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Maggi J, Feil S, Gloggnitzer J, Maggi K, Bachmann-Gagescu R, Gerth-Kahlert C, Koller S, Berger W. Nanopore Deep Sequencing as a Tool to Characterize and Quantify Aberrant Splicing Caused by Variants in Inherited Retinal Dystrophy Genes. Int J Mol Sci 2024; 25:9569. [PMID: 39273516 PMCID: PMC11395040 DOI: 10.3390/ijms25179569] [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: 08/08/2024] [Revised: 08/22/2024] [Accepted: 08/23/2024] [Indexed: 09/15/2024] Open
Abstract
The contribution of splicing variants to molecular diagnostics of inherited diseases is reported to be less than 10%. This figure is likely an underestimation due to several factors including difficulty in predicting the effect of such variants, the need for functional assays, and the inability to detect them (depending on their locations and the sequencing technology used). The aim of this study was to assess the utility of Nanopore sequencing in characterizing and quantifying aberrant splicing events. For this purpose, we selected 19 candidate splicing variants that were identified in patients affected by inherited retinal dystrophies. Several in silico tools were deployed to predict the nature and estimate the magnitude of variant-induced aberrant splicing events. Minigene assay or whole blood-derived cDNA was used to functionally characterize the variants. PCR amplification of minigene-specific cDNA or the target gene in blood cDNA, combined with Nanopore sequencing, was used to identify the resulting transcripts. Thirteen out of nineteen variants caused aberrant splicing events, including cryptic splice site activation, exon skipping, pseudoexon inclusion, or a combination of these. Nanopore sequencing allowed for the identification of full-length transcripts and their precise quantification, which were often in accord with in silico predictions. The method detected reliably low-abundant transcripts, which would not be detected by conventional strategies, such as RT-PCR followed by Sanger sequencing.
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Affiliation(s)
- Jordi Maggi
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Silke Feil
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Jiradet Gloggnitzer
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Kevin Maggi
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Ruxandra Bachmann-Gagescu
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren, Switzerland
- Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
- Neuroscience Center Zurich (ZNZ), University and ETH Zurich, 8057 Zurich, Switzerland
| | - Christina Gerth-Kahlert
- Department of Ophthalmology, University Hospital Zurich and University of Zurich, 8091 Zurich, Switzerland
| | - Samuel Koller
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Wolfgang Berger
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
- Neuroscience Center Zurich (ZNZ), University and ETH Zurich, 8057 Zurich, Switzerland
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, 8057 Zurich, Switzerland
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2
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Chacon-Camacho OF, Xilotl-de Jesús N, Calderón-Martínez E, Ordoñez-Labastida V, Neria-Gonzalez MI, Villafuerte-de la Cruz R, Martinez-Rojas A, Zenteno JC. Genotypic spectrum of ABCA4-associated retinal degenerations in 211 unrelated Mexican patients: identification of 22 novel disease-causing variants. Mol Genet Genomics 2024; 299:79. [PMID: 39162841 PMCID: PMC11335775 DOI: 10.1007/s00438-024-02174-x] [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: 07/19/2023] [Accepted: 08/02/2024] [Indexed: 08/21/2024]
Abstract
The purpose of this study was to analyze and molecularly describe the largest group of patients with ABCA4-associated retinal degeneration in Latin America. Pathogenic variants in ABCA4, a member of the ATP Binding Cassette (ABC) transporters superfamily, is one of the most common causes of inherited visual deficiency in humans. Retinal phenotypes associated with genetic defects in ABCA4 are collectively known as ABCA4-associated retinal degenerations (ABCA4R), a group of recessively inherited disorders associated with a high allelic heterogeneity. While large groups of Caucasian and Asiatic individuals suffering from ABCA4R have been well characterized, molecular information from certain ethnic groups is limited or unavailable, precluding a more realistic knowledge of ABCA4-related mutational profile worldwide. In this study, we describe the molecular findings of a large group of 211 ABCA4R index cases from Mexico. Genotyping was performed using either next generation sequencing (NGS) of a retinal dystrophy genes panel or exome. ABCA4 targeted mutation testing was applied to a subgroup of subjects in whom founder mutations were suspected. A total of 128 different ABCA4 pathogenic variants were identified, including 22 previously unpublished variants. The most common type of genetic variation was single nucleotide substitutions which occurred in 92.7% (408/440 alleles). According to the predicted protein effect, the most frequent variant type was missense, occurring in 83.5% of disease-causing alleles (368/440). Mutations such as p.Ala1773Val are fully demonstrated as a founder effect in native inhabitants of certain regions of Mexico. This study also gives us certain indications of other founder effects that need to be further studied in the near future. This is the largest molecularly characterized ABCA4R Latin American cohort, and our results supports the value of conducting genetic screening in underrepresented populations for a better knowledge of the mutational profile leading to monogenic diseases.
