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Thuma TBT, Procopio RA, Jimenez HJ, Gunton KB, Pulido JS. Hypomorphic variants in inherited retinal and ocular diseases: A review of the literature with clinical cases. Surv Ophthalmol 2024; 69:337-348. [PMID: 38036193 DOI: 10.1016/j.survophthal.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/02/2023]
Abstract
Hypomorphic variants decrease, but do not eliminate, gene function via a reduction in the amount of mRNA or protein product produced by a gene or by production of a gene product with reduced function. Many hypomorphic variants have been implicated in inherited retinal diseases (IRDs) and other genetic ocular conditions; however, there is heterogeneity in the use of the term "hypomorphic" in the scientific literature. We searched for all hypomorphic variants reported to cause IRDs and ocular disorders. We also discuss the presence of hypomorphic variants in the patient population of our ocular genetics department over the past decade. We propose that standardized criteria should be adopted for use of the term "hypomorphic" to describe gene variants to improve genetic counseling and patient care outcomes.
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Affiliation(s)
- Tobin B T Thuma
- Department of Pediatric Ophthalmology and Strabismus, Wills Eye Hospital, Philadelphia, PA, USA
| | | | - Hiram J Jimenez
- Vickie and Jack Farber Vision Research Center, Wills Eye Hospital, Philadelphia, PA, USA
| | - Kammi B Gunton
- Department of Pediatric Ophthalmology and Strabismus, Wills Eye Hospital, Philadelphia, PA, USA
| | - Jose S Pulido
- Vickie and Jack Farber Vision Research Center, Wills Eye Hospital, Philadelphia, PA, USA; Retina Service, Wills Eye Hospital, Philadelphia, PA, USA.
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2
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Cevik S, Wangtiraumnuay N, Van Schelvergem K, Tsukikawa M, Capasso J, Biswas SB, Bodt B, Levin AV, Biswas-Fiss E. Protein modeling and in silico analysis to assess pathogenicity of ABCA4 variants in patients with inherited retinal disease. Mol Vis 2023; 29:217-233. [PMID: 38222458 PMCID: PMC10784225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/23/2023] [Indexed: 01/16/2024] Open
Abstract
Purpose The retina-specific ABCA transporter, ABCA4, plays an essential role in translocating retinoids required by the visual cycle. ABCA4 genetic variants are known to cause a wide range of inherited retinal disorders, including Stargardt disease and cone-rod dystrophy. More than 1,400 ABCA4 missense variants have been identified; however, more than half of these remain variants of uncertain significance (VUS). The purpose of this study was to employ a predictive strategy to assess the pathogenicity of ABCA4 variants in inherited retinal diseases using protein modeling and computational approaches. Methods We studied 13 clinically well-defined patients with ABCA4 retinopathies and identified the presence of 10 missense variants, including one novel variant in the ABCA4 gene, by next-generation sequencing (NGS). All variants were structurally analyzed using AlphaFold2 models and existing experimental structures of human ABCA4 protein. The results of these analyses were compared with patient clinical presentations to test the effectiveness of the methods employed in predicting variant pathogenicity. Results We conducted a phenotype-genotype comparison of 13 genetically and phenotypically well-defined retinal disease patients. The in silico protein structure analyses we employed successfully detected the deleterious effect of missense variants found in this affected patient cohort. Our study provides American College of Medical Genetics and Genomics (ACMG)-defined supporting evidence of the pathogenicity of nine missense ABCA4 variants, aligning with the observed clinical phenotypes in this cohort. Conclusions In this report, we describe a systematic approach to predicting the pathogenicity of ABCA4 variants by means of three-dimensional (3D) protein modeling and in silico structure analysis. Our results demonstrate concordance between disease severity and structural changes in protein models induced by genetic variations. Furthermore, the present study suggests that in silico protein structure analysis can be used as a predictor of pathogenicity and may facilitate the assessment of genetic VUS.
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Affiliation(s)
- Senem Cevik
- Department of Medical and Molecular Sciences, University of Delaware College of Health Sciences, Newark, DE
| | - Nutsuchar Wangtiraumnuay
- Department of Ophthalmology, Queen Sirikit National Institute of Child Health, Bangkok, Thailand
| | | | - Mai Tsukikawa
- Department of Ophthalmology, Duke University, Durham, NC
| | - Jenina Capasso
- Departments of Ophthalmology and Pediatrics, Flaum Eye Institute and Golisano Children's Hospital, University of Rochester, Rochester, NY
| | - Subhasis B Biswas
- Department of Medical and Molecular Sciences, University of Delaware College of Health Sciences, Newark, DE
| | - Barry Bodt
- College of Health Sciences Biostatistics Core Facility, University of Delaware, Newark, DE
| | - Alex V Levin
- Departments of Ophthalmology and Pediatrics, Flaum Eye Institute and Golisano Children's Hospital, University of Rochester, Rochester, NY
| | - Esther Biswas-Fiss
- Department of Medical and Molecular Sciences, University of Delaware College of Health Sciences, Newark, DE
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3
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Kaltak M, Corradi Z, Collin RWJ, Swildens J, Cremers FPM. Stargardt disease-associated missense and synonymous ABCA4 variants result in aberrant splicing. Hum Mol Genet 2023; 32:3078-3089. [PMID: 37555651 PMCID: PMC10586196 DOI: 10.1093/hmg/ddad129] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/03/2023] [Accepted: 08/03/2023] [Indexed: 08/10/2023] Open
Abstract
Missense variants in ABCA4 constitute ~50% of causal variants in Stargardt disease (STGD1). Their pathogenicity is attributed to their direct effect on protein function, whilst their potential impact on pre-mRNA splicing disruption remains poorly understood. Interestingly, synonymous ABCA4 variants have previously been classified as 'severe' variants based on in silico analyses. Here, we systemically investigated the role of synonymous and missense variants in ABCA4 splicing by combining computational predictions and experimental assays. To identify variants of interest, we used SpliceAI to ascribe defective splice predictions on a dataset of 5579 biallelic STGD1 probands. We selected those variants with predicted delta scores for acceptor/donor gain > 0.20, and no previous reports on their effect on splicing. Fifteen ABCA4 variants were selected, 4 of which were predicted to create a new splice acceptor site and 11 to create a new splice donor site. In addition, three variants of interest with delta scores < 0.20 were included. The variants were introduced in wild-type midigenes that contained 4-12 kb of ABCA4 genomic sequence, which were subsequently expressed in HEK293T cells. By using RT-PCR and Sanger sequencing, we identified splice aberrations for 16 of 18 analyzed variants. SpliceAI correctly predicted the outcomes for 15 out of 18 variants, illustrating its reliability in predicting the impact of coding ABCA4 variants on splicing. Our findings highlight a causal role for coding ABCA4 variants in splicing aberrations, improving the severity assessment of missense and synonymous ABCA4 variants, and guiding to new treatment strategies for STGD1.
