, Messahel S, Minassian BA, Greenberg BM. Neuronal Ceroid Lipofuscinoses Type 7 (CLN7)- A Case Series Reporting Cross Sectional and Retrospective Clinical Data to Evaluate Validity of Standardized Tools to Assess Disease Progression, Quality of Life, and Adaptive Skills. RESEARCH SQUARE 2024:rs.3.rs-3983366. [PMID: 38978590 PMCID: PMC11230482 DOI: 10.21203/rs.3.rs-3983366/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Background This study evaluated the clinical characteristics of neuronal ceroid lipofuscinosis type 7 or CLN7 disease spectrum to characterize the clinical, electrophysiologic and neuroimaging phenotypes. Methods We performed a single-center cross sectional data collection along with retrospective medical chart review in patients with a genetic diagnosis of CLN7. This study received ethical approval by the University of Texas Southwestern Medical Center Institutional Review Board. A total of 8 patients were included between the ages of 4 to 6 years. All patients had a genetic diagnosis of CLN7 with homozygous or compound heterozygous mutations in the MFSD8 gene. The information collected includes patient demographics, developmental history, neurological events including seizures and neurodevelopmental regression along with further evaluation of brain magnetic resonance imaging and electrophysiological findings. The clinical phenotype is described through cross sectional and retrospective data collection and standardized tools assessing quality of life and functional skills. Conclusions Our findings in this cohort of CLN7 patients indicated that development is initially normal with onset of clinical symptoms as early as two years of age. Language problems were noted prior to or at the onset of seizures in all cases. Gait problems were noted prior to seizure onset in 3 of 8 patients, and at or within 6 months after the onset of seizures in 5 of 8 patients. All patients followed a progressive course of language, motor, and neurocognitive deterioration. Congruent with the medical history, our patients had significantly low scores on adaptive abilities. Natural history data such as this can be used to support future clinical trial designs.
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Affiliation(s)
- Saima Kayani
- UT Southwestern: The University of Texas Southwestern Medical Center
| | | | - Andrea Lowden
- UT Southwestern: The University of Texas Southwestern Medical Center
| | | | - Hamza Dahshi
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Souad Messahel
- UT Southwestern: The University of Texas Southwestern Medical Center
| | - Berge A Minassian
- UT Southwestern: The University of Texas Southwestern Medical Center
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2
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Lin S, Robson AG, Thompson DA, Stepien KM, Lachmann R, Footitt E, Czyz O, Chandrasekhar S, Schiff E, Iosifidis C, Black GC, Michaelides M, Mahroo OA, Arno G, Webster AR. Non-syndromic retinal dystrophy associated with biallelic variation of SUMF1 and reduced leukocyte sulfatase activity. Clin Genet 2024. [PMID: 38863195 DOI: 10.1111/cge.14573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/13/2024]
Abstract
Biallelic variants in SUMF1 are associated with multiple sulfatase deficiency (MSD), a rare lysosomal storage disorder typically diagnosed in early infancy or childhood, marked by severe neurodegeneration and early mortality. We present clinical and molecular characterisation of three unrelated patients aged 13 to 58 years with milder clinical manifestations due to SUMF1 disease variants, including two adult patients presenting with apparent non-syndromic retinal dystrophy. Whole genome sequencing identified biallelic SUMF1 variants in all three patients; Patient 1 homozygous for a complex allele c.[290G>T;293T>A]; p.[(Gly97Val);(Val98Glu)], Patient 2 homozygous for c.866A>G; p.(Tyr289Cys), and Patient 3 compound heterozygous for c.726-1G>C and p.(Tyr289Cys). Electroretinography indicated a rod-cone dystrophy with additional possible inner retinal dysfunction in all three patients. Biochemical studies confirmed reduced, but not absent, sulfatase enzyme activity in the absence of extra-ocular disease (Patient 1) or only mild systemic disease (Patients 2, 3). These cases are suggestive that non-null SUMF1 genotypes can cause an attenuated clinical phenotype, including retinal dystrophy without systemic complications, in adulthood.
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Affiliation(s)
- Siying Lin
- NIHR Biomedical Research Centre, Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Anthony G Robson
- NIHR Biomedical Research Centre, Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Dorothy A Thompson
- Tony Kriss Visual Electrophysiology Unit, Department of Clinical and Academic Department of Ophthalmology, Sight and Sound Centre, Great Ormond Street Hospital for Children, London, UK
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Karolina M Stepien
- Adult Inherited Metabolic Disorders, Salford Royal Organisation, Northern Care Alliance NHS Foundation Trust, London, UK
| | - Robin Lachmann
- Charles Dent Metabolic Unit, National Hospital for Neurology and Neurosurgery, London, UK
| | - Emma Footitt
- Department of Metabolic Paediatrics, Great Ormond Street Hospital, London, UK
| | - Ola Czyz
- Department of Metabolic Paediatrics, Great Ormond Street Hospital, London, UK
| | | | - Elena Schiff
- NIHR Biomedical Research Centre, Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Christos Iosifidis
- Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Graeme C Black
- Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Michel Michaelides
- NIHR Biomedical Research Centre, Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Omar A Mahroo
- NIHR Biomedical Research Centre, Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
- Department of Ophthalmology, St Thomas' Hospital, London, UK
| | - Gavin Arno
- NIHR Biomedical Research Centre, Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
- Division of Research, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Andrew R Webster
- NIHR Biomedical Research Centre, Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
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3
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Thuma TBT, Procopio RA, Jimenez HJ, Gunton KB, Pulido JS. Hypomorphic variants in inherited retinal and ocular diseases: A review of the literature with clinical cases. Surv Ophthalmol 2024; 69:337-348. [PMID: 38036193 DOI: 10.1016/j.survophthal.2023.11.006] [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: 06/20/2022] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/02/2023]
Abstract
Hypomorphic variants decrease, but do not eliminate, gene function via a reduction in the amount of mRNA or protein product produced by a gene or by production of a gene product with reduced function. Many hypomorphic variants have been implicated in inherited retinal diseases (IRDs) and other genetic ocular conditions; however, there is heterogeneity in the use of the term "hypomorphic" in the scientific literature. We searched for all hypomorphic variants reported to cause IRDs and ocular disorders. We also discuss the presence of hypomorphic variants in the patient population of our ocular genetics department over the past decade. We propose that standardized criteria should be adopted for use of the term "hypomorphic" to describe gene variants to improve genetic counseling and patient care outcomes.
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Affiliation(s)
- Tobin B T Thuma
- Department of Pediatric Ophthalmology and Strabismus, Wills Eye Hospital, Philadelphia, PA, USA
| | | | - Hiram J Jimenez
- Vickie and Jack Farber Vision Research Center, Wills Eye Hospital, Philadelphia, PA, USA
| | - Kammi B Gunton
- Department of Pediatric Ophthalmology and Strabismus, Wills Eye Hospital, Philadelphia, PA, USA
| | - Jose S Pulido
- Vickie and Jack Farber Vision Research Center, Wills Eye Hospital, Philadelphia, PA, USA; Retina Service, Wills Eye Hospital, Philadelphia, PA, USA.
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4
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da Palma MM, Marra M, Igelman AD, Ku CA, Burr A, Andersen K, Everett LA, Porto FBO, Sallum JMF, Yang P, Pennesi ME. Expanding the phenotypic and genotypic spectrum of patients with HGSNAT-related retinopathy. Ophthalmic Genet 2024; 45:167-174. [PMID: 37592806 DOI: 10.1080/13816810.2023.2245035] [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: 03/12/2023] [Accepted: 08/01/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND Variants in HGSNAT have historically been associated with syndromic mucopolysaccharidosis type IIIC (MPSIIIC) but more recent studies demonstrate cases of HGSNAT-related non-syndromic retinitis pigmentosa. We describe and expand the genotypic and phenotypic spectrum of this disease. MATERIALS AND METHODS This is a retrospective, observational, case series of 11 patients with pericentral retinitis pigmentosa due to variants in HGSNAT gene without a syndromic diagnosis of MPSIIIC. We reviewed ophthalmologic data extracted from medical records, genetic testing, color fundus photos, fundus autofluorescence (FAF), and optical coherence tomography (OCT). RESULTS Of the 11 patients, the mean age was 52 years (range: 26-78). The mean age of ophthalmologic symptoms onset was 45 years (range: 15-72). The visual acuity varied from 20/20 to 20/80 (mean 20/30 median 20/20). We described five novel variants in HGSNAT: c.715del (p.Arg239Alafs *37), c.118 G>A (p.Asp40Asn), c.1218_1220delinsTAT, c.1297A>G (p.Asn433Asp), and c.1726 G>T (p.Gly576*). CONCLUSIONS HGSNAT has high phenotypic heterogeneity. Data from our cohort showed that all patients who had at least one variant of c.1843 G>A (p.Ala615Thr) presented with the onset of ocular symptoms after the fourth decade of life. The two patients with onset of ocular symptoms before the fourth decade did not carry this variant. This may suggest that c.1843 G>A variant is associated with a later onset of retinopathy.
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Affiliation(s)
- Mariana Matioli da Palma
- Department of Ophthalmology, Casey Eye Institute at Oregon Health & Science University (OHSU), Portland, Oregon, USA
- Department of Ophthalmology and Visual Sciences, Universidade Federal de São Paulo Escola Paulista de Medicina (UNIFESP), São Paulo, Brazil
- Instituto de Genética Ocular, São Paulo, Brazil
- Department of Surgery & Hospital Clinic of Barcelona, School of Medicine, Universitat de Barcelona, Barcelona, Spain
| | - Molly Marra
- Department of Ophthalmology, Casey Eye Institute at Oregon Health & Science University (OHSU), Portland, Oregon, USA
| | - Austin D Igelman
- Department of Ophthalmology, Casey Eye Institute at Oregon Health & Science University (OHSU), Portland, Oregon, USA
| | - Cristy A Ku
- Department of Ophthalmology, Casey Eye Institute at Oregon Health & Science University (OHSU), Portland, Oregon, USA
- Department of Ophthalmology & Vision Science, University of California Davis, Sacramento, California, USA
| | - Amanda Burr
- Department of Ophthalmology, Casey Eye Institute at Oregon Health & Science University (OHSU), Portland, Oregon, USA
| | - Katherine Andersen
- Department of Ophthalmology, Casey Eye Institute at Oregon Health & Science University (OHSU), Portland, Oregon, USA
| | - Lesley A Everett
- Department of Ophthalmology, Casey Eye Institute at Oregon Health & Science University (OHSU), Portland, Oregon, USA
| | | | - Juliana Maria Ferraz Sallum
- Department of Ophthalmology and Visual Sciences, Universidade Federal de São Paulo Escola Paulista de Medicina (UNIFESP), São Paulo, Brazil
- Instituto de Genética Ocular, São Paulo, Brazil
| | - Paul Yang
- Department of Ophthalmology, Casey Eye Institute at Oregon Health & Science University (OHSU), Portland, Oregon, USA
| | - Mark E Pennesi
- Department of Ophthalmology, Casey Eye Institute at Oregon Health & Science University (OHSU), Portland, Oregon, USA
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5
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Beckman M, Clevenger L, DeBenedictis MJ, Yuan A, Sharma S. A novel ocular phenotype associated with pathogenic variants in MFSD8 leading to macular dystrophy. Ophthalmic Genet 2023; 44:606-609. [PMID: 36861499 DOI: 10.1080/13816810.2023.2183224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/02/2023] [Accepted: 02/16/2023] [Indexed: 03/03/2023]
Abstract
BACKGROUND The major facilitator superfamily domain-containing protein 8 (MFSD8) pathogenic variants are classically associated with autosomal recessive neuronal ceroid lipofuscinosis-7. Case reports have recently demonstrated an association of MFSD8 variants causing autosomal recessive macular dystrophy with central cone involvement without neurologic sequelae. We report a patient with a novel ocular phenotype associated with MFSD8 pathogenic variants causing macular dystrophy without systemic findings. CASE PRESENTATION A 37-year-old female presented with a 20-year history of progressive bilateral vision loss. Fundus examination was notable for a slight pigmentary ring around the fovea in both eyes. Optical coherence tomography (OCT) of the macula showed bilateral subfoveal ellipsoid zone loss without outer retinal changes. Fundus autofluorescence (FAF) demonstrated foveal hypo-autofluorescence (AF) in both eyes as well as hyper-AF nasally to the optic nerve in the perifoveal area. Full-field and multifocal electroretinography demonstrated cone dysfunction with diffuse macular changes in both eyes. Subsequent genetic testing identified two pathogenic MFSD8 variants. The patient had no neurologic symptoms consistent with variant-late infantile neuronal ceroid lipofuscinosis. CONCLUSION MFSD8 pathogenic variants are known to cause macular dystrophies. We report a novel MFSD8-associated macular dystrophy phenotype demonstrating foveal-limited disease with cavitary changes on OCT without inner retinal atrophy and foveal-specific changes on FAF. A threshold model can explain how a hypomorphic missense variant heterozygous with a loss-of-function nonsense variant can lead to a predominantly ocular phenotype with preserved neurologic function. We recommend careful monitoring of these patients for future signs of both retinal and systemic disease progression.
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Affiliation(s)
- Madeline Beckman
- School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | | | | | - Alex Yuan
- Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Sumit Sharma
- Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, USA
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6
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Klein M, Hermey G. Converging links between adult-onset neurodegenerative Alzheimer's disease and early life neurodegenerative neuronal ceroid lipofuscinosis? Neural Regen Res 2023; 18:1463-1471. [PMID: 36571343 PMCID: PMC10075119 DOI: 10.4103/1673-5374.361544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Evidence from genetics and from analyzing cellular and animal models have converged to suggest links between neurodegenerative disorders of early and late life. Here, we summarize emerging links between the most common late life neurodegenerative disease, Alzheimer's disease, and the most common early life neurodegenerative diseases, neuronal ceroid lipofuscinoses. Genetic studies reported an overlap of clinically diagnosed Alzheimer's disease and mutations in genes known to cause neuronal ceroid lipofuscinoses. Accumulating data strongly suggest dysfunction of intracellular trafficking mechanisms and the autophagy-endolysosome system in both types of neurodegenerative disorders. This suggests shared cytopathological processes underlying these different types of neurodegenerative diseases. A better understanding of the common mechanisms underlying the different diseases is important as this might lead to the identification of novel targets for therapeutic concepts, the transfer of therapeutic strategies from one disease to the other and therapeutic approaches tailored to patients with specific mutations. Here, we review dysfunctions of the endolysosomal autophagy pathway in Alzheimer's disease and neuronal ceroid lipofuscinoses and summarize emerging etiologic and genetic overlaps.
