1
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Zeuli R, Karali M, de Bruijn SE, Rodenburg K, Scarpato M, Capasso D, Astuti GDN, Gilissen C, Rodríguez-Hidalgo M, Ruiz-Ederra J, Testa F, Simonelli F, Cremers FPM, Banfi S, Roosing S. Whole genome sequencing identifies elusive variants in genetically unsolved Italian inherited retinal disease patients. HGG ADVANCES 2024; 5:100314. [PMID: 38816995 PMCID: PMC11225895 DOI: 10.1016/j.xhgg.2024.100314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/01/2024] Open
Abstract
Inherited retinal diseases (IRDs) are a group of rare monogenic diseases with high genetic heterogeneity (pathogenic variants identified in over 280 causative genes). The genetic diagnostic rate for IRDs is around 60%, mainly thanks to the routine application of next-generation sequencing (NGS) approaches such as extensive gene panels or whole exome analyses. Whole-genome sequencing (WGS) has been reported to improve this diagnostic rate by revealing elusive variants, such as structural variants (SVs) and deep intronic variants (DIVs). We performed WGS on 33 unsolved cases with suspected autosomal recessive IRD, aiming to identify causative genetic variants in non-coding regions or to detect SVs that were unexplored in the initial screening. Most of the selected cases (30 of 33, 90.9%) carried monoallelic pathogenic variants in genes associated with their clinical presentation, hence we first analyzed the non-coding regions of these candidate genes. Whenever additional pathogenic variants were not identified with this approach, we extended the search for SVs and DIVs to all IRD-associated genes. Overall, we identified the missing causative variants in 11 patients (11 of 33, 33.3%). These included three DIVs in ABCA4, CEP290 and RPGRIP1; one non-canonical splice site (NCSS) variant in PROM1 and three SVs (large deletions) in EYS, PCDH15 and USH2A. For the previously unreported DIV in CEP290 and for the NCCS variant in PROM1, we confirmed the effect on splicing by reverse transcription (RT)-PCR on patient-derived RNA. This study demonstrates the power and clinical utility of WGS as an all-in-one test to identify disease-causing variants missed by standard NGS diagnostic methodologies.
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Affiliation(s)
- Roberta Zeuli
- Medical Genetics, Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Marianthi Karali
- Medical Genetics, Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy; Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Suzanne E de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Kim Rodenburg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Margherita Scarpato
- Medical Genetics, Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Dalila Capasso
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomic and Experimental Medicine Program, Naples, Italy
| | - Galuh D N Astuti
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - 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
| | - María Rodríguez-Hidalgo
- Department of Neuroscience, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Department of Dermatology, Ophthalmology, and Otorhinolaryngology, University of the Basque Country (UPV/EHU), Donostia-San Sebastián, Spain
| | - Javier Ruiz-Ederra
- Department of Neuroscience, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Department of Dermatology, Ophthalmology, and Otorhinolaryngology, University of the Basque Country (UPV/EHU), Donostia-San Sebastián, Spain
| | - Francesco Testa
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sandro Banfi
- Medical Genetics, Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
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2
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Corradi Z, Dhaenens CM, Grunewald O, Kocabaş IS, Meunier I, Banfi S, Karali M, Cremers FPM, Hitti-Malin RJ. Novel and Recurrent Copy Number Variants in ABCA4-Associated Retinopathy. Int J Mol Sci 2024; 25:5940. [PMID: 38892127 PMCID: PMC11173210 DOI: 10.3390/ijms25115940] [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: 04/22/2024] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
ABCA4 is the most frequently mutated gene leading to inherited retinal disease (IRD) with over 2200 pathogenic variants reported to date. Of these, ~1% are copy number variants (CNVs) involving the deletion or duplication of genomic regions, typically >50 nucleotides in length. An in-depth assessment of the current literature based on the public database LOVD, regarding the presence of known CNVs and structural variants in ABCA4, and additional sequencing analysis of ABCA4 using single-molecule Molecular Inversion Probes (smMIPs) for 148 probands highlighted recurrent and novel CNVs associated with ABCA4-associated retinopathies. An analysis of the coverage depth in the sequencing data led to the identification of eleven deletions (six novel and five recurrent), three duplications (one novel and two recurrent) and one complex CNV. Of particular interest was the identification of a complex defect, i.e., a 15.3 kb duplicated segment encompassing exon 31 through intron 41 that was inserted at the junction of a downstream 2.7 kb deletion encompassing intron 44 through intron 47. In addition, we identified a 7.0 kb tandem duplication of intron 1 in three cases. The identification of CNVs in ABCA4 can provide patients and their families with a genetic diagnosis whilst expanding our understanding of the complexity of diseases caused by ABCA4 variants.
