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Lin S, Vermeirsch S, Pontikos N, Martin-Gutierrez MP, Daich Varela M, Malka S, Schiff E, Knight H, Wright G, Jurkute N, Simcoe MJ, Yu-Wai-Man P, Moosajee M, Michaelides M, Mahroo OA, Webster AR, Arno G. Spectrum of Genetic Variants in the Most Common Genes Causing Inherited Retinal Disease in a Large Molecularly Characterized United Kingdom Cohort. Ophthalmol Retina 2024; 8:699-709. [PMID: 38219857 DOI: 10.1016/j.oret.2024.01.012] [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: 09/14/2023] [Revised: 12/12/2023] [Accepted: 01/08/2024] [Indexed: 01/16/2024]
Abstract
PURPOSE Inherited retinal disease (IRD) is a leading cause of blindness. Recent advances in gene-directed therapies highlight the importance of understanding the genetic basis of these disorders. This study details the molecular spectrum in a large United Kingdom (UK) IRD patient cohort. DESIGN Retrospective study of electronic patient records. PARTICIPANTS Patients with IRD who attended the Genetics Service at Moorfields Eye Hospital between 2003 and July 2020, in whom a molecular diagnosis was identified. METHODS Genetic testing was undertaken via a combination of single-gene testing, gene panel testing, whole exome sequencing, and more recently, whole genome sequencing. Likely disease-causing variants were identified from entries within the genetics module of the hospital electronic patient record (OpenEyes Electronic Medical Record). Analysis was restricted to only genes listed in the Genomics England PanelApp R32 Retinal Disorders panel (version 3.24), which includes 412 genes associated with IRD. Manual curation ensured consistent variant annotation and included only plausible disease-associated variants. MAIN OUTCOME MEASURES Detailed analysis was performed for variants in the 5 most frequent genes (ABCA4, USH2A, RPGR, PRPH2, and BEST1), as well as for the most common variants encountered in the IRD study cohort. RESULTS We identified 4415 individuals from 3953 families with molecularly diagnosed IRD (variants in 166 genes). Of the families, 42.7% had variants in 1 of the 5 most common IRD genes. Complex disease alleles contributed to disease in 16.9% of affected families with ABCA4-associated retinopathy. USH2A exon 13 variants were identified in 43% of affected individuals with USH2A-associated IRD. Of the RPGR variants, 71% were clustered in the ORF15 region. PRPH2 and BEST1 variants were associated with a range of dominant and recessive IRD phenotypes. Of the 20 most prevalent variants identified, 5 were not in the most common genes; these included founder variants in CNGB3, BBS1, TIMP3, EFEMP1, and RP1. CONCLUSIONS We describe the most common pathogenic IRD alleles in a large single-center multiethnic UK cohort and the burden of disease, in terms of families affected, attributable to these variants. Our findings will inform IRD diagnoses in future patients and help delineate the cohort of patients eligible for gene-directed therapies under development. FINANCIAL DISCLOSURE(S) Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
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Affiliation(s)
- Siying Lin
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Sandra Vermeirsch
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom
| | - Nikolas Pontikos
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Maria Pilar Martin-Gutierrez
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom
| | - Malena Daich Varela
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Samantha Malka
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Elena Schiff
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Hannah Knight
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Genevieve Wright
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Neringa Jurkute
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom; Department of Neuro-Ophhalmology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Mark J Simcoe
- UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Patrick Yu-Wai-Man
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Mariya Moosajee
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Michel Michaelides
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Omar A Mahroo
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom; Department of Ophthalmology, St Thomas' Hospital, London, United Kingdom
| | - Andrew R Webster
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Gavin Arno
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom.
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Hitti-Malin RJ, Panneman DM, Corradi Z, Boonen EGM, Astuti G, Dhaenens CM, Stöhr H, Weber BHF, Sharon D, Banin E, Karali M, Banfi S, Ben-Yosef T, Glavač D, Farrar GJ, Ayuso C, Liskova P, Dudakova L, Vajter M, Ołdak M, Szaflik JP, Matynia A, Gorin MB, Kämpjärvi K, Bauwens M, De Baere E, Hoyng CB, Li CHZ, Klaver CCW, Inglehearn CF, Fujinami K, Rivolta C, Allikmets R, Zernant J, Lee W, Podhajcer OL, Fakin A, Sajovic J, AlTalbishi A, Valeina S, Taurina G, Vincent AL, Roberts L, Ramesar R, Sartor G, Luppi E, Downes SM, van den Born LI, McLaren TL, De Roach JN, Lamey TM, Thompson JA, Chen FK, Tracewska AM, Kamakari S, Sallum JMF, Bolz HJ, Kayserili H, Roosing S, Cremers FPM. Towards Uncovering the Role of Incomplete Penetrance in Maculopathies through Sequencing of 105 Disease-Associated Genes. Biomolecules 2024; 14:367. [PMID: 38540785 PMCID: PMC10967834 DOI: 10.3390/biom14030367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 05/02/2024] Open
Abstract
Inherited macular dystrophies (iMDs) are a group of genetic disorders, which affect the central region of the retina. To investigate the genetic basis of iMDs, we used single-molecule Molecular Inversion Probes to sequence 105 maculopathy-associated genes in 1352 patients diagnosed with iMDs. Within this cohort, 39.8% of patients were considered genetically explained by 460 different variants in 49 distinct genes of which 73 were novel variants, with some affecting splicing. The top five most frequent causative genes were ABCA4 (37.2%), PRPH2 (6.7%), CDHR1 (6.1%), PROM1 (4.3%) and RP1L1 (3.1%). Interestingly, variants with incomplete penetrance were revealed in almost one-third of patients considered solved (28.1%), and therefore, a proportion of patients may not be explained solely by the variants reported. This includes eight previously reported variants with incomplete penetrance in addition to CDHR1:c.783G>A and CNGB3:c.1208G>A. Notably, segregation analysis was not routinely performed for variant phasing-a limitation, which may also impact the overall diagnostic yield. The relatively high proportion of probands without any putative causal variant (60.2%) highlights the need to explore variants with incomplete penetrance, the potential modifiers of disease and the genetic overlap between iMDs and age-related macular degeneration. Our results provide valuable insights into the genetic landscape of iMDs and warrant future exploration to determine the involvement of other maculopathy genes.
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Affiliation(s)
- Rebekkah J. Hitti-Malin
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Daan M. Panneman
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Zelia Corradi
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Erica G. M. Boonen
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Galuh Astuti
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Claire-Marie Dhaenens
- Univ. Lille, Inserm, CHU Lille, U1172-LilNCog-Lille Neuroscience & Cognition, F-59000 Lille, France
| | - Heidi Stöhr
- Institute of Human Genetics, University of Regensburg, 93053 Regensburg, Germany
| | - Bernhard H. F. Weber
- Institute of Human Genetics, University of Regensburg, 93053 Regensburg, Germany
- Institute of Clinical Human Genetics, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Marianthi Karali
- Department of Precision Medicine, University of Campania ‘Luigi Vanvitelli’, 80138 Naples, Italy
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania ‘Luigi Vanvitelli’, 80131 Naples, Italy
| | - Sandro Banfi
- Department of Precision Medicine, University of Campania ‘Luigi Vanvitelli’, 80138 Naples, Italy
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania ‘Luigi Vanvitelli’, 80131 Naples, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Tamar Ben-Yosef
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Damjan Glavač
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Center for Human Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, 2000 Maribor, Slovenia
| | - G. Jane Farrar
- The School of Genetics and Microbiology, The University of Dublin Trinity College, D02 VF25 Dublin, Ireland
| | - Carmen Ayuso
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28049 Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Petra Liskova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 08 Prague, Czech Republic
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 08 Prague, Czech Republic
| | - Lubica Dudakova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 08 Prague, Czech Republic
| | - Marie Vajter
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 08 Prague, Czech Republic
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 08 Prague, Czech Republic
| | - Monika Ołdak
- Department of Histology and Embryology, Medical University of Warsaw, 02-004 Warsaw, Poland
| | - Jacek P. Szaflik
- Department of Ophthalmology, Medical University of Warsaw, SPKSO Ophthalmic University Hospital, 03-709 Warsaw, Poland
| | - Anna Matynia
- College of Optometry, University of Houston, Houston, TX 77004, USA
- Jules Stein Eye Institute, Los Angeles, CA 90095, USA
- Ophthalmology, University of California Los Angeles David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | | | | | - Miriam Bauwens
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Elfride De Baere
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Carel B. Hoyng
- Department of Ophthalmology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Catherina H. Z. Li
- Department of Ophthalmology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Caroline C. W. Klaver
- Department of Ophthalmology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Chris F. Inglehearn
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Kaoru Fujinami
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo 105-8461, Japan
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, NY 10027, USA
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10027, USA
| | - Jana Zernant
- Department of Ophthalmology, Columbia University, New York, NY 10027, USA
| | - Winston Lee
- Department of Ophthalmology, Columbia University, New York, NY 10027, USA
| | - Osvaldo L. Podhajcer
- Laboratorio de Terapia Molecular y Celular (Genocan), Fundación Instituto Leloir, CONICET, Buenos Aires 1405, Argentina
| | - Ana Fakin
- Eye Hospital, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Jana Sajovic
- Eye Hospital, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Alaa AlTalbishi
- St John of Jerusalem Eye Hospital Group, East Jerusalem 91198, Palestine
| | - Sandra Valeina
- Department of Ophthalmology, Riga Stradins University, LV-1007 Riga, Latvia
- Children’s Clinical University Hospital, LV-1004 Riga, Latvia
| | - Gita Taurina
- Children’s Clinical University Hospital, LV-1004 Riga, Latvia
| | - Andrea L. Vincent
- Department of Ophthalmology, New Zealand National Eye Centre, Faculty of Medical and Health Sciences, The University of Auckland, Grafton, Auckland 1023, New Zealand
- Eye Department, Greenlane Clinical Centre, Auckland District Health Board, Auckland 1142, New Zealand
| | - Lisa Roberts
- University of Cape Town/MRC Precision and Genomic Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Raj Ramesar
- University of Cape Town/MRC Precision and Genomic Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Giovanna Sartor
- Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy
| | - Elena Luppi
- Department of Medical and Surgical Sciences, University of Bologna, 40127 Bologna, Italy
- Unit of Medical Genetics, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Susan M. Downes
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, Oxford University, Oxford OX3 9DU, UK
- Oxford Eye Hospital, Oxford University NHS Foundation Trust, Oxford OX3 9DU, UK
| | | | - Terri L. McLaren
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Nedlands, WA 6009, Australia
| | - John N. De Roach
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Tina M. Lamey
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Jennifer A. Thompson
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
| | - Fred K. Chen
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Nedlands, WA 6009, Australia
| | | | - Smaragda Kamakari
- Ophthalmic Genetics Unit, OMMA Ophthalmological Institute of Athens, 115 25 Athens, Greece
| | - Juliana Maria Ferraz Sallum
- Department of Ophthalmology and Visual Sciences, Universidade Federal de São Paulo, São Paulo 04023-062, SP, Brazil
- Instituto de Genética Ocular, São Paulo 04552-050, SP, Brazil
| | - Hanno J. Bolz
- Institute of Human Genetics, University Hospital of Cologne, 50937 Cologne, Germany
| | - Hülya Kayserili
- Department of Medical Genetics, Koc University School of Medicine (KUSOM), 34450 Istanbul, Turkey
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
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Zeng B, Liu DC, Huang JG, Xia XB, Qin B. PdmIRD: missense variants pathogenicity prediction for inherited retinal diseases in a disease-specific manner. Hum Genet 2024; 143:331-342. [PMID: 38478153 DOI: 10.1007/s00439-024-02645-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/17/2024] [Indexed: 04/25/2024]
Abstract
Accurate discrimination of pathogenic and nonpathogenic variation remains an enormous challenge in clinical genetic testing of inherited retinal diseases (IRDs) patients. Computational methods for predicting variant pathogenicity are the main solutions for this dilemma. The majority of the state-of-the-art variant pathogenicity prediction tools disregard the differences in characteristics among different genes and treat all types of mutations equally. Since missense variants are the most common type of variation in the coding region of the human genome, we developed a novel missense mutation pathogenicity prediction tool, named Prediction of Deleterious Missense Mutation for IRDs (PdmIRD) in this study. PdmIRD was tailored for IRDs-related genes and constructed with the conditional random forest model. Population frequencies and a newly available prediction tool were incorporated into PdmIRD to improve the performance of the model. The evaluation of PdmIRD demonstrated its superior performance over nonspecific tools (areas under the curves, 0.984 and 0.910) and an existing eye abnormalities-specific tool (areas under the curves, 0.975 and 0.891). We also demonstrated the submodel that used a smaller gene panel further slightly improved performance. Our study provides evidence that a disease-specific model can enhance the prediction of missense mutation pathogenicity, especially when new and important features are considered. Additionally, this study provides guidance for exploring the characteristics and functions of the mutated proteins in a greater number of Mendelian disorders.
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Affiliation(s)
- Bing Zeng
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, 518031, Guangdong, China
- Shenzhen Aier Ophthalmic Technology Institute, Shenzhen, 518031, Guangdong, China
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Dong Cheng Liu
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, 518031, Guangdong, China
- Shenzhen Aier Ophthalmic Technology Institute, Shenzhen, 518031, Guangdong, China
| | - Jian Guo Huang
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, 518031, Guangdong, China
- Shenzhen Aier Ophthalmic Technology Institute, Shenzhen, 518031, Guangdong, China
| | - Xiao Bo Xia
- Eye Center of Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Bo Qin
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, 518031, Guangdong, China.
- Shenzhen Aier Ophthalmic Technology Institute, Shenzhen, 518031, Guangdong, China.
- Aier School of Ophthalmology, Central South University, Changsha, Hunan, China.
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Tian L, Chen CJ, Song YN, Xu K, Li NE, Zhang XH, Xie Y, Jin ZB, Li Y. Comprehensive genetic analysis reveals the mutational landscape of ABCA4-associated retinal dystrophy in a Chinese cohort. Gene 2024; 891:147832. [PMID: 37774808 DOI: 10.1016/j.gene.2023.147832] [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: 06/25/2023] [Revised: 09/15/2023] [Accepted: 09/25/2023] [Indexed: 10/01/2023]
Abstract
PURPOSE To depict the variant profiles of the ABCA4 gene in a large Chinese cohort of patients with ABCA4-associated retinal dystrophy (ABCA4-RD). METHODS We recruited 290 unrelated Chinese patients with ABCA4-RD and did ABCA4 mutational screening by a combination of Sanger sequencing, targeted exome sequencing, entire ABCA4 locus sequencing, and whole genome sequencing (WGS). The pathogenicity of variants was assessed using in silico tools or in vitro splicing assays following the American College of Medical Genetics and Genomics guidelines. RESULTS Two hundred sixty-eight distinct pathogenic variants were identified, and 57 were novel. In 580 alleles, 22 noncoding region variants outside canonical splice sites and 4 structural variations were found in 44 alleles accounting for 7.6% of all alleles. Bioinformatics analysis showed the complex mechanism of aberrant splicing productsnatural splice site disruption, branch point destruction, and cryptic splice site activation. Correspondingly, minigene assays validated the various abnormal splicing products, including exon skipping, exon elongation, partial exon deletion, and pseudoexon insertion. WGS identified the first inversion variation in ABCA4. CONCLUSIONS This study systematically depicted the variant profiles of ABCA4 and revealed the missing alleles of patients with ABCA4-RD in a large Chinese cohort. Our findings demonstrated the complexity of molecular diagnosis of Mendelian diseases and the efficiency of WGS for detecting structural variants.
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Affiliation(s)
- Lu Tian
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China; Department of Ophthalmology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Chun-Jie Chen
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Yu-Ning Song
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Ke Xu
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Ni-En Li
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Xiao-Hui Zhang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Yue Xie
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Zi-Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Yang Li
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China.