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Affiliation(s)
- Melita Kaltak
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
- R&D Department, ProQR Therapeutics, Leiden, 2333 CK, The Netherlands
| | - Zelia Corradi
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
| | - Jim Swildens
- R&D Department, ProQR Therapeutics, Leiden, 2333 CK, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6525 GA, The Netherlands
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4
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Kaltak M, Blanco-Garavito R, Molday LL, Dhaenens CM, Souied EE, Platenburg G, Swildens J, Molday RS, Cremers FPM. Stargardt disease-associated in-frame ABCA4 exon 17 skipping results in significant ABCA4 function. J Transl Med 2023; 21:546. [PMID: 37587475 PMCID: PMC10428568 DOI: 10.1186/s12967-023-04406-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 08/01/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND ABCA4, the gene implicated in Stargardt disease (STGD1), contains 50 exons, of which 17 contain multiples of three nucleotides. The impact of in-frame exon skipping is yet to be determined. Antisense oligonucleotides (AONs) have been investigated in Usher syndrome-associated genes to induce skipping of in-frame exons carrying severe variants and mitigate their disease-linked effect. Upon the identification of a STGD1 proband carrying a novel exon 17 canonical splice site variant, the activity of ABCA4 lacking 22 amino acids encoded by exon 17 was examined, followed by design of AONs able to induce exon 17 skipping. METHODS A STGD1 proband was compound heterozygous for the splice variant c.2653+1G>A, that was predicted to result in in-frame skipping of exon 17, and a null variant [c.735T>G, p.(Tyr245*)]. Clinical characteristics of this proband were studied using multi-modal imaging and complete ophthalmological examination. The aberrant splicing of c.2653+1G>A was investigated in vitro in HEK293T cells with wild-type and mutant midigenes. The residual activity of the mutant ABCA4 protein lacking Asp864-Gly885 encoded by exon 17 was analyzed with all-trans-retinal-activated ATPase activity assay, along with its subcellular localization. To induce exon 17 skipping, the effect of 40 AONs was examined in vitro in WT WERI-Rb-1 cells and 3D human retinal organoids. RESULTS Late onset STGD1 in the proband suggests that c.2653+1G>A does not have a fully deleterious effect. The in vitro splice assay confirmed that this variant leads to ABCA4 transcripts without exon 17. ABCA4 Asp864_Gly863del was stable and retained 58% all-trans-retinal-activated ATPase activity compared to WT ABCA4. This sequence is located in an unstructured linker region between transmembrane domain 6 and nucleotide-binding domain-1 of ABCA4. AONs were designed to possibly reduce pathogenicity of severe variants harbored in exon 17. The best AON achieved 59% of exon 17 skipping in retinal organoids. CONCLUSIONS Exon 17 deletion in ABCA4 does not result in the absence of protein activity and does not cause a severe STGD1 phenotype when in trans with a null allele. By applying AONs, the effect of severe variants in exon 17 can potentially be ameliorated by exon skipping, thus generating partial ABCA4 activity in STGD1 patients.