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Affiliation(s)
- Zelia Corradi
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Claire-Marie Dhaenens
- Université de Lille, Inserm, CHU Lille, U1172-LilNCog-Lille Neuroscience & Cognition, F-59000 Lille, France
| | - Olivier Grunewald
- Université de Lille, Inserm, CHU Lille, U1172-LilNCog-Lille Neuroscience & Cognition, F-59000 Lille, France
| | - Ipek Selen Kocabaş
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Isabelle Meunier
- Institute des Neurosciences de Montpellier, INSERM, Université de Montpellier, F-34295 Montpellier, France
| | - Sandro Banfi
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 81031 Naples, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Marianthi Karali
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 81031 Naples, Italy
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania “Luigi Vanvitelli”, 81031 Naples, Italy
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Rebekkah J. Hitti-Malin
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
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3
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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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4
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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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5
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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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6
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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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7
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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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8
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Panneman DM, Hitti-Malin RJ, Holtes LK, de Bruijn SE, Reurink J, Boonen EGM, Khan MI, Ali M, Andréasson S, De Baere E, Banfi S, Bauwens M, Ben-Yosef T, Bocquet B, De Bruyne M, de la Cerda B, Coppieters F, Farinelli P, Guignard T, Inglehearn CF, Karali M, Kjellström U, Koenekoop R, de Koning B, Leroy BP, McKibbin M, Meunier I, Nikopoulos K, Nishiguchi KM, Poulter JA, Rivolta C, Rodríguez de la Rúa E, Saunders P, Simonelli F, Tatour Y, Testa F, Thiadens AAHJ, Toomes C, Tracewska AM, Tran HV, Ushida H, Vaclavik V, Verhoeven VJM, van de Vorst M, Gilissen C, Hoischen A, Cremers FPM, Roosing S. Cost-effective sequence analysis of 113 genes in 1,192 probands with retinitis pigmentosa and Leber congenital amaurosis. Front Cell Dev Biol 2023; 11:1112270. [PMID: 36819107 PMCID: PMC9936074 DOI: 10.3389/fcell.2023.1112270] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/20/2023] [Indexed: 02/05/2023] Open
Abstract
Introduction: Retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA) are two groups of inherited retinal diseases (IRDs) where the rod photoreceptors degenerate followed by the cone photoreceptors of the retina. A genetic diagnosis for IRDs is challenging since >280 genes are associated with these conditions. While whole exome sequencing (WES) is commonly used by diagnostic facilities, the costs and required infrastructure prevent its global applicability. Previous studies have shown the cost-effectiveness of sequence analysis using single molecule Molecular Inversion Probes (smMIPs) in a cohort of patients diagnosed with Stargardt disease and other maculopathies. Methods: Here, we introduce a smMIPs panel that targets the exons and splice sites of all currently known genes associated with RP and LCA, the entire RPE65 gene, known causative deep-intronic variants leading to pseudo-exons, and part of the RP17 region associated with autosomal dominant RP, by using a total of 16,812 smMIPs. The RP-LCA smMIPs panel was used to screen 1,192 probands from an international cohort of predominantly RP and LCA cases. Results and discussion: After genetic analysis, a diagnostic yield of 56% was obtained which is on par with results from WES analysis. The effectiveness and the reduced costs compared to WES renders the RP-LCA smMIPs panel a competitive approach to provide IRD patients with a genetic diagnosis, especially in countries with restricted access to genetic testing.
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Affiliation(s)
- Daan M. Panneman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands,*Correspondence: Daan M. Panneman,
| | - Rebekkah J. Hitti-Malin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Lara K. Holtes
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Suzanne E. de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Janine Reurink
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Erica G. M. Boonen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Muhammad Imran Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Manir Ali
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, United Kingdom
| | - Sten Andréasson
- Department of Ophthalmology and Clinical Sciences Lund, Lund University, Skane University Hospital, Lund, Sweden
| | - Elfride De Baere
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy,Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Miriam Bauwens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Tamar Ben-Yosef
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Béatrice Bocquet
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, Montpellier University Hospital, Sensgene Care Network, ERN-EYE Network, Montpellier, France,Institute for Neurosciences of Montpellier (INM), L’Institut National de la Santé et de la Recherche Médicale, University of Montpellier, L’Institut National de la Santé et de la Recherche Médicale, Montpellier, France
| | - Marieke De Bruyne
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Berta de la Cerda
- Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), Seville, Spain
| | - Frauke Coppieters
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium,Department of Pharmaceutics, Ghent University, Ghent, Belgium
| | - Pietro Farinelli
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Thomas Guignard
- Chromosomal Genetics Unit, University Hospital of Montpellier, Montpellier, France
| | - Chris F. Inglehearn
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, United Kingdom
| | - Marianthi Karali
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy,Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Ulrika Kjellström
- Department of Ophthalmology and Clinical Sciences Lund, Lund University, Skane University Hospital, Lund, Sweden
| | - Robert Koenekoop
- McGill University Health Center (MUHC) Research Institute, Montreal, QC, Canada,Departments of Paediatric Surgery, Human Genetics, and Adult Ophthalmology, McGill University Health Center, Montreal, QC, Canada
| | - Bart de Koning
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, Netherlands
| | - Bart P. Leroy
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium,Department of Head & Skin, Ghent University, Ghent, Belgium,Division of Ophthalmology & Center for Cellular & Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Martin McKibbin
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, United Kingdom,Department of Ophthalmology, St. James’s University Hospital, Leeds, United Kingdom
| | - Isabelle Meunier
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, Montpellier University Hospital, Sensgene Care Network, ERN-EYE Network, Montpellier, France,Institute for Neurosciences of Montpellier (INM), L’Institut National de la Santé et de la Recherche Médicale, University of Montpellier, L’Institut National de la Santé et de la Recherche Médicale, Montpellier, France
| | | | - Koji M. Nishiguchi
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - James A. Poulter
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, United Kingdom
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland,Department of Ophthalmology, University of Basel, Basel, Switzerland,Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Enrique Rodríguez de la Rúa
- Department of Ophthalmology, Retics Patologia Ocular, OFTARED, Instituto de Salud Carlos III, University Hospital Virgen Macarena, Madrid, Spain
| | | | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Yasmin Tatour
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Francesco Testa
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, Naples, Italy
| | | | - Carmel Toomes
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds, United Kingdom
| | - Anna M. Tracewska
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Hoai Viet Tran
- Oculogenetic Unit, University Eye Hospital Jules Gonin, Geneva, Switzerland
| | - Hiroaki Ushida
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Veronika Vaclavik
- Oculogenetic Unit, University Eye Hospital Jules Gonin, Geneva, Switzerland
| | - Virginie J. M. Verhoeven
- Department of Ophthalmology, Erasmus, Rotterdam, Netherlands,Department of Clinical Genetics, Erasmus, Rotterdam, Netherlands
| | - Maartje van de Vorst
- Department of Human Genetics, 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
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands,Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, Netherlands
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9
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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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10
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Kim BM, Song HS, Kim JY, Kwon EY, Ha SY, Kim M, Choi JH. Functional characterization of ABCA4 genetic variants related to Stargardt disease. Sci Rep 2022; 12:22282. [PMID: 36566289 PMCID: PMC9790013 DOI: 10.1038/s41598-022-26912-6] [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: 07/28/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022] Open
Abstract
The ATP-binding cassette subfamily 4 (ABCA4), a transporter, is localized within the photoreceptors of the retina, and its genetic variants cause retinal dystrophy. Despite the clinical importance of the ABCA4 transporter, a few studies have investigated the function of each variant. In this study, we functionally characterized ABCA4 variants found in Korean patients with Stargardt disease or variants of the ABCA4 promoter region. We observed that four missense variants-p.Arg290Gln, p.Thr1117Ala, p.Cys1140Trp, and p.Asn1588Tyr-significantly decreased ABCA4 expression on the plasma membrane, which could be due to intracellular degradation. There are four major haplotypes in the ABCA4 proximal promoter. We observed that the H1 haplotype (c.-761C>A) indicated significantly increased luciferase activity compared to that of the wild-type, whereas the H3 haplotype (c.-1086A>C) indicated significantly decreased luciferase activity (P < 0.01 and 0.001, respectively). In addition, c.-900A>T in the H2 haplotype exhibited significantly increased luciferase activity compared with that of the wild-type. Two transcription factors, GATA-2 and HLF, were found to function as enhancers of ABCA4 transcription. Our findings suggest that ABCA4 variants in patients with Stargardt disease affect ABCA4 expression. Furthermore, common variants of the ABCA4 proximal promoter alter the ABCA4 transcriptional activity, which is regulated by GATA-2 and HLF transcription factors.