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Affiliation(s)
- Oscar F Chacon-Camacho
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Chimalpopoca 14, Col. Obrera, Cuauhtemoc, Mexico City, CP06800, Mexico
- Laboratorio 5, Edificio A-4, Carrera de Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Laboratorio 5, Edificio A-4, Mexico City, Mexico
| | - Nancy Xilotl-de Jesús
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Chimalpopoca 14, Col. Obrera, Cuauhtemoc, Mexico City, CP06800, Mexico
| | - Ernesto Calderón-Martínez
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Chimalpopoca 14, Col. Obrera, Cuauhtemoc, Mexico City, CP06800, Mexico
- Department of Biomedical Informatics, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Vianey Ordoñez-Labastida
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Chimalpopoca 14, Col. Obrera, Cuauhtemoc, Mexico City, CP06800, Mexico
- Rare Disease Diagnostic Unit, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
- Faculty of Medicine, Autonomous University of the State of Morelos (UAEM), Morelos, Mexico
| | - M Isabel Neria-Gonzalez
- Laboratory of Integrative Microbiology and Molecular Biology, Division of Chemical and Biochemical Engineering, TecNm: Tecnológico de Estudios Superiores de Ecatepec. Ecatepec de Morelos, Morelos, Edo. México, Mexico
| | | | | | - Juan Carlos Zenteno
- Department of Genetics, Institute of Ophthalmology "Conde de Valenciana", Chimalpopoca 14, Col. Obrera, Cuauhtemoc, Mexico City, CP06800, Mexico.
- Rare Disease Diagnostic Unit, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico.
- Biochemistry Department, Faculty of Medicine, UNAM, Mexico City, Mexico.
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3
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Ghenciu LA, Hațegan OA, Stoicescu ER, Iacob R, Șișu AM. Emerging Therapeutic Approaches and Genetic Insights in Stargardt Disease: A Comprehensive Review. Int J Mol Sci 2024; 25:8859. [PMID: 39201545 PMCID: PMC11354485 DOI: 10.3390/ijms25168859] [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: 07/21/2024] [Revised: 08/09/2024] [Accepted: 08/12/2024] [Indexed: 09/02/2024] Open
Abstract
Stargardt disease, one of the most common forms of inherited retinal diseases, affects individuals worldwide. The primary cause is mutations in the ABCA4 gene, leading to the accumulation of toxic byproducts in the retinal pigment epithelium (RPE) and subsequent photoreceptor cell degeneration. Over the past few years, research on Stargardt disease has advanced significantly, focusing on clinical and molecular genetics. Recent studies have explored various innovative therapeutic approaches, including gene therapy, stem cell therapy, and pharmacological interventions. Gene therapy has shown promise, particularly with adeno-associated viral (AAV) vectors capable of delivering the ABCA4 gene to retinal cells. However, challenges remain due to the gene's large size. Stem cell therapy aims to replace degenerated RPE and photoreceptor cells, with several clinical trials demonstrating safety and preliminary efficacy. Pharmacological approaches focus on reducing toxic byproduct accumulation and modulating the visual cycle. Precision medicine, targeting specific genetic mutations and pathways, is becoming increasingly important. Novel techniques such as clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 offer potential for directly correcting genetic defects. This review aims to synthesize recent advancements in understanding and treating Stargardt disease. By highlighting breakthroughs in genetic therapies, stem cell treatments, and novel pharmacological strategies, it provides a comprehensive overview of emerging therapeutic options.
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Affiliation(s)
- Laura Andreea Ghenciu
- Department of Functional Sciences, “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timișoara, Romania;
| | - Ovidiu Alin Hațegan
- Discipline of Anatomy and Embriology, Medicine Faculty, Vasile Goldis Western University of Arad, Revolution Boulevard 94, 310025 Arad, Romania
| | - Emil Robert Stoicescu
- Field of Applied Engineering Sciences, Specialization Statistical Methods and Techniques in Health and Clinical Research, Faculty of Mechanics, ‘Politehnica’ University Timișoara, Mihai Viteazul Boulevard No. 1, 300222 Timișoara, Romania; (E.R.S.); (R.I.)
- Department of Radiology and Medical Imaging, ‘Victor Babeș’ University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timișoara, Romania
- Research Center for Pharmaco-Toxicological Evaluations, ‘Victor Babeș’ University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timișoara, Romania
| | - Roxana Iacob
- Field of Applied Engineering Sciences, Specialization Statistical Methods and Techniques in Health and Clinical Research, Faculty of Mechanics, ‘Politehnica’ University Timișoara, Mihai Viteazul Boulevard No. 1, 300222 Timișoara, Romania; (E.R.S.); (R.I.)