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Affiliation(s)
- Melita Kaltak
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- ProQR Therapeutics, Leiden, The Netherlands
| | - Rocio Blanco-Garavito
- Department of Ophthalmology, Intercommunal Hospital Center and Henri Mondor Hospital, Paris-Est Créteil University, Creteil, France
| | - Laurie L Molday
- Department of Biochemistry and Molecular Biology, Department of Ophthalmology and Visual Sciences, Centre for Macular Research, University of British Columbia, Vancouver, BC, Canada
| | - Claire-Marie Dhaenens
- University of Lille, Inserm, CHU Lille, U1172-LilNCog-Lille Neuroscience & Cognition, Lille, France
| | - Eric E Souied
- Department of Ophthalmology, Intercommunal Hospital Center and Henri Mondor Hospital, Paris-Est Créteil University, Creteil, France
| | | | | | - Robert S Molday
- Department of Biochemistry and Molecular Biology, Department of Ophthalmology and Visual Sciences, Centre for Macular Research, University of British Columbia, Vancouver, BC, Canada
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
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Cevik S, Biswas SB, Biswas-Fiss EE. Structural and Pathogenic Impacts of ABCA4 Variants in Retinal Degenerations-An In-Silico Study. Int J Mol Sci 2023; 24:ijms24087280. [PMID: 37108442 PMCID: PMC10138569 DOI: 10.3390/ijms24087280] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The retina-specific ATP-binding cassette transporter protein ABCA4 is responsible for properly continuing the visual cycle by removing toxic retinoid byproducts of phototransduction. Functional impairment caused by ABCA4 sequence variations is the leading cause of autosomal recessive inherited retinal disorders, including Stargardt disease, retinitis pigmentosa, and cone-rod dystrophy. To date, more than 3000 ABCA4 genetic variants have been identified, approximately 40 percent of which have not been able to be classified for pathogenicity assessments. This study examined 30 missense ABCA4 variants using AlphaFold2 protein modeling and computational structure analysis for pathogenicity prediction. All variants classified as pathogenic (n = 10) were found to have deleterious structural consequences. Eight of the ten benign variants were structurally neutral, while the remaining two resulted in mild structural changes. This study's results provided multiple lines of computational pathogenicity evidence for eight ABCA4 variants of uncertain clinical significance. Overall, in silico analyses of ABCA4 can provide a valuable tool for understanding the molecular mechanisms of retinal degeneration and their pathogenic impact.
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Affiliation(s)
- Senem Cevik
- Department of Medical and Molecular Sciences, College of Health Sciences, University of Delaware, 16 West Main Street, Suite 302 WHL, Newark, DE 19716, USA
- Ammon Pinizzotto Biopharmaceutical Innovation Center, 590 Avenue 1743, Newark, DE 19713, USA
| | - Subhasis B Biswas
- Department of Medical and Molecular Sciences, College of Health Sciences, University of Delaware, 16 West Main Street, Suite 302 WHL, Newark, DE 19716, USA
- Ammon Pinizzotto Biopharmaceutical Innovation Center, 590 Avenue 1743, Newark, DE 19713, USA
| | - Esther E Biswas-Fiss
- Department of Medical and Molecular Sciences, College of Health Sciences, University of Delaware, 16 West Main Street, Suite 302 WHL, Newark, DE 19716, USA
- Ammon Pinizzotto Biopharmaceutical Innovation Center, 590 Avenue 1743, Newark, DE 19713, USA
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6
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Xu T, Molday L, Molday R. Retinal-phospholipid Schiff-base conjugates and their interaction with ABCA4, the ABC transporter associated with Stargardt Disease. J Biol Chem 2023; 299:104614. [PMID: 36931393 PMCID: PMC10127136 DOI: 10.1016/j.jbc.2023.104614] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/10/2023] [Accepted: 03/11/2023] [Indexed: 03/17/2023] Open
Abstract
N-retinylidene-phosphatidylethanolamine (N-Ret-PE), the Schiff-base conjugate formed through the reversible reaction of retinal (Vitamin A-aldehyde) and phosphatidylethanolamine, plays a crucial role in the visual cycle and visual pigment photoregeneration. However, N-Ret-PE can react with another molecule of retinal to form toxic di-retinoids if not removed from photoreceptors through its transport across photoreceptor membranes by the ATP-binding-cassette transporter ABCA4. Loss-of-function mutations in ABCA4 are known to cause Stargardt disease (STGD1), an inherited retinal degenerative disease associated with the accumulation of fluorescent di-retinoids and severe loss in vision. A larger assessment of retinal-phospholipid Schiff-base conjugates in photoreceptors is needed, along with further investigation of ABCA4 residues important for N-Ret-PE binding. In this study we show that N-Ret-PE formation is dependent on pH and phospholipid content. When retinal is added to liposomes or photoreceptor membranes, 40-60% is converted to N-Ret-PE at physiological pH. Phosphatidylserine and taurine also react with retinal to form N-retinylidene-phosphatidylserine (N-Ret-PS) and N-retinylidene-taurine, respectively, but at significantly lower levels. N-Ret-PS is not a substrate for ABCA4 and reacts poorly with retinal to form di-retinoids. Additionally, amino acid residues within the binding pocket of ABCA4 that contribute to its interaction with N-Ret-PE were identified and characterized using site-directed mutagenesis together with functional and binding assays. Substitution of arginine residues and hydrophobic residues with alanine or residues implicated in STGD1 significantly reduced or in some cases eliminated substrate-activated ATPase activity and substrate binding. Collectively, this study provides important insight into conditions which affect retinal-phospholipid Schiff-base formation and mechanisms underlying the pathogenesis of STGD1.
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Affiliation(s)
- Tongzhou Xu
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, B.C. V6T 1Z3 Canada
| | - LaurieL Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, B.C. V6T 1Z3 Canada
| | - RobertS Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, B.C. V6T 1Z3 Canada.
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Liu Q, Liu J, Higuchi A. hPSC-derived RPE transplantation for the treatment of macular degeneration. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 199:227-269. [PMID: 37678973 DOI: 10.1016/bs.pmbts.2023.02.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Macular degeneration (MD) is a group of diseases characterized by irreversible and progressive vision loss. Patients with MD suffer from severely impaired central vision, especially elderly people. Currently, only one type of MD, wet age-related macular degeneration (AMD), can be treated with anti-vascular endothelium growth factor (VEGF) drugs. Other types of MD remain difficult to treat. With the advent of human pluripotent stem cells (hPSCs) and their differentiation into retinal pigmented epithelium (RPE), it is promising to treat patients with MD by transplantation of hPSC-derived RPE into the subretinal space. In this review, the current progress in hPSC-derived RPE transplantation for the treatment of patients with MD is described from bench to bedside, including hPSC differentiation into RPE and the characterization and usage of hPSC-derived RPE for transplantation into patients with MD.