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Affiliation(s)
- Bo Min Kim
- grid.255649.90000 0001 2171 7754Department of Pharmacology, Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, 25 Magokdong-Ro 2-Gil, Gangseo-Gu, Seoul, 07804 Korea
| | - Hyo Sook Song
- grid.255649.90000 0001 2171 7754Department of Pharmacology, Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, 25 Magokdong-Ro 2-Gil, Gangseo-Gu, Seoul, 07804 Korea
| | - Jin-Young Kim
- grid.255649.90000 0001 2171 7754Department of Pharmacology, Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, 25 Magokdong-Ro 2-Gil, Gangseo-Gu, Seoul, 07804 Korea
| | - Eun Young Kwon
- grid.255649.90000 0001 2171 7754Department of Pharmacology, Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, 25 Magokdong-Ro 2-Gil, Gangseo-Gu, Seoul, 07804 Korea
| | - Seung Yeon Ha
- grid.255649.90000 0001 2171 7754Department of Pharmacology, Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, 25 Magokdong-Ro 2-Gil, Gangseo-Gu, Seoul, 07804 Korea
| | - Minsuk Kim
- grid.255649.90000 0001 2171 7754Department of Pharmacology, Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, 25 Magokdong-Ro 2-Gil, Gangseo-Gu, Seoul, 07804 Korea
| | - Ji Ha Choi
- grid.255649.90000 0001 2171 7754Department of Pharmacology, Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, 25 Magokdong-Ro 2-Gil, Gangseo-Gu, Seoul, 07804 Korea
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11
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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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12
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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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13
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Zernant J, Lee W, Wang J, Goetz K, Ullah E, Nagasaki T, Su PY, Fishman GA, Tsang SH, Tumminia SJ, Brooks BP, Hufnagel RB, Chen R, Allikmets R. Rare and common variants in ROM1 and PRPH2 genes trans-modify Stargardt/ABCA4 disease. PLoS Genet 2022; 18:e1010129. [PMID: 35353811 PMCID: PMC9000055 DOI: 10.1371/journal.pgen.1010129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 04/11/2022] [Accepted: 03/02/2022] [Indexed: 11/18/2022] Open
Abstract
Over 1,500 variants in the ABCA4 locus cause phenotypes ranging from severe, early-onset retinal degeneration to very late-onset maculopathies. The resulting ABCA4/Stargardt disease is the most prevalent Mendelian eye disorder, although its underlying clinical heterogeneity, including penetrance of many alleles, are not well-understood. We hypothesized that a share of this complexity is explained by trans-modifiers, i.e., variants in unlinked loci, which are currently unknown. We sought to identify these by performing exome sequencing in a large cohort for a rare disease of 622 cases and compared variation in seven genes known to clinically phenocopy ABCA4 disease to cohorts of ethnically matched controls. We identified a significant enrichment of variants in 2 out of the 7 genes. Moderately rare, likely functional, variants, at the minor allele frequency (MAF) <0.005 and CADD>25, were enriched in ROM1, where 1.3% of 622 patients harbored a ROM1 variant compared to 0.3% of 10,865 controls (p = 2.41E04; OR 3.81 95% CI [1.77; 8.22]). More importantly, analysis of common variants (MAF>0.1) identified a frequent haplotype in PRPH2, tagged by the p.Asp338 variant with MAF = 0.21 in the matched general population that was significantly increased in the patient cohort, MAF 0.25, p = 0.0014. Significant differences were also observed between ABCA4 disease subgroups. In the late-onset subgroup, defined by the hypomorphic p.Asn1868Ile variant and including c.4253+43G>A, the allele frequency for the PRPH2 p.Asp338 variant was 0.15 vs 0.27 in the remaining cohort, p = 0.00057. Known functional data allowed suggesting a mechanism by which the PRPH2 haplotype influences the ABCA4 disease penetrance. These associations were replicated in an independent cohort of 408 patients. The association was highly statistically significant in the combined cohorts of 1,030 cases, p = 4.00E-05 for all patients and p = 0.00014 for the hypomorph subgroup, suggesting a substantial trans-modifying role in ABCA4 disease for both rare and common variants in two unlinked loci.