- Department of Anatomy and Embriology, ‘Victor Babeș’ University of Medicine and Pharmacy Timișoara, 300041 Timișoara, Romania;
| | - Alina Maria Șișu
- Department of Anatomy and Embriology, ‘Victor Babeș’ University of Medicine and Pharmacy Timișoara, 300041 Timișoara, Romania;
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Vázquez-Domínguez I, Anido AA, Duijkers L, Hoppenbrouwers T, Hoogendoorn ADM, Koster C, Collin RWJ, Garanto A. Efficacy, biodistribution and safety comparison of chemically modified antisense oligonucleotides in the retina. Nucleic Acids Res 2024:gkae686. [PMID: 39119918 DOI: 10.1093/nar/gkae686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 06/25/2024] [Accepted: 07/26/2024] [Indexed: 08/10/2024] Open
Abstract
Antisense oligonucleotides (AONs) are a versatile tool for treating inherited retinal diseases. However, little is known about how different chemical modifications of AONs can affect their biodistribution, toxicity, and uptake in the retina. Here, we addressed this question by comparing splice-switching AONs with three different chemical modifications commonly used in a clinical setting (2'O-methyl-phosphorothioate (2-OMe/PS), 2'O-methoxyethyl-phosphoriate (2-MOE/PS), and phosphorodiamidite morpholino oligomers (PMO)). These AONs targeted genes exclusively expressed in certain types of retinal cells. Overall, studies in vitro and in vivo in C57BL/6J wild-type mouse retinas showed that 2-OMe/PS and 2-MOE/PS AONs have comparable efficacy and safety profiles. In contrast, octa-guanidine-dendrimer-conjugated in vivo PMO-oligonucleotides (ivPMO) caused toxicity. This was evidenced by externally visible ocular phenotypes in 88.5% of all ivPMO-treated animals, accompanied by severe alterations at the morphological level. However, delivery of unmodified PMO-AONs did not cause any toxicity, although it clearly reduced the efficacy. We conducted the first systematic comparison of different chemical modifications of AONs in the retina. Our results showed that the same AON sequence with different chemical modifications displayed different splicing modulation efficacies, suggesting the 2'MOE/PS modification as the most efficacious in these conditions. Thereby, our work provides important insights for future clinical applications.
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Affiliation(s)
| | - Alejandro Allo Anido
- Radboud university medical center, Department of Human Genetics, Nijmegen, The Netherlands
| | - Lonneke Duijkers
- Radboud university medical center, Department of Human Genetics, Nijmegen, The Netherlands
| | - Tamara Hoppenbrouwers
- Radboud university medical center, Department of Human Genetics, Nijmegen, The Netherlands
| | - Anita D M Hoogendoorn
- Radboud university medical center, Amalia Children's Hospital, Department of Pediatrics, Nijmegen, The Netherlands
| | - Céline Koster
- Departments of Human Genetics and Ophthalmology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Rob W J Collin
- Radboud university medical center, Department of Human Genetics, Nijmegen, The Netherlands
| | - Alejandro Garanto
- Radboud university medical center, Department of Human Genetics, Nijmegen, The Netherlands
- Radboud university medical center, Amalia Children's Hospital, Department of Pediatrics, Nijmegen, The Netherlands
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5
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Burnight ER, Fenner BJ, Han IC, DeLuca AP, Whitmore SS, Bohrer LR, Andorf JL, Sohn EH, Mullins RF, Tucker BA, Stone EM. Demonstration of the pathogenicity of a common non-exomic mutation in ABCA4 using iPSC-derived retinal organoids and retrospective clinical data. Hum Mol Genet 2024; 33:1379-1390. [PMID: 37930186 PMCID: PMC11305681 DOI: 10.1093/hmg/ddad176] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/25/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023] Open
Abstract
Mutations in ABCA4 are the most common cause of Mendelian retinal disease. Clinical evaluation of this gene is challenging because of its extreme allelic diversity, the large fraction of non-exomic mutations, and the wide range of associated disease. We used patient-derived retinal organoids as well as DNA samples and clinical data from a large cohort of patients with ABCA4-associated retinal disease to investigate the pathogenicity of a variant in ABCA4 (IVS30 + 1321 A>G) that occurs heterozygously in 2% of Europeans. We found that this variant causes mis-splicing of the gene in photoreceptor cells such that the resulting protein contains 36 incorrect amino acids followed by a premature stop. We also investigated the phenotype of 10 patients with compound genotypes that included this mutation. Their median age of first vision loss was 39 years, which is in the mildest quintile of a large cohort of patients with ABCA4 disease. We conclude that the IVS30 + 1321 A>G variant can cause disease when paired with a sufficiently deleterious opposing allele in a sufficiently permissive genetic background.