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Affiliation(s)
- Marcel Klein
- Institute for Molecular and Cellular Cognition, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Guido Hermey
- Institute for Molecular and Cellular Cognition, Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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7
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Priluck AZ, Breazzano MP. Novel MFSD8 mutation causing non-syndromic asymmetric adult-onset macular dystrophy. Ophthalmic Genet 2023; 44:186-190. [PMID: 35801630 DOI: 10.1080/13816810.2022.2092758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
BACKGROUND MFSD8 mutations can cause type 7 neuronal ceroid lipofuscinosis, a systemic disorder that includes vision loss; however, such mutations can also cause isolated retinal dystrophy with vision loss without systemic signs or symptoms as first identified in 2015. This report details a previously unreported combination of compound heterozygous variants in the MFSD8 gene causing a non-syndromic, bilateral central macular dystrophy presenting in adulthood. MATERIALS AND METHODS We present a case of MFSD8-associated retinal dystrophy with multimodal imaging and a review of relevant literature. RESULTS A 57-year-old female presented for subacute, unilateral blurriness in her right eye. Best corrected visual acuity was 20/250 and 20/50 in the right and left eyes, respectively. Fundus examination and multimodal imaging revealed blunted foveal reflexes and optical gap with subfoveal ellipsoid zone loss in both eyes, right greater than left. Full field electroretinography results were within normal limits while the Arden ratio on electro-oculography was abnormal in both eyes, right more so than left. Genetic testing revealed apparently causative compound heterozygous mutations in the MFSD8 gene: c.154G>A, p.(Gly52Arg) and c.1006G>C, p.(Gluc336Gln). Visual acuity over one year of follow-up has remained stable. CONCLUSIONS To authors' knowledge, this report is first description of this combination of mutations in the MFSD8 gene leading to non-syndromic adult-onset macular dystrophy.
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Affiliation(s)
- Aaron Z Priluck
- Wilmer Eye Institute, Johns Hopkins Hospital, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mark P Breazzano
- Wilmer Eye Institute, Johns Hopkins Hospital, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Retina-Vitreous Surgeons of Central New York, Liverpool, NY, USA
- Department of Ophthalmology and Visual Sciences, State University of New York Upstate Medical University, Syracuse, NY, USA
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8
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Kolesnikova M, Lima de Carvalho JR, Oh JK, Soucy M, Demirkol A, Kim AH, Tsang SH, Breazzano MP. Phenotypic Variability of Retinal Disease Among a Cohort of Patients With Variants in the CLN Genes. Invest Ophthalmol Vis Sci 2023; 64:23. [PMID: 36912596 PMCID: PMC10019488 DOI: 10.1167/iovs.64.3.23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023] Open
Abstract
Purpose To describe the phenotype of CLN-associated retinal dystrophy in a subset of patients at the Columbia University Medical Center, United States, and the Hospital das Clínicas de Pernambuco, Brazil, in comparison to the published literature. Methods Eleven patients with confirmed biallelic variants in the CLN genes were evaluated via dilated fundus examination, clinical imaging, and full-field electroretinogram. A thorough literature search was conducted to determine previously published variants and associated phenotypes. Results Genetic testing confirmed the presence of variants in CLN3, CLN7/MFSD8, CLN8, and GRN/CLN11. Five novel variants were identified, and four novel phenotypes of previously published alleles were described. The phenotype differed among patients with variants in the same gene and sometimes among patients with the same allele. Conclusions Substantial phenotypic variability among variants in the CLN genes makes identification of genotype-phenotype or allele-phenotype correlations challenging. Further study is required to establish an extensive database for adequate patient counseling.
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Affiliation(s)
- Masha Kolesnikova
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, New York-Presbyterian Hospital, New York, New York, United States.,College of Medicine at the State University of New York at Downstate Medical Center, Brooklyn, New York, United States
| | - Jose Ronaldo Lima de Carvalho
- Department of Ophthalmology, Hospital das Clínicas de Pernambuco, Empresa Brasileira de Serviços Hospitalares, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | - Jin Kyun Oh
- Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University Medical Center, New York-Presbyterian Hospital, New York, New York, United States
| | - Megan Soucy
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, United States
| | - Aykut Demirkol
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, New York-Presbyterian Hospital, New York, New York, United States.,Usküdar University Vocational School of Health Services, Department of Opticianry, Istanbul, Turkey
| | - Angela H Kim
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, New York-Presbyterian Hospital, New York, New York, United States.,College of Medicine at the State University of New York at Downstate Medical Center, Brooklyn, New York, United States
| | - Stephen H Tsang
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, New York-Presbyterian Hospital, New York, New York, United States.,Department of Ophthalmology, Edward S. Harkness Eye Institute, Columbia University Medical Center, New York-Presbyterian Hospital, New York, New York, United States.,Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, United States
| | - Mark P Breazzano
- Wilmer Eye Institute, Johns Hopkins Hospital, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States.,Retina-Vitreous Surgeons of Central New York, Liverpool, New York, United States.,Department of Ophthalmology & Visual Sciences, State University of New York Upstate Medical University, Syracuse, New York, United States
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9
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Web-accessible application for identifying pathogenic transcripts with RNA-seq: Increased sensitivity in diagnosis of neurodevelopmental disorders. Am J Hum Genet 2023; 110:251-272. [PMID: 36669495 PMCID: PMC9943747 DOI: 10.1016/j.ajhg.2022.12.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/21/2022] [Indexed: 01/20/2023] Open
Abstract
For neurodevelopmental disorders (NDDs), a molecular diagnosis is key for management, predicting outcome, and counseling. Often, routine DNA-based tests fail to establish a genetic diagnosis in NDDs. Transcriptome analysis (RNA sequencing [RNA-seq]) promises to improve the diagnostic yield but has not been applied to NDDs in routine diagnostics. Here, we explored the diagnostic potential of RNA-seq in 96 individuals including 67 undiagnosed subjects with NDDs. We performed RNA-seq on single individuals' cultured skin fibroblasts, with and without cycloheximide treatment, and used modified OUTRIDER Z scores to detect gene expression outliers and mis-splicing by exonic and intronic outliers. Analysis was performed by a user-friendly web application, and candidate pathogenic transcriptional events were confirmed by secondary assays. We identified intragenic deletions, monoallelic expression, and pseudoexonic insertions but also synonymous and non-synonymous variants with deleterious effects on transcription, increasing the diagnostic yield for NDDs by 13%. We found that cycloheximide treatment and exonic/intronic Z score analysis increased detection and resolution of aberrant splicing. Importantly, in one individual mis-splicing was found in a candidate gene nearly matching the individual's specific phenotype. However, pathogenic splicing occurred in another neuronal-expressed gene and provided a molecular diagnosis, stressing the need to customize RNA-seq. Lastly, our web browser application allowed custom analysis settings that facilitate diagnostic application and ranked pathogenic transcripts as top candidates. Our results demonstrate that RNA-seq is a complementary method in the genomic diagnosis of NDDs and, by providing accessible analysis with improved sensitivity, our transcriptome analysis approach facilitates wider implementation of RNA-seq in routine genome diagnostics.
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10
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Clinical-genetic findings in a group of subjects with macular dystrophies due to mutations in rare inherited retinopathy genes. Graefes Arch Clin Exp Ophthalmol 2023; 261:353-365. [PMID: 35947183 DOI: 10.1007/s00417-022-05786-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 07/03/2022] [Accepted: 07/22/2022] [Indexed: 01/25/2023] Open
Abstract
PURPOSE To describe the results of clinical and molecular analyses in a group of patients suffering from inherited macular dystrophies, in which next-generation sequencing (NGS) efficiently detected rare causative mutations. METHODS A total of eight unrelated Mexican subjects with a clinical and multimodal imaging diagnosis of macular dystrophy were included. Visual assessment methods included best corrected visual acuity, color fundus photography, Goldmann visual field tests, kinetic perimetry, dark/light adapted chromatic perimetry, full-field electroretinography, autofluorescence imaging, and spectral domain-optical coherence tomography imaging. Genetic screening was performed by means of whole exome sequencing with subsequent Sanger sequencing validation of causal variants. RESULTS All patients exhibited a predominantly macular or cone-dominant disease. Patients' ages ranged from 12 to 60 years. Three cases had mutations in genes associated with autosomal dominant inheritance (UNC119 and PRPH2) while the remaining five cases had mutations in genes associated with autosomal recessive inheritance (CNGA3, POC1B, BEST1, CYP2U1, and PROM1). Of the total of 11 different pathogenic alleles identified, three were previously unreported disease-causing variants. CONCLUSIONS Macular dystrophies can be caused by defects in genes that are not routinely analyzed or not included in NGS gene panels. In this group of patients, whole exome sequencing efficiently detected rare genetic causes of hereditary maculopathies, and our findings contribute to expanding the current knowledge of the clinical and mutational spectrum associated with these disorders.
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11
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Linear Diagnostic Procedure Elicited by Clinical Genetics and Validated by mRNA Analysis in Neuronal Ceroid Lipofuscinosis 7 Associated with a Novel Non-Canonical Splice Site Variant in MFSD8. Genes (Basel) 2023; 14:genes14020245. [PMID: 36833170 PMCID: PMC9956376 DOI: 10.3390/genes14020245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/08/2023] [Accepted: 01/16/2023] [Indexed: 01/19/2023] Open
Abstract
Neuronal ceroid lipofuscinoses (CNL) are lysosomal storage diseases that represent the most common cause of dementia in children. To date, 13 autosomal recessive (AR) and 1 autosomal dominant (AD) gene have been characterized. Biallelic variants in MFSD8 cause CLN7 type, with nearly 50 pathogenic variants, mainly truncating and missense, reported so far. Splice site variants require functional validation. We detected a novel homozygous non-canonical splice-site variant in MFSD8 in a 5-year-old girl who presented with progressive neurocognitive impairment and microcephaly. The diagnostic procedure was elicited by clinical genetics first, and then confirmed by cDNA sequencing and brain imaging. Inferred by the common geographic origin of the parents, an autosomal recessive inheritance was hypothesized, and SNP-array was performed as the first-line genetic test. Only three AR genes lying within the observed 24 Mb regions of homozygosity were consistent with the clinical phenotype, including EXOSC9, SPATA5 and MFSD8. The cerebral and cerebellar atrophy detected in the meantime by MRI, along with the suspicion of accumulation of ceroid lipopigment in neurons, prompted us to perform targeted MFSD8 sequencing. Following the detection of a splice site variant of uncertain significance, skipping of exon 8 was demonstrated by cDNA sequencing, and the variant was redefined as pathogenic.
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12
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Sangermano R, Galdikaité-Braziené E, Bujakowska KM. Non-syndromic Retinal Degeneration Caused by Pathogenic Variants in Joubert Syndrome Genes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1415:173-182. [PMID: 37440031 DOI: 10.1007/978-3-031-27681-1_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Inherited retinal degenerations (IRDs) are a group of genetic disorders characterized by progressive dysfunction and loss of photoreceptors. IRDs are classified as non-syndromic or syndromic, depending on whether retinal degeneration manifests alone or in combination with other associated symptoms. Joubert syndrome (JBTS) is a genetically and clinically heterogeneous disorder affecting the central nervous system and other organs and tissues, including the neuroretina. To date, 39 genes have been associated with JBTS, a majority of which encode structural or functional components of the primary cilium, a specialized sensory organelle present in most post-mitotic cells, including photoreceptors. The use of whole exome and IRD panel next-generation sequencing in routine diagnostics of non-syndromic IRD cases led to the discovery of pathogenic variants in JBTS genes that cause photoreceptor loss without other syndromic features. Here, we recapitulate these findings, describing the JBTS gene defects leading to non-syndromic IRDs.
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Affiliation(s)
- Riccardo Sangermano
- Ocular Genomics Institute, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Egle Galdikaité-Braziené
- Ocular Genomics Institute, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Kinga M Bujakowska
- Ocular Genomics Institute, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA.
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13
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Bartsch U, Storch S. Experimental Therapeutic Approaches for the Treatment of Retinal Pathology in Neuronal Ceroid Lipofuscinoses. Front Neurol 2022; 13:866983. [PMID: 35509995 PMCID: PMC9058077 DOI: 10.3389/fneur.2022.866983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/17/2022] [Indexed: 11/13/2022] Open
Abstract
The neuronal ceroid lipofuscinoses (NCLs) are a group of childhood-onset neurodegenerative lysosomal storage disorders mainly affecting the brain and the retina. In the NCLs, disease-causing mutations in 13 different ceroid lipofuscinoses genes (CLN) have been identified. The clinical symptoms include seizures, progressive neurological decline, deterioration of motor and language skills, and dementia resulting in premature death. In addition, the deterioration and loss of vision caused by progressive retinal degeneration is another major hallmark of NCLs. To date, there is no curative therapy for the treatment of retinal degeneration and vision loss in patients with NCL. In this review, the key findings of different experimental approaches in NCL animal models aimed at attenuating progressive retinal degeneration and the decline in retinal function are discussed. Different approaches, including experimental enzyme replacement therapy, gene therapy, cell-based therapy, and immunomodulation therapy were evaluated and showed encouraging therapeutic benefits. Recent experimental ocular gene therapies in NCL animal models with soluble lysosomal enzyme deficiencies and transmembrane protein deficiencies have shown the strong potential of gene-based approaches to treat retinal dystrophies in NCLs. In CLN3 and CLN6 mouse models, an adeno-associated virus (AAV) vector-mediated delivery of CLN3 and CLN6 to bipolar cells has been shown to attenuate the retinal dysfunction. Therapeutic benefits of ocular enzyme replacement therapies were evaluated in CLN2 and CLN10 animal models. Since brain-targeted gene or enzyme replacement therapies will most likely not attenuate retinal neurodegeneration, there is an unmet need for treatment options additionally targeting the retina in patients with NCL. The long-term benefits of these therapeutic interventions aimed at attenuating retinal degeneration and vision loss in patients with NCL remain to be investigated in future clinical studies.
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Affiliation(s)
- Udo Bartsch
- Department of Ophthalmology, Experimental Ophthalmology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephan Storch
- University Children's Research@Kinder-UKE, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- *Correspondence: Stephan Storch
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14
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Poncet AF, Grunewald O, Vaclavik V, Meunier I, Drumare I, Pelletier V, Bocquet B, Todorova MG, Le Moing AG, Devos A, Schorderet DF, Jobic F, Defoort-Dhellemmes S, Dollfus H, Smirnov VM, Dhaenens CM. Contribution of Whole-Genome Sequencing and Transcript Analysis to Decipher Retinal Diseases Associated with MFSD8 Variants. Int J Mol Sci 2022; 23:ijms23084294. [PMID: 35457110 PMCID: PMC9032189 DOI: 10.3390/ijms23084294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/25/2022] [Accepted: 04/11/2022] [Indexed: 01/01/2023] Open
Abstract
Biallelic gene defects in MFSD8 are not only a cause of the late-infantile form of neuronal ceroid lipofuscinosis, but also of rare isolated retinal degeneration. We report clinical and genetic data of seven patients compound heterozygous or homozygous for variants in MFSD8, issued from a French cohort with inherited retinal degeneration, and two additional patients retrieved from a Swiss cohort. Next-generation sequencing of large panels combined with whole-genome sequencing allowed for the identification of twelve variants from which seven were novel. Among them were one deep intronic variant c.998+1669A>G, one large deletion encompassing exon 9 and 10, and a silent change c.750A>G. Transcript analysis performed on patients’ lymphoblastoid cell lines revealed the creation of a donor splice site by c.998+1669A>G, resulting in a 140 bp pseudoexon insertion in intron 10. Variant c.750A>G produced exon 8 skipping. In silico and in cellulo studies of these variants allowed us to assign the pathogenic effect, and showed that the combination of at least one severe variant with a moderate one leads to isolated retinal dystrophy, whereas the combination in trans of two severe variants is responsible for early onset severe retinal dystrophy in the context of late-infantile neuronal ceroid lipofuscinosis.