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de Guimaraes TAC, Georgiou M, Robson AG, Fujinami K, Vincent A, Nasser F, Khateb S, Mahroo OA, Pontikos N, Vargas ME, Thiadens AAHJ, Carvalho ERD, Nguyen XTA, Arno G, Fujinami-Yokokawa Y, Liu X, Tsunoda K, Hayashi T, Jiménez-Rolando B, Martin-Merida MI, Avila-Fernandez A, Salas EC, Garcia-Sandoval B, Ayuso C, Sharon D, Kohl S, Huckfeldt RM, Banin E, Pennesi ME, Khan AO, Wissinger B, Webster AR, Heon E, Boon CJF, Zrenner E, Michaelides M. KCNV2-associated retinopathy: genotype-phenotype correlations - KCNV2 study group report 3. Br J Ophthalmol 2023:bjo-2023-323640. [PMID: 37852740 DOI: 10.1136/bjo-2023-323640] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 09/15/2023] [Indexed: 10/20/2023]
Abstract
BACKGROUND/AIMS To investigate genotype-phenotype associations in patients with KCNV2 retinopathy. METHODS Review of clinical notes, best-corrected visual acuity (BCVA), molecular variants, electroretinography (ERG) and retinal imaging. Subjects were grouped according to the combination of KCNV2 variants-two loss-of-function (TLOF), two missense (TM) or one of each (MLOF)-and parameters were compared. RESULTS Ninety-two patients were included. The mean age of onset (mean±SD) in TLOF (n=55), TM (n=23) and MLOF (n=14) groups was 3.51±0.58, 4.07±2.76 and 5.54±3.38 years, respectively. The mean LogMAR BCVA (±SD) at baseline in TLOF, TM and MLOF groups was 0.89±0.25, 0.67±0.38 and 0.81±0.35 for right, and 0.88±0.26, 0.69±0.33 and 0.78±0.33 for left eyes, respectively. The difference in BCVA between groups at baseline was significant in right (p=0.03) and left eyes (p=0.035). Mean outer nuclear layer thickness (±SD) at baseline in TLOF, MLOF and TM groups was 37.07±15.20 µm, 40.67±12.53 and 40.38±18.67, respectively, which was not significantly different (p=0.85). The mean ellipsoid zone width (EZW) loss (±SD) was 2051 µm (±1318) for patients in the TLOF, and 1314 µm (±965) for MLOF. Only one patient in the TM group had EZW loss at presentation. There was considerable overlap in ERG findings, although the largest DA 10 ERG b-waves were associated with TLOF and the smallest with TM variants. CONCLUSIONS Patients with missense alterations had better BCVA and greater structural integrity. This is important for patient prognostication and counselling, as well as stratification for future gene therapy trials.
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Affiliation(s)
- Thales A C de Guimaraes
- Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Michalis Georgiou
- Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Anthony G Robson
- Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Kaoru Fujinami
- Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, Tokyo, Japan
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
| | - Ajoy Vincent
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Fadi Nasser
- Centre for Ophthalmology, University Hospital Tubingen Institute for Ophthalmic Research, Tubingen, Germany
| | - Samer Khateb
- Department of Ophthalmology, Hadassah Medical Center, Jerusalem, Israel
| | - Omar A Mahroo
- Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Nikolas Pontikos
- Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | | | - Alberta A H J Thiadens
- Department of Opthalmology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Emanuel R de Carvalho
- Institute of Ophthalmology, University College London, London, UK
- Department of Ophthalmology, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | - Xuan-Than-An Nguyen
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Gavin Arno
- Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Yu Fujinami-Yokokawa
- Institute of Ophthalmology, University College London, London, UK
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, Tokyo, Japan
- Department of Health Policy and Management, Keio University School of Medicine, Tokyo, Japan
| | - Xiao Liu
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, Tokyo, Japan
| | - Kazushige Tsunoda
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, Tokyo, Japan
| | - Takaaki Hayashi
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, Japan
| | | | - Maria Inmaculada Martin-Merida
- Instituto de Investigacion Sanitaria de la Fundacion Jimenez Diaz, Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Almudena Avila-Fernandez
- Instituto de Investigacion Sanitaria de la Fundacion Jimenez Diaz, Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Ester Carreño Salas
- Instituto de Investigacion Sanitaria de la Fundacion Jimenez Diaz, Madrid, Spain
| | | | - Carmen Ayuso
- Instituto de Investigacion Sanitaria de la Fundacion Jimenez Diaz, Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Jerusalem, Israel
| | - Susanne Kohl
- Centre for Ophthalmology, University Hospital Tubingen Institute for Ophthalmic Research, Tubingen, Germany
| | - Rachel M Huckfeldt
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard, Massachusetts, USA
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Jerusalem, Israel
| | - Mark E Pennesi
- Department of Ophthalmology, Oregon Health & Science University - Casey Eye Institute, Portland, Oregon, USA
| | - Arif O Khan
- Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, UAE
- Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, USA
| | - Bernd Wissinger
- Centre for Ophthalmology, University Hospital Tubingen Institute for Ophthalmic Research, Tubingen, Germany
| | - Andrew R Webster
- Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Elise Heon
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Camiel J F Boon
- Department of Ophthalmology, Amsterdam University Medical Centres, Amsterdam, The Netherlands
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eberhard Zrenner
- Centre for Ophthalmology, University Hospital Tubingen Institute for Ophthalmic Research, Tubingen, Germany
| | - Michel Michaelides
- Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
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6
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Corradi Z, Khan M, Hitti-Malin R, Mishra K, Whelan L, Cornelis SS, Hoyng CB, Kämpjärvi K, Klaver CCW, Liskova P, Stöhr H, Weber BHF, Banfi S, Farrar GJ, Sharon D, Zernant J, Allikmets R, Dhaenens CM, Cremers FPM. Targeted sequencing and in vitro splice assays shed light on ABCA4-associated retinopathies missing heritability. HGG ADVANCES 2023; 4:100237. [PMID: 37705246 PMCID: PMC10534262 DOI: 10.1016/j.xhgg.2023.100237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/15/2023] Open
Abstract
The ABCA4 gene is the most frequently mutated Mendelian retinopathy-associated gene. Biallelic variants lead to a variety of phenotypes, however, for thousands of cases the underlying variants remain unknown. Here, we aim to shed further light on the missing heritability of ABCA4-associated retinopathy by analyzing a large cohort of macular dystrophy probands. A total of 858 probands were collected from 26 centers, of whom 722 carried no or one pathogenic ABCA4 variant, while 136 cases carried two ABCA4 alleles, one of which was a frequent mild variant, suggesting that deep-intronic variants (DIVs) or other cis-modifiers might have been missed. After single molecule molecular inversion probes (smMIPs)-based sequencing of the complete 128-kb ABCA4 locus, the effect of putative splice variants was assessed in vitro by midigene splice assays in HEK293T cells. The breakpoints of copy number variants (CNVs) were determined by junction PCR and Sanger sequencing. ABCA4 sequence analysis solved 207 of 520 (39.8%) naive or unsolved cases and 70 of 202 (34.7%) monoallelic cases, while additional causal variants were identified in 54 of 136 (39.7%) probands carrying two variants. Seven novel DIVs and six novel non-canonical splice site variants were detected in a total of 35 alleles and characterized, including the c.6283-321C>G variant leading to a complex splicing defect. Additionally, four novel CNVs were identified and characterized in five alleles. These results confirm that smMIPs-based sequencing of the complete ABCA4 gene provides a cost-effective method to genetically solve retinopathy cases and that several rare structural and splice altering defects remain undiscovered in Stargardt disease cases.
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Affiliation(s)
- Zelia Corradi
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Mubeen Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Rebekkah Hitti-Malin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ketan Mishra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Laura Whelan
- The School of Genetics & Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Stéphanie S Cornelis
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Caroline C W Klaver
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands; Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands; Institute of Molecular & Clinical Ophthalmology, Basel, Switzerland
| | - Petra Liskova
- Research Unit for Rare Diseases, Department of Paediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic; Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Heidi Stöhr
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Bernhard H F Weber
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany; Institute of Clinical Human Genetics, University Hospital Regensburg, Regensburg, Germany
| | - Sandro Banfi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli," Naples and Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - G Jane Farrar
- The School of Genetics & Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jana Zernant
- Department of Ophthalmology, Columbia University, New York, NY, USA
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, NY, USA; Department of Pathology & Cell Biology, Columbia University, New York, NY, USA
| | - Claire-Marie Dhaenens
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; University Lille, Inserm, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, 59000 Lille, France
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
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7
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Rodríguez-Hidalgo M, de Bruijn SE, Corradi Z, Rodenburg K, Lara-López A, Valverde-Megías A, Ávila-Fernández A, Fernandez-Caballero L, Del Pozo-Valero M, Corominas J, Gilissen C, Irigoyen C, Cremers FPM, Ayuso C, Ruiz-Ederra J, Roosing S. ABCA4 c.6480-35A>G, a novel branchpoint variant associated with Stargardt disease. Front Genet 2023; 14:1234032. [PMID: 37779911 PMCID: PMC10539688 DOI: 10.3389/fgene.2023.1234032] [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: 06/03/2023] [Accepted: 08/15/2023] [Indexed: 10/03/2023] Open
Abstract
Introduction: Inherited retinal dystrophies (IRDs) can be caused by variants in more than 280 genes. The ATP-binding cassette transporter type A4 (ABCA4) gene is one of these genes and has been linked to Stargardt disease type 1 (STGD1), fundus flavimaculatus, cone-rod dystrophy (CRD), and pan-retinal CRD. Approximately 25% of the reported ABCA4 variants affect RNA splicing. In most cases, it is necessary to perform a functional assay to determine the effect of these variants. Methods: Whole genome sequencing (WGS) was performed in one Spanish proband with Stargardt disease. The putative pathogenicity of c.6480-35A>G on splicing was investigated both in silico and in vitro. The in silico approach was based on the deep-learning tool SpliceAI. For the in vitro approach we used a midigene splice assay in HEK293T cells, based on a previously established wild-type midigene (BA29) containing ABCA4 exons 46 to 48. Results: Through the analysis of WGS data, we identified two candidate variants in ABCA4 in one proband: a previously described deletion, c.699_768+342del (p.(Gln234Phefs*5)), and a novel branchpoint variant, c.6480-35A>G. Segregation analysis confirmed that the variants were in trans. For the branchpoint variant, SpliceAI predicted an acceptor gain with a high score (0.47) at position c.6480-47. A midigene splice assay in HEK293T cells revealed the inclusion of the last 47 nucleotides of intron 47 creating a premature stop codon and allowed to categorize the variant as moderately severe. Subsequent analysis revealed the presence of this variant as a second allele besides c.1958G>A p.(Arg653His) in an additional Spanish proband in a large cohort of IRD cases. Conclusion: A splice-altering effect of the branchpoint variant, confirmed by the midigene splice assay, along with the identification of this variant in a second unrelated individual affected with STGD, provides sufficient evidence to classify the variant as likely pathogenic. In addition, this research highlights the importance of studying non-coding regions and performing functional assays to provide a conclusive molecular diagnosis.
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Affiliation(s)
- María Rodríguez-Hidalgo
- Department of Neuroscience, Biodonostia Health Research Institute, Donostia-San Sebastián, Spain
- Department of Genetic, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Suzanne E. de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Zelia Corradi
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Kim Rodenburg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | | | | | - Almudena Ávila-Fernández
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Lidia Fernandez-Caballero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Del Pozo-Valero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Jordi Corominas
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Cristina Irigoyen
- Department of Neuroscience, Biodonostia Health Research Institute, Donostia-San Sebastián, Spain
- Ophthalmology Service, Donostia Universy Hospital, Donostia-San Sebastián, Spain
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Carmen Ayuso
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Javier Ruiz-Ederra
- Department of Neuroscience, Biodonostia Health Research Institute, Donostia-San Sebastián, Spain
- Department of Ophthalmology, University of the Basque Country (UPV/EHU), San Sebastián, Spain
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
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8
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Kaltak M, Blanco-Garavito R, Molday LL, Dhaenens CM, Souied EE, Platenburg G, Swildens J, Molday RS, Cremers FPM. Stargardt disease-associated in-frame ABCA4 exon 17 skipping results in significant ABCA4 function. J Transl Med 2023; 21:546. [PMID: 37587475 PMCID: PMC10428568 DOI: 10.1186/s12967-023-04406-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 08/01/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND ABCA4, the gene implicated in Stargardt disease (STGD1), contains 50 exons, of which 17 contain multiples of three nucleotides. The impact of in-frame exon skipping is yet to be determined. Antisense oligonucleotides (AONs) have been investigated in Usher syndrome-associated genes to induce skipping of in-frame exons carrying severe variants and mitigate their disease-linked effect. Upon the identification of a STGD1 proband carrying a novel exon 17 canonical splice site variant, the activity of ABCA4 lacking 22 amino acids encoded by exon 17 was examined, followed by design of AONs able to induce exon 17 skipping. METHODS A STGD1 proband was compound heterozygous for the splice variant c.2653+1G>A, that was predicted to result in in-frame skipping of exon 17, and a null variant [c.735T>G, p.(Tyr245*)]. Clinical characteristics of this proband were studied using multi-modal imaging and complete ophthalmological examination. The aberrant splicing of c.2653+1G>A was investigated in vitro in HEK293T cells with wild-type and mutant midigenes. The residual activity of the mutant ABCA4 protein lacking Asp864-Gly885 encoded by exon 17 was analyzed with all-trans-retinal-activated ATPase activity assay, along with its subcellular localization. To induce exon 17 skipping, the effect of 40 AONs was examined in vitro in WT WERI-Rb-1 cells and 3D human retinal organoids. RESULTS Late onset STGD1 in the proband suggests that c.2653+1G>A does not have a fully deleterious effect. The in vitro splice assay confirmed that this variant leads to ABCA4 transcripts without exon 17. ABCA4 Asp864_Gly863del was stable and retained 58% all-trans-retinal-activated ATPase activity compared to WT ABCA4. This sequence is located in an unstructured linker region between transmembrane domain 6 and nucleotide-binding domain-1 of ABCA4. AONs were designed to possibly reduce pathogenicity of severe variants harbored in exon 17. The best AON achieved 59% of exon 17 skipping in retinal organoids. CONCLUSIONS Exon 17 deletion in ABCA4 does not result in the absence of protein activity and does not cause a severe STGD1 phenotype when in trans with a null allele. By applying AONs, the effect of severe variants in exon 17 can potentially be ameliorated by exon skipping, thus generating partial ABCA4 activity in STGD1 patients.
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Affiliation(s)
- Melita Kaltak
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- ProQR Therapeutics, Leiden, The Netherlands
| | - Rocio Blanco-Garavito
- Department of Ophthalmology, Intercommunal Hospital Center and Henri Mondor Hospital, Paris-Est Créteil University, Creteil, France
| | - Laurie L Molday
- Department of Biochemistry and Molecular Biology, Department of Ophthalmology and Visual Sciences, Centre for Macular Research, University of British Columbia, Vancouver, BC, Canada
| | - Claire-Marie Dhaenens
- University of Lille, Inserm, CHU Lille, U1172-LilNCog-Lille Neuroscience & Cognition, Lille, France
| | - Eric E Souied
- Department of Ophthalmology, Intercommunal Hospital Center and Henri Mondor Hospital, Paris-Est Créteil University, Creteil, France
| | | | | | - Robert S Molday
- Department of Biochemistry and Molecular Biology, Department of Ophthalmology and Visual Sciences, Centre for Macular Research, University of British Columbia, Vancouver, BC, Canada
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
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9
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Watson A, Lako M. Retinal organoids provide unique insights into molecular signatures of inherited retinal disease throughout retinogenesis. J Anat 2023; 243:186-203. [PMID: 36177499 PMCID: PMC10335378 DOI: 10.1111/joa.13768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 09/06/2022] [Accepted: 09/06/2022] [Indexed: 10/14/2022] Open
Abstract
The demand for induced pluripotent stem cells (iPSC)-derived retinal organoid and retinal pigment epithelium (RPE) models for the modelling of inherited retinopathies has increased significantly in the last decade. These models are comparable with foetal retinas up until the later stages of retinogenesis, expressing all of the key neuronal markers necessary for retinal function. These models have proven to be invaluable in the understanding of retinogenesis, particular in the context of patient-specific diseases. Inherited retinopathies are infamously described as clinically and phenotypically heterogeneous, such that developing gene/mutation-specific animal models in each instance of retinal disease is not financially or ethically feasible. Further to this, many animal models are insufficient in the study of disease pathogenesis due to anatomical differences and failure to recapitulate human disease phenotypes. In contrast, iPSC-derived retinal models provide a high throughput platform which is physiologically relevant for studying human health and disease. They also serve as a platform for drug screening, gene therapy approaches and in vitro toxicology of novel therapeutics in pre-clinical studies. One unique characteristic of stem cell-derived retinal models is the ability to mimic in vivo retinogenesis, providing unparalleled insights into the effects of pathogenic mutations in cells of the developing retina, in a highly accessible way. This review aims to give the reader an overview of iPSC-derived retinal organoids and/or RPE in the context of disease modelling of several inherited retinopathies including Retinitis Pigmentosa, Stargardt disease and Retinoblastoma. We describe the ability of each model to recapitulate in vivo disease phenotypes, validate previous findings from animal models and identify novel pathomechanisms that underpin individual IRDs.