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Affiliation(s)
- Erin R Burnight
- Institute for Vision Research, Carver College of Medicine, University of Iowa, 375 Newton Road, Iowa City, IA 52242, United States
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, United States
| | - Beau J Fenner
- Institute for Vision Research, Carver College of Medicine, University of Iowa, 375 Newton Road, Iowa City, IA 52242, United States
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, United States
| | - Ian C Han
- Institute for Vision Research, Carver College of Medicine, University of Iowa, 375 Newton Road, Iowa City, IA 52242, United States
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, United States
| | - Adam P DeLuca
- Institute for Vision Research, Carver College of Medicine, University of Iowa, 375 Newton Road, Iowa City, IA 52242, United States
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, United States
| | - S Scott Whitmore
- Institute for Vision Research, Carver College of Medicine, University of Iowa, 375 Newton Road, Iowa City, IA 52242, United States
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, United States
| | - Laura R Bohrer
- Institute for Vision Research, Carver College of Medicine, University of Iowa, 375 Newton Road, Iowa City, IA 52242, United States
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, United States
| | - Jeaneen L Andorf
- Institute for Vision Research, Carver College of Medicine, University of Iowa, 375 Newton Road, Iowa City, IA 52242, United States
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, United States
| | - Elliott H Sohn
- Institute for Vision Research, Carver College of Medicine, University of Iowa, 375 Newton Road, Iowa City, IA 52242, United States
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, United States
| | - Robert F Mullins
- Institute for Vision Research, Carver College of Medicine, University of Iowa, 375 Newton Road, Iowa City, IA 52242, United States
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, United States
| | - Budd A Tucker
- Institute for Vision Research, Carver College of Medicine, University of Iowa, 375 Newton Road, Iowa City, IA 52242, United States
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, United States
| | - Edwin M Stone
- Institute for Vision Research, Carver College of Medicine, University of Iowa, 375 Newton Road, Iowa City, IA 52242, United States
- Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, 200 Hawkins Drive, Iowa City, IA 52242, United States
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Aslaksen S, Aukrust I, Molday L, Holtan JP, Jansson RW, Berland S, Rødahl E, Bredrup C, Bragadóttir R, Bratland E, Molday RS, Knappskog PM. Functional Characterization of ABCA4 Missense Variants Aids Variant Interpretation and Phenotype Prediction in Patients With ABCA4-Retinal Dystrophies. Invest Ophthalmol Vis Sci 2024; 65:2. [PMID: 39087934 PMCID: PMC11305421 DOI: 10.1167/iovs.65.10.2] [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: 12/18/2023] [Accepted: 07/01/2024] [Indexed: 08/02/2024] Open
Abstract
Purpose Biallelic pathogenic variants in the gene encoding the ATP-binding cassette transporter ABCA4 are the leading cause of irreversible vision loss in inherited retinal dystrophies (IRDs). Interpretation of ABCA4 variants is challenging, due to cis-modifying and hypomorphic variants. We have previously detected 10 missense variants of unknown significance (VUS) in patients with suspected ABCA4-retinal dystrophies (ABCA4-RDs) in Norway. In this study, we functionally characterized the VUS to aid interpretation of the variants and to determine if they are associated with the disease. Methods The ABCA4 VUS were expressed in HEK293T cells and the ABCA4 expression level and ATPase activity were determined and correlated with the patients' phenotype. The functional data further used for reclassification of the VUS following the American College of Medical Genetics and Genomics (ACMG) guidelines. Results Of the 10 VUSs, 2 variants, Cys205Phe and Asn415Thr, were categorized as functionally severe. The age at presentation in the 2 patients carrying these variants was divergent and seemed to be driven by the patients' second pathogenic variants Gly1961Glu and c.5461-10T>C, respectively. Three variants, Val643Gly, Pro799Leu, and Val1433Ile were categorized as functionally moderate, and were found in patients with intermediate/late age at presentation. The remaining five variants were categorized as functionally normal/mild. Based on our data, c.614G>T p.(Cys205Phe), c.1244A>C p.(Asn415Thr), and c.2396C>T p.(Pro799Leu) were reclassified to (likely) pathogenic, while 4 of the functionally normal/mild variants could be reclassified to likely benign. Conclusions Functional analyses of ABCA4 variants are a helpful tool in variant classification and enable us to better predict the disease severity in patients with ABCA4-RDs.
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Affiliation(s)
- Sigrid Aslaksen
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Ingvild Aukrust
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Laurie Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | | | | | - Siren Berland
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Eyvind Rødahl
- Department of Ophthalmology, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Cecilie Bredrup
- Department of Ophthalmology, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Ragnheiður Bragadóttir
- Department of Ophthalmology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Eirik Bratland
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - 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
| | - Per Morten Knappskog
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
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Bjeloš M, Ćurić A, Bušić M, Rak B, Kuzmanović Elabjer B. Genotype-Phenotype Correlation Model for the Spectrum of TYR-Associated Albinism. Diagnostics (Basel) 2024; 14:1583. [PMID: 39125459 PMCID: PMC11311874 DOI: 10.3390/diagnostics14151583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Revised: 07/16/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024] Open
Abstract
We present two children aged 3 and 5 years who share identical TYR genotype, yet exhibit contrasting phenotypic manifestations in terms of eye, skin, and hair coloration. The patients are heterozygous for TYR c.1A>G, p. (Met1?), which is pathogenic, and homozygous for TYR c.1205G>A, p. (Arg402Gln), which is classified as a risk factor. The children manifested diminished visual acuity, nystagmus, and foveal hypoplasia. The first patient presented with hypopigmentation of the skin, hair, and ocular tissues, while the second patient presented with hypopigmentation of the skin, hair, retinal pigment epithelium, and choroid with dark brown irises. Furthermore, the brown-eyed subject presented astigmatic refractive error and both global and local stereopsis capabilities, contrasting with the presentation of hypermetropia, strabismus, and the absence of stereopsis in the blue-eyed individual. Herein, we propose a genotype-phenotype correlation model to elucidate the diverse clinical presentations stemming from biallelic and triallelic pathogenic variants in TYR, establishing a link between the residual tyrosinase activity and resultant phenotypes. According to our proposed model, the severity of TYR variants correlates with distinct albino phenotypes. Our findings propose the potential association between reduced pigmentation levels in ocular tissues and binocular functions, suggesting pigmentation as a possible independent variable influencing the onset of strabismus-an association unreported until now in the existing literature.