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Affiliation(s)
- Qian Liu
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Jun Liu
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Akon Higuchi
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China; Department of Chemical and Materials Engineering, National Central University, Jhongli, Taoyuan, Taiwan.
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8
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Farnoodian M, Bose D, Khristov V, Susaimanickam PJ, Maddileti S, Mariappan I, Abu-Asab M, Campos M, Villasmil R, Wan Q, Maminishkis A, McGaughey D, Barone F, Gundry RL, Riordon DR, Boheler KR, Sharma R, Bharti K. Cell-autonomous lipid-handling defects in Stargardt iPSC-derived retinal pigment epithelium cells. Stem Cell Reports 2022; 17:2438-2450. [DOI: 10.1016/j.stemcr.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022] Open
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Kamenarova K, Mihova K, Veleva N, Mermeklieva E, Mihaylova B, Dimitrova G, Oscar A, Shandurkov I, Cherninkova S, Kaneva R. Panel-based next-generation sequencing identifies novel mutations in Bulgarian patients with inherited retinal dystrophies. Mol Genet Genomic Med 2022; 10:e1997. [PMID: 35656873 PMCID: PMC9356554 DOI: 10.1002/mgg3.1997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 04/07/2022] [Accepted: 05/13/2022] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Next-generation sequencing (NGS)-based method is being used broadly for genetic testing especially for clinically and genetically heterogeneous disorders, such as inherited retinal degenerations (IRDs) but still not routinely used for molecular diagnostics in Bulgaria. Consequently, the purpose of this study was to evaluate the effectiveness of a molecular diagnostic approach, based on targeted NGS for the identification of the disease-causing mutations in 16 Bulgarian patients with different IRDs. METHODS We applied a customized NGS panel, including 125 genes associated with retinal and other eye diseases to the patients with hereditary retinopathies. RESULTS Systematic filtering approach coupled with copy number variation analysis and segregation study lead to the identification of 16 pathogenic and likely pathogenic variants in 12/16 (75%) of IRD patients, 2 of which novel (12.5%): ABCA4-c.668delA (p.K223Rfs18) and RР1-c.2015dupA (p.K673Efs*25). Mutations in the ABCA4, PRPH2, USH2A, BEST1, RР1, CDHR1, and RHO genes were detected reaching a diagnostic yield between 42.9% for Retinitis pigmentosa cases and 100% for macular degeneration, Usher syndrome, and cone-rod dystrophy patients. CONCLUSION Our results confirm the usefulness of targeted NGS approach based on frequently mutated genes as a comprehensive and successful genetic diagnostic tool for IRDs with significant impact on patients counseling.
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Affiliation(s)
- Kunka Kamenarova
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria.,Laboratory of Genomic Diagnostics, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
| | - Kalina Mihova
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria.,Laboratory of Genomic Diagnostics, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
| | - Nevyana Veleva
- Department of Ophthalmology, University Hospital "Alexandrovska", Medical University of Sofia, Sofia, Bulgaria
| | - Elena Mermeklieva
- Clinic of Ophthalmology, University Hospital "Lozenetz", Medical Faculty, Sofia University "St. Kliment Ohridski", Sofia, Bulgaria
| | | | - Galina Dimitrova
- Department of Ophthalmology, University Hospital "Alexandrovska", Medical University of Sofia, Sofia, Bulgaria
| | - Alexander Oscar
- Department of Ophthalmology, University Hospital "Alexandrovska", Medical University of Sofia, Sofia, Bulgaria
| | | | - Sylvia Cherninkova
- Department of Neurology, University hospital "Alexandrovska", Medical University of Sofia, Sofia, Bulgaria
| | - Radka Kaneva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria.,Laboratory of Genomic Diagnostics, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
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10
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Molday RS, Garces FA, Scortecci JF, Molday LL. Structure and function of ABCA4 and its role in the visual cycle and Stargardt macular degeneration. Prog Retin Eye Res 2021; 89:101036. [PMID: 34954332 DOI: 10.1016/j.preteyeres.2021.101036] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/07/2021] [Accepted: 12/13/2021] [Indexed: 12/17/2022]
Abstract
ABCA4 is a member of the superfamily of ATP-binding cassette (ABC) transporters that is preferentially localized along the rim region of rod and cone photoreceptor outer segment disc membranes. It uses the energy from ATP binding and hydrolysis to transport N-retinylidene-phosphatidylethanolamine (N-Ret-PE), the Schiff base adduct of retinal and phosphatidylethanolamine, from the lumen to the cytoplasmic leaflet of disc membranes. This ensures that all-trans-retinal and excess 11-cis-retinal are efficiently cleared from photoreceptor cells thereby preventing the accumulation of toxic retinoid compounds. Loss-of-function mutations in the gene encoding ABCA4 cause autosomal recessive Stargardt macular degeneration, also known as Stargardt disease (STGD1), and related autosomal recessive retinopathies characterized by impaired central vision and an accumulation of lipofuscin and bis-retinoid compounds. High resolution structures of ABCA4 in its substrate and nucleotide free state and containing bound N-Ret-PE or ATP have been determined by cryo-electron microscopy providing insight into the molecular architecture of ABCA4 and mechanisms underlying substrate recognition and conformational changes induced by ATP binding. The expression and functional characterization of a large number of disease-causing missense ABCA4 variants have been determined. These studies have shed light into the molecular mechanisms underlying Stargardt disease and a classification that reliably predicts the effect of a specific missense mutation on the severity of the disease. They also provide a framework for developing rational therapeutic treatments for ABCA4-associated diseases.