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Affiliation(s)
- Jana Zernant
- Department of Ophthalmology, Columbia University, New York, New York, United States of America
| | - Winston Lee
- Department of Ophthalmology, Columbia University, New York, New York, United States of America
- Department of Genetics & Development, Columbia University, New York, New York, United States of America
| | - Jun Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kerry Goetz
- National Eye Institute, NIH, Bethesda, Maryland, United States of America
| | - Ehsan Ullah
- National Eye Institute, NIH, Bethesda, Maryland, United States of America
| | - Takayuki Nagasaki
- Department of Ophthalmology, Columbia University, New York, New York, United States of America
| | - Pei-Yin Su
- Department of Ophthalmology, Columbia University, New York, New York, United States of America
| | - Gerald A. Fishman
- The Pangere Center for Inherited Retinal Diseases, The Chicago Lighthouse, Chicago, Illinois, United States of America
| | - Stephen H. Tsang
- Department of Ophthalmology, Columbia University, New York, New York, United States of America
- Department of Pathology & Cell Biology, Columbia University, New York, New York, United States of America
| | - Santa J. Tumminia
- National Eye Institute, NIH, Bethesda, Maryland, United States of America
| | - Brian P. Brooks
- National Eye Institute, NIH, Bethesda, Maryland, United States of America
| | - Robert B. Hufnagel
- National Eye Institute, NIH, Bethesda, Maryland, United States of America
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, New York, United States of America
- Department of Pathology & Cell Biology, Columbia University, New York, New York, United States of America
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14
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Del Pozo-Valero M, Riveiro-Alvarez R, Martin-Merida I, Blanco-Kelly F, Swafiri S, Lorda-Sanchez I, Trujillo-Tiebas MJ, Carreño E, Jimenez-Rolando B, Garcia-Sandoval B, Corton M, Avila-Fernandez A, Ayuso C. Impact of Next Generation Sequencing in Unraveling the Genetics of 1036 Spanish Families With Inherited Macular Dystrophies. Invest Ophthalmol Vis Sci 2022; 63:11. [PMID: 35119454 PMCID: PMC8819279 DOI: 10.1167/iovs.63.2.11] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Purpose To assess the potential of next-generation sequencing (NGS) technologies to characterize cases diagnosed with autosomal recessive (ar) or sporadic (s) macular dystrophies (ar/sMD) and describe their mutational spectrum. Methods A cohort of 1036 families was classified according to their suspected clinical diagnosis—Stargardt disease (STGD), cone and cone-rod dystrophy (CCRD) or other maculopathies (otherMD). Molecular studies included genotyping microarrays, Sanger sequencing, NGS, and sequencing of intronic regions of the ABCA4 gene. Clinical reclassification was done after the genetic study. Results At the end of the study, 677 patients (65%) had a confirmed genetic diagnosis, representing 78%, 63%, and 38% of STGD, CCRD, and otherMD groups of patients, respectively. ABCA4 is the most mutated gene in all groups, and a second pathogenic variant was found in 76% of STGD patients with one previously identified mutated ABCA4 allele. Autosomal dominant or X-linked mutations were found in 5% of cases together with not-MD genes (CHM, EYS, RHO, RPGR, RLBP1, OPA1, and USH2A among others) leading to their reclassification. Novel variants in the very rare genes PLA2G5 and TTLL5 revealed additional phenotypic associations. Conclusions This study provides for the first time a genetic landscape of 1036 ar/sMD families according to their suspected diagnosis. The analysis of >200 genes associated with retinal dystrophies and the entire locus of ABCA4 increase the rate of characterization, even regardless of available clinical and familiar data. The use of the suspected a priori diagnosis referred by the clinicians, especially in the past, could lead to clinical reclassifications to other inherited retinal dystrophies.
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Affiliation(s)
- Marta Del Pozo-Valero
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Rosa Riveiro-Alvarez
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Inmaculada Martin-Merida
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Fiona Blanco-Kelly
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Saoud Swafiri
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Isabel Lorda-Sanchez
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Maria José Trujillo-Tiebas
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Ester Carreño
- Department of Ophthalmology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Belen Jimenez-Rolando
- Department of Ophthalmology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Blanca Garcia-Sandoval
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain.,Department of Ophthalmology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Marta Corton
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Almudena Avila-Fernandez
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
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15
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Keegan NP, Wilton SD, Fletcher S. Analysis of Pathogenic Pseudoexons Reveals Novel Mechanisms Driving Cryptic Splicing. Front Genet 2022; 12:806946. [PMID: 35140743 PMCID: PMC8819188 DOI: 10.3389/fgene.2021.806946] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/09/2021] [Indexed: 12/16/2022] Open
Abstract
Understanding pre-mRNA splicing is crucial to accurately diagnosing and treating genetic diseases. However, mutations that alter splicing can exert highly diverse effects. Of all the known types of splicing mutations, perhaps the rarest and most difficult to predict are those that activate pseudoexons, sometimes also called cryptic exons. Unlike other splicing mutations that either destroy or redirect existing splice events, pseudoexon mutations appear to create entirely new exons within introns. Since exon definition in vertebrates requires coordinated arrangements of numerous RNA motifs, one might expect that pseudoexons would only arise when rearrangements of intronic DNA create novel exons by chance. Surprisingly, although such mutations do occur, a far more common cause of pseudoexons is deep-intronic single nucleotide variants, raising the question of why these latent exon-like tracts near the mutation sites have not already been purged from the genome by the evolutionary advantage of more efficient splicing. Possible answers may lie in deep intronic splicing processes such as recursive splicing or poison exon splicing. Because these processes utilize intronic motifs that benignly engage with the spliceosome, the regions involved may be more susceptible to exonization than other intronic regions would be. We speculated that a comprehensive study of reported pseudoexons might detect alignments with known deep intronic splice sites and could also permit the characterisation of novel pseudoexon categories. In this report, we present and analyse a catalogue of over 400 published pseudoexon splice events. In addition to confirming prior observations of the most common pseudoexon mutation types, the size of this catalogue also enabled us to suggest new categories for some of the rarer types of pseudoexon mutation. By comparing our catalogue against published datasets of non-canonical splice events, we also found that 15.7% of pseudoexons exhibit some splicing activity at one or both of their splice sites in non-mutant cells. Importantly, this included seven examples of experimentally confirmed recursive splice sites, confirming for the first time a long-suspected link between these two splicing phenomena. These findings have the potential to improve the fidelity of genetic diagnostics and reveal new targets for splice-modulating therapies.
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Affiliation(s)
- Niall P. Keegan
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
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16
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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: 26] [Impact Index Per Article: 8.7] [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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17
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Duzkale N, Arslan U. Investigation of genotype-phenotype relationship in Turkish patients with inherited retinal disease by next generation sequencing. Ophthalmic Genet 2021; 42:674-684. [PMID: 34315337 DOI: 10.1080/13816810.2021.1952616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Inherited retinal dystrophies (IRDs) are a group of retinal diseases genetically and clinically highly heterogeneous and associated with more than 300 genes. This study aims to investigate the genetic basis of Turkish patients with IRDs. MATERIALS AND METHODS In the study, genes related to retinal diseases in 86 IRDs patients were analyzed using the Next Generations Sequencing method (NGS). RESULTS The mean age of 86 patients was 35 and the mean age at diagnosis was 18. There was consanguinity between the parents of 62% of these patients. Fifty-six retinal disease-associated genes of 46 patients and 230 retinal disease-associated genes of 40 patients were examined. Genetic analysis provides a molecular diagnosis in a total of 53 (61.6%) patients. The genes responsible for the IRDs phenotype were frequently identified as ABCA4 (25%), EYS (11%), and RDH12 (9%). There was no significant difference between those with and without a molecular diagnosis in terms of demographic characteristics and family history. CONCLUSIONS Determination of genetic cause by NGS method in IRDs subgroups that are difficult to define by ophthalmic examination ensures that patients receive accurate diagnosis, treatment and counseling. This study contributed to the understanding of the genotype-phenotype relationship of Turkish patients with IRDs.