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Affiliation(s)
- Anaïs F. Poncet
- Univ. Lille, Inserm, CHU Lille, U1172-LilNCog-Lille Neuroscience & Cognition, F-59000 Lille, France; (A.F.P.); (O.G.); (A.D.)
| | - Olivier Grunewald
- Univ. Lille, Inserm, CHU Lille, U1172-LilNCog-Lille Neuroscience & Cognition, F-59000 Lille, France; (A.F.P.); (O.G.); (A.D.)
| | - Veronika Vaclavik
- University of Lausanne, Jules-Gonin Eye Hospital, 1004 Lausanne, Switzerland;
- Cantonal Hospital, Department of Ophthalmology, 1700 Fribourg, Switzerland
| | - Isabelle Meunier
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, Montpellier University Hospital, Sensgene Care Network, ERN-EYE Network, F-34000 Montpellier, France; (I.M.); (B.B.)
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, INSERM, F-34000 Montpellier, France
| | - Isabelle Drumare
- Exploration de la Vision et Neuro-Ophtalmology, CHU de Lille, F-59000 Lille, France; (I.D.); (S.D.-D.); (V.M.S.)
| | - Valérie Pelletier
- Centre de Référence pour les Affections Rares en Génétique Ophtalmologiques, Hopitaux Universitaires de Strasbourg, F-67000 Strasbourg, France; (V.P.); (H.D.)
| | - Béatrice Bocquet
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, Montpellier University Hospital, Sensgene Care Network, ERN-EYE Network, F-34000 Montpellier, France; (I.M.); (B.B.)
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, INSERM, F-34000 Montpellier, France
| | - Margarita G. Todorova
- Department of Ophthalmology, Cantonal Hospital, 9007 St. Gallen, Switzerland;
- Department of Ophthalmology, University of Zürich, 8091 Zürich, Switzerland
- Department of Ophthalmology, University of Basel, 4056 Basel, Switzerland
| | - Anne-Gaëlle Le Moing
- Department of Child Neurology, Amiens-Picardy University Hospital, F-80000 Amiens, France;
| | - Aurore Devos
- Univ. Lille, Inserm, CHU Lille, U1172-LilNCog-Lille Neuroscience & Cognition, F-59000 Lille, France; (A.F.P.); (O.G.); (A.D.)
| | - Daniel F. Schorderet
- Faculty of Biology and Medicine, University of Lausanne and Faculty of Life Sciences, Ecole Polytechnique Fédérale of Lausanne, 1004 Lausanne, Switzerland;
| | - Florence Jobic
- Unité de Génétique Médicale et Oncogénétique, Centre Hospitalier Universitaire Amiens Picardie, F-80000 Amiens, France;
| | - Sabine Defoort-Dhellemmes
- Exploration de la Vision et Neuro-Ophtalmology, CHU de Lille, F-59000 Lille, France; (I.D.); (S.D.-D.); (V.M.S.)
| | - Hélène Dollfus
- Centre de Référence pour les Affections Rares en Génétique Ophtalmologiques, Hopitaux Universitaires de Strasbourg, F-67000 Strasbourg, France; (V.P.); (H.D.)
| | - Vasily M. Smirnov
- Exploration de la Vision et Neuro-Ophtalmology, CHU de Lille, F-59000 Lille, France; (I.D.); (S.D.-D.); (V.M.S.)
- Université de Lille, Faculté de Médecine, F-59000 Lille, France
| | - Claire-Marie Dhaenens
- Univ. Lille, Inserm, CHU Lille, U1172-LilNCog-Lille Neuroscience & Cognition, F-59000 Lille, France; (A.F.P.); (O.G.); (A.D.)
- Correspondence: ; Tel.: +33-320444953
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15
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Garanto A, Ferreira CR, Boon CJF, van Karnebeek CDM, Blau N. Clinical and biochemical footprints of inherited metabolic disorders. VII. Ocular phenotypes. Mol Genet Metab 2022; 135:311-319. [PMID: 35227579 PMCID: PMC10518078 DOI: 10.1016/j.ymgme.2022.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 01/19/2022] [Accepted: 02/11/2022] [Indexed: 12/11/2022]
Abstract
Ocular manifestations are observed in approximately one third of all inherited metabolic disorders (IMDs). Although ocular involvement is not life-threatening, it can result in severe vision loss, thereby leading to an additional burden for the patient. Retinal degeneration with or without optic atrophy is the most frequent phenotype, followed by oculomotor problems, involvement of the cornea and lens, and refractive errors. These phenotypes can provide valuable clues that contribute to its diagnosis. In this issue we found 577 relevant IMDs leading to ophthalmologic manifestations. This article is the seventh of a series attempting to create and maintain a comprehensive list of clinical and metabolic differential diagnoses according to system involvement.
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Affiliation(s)
- Alejandro Garanto
- Department of Pediatrics, Amalia Children's Hospital Radboud Center for Mitochondrial and Metabolic Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Carlos R Ferreira
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Camiel J F Boon
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands and Amsterdam University Medical Centers, Academic Medical Center, Department of Ophthalmology, University of Amsterdam, Amsterdam, the Netherlands.
| | - Clara D M van Karnebeek
- Department of Pediatrics, Amalia Children's Hospital Radboud Center for Mitochondrial and Metabolic Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands; Departments of Pediatrics and Human Genetics, Emma Children's Hospital, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, Amsterdam, the Netherlands.
| | - Nenad Blau
- Division of Metabolism, University Children's Hospital, Zürich, Switzerland.
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16
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Chen X, Dong T, Hu Y, Shaffo FC, Belur NR, Mazzulli JR, Gray SJ. AAV9/MFSD8 gene therapy is effective in preclinical models of neuronal ceroid lipofuscinosis type 7 disease. J Clin Invest 2022; 132:146286. [PMID: 35025759 PMCID: PMC8884910 DOI: 10.1172/jci146286] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/11/2022] [Indexed: 11/17/2022] Open
Abstract
Neuronal ceroid lipofuscinosis type 7 (CLN7) disease is a lysosomal storage disease caused by mutations in the facilitator superfamily domain containing 8 (MFSD8) gene, which encodes a membrane-bound lysosomal protein, MFSD8. To test the effectiveness and safety of adeno-associated viral (AAV) gene therapy, an in vitro study demonstrated that AAV2/MFSD8 dose dependently rescued lysosomal function in fibroblasts from a CLN7 patient. An in vivo efficacy study using intrathecal administration of AAV9/MFSD8 to Mfsd8- /- mice at P7-P10 or P120 with high or low dose led to clear age- and dose-dependent effects. A high dose of AAV9/MFSD8 at P7-P10 resulted in widespread MFSD8 mRNA expression, tendency of amelioration of subunit c of mitochondrial ATP synthase accumulation and glial fibrillary acidic protein immunoreactivity, normalization of impaired behaviors, doubled median life span, and extended normal body weight gain. In vivo safety studies in rodents concluded that intrathecal administration of AAV9/MFSD8 was safe and well tolerated. In summary, these results demonstrated that the AAV9/MFSD8 vector is both effective and safe in preclinical models.
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Affiliation(s)
- Xin Chen
- Department of Pediatrics, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - Thomas Dong
- Department of Pediatrics, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - Yuhui Hu
- Department of Pediatrics, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - Frances C Shaffo
- Department of Pediatrics, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - Nandkishore R Belur
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Joseph R Mazzulli
- The Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Steven J Gray
- Department of Pediatrics, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
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17
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A Novel, Apparently Silent Variant in MFSD8 Causes Neuronal Ceroid Lipofuscinosis with Marked Intrafamilial Variability. Int J Mol Sci 2022; 23:ijms23042271. [PMID: 35216386 PMCID: PMC8877174 DOI: 10.3390/ijms23042271] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/09/2022] [Accepted: 02/16/2022] [Indexed: 02/06/2023] Open
Abstract
Variants in MFSD8 can cause neuronal ceroid lipofuscinoses (NCLs) as well as nonsyndromic retinopathy. The mutation spectrum includes mainly missense and stop variants, but splice sites and frameshift variants have also been reported. To date, apparently synonymous substitutions have not been shown to cause MFSD8-associated diseases. We report two closely related subjects from a consanguineous Turkish family who presented classical features of NCLs but demonstrated marked intrafamilial variability in age at the onset and severity of symptoms. In fact, the difference in the onset of first neurologic symptoms was 15 years and that of ophthalmologic symptoms was 12 years. One subject presented an intellectual disability and a considerable cerebellar ataxia syndrome, while the other subject showed no intellectual disability and only a mild atactic syndrome. The diagnostic genetic testing of both subjects based on genome sequencing prioritized a novel, apparently synonymous variant in MFSD8, which was found in homozygosity in both subjects. The variant was not located within an integral part of the splice site consensus sequences. However, the bioinformatic analyses suggested that the mutant allele is more likely to cause exon skipping due to an altered ratio of exonic splice enhancer and silencer motifs. Exon skipping was confirmed in vitro by minigene assays and in vivo by RNA analysis from patient lymphocytes. The mutant transcript is predicted to result in a frameshift and, if translated, in a truncated protein. Synonymous variants are often given a low priority in genetic diagnostics because of their expected lack of functional impact. This study highlights the importance of investigating the impact of synonymous variants on splicing.
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18
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Qiao Y, Gu Y, Cheng Y, Su Y, Lv N, Shang Q, Xing Q. Case Report: Novel MFSD8 Variants in a Chinese Family With Neuronal Ceroid Lipofuscinoses 7. Front Genet 2022; 13:807515. [PMID: 35154277 PMCID: PMC8826235 DOI: 10.3389/fgene.2022.807515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/06/2022] [Indexed: 11/24/2022] Open
Abstract
Neuronal ceroid lipofuscinoses (NCLs) are among the most common progressive encephalopathies of childhood. Neuronal ceroid lipofuscinosis 7 (CLN7), one of the late infantile-onset NCLs, is an autosomal recessive disorder caused by mutations in the MFSD8 gene on chromosome 4q28. Almost all reported mutations of MFSD8 in CLN7 patients were SNVs. However, we report a 4-year-old boy with CLN7 harboring compound heterozygous mutations in the MFSD8 gene, including one novel two-nucleotide deletion c.136_137delAT (p. M46Vfs*22) and one whole gene deletion of MFSD8 confirmed by Sanger sequencing, genomic quantitative PCR and CNV-seq. Therefore, for nonconsanguineous CLN7 patients with homozygous mutations in the MFSD8 gene, genetic counseling staff should focus on the possibility of whole gene deletion. This is one case report describing a whole gene deletion in a Chinese patient with CLN7, suggesting the diagnosis of CLN7 should be based on clinical suspicion and genetic testing.
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Affiliation(s)
- Yimeng Qiao
- Institutes of Biomedical Sciences and Children's Hospital, Fudan University, Shanghai, China
| | - Yang Gu
- Children's Hospital of Zhengzhou University and Henan Children's Hospital, Zhengzhou, China
| | - Ye Cheng
- Institutes of Biomedical Sciences and Children's Hospital, Fudan University, Shanghai, China
| | - Yu Su
- Institutes of Biomedical Sciences and Children's Hospital, Fudan University, Shanghai, China
| | - Nan Lv
- Children's Hospital of Zhengzhou University and Henan Children's Hospital, Zhengzhou, China
| | - Qing Shang
- Children's Hospital of Zhengzhou University and Henan Children's Hospital, Zhengzhou, China
| | - Qinghe Xing
- Institutes of Biomedical Sciences and Children's Hospital, Fudan University, Shanghai, China.,Shanghai Center for Women and Children's Health, Shanghai, China
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19
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Gardner E, Mole SE. The Genetic Basis of Phenotypic Heterogeneity in the Neuronal Ceroid Lipofuscinoses. Front Neurol 2021; 12:754045. [PMID: 34733232 PMCID: PMC8558747 DOI: 10.3389/fneur.2021.754045] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022] Open
Abstract
The neuronal ceroid lipofuscinoses (NCLs) are a group of inherited neurodegenerative disorders that affect children and adults. They share some similar clinical features and the accumulation of autofluorescent storage material. Since the discovery of the first causative genes, more than 530 mutations have been identified across 13 genes in cases diagnosed with NCL. These genes encode a variety of proteins whose functions have not been fully defined; most are lysosomal enzymes, or transmembrane proteins of the lysosome or other organelles. Many mutations in these genes are associated with a typical NCL disease phenotype. However, increasing numbers of variant disease phenotypes are being described, affecting age of onset, severity or progression, and including some distinct clinical phenotypes. This data is collated by the NCL Mutation Database which allows analysis from many perspectives. This article will summarise and interpret current knowledge and understanding of their genetic basis and phenotypic heterogeneity.
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Affiliation(s)
- Emily Gardner
- MRC Laboratory for Molecular Cell Biology and Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Sara E Mole
- MRC Laboratory for Molecular Cell Biology and Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
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20
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Wang Y, Teng Y, Liang D, Li Z, Wu L. Simultaneous Identification of Both MFSD8 and RDH12 Pathogenic Variants in a Chinese Family Affected With Retinitis Pigmentosa. Front Genet 2021; 12:715100. [PMID: 34567070 PMCID: PMC8458757 DOI: 10.3389/fgene.2021.715100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/16/2021] [Indexed: 11/13/2022] Open
Abstract
Retinitis pigmentosa (RP) is characterized by tremendous genetic and phenotypic heterogeneity. Here, we investigate the pathogeny of RP in a family to provide evidence for genetic and reproductive counseling for families. Although this pregnant woman of 8+3 weeks presented with RP, her first baby was born with RP, epilepsy, and cerebellar atrophy. The research identified a compound heterozygous mutation (c.998+3_998+6del/deletion) in the MFSD8 gene of the first born, explaining the cause of the proband’s disease, which cannot explain the mother’s. Then, a homozygous mutation c.343+1G > A in RDH12 of the mother was found. RT-PCR is employed to find that there is a skipping of exon 10 in MFSD8 and a 15-nucleotide retention of intron5 in RDH12. The coexistence of two independent instances of RP caused by distinct genes in one pedigree is demonstrated. Based on the diagnosis, a prenatal diagnosis performed on the fetus found that the fetus’s MFSD8 is affected by the same mutation as the proband. The research underscoring the complexity of RP and the need for the combination of extensive molecular genetic testing and clinical characterization in addition expands the spectrum of MFSD8 mutations. Finally, it is expected that the family members would be prevented from reproducing children with the similar disease.