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Affiliation(s)
- Robert S Molday
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, B.C., Canada; Department of Ophthalmology & Visual Sciences, University of British Columbia, Vancouver, B.C., Canada.
| | - Fabian A Garces
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, B.C., Canada
| | | | - Laurie L Molday
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, B.C., Canada
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11
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Heath Jeffery RC, Thompson JA, Lo J, Lamey TM, McLaren TL, McAllister IL, Constable IJ, De Roach JN, Chen FK. Genotype-Specific Lesion Growth Rates in Stargardt Disease. Genes (Basel) 2021; 12:1981. [PMID: 34946930 PMCID: PMC8701386 DOI: 10.3390/genes12121981] [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: 11/09/2021] [Revised: 12/03/2021] [Accepted: 12/10/2021] [Indexed: 01/10/2023] Open
Abstract
Reported growth rates (GR) of atrophic lesions in Stargardt disease (STGD1) vary widely. In the present study, we report the longitudinal natural history of patients with confirmed biallelic ABCA4 mutations from five genotype groups: c.6079C>T, c.[2588G>C;5603A>T], c.3113C>T, c.5882G>A and c.5603A>T. Fundus autofluorescence (AF) 30° × 30° images were manually segmented for boundaries of definitely decreased autofluorescence (DDAF). The primary outcome was the effective radius GR across five genotype groups. The age of DDAF formation in each eye was calculated using the x-intercept of the DDAF effective radius against age. Discordance between age at DDAF formation and symptom onset was compared. A total of 75 eyes from 39 STGD1 patients (17 male [44%]; mean ± SD age 45 ± 19 years; range 21-86) were recruited. Patients with c.3113C>T or c.6079C>T had a significantly faster effective radius GR at 0.17 mm/year (95% CI 0.12 to 0.22; p < 0.001 and 0.14 to 0.21; p < 0.001) respectively, as compared to those patients harbouring c.5882G>A at 0.06 mm/year (95% CI 0.03-0.09), respectively. Future clinical trial design should consider the effect of genotype on the effective radius GR and the timing of DDAF formation relative to symptom onset.
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Affiliation(s)
- Rachael C. Heath Jeffery
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Nedlands, WA 6009, Australia; (R.C.H.J.); (T.M.L.); (T.L.M.); (I.L.M.); (I.J.C.); (J.N.D.R.)
- Department of Ophthalmology, Royal Perth Hospital, Perth, WA 6000, 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;
| | - Johnny Lo
- School of Science, Edith Cowan University, Joondalup, WA 6027, Australia;
| | - Tina M. Lamey
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Nedlands, WA 6009, Australia; (R.C.H.J.); (T.M.L.); (T.L.M.); (I.L.M.); (I.J.C.); (J.N.D.R.)
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia;
| | - Terri L. McLaren
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Nedlands, WA 6009, Australia; (R.C.H.J.); (T.M.L.); (T.L.M.); (I.L.M.); (I.J.C.); (J.N.D.R.)
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia;
| | - Ian L. McAllister
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Nedlands, WA 6009, Australia; (R.C.H.J.); (T.M.L.); (T.L.M.); (I.L.M.); (I.J.C.); (J.N.D.R.)
| | - Ian J. Constable
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Nedlands, WA 6009, Australia; (R.C.H.J.); (T.M.L.); (T.L.M.); (I.L.M.); (I.J.C.); (J.N.D.R.)
| | - John N. De Roach
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Nedlands, WA 6009, Australia; (R.C.H.J.); (T.M.L.); (T.L.M.); (I.L.M.); (I.J.C.); (J.N.D.R.)
- 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 (Incorporating Lions Eye Institute), The University of Western Australia, Nedlands, WA 6009, Australia; (R.C.H.J.); (T.M.L.); (T.L.M.); (I.L.M.); (I.J.C.); (J.N.D.R.)
- Department of Ophthalmology, Royal Perth Hospital, Perth, WA 6000, Australia
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia;
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12
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Heath Jeffery RC, Thompson JA, Lamey TM, McLaren TL, McAllister IL, Constable IJ, Mackey DA, De Roach JN, Chen FK. CLASSIFYING ABCA4 MUTATION SEVERITY USING AGE-DEPENDENT ULTRA-WIDEFIELD FUNDUS AUTOFLUORESCENCE-DERIVED TOTAL LESION SIZE. Retina 2021; 41:2578-2588. [PMID: 34125082 DOI: 10.1097/iae.0000000000003227] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
PURPOSE To establish a mutation-specific age-dependent ultra-widefield fundus autofluorescence (UWF-FAF) trajectory in a large Stargardt disease (STGD1) cohort using total lesion size (TLS) and to develop a clinical method for variant classification. METHODS A retrospective study of patients with biallelic ABCA4 mutations that were evaluated with UWF-FAF. Boundaries of TLS, defined by stippled hyper/hypoautofluorescence, were outlined manually. Pathogenicity was assessed according to ACMG/AMP criteria, and mutation severities were classified based on the current literature. Age-dependent trajectories in TLS were examined in patients with nullizygous, mild, and intermediate mutations. Mutations of uncertain severities were classified using a clinical criterion based on age of symptom onset and TLS. RESULTS Eighty-one patients with STGD1 (mean age = 42 ± 20 years and mean visual acuity = 20/200) were recruited from 65 unrelated families. Patients with biallelic null/severe variants (n = 6) demonstrated an increase in TLS during their second decade reaching a mean ± SD of 796 ± 29 mm2 by age 40. Those harboring mild mutations c.5882G>A or c.5603A>T had lesions confined to the posterior pole with a mean ± SD TLS of 30 ± 39 mm2. Intermediate mutations c.6079C>T or c.[2588G>C;5603A>T] in trans with a null/severe mutation had a mean ± SD TLS of 397 ± 29 mm2. Thirty-two mutations were predicted to cause severe (n = 22), intermediate (n = 6), and mild (n = 5) impairment of ABCA4 function based on age of symptom onset and TLS. CONCLUSION Age-dependent TLS showed unique ABCA4 mutation-specific trajectories. Our novel clinical criterion using age of symptom onset and TLS to segregate ABCA4 mutations into three severity groups requires further molecular studies to confirm its validity.