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Affiliation(s)
- Avril Watson
- Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Majlinda Lako
- Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
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10
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Whelan L, Dockery A, Stephenson KAJ, Zhu J, Kopčić E, Post IJM, Khan M, Corradi Z, Wynne N, O' Byrne JJ, Duignan E, Silvestri G, Roosing S, Cremers FPM, Keegan DJ, Kenna PF, Farrar GJ. Detailed analysis of an enriched deep intronic ABCA4 variant in Irish Stargardt disease patients. Sci Rep 2023; 13:9380. [PMID: 37296172 PMCID: PMC10256698 DOI: 10.1038/s41598-023-35889-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Over 15% of probands in a large cohort of more than 1500 inherited retinal degeneration patients present with a clinical diagnosis of Stargardt disease (STGD1), a recessive form of macular dystrophy caused by biallelic variants in the ABCA4 gene. Participants were clinically examined and underwent either target capture sequencing of the exons and some pathogenic intronic regions of ABCA4, sequencing of the entire ABCA4 gene or whole genome sequencing. ABCA4 c.4539 + 2028C > T, p.[= ,Arg1514Leufs*36] is a pathogenic deep intronic variant that results in a retina-specific 345-nucleotide pseudoexon inclusion. Through analysis of the Irish STGD1 cohort, 25 individuals across 18 pedigrees harbour ABCA4 c.4539 + 2028C > T and another pathogenic variant. This includes, to the best of our knowledge, the only two homozygous patients identified to date. This provides important evidence of variant pathogenicity for this deep intronic variant, highlighting the value of homozygotes for variant interpretation. 15 other heterozygous incidents of this variant in patients have been reported globally, indicating significant enrichment in the Irish population. We provide detailed genetic and clinical characterization of these patients, illustrating that ABCA4 c.4539 + 2028C > T is a variant of mild to intermediate severity. These results have important implications for unresolved STGD1 patients globally with approximately 10% of the population in some western countries claiming Irish heritage. This study exemplifies that detection and characterization of founder variants is a diagnostic imperative.
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Affiliation(s)
- Laura Whelan
- The School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland.
| | - Adrian Dockery
- The School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
- Next Generation Sequencing Laboratory, Pathology Department, The Mater Misericordiae University Hospital, Dublin 7, Ireland
| | - Kirk A J Stephenson
- Department of Ophthalmology, Royal Victoria Eye and Ear Hospital, Dublin 2, Ireland
- Mater Clinical Ophthalmic Genetics Unit, The Mater Misericordiae University Hospital, Dublin 7, Ireland
| | - Julia Zhu
- Mater Clinical Ophthalmic Genetics Unit, The Mater Misericordiae University Hospital, Dublin 7, Ireland
| | - Ella Kopčić
- The School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
| | - Iris J M Post
- The School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
| | - Mubeen Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- International Max Planck Research School for Language Sciences, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Zelia Corradi
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Academic Alliance Genetics, Radboud University Medical Center, Nijmegen, and Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Niamh Wynne
- Department of Ophthalmology, Royal Victoria Eye and Ear Hospital, Dublin 2, Ireland
| | - James J O' Byrne
- Mater Clinical Ophthalmic Genetics Unit, The Mater Misericordiae University Hospital, Dublin 7, Ireland
- International Max Planck Research School for Language Sciences, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- National Centre for Inherited Metabolic Disorders, The Mater Misericordiae University Hospital, Dublin 7, Ireland
- School of Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Emma Duignan
- Department of Ophthalmology, Royal Victoria Eye and Ear Hospital, Dublin 2, Ireland
| | - Giuliana Silvestri
- Centre for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK
- School of Medicine, University College Dublin, Dublin 4, Ireland
- Department of Ophthalmology, The Royal Victoria Hospital, Belfast, Northern Ireland, UK
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Academic Alliance Genetics, Radboud University Medical Center, Nijmegen, and Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Academic Alliance Genetics, Radboud University Medical Center, Nijmegen, and Maastricht University Medical Center+, Maastricht, The Netherlands
| | - David J Keegan
- Mater Clinical Ophthalmic Genetics Unit, The Mater Misericordiae University Hospital, Dublin 7, Ireland
| | - Paul F Kenna
- The School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
- Department of Ophthalmology, Royal Victoria Eye and Ear Hospital, Dublin 2, Ireland
| | - G Jane Farrar
- The School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
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11
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Cevik S, Biswas SB, Biswas-Fiss EE. Structural and Pathogenic Impacts of ABCA4 Variants in Retinal Degenerations-An In-Silico Study. Int J Mol Sci 2023; 24:ijms24087280. [PMID: 37108442 PMCID: PMC10138569 DOI: 10.3390/ijms24087280] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The retina-specific ATP-binding cassette transporter protein ABCA4 is responsible for properly continuing the visual cycle by removing toxic retinoid byproducts of phototransduction. Functional impairment caused by ABCA4 sequence variations is the leading cause of autosomal recessive inherited retinal disorders, including Stargardt disease, retinitis pigmentosa, and cone-rod dystrophy. To date, more than 3000 ABCA4 genetic variants have been identified, approximately 40 percent of which have not been able to be classified for pathogenicity assessments. This study examined 30 missense ABCA4 variants using AlphaFold2 protein modeling and computational structure analysis for pathogenicity prediction. All variants classified as pathogenic (n = 10) were found to have deleterious structural consequences. Eight of the ten benign variants were structurally neutral, while the remaining two resulted in mild structural changes. This study's results provided multiple lines of computational pathogenicity evidence for eight ABCA4 variants of uncertain clinical significance. Overall, in silico analyses of ABCA4 can provide a valuable tool for understanding the molecular mechanisms of retinal degeneration and their pathogenic impact.
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Affiliation(s)
- Senem Cevik
- Department of Medical and Molecular Sciences, College of Health Sciences, University of Delaware, 16 West Main Street, Suite 302 WHL, Newark, DE 19716, USA
- Ammon Pinizzotto Biopharmaceutical Innovation Center, 590 Avenue 1743, Newark, DE 19713, USA
| | - Subhasis B Biswas
- Department of Medical and Molecular Sciences, College of Health Sciences, University of Delaware, 16 West Main Street, Suite 302 WHL, Newark, DE 19716, USA
- Ammon Pinizzotto Biopharmaceutical Innovation Center, 590 Avenue 1743, Newark, DE 19713, USA
| | - Esther E Biswas-Fiss
- Department of Medical and Molecular Sciences, College of Health Sciences, University of Delaware, 16 West Main Street, Suite 302 WHL, Newark, DE 19716, USA
- Ammon Pinizzotto Biopharmaceutical Innovation Center, 590 Avenue 1743, Newark, DE 19713, USA
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12
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Kaltak M, de Bruijn P, Piccolo D, Lee SE, Dulla K, Hoogenboezem T, Beumer W, Webster AR, Collin RW, Cheetham ME, Platenburg G, Swildens J. Antisense oligonucleotide therapy corrects splicing in the common Stargardt disease type 1-causing variant ABCA4 c.5461-10T>C. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:674-688. [PMID: 36910710 PMCID: PMC9999166 DOI: 10.1016/j.omtn.2023.02.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 02/15/2023] [Indexed: 02/20/2023]
Abstract
Stargardt disease type 1 (STGD1) is the most common hereditary form of maculopathy and remains untreatable. STGD1 is caused by biallelic variants in the ABCA4 gene, which encodes the ATP-binding cassette (type 4) protein (ABCA4) that clears toxic byproducts of the visual cycle. The c.5461-10T>C p.[Thr1821Aspfs∗6,Thr1821Valfs∗13] variant is the most common severe disease-associated variant, and leads to exon skipping and out-of-frame ABCA4 transcripts that prevent translation of functional ABCA4 protein. Homozygous individuals typically display early onset STGD1 and are legally blind by early adulthood. Here, we applied antisense oligonucleotides (AONs) to promote exon inclusion and restore wild-type RNA splicing of ABCA4 c.5461-10T>C. The effect of AONs was first investigated in vitro using an ABCA4 midigene model. Subsequently, the best performing AONs were administered to homozygous c.5461-10T>C 3D human retinal organoids. Isoform-specific digital polymerase chain reaction revealed a significant increase in correctly spliced transcripts after treatment with the lead AON, QR-1011, up to 53% correct transcripts at a 3 μM dose. Furthermore, western blot and immunohistochemistry analyses identified restoration of ABCA4 protein after treatment. Collectively, we identified QR-1011 as a potent splice-correcting AON and a possible therapeutic intervention for patients harboring the severe ABCA4 c.5461-10T>C variant.
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Affiliation(s)
- Melita Kaltak
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, the Netherlands
- Academic Alliance Genetics, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, and Maastricht University Medical Center+, P. Debyelaan 25, 6229 HX Maastricht, the Netherlands
| | - Petra de Bruijn
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | - Davide Piccolo
- UCL, Institute of Ophthalmology, 11-43 Bath Street, EC1V 9EL London, UK
| | - Sang-Eun Lee
- UCL, Institute of Ophthalmology, 11-43 Bath Street, EC1V 9EL London, UK
| | - Kalyan Dulla
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | | | - Wouter Beumer
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | - Andrew R. Webster
- UCL, Institute of Ophthalmology, 11-43 Bath Street, EC1V 9EL London, UK
- Moorfields Eye Hospital, 162 City Road, EC1V 2PD London, UK
| | - Rob W.J. Collin
- Department of Human Genetics, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, the Netherlands
- Academic Alliance Genetics, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, and Maastricht University Medical Center+, P. Debyelaan 25, 6229 HX Maastricht, the Netherlands
| | | | | | - Jim Swildens
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
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13
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Mc Clinton B, Corradi Z, McKibbin M, Panneman DM, Roosing S, Boonen EGM, Ali M, Watson CM, Steel DH, Cremers FPM, Inglehearn CF, Hitti-Malin RJ, Toomes C. Effective smMIPs-Based Sequencing of Maculopathy-Associated Genes in Stargardt Disease Cases and Allied Maculopathies from the UK. Genes (Basel) 2023; 14:191. [PMID: 36672932 PMCID: PMC9859292 DOI: 10.3390/genes14010191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/13/2023] Open
Abstract
Macular dystrophies are a group of individually rare but collectively common inherited retinal dystrophies characterised by central vision loss and loss of visual acuity. Single molecule Molecular Inversion Probes (smMIPs) have proved effective in identifying genetic variants causing macular dystrophy. Here, a previously established smMIPs panel tailored for genes associated with macular diseases has been used to examine 57 UK macular dystrophy cases, achieving a high solve rate of 63.2% (36/57). Among 27 bi-allelic STGD1 cases, only three novel ABCA4 variants were identified, illustrating that the majority of ABCA4 variants in Caucasian STGD1 cases are currently known. We examined cases with ABCA4-associated disease in detail, comparing our results with a previously reported variant grading system, and found this model to be accurate and clinically useful. In this study, we showed that ABCA4-associated disease could be distinguished from other forms of macular dystrophy based on clinical evaluation in the majority of cases (34/36).
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Affiliation(s)
- Benjamin Mc Clinton
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
| | - Zelia Corradi
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Martin McKibbin
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
- Department of Ophthalmology, St. James’s University Hospital, Leeds LS9 7TF, UK
| | - Daan M. Panneman
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Erica G. M. Boonen
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Manir Ali
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
| | - Christopher M. Watson
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
- North East and Yorkshire Genomic Laboratory Hub, Central Lab, St. James’s University Hospital, Leeds LS9 7TF, UK
| | - David H. Steel
- Sunderland Eye Infirmary, Sunderland SR2 9HP, UK
- The Bioscience Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Chris F. Inglehearn
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
| | - Rebekkah J. Hitti-Malin
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Carmel Toomes
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
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14
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Tomkiewicz TZ, Nieuwenhuis SE, Cremers FPM, Garanto A, Collin RWJ. Correction of the Splicing Defect Caused by a Recurrent Variant in ABCA4 (c.769-784C>T) That Underlies Stargardt Disease. Cells 2022; 11:3947. [PMID: 36552712 PMCID: PMC9777113 DOI: 10.3390/cells11243947] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/23/2022] [Accepted: 11/26/2022] [Indexed: 12/13/2022] Open
Abstract
Stargardt disease is an inherited retinal disease caused by biallelic mutations in the ABCA4 gene, many of which affect ABCA4 splicing. In this study, nine antisense oligonucleotides (AONs) were designed to correct pseudoexon (PE) inclusion caused by a recurrent deep-intronic variant in ABCA4 (c.769-784C>T). First, the ability of AONs to skip the PE from the final ABCA4 mRNA transcript was assessed in two cellular models carrying the c.769-784C>T variant: a midigene assay using HEK293T cells and patient-derived fibroblasts. Based on the splicing-correcting ability of each individual AON, the three most efficacious AONs targeting independent regions of the PE were selected for a final assessment in photoreceptor precursor cells (PPCs). The final analysis in the PPC model confirmed high efficacy of AON2, -5, and -7 in promoting PE exclusion. Among the three AONs, AON2 is chosen as the lead candidate for further optimization, hereby showcasing the high potential of AONs to correct aberrant splicing events driven by deep-intronic variants.
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Affiliation(s)
- Tomasz Z. Tomkiewicz
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Sara E. Nieuwenhuis
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Frans P. M. Cremers
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Alejandro Garanto
- Departments of Pediatrics, Amalia Children’s Hospital, Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Rob W. J. Collin
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
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15
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Hitti-Malin RJ, Dhaenens CM, Panneman DM, Corradi Z, Khan M, den Hollander AI, Farrar GJ, Gilissen C, Hoischen A, van de Vorst M, Bults F, Boonen EGM, Saunders P, Roosing S, Cremers FPM. Using single molecule Molecular Inversion Probes as a cost-effective, high-throughput sequencing approach to target all genes and loci associated with macular diseases. Hum Mutat 2022; 43:2234-2250. [PMID: 36259723 PMCID: PMC10092144 DOI: 10.1002/humu.24489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 09/06/2022] [Accepted: 10/17/2022] [Indexed: 01/25/2023]
Abstract
Macular degenerations (MDs) are a subgroup of retinal disorders characterized by central vision loss. Knowledge is still lacking on the extent of genetic and nongenetic factors influencing inherited MD (iMD) and age-related MD (AMD) expression. Single molecule Molecular Inversion Probes (smMIPs) have proven effective in sequencing the ABCA4 gene in patients with Stargardt disease to identify associated coding and noncoding variation, however many MD patients still remain genetically unexplained. We hypothesized that the missing heritability of MDs may be revealed by smMIPs-based sequencing of all MD-associated genes and risk factors. Using 17,394 smMIPs, we sequenced the coding regions of 105 iMD and AMD-associated genes and noncoding or regulatory loci, known pseudo-exons, and the mitochondrial genome in two test cohorts that were previously screened for variants in ABCA4. Following detailed sequencing analysis of 110 probands, a diagnostic yield of 38% was observed. This established an ''MD-smMIPs panel," enabling a genotype-first approach in a high-throughput and cost-effective manner, whilst achieving uniform and high coverage across targets. Further analysis will identify known and novel variants in MD-associated genes to offer an accurate clinical diagnosis to patients. Furthermore, this will reveal new genetic associations for MD and potential genetic overlaps between iMD and AMD.