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Affiliation(s)
- Yihui Wang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China
| | - Yanling Teng
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China
| | - Desheng Liang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China.,Hunan Jiahui Genetics Hospital, Changsha, China
| | - Zhuo Li
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China
| | - Lingqian Wu
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China.,Hunan Jiahui Genetics Hospital, Changsha, China
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21
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Novel MFSD8 Variants in a Chinese Family with Nonsyndromic Macular Dystrophy. J Ophthalmol 2021; 2021:6684045. [PMID: 34457359 PMCID: PMC8387190 DOI: 10.1155/2021/6684045] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 07/04/2021] [Accepted: 07/05/2021] [Indexed: 11/25/2022] Open
Abstract
Purpose To identify the molecular etiology of a Chinese family with nonsyndromic macular dystrophy. Methods Ophthalmic examinations were performed, and genomic DNA was extracted from available family members. Whole exome sequencing of two members (the proband and her unaffected mother) and Sanger sequencing in available family members were performed to screen potential pathogenic variants. Results Novel compound heterozygous variants, c.1066C>T (p.Pro356Ser) and c.1102+2T>C, in the major facilitator superfamily domain containing 8 gene (MFSD8) were suspected to be involved in this family's macular dystrophy phenotype. The novel c.1066C>T variant in the MFSD8 gene probably resulted in substitution of serine for proline at the 356th residue and was predicted to be “uncertain significance” through in silico analyses. The novel c.1102+2T>C variant in the MFSD8 gene was likely to affect the splicing form and predicted to be “pathogenic.” Conclusion The novel compound heterozygous variants, c.1066C>T (p.Pro356Ser) and c.1102+2T>C, in the MFSD8 gene are likely responsible for the isolated macular dystrophy phenotype in this family. This study enlarged the MFSD8 gene mutant spectrum and might provide more accurate genetic counseling for this family.
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22
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Lo Faro V, Ten Brink JB, Snieder H, Jansonius NM, Bergen AA. Genome-wide CNV investigation suggests a role for cadherin, Wnt, and p53 pathways in primary open-angle glaucoma. BMC Genomics 2021; 22:590. [PMID: 34348663 PMCID: PMC8336345 DOI: 10.1186/s12864-021-07846-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/18/2021] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND To investigate whether copy number variations (CNVs) are implicated in molecular mechanisms underlying primary open-angle glaucoma (POAG), we used genotype data of POAG individuals and healthy controls from two case-control studies, AGS (n = 278) and GLGS-UGLI (n = 1292). PennCNV, QuantiSNP, and cnvPartition programs were used to detect CNV. Stringent quality controls at both sample and marker levels were applied. The identified CNVs were intersected in CNV region (CNVR). After, we performed burden analysis, CNV-genome-wide association analysis, gene set overrepresentation and pathway analysis. In addition, in human eye tissues we assessed the expression of the genes lying within significant CNVRs. RESULTS We reported a statistically significant greater burden of CNVs in POAG cases compared to controls (p-value = 0,007). In common between the two cohorts, CNV-association analysis identified statistically significant CNVRs associated with POAG that span 11 genes (APC, BRCA2, COL3A1, HLA-DRB1, HLA-DRB5, HLA-DRB6, MFSD8, NIPBL, SCN1A, SDHB, and ZDHHC11). Functional annotation and pathway analysis suggested the involvement of cadherin, Wnt signalling, and p53 pathways. CONCLUSIONS Our data suggest that CNVs may have a role in the susceptibility of POAG and they can reveal more information on the mechanism behind this disease. Additional genetic and functional studies are warranted to ascertain the contribution of CNVs in POAG.
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Affiliation(s)
- Valeria Lo Faro
- Department of Ophthalmology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Departments of Clinical Genetics and Ophthalmology, Amsterdam University Medical Center (AMC), Location AMC K2-217
- AMC-UvA, P.O.Box 22700, 1100 DE, Amsterdam, The Netherlands
| | - Jacoline B Ten Brink
- Departments of Clinical Genetics and Ophthalmology, Amsterdam University Medical Center (AMC), Location AMC K2-217
- AMC-UvA, P.O.Box 22700, 1100 DE, Amsterdam, The Netherlands
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Nomdo M Jansonius
- Department of Ophthalmology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Arthur A Bergen
- Departments of Clinical Genetics and Ophthalmology, Amsterdam University Medical Center (AMC), Location AMC K2-217
- AMC-UvA, P.O.Box 22700, 1100 DE, Amsterdam, The Netherlands. .,Department of Ophthalmology, Amsterdam UMC, Location AMC, Amsterdam, The Netherlands. .,Netherlands Institute for Neuroscience (NIN-KNAW), Amsterdam, The Netherlands.
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23
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Bolz HJ. Diagnostic Analyses of Retinal Dystrophy Genes: Current Status and Perspective. Klin Monbl Augenheilkd 2021; 238:261-266. [PMID: 33784789 DOI: 10.1055/a-1386-5361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Over the past decade, novel high-throughput DNA sequencing technologies have revolutionised both research and diagnostic testing for monogenic disorders. This applies particularly to genetically very heterogeneous disorders like retinal dystrophies (RDs). Next-generation sequencing (NGS) today is considered as reliable as Sanger sequencing, which had been the gold standard for decades. Today, comprehensive NGS-based diagnostic testing reveals the causative mutations in the majority of RD patients, with important implications for genetic counselling for recurrence risks and personalised medical management (from interdisciplinary surveillance to prophylactic measures and, albeit yet rare, [gene] therapy). While DNA sequencing is - in most cases - no longer the diagnostic bottleneck, one needs to be aware of interpretation pitfalls and dead ends. The advent of new (NGS) technologies will solve some of these issues. However, specialised medical geneticists who are familiar with the peculiarities of certain RD genes and closely interact with ophthalmologists will remain key to successful RD research and diagnostic testing for the benefit of the patients. This review sheds light on the current state of the field, its challenges and potential solutions.
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Affiliation(s)
- Hanno Jörn Bolz
- Humangenetik, Senckenberg Zentrum für Humangenetik, Frankfurt, Germany.,Humangenetik, University Hospital of Cologne, Cologne, Germany
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Bassal M, Liu J, Jankowiak W, Saftig P, Bartsch U. Rapid and Progressive Loss of Multiple Retinal Cell Types in Cathepsin D-Deficient Mice-An Animal Model of CLN10 Disease. Cells 2021; 10:696. [PMID: 33800998 PMCID: PMC8003850 DOI: 10.3390/cells10030696] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/11/2021] [Accepted: 03/19/2021] [Indexed: 12/18/2022] Open
Abstract
Vision loss is among the characteristic symptoms of neuronal ceroid lipofuscinosis (NCL), a fatal neurodegenerative lysosomal storage disorder. Here, we performed an in-depth analysis of retinal degeneration at the molecular and cellular levels in mice lacking the lysosomal aspartyl protease cathepsin D, an animal model of congenital CLN10 disease. We observed an early-onset accumulation of storage material as indicated by elevated levels of saposin D and subunit C of the mitochondrial ATP synthase. The accumulation of storage material was accompanied by reactive astrogliosis and microgliosis, elevated expression of the autophagy marker sequestosome 1/p62 and a dysregulated expression of several lysosomal proteins. The number of cone photoreceptor cells was reduced as early as at postnatal day 5. At the end stage of the disease, the outer nuclear layer was almost atrophied, and all cones were lost. A significant loss of rod and cone bipolar cells, amacrine cells and ganglion cells was found at advanced stages of the disease. Results demonstrate that cathepsin D deficiency results in an early-onset and rapidly progressing retinal dystrophy that involves all retinal cell types. Data of the present study will serve as a reference for studies aimed at developing treatments for retinal degeneration in CLN10 disease.
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Affiliation(s)
- Mahmoud Bassal
- Department of Ophthalmology, Experimental Ophthalmology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.B.); (J.L.); (W.J.)
| | - Junling Liu
- Department of Ophthalmology, Experimental Ophthalmology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.B.); (J.L.); (W.J.)
| | - Wanda Jankowiak
- Department of Ophthalmology, Experimental Ophthalmology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.B.); (J.L.); (W.J.)
| | - Paul Saftig
- Institute of Biochemistry, Christian-Albrechts-University Kiel, 24118 Kiel, Germany;
| | - Udo Bartsch
- Department of Ophthalmology, Experimental Ophthalmology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (M.B.); (J.L.); (W.J.)
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25
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Magliyah MS, Geuer S, Alsalamah AK, Lenzner S, Drasdo M, Schatz P. Association of the Recurrent Rare Variant c.415T>C p.Phe139Leu in CLN5 With a Recessively Inherited Macular Dystrophy. JAMA Ophthalmol 2021; 139:339-343. [PMID: 33507209 PMCID: PMC7844694 DOI: 10.1001/jamaophthalmol.2020.6085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/10/2020] [Indexed: 01/10/2023]
Abstract
Importance Homozygous variants in the neuronal ceroid lipofuscinosis type 5 (CLN5) gene are associated with neuronal ceroid lipofuscinosis, a progressive neurologic disorder that leads to ataxia, seizures, and early death. The association between a homozygous variant in this gene and a macular dystrophy is described here. Objective To describe an autosomal recessive macular dystrophy associated with a recurrent variant in CLN5. Design, Setting, and Participants This cohort study took place at a national referral center and had a follow-up duration ranging between 1 and 5 years. All patients who were identified to carry a specific homozygous missense variant in CLN5, among more than 2000 patients who were diagnosed with or suspected to have retinal dystrophies, who did not carry this variant, were included. Data were collected between June 2014 and September 2020. Exposures All patients who were sampled for DNA analysis due to molecularly unconfirmed retinal dystrophy and who were subsequently identified to carry the homozygous missense variant c.415T>C (p.Phe139Leu) in CLN5 were included, while patients who did not carry the variant were excluded. Main Outcomes and Measures Retinal phenotype associated with this specific homozygous missense variant in CLN5. Results Seven affected patients (mean [SD] age, 43 [18] years; age range, 33-52 years; 5 male) carried the homozygous missense in CLN5. All patients were diagnosed as having a macular dystrophy. Four patients had mild electroretinographic alterations. All patients had hypoautofluorescent maculas with retinal thinning (central subfield thickness, 80 µm). Visual acuity ranged between 2/200 and 20/100. Neurologic symptoms were mild (dizziness) in 5 patients and absent in 2 patients. Neuroimaging demonstrated cerebellar atrophy and white matter lesions, respectively, in 2 patients. Conclusions and Relevance These results suggest that CLN5, similar to CLN7, may be associated with isolated macular dystrophy as well as neuronal ceroid lipofuscinosis. The variant c.415T>C p.Phe139Leu does not seem to be associated with any prominent neurologic disease at least until the fourth to sixth decades of life. These findings may imply a specific role of CLN5 in macular neurons. Additional study is suggested, such as molecular screening for this variant in cohorts of patients with undiagnosed macular dystrophies and biological studies of its molecular effects.
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Affiliation(s)
- Moustafa S. Magliyah
- Vitreoretinal Division, King Khaled Eye Specialist Hospital, Riyadh, Kingdom of Saudi Arabia
- Ophthalmology Department, Prince Mohammed Medical City, AlJouf, Saudi Arabia
| | - Sinje Geuer
- Human Genetics Bioscientia Ingelheim, Ingelheim am Rhein, Germany
| | - Abrar K. Alsalamah
- Vitreoretinal Division, King Khaled Eye Specialist Hospital, Riyadh, Kingdom of Saudi Arabia
| | - Steffen Lenzner
- Human Genetics Bioscientia Ingelheim, Ingelheim am Rhein, Germany
| | - Mojgan Drasdo
- Human Genetics Bioscientia Ingelheim, Ingelheim am Rhein, Germany
| | - Patrik Schatz
- Vitreoretinal Division, King Khaled Eye Specialist Hospital, Riyadh, Kingdom of Saudi Arabia
- Department of Ophthalmology, Clinical Sciences, Scane County University Hospital, University of Lund, Lund, Sweden
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Maggi J, Koller S, Bähr L, Feil S, Kivrak Pfiffner F, Hanson JVM, Maspoli A, Gerth-Kahlert C, Berger W. Long-Range PCR-Based NGS Applications to Diagnose Mendelian Retinal Diseases. Int J Mol Sci 2021; 22:ijms22041508. [PMID: 33546218 PMCID: PMC7913364 DOI: 10.3390/ijms22041508] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 12/27/2022] Open
Abstract
The purpose of this study was to develop a flexible, cost-efficient, next-generation sequencing (NGS) protocol for genetic testing. Long-range polymerase chain reaction (PCR) amplicons of up to 20 kb in size were designed to amplify entire genomic regions for a panel (n = 35) of inherited retinal disease (IRD)-associated loci. Amplicons were pooled and sequenced by NGS. The analysis was applied to 227 probands diagnosed with IRD: (A) 108 previously molecularly diagnosed, (B) 94 without previous genetic testing, and (C) 25 undiagnosed after whole-exome sequencing (WES). The method was validated with 100% sensitivity on cohort A. Long-range PCR-based sequencing revealed likely causative variant(s) in 51% and 24% of proband from cohorts B and C, respectively. Breakpoints of 3 copy number variants (CNVs) could be characterized. Long-range PCR libraries spike-in extended coverage of WES. Read phasing confirmed compound heterozygosity in 5 probands. The proposed sequencing protocol provided deep coverage of the entire gene, including intronic and promoter regions. Our method can be used (i) as a first-tier assay to reduce genetic testing costs, (ii) to elucidate missing heritability cases, (iii) to characterize breakpoints of CNVs at nucleotide resolution, (iv) to extend WES data to non-coding regions by spiking-in long-range PCR libraries, and (v) to help with phasing of candidate variants.
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Affiliation(s)
- Jordi Maggi
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.); (L.B.); (S.F.); (F.K.P.); (A.M.)
| | - Samuel Koller
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.); (L.B.); (S.F.); (F.K.P.); (A.M.)
| | - Luzy Bähr
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.); (L.B.); (S.F.); (F.K.P.); (A.M.)
| | - Silke Feil
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.); (L.B.); (S.F.); (F.K.P.); (A.M.)
| | - Fatma Kivrak Pfiffner
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.); (L.B.); (S.F.); (F.K.P.); (A.M.)
| | - James V. M. Hanson
- Department of Ophthalmology, University Hospital Zurich and University of Zurich, 8091 Zurich, Switzerland; (J.V.M.H.); (C.G.-K.)
| | - Alessandro Maspoli
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.); (L.B.); (S.F.); (F.K.P.); (A.M.)
| | - Christina Gerth-Kahlert
- Department of Ophthalmology, University Hospital Zurich and University of Zurich, 8091 Zurich, Switzerland; (J.V.M.H.); (C.G.-K.)
| | - Wolfgang Berger
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (J.M.); (S.K.); (L.B.); (S.F.); (F.K.P.); (A.M.)