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Affiliation(s)
- Rachael C Heath Jeffery
- Centre for Ophthalmology and Visual Science (incorporating Lions Eye Institute), The University of Western Australia, Australia
- Department of Ophthalmology, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Jennifer A Thompson
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia; and
| | - Tina M Lamey
- Centre for Ophthalmology and Visual Science (incorporating Lions Eye Institute), The University of Western Australia, Australia
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia; and
| | - Terri L McLaren
- Centre for Ophthalmology and Visual Science (incorporating Lions Eye Institute), The University of Western Australia, Australia
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia; and
| | - Ian L McAllister
- Centre for Ophthalmology and Visual Science (incorporating Lions Eye Institute), The University of Western Australia, Australia
| | - Ian J Constable
- Centre for Ophthalmology and Visual Science (incorporating Lions Eye Institute), The University of Western Australia, Australia
| | - David A Mackey
- Centre for Ophthalmology and Visual Science (incorporating Lions Eye Institute), The University of Western Australia, Australia
| | - John N De Roach
- Centre for Ophthalmology and Visual Science (incorporating Lions Eye Institute), The University of Western Australia, Australia
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia; and
| | - Fred K Chen
- Centre for Ophthalmology and Visual Science (incorporating Lions Eye Institute), The University of Western Australia, Australia
- Department of Ophthalmology, Royal Perth Hospital, Perth, Western Australia, Australia
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia; and
- Department of Ophthalmology, Perth Children's Hospital, Nedlands, Western Australia, Australia
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13
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Schneider N, Sundaresan Y, Gopalakrishnan P, Beryozkin A, Hanany M, Levanon EY, Banin E, Ben-Aroya S, Sharon D. Inherited retinal diseases: Linking genes, disease-causing variants, and relevant therapeutic modalities. Prog Retin Eye Res 2021; 89:101029. [PMID: 34839010 DOI: 10.1016/j.preteyeres.2021.101029] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/11/2022]
Abstract
Inherited retinal diseases (IRDs) are a clinically complex and heterogenous group of visual impairment phenotypes caused by pathogenic variants in at least 277 nuclear and mitochondrial genes, affecting different retinal regions, and depleting the vision of affected individuals. Genes that cause IRDs when mutated are unique by possessing differing genotype-phenotype correlations, varying inheritance patterns, hypomorphic alleles, and modifier genes thus complicating genetic interpretation. Next-generation sequencing has greatly advanced the identification of novel IRD-related genes and pathogenic variants in the last decade. For this review, we performed an in-depth literature search which allowed for compilation of the Global Retinal Inherited Disease (GRID) dataset containing 4,798 discrete variants and 17,299 alleles published in 31 papers, showing a wide range of frequencies and complexities among the 194 genes reported in GRID, with 65% of pathogenic variants being unique to a single individual. A better understanding of IRD-related gene distribution, gene complexity, and variant types allow for improved genetic testing and therapies. Current genetic therapeutic methods are also quite diverse and rely on variant identification, and range from whole gene replacement to single nucleotide editing at the DNA or RNA levels. IRDs and their suitable therapies thus require a range of effective disease modelling in human cells, granting insight into disease mechanisms and testing of possible treatments. This review summarizes genetic and therapeutic modalities of IRDs, provides new analyses of IRD-related genes (GRID and complexity scores), and provides information to match genetic-based therapies such as gene-specific and variant-specific therapies to the appropriate individuals.
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Affiliation(s)
- Nina Schneider
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Yogapriya Sundaresan
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Prakadeeswari Gopalakrishnan
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Avigail Beryozkin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Mor Hanany
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Shay Ben-Aroya
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel.
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14
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Scortecci JF, Molday LL, Curtis SB, Garces FA, Panwar P, Van Petegem F, Molday RS. Cryo-EM structures of the ABCA4 importer reveal mechanisms underlying substrate binding and Stargardt disease. Nat Commun 2021; 12:5902. [PMID: 34625547 PMCID: PMC8501128 DOI: 10.1038/s41467-021-26161-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 09/20/2021] [Indexed: 12/04/2022] Open
Abstract
ABCA4 is an ATP-binding cassette (ABC) transporter that flips N-retinylidene-phosphatidylethanolamine (N-Ret-PE) from the lumen to the cytoplasmic leaflet of photoreceptor membranes. Loss-of-function mutations cause Stargardt disease (STGD1), a macular dystrophy associated with severe vision loss. To define the mechanisms underlying substrate binding and STGD1, we determine the cryo-EM structure of ABCA4 in its substrate-free and bound states. The two structures are similar and delineate an elongated protein with the two transmembrane domains (TMD) forming an outward facing conformation, extended and twisted exocytoplasmic domains (ECD), and closely opposed nucleotide binding domains. N-Ret-PE is wedged between the two TMDs and a loop from ECD1 within the lumen leaflet consistent with a lateral access mechanism and is stabilized through hydrophobic and ionic interactions with residues from the TMDs and ECDs. Our studies provide a framework for further elucidating the molecular mechanism associated with lipid transport and disease and developing promising disease interventions.