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Affiliation(s)
- Rebekkah J Hitti-Malin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Claire-Marie Dhaenens
- Inserm, CHU Lille, U1172-LilNCog-Lille Neuroscience & Cognition, Univ. Lille, Lille, France
| | - Daan M Panneman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Zelia Corradi
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mubeen Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anneke I den Hollander
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - G Jane Farrar
- The School of Genetics & Microbiology, The University of Dublin Trinity College, Dublin, Ireland
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Internal Medicine, Radboud University Medical Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maartje van de Vorst
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Femke Bults
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Erica G M Boonen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
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16
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Lee W, Su PY, Zernant J, Nagasaki T, Tsang SH, Allikmets R. Longitudinal Analysis of a Resolving Foveomacular Vitelliform Lesion in ABCA4 Disease. Ophthalmol Retina 2022; 6:847-860. [PMID: 35413457 PMCID: PMC9464664 DOI: 10.1016/j.oret.2022.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/27/2022] [Accepted: 04/05/2022] [Indexed: 11/26/2022]
Abstract
PURPOSE To describe the longitudinal progression and phenotypic association of bilateral foveomacular vitelliform lesions in the setting of ABCA4 disease. DESIGN Case report and cross-sectional cohort study. PARTICIPANTS Nineteen patients with confirmed ABCA4 disease exhibiting an optical gap phenotype. METHODS Multimodal retinal imaging across multiple visits included autofluorescence imaging, spectral-domain OCT (SD-OCT), and OCT angiography. Electro-oculogram (EOG) and full-field electroretinogram testing results were analyzed. Exome sequencing was performed for diagnostic confirmation and the verification of other variations. MAIN OUTCOME MEASURES Light-peak-to-dark-trough ratio (Arden ratio) on EOG; thickness and en face maps of various retinal layers on SD-OCT; area measurements on 488- and 787-nm autofluorescence images; and the presence of variation in vitelliform-associated genes identified using exome sequencing. RESULTS A 25-year-old White man presented with bilateral central vision loss due to foveal lesions consisting of vitelliform fluid. The result of EOG testing was inconsistent with bestrophinopathy (Arden ratio = 1.62), and no generalized rod or cone dysfunction was detected on full-field electroretinogram. Exome sequencing identified the pathogenic variants c.5882G>A (p.(Gly1961Glu)) and c.4139C>T (p.(Pro1380Leu)) in ABCA4 and no other vitelliform-associated genes. Significant thinning and abnormal reflectivity of photoreceptor-attributable layers as well as near-infrared autofluorescence abnormalities were found in lesion-adjacent areas. Complete resorption of the vitelliform fluid occurred after 30 months, after which the optical gap lesions exhibited an enlarged and "cavitated" appearance. Phenotypic screening for additional cases from a large ABCA4 disease database (n = 602) identified 18 additional patients at various stages of optical gap lesion formation, most of whom harbored the c.5882G>A (p.(Gly1961Glu)) variant (P < 0.001), although none had apparent vitelliform fluid. At least 5 of the 18 (31.6%) patients exhibited optical gap lesions with the distinct "cavitated" appearance, whereas the lesions remained unperturbed in the other patients over the course of examination. CONCLUSIONS Foveomacular vitelliform deposition is a mechanistically congruent but rare manifestation of ABCA4 disease. Specifically, this disease phenotype may be clinically associated with the c.5882G>A (p.(Gly1961Glu)) allele and optical gap lesions.
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Affiliation(s)
- Winston Lee
- Department of Genetics & Development, Columbia University, New York, New York; Department of Ophthalmology, Columbia University, New York, New York
| | - Pei-Yin Su
- Department of Ophthalmology, Columbia University, New York, New York
| | - Jana Zernant
- Department of Ophthalmology, Columbia University, New York, New York
| | - Takayuki Nagasaki
- Department of Ophthalmology, Columbia University, New York, New York
| | - Stephen H Tsang
- Department of Genetics & Development, Columbia University, New York, New York; Department of Pathology & Cell Biology, Columbia University, New York, New York
| | - Rando Allikmets
- Department of Genetics & Development, Columbia University, New York, New York; Department of Pathology & Cell Biology, Columbia University, New York, New York.
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17
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Hall JC, Paull D, Pébay A, Lidgerwood GE. Human pluripotent stem cells for the modelling of retinal pigment epithelium homeostasis and disease: A review. Clin Exp Ophthalmol 2022; 50:667-677. [PMID: 35739648 PMCID: PMC9546239 DOI: 10.1111/ceo.14128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/06/2022] [Accepted: 06/19/2022] [Indexed: 12/05/2022]
Abstract
Human pluripotent stem cells (hPSCs), which include induced pluripotent stem cells and embryonic stem cells, are powerful tools for studying human development, physiology and disease, including those affecting the retina. Cells from selected individuals, or specific genetic backgrounds, can be differentiated into distinct cell types allowing the modelling of diseases in a dish for therapeutic development. hPSC‐derived retinal cultures have already been used to successfully model retinal pigment epithelium (RPE) degeneration for various retinal diseases including monogenic conditions and complex disease such as age‐related macular degeneration. Here, we will review the current knowledge gained in understanding the molecular events involved in retinal disease using hPSC‐derived retinal models, in particular RPE models. We will provide examples of various conditions to illustrate the scope of applications associated with the use of hPSC‐derived RPE models.
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Affiliation(s)
- Jenna C Hall
- Department of Anatomy and Physiology The University of Melbourne Parkville Victoria Australia
| | - Daniel Paull
- The New York Stem Cell Foundation Research Institute New York New York USA
| | - Alice Pébay
- Department of Anatomy and Physiology The University of Melbourne Parkville Victoria Australia
- Department of Surgery, Royal Melbourne Hospital The University of Melbourne Parkville Victoria Australia
| | - Grace E. Lidgerwood
- Department of Anatomy and Physiology The University of Melbourne Parkville Victoria Australia
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18
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Runhart EH, Dhooge P, Meester‐Smoor M, Pas J, Pott JWR, Leeuwen R, Kroes HY, Bergen AA, Jong‐Hesse Y, Thiadens AA, Schooneveld MJ, Genderen M, Boon C, Klaver C, den Born LI, Cremers FPM, Hoyng CB. Stargardt disease: monitoring incidence and diagnostic trends in the Netherlands using a nationwide disease registry. Acta Ophthalmol 2022; 100:395-402. [PMID: 34431609 PMCID: PMC9291619 DOI: 10.1111/aos.14996] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/20/2021] [Accepted: 08/04/2021] [Indexed: 01/06/2023]
Abstract
Purpose To assess the incidence of Stargardt disease (STGD1) and to evaluate demographics of incident cases. Methods For this retrospective cohort study, demographic, clinical and genetic data of patients with a clinical diagnosis of STGD1 were registered between September 2010 and January 2020 in a nationwide disease registry. Annual incidence (2014‐2018) and point prevalence (2018) were assessed on the basis of this registry. Results A total of 800 patients were registered, 56% were female and 83% were of European ancestry. The incidence was 1.67‐1.95:1,000,000 per year and the point prevalence in 2018 was approximately 1:22,000‐1:19,000 (with and without 10% of potentially unregistered cases). Age at onset was associated with sex (p = 0.027, Fisher’s exact); 1.9x more women than men were observed (140 versus 74) amongst patients with an age at onset between 10 and 19 years, while the sex ratio in other age‐at‐onset categories approximated one. Late‐onset STGD1 (≥45 years) constituted 33% of the diagnoses in 2014‐2018 compared to 19% in 2004‐2008. Diagnostic delay (≥2 years between the first documentation of macular abnormalities and diagnosis) was associated with older age of onset (p = 0.001, Mann–Whitney). Misdiagnosis for age‐related macular degeneration (22%) and incidental STGD1 findings (14%) was common in patients with late‐onset STGD1. Conclusion The observed prevalence of STGD1 in real‐world data was lower than expected on the basis of population ABCA4 allele frequencies. Late‐onset STGD1 was more frequently diagnosed in recent years, likely due to higher awareness of its phenotype. In this pretherapeutic era, mis‐ and underdiagnosis of especially late‐onset STGD1 and the role of sex in STGD1 should receive special attention.
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Affiliation(s)
- Esmee H. Runhart
- Department of Ophthalmology Radboud University Medical Centre Nijmegen the Netherlands
- Donders Institute for Brain Cognition and Behaviour Radboud University Medical Centre Nijmegen the Netherlands
| | - Patty Dhooge
- Department of Ophthalmology Radboud University Medical Centre Nijmegen the Netherlands
- Donders Institute for Brain Cognition and Behaviour Radboud University Medical Centre Nijmegen the Netherlands
| | - Magda Meester‐Smoor
- Department of Ophthalmology Erasmus University Medical Centre Rotterdam the Netherlands
| | - Jeroen Pas
- Department of Ophthalmology Radboud University Medical Centre Nijmegen the Netherlands
| | - Jan Willem R. Pott
- Department of Ophthalmology University Medical Centre Groningen University of Groningen Groningen the Netherlands
| | - Redmer Leeuwen
- Department of Ophthalmology University Medical Centre Utrecht Utrecht the Netherlands
| | - Hester Y. Kroes
- Department of Genetics University Medical Centre Utrecht Utrecht the Netherlands
| | - Arthur A. Bergen
- Department of Clinical Genetics Academic Medical Centre Amsterdam the Netherlands
- The Netherlands Institute for Neuroscience (NIN‐KNAW) Amsterdam the Netherlands
| | - Yvonne Jong‐Hesse
- Department of Ophthalmology Amsterdam University Medical Centres Amsterdam the Netherlands
| | - Alberta A. Thiadens
- Department of Ophthalmology Erasmus University Medical Centre Rotterdam the Netherlands
| | - Mary J. Schooneveld
- Department of Ophthalmology Amsterdam University Medical Centres Amsterdam the Netherlands
- Bartiméus Diagnostic Centre for Complex Visual Disorders Zeist the Netherlands
| | - Maria Genderen
- Department of Ophthalmology University Medical Centre Utrecht Utrecht the Netherlands
- Bartiméus Diagnostic Centre for Complex Visual Disorders Zeist the Netherlands
| | - Camiel Boon
- Department of Ophthalmology Amsterdam University Medical Centres Amsterdam the Netherlands
- Department of Ophthalmology Leiden University Medical Centre Leiden the Netherlands
| | - Caroline Klaver
- Department of Ophthalmology Radboud University Medical Centre Nijmegen the Netherlands
- Department of Ophthalmology Erasmus University Medical Centre Rotterdam the Netherlands
- Department of Epidemiology Erasmus University Medical Centre Rotterdam the Netherlands
| | - L. Ingeborg den Born
- The Rotterdam Eye Hospital Rotterdam the Netherlands
- Rotterdam Ophthalmic Institute Rotterdam the Netherlands
| | - Frans P. M. Cremers
- Donders Institute for Brain Cognition and Behaviour Radboud University Medical Centre Nijmegen the Netherlands
- Department of Human Genetics Radboud University Medical Centre Nijmegen the Netherlands
| | - Carel B. Hoyng
- Department of Ophthalmology Radboud University Medical Centre Nijmegen the Netherlands
- Donders Institute for Brain Cognition and Behaviour Radboud University Medical Centre Nijmegen the Netherlands
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19
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Corradi Z, Salameh M, Khan M, Héon E, Mishra K, Hitti-Malin RJ, AlSwaiti Y, Aslanian A, Banin E, Brooks BP, Zein WM, Hufnagel RB, Roosing S, Dhaenens C, Sharon D, Cremers FPM, AlTalbishi A. ABCA4 c.859-25A>G, a Frequent Palestinian Founder Mutation Affecting the Intron 7 Branchpoint, Is Associated With Early-Onset Stargardt Disease. Invest Ophthalmol Vis Sci 2022; 63:20. [PMID: 35475888 PMCID: PMC9055564 DOI: 10.1167/iovs.63.4.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/02/2022] [Indexed: 11/24/2022] Open
Abstract
Purpose The effect of noncoding variants is often unknown in the absence of functional assays. Here, we characterized an ABCA4 intron 7 variant, c.859-25A>G, identified in Palestinian probands with Stargardt disease (STGD) or cone-rod dystrophy (CRD). We investigated the effect of this variant on the ABCA4 mRNA and retinal phenotype, and its prevalence in Palestine. Methods The ABCA4 gene was sequenced completely or partially in 1998 cases with STGD or CRD. The effect of c.859-25A>G on splicing was investigated in silico using SpliceAI and in vitro using splice assays. Homozygosity mapping was performed for 16 affected individuals homozygous for c.859-25A>G. The clinical phenotype was assessed using functional and structural analyses including visual acuity, full-field electroretinography, and multimodal imaging. Results The smMIPs-based ABCA4 sequencing revealed c.859-25A>G in 10 Palestinian probands from Hebron and Jerusalem. SpliceAI predicted a significant effect of this putative branchpoint-inactivating variant on the nearby intron 7 splice acceptor site. Splice assays revealed exon 8 skipping and two partial inclusions of intron 7, each having a deleterious effect. Additional genotyping revealed another 46 affected homozygous or compound heterozygous individuals carrying variant c.859-25A>G. Homozygotes shared a genomic segment of 59.6 to 87.9 kb and showed severe retinal defects on ophthalmoscopic evaluation. Conclusions The ABCA4 variant c.859-25A>G disrupts a predicted branchpoint, resulting in protein truncation because of different splice defects, and is associated with early-onset STGD1 when present in homozygosity. This variant was found in 25/525 Palestinian inherited retinal dystrophy probands, representing one of the most frequent inherited retinal disease-causing variants in West-Bank Palestine.
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Affiliation(s)
- Zelia Corradi
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Manar Salameh
- St John of Jerusalem Eye Hospital Group, East Jerusalem, Palestine
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mubeen Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Elise Héon
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Ontario, Canada
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ketan Mishra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rebekkah J. Hitti-Malin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Yahya AlSwaiti
- St John of Jerusalem Eye Hospital Group, East Jerusalem, Palestine
| | - Alice Aslanian
- St John of Jerusalem Eye Hospital Group, East Jerusalem, Palestine
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Brian P. Brooks
- Ophthalmic Genetics and Visual Function Branch, National Eye Institutes, National Institutes of Health, Bethesda, Maryland, United States
| | - Wadih M. Zein
- Ophthalmic Genetics and Visual Function Branch, National Eye Institutes, National Institutes of Health, Bethesda, Maryland, United States
| | - Robert B. Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institutes, National Institutes of Health, Bethesda, Maryland, United States
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Claire‐Marie Dhaenens
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Univ. Lille, Inserm, CHU Lille, U1172 - LilNCog - Lille Neuroscience & Cognition, Lille, France
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alaa AlTalbishi
- St John of Jerusalem Eye Hospital Group, East Jerusalem, Palestine
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20
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Cornelis SS, Runhart EH, Bauwens M, Corradi Z, De Baere E, Roosing S, Haer-Wigman L, Dhaenens CM, Vulto-van Silfhout AT, Cremers FP. Personalized genetic counseling for Stargardt disease: Offspring risk estimates based on variant severity. Am J Hum Genet 2022; 109:498-507. [PMID: 35120629 DOI: 10.1016/j.ajhg.2022.01.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/11/2022] [Indexed: 12/21/2022] Open
Abstract
Recurrence risk calculations in autosomal recessive diseases are complicated when the effect of genetic variants and their population frequencies and penetrances are unknown. An example of this is Stargardt disease (STGD1), a frequent recessive retinal disease caused by bi-allelic pathogenic variants in ABCA4. In this cross-sectional study, 1,619 ABCA4 variants from 5,579 individuals with STGD1 were collected and categorized by (1) severity based on statistical comparisons of their frequencies in STGD1-affected individuals versus the general population, (2) their observed versus expected homozygous occurrence in STGD1-affected individuals, (3) their occurrence in combination with established mild alleles in STGD1-affected individuals, and (4) previous functional and clinical studies. We used the sum allele frequencies of these severity categories to estimate recurrence risks for offspring of STGD1-affected individuals and carriers of pathogenic ABCA4 variants. The risk for offspring of an STGD1-affected individual with the "severe|severe" genotype or a "severe|mild with complete penetrance" genotype to develop STGD1 at some moment in life was estimated at 2.8%-3.1% (1 in 36-32 individuals) and 1.6%-1.8% (1 in 62-57 individuals), respectively. The risk to develop STGD1 in childhood was estimated to be 2- to 4-fold lower: 0.68%-0.79% (1 in 148-126) and 0.34%-0.39% (1 in 296-252), respectively. In conclusion, we established personalized recurrence risk calculations for STGD1-affected individuals with different combinations of variants. We thus propose an expanded genotype-based personalized counseling to appreciate the variable recurrence risks for STGD1-affected individuals. This represents a conceptual breakthrough because risk calculations for STGD1 may be exemplary for many other inherited diseases.