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, 8057 Zurich, Switzerland
- Neuroscience Center Zurich (ZNZ), University and ETH Zurich, 8057 Zurich, Switzerland
- Correspondence: ; Tel.: +41-44-556-33-50
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Butz ES, Chandrachud U, Mole SE, Cotman SL. Moving towards a new era of genomics in the neuronal ceroid lipofuscinoses. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165571. [DOI: 10.1016/j.bbadis.2019.165571] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 10/12/2019] [Accepted: 10/14/2019] [Indexed: 12/15/2022]
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Huizing M, Gahl WA. Inherited disorders of lysosomal membrane transporters. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183336. [PMID: 32389669 DOI: 10.1016/j.bbamem.2020.183336] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/01/2020] [Accepted: 04/28/2020] [Indexed: 02/07/2023]
Abstract
Disorders caused by defects in lysosomal membrane transporters form a distinct subgroup of lysosomal storage disorders (LSDs). To date, defects in only 10 lysosomal membrane transporters have been associated with inherited disorders. The clinical presentations of these diseases resemble the phenotypes of other LSDs; they are heterogeneous and often present in children with neurodegenerative manifestations. However, for pathomechanistic and therapeutic studies, lysosomal membrane transport defects should be distinguished from LSDs caused by defective hydrolytic enzymes. The involved proteins differ in function, localization, and lysosomal targeting, and the diseases themselves differ in their stored material and therapeutic approaches. We provide an overview of the small group of disorders of lysosomal membrane transporters, emphasizing discovery, pathomechanism, clinical features, diagnostic methods and therapeutic aspects. We discuss common aspects of lysosomal membrane transporter defects that can provide the basis for preclinical research into these disorders.
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Affiliation(s)
- Marjan Huizing
- Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - William A Gahl
- Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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29
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Bauwens M, Storch S, Weisschuh N, Ceuterick‐de Groote C, De Rycke R, Guillemyn B, De Jaegere S, Coppieters F, Van Coster R, Leroy BP, De Baere E. Functional characterization of novel MFSD8 pathogenic variants anticipates neurological involvement in juvenile isolated maculopathy. Clin Genet 2020; 97:426-436. [PMID: 31721179 PMCID: PMC7064892 DOI: 10.1111/cge.13673] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/30/2019] [Accepted: 11/01/2019] [Indexed: 12/22/2022]
Abstract
Biallelic MFSD8 variants are an established cause of severe late-infantile subtype of neuronal ceroid lipofuscinosis (v-LINCL), a severe lysosomal storage disorder, but have also been associated with nonsyndromic adult-onset maculopathy. Here, we functionally characterized two novel MFSD8 variants found in a child with juvenile isolated maculopathy, in order to establish a refined prognosis. ABCA4 locus resequencing was followed by the analysis of other inherited retinal disease genes by whole exome sequencing (WES). Minigene assays and cDNA sequencing were used to assess the effect of a novel MFSD8 splice variant. MFSD8 expression was quantified with qPCR and overexpression studies were analyzed by immunoblotting. Transmission electron microscopy (TEM) was performed on a skin biopsy and ophthalmological and neurological re-examinations were conducted. WES revealed two novel MFSD8 variants: c.[590del];[439+3A>C] p.[Gly197Valfs*2];[Ile67Glufs*3]. Characterization of the c.439+3A>C variant via splice assays showed exon-skipping (p.Ile67Glufs*3), while overexpression studies of the corresponding protein indicated expression of a truncated polypeptide. In addition, a significantly reduced MFSD8 RNA expression was noted in patient's lymphocytes. TEM of a skin biopsy revealed typical v-LINCL lipopigment inclusions while neurological imaging of the proband displayed subtle cerebellar atrophy. Functional characterization demonstrated the pathogenicity of two novel MFSD8 variants, found in a child with an initial diagnosis of juvenile isolated maculopathy but likely evolving to v-LINCL with a protracted disease course. Our study allowed a refined neurological prognosis in the proband and expands the natural history of MFSD8-associated disease.
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Affiliation(s)
| | - Stephan Storch
- Department of Biochemistry, Children's HospitalUniversity Medical Center Hamburg‐EppendorfHamburgGermany
| | - Nicole Weisschuh
- Molecular Genetics Laboratory, Institute for Ophthalmic ResearchUniversity of TuebingenTuebingenGermany
| | | | - Riet De Rycke
- Department of Biomedical Molecular BiologyGhent UniversityGhentBelgium
- VIB‐UGent Center for Inflammation ResearchGhentBelgium
- Ghent University Expertise Centre for Transmission Electron Microscopy and VIB BioImaging CoreGhentBelgium
| | | | - Sarah De Jaegere
- Center for Medical GeneticsGhent University HospitalGhentBelgium
| | | | - Rudy Van Coster
- Department of Pediatrics, Division of Pediatric Neurology and MetabolismGhent University HospitalGhentBelgium
| | - Bart P. Leroy
- Center for Medical GeneticsGhent University HospitalGhentBelgium
- Department of OphthalmologyGhent University and Ghent University HospitalGhentBelgium
- Division of Ophthalmology and Center for Cellular & Molecular TherapeuticsThe Children's Hospital of PhiladelphiaPhiladelphiaPennsylvania
| | - Elfride De Baere
- Center for Medical GeneticsGhent UniversityGhentBelgium
- Center for Medical GeneticsGhent University HospitalGhentBelgium
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30
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Magliyah M, AlRaddadi O, Balbaid A, Schatz P. Multimodal retinal imaging in MFSD8-neuronal ceroid lipofuscinosis. Ophthalmic Genet 2020; 40:588-590. [PMID: 31909682 DOI: 10.1080/13816810.2019.1709125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Moustafa Magliyah
- Vitreoretinal Division, King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia.,Ophthalmology Department, Prince Mohammed Medical City, AlJouf, Saudi Arabia
| | - Osama AlRaddadi
- Vitreoretinal Division, King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia.,Ophthalmology Department, Ohud Hospital, Madinah, Saudi Arabia
| | - Abdullah Balbaid
- Vitreoretinal Division, King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia.,Retina Department, Jeddah Eye Hospital, Jeddah, Saudi Arabia
| | - Patrik Schatz
- Vitreoretinal Division, King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia.,Department of Ophthalmology, Clinical Sciences, Skane County University Hospital, Lund University, Lund, Sweden
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31
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Guo J, Johnson GS, Cook J, Harris OK, Mhlanga-Mutangadura T, Schnabel RD, Jensen CA, Katz ML. Neuronal ceroid lipofuscinosis in a German Shorthaired Pointer associated with a previously reported CLN8 nonsense variant. Mol Genet Metab Rep 2019; 21:100521. [PMID: 31687336 PMCID: PMC6819867 DOI: 10.1016/j.ymgmr.2019.100521] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 09/11/2019] [Indexed: 12/23/2022] Open
Abstract
Two littermate German Shorthaired Pointers, a male and a female, were adopted as puppies from an animal shelter. Both puppies developed normally until approximately 11 months of age when the male began to exhibit neurological signs including ataxia, vision loss, and behavioral changes indicative of cognitive decline. These signs increased in severity over time. The female remained neurologically normal and healthy. The affected dog was euthanized at approximately 21 months of age. Autofluorescent cytoplasmic storage bodies were detected in neurons in unstained tissue sections from the cerebellum, the cerebrum, and the retina. Electron micrographs of these storage bodies showed that they were membrane bound and that most contained tightly packed aggregates of membranous whorls along with a variety of other ultrastructural features. This ultrastructure, along with the autofluorescence and the clinical signs supported a diagnosis of neuronal ceroid lipofuscinosis (NCL). Unlike earlier investigated forms of canine NCL with causal alleles in ATP13A2, TPP1, MFSD8 and CLN5 that had autofluorescent cytoplasmic storage bodies in cardiac muscle, no autofluorescence was detected in cardiac muscle from the affected German Shorthaired Pointer. A 39-fold average coverage whole genome sequence indicated that the affected German Shorthaired Pointer was homozygous for the A allele of a G > A transversion at position 30,895,648 chromosome 37. This 37:30895648G > A mutation created a CLN8 termination codon that had been previously reported to cause NCL in a mixed breed dog with Australian Shepherd and Australian Cattle Dog ancestry. This nonsense allele was heterozygous in the clinically normal female sibling, while archived DNA samples from 512 other German Shorthaired Pointers were all homozygous for the reference allele. The affected German Shorthaired Pointer and the previously diagnosed mixed breed dog with the same nonsense mutation shaired an identical homozygous haplotype that extended for 4.41 Mb at the telomeric end of chromosome 37, indicating the both dogs inherited the nonsense mutation from a common ancestor.
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Affiliation(s)
- Juyuan Guo
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
| | - Gary S. Johnson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
| | - James Cook
- Specialists in Companion Animal Neurology, Clearwater, FL, USA
| | - Olivia K. Harris
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
| | | | - Robert D. Schnabel
- Division of Animal Sciences and Informatics Institute, University of Missouri, Columbia, MO, USA
| | - Cheryl A. Jensen
- Neurodegenerative Diseases Research Laboratory, Department of Ophthalmology, University of Missouri, Columbia, MO, USA
| | - Martin L. Katz
- Neurodegenerative Diseases Research Laboratory, Department of Ophthalmology, University of Missouri, Columbia, MO, USA
- Corresponding author at: Mason Eye Institute, Room EC-203, University of Missouri School of Medicine, Columbia, MO 65121, USA.
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Zare-Abdollahi D, Bushehri A, Alavi A, Dehghani A, Mousavi-Mirkala M, Effati J, Miratashi SAM, Dehani M, Jamali P, Khorram Khorshid HR. MFSD8 gene mutations; evidence for phenotypic heterogeneity. Ophthalmic Genet 2019; 40:141-145. [PMID: 31006324 DOI: 10.1080/13816810.2019.1592200] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
BACKGROUND Cone-rod dystrophies are a group of genetically and phenotypically heterogeneous inherited degenerative retinal diseases primarily affecting macular and cone system function. MFSD8 loss-of-function variants are mainly related to the variant late-infantile neuronal ceroid lipofuscinoses which present with progressive motor and mental regression in combination with seizures, ataxia, and visual impairment. MATERIAL AND METHODS Clinical examination and genomic DNA extraction were collected from two unrelated Iranian families presenting with autosomal recessive cone-rod dystrophy. The candidate disease-causing variant was screened with whole-exome sequencing and bioinformatics analyses. Sanger sequencing was used for validation and co-segregation analysis. RESULTS Two previously reported variants (c.1361T>C; p.M454T and c.1235C>T; p.P412L) and in a compound heterozygous pattern in one family and a homozygous variant (c.1361T>C; p.M454T) identical to one of the variants in the first family in MFSD8 gene were identified. Both confirmed by Sanger sequencing and co-segregated with disease status. CONCLUSIONS Here and for the first time, we reported on two previously variant late-infantile neuronal ceroid lipofuscinoses-associated variants in MFSD8 but in association with a form of cone-rod dystrophy known as non-syndromic macular dystrophy with central cone involvement. Our results support this concept that variant late-infantile neuronal ceroid lipofuscinoses and non-syndromic macular dystrophy with central cone involvement are not different disease entities, but rather allelic diseases and phenotypic variants of the same mutation. Consideration of the milder MFSD8 phenotypes is important against the potentially severe consequences of life-threatening conditions associated with MFSD8 mutations in order to prevent the danger of misdiagnosis as well as the accuracy of genetic counseling.
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Affiliation(s)
- Davood Zare-Abdollahi
- a Genetics Research Center , University of Social Welfare and Rehabilitation Sciences , Tehran , Iran
| | - Ata Bushehri
- a Genetics Research Center , University of Social Welfare and Rehabilitation Sciences , Tehran , Iran
| | - Afagh Alavi
- a Genetics Research Center , University of Social Welfare and Rehabilitation Sciences , Tehran , Iran
| | - Alireza Dehghani
- b Department of Ophthalmology , Eye Research Center, Isfahan University of Medical Sciences , Isfahan , Iran
| | | | - Jalil Effati
- d Meybod Genetic Research Center, State Welfare Organization of Yazd , Yazd , Iran
| | | | - Mohammad Dehani
- a Genetics Research Center , University of Social Welfare and Rehabilitation Sciences , Tehran , Iran
| | - Payman Jamali
- f Shahrood Genetic Counseling Center , Welfare Office , Semnan , Iran
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Geier EG, Bourdenx M, Storm NJ, Cochran JN, Sirkis DW, Hwang JH, Bonham LW, Ramos EM, Diaz A, Van Berlo V, Dokuru D, Nana AL, Karydas A, Balestra ME, Huang Y, Russo SP, Spina S, Grinberg LT, Seeley WW, Myers RM, Miller BL, Coppola G, Lee SE, Cuervo AM, Yokoyama JS. Rare variants in the neuronal ceroid lipofuscinosis gene MFSD8 are candidate risk factors for frontotemporal dementia. Acta Neuropathol 2019; 137:71-88. [PMID: 30382371 PMCID: PMC6371791 DOI: 10.1007/s00401-018-1925-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/23/2018] [Accepted: 10/24/2018] [Indexed: 12/21/2022]
Abstract
Pathogenic variation in MAPT, GRN, and C9ORF72 accounts for at most only half of frontotemporal lobar degeneration (FTLD) cases with a family history of neurological disease. This suggests additional variants and genes that remain to be identified as risk factors for FTLD. We conducted a case-control genetic association study comparing pathologically diagnosed FTLD patients (n = 94) to cognitively normal older adults (n = 3541), and found suggestive evidence that gene-wide aggregate rare variant burden in MFSD8 is associated with FTLD risk. Because homozygous mutations in MFSD8 cause neuronal ceroid lipofuscinosis (NCL), similar to homozygous mutations in GRN, we assessed rare variants in MFSD8 for relevance to FTLD through experimental follow-up studies. Using post-mortem tissue from middle frontal gyrus of patients with FTLD and controls, we identified increased MFSD8 protein levels in MFSD8 rare variant carriers relative to non-variant carrier patients with sporadic FTLD and healthy controls. We also observed an increase in lysosomal and autophagy-related proteins in MFSD8 rare variant carrier and sporadic FTLD patients relative to controls. Immunohistochemical analysis revealed that MFSD8 was expressed in neurons and astrocytes across subjects, without clear evidence of abnormal localization in patients. Finally, in vitro studies identified marked disruption of lysosomal function in cells from MFSD8 rare variant carriers, and identified one rare variant that significantly increased the cell surface levels of MFSD8. Considering the growing evidence for altered autophagy in the pathogenesis of neurodegenerative disorders, our findings support a role of NCL genes in FTLD risk and suggest that MFSD8-associated lysosomal dysfunction may contribute to FTLD pathology.