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Affiliation(s)
- Neslihan Duzkale
- Department of Medical Genetic, Diskapi Yildirim Beyazit Training and Research Hospital, Ankara, Turkey
| | - Umut Arslan
- Department of Bioretina, Ankara University Technopolis, Ankara, Turkey
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18
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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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19
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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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20
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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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21
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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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22
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Liu F, Lee J, Chen J. Molecular structures of the eukaryotic retinal importer ABCA4. eLife 2021; 10:63524. [PMID: 33605212 PMCID: PMC7932691 DOI: 10.7554/elife.63524] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/18/2021] [Indexed: 12/20/2022] Open
Abstract
The ATP-binding cassette (ABC) transporter family contains thousands of members with diverse functions. Movement of the substrate, powered by ATP hydrolysis, can be outward (export) or inward (import). ABCA4 is a eukaryotic importer transporting retinal to the cytosol to enter the visual cycle. It also removes toxic retinoids from the disc lumen. Mutations in ABCA4 cause impaired vision or blindness. Despite decades of clinical, biochemical, and animal model studies, the molecular mechanism of ABCA4 is unknown. Here, we report the structures of human ABCA4 in two conformations. In the absence of ATP, ABCA4 adopts an outward-facing conformation, poised to recruit substrate. The presence of ATP induces large conformational changes that could lead to substrate release. These structures provide a molecular basis to understand many disease-causing mutations and a rational guide for new experiments to uncover how ABCA4 recruits, flips, and releases retinoids.
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Affiliation(s)
- Fangyu Liu
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University, New York, United States.,Tri-Institutional Training Program in Chemical Biology, New York, United States
| | - James Lee
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University, New York, United States
| | - Jue Chen
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University, New York, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
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23
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Perrault I, Hanein S, Gérard X, Mounguengue N, Bouyakoub R, Zarhrate M, Fourrage C, Jabot-Hanin F, Bocquet B, Meunier I, Zanlonghi X, Kaplan J, Rozet JM. Whole Locus Sequencing Identifies a Prevalent Founder Deep Intronic RPGRIP1 Pathologic Variant in the French Leber Congenital Amaurosis Cohort. Genes (Basel) 2021; 12:genes12020287. [PMID: 33670832 PMCID: PMC7922592 DOI: 10.3390/genes12020287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/10/2021] [Accepted: 02/16/2021] [Indexed: 01/04/2023] Open
Abstract
Leber congenital amaurosis (LCA) encompasses the earliest and most severe retinal dystrophies and can occur as a non-syndromic or a syndromic disease. Molecular diagnosis in LCA is of particular importance in clinical decision-making and patient care since it can provide ocular and extraocular prognostics and identify patients eligible to develop gene-specific therapies. Routine high-throughput molecular testing in LCA yields 70%–80% of genetic diagnosis. In this study, we aimed to investigate the non-coding regions of one non-syndromic LCA gene, RPGRIP1, in a series of six families displaying one single disease allele after a gene-panel screening of 722 LCA families which identified 26 biallelic RPGRIP1 families. Using trio-based high-throughput whole locus sequencing (WLS) for second disease alleles, we identified a founder deep intronic mutation (NM_020366.3:c.1468-128T>G) in 3/6 families. We employed Sanger sequencing to search for the pathologic variant in unresolved LCA cases (106/722) and identified three additional families (two homozygous and one compound heterozygous with the NM_020366.3:c.930+77A>G deep intronic change). This makes the c.1468-128T>G the most frequent RPGRIP1 disease allele (8/60, 13%) in our cohort. Studying patient lymphoblasts, we show that the pathologic variant creates a donor splice-site and leads to the insertion of the pseudo-exon in the mRNA, which we were able to hamper using splice-switching antisense oligonucleotides (AONs), paving the way to therapies.
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Affiliation(s)
- Isabelle Perrault
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (X.G.); (N.M.); (R.B.); (J.K.); (J.-M.R.)
- Correspondence:
| | - Sylvain Hanein
- Translational Genetics, Institute of Genetic Diseases, INSERM UMR1163, Imagine and Paris Descartes University, 75015 Paris, France;
| | - Xavier Gérard
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (X.G.); (N.M.); (R.B.); (J.K.); (J.-M.R.)
| | - Nelson Mounguengue
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (X.G.); (N.M.); (R.B.); (J.K.); (J.-M.R.)
| | - Ryme Bouyakoub
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (X.G.); (N.M.); (R.B.); (J.K.); (J.-M.R.)
| | - Mohammed Zarhrate
- Genomics Platform, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France;
| | - Cécile Fourrage
- Bioinformatic Platform, Institute of Genetic Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (C.F.); (F.J.-H.)
| | - Fabienne Jabot-Hanin
- Bioinformatic Platform, Institute of Genetic Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (C.F.); (F.J.-H.)
- Bioinformatics Core Facility, Université Paris Descartes-Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, 75015 Paris, France
| | - Béatrice Bocquet
- Centre de Référence des Affections Sensorielles Génétiques, Institut des Neurosciences de Montpellier, CHU-Saint Eloi Montpellier, 34091 Montpellier, France; (B.B.); (I.M.)
| | - Isabelle Meunier
- Centre de Référence des Affections Sensorielles Génétiques, Institut des Neurosciences de Montpellier, CHU-Saint Eloi Montpellier, 34091 Montpellier, France; (B.B.); (I.M.)
- National Reference Centre for Inherited Sensory Diseases, Univ Montpellier, CHU, 34091 Montpellier, France
| | - Xavier Zanlonghi
- Eye Clinic Jules Verne, 44300 Nantes, France;
- CHU, 35000 Rennes, France
| | - Josseline Kaplan
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (X.G.); (N.M.); (R.B.); (J.K.); (J.-M.R.)
- Ophthalmology Department, University Hospital Henri Mondor, APHP, 94000 Créteil, France
| | - Jean-Michel Rozet
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (X.G.); (N.M.); (R.B.); (J.K.); (J.-M.R.)