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21
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Piotter E, McClements ME, MacLaren RE. The Scope of Pathogenic ABCA4 Mutations Targetable by CRISPR DNA Base Editing Systems—A Systematic Review. Front Genet 2022; 12:814131. [PMID: 35154257 PMCID: PMC8830518 DOI: 10.3389/fgene.2021.814131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/14/2021] [Indexed: 12/26/2022] Open
Abstract
Stargardt macular dystrophy (STGD1) is the most common form of inherited childhood blindness worldwide and for which no current treatments exist. It is an autosomal recessive disease caused by mutations in ABCA4. To date, a variety of gene supplementation approaches have been tested to create a therapy, with some reaching clinical trials. New technologies, such as CRISPR-Cas based editing systems, provide an exciting frontier for addressing genetic disease by allowing targeted DNA or RNA base editing of pathogenic mutations. ABCA4 has ∼1,200 known pathogenic mutations, of which ∼63% are transition mutations amenable to this editing technology. In this report, we screened the known “pathogenic” and “likely pathogenic” mutations in ABCA4 from available data in gnomAD, Leiden Open Variation Database (LOVD), and ClinVar for potential PAM sites of relevant base editors, including Streptococcus pyogenes Cas (SpCas), Staphylococcus aureus Cas (SaCas), and the KKH variant of SaCas (Sa-KKH). Overall, of the mutations screened, 53% (ClinVar), 71% (LOVD), and 71% (gnomAD), were editable, pathogenic transition mutations, of which 35–47% had “ideal” PAM sites. Of these mutations, 16–20% occur within a range of multiple PAM sites, enabling a variety of editing strategies. Further, in relevant patient data looking at three cohorts from Germany, Denmark, and China, we find that 44–76% of patients, depending on the presence of complex alleles, have at least one transition mutation with a nearby SaCas, SpCas, or Sa-KKH PAM site, which would allow for potential DNA base editing as a treatment strategy. Given the complexity of the genetic landscape of Stargardt, these findings provide a clearer understanding of the potential for DNA base editing approaches to be applied as ABCA4 gene therapy strategies.
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Affiliation(s)
- Elena Piotter
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- *Correspondence: Elena Piotter,
| | - Michelle E. McClements
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Robert E. MacLaren
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust and NIHR Biomedical Research Centre, Oxford, United Kingdom
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22
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Functional assays of non-canonical splice-site variants in inherited retinal dystrophies genes. Sci Rep 2022; 12:68. [PMID: 34996991 PMCID: PMC8742059 DOI: 10.1038/s41598-021-03925-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 12/10/2021] [Indexed: 11/17/2022] Open
Abstract
Inherited retinal dystrophies are a group of disorders characterized by the progressive degeneration of photoreceptors leading to loss of the visual function and eventually to legal blindness. Although next generation sequencing (NGS) has revolutionized the molecular diagnosis of these diseases, the pathogenicity of some mutations casts doubts. After the screening of 208 patients with a panel of 117 genes, we obtained 383 variants that were analysed in silico with bioinformatic prediction programs. Based on the results of these tools, we selected 15 variants for their functional assessment. Therefore, we carried out minigene assays to unveil whether they could affect the splicing of the corresponding gene. As a whole, seven variants were found to induce aberrant splicing in the following genes: BEST1, CACNA2D4, PRCD, RIMS1, FSCN2, MERTK and MAK. This study shows the efficacy of a workflow, based on the association of the Minimum Allele Frequency, family co-segregation, in silico predictions and in vitro assays to determine the effect of potential splice site variants identified by DNA-based NGS. These findings improve the molecular diagnosis of inherited retinal dystrophies and will allow some patients to benefit from the upcoming gene-based therapeutic strategies.
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23
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Schönbach EM, Strauss RW, Cattaneo ME, Fujinami K, Birch DG, Cideciyan AV, Sunness JS, Zrenner E, Sadda SR, Scholl HP. Longitudinal Changes of Fixation Stability and Location Within 24 Months in Stargardt Disease: ProgStar Report No. 16. Am J Ophthalmol 2022; 233:78-89. [PMID: 34298008 DOI: 10.1016/j.ajo.2021.07.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 11/25/2022]
Abstract
PURPOSE Stargardt disease type 1 (STGD1) is the most common macular dystrophy. The assessment of fixation describes an important dimension of visual function, but data on its progression over time are limited. We present longitudinal changes and investigate its usefulness for clinical trials. DESIGN International, multicenter, prospective cohort study. METHODS Included were 239 individuals with genetically confirmed STGD1 (one or more disease-causing ATP binding cassette subfamily A member 4 [ABCA4] variant). We determined the fixation stability (FS) using 1 SD of the bivariate contour ellipse area (1 SD-BCEA) and fixation location (FL) using the eccentricity of fixation from the fovea during five study visits every 6 months. RESULTS At baseline, 239 patients (105 males [44%]) and 459 eyes, with a median age of 32 years, were included. The baseline mean logBCEA was 0.70 ± 1.41 log deg2 and the mean FL was 6.25° ± 4.40°. Although the mean logBCEA did not monotonically increase from visit to visit, the overall yearly increase in the logBCEA was 0.124 log deg2 (95% CI, 0.063-0.185 log deg2). The rate of change was not different between the 2 years but increased faster in eyes without flecks outside of the vascular arcades and depended on baseline logBCEA. FL did not change statistically significantly over time. CONCLUSIONS Fixation parameters are unlikely to be sensitive outcome measures for clinical trials in STGD1 but may provide useful ancillary information in selected cases to longitudinally describe and understand an eye's visual function.
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24
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Molday RS, Garces FA, Scortecci JF, Molday LL. Structure and function of ABCA4 and its role in the visual cycle and Stargardt macular degeneration. Prog Retin Eye Res 2021; 89:101036. [PMID: 34954332 DOI: 10.1016/j.preteyeres.2021.101036] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/07/2021] [Accepted: 12/13/2021] [Indexed: 12/17/2022]
Abstract
ABCA4 is a member of the superfamily of ATP-binding cassette (ABC) transporters that is preferentially localized along the rim region of rod and cone photoreceptor outer segment disc membranes. It uses the energy from ATP binding and hydrolysis to transport N-retinylidene-phosphatidylethanolamine (N-Ret-PE), the Schiff base adduct of retinal and phosphatidylethanolamine, from the lumen to the cytoplasmic leaflet of disc membranes. This ensures that all-trans-retinal and excess 11-cis-retinal are efficiently cleared from photoreceptor cells thereby preventing the accumulation of toxic retinoid compounds. Loss-of-function mutations in the gene encoding ABCA4 cause autosomal recessive Stargardt macular degeneration, also known as Stargardt disease (STGD1), and related autosomal recessive retinopathies characterized by impaired central vision and an accumulation of lipofuscin and bis-retinoid compounds. High resolution structures of ABCA4 in its substrate and nucleotide free state and containing bound N-Ret-PE or ATP have been determined by cryo-electron microscopy providing insight into the molecular architecture of ABCA4 and mechanisms underlying substrate recognition and conformational changes induced by ATP binding. The expression and functional characterization of a large number of disease-causing missense ABCA4 variants have been determined. These studies have shed light into the molecular mechanisms underlying Stargardt disease and a classification that reliably predicts the effect of a specific missense mutation on the severity of the disease. They also provide a framework for developing rational therapeutic treatments for ABCA4-associated diseases.
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Affiliation(s)
- Robert S Molday
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, B.C., Canada; Department of Ophthalmology & Visual Sciences, University of British Columbia, Vancouver, B.C., Canada.
| | - Fabian A Garces
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, B.C., Canada
| | | | - Laurie L Molday
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, B.C., Canada
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25
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Choi H, Cloutier A, Lally D. PRPH2-Associated Macular Dystrophy in 4 Family Members with a Novel Mutation. Ophthalmic Genet 2021; 43:235-239. [PMID: 34906036 DOI: 10.1080/13816810.2021.2015790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Peripherin-2 (PRPH2) gene variants are a well-established cause of multiple inherited maculopathies including central areolar choroidal dystrophy (CACD) and pattern dystrophy. In this familial case study, we present a 63-year-old proband who presented with visual acuity of 20/63 right eye and 20/100 left eye with a complaint of lowered visual acuity in the left eye for unknown duration. Fundus examination presented with unifocal atrophic lesions bilaterally. Multi-modal imaging was obtained and genetic testing (My Retina Tracker; Blueprint Genetics) was performed. The proband was monoallelic for a novel missense mutation within the PRPH2 gene (Arg203Pro) not previously found in the literature or large databases (gnomAD, ClinVar, and HGMD). Subsequent examination of the proband's mother, older sister (65 years old), younger sister (53), and daughter (35) found the novel mutation to segregate with maculopathy ranging from speckled fundus autofluorescence with EZ disruption and RPE attenuation on spectral domain optical coherence tomography to large unifocal atrophic lesions throughout the macula bilaterally. The purpose of this case report is to add to the literature of PRPH2-associated disease by providing a comprehensive fundus examination of a family with autosomal dominant PRPH2-associated maculopathy diagnosed as central areolar choroidal dystrophy and pattern dystrophy.
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Affiliation(s)
- Hanna Choi
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA.,New England Retina Consultants, Springfield, Massachusetts, USA
| | - Alan Cloutier
- New England Retina Consultants, Springfield, Massachusetts, USA
| | - David Lally
- New England Retina Consultants, Springfield, Massachusetts, USA.,Department of Surgery, University of Massachusetts Medical School-Baystate, Springfield, Massachusetts, USA
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26
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Asaoka R, Oishi A, Fujino Y, Murata H, Azuma K, Miyata M, Obata R, Inoue T. Association between the number of visual fields and the accuracy of future prediction in eyes with retinitis pigmentosa. BMJ Open Ophthalmol 2021; 6:e000900. [PMID: 34869907 PMCID: PMC8603256 DOI: 10.1136/bmjophth-2021-000900] [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: 09/07/2021] [Accepted: 10/21/2021] [Indexed: 11/15/2022] Open
Abstract
Purpose To evaluate the minimum number of visual fields (VFs) required to precisely predict future VFs in eyes with retinitis pigmentosa (RP). Methods A series of 12 VFs (Humphrey Field Analyzer 10–2 test (8.9 years in average) were analysed from 102 eyes of 52 patients with RP. The absolute error to predict the 12th VF using the prior 11 VFs was calculated in a pointwise manner, using the linear regression, and the 95% CI range was determined. Then, using 3–10 initial VFs, next VFs (4th to 11th VFs, respectively) were also predicted. The minimum number of VFs required for the mean absolute prediction error to reach the 95% CI was identified. Similar analyses were iterated for the second and third next VF predictions. Similar analyses were conducted using mean deviation (MD). Results In the pointwise analysis, the minimum number of VFs required to reach the 95% CI for the 12th VF was five (first and second next VF predictions) and six (third next VF prediction). For the MD analysis, three (first and second next VF predictions) and four (third next VF prediction) VFs were required to reach 95% CI for the 12th VF. Conclusions The minimum number of VFs required to obtain accurate predictions of the future VF was five or six in the pointwise analysis and three or four in the analysis with MD.
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Affiliation(s)
- Ryo Asaoka
- Department of Ophthalmology, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan.,Nanovision Research Division, Research Institute of Electronics, Shizuoka University, Shizuoka, Japan.,The Graduate School for the Creation of New Photonics Industries, Shizuoka, Japan.,Seirei Christopher University, Shizuoka, Japan
| | - Akio Oishi
- Department of Ophthalmology, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Yuri Fujino
- Department of Ophthalmology, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan.,Department of Ophthalmology, Shimane University Faculty of Medicine, Izumo, Japan
| | - Hiroshi Murata
- Department of Ophthalmology, University of Tokyo, Tokyo, Japan.,Department of Ophthalmology, National Center for Global Health and Medicine, Tokyo, Japan
| | - Keiko Azuma
- Department of Ophthalmology, Graduate School of Medicine, Tokyo, Japan
| | - Manabu Miyata
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto City, Kyoto Prefecture, Japan
| | - Ryo Obata
- Department of Ophthalmology, University of Tokyo Graduate School of Medichine, Tokyo, Japan
| | - Tatsuya Inoue
- Department of Ophthalmology, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan.,Department of Ophthalmology and Micro-Technology, Yokohama City University, Kanagawa, Japan
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27
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Lee W, Zernant J, Su PY, Nagasaki T, Tsang SH, Allikmets R. A genotype-phenotype correlation matrix for Stargardt/ABCA4 disease based on long-term prognostic outcomes. JCI Insight 2021; 7:156154. [PMID: 34874912 PMCID: PMC8855796 DOI: 10.1172/jci.insight.156154] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/01/2021] [Indexed: 11/26/2022] Open
Abstract
Background More than 1500 variants in the ATP-binding cassette, sub-family A, member 4 (ABCA4), locus underlie a heterogeneous spectrum of retinal disorders ranging from aggressive childhood-onset chorioretinopathy to milder late-onset macular disease. Genotype-phenotype correlation studies have been limited in clinical applicability as patient cohorts are typically small and seldom capture the full natural history of individual genotypes. To overcome these limitations, we constructed a genotype-phenotype correlation matrix that provides quantifiable probabilities of long-term disease outcomes associated with specific ABCA4 genotypes from a large, age-restricted patient cohort. Methods The study included 112 unrelated patients at least 50 years of age in whom 2 pathogenic variants were identified after sequencing of the ABCA4 locus. Clinical characterization was performed using the results of best corrected visual acuity, retinal imaging, and full-field electroretinogram testing. Results Four distinct prognostic groups were defined according to the spatial severity of disease features across the fundus. Recurring genotypes were observed in milder prognoses, including a newly defined class of rare hypomorphic alleles. PVS1 (predicted null) variants were enriched in the most severe prognoses; however, missense variants were present in a larger-than-expected fraction of these patients. Analysis of allele combinations and their respective prognostic severity showed that certain variants, such as p.(Gly1961Glu), and both rare and frequent hypomorphic alleles, were “clinically dominant” with respect to patient phenotypes irrespective of the allele in trans. Conclusion These results provide much-needed structure to the complex genetic and clinical landscape of ABCA4 disease and add a tool to the clinical repertoire to quantitatively assess individual genotype-specific prognoses in patients. FUNDING National Eye Institute, NIH, grants R01 EY028203, R01 EY028954, R01 EY029315, P30 19007 (Core Grant for Vision Research); the Foundation Fighting Blindness USA, grant no. PPA-1218-0751-COLU; and Research to Prevent Blindness.
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Affiliation(s)
- Winston Lee
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, United States of America
| | - Jana Zernant
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, United States of America
| | - Pei-Yin Su
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, United States of America
| | - Takayuki Nagasaki
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, United States of America
| | - Stephen H Tsang
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, United States of America
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University Irving Medical Center, New York, United States of America
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28
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Asano S, Oishi A, Asaoka R, Fujino Y, Murata H, Azuma K, Miyata M, Obata R, Inoue T. Detecting Progression of Retinitis Pigmentosa Using the Binomial Pointwise Linear Regression Method. Transl Vis Sci Technol 2021; 10:15. [PMID: 34757391 PMCID: PMC8590177 DOI: 10.1167/tvst.10.13.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Purpose A method of evaluating central visual field (VF) progression in eyes with retinitis pigmentosa (RP) has still to be established. We previously reported the potential merit of applying a binomial test to pointwise linear regression (binomial PLR) in glaucoma progression. In the current study, we investigated the usefulness of binomial PLR in eyes with RP. Methods A series of 10 VFs (VF 1–10, Humphrey field analyzer, 10-2 test) from 196 eyes of 103 patients with RP were collected retrospectively. The PLR was performed by regressing the total deviation of all test points with the complete series of 10 VFs. The accuracy (positive predictive value, negative predictive value, and false-positive rate) and the time required to detect VF progression with shorter VF series (from VF 1–5 to VF 1–9) were compared across the binomial PLR, a permutation analysis of PLR (PoPLR), and a mean deviation (MD) trend analysis. Results In evaluating VF progression, the binomial PLR was comparable with the PoPLR and MD trend analyses in its positive predictive value (0.55 to 0.95), negative predictive value (0.67 to 0.92), and false-positive rate (0.01 to 0.05). The binomial PLR required significantly less time to detect VF progression (5.0 ± 2.0 years) than the PoPLR and MD trend analyses (P < 0.01, P < 0.001, respectively). Conclusions The application of a binomial PLR achieved reliable and earlier detection of central VF progression in eyes with RP. Translational Relevance A binomial PLR was useful in assessing VF progression in RP.