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Affiliation(s)
- Ethan G Geier
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, 675 Nelson Rising Lane, Suite 190, San Francisco, CA, 94158, USA
| | - Mathieu Bourdenx
- Department of Development and Molecular Biology, Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY, 10461, USA
| | - Nadia J Storm
- Department of Development and Molecular Biology, Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY, 10461, USA
| | | | - Daniel W Sirkis
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Ji-Hye Hwang
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, 675 Nelson Rising Lane, Suite 190, San Francisco, CA, 94158, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Luke W Bonham
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, 675 Nelson Rising Lane, Suite 190, San Francisco, CA, 94158, USA
| | - Eliana Marisa Ramos
- Department of Psychiatry and Semel Institute for Neuroscience and Human Behavior, The David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Antonio Diaz
- Department of Development and Molecular Biology, Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY, 10461, USA
| | - Victoria Van Berlo
- Department of Psychiatry and Semel Institute for Neuroscience and Human Behavior, The David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Deepika Dokuru
- Department of Psychiatry and Semel Institute for Neuroscience and Human Behavior, The David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Alissa L Nana
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, 675 Nelson Rising Lane, Suite 190, San Francisco, CA, 94158, USA
| | - Anna Karydas
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, 675 Nelson Rising Lane, Suite 190, San Francisco, CA, 94158, USA
| | | | - Yadong Huang
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Silvia P Russo
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, 675 Nelson Rising Lane, Suite 190, San Francisco, CA, 94158, USA
| | - Salvatore Spina
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, 675 Nelson Rising Lane, Suite 190, San Francisco, CA, 94158, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Lea T Grinberg
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, 675 Nelson Rising Lane, Suite 190, San Francisco, CA, 94158, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - William W Seeley
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, 675 Nelson Rising Lane, Suite 190, San Francisco, CA, 94158, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Bruce L Miller
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, 675 Nelson Rising Lane, Suite 190, San Francisco, CA, 94158, USA
| | - Giovanni Coppola
- Department of Psychiatry and Semel Institute for Neuroscience and Human Behavior, The David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Suzee E Lee
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, 675 Nelson Rising Lane, Suite 190, San Francisco, CA, 94158, USA
| | - Ana Maria Cuervo
- Department of Development and Molecular Biology, Institute for Aging Studies, Albert Einstein College of Medicine, New York, NY, 10461, USA
| | - Jennifer S Yokoyama
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, 675 Nelson Rising Lane, Suite 190, San Francisco, CA, 94158, USA.
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Birtel J, Gliem M, Mangold E, Müller PL, Holz FG, Neuhaus C, Lenzner S, Zahnleiter D, Betz C, Eisenberger T, Bolz HJ, Charbel Issa P. Next-generation sequencing identifies unexpected genotype-phenotype correlations in patients with retinitis pigmentosa. PLoS One 2018; 13:e0207958. [PMID: 30543658 PMCID: PMC6292620 DOI: 10.1371/journal.pone.0207958] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/08/2018] [Indexed: 12/13/2022] Open
Abstract
Retinitis pigmentosa (RP) is an inherited degenerative disease causing severe retinal dystrophy and visual impairment mainly with onset in infancy or adolescence. Targeted next-generation sequencing (NGS) has become an efficient tool to encounter the enormous genetic heterogeneity of diverse retinal dystrophies, including RP. To identify disease-causing mutations in unselected, consecutive RP patients, we conducted Sanger sequencing of genes commonly involved in the suspected genetic RP subtype, followed by targeted large-panel NGS if no mutation was identified, or NGS as primary analysis. A high (70%) detection rate of disease-causing mutations was achieved in a large cohort of 116 unrelated patients. About half (48%) of the solved RP cases were explained by mutations in four genes: RPGR, EYS, PRPF31 and USH2A. Overall, 110 different mutations distributed across 30 different genes were detected, and 46 of these mutations were novel. A molecular diagnosis was achieved in the majority (82–100%) of patients if the family history was suggestive for a particular mode of inheritance, but only in 60% in cases of sporadic RP. The diagnostic potential of extensive molecular analysis in a routine setting is also illustrated by the identification of unexpected genotype-phenotype correlations for RP patients with mutations in CRX, CEP290, RPGRIP1, MFSD8. Furthermore, we identified numerous mutations in autosomal dominant (PRPF31, PRPH2, CRX) and X-linked (RPGR) RP genes in patients with sporadic RP. Variants in RP2 and RPGR were also found in female RP patients with apparently sporadic or dominant disease. In summary, this study demonstrates that massively parallel sequencing of all known retinal dystrophy genes is a valuable diagnostic approach for RP patients.
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Affiliation(s)
- Johannes Birtel
- Department of Ophthalmology, University of Bonn, Bonn, Germany
- Center for Rare Diseases Bonn (ZSEB), University of Bonn, Bonn, Germany
| | - Martin Gliem
- Department of Ophthalmology, University of Bonn, Bonn, Germany
- Center for Rare Diseases Bonn (ZSEB), University of Bonn, Bonn, Germany
| | | | - Philipp L. Müller
- Department of Ophthalmology, University of Bonn, Bonn, Germany
- Center for Rare Diseases Bonn (ZSEB), University of Bonn, Bonn, Germany
| | - Frank G. Holz
- Department of Ophthalmology, University of Bonn, Bonn, Germany
- Center for Rare Diseases Bonn (ZSEB), University of Bonn, Bonn, Germany
| | | | | | | | - Christian Betz
- Bioscientia Center for Human Genetics, Ingelheim, Germany
| | | | - Hanno J. Bolz
- Bioscientia Center for Human Genetics, Ingelheim, Germany
- Institute of Human Genetics, University Hospital of Cologne, Cologne, Germany
| | - Peter Charbel Issa
- Department of Ophthalmology, University of Bonn, Bonn, Germany
- Center for Rare Diseases Bonn (ZSEB), University of Bonn, Bonn, Germany
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, and Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- * E-mail:
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Wang J, Zhao L, Wang X, Chen Y, Xu M, Soens ZT, Ge Z, Wang PR, Wang F, Chen R. GRIPT: a novel case-control analysis method for Mendelian disease gene discovery. Genome Biol 2018; 19:203. [PMID: 30477545 PMCID: PMC6258408 DOI: 10.1186/s13059-018-1579-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 11/02/2018] [Indexed: 11/10/2022] Open
Abstract
Despite rapid progress of next-generation sequencing (NGS) technologies, the disease-causing genes underpinning about half of all Mendelian diseases remain elusive. One main challenge is the high genetic heterogeneity of Mendelian diseases in which similar phenotypes are caused by different genes and each gene only accounts for a small proportion of the patients. To overcome this gap, we developed a novel method, the Gene Ranking, Identification and Prediction Tool (GRIPT), for performing case-control analysis of NGS data. Analyses of simulated and real datasets show that GRIPT is well-powered for disease gene discovery, especially for diseases with high locus heterogeneity.
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Affiliation(s)
- Jun Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Li Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Structural and Computational Biology and Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, TX 77030 USA
| | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Miraca Genetics Laboratories, Houston, TX 77030 USA
| | - Yong Chen
- Shanghai Key Lab of Intelligent Information Processing, School of Computer Science and Technology, Fudan University, Shanghai, China
| | - Mingchu Xu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Zachry T. Soens
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Zhongqi Ge
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Peter Ronghan Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Fei Wang
- Shanghai Key Lab of Intelligent Information Processing, School of Computer Science and Technology, Fudan University, Shanghai, China
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Structural and Computational Biology and Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, TX 77030 USA
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36
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A homozygous founder missense variant in arylsulfatase G abolishes its enzymatic activity causing atypical Usher syndrome in humans. Genet Med 2018; 20:1004-1012. [PMID: 29300381 DOI: 10.1038/gim.2017.227] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/06/2017] [Indexed: 12/28/2022] Open
Abstract
PURPOSE We aimed to identify the cause of disease in patients suffering from a distinctive, atypical form of Usher syndrome. METHODS Whole-exome and genome sequencing were performed in five patients from three families of Yemenite Jewish origin, suffering from distinctive retinal degeneration phenotype and sensorineural hearing loss. Functional analysis of the wild-type and mutant proteins was performed in human fibrosarcoma cells. RESULTS We identified a homozygous founder missense variant, c.133G>T (p.D45Y) in arylsulfatase G (ARSG). All patients shared a distinctive retinal phenotype with ring-shaped atrophy along the arcades engirdling the fovea, resulting in ring scotoma. In addition, patients developed moderate to severe sensorineural hearing loss. Both vision and hearing loss appeared around the age of 40 years. The identified variant affected a fully conserved amino acid that is part of the catalytic site of the enzyme. Functional analysis of the wild-type and mutant proteins showed no basal activity of p.D45Y. CONCLUSION Homozygosity for ARSG-p.D45Y in humans leads to protein dysfunction, causing an atypical combination of late-onset Usher syndrome. Although there is no evidence for generalized clinical manifestations of lysosomal storage diseases in this set of patients, we cannot rule out the possibility that mild and late-onset symptoms may appear.
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Ku CA, Hull S, Arno G, Vincent A, Carss K, Kayton R, Weeks D, Anderson GW, Geraets R, Parker C, Pearce DA, Michaelides M, MacLaren RE, Robson AG, Holder GE, Heon E, Raymond FL, Moore AT, Webster AR, Pennesi ME. Detailed Clinical Phenotype and Molecular Genetic Findings in CLN3-Associated Isolated Retinal Degeneration. JAMA Ophthalmol 2017; 135:749-760. [PMID: 28542676 DOI: 10.1001/jamaophthalmol.2017.1401] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Importance Mutations in genes traditionally associated with syndromic retinal disease are increasingly found to cause nonsyndromic inherited retinal degenerations. Mutations in CLN3 are classically associated with juvenile neuronal ceroid lipofuscinosis, a rare neurodegenerative disease with early retinal degeneration and progressive neurologic deterioration, but have recently also been identified in patients with nonsyndromic inherited retinal degenerations. To our knowledge, detailed clinical characterization of such cases has yet to be reported. Objective To provide detailed clinical, electrophysiologic, structural, and molecular genetic findings in nonsyndromic inherited retinal degenerations associated with CLN3 mutations. Design, Setting, and Participants A multi-institutional case series of 10 patients who presented with isolated nonsyndromic retinal disease and mutations in CLN3. Patient ages ranged from 16 to 70 years; duration of follow-up ranged from 3 to 29 years. Main Outcomes and Measures Longitudinal clinical evaluation, including full ophthalmic examination, multimodal retinal imaging, perimetry, and electrophysiology. Molecular analyses were performed using whole-genome sequencing or whole-exome sequencing. Electron microscopy studies of peripheral lymphocytes and CLN3 transcript analysis with polymerase chain reaction amplification were performed in a subset of patients. Results There were 7 females and 3 males in this case series, with a mean (range) age at last review of 37.1 (16-70) years. Of the 10 patients, 4 had a progressive late-onset rod-cone dystrophy, with a mean (range) age at onset of 29.7 (20-40) years, and 6 had an earlier onset rod-cone dystrophy, with a mean (range) age at onset of 12.1 (7-17) years. Ophthalmoscopic examination features included macular edema, mild intraretinal pigment migration, and widespread atrophy in advanced disease. Optical coherence tomography imaging demonstrated significant photoreceptor loss except in patients with late-onset disease who had a focal preservation of the ellipsoid zone and outer nuclear layer in the fovea. Electroretinography revealed a rod-cone pattern of dysfunction in 6 patients and were completely undetectable in 2 patients. Six novel CLN3 variants were identified in molecular analyses. Conclusions and Relevance This report describes detailed clinical, imaging, and genetic features of CLN3-associated nonsyndromic retinal degeneration. The age at onset and natural progression of retinal disease differs greatly between syndromic and nonsyndromic CLN3 disease, which may be associated with genotypic differences.
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Affiliation(s)
- Cristy A Ku
- Casey Eye Institute, Oregon Health & Science University, Portland
| | - Sarah Hull
- University College London Institute of Ophthalmology, London, England3Moorfields Eye Hospital, London, England
| | - Gavin Arno
- University College London Institute of Ophthalmology, London, England3Moorfields Eye Hospital, London, England
| | - Ajoy Vincent
- Department of Ophthalmology and Vision Sciences, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Keren Carss
- National Health Service Blood and Transplant Centre, Department of Haematology, University of Cambridge, Cambridge, England6National Institute for Health Research BioResource: Rare Diseases, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, England
| | - Robert Kayton
- Pathology Department, Oregon Health & Science University, Portland
| | - Douglas Weeks
- Pathology Department, Oregon Health & Science University, Portland
| | - Glenn W Anderson
- Histopathology Department, Great Ormond Street Hospital for Children, London, England
| | - Ryan Geraets
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota
| | - Camille Parker
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota
| | - David A Pearce
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota10Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls
| | - Michel Michaelides
- University College London Institute of Ophthalmology, London, England3Moorfields Eye Hospital, London, England
| | - Robert E MacLaren
- Moorfields Eye Hospital, London, England11Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford, England12Oxford University Hospitals National Health Service Foundation Trust, Oxford, England
| | - Anthony G Robson
- University College London Institute of Ophthalmology, London, England3Moorfields Eye Hospital, London, England
| | - Graham E Holder
- University College London Institute of Ophthalmology, London, England3Moorfields Eye Hospital, London, England
| | - Elise Heon
- Department of Ophthalmology and Vision Sciences, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - F Lucy Raymond
- National Health Service Blood and Transplant Centre, Department of Haematology, University of Cambridge, Cambridge, England6National Institute for Health Research BioResource: Rare Diseases, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, England13Cambridge Institute for Medical Research, Department of Medical Genetics, University of Cambridge, Cambridge, England
| | - Anthony T Moore
- University College London Institute of Ophthalmology, London, England3Moorfields Eye Hospital, London, England14Department of Ophthalmology, University of California, San Francisco Medical School, San Francisco
| | - Andrew R Webster
- University College London Institute of Ophthalmology, London, England3Moorfields Eye Hospital, London, England
| | - Mark E Pennesi
- Casey Eye Institute, Oregon Health & Science University, Portland
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Efficacy of rituximab in non-paraneoplastic autoimmune retinopathy. Orphanet J Rare Dis 2017; 12:129. [PMID: 28709429 PMCID: PMC5512938 DOI: 10.1186/s13023-017-0680-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 07/05/2017] [Indexed: 12/27/2022] Open
Abstract
Background Autoimmune retinopathy (AIR) is a rare but potentially blinding condition that is often underdiagnosed. Common features in AIR presentation include rapidly progressive vision loss with abnormal electrophysiological responses of the retina associated with positive anti-retinal antibodies. AIR is also challenging to treat, and thus, the introduction of new potential therapeutic agents is welcomed. The goal of this communication is to assess the effects of rituximab infusions on electroretinogram (ERG) responses and visual function outcomes in patients with non-paraneoplastic autoimmune retinopathy (npAIR). Results Following infusion(s), three out of five patients showed no evidence of disease progression or improved, while two patients continued to progress on ERG. One patient demonstrated improvement in visual acuity (2 lines) in both eyes. ERG responses provided objective monitoring of patients’ visual function and response to immunosuppression over time. Conclusions These findings suggest that patients with npAIR unresponsive to other immunosuppression therapies may benefit from rituximab infusion, although stabilization rather than improvement was more frequently the outcome in our case series. Furthermore, regularly scheduled ERG follow-up examinations are recommended for monitoring patients’ progression during treatment.