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Affiliation(s)
| | - Laurie L Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Susan B Curtis
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Fabian A Garces
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Pankaj Panwar
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Robert S Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, BC, Canada.
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15
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Huang D, Heath Jeffery RC, Aung-Htut MT, McLenachan S, Fletcher S, Wilton SD, Chen FK. Stargardt disease and progress in therapeutic strategies. Ophthalmic Genet 2021; 43:1-26. [PMID: 34455905 DOI: 10.1080/13816810.2021.1966053] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background: Stargardt disease (STGD1) is an autosomal recessive retinal dystrophy due to mutations in ABCA4, characterized by subretinal deposition of lipofuscin-like substances and bilateral centrifugal vision loss. Despite the tremendous progress made in the understanding of STGD1, there are no approved treatments to date. This review examines the challenges in the development of an effective STGD1 therapy.Materials and Methods: A literature review was performed through to June 2021 summarizing the spectrum of retinal phenotypes in STGD1, the molecular biology of ABCA4 protein, the in vivo and in vitro models used to investigate the mechanisms of ABCA4 mutations and current clinical trials.Results: STGD1 phenotypic variability remains an challenge for clinical trial design and patient selection. Pre-clinical development of therapeutic options has been limited by the lack of animal models reflecting the diverse phenotypic spectrum of STDG1. Patient-derived cell lines have facilitated the characterization of splice mutations but the clinical presentation is not always predicted by the effect of specific mutations on retinoid metabolism in cellular models. Current therapies primarily aim to delay vision loss whilst strategies to restore vision are less well developed.Conclusions: STGD1 therapy development can be accelerated by a deeper understanding of genotype-phenotype correlations.
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Affiliation(s)
- Di Huang
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Western Australia, Australia.,Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), the University of Western Australia, Nedlands, Western Australia, Australia.,Perron Institute for Neurological and Translational Science & the University of Western Australia, Nedlands, Western Australia, Australia
| | - Rachael C Heath Jeffery
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), the University of Western Australia, Nedlands, Western Australia, Australia
| | - May Thandar Aung-Htut
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Western Australia, Australia.,Perron Institute for Neurological and Translational Science & the University of Western Australia, Nedlands, Western Australia, Australia
| | - Samuel McLenachan
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), the University of Western Australia, Nedlands, Western Australia, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Western Australia, Australia.,Perron Institute for Neurological and Translational Science & the University of Western Australia, Nedlands, Western Australia, Australia
| | - Steve D Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Western Australia, Australia.,Perron Institute for Neurological and Translational Science & the University of Western Australia, Nedlands, Western Australia, Australia
| | - Fred K Chen
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), the University of Western Australia, Nedlands, Western Australia, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia.,Department of Ophthalmology, Royal Perth Hospital, Perth, Western Australia, Australia.,Department of Ophthalmology, Perth Children's Hospital, Nedlands, Western Australia, Australia
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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: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 11/16/2022] Open
Abstract
Stargardt disease (STGD1) and ABCA4 retinopathies (ABCA4R) are caused by pathogenic variants in the ABCA4 gene inherited in an autosomal recessive manner. The gene encodes an importer flippase protein that prevents the build-up of vitamin A derivatives that are toxic to the RPE. Diagnosing ABCA4R is complex due to its phenotypic variability and the presence of other inherited retinal dystrophy phenocopies. ABCA4 is a large gene, comprising 50 exons; to date > 2000 variants have been described. These include missense, nonsense, splicing, structural, and deep intronic variants. Missense variants account for the majority of variants in ABCA4. However, in a significant proportion of patients with an ABCA4R phenotype, a second variant in ABCA4 is not identified. This could be due to the presence of yet unknown variants, or hypomorphic alleles being incorrectly classified as benign, or the possibility that the disease is caused by a variant in another gene. This underlines the importance of accurate genetic testing. The pathogenicity of novel variants can be predicted using in silico programs, but these rely on databases that are not ethnically diverse, thus highlighting the need for studies in differing populations. Functional studies in vitro are useful towards assessing protein function but do not directly measure the flippase activity. Obtaining an accurate molecular diagnosis is becoming increasingly more important as targeted therapeutic options become available; these include pharmacological, gene-based, and cell replacement-based therapies. The aim of this review is to provide an update on the current status of genotyping in ABCA4 and the status of the therapeutic approaches being investigated.