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Affiliation(s)
- Shotaro Asano
- Department of Ophthalmology, The University of Tokyo, Graduate School of Medicine, Tokyo, Japan.,Department of Ophthalmology, Asahi General Hospital, Asahi, Chiba, Japan
| | - Akio Oishi
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Department of Ophthalmology and Visual Sciences, Nagasaki University, Nagasaki, Japan
| | - Ryo Asaoka
- Department of Ophthalmology, The University of Tokyo, Graduate School of Medicine, Tokyo, Japan.,Department of Ophthalmology, Seirei Hamamatsu General Hospital, Shizuoka, Japan.,Seirei Christopher University, Shizuoka, Japan.,Nanovision Research Division, Research Institute of Electronics, Shizuoka University, Shizuoka, Japan.,The Graduate School for the Creation of New Photonics Industries, Shizuoka, Japan
| | - Yuri Fujino
- Department of Ophthalmology, The University of Tokyo, Graduate School of Medicine, Tokyo, Japan.,Department of Ophthalmology, Seirei Hamamatsu General Hospital, Shizuoka, Japan.,Department of Ophthalmology, Shimane University Faculty of Medicine, Izumo, Japan
| | - Hiroshi Murata
- Department of Ophthalmology, The University of Tokyo, Graduate School of Medicine, Tokyo, Japan
| | - Keiko Azuma
- Department of Ophthalmology, The University of Tokyo, Graduate School of Medicine, Tokyo, Japan
| | - Manabu Miyata
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Ryo Obata
- Department of Ophthalmology, The University of Tokyo, Graduate School of Medicine, Tokyo, Japan
| | - Tatsuya Inoue
- Department of Ophthalmology, The University of Tokyo, Graduate School of Medicine, Tokyo, Japan.,Department of Ophthalmology and Micro-Technology, Yokohama City University, Kanagawa, Japan
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29
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Schönbach EM, Janeschitz-Kriegl L, Strauss RW, Cattaneo ME, Fujinami K, Birch DG, Cideciyan AV, Sunness JS, Weleber RG, Ip MS, Sadda SR, Scholl HP. The Progression of Stargardt Disease Using Volumetric Hill of Vision Analyses Over 24 Months: ProgStar Report No.15. Am J Ophthalmol 2021; 230:123-133. [PMID: 33951446 DOI: 10.1016/j.ajo.2021.04.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/06/2021] [Accepted: 04/16/2021] [Indexed: 12/21/2022]
Abstract
PURPOSE To report the yearly rate of change in macular function in patients with Stargardt disease type 1 (STGD1) over 24 months and to establish a new volumetric visual function index for use in clinical trials investigating the efficacy on retinal sensitivity. METHODS Design: International, multicenter, prospective cohort study with 5 study visits every 6 months over 24 months. PARTICIPANTS A total of 233 individuals with genetically confirmed STGD1 (≥1 disease-causing ABCA4 variant). MAIN OUTCOME MEASURES The total volume (VTOT) beneath the sensitivity surface of a 3-D model of the hill of vision and mean sensitivity (MS) derived from mesopic microperimetry performed with a white stimulus. Changes of VTOT over time and its correlation with the ABCA4 genotype and baseline features. RESULTS At baseline, 440 eyes (233 patients) with a mean (SD) age of 33.7 (15.0) years, mean (SD) visual acuity of 46.08 (16.03) ETDRS letters were analyzed with an average VTOT of 0.91 decibel-steradian (dB-sr) and an MS of 10.73 dB. The overall mean rate of decrease in sensitivity [95% confidence interval] was 0.077 [0.064, 0.090] dB-sr/y for VTOT and 0.87 [0.72, 1.02] dB/year for MS. The progression rate of VTOT depended on baseline visual function (0.029 dB-sr/year for low and 0.120 dB-sr/year for high baseline VTOT; P < .001) and exhibited a difference in the first vs second year of follow-up (0.065 dB-sr/year vs 0.089 dB-sr/year, respectively; P < .001). The absence of pigmentary abnormalities of the retinal pigment epithelium at baseline was found to be associated with a faster progression rate (P < .001), whereas a significant association with the genotype was not detected (P = .7). CONCLUSION In STGD1, both microperimetric outcomes demonstrate statistically significant and clinically meaningful changes after relatively short follow-up periods. Volumetric modeling may be useful in future interventional clinical trials that aim to improve retinal sensitivity or to slow down its decline and for structure-function correlations.
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30
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Huang D, Heath Jeffery RC, Aung-Htut MT, McLenachan S, Fletcher S, Wilton SD, Chen FK. Stargardt disease and progress in therapeutic strategies. Ophthalmic Genet 2021; 43:1-26. [PMID: 34455905 DOI: 10.1080/13816810.2021.1966053] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background: Stargardt disease (STGD1) is an autosomal recessive retinal dystrophy due to mutations in ABCA4, characterized by subretinal deposition of lipofuscin-like substances and bilateral centrifugal vision loss. Despite the tremendous progress made in the understanding of STGD1, there are no approved treatments to date. This review examines the challenges in the development of an effective STGD1 therapy.Materials and Methods: A literature review was performed through to June 2021 summarizing the spectrum of retinal phenotypes in STGD1, the molecular biology of ABCA4 protein, the in vivo and in vitro models used to investigate the mechanisms of ABCA4 mutations and current clinical trials.Results: STGD1 phenotypic variability remains an challenge for clinical trial design and patient selection. Pre-clinical development of therapeutic options has been limited by the lack of animal models reflecting the diverse phenotypic spectrum of STDG1. Patient-derived cell lines have facilitated the characterization of splice mutations but the clinical presentation is not always predicted by the effect of specific mutations on retinoid metabolism in cellular models. Current therapies primarily aim to delay vision loss whilst strategies to restore vision are less well developed.Conclusions: STGD1 therapy development can be accelerated by a deeper understanding of genotype-phenotype correlations.
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Affiliation(s)
- Di Huang
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Western Australia, Australia.,Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), the University of Western Australia, Nedlands, Western Australia, Australia.,Perron Institute for Neurological and Translational Science & the University of Western Australia, Nedlands, Western Australia, Australia
| | - Rachael C Heath Jeffery
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), the University of Western Australia, Nedlands, Western Australia, Australia
| | - May Thandar Aung-Htut
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Western Australia, Australia.,Perron Institute for Neurological and Translational Science & the University of Western Australia, Nedlands, Western Australia, Australia
| | - Samuel McLenachan
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), the University of Western Australia, Nedlands, Western Australia, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Western Australia, Australia.,Perron Institute for Neurological and Translational Science & the University of Western Australia, Nedlands, Western Australia, Australia
| | - Steve D Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Western Australia, Australia.,Perron Institute for Neurological and Translational Science & the University of Western Australia, Nedlands, Western Australia, Australia
| | - Fred K Chen
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), the University of Western Australia, Nedlands, Western Australia, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia.,Department of Ophthalmology, Royal Perth Hospital, Perth, Western Australia, Australia.,Department of Ophthalmology, Perth Children's Hospital, Nedlands, Western Australia, Australia
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Al-Khuzaei S, Broadgate S, Foster CR, Shah M, Yu J, Downes SM, Halford S. An Overview of the Genetics of ABCA4 Retinopathies, an Evolving Story. Genes (Basel) 2021; 12:1241. [PMID: 34440414 PMCID: PMC8392661 DOI: 10.3390/genes12081241] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 11/16/2022] Open
Abstract
Stargardt disease (STGD1) and ABCA4 retinopathies (ABCA4R) are caused by pathogenic variants in the ABCA4 gene inherited in an autosomal recessive manner. The gene encodes an importer flippase protein that prevents the build-up of vitamin A derivatives that are toxic to the RPE. Diagnosing ABCA4R is complex due to its phenotypic variability and the presence of other inherited retinal dystrophy phenocopies. ABCA4 is a large gene, comprising 50 exons; to date > 2000 variants have been described. These include missense, nonsense, splicing, structural, and deep intronic variants. Missense variants account for the majority of variants in ABCA4. However, in a significant proportion of patients with an ABCA4R phenotype, a second variant in ABCA4 is not identified. This could be due to the presence of yet unknown variants, or hypomorphic alleles being incorrectly classified as benign, or the possibility that the disease is caused by a variant in another gene. This underlines the importance of accurate genetic testing. The pathogenicity of novel variants can be predicted using in silico programs, but these rely on databases that are not ethnically diverse, thus highlighting the need for studies in differing populations. Functional studies in vitro are useful towards assessing protein function but do not directly measure the flippase activity. Obtaining an accurate molecular diagnosis is becoming increasingly more important as targeted therapeutic options become available; these include pharmacological, gene-based, and cell replacement-based therapies. The aim of this review is to provide an update on the current status of genotyping in ABCA4 and the status of the therapeutic approaches being investigated.
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Affiliation(s)
- Saoud Al-Khuzaei
- Oxford Eye Hospital, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK; (S.A.-K.); (M.S.)
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Level 6 John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (S.B.); (J.Y.)
| | - Suzanne Broadgate
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Level 6 John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (S.B.); (J.Y.)
| | | | - Mital Shah
- Oxford Eye Hospital, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK; (S.A.-K.); (M.S.)
| | - Jing Yu
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Level 6 John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (S.B.); (J.Y.)
| | - Susan M. Downes
- Oxford Eye Hospital, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK; (S.A.-K.); (M.S.)
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Level 6 John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (S.B.); (J.Y.)
| | - Stephanie Halford
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Level 6 John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (S.B.); (J.Y.)
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García Bohórquez B, Aller E, Rodríguez Muñoz A, Jaijo T, García García G, Millán JM. Updating the Genetic Landscape of Inherited Retinal Dystrophies. Front Cell Dev Biol 2021; 9:645600. [PMID: 34327195 PMCID: PMC8315279 DOI: 10.3389/fcell.2021.645600] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/30/2021] [Indexed: 12/24/2022] Open
Abstract
Inherited retinal dystrophies (IRD) are a group of diseases characterized by the loss or dysfunction of photoreceptors and a high genetic and clinical heterogeneity. Currently, over 270 genes have been associated with IRD which makes genetic diagnosis very difficult. The recent advent of next generation sequencing has greatly facilitated the diagnostic process, enabling to provide the patients with accurate genetic counseling in some cases. We studied 92 patients who were clinically diagnosed with IRD with two different custom panels. In total, we resolved 53 patients (57.6%); in 12 patients (13%), we found only one mutation in a gene with a known autosomal recessive pattern of inheritance; and 27 patients (29.3%) remained unsolved. We identified 120 pathogenic or likely pathogenic variants; 30 of them were novel. Among the cone-rod dystrophy patients, ABCA4 was the most common mutated gene, meanwhile, USH2A was the most prevalent among the retinitis pigmentosa patients. Interestingly, 10 families carried pathogenic variants in more than one IRD gene, and we identified two deep-intronic variants previously described as pathogenic in ABCA4 and CEP290. In conclusion, the IRD study through custom panel sequencing demonstrates its efficacy for genetic diagnosis, as well as the importance of including deep-intronic regions in their design. This genetic diagnosis will allow patients to make accurate reproductive decisions, enroll in gene-based clinical trials, and benefit from future gene-based treatments.
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Affiliation(s)
- Belén García Bohórquez
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- CIBER of Rare Diseases, Madrid, Spain
| | - Elena Aller
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- CIBER of Rare Diseases, Madrid, Spain
- Unit of Genetics, University Hospital La Fe, Valencia, Spain
| | - Ana Rodríguez Muñoz
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- CIBER of Rare Diseases, Madrid, Spain
| | - Teresa Jaijo
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- CIBER of Rare Diseases, Madrid, Spain
- Unit of Genetics, University Hospital La Fe, Valencia, Spain
| | - Gema García García
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- CIBER of Rare Diseases, Madrid, Spain
| | - José M. Millán
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- CIBER of Rare Diseases, Madrid, Spain
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Absence of Genotype/Phenotype Correlations Requires Molecular Diagnostic to Ascertain Stargardt and Stargardt-Like Swiss Patients. Genes (Basel) 2021; 12:genes12060812. [PMID: 34073554 PMCID: PMC8229718 DOI: 10.3390/genes12060812] [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: 05/04/2021] [Revised: 05/20/2021] [Accepted: 05/25/2021] [Indexed: 11/25/2022] Open
Abstract
We genetically characterized 22 Swiss patients who had been diagnosed with Stargardt disease after clinical examination. We identified in 11 patients (50%) pathogenic bi-allelic ABCA4 variants, c.1760+2T>C and c.4496T>C being novel. The dominantly inherited pathogenic ELOVL4 c.810C>G p.(Tyr270*) and PRPH2-c.422A>G p.(Tyr141Cys) variants were identified in eight (36%) and three patients (14%), respectively. All patients harboring the ELOVL4 c.810C>G p.(Tyr270*) variant originated from the same small Swiss area, identifying a founder mutation. In the ABCA4 and ELOVL4 cohorts, the clinical phenotypes of “flecks”, “atrophy”, and “bull’s eye like” were observed by fundus examination. In the small number of patients harboring the pathogenic PRPH2 variant, we could observe both “flecks” and “atrophy” clinical phenotypes. The onset of disease, progression of visual acuity and clinical symptoms, inheritance patterns, fundus autofluorescence, and optical coherence tomography did not allow discrimination between the genetically heterogeneous Stargardt patients. The genetic heterogeneity observed in the relatively small Swiss population should prompt systematic genetic testing of clinically diagnosed Stargardt patients. The resulting molecular diagnostic is required to prevent potentially harmful vitamin A supplementation, to provide genetic counseling with respect to inheritance, and to schedule appropriate follow-up visits in the presence of increased risk of choroidal neovascularization.
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Thorsteinsson DA, Stefansdottir V, Eysteinsson T, Thorisdottir S, Jonsson JJ. Molecular genetics of inherited retinal degenerations in Icelandic patients. Clin Genet 2021; 100:156-167. [PMID: 33851411 PMCID: PMC8360171 DOI: 10.1111/cge.13967] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 04/07/2021] [Accepted: 04/10/2021] [Indexed: 12/22/2022]
Abstract
The study objective was to delineate the genetics of inherited retinal degenerations (IRDs) in Iceland, a small nation of 364.000 and a genetic isolate. Benefits include delineating novel pathogenic genetic variants and defining genetically homogenous patients as potential investigative molecular therapy candidates. The study sample comprised patients with IRD in Iceland ascertained through national centralized genetic and ophthalmological services at Landspitali, a national social support institute, and the Icelandic patient association. Information on patients' disease, syndrome, and genetic testing was collected in a clinical registry. Variants were reevaluated according to ACMG/AMP guidelines. Overall, 140 IRD patients were identified (point prevalence of 1/2.600), of which 70 patients had a genetic evaluation where two-thirds had an identified genetic cause. Thirteen disease genes were found in patients with retinitis pigmentosa, with the RLBP1 gene most common (n = 4). The c.1073 + 5G > A variant in the PRPF31 gene was homozygous in two RP patients. All tested patients with X-linked retinoschisis (XLRS) had the same possibly unique RS1 pathogenic variant, c.441G > A (p.Trp147X). Pathologic variants and genes for IRDs in Iceland did not resemble those described in ancestral North-Western European nations. Four variants were reclassified as likely pathogenic. One novel pathogenic variant defined a genetically homogenous XLRS patient group.
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Affiliation(s)
| | - Vigdis Stefansdottir
- Department of Genetics and Molecular Medicine, Landspitali - National University Hospital of Iceland, Reykjavik, Iceland
| | - Thor Eysteinsson
- Department of Physiology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland.,Department of Ophthalmology, Landspitali - National University Hospital of Iceland, Reykjavik, Iceland
| | - Sigridur Thorisdottir
- Department of Ophthalmology, Landspitali - National University Hospital of Iceland, Reykjavik, Iceland
| | - Jon J Jonsson
- Department of Genetics and Molecular Medicine, Landspitali - National University Hospital of Iceland, Reykjavik, Iceland.,Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
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Lee W, Zernant J, Nagasaki T, Molday LL, Su PY, Fishman GA, Tsang SH, Molday RS, Allikmets R. Cis-acting modifiers in the ABCA4 locus contribute to the penetrance of the major disease-causing variant in Stargardt disease. Hum Mol Genet 2021; 30:1293-1304. [PMID: 33909047 DOI: 10.1093/hmg/ddab122] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/01/2021] [Accepted: 04/20/2021] [Indexed: 11/14/2022] Open
Abstract
Over 1200 variants in the ABCA4 gene cause a wide variety of retinal disease phenotypes, the best known of which is autosomal recessive Stargardt disease (STGD1). Disease-causing variation encompasses all mutation categories, from large copy number variants to very mild, hypomorphic missense variants. The most prevalent disease-causing ABCA4 variant, present in ~ 20% of cases of European descent, c.5882G > A p.(Gly1961Glu), has been a subject of controversy since its minor allele frequency (MAF) is as high as ~ 0.1 in certain populations, questioning its pathogenicity, especially in homozygous individuals. We sequenced the entire ~140Kb ABCA4 genomic locus in an extensive cohort of 644 bi-allelic, i.e. genetically confirmed, patients with ABCA4 disease and analyzed all variants in 140 compound heterozygous and 10 homozygous cases for the p.(Gly1961Glu) variant. A total of 23 patients in this cohort additionally harbored the deep intronic c.769-784C > T variant on the p.(Gly1961Glu) allele, which appears on a specific haplotype in ~ 15% of p.(Gly1961Glu) alleles. This haplotype was present in 5/7 of homozygous cases, where the p.(Gly1961Glu) was the only known pathogenic variant. Three cases had an exonic variant on the same allele with the p.(Gly1961Glu). Patients with the c.[769-784C > T;5882G > A] complex allele exhibit a more severe clinical phenotype, as seen in compound heterozygotes with some more frequent ABCA4 mutations, e.g. p.(Pro1380Leu). Our findings indicate that the c.769-784C > T variant is major cis-acting modifier of the p.(Gly1961Glu) allele. The absence of such additional allelic variation on most p.(Gly1961Glu) alleles largely explains the observed paucity of affected homozygotes in the population.