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Affiliation(s)
- Mirjana Bjeloš
- University Eye Department, Reference Center of the Ministry of Health of the Republic of Croatia for Inherited Retinal Dystrophies, Reference Center of the Ministry of Health of the Republic of Croatia for Pediatric Ophthalmology and Strabismus, University Hospital “Sveti Duh”, 10000 Zagreb, Croatia; (M.B.); (M.B.); (B.R.); (B.K.E.)
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Ana Ćurić
- University Eye Department, Reference Center of the Ministry of Health of the Republic of Croatia for Inherited Retinal Dystrophies, Reference Center of the Ministry of Health of the Republic of Croatia for Pediatric Ophthalmology and Strabismus, University Hospital “Sveti Duh”, 10000 Zagreb, Croatia; (M.B.); (M.B.); (B.R.); (B.K.E.)
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Mladen Bušić
- University Eye Department, Reference Center of the Ministry of Health of the Republic of Croatia for Inherited Retinal Dystrophies, Reference Center of the Ministry of Health of the Republic of Croatia for Pediatric Ophthalmology and Strabismus, University Hospital “Sveti Duh”, 10000 Zagreb, Croatia; (M.B.); (M.B.); (B.R.); (B.K.E.)
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Benedict Rak
- University Eye Department, Reference Center of the Ministry of Health of the Republic of Croatia for Inherited Retinal Dystrophies, Reference Center of the Ministry of Health of the Republic of Croatia for Pediatric Ophthalmology and Strabismus, University Hospital “Sveti Duh”, 10000 Zagreb, Croatia; (M.B.); (M.B.); (B.R.); (B.K.E.)
| | - Biljana Kuzmanović Elabjer
- University Eye Department, Reference Center of the Ministry of Health of the Republic of Croatia for Inherited Retinal Dystrophies, Reference Center of the Ministry of Health of the Republic of Croatia for Pediatric Ophthalmology and Strabismus, University Hospital “Sveti Duh”, 10000 Zagreb, Croatia; (M.B.); (M.B.); (B.R.); (B.K.E.)
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
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Smith CEL, Laugel-Haushalter V, Hany U, Best S, Taylor RL, Poulter JA, Wortmann SB, Feichtinger RG, Mayr JA, Al Bahlani S, Nikolopoulos G, Rigby A, Black GC, Watson CM, Mansour S, Inglehearn CF, Mighell AJ, Bloch-Zupan A. Biallelic variants in Plexin B2 ( PLXNB2) cause amelogenesis imperfecta, hearing loss and intellectual disability. J Med Genet 2024; 61:689-698. [PMID: 38458752 PMCID: PMC11228227 DOI: 10.1136/jmg-2023-109728] [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: 11/02/2023] [Accepted: 02/22/2024] [Indexed: 03/10/2024]
Abstract
BACKGROUND Plexins are large transmembrane receptors for the semaphorin family of signalling proteins. Semaphorin-plexin signalling controls cellular interactions that are critical during development as well as in adult life stages. Nine plexin genes have been identified in humans, but despite the apparent importance of plexins in development, only biallelic PLXND1 and PLXNA1 variants have so far been associated with Mendelian genetic disease. METHODS Eight individuals from six families presented with a recessively inherited variable clinical condition, with core features of amelogenesis imperfecta (AI) and sensorineural hearing loss (SNHL), with variable intellectual disability. Probands were investigated by exome or genome sequencing. Common variants and those unlikely to affect function were excluded. Variants consistent with autosomal recessive inheritance were prioritised. Variant segregation analysis was performed by Sanger sequencing. RNA expression analysis was conducted in C57Bl6 mice. RESULTS Rare biallelic pathogenic variants in plexin B2 (PLXNB2), a large transmembrane semaphorin receptor protein, were found to segregate with disease in all six families. The variants identified include missense, nonsense, splicing changes and a multiexon deletion. Plxnb2 expression was detected in differentiating ameloblasts. CONCLUSION We identify rare biallelic pathogenic variants in PLXNB2 as a cause of a new autosomal recessive, phenotypically diverse syndrome with AI and SNHL as core features. Intellectual disability, ocular disease, ear developmental abnormalities and lymphoedema were also present in multiple cases. The variable syndromic human phenotype overlaps with that seen in Plxnb2 knockout mice, and, together with the rarity of human PLXNB2 variants, may explain why pathogenic variants in PLXNB2 have not been reported previously.