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24
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Lorenz B, Tavares J, van den Born LI, Marques JP, Scholl HPN. Current Management of Inherited Retinal Degeneration Patients in Europe: Results of a Multinational Survey by the European Vision Institute Clinical Research Network. Ophthalmic Res 2021; 64:622-638. [PMID: 33465765 DOI: 10.1159/000514540] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/15/2021] [Indexed: 11/19/2022]
Abstract
PURPOSE An increasing number of gene therapies are developed for Inherited Retinal Degenerations (IRD). To date, 1 treatment has been approved for clinical use (FDA USA 2017, EMA Europe 2018, MoHAP UAE 2019, SFDA Saudi Arabia 2019, Swiss Medic Switzerland 2020, TGA Australia 2020, and BFR Brazil 2020). While such therapies do not provide complete cure, they may halt degeneration or partially restore function. Identification of well-characterized patients is an emerging need. We conducted the first multinational survey to understand the management of IRDs in Europe. METHODS An electronic survey questionnaire containing 112 questions was developed and sent to the 101 EVICR.net clinical centers (14 European countries and Israel). RESULTS The overall response rate was 49%. Only 14% of responding centers do not see IRD patients; 52% that manage IRD patients follow ≥200 patients, 16% > 1,000. Databases exist in 86% of the centers; of these, 75% are local files, 28% local Web-based database, and 19% national Web-based. IRD patients are referred to EVICR.net centers mainly by general ophthalmologists, patient self-referrals, and medical retina specialists. Most IRD patients are first seen in adulthood. Most prominent signs and symptoms depend on the age of onset, for example, nystagmus in infancy, or night blindness, and reduced visual acuity at older age. The time from inquiring for first appointment and clinical diagnosis varies among countries: in 29% of centers, the mean time is <4 weeks, although can be up to 35 months in others. The time to genetic diagnosis is ≥4 weeks, the maximum 10 years, likely depending on access to genetic testing, and the improvement of the tests available. Comprehensive eye examination always includes autofluorescence imaging and perimetry (86% static, 76% kinetic, and 21% microperimetry), and frequently optical coherence tomography (OCT) (95%), electroretinography (93%), and fundus photography (93%). Identified genotypes were reported in 40-80% patients by 69% of centers, and in 80-100% by 5%. Genetic testing is provided by public health insurance in 77% of centers, private health insurance in 38%, center budget in 13%, research funds in 18%; and 15% of centers do not have access to genetic testing. CONCLUSION At the start of this era of ocular gene therapy for IRD patients, this first international survey on management of IRDs in Europe highlights significant heterogeneity between centers and across countries and provides important baseline data for researchers, clinicians, pharmaceutical companies, and investors.
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Affiliation(s)
- Birgit Lorenz
- Department of Ophthalmology, Justus-Liebig-University Giessen, Giessen, Germany.,Department of Ophthalmology, University Hospital Bonn, Bonn, Germany
| | - Joana Tavares
- Association for Innovation and Biomedical Research on Light and Image (AIBILI), Coimbra, Portugal
| | | | - João P Marques
- Center for Clinical Trials, Association for Innovation and Biomedical Research on Light and Image (AIBILI), Coimbra, Portugal.,Department of Ophthalmology, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal.,Faculty of Medicine, University of Coimbra (FMUC), Coimbra, Portugal
| | - Hendrik P N Scholl
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Wilmer Eye Institute, Johns Hopkins University, Baltimore, Maryland, USA
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25
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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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26
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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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Cremers FPM, Lee W, Collin RWJ, Allikmets R. Clinical spectrum, genetic complexity and therapeutic approaches for retinal disease caused by ABCA4 mutations. Prog Retin Eye Res 2020; 79:100861. [PMID: 32278709 PMCID: PMC7544654 DOI: 10.1016/j.preteyeres.2020.100861] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/13/2020] [Accepted: 03/18/2020] [Indexed: 12/18/2022]
Abstract
The ABCA4 protein (then called a “rim protein”) was first
identified in 1978 in the rims and incisures of rod photoreceptors. The
corresponding gene, ABCA4, was cloned in 1997, and variants
were identified as the cause of autosomal recessive Stargardt disease (STGD1).
Over the next two decades, variation in ABCA4 has been
attributed to phenotypes other than the classically defined STGD1 or fundus
flavimaculatus, ranging from early onset and fast progressing cone-rod dystrophy
and retinitis pigmentosa-like phenotypes to very late onset cases of mostly mild
disease sometimes resembling, and confused with, age-related macular
degeneration. Similarly, analysis of the ABCA4 locus uncovered
a trove of genetic information, including >1200 disease-causing mutations
of varying severity, and of all types – missense, nonsense, small
deletions/insertions, and splicing affecting variants, of which many are located
deep-intronic. Altogether, this has greatly expanded our understanding of
complexity not only of the diseases caused by ABCA4 mutations,
but of all Mendelian diseases in general. This review provides an in depth
assessment of the cumulative knowledge of ABCA4-associated retinopathy –
clinical manifestations, genetic complexity, pathophysiology as well as current
and proposed therapeutic approaches.
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Affiliation(s)
- Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, PO Box 9104, 6500 HE, Nijmegen, the Netherlands.
| | - Winston Lee
- Department of Ophthalmology, Columbia University, New York, NY, 10032, USA; Department of Genetics & Development, Columbia University, New York, NY, 10032, USA
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, PO Box 9104, 6500 HE, Nijmegen, the Netherlands
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, NY, 10032, USA; Department of Pathology & Cell Biology, Columbia University, New York, NY, 10032, USA.