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Affiliation(s)
- Winston Lee
- Department of Genetics & Development, Columbia University, New York, NY 10032, USA
- Department of Ophthalmology, Columbia University, New York, NY 10032, USA
| | - Jana Zernant
- Department of Ophthalmology, Columbia University, New York, NY 10032, USA
| | - Takayuki Nagasaki
- Department of Ophthalmology, Columbia University, New York, NY 10032, USA
| | - Laurie L Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Pei-Yin Su
- Department of Ophthalmology, Columbia University, New York, NY 10032, USA
| | - Gerald A Fishman
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- The Pangere Center for Inherited Retinal Diseases, The Chicago Lighthouse, Chicago, IL 60608, USA
| | - Stephen H Tsang
- Department of Ophthalmology, Columbia University, New York, NY 10032, USA
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
| | - Robert S Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, NY 10032, USA
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
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Tomkiewicz TZ, Suárez-Herrera N, Cremers FPM, Collin RWJ, Garanto A. Antisense Oligonucleotide-Based Rescue of Aberrant Splicing Defects Caused by 15 Pathogenic Variants in ABCA4. Int J Mol Sci 2021; 22:ijms22094621. [PMID: 33924840 PMCID: PMC8124656 DOI: 10.3390/ijms22094621] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/16/2022] Open
Abstract
The discovery of novel intronic variants in the ABCA4 locus has contributed significantly to solving the missing heritability in Stargardt disease (STGD1). The increasing number of variants affecting pre-mRNA splicing makes ABCA4 a suitable candidate for antisense oligonucleotide (AON)-based splicing modulation therapies. In this study, AON-based splicing modulation was assessed for 15 recently described intronic variants (three near-exon and 12 deep-intronic variants). In total, 26 AONs were designed and tested in vitro using a midigene-based splice system. Overall, partial or complete splicing correction was observed for two variants causing exon elongation and all variants causing pseudoexon inclusion. Together, our results confirm the high potential of AONs for the development of future RNA therapies to correct splicing defects causing STGD1.
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Affiliation(s)
- Tomasz Z. Tomkiewicz
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands; (T.Z.T.); (N.S.-H.); (F.P.M.C.); (R.W.J.C.)
| | - Nuria Suárez-Herrera
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands; (T.Z.T.); (N.S.-H.); (F.P.M.C.); (R.W.J.C.)
| | - Frans P. M. Cremers
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands; (T.Z.T.); (N.S.-H.); (F.P.M.C.); (R.W.J.C.)
| | - Rob W. J. Collin
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands; (T.Z.T.); (N.S.-H.); (F.P.M.C.); (R.W.J.C.)
| | - Alejandro Garanto
- Departments of Pediatrics and Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands
- Correspondence:
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Camp DA, Gemayel MC, Ciulla TA. Understanding the genetic pathology of Stargardt disease: a review of current findings and challenges. Expert Opin Orphan Drugs 2021. [DOI: 10.1080/21678707.2021.1898373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- David A. Camp
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Michael C. Gemayel
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Thomas A. Ciulla
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN, USA
- Retina Service, Midwest Eye Institute, Indianapolis, IN, USA
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de Bruijn SE, Fadaie Z, Cremers FPM, Kremer H, Roosing S. The Impact of Modern Technologies on Molecular Diagnostic Success Rates, with a Focus on Inherited Retinal Dystrophy and Hearing Loss. Int J Mol Sci 2021; 22:2943. [PMID: 33799353 PMCID: PMC7998853 DOI: 10.3390/ijms22062943] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/04/2021] [Accepted: 03/09/2021] [Indexed: 02/07/2023] Open
Abstract
The identification of pathogenic variants in monogenic diseases has been of interest to researchers and clinicians for several decades. However, for inherited diseases with extremely high genetic heterogeneity, such as hearing loss and retinal dystrophies, establishing a molecular diagnosis requires an enormous effort. In this review, we use these two genetic conditions as examples to describe the initial molecular genetic identification approaches, as performed since the early 90s, and subsequent improvements and refinements introduced over the years. Next, the history of DNA sequencing from conventional Sanger sequencing to high-throughput massive parallel sequencing, a.k.a. next-generation sequencing, is outlined, including their advantages and limitations and their impact on identifying the remaining genetic defects. Moreover, the development of recent technologies, also coined "third-generation" sequencing, is reviewed, which holds the promise to overcome these limitations. Furthermore, we outline the importance and complexity of variant interpretation in clinical diagnostic settings concerning the massive number of different variants identified by these methods. Finally, we briefly mention the development of novel approaches such as optical mapping and multiomics, which can help to further identify genetic defects in the near future.
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Affiliation(s)
- Suzanne E. de Bruijn
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (S.E.d.B.); (Z.F.); (F.P.M.C.)
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands;
| | - Zeinab Fadaie
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (S.E.d.B.); (Z.F.); (F.P.M.C.)
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands;
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (S.E.d.B.); (Z.F.); (F.P.M.C.)
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands;
| | - Hannie Kremer
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands;
- Department of Otorhinolaryngology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; (S.E.d.B.); (Z.F.); (F.P.M.C.)
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands;
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Al-Ani HH, Sheck L, Vincent AL. Peripheral pigmented lesions in ABCA4-associated retinopathy. Ophthalmic Genet 2021; 42:383-391. [PMID: 33706644 DOI: 10.1080/13816810.2021.1897850] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Purpose: To investigate the prevalence and characteristics of peripheral pigmented retinal lesions and the associated clinical and genetic findings in patients with pathogenic variants in the ABCA4 gene.Methods: Records at a single tertiary hospital were retrospectively reviewed to identify the presence of peripheral pigmented retinal lesions on wide-field retinal imaging in patients with ABCA4-associated disease, compared with an RDS/PRPH2 cohort, and an age-matched control group. Data on patient demographics, genetic variants, severity of disease, and phenotype were collected and assessed.Results: Of 91 patients with at least one pathogenic variant in the ABCA4 gene and fundal changes consistent with ABCA4 retinal dystrophy, 15 (16.5%) had peripheral pigmented retinal lesions in 20 eyes, and were bilateral in 6 patients. These flat, subretinal lesions were located in the mid- or far periphery, not involving the macula, and had well-defined borders. Most affected eyes had a solitary lesion (n = 18) with lesions more commonly present in the temporal half of the retina. Twenty-one unique genetic variants in ABCA4 were associated with these lesions. In 26 subjects (52 eyes) with RDS/PRPH-2-associated IRD, and in 30 age-matched controls (60 eyes), only one control eye had a pigmented lesion consistent with congenital hypertrophy of the retinal pigment epithelium and there were no peripheral pigmented lesions.Conclusions: Almost one-fifth of patients with ABCA4-associated retinopathy have peripheral pigmented retinal lesions. The presence of these lesions is associated with more severe disease with an earlier onset than in patients without the lesions, and is an aid to diagnosis.
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Affiliation(s)
- Haya H Al-Ani
- Eye Department, Greenlane Clinical Centre, Auckland District Health Board, Auckland, New Zealand.,Department of Ophthalmology, FMHS, New Zealand National Eye Centre, University of Auckland, Auckland, New Zealand
| | - Leo Sheck
- Eye Department, Greenlane Clinical Centre, Auckland District Health Board, Auckland, New Zealand
| | - Andrea L Vincent
- Eye Department, Greenlane Clinical Centre, Auckland District Health Board, Auckland, New Zealand.,Department of Ophthalmology, FMHS, New Zealand National Eye Centre, University of Auckland, Auckland, New Zealand
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40
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Runhart EH, Khan M, Cornelis SS, Roosing S, Del Pozo-Valero M, Lamey TM, Liskova P, Roberts L, Stöhr H, Klaver CCW, Hoyng CB, Cremers FPM, Dhaenens CM. Association of Sex With Frequent and Mild ABCA4 Alleles in Stargardt Disease. JAMA Ophthalmol 2021; 138:1035-1042. [PMID: 32815999 DOI: 10.1001/jamaophthalmol.2020.2990] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Importance The mechanisms behind the phenotypic variability and reduced penetrance in autosomal recessive Stargardt disease (STGD1), often a blinding disease, are poorly understood. Identification of the unknown disease modifiers can improve patient and family counseling and provide valuable information for disease management. Objective To assess the association of incompletely penetrant ABCA4 alleles with sex in STGD1. Design, Setting, and Participants Genetic data for this cross-sectional study were obtained from 2 multicenter genetic studies of 1162 patients with clinically suspected STGD1. Unrelated patients with genetically confirmed STGD1 were selected. The data were collected from June 2016 to June 2019, and post hoc analysis was performed between July 2019 and January 2020. Main Outcomes and Measures Penetrance of reported mild ABCA4 variants was calculated by comparing the allele frequencies in the general population (obtained from the Genome Aggregation Database) with the genotyping data in the patient population (obtained from the ABCA4 Leiden Open Variation Database). The sex ratio among patients with and patients without an ABCA4 allele with incomplete penetrance was assessed. Results A total of 550 patients were included in the study, among which the mean (SD) age was 45.7 (18.0) years and most patients were women (311 [57%]). Five of the 5 mild ABCA4 alleles, including c.5603A>T and c.5882G>A, were calculated to have incomplete penetrance. The women to men ratio in the subgroup carrying c.5603A>T was 1.7 to 1; the proportion of women in this group was higher compared with the subgroup not carrying a mild allele (difference, 13%; 95% CI, 3%-23%; P = .02). The women to men ratio in the c.5882G>A subgroup was 2.1 to 1, and the women were overrepresented compared with the group carrying no mild allele (difference, 18%; 95% CI, 6%-30%; P = .005). Conclusions and Relevance This study found an imbalance in observed sex ratio among patients harboring a mild ABCA4 allele, which concerns approximately 25% of all patients with STGD1, suggesting that STGD1 should be considered a polygenic or multifactorial disease rather than a disease caused by ABCA4 gene mutations alone. The findings suggest that sex should be considered as a potential disease-modifying variable in both basic research and clinical trials on STGD1.
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Affiliation(s)
- Esmee H Runhart
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands.,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Mubeen Khan
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Stéphanie S Cornelis
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Susanne Roosing
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marta Del Pozo-Valero
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Tina M Lamey
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Nedlands, Western Australia, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Petra Liskova
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic.,Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Lisa Roberts
- University of Cape Town/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Heidi Stöhr
- Institute of Human Genetics, University of Regensburg, Regensburg, Germany
| | - Caroline C W Klaver
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands.,Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands.,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Frans P M Cremers
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Claire-Marie Dhaenens
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,University Lille, Inserm, CHU Lille, U1172-LilNCog-Lille Neuroscience & Cognition, Lille, France
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Garces FA, Scortecci JF, Molday RS. Functional Characterization of ABCA4 Missense Variants Linked to Stargardt Macular Degeneration. Int J Mol Sci 2020; 22:ijms22010185. [PMID: 33375396 PMCID: PMC7796138 DOI: 10.3390/ijms22010185] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 12/17/2022] Open
Abstract
ABCA4 is an ATP-binding cassette (ABC) transporter expressed in photoreceptors, where it transports its substrate, N-retinylidene-phosphatidylethanolamine (N-Ret-PE), across outer segment membranes to facilitate the clearance of retinal from photoreceptors. Mutations in ABCA4 cause Stargardt macular degeneration (STGD1), an autosomal recessive disorder characterized by a loss of central vision and the accumulation of bisretinoid compounds. The purpose of this study was to determine the molecular properties of ABCA4 variants harboring disease-causing missense mutations in the transmembrane domains. Thirty-eight variants expressed in culture cells were analyzed for expression, ATPase activities, and substrate binding. On the basis of these properties, the variants were divided into three classes: Class 1 (severe variants) exhibited significantly reduced ABCA4 expression and basal ATPase activity that was not stimulated by its substrate N-Ret-PE; Class 2 (moderate variants) showed a partial reduction in expression and basal ATPase activity that was modestly stimulated by N-Ret-PE; and Class 3 (mild variants) displayed expression and functional properties comparable to normal ABCA4. The p.R653C variant displayed normal expression and basal ATPase activity, but lacked substrate binding and ATPase activation, suggesting that arginine 653 contributes to N-Ret-PE binding. Our classification provides a basis for better understanding genotype–phenotype correlations and evaluating therapeutic treatments for STGD1.
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Affiliation(s)
- Fabian A. Garces
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (F.A.G.); (J.F.S.)
| | - Jessica F. Scortecci
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (F.A.G.); (J.F.S.)
| | - Robert S. Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (F.A.G.); (J.F.S.)
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, BC V5Z 3N9, Canada
- Correspondence: ; Tel.: +1-604-822-6173
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42
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Starace V, Battista M, Brambati M, Pederzolli M, Viganò C, Arrigo A, Cicinelli MV, Bandello F, Parodi MB. Genotypic and phenotypic factors influencing the rate of progression in ABCA-4-related Stargardt disease. EXPERT REVIEW OF OPHTHALMOLOGY 2020. [DOI: 10.1080/17469899.2021.1860753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Vincenzo Starace
- Department of Ophthalmology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marco Battista
- Department of Ophthalmology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maria Brambati
- Department of Ophthalmology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Matteo Pederzolli
- Department of Ophthalmology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Chiara Viganò
- Department of Ophthalmology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alessandro Arrigo
- Department of Ophthalmology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maria Vittoria Cicinelli
- Department of Ophthalmology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
| | - Francesco Bandello
- Department of Ophthalmology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
| | - Maurizio Battaglia Parodi
- Department of Ophthalmology, IRCCS San Raffaele Scientific Institute, Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Milan, Italy
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43
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Sun Z, Yang L, Li H, Zou X, Wang L, Wu S, Zhu T, Wei X, Zhong Y, Sui R. Clinical and genetic analysis of the ABCA4 gene associated retinal dystrophy in a large Chinese cohort. Exp Eye Res 2020; 202:108389. [PMID: 33301772 DOI: 10.1016/j.exer.2020.108389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/30/2020] [Accepted: 12/04/2020] [Indexed: 12/31/2022]
Abstract
ABCA4 gene associated retinal dystrophies (ABCA4-RD) are a group of inherited eye diseases caused by ABCA4 gene mutations, including Stargardt disease, cone-rod dystrophy and retinitis pigmentosa. With the development of next-generation sequencing (NGS), numerous clinical and genetic studies on ABCA4-RD have been performed, and the genotype and phenotype spectra have been elucidated. However, most of the studies focused on the Caucasian population and limited studies of large Chinese ABCA4-RD cohorts were reported. In this study, we summarized the phenotypic and genotypic characteristics of 129 Chinese patients with ABCA4-RD. We found a mutation spectrum of Chinese patients which is considerably different from that of the Caucasian population and identified 35 novel ABCA4 mutations. We also reported some rare and special cases, such as, pedigrees with patients in two generations, patients diagnosed with cone-rod dystrophy or retinitis pigmentosa, patients with subretinal fibrosis and patients with preserved foveal structure. At the same time, we focused on the correlation between the genotypes and phenotypes. By the comprehensive analysis of multiple clinical examinations and the application of multiple regression analysis, we proved that patients with two "null" variants had a younger onset age and reached legal blindness earlier than patients with two "none-null" variants. Patients with one or more "none-null" variants tended to have better visual acuity and presented with milder fundus autofluorescence changes and more preserved rod functions on the full-field electroretinography than patients with two "null" variants. Furthermore, most patients with the p.(Phe2188Ser) variant shared a mild phenotype with a low fundus autofluorescence signal limited to the fovea and with normal full-field electroretinography responses. Our findings expand the variant spectrum of the ABCA4 gene and enhance the knowledge of Chinese patients with ABCA4-RD.
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Affiliation(s)
- Zixi Sun
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Lizhu Yang
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China; Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization, Tokyo Medical Center, Tokyo, 152-8902, Japan; Department of Ophthalmology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Hui Li
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xuan Zou
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Lei Wang
- Beijing Mei'ermu Hospital, Beijing, China
| | - Shijing Wu
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Tian Zhu
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xing Wei
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Yong Zhong
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Ruifang Sui
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China.