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39
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Nguyen TMT, Hull S, Roepman R, van den Born LI, Oud MM, de Vrieze E, Hetterschijt L, Letteboer SJF, van Beersum SEC, Blokland EA, Yntema HG, Cremers FPM, van der Zwaag PA, Arno G, van Wijk E, Webster AR, Haer-Wigman L. Missense mutations in the WD40 domain of AHI1 cause non-syndromic retinitis pigmentosa. J Med Genet 2017; 54:624-632. [PMID: 28442542 PMCID: PMC5574394 DOI: 10.1136/jmedgenet-2016-104200] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 02/02/2017] [Accepted: 02/27/2017] [Indexed: 12/31/2022]
Abstract
Background Recent findings suggesting that Abelson helper integration site 1 (AHI1) is involved in non-syndromic retinal disease have been debated, as the functional significance of identified missense variants was uncertain. We assessed whether AHI1 variants cause non-syndromic retinitis pigmentosa (RP). Methods Exome sequencing was performed in three probands with RP. The effects of the identified missense variants in AHI1 were predicted by three-dimensional structure homology modelling. Ciliary parameters were evaluated in patient’s fibroblasts, and recombinant mutant proteins were expressed in ciliated retinal pigmented epithelium cells. Results In the three patients with RP, three sets of compound heterozygous variants were detected in AHI1 (c.2174G>A; p.Trp725* and c.2258A>T; p.Asp753Val, c.660delC; p.Ser221Glnfs*10 and c.2090C>T; p.Pro697Leu, c.2087A>G; p.His696Arg and c.2429C>T; p.Pro810Leu). All four missense variants were present in the conserved WD40 domain of Jouberin, the ciliary protein encoded by AHI1, with variable predicted implications for the domain structure. No significant changes in the percentage of ciliated cells, nor in cilium length or intraflagellar transport were detected. However, expression of mutant recombinant Jouberin in ciliated cells showed a significantly decreased enrichment at the ciliary base. Conclusions This report confirms that mutations in AHI1 can underlie autosomal recessive RP. Moreover, it structurally and functionally validates the effect of the RP-associated AHI1 variants on protein function, thus proposing a new genotype–phenotype correlation for AHI1 mutation associated retinal ciliopathies.
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Affiliation(s)
- Thanh-Minh T Nguyen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sarah Hull
- UniversityCollege London, Instituteof Ophthalmology, London, United Kingdom.,Moorfields Eye Hospital, London, United Kingdom
| | - Ronald Roepman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Machteld M Oud
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Erik de Vrieze
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Lisette Hetterschijt
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Stef J F Letteboer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sylvia E C van Beersum
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ellen A Blokland
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Paul A van der Zwaag
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Gavin Arno
- UniversityCollege London, Instituteof Ophthalmology, London, United Kingdom.,Moorfields Eye Hospital, London, United Kingdom
| | - Erwin van Wijk
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Andrew R Webster
- UniversityCollege London, Instituteof Ophthalmology, London, United Kingdom.,Moorfields Eye Hospital, London, United Kingdom
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
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Broadgate S, Yu J, Downes SM, Halford S. Unravelling the genetics of inherited retinal dystrophies: Past, present and future. Prog Retin Eye Res 2017; 59:53-96. [PMID: 28363849 DOI: 10.1016/j.preteyeres.2017.03.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 03/21/2017] [Accepted: 03/23/2017] [Indexed: 02/07/2023]
Abstract
The identification of the genes underlying monogenic diseases has been of interest to clinicians and scientists for many years. Using inherited retinal dystrophies as an example of monogenic disease we describe the history of molecular genetic techniques that have been pivotal in the discovery of disease causing genes. The methods that were developed in the 1970's and 80's are still in use today but have been refined and improved. These techniques enabled the concept of the Human Genome Project to be envisaged and ultimately realised. When the successful conclusion of the project was announced in 2003 many new tools and, as importantly, many collaborations had been developed that facilitated a rapid identification of disease genes. In the post-human genome project era advances in computing power and the clever use of the properties of DNA replication has allowed the development of next-generation sequencing technologies. These methods have revolutionised the identification of disease genes because for the first time there is no need to define the position of the gene in the genome. The use of next generation sequencing in a diagnostic setting has allowed many more patients with an inherited retinal dystrophy to obtain a molecular diagnosis for their disease. The identification of novel genes that have a role in the development or maintenance of retinal function is opening up avenues of research which will lead to the development of new pharmacological and gene therapy approaches. Neither of which can be used unless the defective gene and protein is known. The continued development of sequencing technologies also holds great promise for the advent of truly personalised medicine.
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Affiliation(s)
- Suzanne Broadgate
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Levels 5 and 6 West Wing, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Jing Yu
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Levels 5 and 6 West Wing, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK
| | - Susan M Downes
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, Oxford, OX3 9DU, UK
| | - Stephanie Halford
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Levels 5 and 6 West Wing, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DU, UK.
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Zhang Q, Li G, Zhang L, Sun X, Zhang D, Lu J, Ma J, Yan J, Chen ZJ. Maternal common variant rs2305957 spanning PLK4 is associated with blastocyst formation and early recurrent miscarriage. Fertil Steril 2017; 107:1034-1040.e5. [PMID: 28238495 DOI: 10.1016/j.fertnstert.2017.01.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 01/05/2017] [Accepted: 01/05/2017] [Indexed: 12/21/2022]
Abstract
OBJECTIVE To investigate whether the common variant rs2305957 spanning PLK4 (Polo-like kinase 4) confers risk to embryo development in Northern Chinese Han (CHN) women. DESIGN Genetic association study. SETTING University hospital. PATIENT(S) A total of 2,015 infertile women who underwent in vitro fertilization (IVF), 530 women with early recurrent miscarriage (ERM), and 600 fertile control women in the CHN population. INTERVENTION(S) Genotyping of rs2305957 was performed by means of high-resolution melting analysis. MAIN OUTCOME MEASURE(S) Blastocyst formation, implantation, early miscarriage, and live birth rates in infertile women; genotype distribution at rs2305957 in ERM case and control subjects. RESULT(S) In the first cohort of this study, infertile women with AA genotype had a lower blastocyst formation rate than those with AG or GG genotype. No significant differences were observed in implantation rate, early miscarriage rate, or live birth rate among AA, AG, and GG subgroups. In the second cohort, common variant rs2305957 was related to ERM. Genotype frequency differences were also significant in both additive model and dominant model. CONCLUSION(S) Common variant rs2305957 is associated with blastocyst formation and ERM in CHN women. Further investigations of PLK4 gene during embryo development could be worthwhile.
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Affiliation(s)
- Qian Zhang
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, People's Republic of China; National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, People's Republic of China; The Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, People's Republic of China; Shandong Provincial Key Laboratory of Reproductive Medicine, Jinan, People's Republic of China
| | - Guangyu Li
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, People's Republic of China; National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, People's Republic of China; The Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, People's Republic of China; Shandong Provincial Key Laboratory of Reproductive Medicine, Jinan, People's Republic of China
| | - Lei Zhang
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, People's Republic of China; National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, People's Republic of China; The Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, People's Republic of China; Shandong Provincial Key Laboratory of Reproductive Medicine, Jinan, People's Republic of China
| | - Xiaohe Sun
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, People's Republic of China; National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, People's Republic of China; The Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, People's Republic of China; Shandong Provincial Key Laboratory of Reproductive Medicine, Jinan, People's Republic of China
| | - Dandan Zhang
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, People's Republic of China; National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, People's Republic of China; The Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, People's Republic of China; Shandong Provincial Key Laboratory of Reproductive Medicine, Jinan, People's Republic of China
| | - Juanjuan Lu
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, People's Republic of China; National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, People's Republic of China; The Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, People's Republic of China; Shandong Provincial Key Laboratory of Reproductive Medicine, Jinan, People's Republic of China
| | - Jinlong Ma
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, People's Republic of China; National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, People's Republic of China; The Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, People's Republic of China; Shandong Provincial Key Laboratory of Reproductive Medicine, Jinan, People's Republic of China
| | - Junhao Yan
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, People's Republic of China; National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, People's Republic of China; The Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, People's Republic of China; Shandong Provincial Key Laboratory of Reproductive Medicine, Jinan, People's Republic of China.
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, People's Republic of China; National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, People's Republic of China; The Key Laboratory of Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, People's Republic of China; Shandong Provincial Key Laboratory of Reproductive Medicine, Jinan, People's Republic of China; Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China; Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, People's Republic of China
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42
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Haer-Wigman L, van Zelst-Stams WA, Pfundt R, van den Born LI, Klaver CC, Verheij JB, Hoyng CB, Breuning MH, Boon CJ, Kievit AJ, Verhoeven VJ, Pott JW, Sallevelt SC, van Hagen JM, Plomp AS, Kroes HY, Lelieveld SH, Hehir-Kwa JY, Castelein S, Nelen M, Scheffer H, Lugtenberg D, Cremers FP, Hoefsloot L, Yntema HG. Diagnostic exome sequencing in 266 Dutch patients with visual impairment. Eur J Hum Genet 2017; 25:591-599. [PMID: 28224992 PMCID: PMC5437915 DOI: 10.1038/ejhg.2017.9] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 12/16/2016] [Accepted: 01/11/2017] [Indexed: 11/13/2022] Open
Abstract
Inherited eye disorders have a large clinical and genetic heterogeneity, which makes genetic diagnosis cumbersome. An exome-sequencing approach was developed in which data analysis was divided into two steps: the vision gene panel and exome analysis. In the vision gene panel analysis, variants in genes known to cause inherited eye disorders were assessed for pathogenicity. If no causative variants were detected and when the patient consented, the entire exome data was analyzed. A total of 266 Dutch patients with different types of inherited eye disorders, including inherited retinal dystrophies, cataract, developmental eye disorders and optic atrophy, were investigated. In the vision gene panel analysis (likely), causative variants were detected in 49% and in the exome analysis in an additional 2% of the patients. The highest detection rate of (likely) causative variants was in patients with inherited retinal dystrophies, for instance a yield of 63% in patients with retinitis pigmentosa. In patients with developmental eye defects, cataract and optic atrophy, the detection rate was 50, 33 and 17%, respectively. An exome-sequencing approach enables a genetic diagnosis in patients with different types of inherited eye disorders using one test. The exome approach has the same detection rate as targeted panel sequencing tests, but offers a number of advantages. For instance, the vision gene panel can be frequently and easily updated with additional (novel) eye disorder genes. Determination of the genetic diagnosis improved the clinical diagnosis, regarding the assessment of the inheritance pattern as well as future disease perspective.
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Affiliation(s)
- Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | | | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | | | - Caroline Cw Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Joke Bgm Verheij
- Department of Medical Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Martijn H Breuning
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Camiel Jf Boon
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Anneke J Kievit
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Virginie Jm Verhoeven
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jan Wr Pott
- Department of Ophthalmology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Suzanne Ceh Sallevelt
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Johanna M van Hagen
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Astrid S Plomp
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | - Hester Y Kroes
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Stefan H Lelieveld
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | - Jayne Y Hehir-Kwa
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | - Steven Castelein
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | - Marcel Nelen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | - Hans Scheffer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | - Dorien Lugtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | - Frans Pm Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | - Lies Hoefsloot
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
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Kletke S, Batmanabane V, Dai T, Vincent A, Li S, Gordon KA, Papsin BC, Cushing SL, Héon E. The combination of vestibular impairment and congenital sensorineural hearing loss predisposes patients to ocular anomalies, including Usher syndrome. Clin Genet 2017; 92:26-33. [PMID: 27743452 DOI: 10.1111/cge.12895] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/05/2016] [Accepted: 10/12/2016] [Indexed: 11/29/2022]
Abstract
The co-occurrence of hearing impairment and visual dysfunction is devastating. Most deaf-blind etiologies are genetically determined, the commonest being Usher syndrome (USH). While studies of the congenitally deaf population reveal a variable degree of visual problems, there are no effective ophthalmic screening guidelines. We hypothesized that children with congenital sensorineural hearing loss (SNHL) and vestibular impairment were at an increased risk of having USH. A retrospective chart review of 33 cochlear implants recipients for severe to profound SNHL and measured vestibular dysfunction was performed to determine the ocular phenotype. All the cases had undergone ocular examination and electroretinogram (ERG). Patients with an abnormal ERG underwent genetic testing for USH. We found an underlying ocular abnormality in 81.81% (27/33) of cases; of which 75% had refractive errors, and 50% of those patients showed visual improvement with refractive correction. A total of 14 cases (42.42%; 14/33) had generalized rod-cone dysfunction on ERG suggestive of Usher syndrome type 1, confirmed by mutational analysis. This work shows that adding vestibular impairment as a criterion for requesting an eye exam and adding the ERG to detect USH increases the chances of detecting ocular anomalies, when compared with previous literature focusing only on congenital SNHL.
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Affiliation(s)
- S Kletke
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Ontario, Canada
| | - V Batmanabane
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - T Dai
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Ontario, Canada
| | - A Vincent
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Ontario, Canada.,Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - S Li
- Program of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - K A Gordon
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Ontario, Canada.,Department of Otolaryngology - Head & Neck Surgery, The Hospital for Sick Children, Toronto, Ontario, Canada.,Archie's Cochlear Implant Laboratory, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - B C Papsin
- Department of Otolaryngology - Head & Neck Surgery, The Hospital for Sick Children, Toronto, Ontario, Canada.,Archie's Cochlear Implant Laboratory, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - S L Cushing
- Department of Otolaryngology - Head & Neck Surgery, The Hospital for Sick Children, Toronto, Ontario, Canada.,Archie's Cochlear Implant Laboratory, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - E Héon
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Ontario, Canada.,Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Ontario, Canada.,Program of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
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44
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Van Cauwenbergh C, Van Schil K, Cannoodt R, Bauwens M, Van Laethem T, De Jaegere S, Steyaert W, Sante T, Menten B, Leroy BP, Coppieters F, De Baere E. arrEYE: a customized platform for high-resolution copy number analysis of coding and noncoding regions of known and candidate retinal dystrophy genes and retinal noncoding RNAs. Genet Med 2016; 19:457-466. [PMID: 27608171 PMCID: PMC5392597 DOI: 10.1038/gim.2016.119] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 07/06/2016] [Indexed: 12/13/2022] Open
Abstract
Purpose: Our goal was to design a customized microarray, arrEYE, for high-resolution copy number variant (CNV) analysis of known and candidate genes for inherited retinal dystrophy (iRD) and retina-expressed noncoding RNAs (ncRNAs). Methods: arrEYE contains probes for the full genomic region of 106 known iRD genes, including those implicated in retinitis pigmentosa (RP) (the most frequent iRD), cone–rod dystrophies, macular dystrophies, and an additional 60 candidate iRD genes and 196 ncRNAs. Eight CNVs in iRD genes identified by other techniques were used as positive controls. The test cohort consisted of 57 patients with autosomal dominant, X-linked, or simplex RP. Results: In an RP patient, a novel heterozygous deletion of exons 7 and 8 of the HGSNAT gene was identified: c.634-408_820+338delinsAGAATATG, p.(Glu212Glyfs*2). A known variant was found on the second allele: c.1843G>A, p.(Ala615Thr). Furthermore, we expanded the allelic spectrum of USH2A and RCBTB1 with novel CNVs. Conclusion: The arrEYE platform revealed subtle single-exon to larger CNVs in iRD genes that could be characterized at the nucleotide level, facilitated by the high resolution of the platform. We report the first CNV in HGSNAT that, combined with another mutation, leads to RP, further supporting its recently identified role in nonsyndromic iRD. Genet Med19 4, 457–466.