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Sun W, Xiao X, Li S, Jia X, Zhang Q. A novel deep intronic COL2A1 mutation in a family with early-onset high myopia/ocular-only Stickler syndrome. Ophthalmic Physiol Opt 2020; 40:281-288. [PMID: 32196734 DOI: 10.1111/opo.12682] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 02/13/2020] [Indexed: 12/13/2022]
Abstract
PURPOSE To identify the genetic defect causing early-onset high myopia (eoHM)/ocular-only Stickler syndrome (ocular-STL) in a large Chinese family. METHODS Genomic DNA and clinical data from a four-generation family with eoHM/ocular-STL were collected. Whole-exome sequencing was performed on one affected member in initial screening. Linkage scan based on microsatellite markers was carried out initially from candidate loci associated with autosomal dominant eoHM and Stickler syndrome. Sanger sequencing was used to detect potential variants. The pathogenicity of candidate variants was evaluated using mini genes ex vivo. RESULTS Eight patients and five unaffected members in the family participated in the study, in which the patients had high myopia with other variable ocular phenotypes but without extraocular abnormalities. Whole exome sequencing did not detect any potential pathogenic variant in all genes known to associate with the disease. The eoHM/ocular-STL in the family was mapped to markers around COL2A1 by candidate loci linkage scan, with a maximum lod score of 3.31 for D12S1590 at θ = 0. A novel deep intronic variant, c.86-50C > G in intron 1 of COL2A1, was detected by Sanger sequencing and co-segregated with eoHM/ocular-STL in the family. Ex vivo splicing test using mini genes confirmed that the variant created a new splicing acceptor 49 bp before the canonical splicing site of exon 2, resulted in addition of 49 bp fragment in the transcript (from c.86-49 to c.86-1) and premature termination. CONCLUSIONS Linkage study, bioinformatics prediction, and ex vivo transcript analysis suggest a novel deep intronic variant adjacent to 5-prime of exon 2 of COL2A1, affecting exon 2 splicing, as a potential cause of ocular-STL in a large family. To our knowledge, this is the first report of an intronic variant around exon 2 as a cause of ocular-STL while a series of variants in the coding region of exon 2, a dispensable alternative-splicing exon for extraocular tissues, in COL2A1 have been reported to cause Stickler syndrome-related ocular phenotype alone.
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Affiliation(s)
- Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaoyun Jia
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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29
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Whelan L, Dockery A, Wynne N, Zhu J, Stephenson K, Silvestri G, Turner J, O’Byrne JJ, Carrigan M, Humphries P, Keegan D, Kenna PF, Farrar GJ. Findings from a Genotyping Study of Over 1000 People with Inherited Retinal Disorders in Ireland. Genes (Basel) 2020; 11:E105. [PMID: 31963381 PMCID: PMC7016747 DOI: 10.3390/genes11010105] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 12/13/2019] [Accepted: 01/13/2020] [Indexed: 12/15/2022] Open
Abstract
The Irish national registry for inherited retinal degenerations (Target 5000) is a clinical and scientific program to identify individuals in Ireland with inherited retinal disorders and to attempt to ascertain the genetic cause underlying the disease pathology. Potential participants first undergo a clinical assessment, which includes clinical history and analysis with multimodal retinal imaging, electrophysiology, and visual field testing. If suitable for recruitment, a sample is taken and used for genetic analysis. Genetic analysis is conducted by use of a retinal gene panel target capture sequencing approach. With over 1000 participants from 710 pedigrees now screened, there is a positive candidate variant detection rate of approximately 70% (495/710). Where an autosomal recessive inheritance pattern is observed, an additional 9% (64/710) of probands have tested positive for a single candidate variant. Many novel variants have also been detected as part of this endeavor. The target capture approach is an economic and effective means of screening patients with inherited retinal disorders. Despite the advances in sequencing technology and the ever-decreasing associated processing costs, target capture remains an attractive option as the data produced is easily processed, analyzed, and stored compared to more comprehensive methods. However, with decreasing costs of whole genome and whole exome sequencing, the focus will likely move towards these methods for more comprehensive data generation.
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Affiliation(s)
- Laura Whelan
- The School of Genetics & Microbiology, Trinity College Dublin, D02 VF25 Dublin, Ireland; (A.D.); (M.C.); (P.H.); (P.F.K.); (G.J.F.)
| | - Adrian Dockery
- The School of Genetics & Microbiology, Trinity College Dublin, D02 VF25 Dublin, Ireland; (A.D.); (M.C.); (P.H.); (P.F.K.); (G.J.F.)
| | - Niamh Wynne
- The Research Foundation, Royal Victoria Eye and Ear Hospital, D02 XK51 Dublin, Ireland;
| | - Julia Zhu
- Clinical Genetics Centre for Ophthalmology, The Mater Misericordiae University Hospital, D07 R2WY Dublin, Ireland; (J.Z.); (K.S.); (J.T.); (J.J.O.); (D.K.)
| | - Kirk Stephenson
- Clinical Genetics Centre for Ophthalmology, The Mater Misericordiae University Hospital, D07 R2WY Dublin, Ireland; (J.Z.); (K.S.); (J.T.); (J.J.O.); (D.K.)
| | - Giuliana Silvestri
- Department of Ophthalmology, The Royal Victoria Hospital, Belfast BT12 6BA, Northern Ireland, UK;
- Centre for Experimental Medicine, Queen’s University Belfast, Belfast BT7 1NN, Northern Ireland, UK
| | - Jacqueline Turner
- Clinical Genetics Centre for Ophthalmology, The Mater Misericordiae University Hospital, D07 R2WY Dublin, Ireland; (J.Z.); (K.S.); (J.T.); (J.J.O.); (D.K.)
| | - James J. O’Byrne
- Clinical Genetics Centre for Ophthalmology, The Mater Misericordiae University Hospital, D07 R2WY Dublin, Ireland; (J.Z.); (K.S.); (J.T.); (J.J.O.); (D.K.)
| | - Matthew Carrigan
- The School of Genetics & Microbiology, Trinity College Dublin, D02 VF25 Dublin, Ireland; (A.D.); (M.C.); (P.H.); (P.F.K.); (G.J.F.)
| | - Peter Humphries
- The School of Genetics & Microbiology, Trinity College Dublin, D02 VF25 Dublin, Ireland; (A.D.); (M.C.); (P.H.); (P.F.K.); (G.J.F.)
| | - David Keegan
- Clinical Genetics Centre for Ophthalmology, The Mater Misericordiae University Hospital, D07 R2WY Dublin, Ireland; (J.Z.); (K.S.); (J.T.); (J.J.O.); (D.K.)
| | - Paul F. Kenna
- The School of Genetics & Microbiology, Trinity College Dublin, D02 VF25 Dublin, Ireland; (A.D.); (M.C.); (P.H.); (P.F.K.); (G.J.F.)
- The Research Foundation, Royal Victoria Eye and Ear Hospital, D02 XK51 Dublin, Ireland;
| | - G. Jane Farrar
- The School of Genetics & Microbiology, Trinity College Dublin, D02 VF25 Dublin, Ireland; (A.D.); (M.C.); (P.H.); (P.F.K.); (G.J.F.)