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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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Structural basis of substrate recognition and translocation by human ABCA4. Nat Commun 2021; 12:3853. [PMID: 34158497 PMCID: PMC8219669 DOI: 10.1038/s41467-021-24194-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/04/2021] [Indexed: 12/29/2022] Open
Abstract
Human ATP-binding cassette (ABC) subfamily A (ABCA) transporters mediate the transport of various lipid compounds across the membrane. Mutations in human ABCA transporters have been described to cause severe hereditary disorders associated with impaired lipid transport. However, little is known about the mechanistic details of substrate recognition and translocation by ABCA transporters. Here, we present three cryo-EM structures of human ABCA4, a retina-specific ABCA transporter, in distinct functional states at resolutions of 3.3–3.4 Å. In the nucleotide-free state, the two transmembrane domains (TMDs) exhibit a lateral-opening conformation, allowing the lateral entry of substrate from the lipid bilayer. The N-retinylidene-phosphatidylethanolamine (NRPE), the physiological lipid substrate of ABCA4, is sandwiched between the two TMDs in the luminal leaflet and is further stabilized by an extended loop from extracellular domain 1. In the ATP-bound state, the two TMDs display a closed conformation, which precludes the substrate binding. Our study provides a molecular basis to understand the mechanism of ABCA4-mediated NRPE recognition and translocation, and suggests a common ‘lateral access and extrusion’ mechanism for ABCA-mediated lipid transport. Here, cryo-EM structures of human retinal ABCA4 transporter, either in apo state, in complex with ATP or with the physiological lipid substrate N-retinylidene-phosphatidylethanolamine (NRPE), reveal lateral opening, substrate recognition and suggest ‘lateral access and extrusion’ mechanism for ABCA-mediated lipid transport.
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18
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Heath Jeffery RC, Thompson JA, Lo J, Lamey TM, McLaren TL, McAllister IL, Mackey DA, Constable IJ, De Roach JN, Chen FK. Atrophy Expansion Rates in Stargardt Disease Using Ultra-Widefield Fundus Autofluorescence. OPHTHALMOLOGY SCIENCE 2021; 1:100005. [PMID: 36246008 PMCID: PMC9559898 DOI: 10.1016/j.xops.2021.100005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/05/2021] [Accepted: 03/01/2021] [Indexed: 01/18/2023]
Abstract
Purpose Design Participants Methods Main Outcome Measures Results Conclusions
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Affiliation(s)
- Rachael C. Heath Jeffery
- Centre for Ophthalmology and Visual Science (incorporating Lions Eye Institute), The University of Western Australia, Perth, Australia
- Department of Ophthalmology, Royal Perth Hospital, Perth, Australia
| | - Jennifer A. Thompson
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Australia
| | - Johnny Lo
- School of Science, Edith Cowan University, Perth, Australia
| | - Tina M. Lamey
- Centre for Ophthalmology and Visual Science (incorporating Lions Eye Institute), The University of Western Australia, Perth, Australia
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Australia
| | - Terri L. McLaren
- Centre for Ophthalmology and Visual Science (incorporating Lions Eye Institute), The University of Western Australia, Perth, Australia
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Australia
| | - Ian L. McAllister
- Centre for Ophthalmology and Visual Science (incorporating Lions Eye Institute), The University of Western Australia, Perth, Australia
| | - David A. Mackey
- Centre for Ophthalmology and Visual Science (incorporating Lions Eye Institute), The University of Western Australia, Perth, Australia
| | - Ian J. Constable
- Centre for Ophthalmology and Visual Science (incorporating Lions Eye Institute), The University of Western Australia, Perth, Australia
| | - John N. De Roach
- Centre for Ophthalmology and Visual Science (incorporating Lions Eye Institute), The University of Western Australia, Perth, Australia
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Australia
| | - Fred K. Chen
- Centre for Ophthalmology and Visual Science (incorporating Lions Eye Institute), The University of Western Australia, Perth, Australia
- Department of Ophthalmology, Royal Perth Hospital, Perth, Australia
- Department of Ophthalmology, Perth Children’s Hospital, Nedlands, Australia
- Correspondence: Fred K. Chen, MBBS, PhD, Lions Eye Institute, 2 Verdun Street, Nedlands WA, Australia.
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19
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Garces FA, Scortecci JF, Molday RS. Functional Characterization of ABCA4 Missense Variants Linked to Stargardt Macular Degeneration. Int J Mol Sci 2020; 22:ijms22010185. [PMID: 33375396 PMCID: PMC7796138 DOI: 10.3390/ijms22010185] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 12/17/2022] Open
Abstract
ABCA4 is an ATP-binding cassette (ABC) transporter expressed in photoreceptors, where it transports its substrate, N-retinylidene-phosphatidylethanolamine (N-Ret-PE), across outer segment membranes to facilitate the clearance of retinal from photoreceptors. Mutations in ABCA4 cause Stargardt macular degeneration (STGD1), an autosomal recessive disorder characterized by a loss of central vision and the accumulation of bisretinoid compounds. The purpose of this study was to determine the molecular properties of ABCA4 variants harboring disease-causing missense mutations in the transmembrane domains. Thirty-eight variants expressed in culture cells were analyzed for expression, ATPase activities, and substrate binding. On the basis of these properties, the variants were divided into three classes: Class 1 (severe variants) exhibited significantly reduced ABCA4 expression and basal ATPase activity that was not stimulated by its substrate N-Ret-PE; Class 2 (moderate variants) showed a partial reduction in expression and basal ATPase activity that was modestly stimulated by N-Ret-PE; and Class 3 (mild variants) displayed expression and functional properties comparable to normal ABCA4. The p.R653C variant displayed normal expression and basal ATPase activity, but lacked substrate binding and ATPase activation, suggesting that arginine 653 contributes to N-Ret-PE binding. Our classification provides a basis for better understanding genotype–phenotype correlations and evaluating therapeutic treatments for STGD1.
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Affiliation(s)
- Fabian A. Garces
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (F.A.G.); (J.F.S.)
| | - Jessica F. Scortecci
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (F.A.G.); (J.F.S.)
| | - Robert S. Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (F.A.G.); (J.F.S.)
- Department of Ophthalmology and Visual Sciences, University of British Columbia, Vancouver, BC V5Z 3N9, Canada
- Correspondence: ; Tel.: +1-604-822-6173
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