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Affiliation(s)
- Claire E L Smith
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
| | - Virginie Laugel-Haushalter
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Strasbourg, France
| | - Ummey Hany
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
| | - Sunayna Best
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Rachel L Taylor
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution and Genomic Sciences, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK
- EMQN CIC, Manchester, UK
| | - James A Poulter
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
| | - Saskia B Wortmann
- Department of Paediatrics, University Children's Hospital, Salzburger Landesklinken (SALK) and Paracelsus Medical University, Salzburg, Austria
- Amalia Children's Hospital, Radboudumc, Nijmegen, The Netherlands
| | - Rene G Feichtinger
- Department of Paediatrics, University Children's Hospital, Salzburger Landesklinken (SALK) and Paracelsus Medical University, Salzburg, Austria
| | - Johannes A Mayr
- Department of Paediatrics, University Children's Hospital, Salzburger Landesklinken (SALK) and Paracelsus Medical University, Salzburg, Austria
| | - Suhaila Al Bahlani
- Dental & OMFS Clinic, Al Nahdha Hospital, Government of Oman Ministry of Health, Muscat, Oman
| | | | - Alice Rigby
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
- School of Dentistry, University of Leeds Faculty of Medicine and Health, Leeds, UK
| | - Graeme C Black
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution and Genomic Sciences, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Christopher M Watson
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
- North East and Yorkshire Genomic Laboratory Hub, Central Lab, St James's University Hospital, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Sahar Mansour
- Lymphovascular Research Unit, Molecular and Clinical Sciences Research Institute, St George's Hospital, University of London, London, UK
- SW Thames Regional Centre for Genomics, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Chris F Inglehearn
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
| | - Alan J Mighell
- School of Dentistry, University of Leeds Faculty of Medicine and Health, Leeds, UK
| | - Agnès Bloch-Zupan
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Strasbourg, France
- Faculté de Chirurgie Dentaire, Université de Strasbourg, Strasbourg, France
- Centre de référence des maladies rares orales et dentaires O-Rares, Filière Santé Maladies rares TETE COU, European Reference Network CRANIO, Pôle de Médecine et Chirurgie Bucco-dentaires, Hôpital Civil, Hôpitaux Universitaires de Strasbourg (HUS), Strasbourg, France
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9
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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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10
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Corradi Z, Hitti-Malin RJ, de Rooij LA, Garanto A, Collin RWJ, Cremers FPM. Antisense Oligonucleotide-Based Rescue of Complex Intronic Splicing Defects in ABCA4. Nucleic Acid Ther 2024; 34:125-133. [PMID: 38800942 DOI: 10.1089/nat.2024.0008] [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] [Indexed: 05/29/2024] Open
Abstract
The ABCA4 gene, involved in Stargardt disease, has a high percentage of splice-altering pathogenic variants, some of which cause complex RNA defects. Although antisense oligonucleotides (AONs) have shown promising results in splicing modulation, they have not yet been used to target complex splicing defects. Here, we performed AON-based rescue studies on ABCA4 complex splicing defects. Intron 13 variants c.1938-724A>G, c.1938-621G>A, c.1938-619A>G, and c.1938-514A>G all lead to the inclusion of different pseudo-exons (PEs) with and without an upstream PE (PE1). Intron 44 variant c.6148-84A>T results in multiple PE inclusions and/or exon skipping events. Five novel AONs were designed to target these defects. AON efficacy was assessed by in vitro splice assays using midigenes containing the variants of interest. All screened complex splicing defects were effectively rescued by the AONs. Although varying levels of efficacy were observed between AONs targeting the same PEs, for all variants at least one AON restored splicing to levels comparable or better than wildtype. In conclusion, AONs are a promising approach to target complex splicing defects in ABCA4.
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Affiliation(s)
- Zelia Corradi
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rebekkah J Hitti-Malin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Laura A de Rooij
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alejandro Garanto
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
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11
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D'haene E, López-Soriano V, Martínez-García PM, Kalayanamontri S, Rey AD, Sousa-Ortega A, Naranjo S, Van de Sompele S, Vantomme L, Mahieu Q, Vergult S, Neto A, Gómez-Skarmeta JL, Martínez-Morales JR, Bauwens M, Tena JJ, De Baere E. Comparative 3D genome analysis between neural retina and retinal pigment epithelium reveals differential cis-regulatory interactions at retinal disease loci. Genome Biol 2024; 25:123. [PMID: 38760655 PMCID: PMC11100165 DOI: 10.1186/s13059-024-03250-6] [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: 06/30/2023] [Accepted: 04/17/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Vision depends on the interplay between photoreceptor cells of the neural retina and the underlying retinal pigment epithelium (RPE). Most genes involved in inherited retinal diseases display specific spatiotemporal expression within these interconnected retinal components through the local recruitment of cis-regulatory elements (CREs) in 3D nuclear space. RESULTS To understand the role of differential chromatin architecture in establishing tissue-specific expression at inherited retinal disease loci, we mapped genome-wide chromatin interactions using in situ Hi-C and H3K4me3 HiChIP on neural retina and RPE/choroid from human adult donor eyes. We observed chromatin looping between active promoters and 32,425 and 8060 candidate CREs in the neural retina and RPE/choroid, respectively. A comparative 3D genome analysis between these two retinal tissues revealed that 56% of 290 known inherited retinal disease genes were marked by differential chromatin interactions. One of these was ABCA4, which is implicated in the most common autosomal recessive inherited retinal disease. We zoomed in on retina- and RPE-specific cis-regulatory interactions at the ABCA4 locus using high-resolution UMI-4C. Integration with bulk and single-cell epigenomic datasets and in vivo enhancer assays in zebrafish revealed tissue-specific CREs interacting with ABCA4. CONCLUSIONS Through comparative 3D genome mapping, based on genome-wide, promoter-centric, and locus-specific assays of human neural retina and RPE, we have shown that gene regulation at key inherited retinal disease loci is likely mediated by tissue-specific chromatin interactions. These findings do not only provide insight into tissue-specific regulatory landscapes at retinal disease loci, but also delineate the search space for non-coding genomic variation underlying unsolved inherited retinal diseases.