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Fadaie Z, Khan M, Del Pozo‐Valero M, Cornelis SS, Ayuso C, Cremers FPM, Roosing S, The ABCA4 study group. Identification of splice defects due to noncanonical splice site or deep-intronic variants in ABCA4. Hum Mutat 2019; 40:2365-2376. [PMID: 31397521 PMCID: PMC6899986 DOI: 10.1002/humu.23890] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/30/2019] [Accepted: 08/04/2019] [Indexed: 12/25/2022]
Abstract
Pathogenic variants in the ATP-binding cassette transporter A4 (ABCA4) gene cause a continuum of retinal disease phenotypes, including Stargardt disease. Noncanonical splice site (NCSS) and deep-intronic variants constitute a large fraction of disease-causing alleles, defining the functional consequences of which remains a challenge. We aimed to determine the effect on splicing of nine previously reported or unpublished NCSS variants, one near exon splice variant and nine deep-intronic variants in ABCA4, using in vitro splice assays in human embryonic kidney 293T cells. Reverse transcription-polymerase chain reaction and Sanger sequence analysis revealed splicing defects for 12 out of 19 variants. Four deep-intronic variants create pseudoexons or elongate the upstream exon. Furthermore, eight NCSS variants cause a partial deletion or skipping of one or more exons in messenger RNAs. Among the 12 variants, nine lead to premature stop codons and predicted truncated ABCA4 proteins. At least two deep-intronic variants affect splice enhancer and silencer motifs and, therefore, these conserved sequences should be carefully evaluated when predicting the outcome of NCSS and deep-intronic variants.
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Affiliation(s)
- Zeinab Fadaie
- Department of Human Genetics, Donders Institute for Brain, Cognition and BehaviorRadboud University Medical CenterNijmegenThe Netherlands
| | - Mubeen Khan
- Department of Human Genetics, Donders Institute for Brain, Cognition and BehaviorRadboud University Medical CenterNijmegenThe Netherlands
| | - Marta Del Pozo‐Valero
- Department of Human Genetics, Donders Institute for Brain, Cognition and BehaviorRadboud University Medical CenterNijmegenThe Netherlands
- Department of Genetics, Instituto de Investigación Sanitaria–Fundación Jiménez Díaz University HospitalUniversidad Autónoma de Madrid (IIS‐FJD, UAM)MadridSpain
| | - Stéphanie S. Cornelis
- Department of Human Genetics, Donders Institute for Brain, Cognition and BehaviorRadboud University Medical CenterNijmegenThe Netherlands
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria–Fundación Jiménez Díaz University HospitalUniversidad Autónoma de Madrid (IIS‐FJD, UAM)MadridSpain
| | - Frans P. M. Cremers
- Department of Human Genetics, Donders Institute for Brain, Cognition and BehaviorRadboud University Medical CenterNijmegenThe Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Donders Institute for Brain, Cognition and BehaviorRadboud University Medical CenterNijmegenThe Netherlands
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Prevalence of ABCA4 Deep-Intronic Variants and Related Phenotype in An Unsolved "One-Hit" Cohort with Stargardt Disease. Int J Mol Sci 2019; 20:ijms20205053. [PMID: 31614660 PMCID: PMC6829239 DOI: 10.3390/ijms20205053] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/24/2019] [Accepted: 10/09/2019] [Indexed: 02/06/2023] Open
Abstract
We investigated the prevalence of reported deep-intronic variants in a French cohort of 70 patients with Stargardt disease harboring a monoallelic pathogenic variant on the exonic regions of ABCA4. Direct Sanger sequencing of selected intronic regions of ABCA4 was conducted. Complete phenotypic analysis and correlation with the genotype was performed in case a known intronic pathogenic variant was identified. All other variants found on the analyzed sequences were queried for minor allele frequency and possible pathogenicity by in silico predictions. The second mutated allele was found in 14 (20%) subjects. The three known deep-intronic variants found were c.5196+1137G>A in intron 36 (6 subjects), c.4539+2064C>T in intron 30 (4 subjects) and c.4253+43G>A in intron 28 (4 subjects). Even though the phenotype depends on the compound effect of the biallelic variants, a genotype-phenotype correlation suggests that the c.5196+1137G>A was mostly associated with a mild phenotype and the c.4539+2064C>T with a more severe one. A variable effect was instead associated with the variant c.4253+43G>A. In addition, two novel variants, c.768+508A>G and c.859-245_859-243delinsTGA never associated with Stargardt disease before, were identified and a possible splice defect was predicted in silico. Our study calls for a larger cohort analysis including targeted locus sequencing and 3D protein modeling to better understand phenotype-genotype correlations associated with deep-intronic changes and patients’ selection for clinical trials.
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Aberrant Splicing Events Associated to CDH23 Noncanonical Splice Site Mutations in a Proband with Atypical Usher Syndrome 1. Genes (Basel) 2019; 10:genes10100732. [PMID: 31546658 PMCID: PMC6826400 DOI: 10.3390/genes10100732] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/17/2019] [Accepted: 09/19/2019] [Indexed: 12/16/2022] Open
Abstract
Aims: The aim of this study was the genetic diagnosis by next generation sequencing (NGS) of a patient diagnosed with Usher syndrome type 2 and the functional evaluation of the identified genetic variants to establish a phenotype–genotype correlation. Methods: Whole exome sequencing (WES) analysis identified two heterozygous intronic variants in CDH23, a gene responsible of Usher syndrome type 1. Evaluation of the putative splicing effects was performed in vivo, in whole blood samples, and in vitro, by transfection of midigene constructs in HEK293T cells. Results: Two intronic variants were identified in intron 45 of CDH23—one novel, c.6050-15G>A, and the other, c.6050-9G>A, already reported as a noncanonical splice site (NCSS) mutation—with partial functional characterization. In vivo and in vitro analyses showed aberrant transcripts by the addition of 13 and 7 nucleotides to exon 46, respectively. Transcript degradation by nonsense mediated decay (NMD) in blood cells could only be prevented by cycloheximide treatment. Midigene constructs showed that the two variants contributed to exon skipping and generated aberrantly spliced transcripts. Conclusions: A combination of in vivo and in vitro assays provided a comprehensive view of the physiological effects of NCSS variants, which in this case led to a clinical reassignment of the proband as affected with atypical USH1 syndrome.
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