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Evidence of complement dysregulation in outer retina of Stargardt disease donor eyes. Redox Biol 2020; 37:101787. [PMID: 33214125 PMCID: PMC7767765 DOI: 10.1016/j.redox.2020.101787] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/30/2020] [Accepted: 11/03/2020] [Indexed: 01/24/2023] Open
Abstract
Stargardt macular degeneration (STGD) is a central blinding disease caused by loss of or dysfunctional ABCA4 transporter in both photoreceptors and retinal pigment epithelial (RPE) cells. Toxic bisretinoid-lipofuscin buildup in the RPE cells is a pathological hallmark of STGD patients and its mouse model, the Abca4-/-. These vitamin A-derived fluorophores have been shown to induce oxidative stress, stimulate complement activity, and cause chronic inflammation of the RPE. In vivo modulation of complement regulatory pathway in the STGD mouse model has partially rescued the STGD phenotype suggesting that complement attack on the RPE is an important etiologic factor in disease pathogenesis. While bisretinoid-dependent complement activation was further evidenced in cultured RPE cells, this pathway has never been investigated directly in the context of RPE from STGD donor eyes. In the current study, we evaluate the complement reactivity in postmortem donor eyes of clinically diagnosed STGD patients. All three STGD donor eyes RPE displayed strong immunoreactivity for an antibody specific to 4-Hydroxynonenal, a lipid peroxidation byproduct. Also, unlike the control eyes, all three STGD donor eyes showed significantly increased membrane attack complex deposition on the RPE cells. In STGD eyes, increased MAC accumulation was mirrored by elevated C3 fragments internalized by the RPE and inversely correlated with the levels of complement factor H, a major complement regulatory protein. Here, we report the first direct evidence of RPE complement dysregulation as a causative factor in developing Stargardt phenotype.
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45
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Del Pozo-Valero M, Riveiro-Alvarez R, Blanco-Kelly F, Aguirre-Lamban J, Martin-Merida I, Iancu IF, Swafiri S, Lorda-Sanchez I, Rodriguez-Pinilla E, Trujillo-Tiebas MJ, Jimenez-Rolando B, Carreño E, Mahillo-Fernandez I, Rivolta C, Corton M, Avila-Fernandez A, Garcia-Sandoval B, Ayuso C. Genotype-Phenotype Correlations in a Spanish Cohort of 506 Families With Biallelic ABCA4 Pathogenic Variants. Am J Ophthalmol 2020; 219:195-204. [PMID: 32619608 DOI: 10.1016/j.ajo.2020.06.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/19/2020] [Accepted: 06/21/2020] [Indexed: 01/28/2023]
Abstract
PURPOSE To define genotype-phenotype correlations in the largest cohort study worldwide of patients with biallelic ABCA4 variants, including 434 patients with Stargardt disease (STGD1) and 72 with cone-rod dystrophy (CRD). DESIGN Cohort study. METHODS We characterized 506 patients with ABCA4 variants using conventional genetic tools and next-generation sequencing technologies. Medical history and ophthalmologic data were obtained from 372 patients. Genotype-phenotype correlation studies were carried out for the following variables: variant type, age at symptom onset (AO), and clinical phenotype. RESULTS A total of 228 different pathogenic variants were identified in 506 ABCA4 patients, 50 of which were novel. Genotype-phenotype correlations showed that most of the patients with biallelic truncating variants presented with CRD and that these cases had a significantly earlier AO than patients with STGD1. Three missense variants are associated with CRD for the first time (c.1804C>T; p.[Arg602Trp], c.3056C>T; p.[Thr1019Met], and c.6320G>C; p.[Arg2107Pro]). Analysis of the most prevalent ABCA4 variant in Spain, c.3386G>T; p.(Arg1129Leu), revealed that is correlated to STGD1, later AO, and foveal sparing. CONCLUSIONS Our study, conducted in the largest ABCA4-associated disease cohort reported to date, updates the genotype-phenotype model established for ABCA4 variants and broadens the mutational spectrum of the gene. According to our observations, patients with ABCA4 presenting with 2 truncating variants may first present features of STGD1 but eventually develop rod dysfunction, and specific missense variants may be associated with a different phenotype, underscoring the importance of an accurate genetic diagnosis. Also, it is a prerequisite for enrollment in clinical trials, and to date, no other treatment has been approved for STGD1.
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Affiliation(s)
- Marta Del Pozo-Valero
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Rosa Riveiro-Alvarez
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Fiona Blanco-Kelly
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Jana Aguirre-Lamban
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain
| | - Inmaculada Martin-Merida
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Ionut-Florin Iancu
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Saoud Swafiri
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Isabel Lorda-Sanchez
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain
| | - Elvira Rodriguez-Pinilla
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain
| | - Maria José Trujillo-Tiebas
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Belen Jimenez-Rolando
- Department of Ophthalmology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ester Carreño
- Department of Ophthalmology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ignacio Mahillo-Fernandez
- Department of Epidemiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Marta Corton
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Almudena Avila-Fernandez
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Blanca Garcia-Sandoval
- Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain; Department of Ophthalmology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid, Spain; Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain.
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Ellingford JM, Hufnagel RB, Arno G. Phenotype and Genotype Correlations in Inherited Retinal Diseases: Population-Guided Variant Interpretation, Variable Expressivity and Incomplete Penetrance. Genes (Basel) 2020; 11:genes11111274. [PMID: 33137882 PMCID: PMC7692259 DOI: 10.3390/genes11111274] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 10/23/2020] [Accepted: 10/25/2020] [Indexed: 12/15/2022] Open
Affiliation(s)
- Jamie M. Ellingford
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WL, UK
- Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
- Correspondence: (J.M.E.); (R.B.H.); (G.A.)
| | - Robert B. Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD 20016, USA
- Correspondence: (J.M.E.); (R.B.H.); (G.A.)
| | - Gavin Arno
- University College London Institute of Ophthalmology, London EC1V 9EL, UK
- Moorfields Eye Hospital, London EC1V 2PD, UK
- Correspondence: (J.M.E.); (R.B.H.); (G.A.)
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47
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Curtis SB, Molday LL, Garces FA, Molday RS. Functional analysis and classification of homozygous and hypomorphic ABCA4 variants associated with Stargardt macular degeneration. Hum Mutat 2020; 41:1944-1956. [PMID: 32845050 DOI: 10.1002/humu.24100] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/06/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022]
Abstract
Stargardt macular degeneration (Stargardt disease 1 [STGD1]) is caused by mutations in the gene encoding ABCA4, an ATP-binding cassette protein that transports N-retinylidene-phosphatidylethanolamine (N-Ret-PE) across photoreceptor membranes. Reduced ABCA4 activity results in retinoid accumulation leading to photoreceptor degeneration. The disease onset and severity vary from severe loss in visual acuity in the first decade to mild visual impairment late in life. We determined the effect of 22 disease-causing missense mutations on the expression and ATPase activity of ABCA4 in the absence and presence of N-Ret-PE. Three classes were identified that correlated with the disease onset in homozygous STGD1 individuals: Class 1 exhibited reduced ABCA4 expression and ATPase activity that was not stimulated by N-Ret-PE; individuals homozygous for these variants had an early disease onset (≤13 years); Class 2 showed reduced ATPase activity with limited stimulation by N-Ret-PE; these correlated with moderate disease onset (14-40 years); and Class 3 displayed high expression and ATPase activity that was strongly activated by N-Ret-PE; these were associated with late disease onset (>40 years). On the basis of our results, we introduce a functionality index for gauging the effect of missense mutations on STGD1 severity. Our studies support the mild phenotype exhibited by the p.Gly863Ala, p.Asn1868Ile, and p.Gly863Ala/p.Asn1868Ile variants.
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Affiliation(s)
- Susan B Curtis
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Laurie L Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Fabian A Garces
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert S Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, British Columbia, Canada
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48
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Khan M, Arno G, Fakin A, Parfitt DA, Dhooge PPA, Albert S, Bax NM, Duijkers L, Niblock M, Hau KL, Bloch E, Schiff ER, Piccolo D, Hogden MC, Hoyng CB, Webster AR, Cremers FPM, Cheetham ME, Garanto A, Collin RWJ. Detailed Phenotyping and Therapeutic Strategies for Intronic ABCA4 Variants in Stargardt Disease. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:412-427. [PMID: 32653833 PMCID: PMC7352060 DOI: 10.1016/j.omtn.2020.06.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/15/2020] [Accepted: 06/09/2020] [Indexed: 01/17/2023]
Abstract
Stargardt disease is a progressive retinal disorder caused by bi-allelic mutations in the ABCA4 gene that encodes the ATP-binding cassette, subfamily A, member 4 transporter protein. Over the past few years, we and others have identified several pathogenic variants that reside within the introns of ABCA4, including a recurrent variant in intron 36 (c.5196+1137G>A) of which the pathogenicity so far remained controversial. Detailed clinical characterization of this variant confirmed its pathogenic nature, and classified it as an allele of intermediate severity. Moreover, we discovered several additional ABCA4 variants clustering in intron 36. Several of these variants resulted in aberrant splicing of ABCA4, i.e., the inclusion of pseudoexons, while the splicing defects caused by the recurrent c.5196+1137G>A variant strongly increased upon differentiation of patient-derived induced pluripotent stem cells into retina-like cells. Finally, all splicing defects could be rescued by the administration of antisense oligonucleotides that were designed to specifically block the pseudoexon insertion, including rescue in 3D retinal organoids harboring the c.5196+1137G>A variant. Our data illustrate the importance of intronic variants in ABCA4 and expand the therapeutic possibilities for overcoming splicing defects in Stargardt disease.
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Affiliation(s)
- Mubeen Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Gavin Arno
- UCL Institute for Ophthalmology, London, UK; Moorfields Eye Hospital, London, UK; Great Ormond Street Hospital for Children, London, UK
| | - Ana Fakin
- UCL Institute for Ophthalmology, London, UK; Moorfields Eye Hospital, London, UK; Eye Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | | | - Patty P A Dhooge
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Silvia Albert
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nathalie M Bax
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lonneke Duijkers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Kwan L Hau
- UCL Institute for Ophthalmology, London, UK
| | - Edward Bloch
- UCL Institute for Ophthalmology, London, UK; Moorfields Eye Hospital, London, UK
| | | | | | | | - Carel B Hoyng
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Andrew R Webster
- UCL Institute for Ophthalmology, London, UK; Moorfields Eye Hospital, London, UK
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Alejandro Garanto
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands.
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de Breuk A, Acar IE, Kersten E, Schijvenaars MMVAP, Colijn JM, Haer-Wigman L, Bakker B, de Jong S, Meester-Smoor MA, Verzijden T, Missotten TOAR, Monés J, Biarnés M, Pauleikhoff D, Hense HW, Silva R, Nunes S, Melo JB, Fauser S, Hoyng CB, Ueffing M, Coenen MJH, Klaver CCW, den Hollander AI. Development of a Genotype Assay for Age-Related Macular Degeneration: The EYE-RISK Consortium. Ophthalmology 2020; 128:1604-1617. [PMID: 32717343 DOI: 10.1016/j.ophtha.2020.07.037] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 06/30/2020] [Accepted: 07/16/2020] [Indexed: 01/23/2023] Open
Abstract
PURPOSE To develop a genotype assay to assess associations with common and rare age-related macular degeneration (AMD) risk variants, to calculate an overall genetic risk score (GRS), and to identify potential misdiagnoses with inherited macular dystrophies that mimic AMD. DESIGN Case-control study. PARTICIPANTS Individuals (n = 4740) from 5 European cohorts. METHODS We designed single-molecule molecular inversion probes for target selection and used next generation sequencing to sequence 87 single nucleotide polymorphisms (SNPs), coding and splice-site regions of 10 AMD-(related) genes (ARMS2, C3, C9, CD46, CFB, CFH, CFI, HTRA1, TIMP3, and SLC16A8), and 3 genes that cause inherited macular dystrophies (ABCA4, CTNNA1, and PRPH2). Genetic risk scores for common AMD risk variants were calculated based on effect size and genotype of 52 AMD-associated variants. Frequency of rare variants was compared between late AMD patients and control individuals with logistic regression analysis. MAIN OUTCOME MEASURES Genetic risk score, association of genetic variants with AMD, and genotype-phenotype correlations. RESULTS We observed high concordance rates between our platform and other genotyping platforms for the 69 successfully genotyped SNPs (>96%) and for the rare variants (>99%). We observed a higher GRS for patients with late AMD compared with patients with early/intermediate AMD (P < 0.001) and individuals without AMD (P < 0.001). A higher proportion of pathogenic variants in the CFH (odds ratio [OR] = 2.88; P = 0.006), CFI (OR = 4.45; P = 0.005), and C3 (OR = 6.56; P = 0.0003) genes was observed in late AMD patients compared with control individuals. In 9 patients, we identified pathogenic variants in the PRPH2, ABCA4, and CTNNA1 genes, which allowed reclassification of these patients as having inherited macular dystrophy. CONCLUSIONS This study reports a genotype assay for common and rare AMD genetic variants, which can identify individuals at intermediate to high genetic risk of late AMD and enables differential diagnosis of AMD-mimicking dystrophies. Our study supports sequencing of CFH, CFI, and C3 genes because they harbor rare high-risk variants. Carriers of these variants could be amendable for new treatments for AMD that currently are under development.
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Affiliation(s)
- Anita de Breuk
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ilhan E Acar
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Eveline Kersten
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mascha M V A P Schijvenaars
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Johanna M Colijn
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Bjorn Bakker
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sarah de Jong
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Magda A Meester-Smoor
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Timo Verzijden
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Jordi Monés
- Barcelona Macula Foundation, Barcelona, Spain; Institut de la Màcula, Barcelona, Spain
| | - Marc Biarnés
- Barcelona Macula Foundation, Barcelona, Spain; Institut de la Màcula, Barcelona, Spain
| | | | - Hans W Hense
- Institute of Epidemiology and Social Medicine, Westfälische Wilhelms University, Münster, Germany
| | - Rufino Silva
- Department of Ophthalmology, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal; Coimbra Institute for Clinical and Biomedical Research, Faculty of Medicine, University of Coimbra (iCBR-FMUC), Coimbra, Portugal; Association for Innovation and Biomedical Research on Light and Image (AIBILI), Coimbra, Portugal
| | - Sandrina Nunes
- Association for Innovation and Biomedical Research on Light and Image (AIBILI), Coimbra, Portugal
| | - Joana B Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Coimbra, Portugal; iCBR-CIMAGO, Center of Investigation on Environment, Genetics and Oncobiology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Sascha Fauser
- Department of Ophthalmology, University Hospital of Cologne, Cologne, Germany
| | - Carel B Hoyng
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marius Ueffing
- Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Marieke J H Coenen
- Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Caroline C W Klaver
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands; Institute of Molecular and Clinical Ophthalmology, Basel, Switzerland
| | - Anneke I den Hollander
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.
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50
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Molecular Analysis of the ABCA4 Gene Mutations in Patients with Stargardt Disease Using Human Hair Follicles. Int J Mol Sci 2020; 21:ijms21103430. [PMID: 32413971 PMCID: PMC7279462 DOI: 10.3390/ijms21103430] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/05/2020] [Accepted: 05/10/2020] [Indexed: 12/17/2022] Open
Abstract
ABCA4 gene mutations are the cause of a spectrum of ABCA4 retinopathies, and the most common juvenile macular degeneration is called Stargardt disease. ABCA4 has previously been observed almost exclusively in the retina. Therefore, studying the functional consequences of ABCA4 variants has required advanced molecular analysis techniques. The aim of the present study was to evaluate whether human hair follicles may be used for molecular analysis of the ABCA4 gene splice-site variants in patients with ABCA4 retinopathies. We assessed ABCA4 expression in hair follicles and skin at mRNA and protein levels by means of real-time PCR and Western blot analyses, respectively. We performed cDNA sequencing to reveal the presence of full-length ABCA4 transcripts and analyzed ABCA4 transcripts from three patients with Stargardt disease carrying different splice-site ABCA4 variants: c.5312+1G>A, c.5312+2T>G and c.5836-3C>A. cDNA analysis revealed that c.5312+1G>A, c.5312+2T>G variants led to the skipping of exon 37, and the c.5836-3C>A variant resulted in the insertion of 30 nucleotides into the transcript. Our results strongly argue for the use of hair follicles as a model for the molecular analysis of the pathogenicity of ABCA4 variants in patients with ABCA4 retinopathies.
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