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Affiliation(s)
- Eva D'haene
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
| | - Víctor López-Soriano
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Pedro Manuel Martínez-García
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain
| | - Soraya Kalayanamontri
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain
| | - Alfredo Dueñas Rey
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Ana Sousa-Ortega
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain
| | - Silvia Naranjo
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain
| | - Stijn Van de Sompele
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Lies Vantomme
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Quinten Mahieu
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Sarah Vergult
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Ana Neto
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain
| | - Juan Ramón Martínez-Morales
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain.
| | - Miriam Bauwens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
| | - Juan Jesús Tena
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain.
| | - Elfride De Baere
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
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12
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Romano F, Lamanna F, Boon CJF, Siligato A, Kalra G, Agarwal A, Medori C, Bertelli M, Pellegrini M, Invernizzi A, Staurenghi G, Salvetti AP. Clinical, Genotypic, and Imaging Characterization of the Spectrum of ABCA4 Retinopathies. Ophthalmol Retina 2024; 8:509-519. [PMID: 37924945 DOI: 10.1016/j.oret.2023.10.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/06/2023]
Abstract
PURPOSE To investigate the clinical and genotypic differences in the spectrum of ABCA4-associated retinopathies (ABCA4Rs). DESIGN Observational, cross sectional case series. PARTICIPANTS Sixty-six patients (132 eyes) carrying biallelic ABCA4 variants. METHODS Patients underwent visual acuity measurement and multimodal imaging. Clinical records were reviewed for age at onset, presenting symptoms, genetic variants, and electroretinogram (ERG). Each eye was assigned to a phenotype based on age at onset, imaging and ERG: cone dystrophy-bull's-eye maculopathy (CD-BEM, 40 eyes), cone-rod dystrophy (CRD, 12 eyes), Stargardt disease (SD, 28 eyes), late-onset SD (LO-SD, 38 eyes), and fundus flavimaculatus (14 eyes). Images were analyzed for: peripapillary sparing, retinal pigment epithelium (RPE) atrophy (definitely decreased autofluorescence, DDAF), flecks patterns using autofluorescence; type of atrophy according to Classification of Atrophy Meeting reports, macular and choroidal thickness on OCT; and choriocapillaris flow deficits on OCT angiography. MAIN OUTCOME MEASURES Primary outcome was to report the demographic, genotypic, and imaging characteristics of the different ABCA4R phenotypes. Secondary objectives included the assessment of imaging biomarkers as outcome measures for clinical trials. RESULTS Age at onset was lower in CRD (12 ± 8 years) and higher in patients with LO-SD (59 ± 9 years) (all P < 0.01). Central vision loss was a common presenting symptom in CD-BEM and SD, whereas patients with LO-SD primarily complained of difficult dark adaptation. Missense variants were more frequent in CD-BEM, and splice site in CRD and LO-SD (P < 0.05). Peripapillary sparing was absent in 3 eyes with LO-SD (8%). Cone dystrophy-bull's-eye maculopathy eyes typically had complete outer retinal atrophy alterations (98%), whereas CRD and SD eyes showed both complete outer retinal atrophy and complete RPE and outer retinal atrophy (cRORA) (71%-100%). Patients with LO-SD had larger areas of DDAF (100% cRORA) and of choriocapillaris flow deficits (all P < 0.01). Repeatability of DDAF measurements was low for some phenotypes (CD-BEM and CRD) and atrophic areas <7.5 mm2. Resorbed flecks were significantly associated with CRD and LO-SD (P < 0.01). CONCLUSIONS This research provides a thorough evaluation of the spectrum of ABCA4R. Our findings suggest that certain phenotypes show preferential photoreceptor degeneration (e.g., CD-BEM), whereas others have substantial RPE and choriocapillaris alterations (e.g., LO-SD). We recommend that clinical trial end points take into consideration these imaging features to improve the interpretation of their results. FINANCIAL DISCLOSURE(S) Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
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Affiliation(s)
- Francesco Romano
- Eye Clinic, Department of Biomedical and Clinical Science, Luigi Sacco Hospital, University of Milan, Milan, Italy; Harvard Retinal Imaging Lab, Retina Service, Department of Ophthalmology, Massachusetts Eye and Ear, Boston, Massachusetts.