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Affiliation(s)
- Caroline Van Cauwenbergh
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Kristof Van Schil
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Robrecht Cannoodt
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.,Data Mining and Modeling for Biomedicine group, VIB Inflammation Research Center, Ghent, Belgium.,Department of Internal Medicine, Ghent University, Ghent, Belgium
| | - Miriam Bauwens
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Thalia Van Laethem
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Sarah De Jaegere
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Wouter Steyaert
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Tom Sante
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Bart P Leroy
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.,Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium.,Division of Ophthalmology and Center for Cellular & Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Frauke Coppieters
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Elfride De Baere
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
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45
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Zhang Q, Xu M, Verriotto JD, Li Y, Wang H, Gan L, Lam BL, Chen R. Next-generation sequencing-based molecular diagnosis of 35 Hispanic retinitis pigmentosa probands. Sci Rep 2016; 6:32792. [PMID: 27596865 PMCID: PMC5011706 DOI: 10.1038/srep32792] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 07/29/2016] [Indexed: 12/13/2022] Open
Abstract
Retinitis pigmentosa (RP) is a heterogeneous group of inherited retinal diseases. The prevalence of RP and the mutation spectrum vary across populations. Hispanic people account for approximately 17% of the United States population, and the genetic etiologies of RP of this ethnic group still remain not well defined. Utilizing next-generation sequencing (NGS), we screened mutations in known retinal disease-causing genes in an RP cohort of 35 unrelated Hispanic probands from the Miami area. We achieved a solving rate of 66% and identified 15 novel putative pathogenic mutations, including a frequent founder mutation disrupting PRPF31 splicing. Our data show that the mutation spectrum of Hispanic RP receives a significant impact from disease-causing alleles of Spanish origin and may also contain population-specific alleles.
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Affiliation(s)
- Qi Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Mingchu Xu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Jennifer D. Verriotto
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Hui Wang
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Lin Gan
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Byron L. Lam
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Structural and Computational Biology and Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, Texas, USA
- The Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA
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46
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Coppieters F, Ascari G, Dannhausen K, Nikopoulos K, Peelman F, Karlstetter M, Xu M, Brachet C, Meunier I, Tsilimbaris M, Tsika C, Blazaki S, Vergult S, Farinelli P, Van Laethem T, Bauwens M, De Bruyne M, Chen R, Langmann T, Sui R, Meire F, Rivolta C, Hamel C, Leroy B, De Baere E. Isolated and Syndromic Retinal Dystrophy Caused by Biallelic Mutations in RCBTB1, a Gene Implicated in Ubiquitination. Am J Hum Genet 2016; 99:470-80. [PMID: 27486781 PMCID: PMC4974088 DOI: 10.1016/j.ajhg.2016.06.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 06/20/2016] [Indexed: 11/24/2022] Open
Abstract
Inherited retinal dystrophies (iRDs) are a group of genetically and clinically heterogeneous conditions resulting from mutations in over 250 genes. Here, homozygosity mapping and whole-exome sequencing (WES) in a consanguineous family revealed a homozygous missense mutation, c.973C>T (p.His325Tyr), in RCBTB1. In affected individuals, it was found to segregate with retinitis pigmentosa (RP), goiter, primary ovarian insufficiency, and mild intellectual disability. Subsequent analysis of WES data in different cohorts uncovered four additional homozygous missense mutations in five unrelated families in whom iRD segregates with or without syndromic features. Ocular phenotypes ranged from typical RP starting in the second decade to chorioretinal dystrophy with a later age of onset. The five missense mutations affect highly conserved residues either in the sixth repeat of the RCC1 domain or in the BTB1 domain. A founder haplotype was identified for mutation c.919G>A (p.Val307Met), occurring in two families of Mediterranean origin. We showed ubiquitous mRNA expression of RCBTB1 and demonstrated predominant RCBTB1 localization in human inner retina. RCBTB1 was very recently shown to be involved in ubiquitination, more specifically as a CUL3 substrate adaptor. Therefore, the effect on different components of the CUL3 and NFE2L2 (NRF2) pathway was assessed in affected individuals’ lymphocytes, revealing decreased mRNA expression of NFE2L2 and several NFE2L2 target genes. In conclusion, our study puts forward mutations in RCBTB1 as a cause of autosomal-recessive non-syndromic and syndromic iRD. Finally, our data support a role for impaired ubiquitination in the pathogenetic mechanism of RCBTB1 mutations.
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47
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Brandenstein L, Schweizer M, Sedlacik J, Fiehler J, Storch S. Lysosomal dysfunction and impaired autophagy in a novel mouse model deficient for the lysosomal membrane protein Cln7. Hum Mol Genet 2016; 25:777-91. [PMID: 26681805 DOI: 10.1093/hmg/ddv615] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 12/14/2015] [Indexed: 12/12/2022] Open
Abstract
CLN7 disease is an autosomal recessive, childhood-onset neurodegenerative lysosomal storage disorder caused by the defective lysosomal membrane protein CLN7. We have disrupted the Cln7/Mfsd8 gene in mice by targeted deletion of exon 2 generating a novel knockout (KO) mouse model for CLN7 disease, which recapitulates key features of human CLN7 disease pathology. Cln7 KO mice showed increased mortality and a neurological phenotype including hind limb clasping and myoclonus. Lysosomal dysfunction in the brain of mutant mice was shown by the storage of autofluorescent lipofuscin-like lipopigments, subunit c of mitochondrial ATP synthase and saposin D and increased expression of lysosomal cathepsins B, D and Z. By immunohistochemical co-stainings, increased cathepsin Z expression restricted to Cln7-deficient microglia and neurons was found. Ultrastructural analyses revealed large storage bodies in Purkinje cells of Cln7 KO mice containing inclusions composed of irregular, curvilinear and rectilinear profiles as well as fingerprint profiles. Generalized astrogliosis and microgliosis in the brain preceded neurodegeneration in the olfactory bulb, cerebral cortex and cerebellum in Cln7 KO mice. Increased levels of LC3-II and the presence of neuronal p62- and ubiquitin-positive protein aggregates suggested that impaired autophagy represents a major pathomechanism in the brain of Cln7 KO mice. The data suggest that loss of the putative lysosomal transporter Cln7 in the brain leads to lysosomal dysfunction, impaired constitutive autophagy and neurodegeneration late in disease.
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Affiliation(s)
| | | | - Jan Sedlacik
- Department of Diagnostics and Interventional Neuroradiology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, Hamburg 20246, Germany
| | - Jens Fiehler
- Department of Diagnostics and Interventional Neuroradiology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, Hamburg 20246, Germany
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48
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Xu M, Yamada T, Sun Z, Eblimit A, Lopez I, Wang F, Manya H, Xu S, Zhao L, Li Y, Kimchi A, Sharon D, Sui R, Endo T, Koenekoop RK, Chen R. Mutations in POMGNT1 cause non-syndromic retinitis pigmentosa. Hum Mol Genet 2016; 25:1479-88. [PMID: 26908613 DOI: 10.1093/hmg/ddw022] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 01/25/2016] [Indexed: 11/12/2022] Open
Abstract
A growing number of human diseases have been linked to defects in protein glycosylation that affects a wide range of organs. Among them, O-mannosylation is an unusual type of protein glycosylation that is largely restricted to the muscular and nerve system. Consistently, mutations in genes involved in the O-mannosylation pathway result in infantile-onset, severe developmental defects involving skeleton muscle, brain and eye, such as the muscle-eye-brain disease (MIM no. 253280). However, the functional importance of O-mannosylation in these tissues at later stages remains largely unknown. In our study, we have identified recessive mutations in POMGNT1, which encodes an essential component in O-mannosylation pathway, in three unrelated families with autosomal recessive retinitis pigmentosa (RP), but without extraocular involvement. Enzymatic assay of these mutant alleles demonstrate that they greatly reduce the POMGNT1 enzymatic activity and are likely to be hypomorphic. Immunohistochemistry shows that POMGNT1 is specifically expressed in photoreceptor basal body. Taken together, our work identifies a novel disease-causing gene for RP and indicates that proper protein O-mannosylation is not only essential for early organ development, but also important for maintaining survival and function of the highly specialized retinal cells at later stages.
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Affiliation(s)
- Mingchu Xu
- Department of Molecular and Human Genetics, Human Genome Sequencing Center
| | - Takeyuki Yamada
- Molecular Glycobiology, Research Team for Mechanism of Aging, Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Tokyo 173-0015, Japan
| | - Zixi Sun
- Department of Ophthalmology, Peking Union Medical College, Beijing 100730, China
| | - Aiden Eblimit
- Department of Molecular and Human Genetics, Human Genome Sequencing Center
| | - Irma Lopez
- McGill Ocular Genetics Laboratory, McGill University Health Centre, Montreal, Quebec H3H 1P3, Canada and
| | - Feng Wang
- Department of Molecular and Human Genetics, Human Genome Sequencing Center
| | - Hiroshi Manya
- Molecular Glycobiology, Research Team for Mechanism of Aging, Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Tokyo 173-0015, Japan
| | - Shan Xu
- Department of Molecular and Human Genetics, Human Genome Sequencing Center
| | - Li Zhao
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Structural and Computational Biology and Molecular Biophysics Graduate Program
| | - Yumei Li
- Department of Molecular and Human Genetics, Human Genome Sequencing Center
| | - Adva Kimchi
- Departments of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Dror Sharon
- Departments of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Ruifang Sui
- Department of Ophthalmology, Peking Union Medical College, Beijing 100730, China
| | - Tamao Endo
- Molecular Glycobiology, Research Team for Mechanism of Aging, Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Tokyo 173-0015, Japan
| | - Robert K Koenekoop
- McGill Ocular Genetics Laboratory, McGill University Health Centre, Montreal, Quebec H3H 1P3, Canada and
| | - Rui Chen
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Structural and Computational Biology and Molecular Biophysics Graduate Program, The Verna and Marrs Mclean Department of Biochemistry and Molecular Biology and Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA,
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49
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Stehr F, van der Putten H. Bridging NCL research gaps. Biochim Biophys Acta Mol Basis Dis 2015; 1852:2324-8. [PMID: 26056946 DOI: 10.1016/j.bbadis.2015.06.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 06/04/2015] [Accepted: 06/05/2015] [Indexed: 01/28/2023]
Abstract
The neuronal ceroid lipofuscinoses, collectively called NCLs, are rare and fatal lysosomal storage diseases that mainly affect children. Due to the fact that NCLs are both rare and heterogeneous (mutations in thirteen different genes) significant gaps exist in both preclinical and clinical research. Altogether, these gaps are major hurdles to bring therapies to patients while the need for new therapies is urgent to help them and their families. To define gaps and discuss solutions, a round table discussion involving teams and different stake holders took place during the 14th International Conference on Neuronal Ceroid Lipofuscinoses (Batten Disease) in Cordóba, Argentina. Topics covered by the teams and their leaders (in parentheses) included basic and translational research gaps with regard to large animal models (I. Tammen, D.N. Palmer), human NCL pathology and access to human tissue (J.D. Cooper, H.H. Goebel), rare NCLs (S. Hofman, I. Noher), links of NCLs to other diseases (F.M. Platt), gaps between clinic and clinical trials (H. Adams, A. Schulz), international collaborative efforts working towards a cure (S.E. Mole, H. Band) perspectives on palliative care from patient organizations (M. Frazier, A. West), and issues NCL researchers face when progressing to independent career in academia (M. Bond). Thoughts presented by the team leaders include previously unpublished opinions and information on the lack of understanding of disease pathomechanisms, gene function, assays for drug discovery and target validation, natural history of disease, and biomarkers for monitoring disease progression and treatment effects. This article is not intended to review the NCL literature. It includes personal opinions of the authors and it provides the reader with a summary of gaps discussed and solutions proposed by the teams. This article is part of a Special Issue entitled: Current Research on the Neuronal Ceroid Lipofuscinoses (Batten Disease).
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Affiliation(s)
- Frank Stehr
- NCL Foundation, Holstenwall 10, 20355 Hamburg, Germany.
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50
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Mole SE, Cotman SL. Genetics of the neuronal ceroid lipofuscinoses (Batten disease). Biochim Biophys Acta Mol Basis Dis 2015; 1852:2237-41. [PMID: 26026925 DOI: 10.1016/j.bbadis.2015.05.011] [Citation(s) in RCA: 214] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/12/2015] [Accepted: 05/18/2015] [Indexed: 11/17/2022]
Abstract
The neuronal ceroid lipofuscinoses (NCLs) are a group of inherited neurodegenerative disorders that affect children and adults and are grouped together by similar clinical features and the accumulation of autofluorescent storage material. More than a dozen genes containing over 430 mutations underlying human NCLs have been identified. These genes encode lysosomal enzymes (CLN1, CLN2, CLN10, CLN13), a soluble lysosomal protein (CLN5), a protein in the secretory pathway (CLN11), two cytoplasmic proteins that also peripherally associate with membranes (CLN4, CLN14), and many transmembrane proteins with different subcellular locations (CLN3, CLN6, CLN7, CLN8, CLN12). For most NCLs, the function of the causative gene has not been fully defined. Most of the mutations in these genes are associated with a typical disease phenotype, but some result in variable disease onset, severity, and progression, including distinct clinical phenotypes. There remain disease subgroups with unknown molecular genetic backgrounds. This article is part of a Special Issue entitled: "Current Research on the Neuronal Ceroid Lipofuscinoses (Batten Disease)."
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Affiliation(s)
- Sara E Mole
- MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London, WC1E 6BT, UK; UCL Institute of Child Health and Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.
| | - Susan L Cotman
- Center for Human Genetic Research, Department of Neurology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
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