| | - Francesca Lamanna
- Eye Clinic, Department of Biomedical and Clinical Science, Luigi Sacco Hospital, University of Milan, Milan, Italy
| | - Camiel J F Boon
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands; Department of Ophthalmology, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Alessandro Siligato
- Eye Clinic, Department of Biomedical and Clinical Science, Luigi Sacco Hospital, University of Milan, Milan, Italy
| | - Gagan Kalra
- Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio
| | | | | | | | - Marco Pellegrini
- Eye Clinic, Department of Biomedical and Clinical Science, Luigi Sacco Hospital, University of Milan, Milan, Italy
| | - Alessandro Invernizzi
- Eye Clinic, Department of Biomedical and Clinical Science, Luigi Sacco Hospital, University of Milan, Milan, Italy; Department of Ophthalmology, Save Sight Institute, University of Sydney, Sydney, Australia
| | - Giovanni Staurenghi
- Eye Clinic, Department of Biomedical and Clinical Science, Luigi Sacco Hospital, University of Milan, Milan, Italy
| | - Anna Paola Salvetti
- Eye Clinic, Department of Biomedical and Clinical Science, Luigi Sacco Hospital, University of Milan, Milan, Italy
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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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Oh R, Woo SJ, Joo K. Whole genome sequencing for inherited retinal diseases in the Korean National Project of Bio Big Data. Graefes Arch Clin Exp Ophthalmol 2024; 262:1351-1359. [PMID: 37947821 DOI: 10.1007/s00417-023-06309-5] [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: 06/25/2023] [Revised: 10/22/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
PURPOSE This study aimed to analyze the genetic results of inherited retinal diseases (IRDs) and evaluate the diagnostic usefulness of whole genome sequencing (WGS) in the Korean National Project of Bio Big Data. METHODS As part of the Korean National Project of Bio Big Data, WGS was performed on 32 individuals with IRDs with no identified pathogenic variants through whole or targeted exome sequencing. RESULTS Individuals with retinitis pigmentosa (n = 23), cone dystrophy (n = 2), cone-rod dystrophy (n = 2), familial exudative vitreoretinopathy (n = 2), pigmented paravenous chorioretinal atrophy (n = 1), North Carolina macular dystrophy (n = 1), and bull's-eye macular dystrophy (n = 1) were included. WGS revealed genetic mutations in the IQCB1, PRPF31, USH2A, and GUCY2D genes in five cases (15.6%). Two large structural variations and an intronic variant were newly detected in three cases. Two individuals had biallelic missense mutations that were not identified in previous exome sequencing. CONCLUSION With WGS, the causative variants in 15.6% of unsolved IRDs from the Korean National Project of Bio Big Data were identified. Further research with a larger cohort might unveil the diagnostic usefulness of WGS in IRDs and other diseases.
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Affiliation(s)
- Richul Oh
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, 82, Gumi-ro 173beon-gil, Bundang-gu, Seongnam, Gyeonggido, Republic of Korea, 13620
| | - Se Joon Woo
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, 82, Gumi-ro 173beon-gil, Bundang-gu, Seongnam, Gyeonggido, Republic of Korea, 13620
| | - Kwangsic Joo
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, 82, Gumi-ro 173beon-gil, Bundang-gu, Seongnam, Gyeonggido, Republic of Korea, 13620.
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15
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Suárez-Herrera N, Garanto A, Collin RWJ. Understanding and Rescuing the Splicing Defect Caused by the Frequent ABCA4 Variant c.4253+43G>A Underlying Stargardt Disease. Nucleic Acid Ther 2024; 34:73-82. [PMID: 38466963 DOI: 10.1089/nat.2023.0076] [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] [Indexed: 03/13/2024] Open
Abstract
Pathogenic variants in ABCA4 are the underlying molecular cause of Stargardt disease (STGD1), an autosomal recessive macular dystrophy characterized by a progressive loss of central vision. Among intronic ABCA4 variants, c.4253+43G>A is frequently detected in STGD1 cases and is classified as a hypomorphic allele, generally associated with late-onset cases. This variant was previously reported to alter splicing regulatory sequences, but the splicing outcome is not fully understood yet. In this study, we attempted to better understand its effect on splicing and to rescue the aberrant splicing via antisense oligonucleotides (AONs). Wild-type and c.4253+43G>A variant-harboring maxigene vectors revealed additional skipping events, which were not previously detected upon transfection in HEK293T cells. To restore exon inclusion, we designed a set of 27 AONs targeting either splicing silencer motifs or the variant region and screened these in maxigene-transfected HEK293T cells. Candidate AONs able to promote exon inclusion were selected for further testing in patient-derived photoreceptor precursor cells. Surprisingly, no robust splicing modulation was observed in this model system. Overall, this research helped to adequately characterize the splicing alteration caused by the c.4253+43G>A variant, although future development of AON-mediated exon inclusion therapy for ABCA4 is needed.
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Affiliation(s)
- Nuria Suárez-Herrera
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alejandro Garanto
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
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Suárez-Herrera N, Riswick IB, Vázquez-Domínguez I, Duijkers L, Karjosukarso DW, Piccolo D, Bauwens M, De Baere E, Cheetham ME, Garanto A, Collin RWJ. Proof-of-concept for multiple AON delivery by a single U7snRNA vector to restore splicing defects in ABCA4. Mol Ther 2024; 32:837-851. [PMID: 38243599 PMCID: PMC10928313 DOI: 10.1016/j.ymthe.2024.01.019] [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: 09/13/2023] [Revised: 12/13/2023] [Accepted: 01/12/2024] [Indexed: 01/21/2024] Open
Abstract
The high allelic heterogeneity in Stargardt disease (STGD1) complicates the design of intervention strategies. A significant proportion of pathogenic intronic ABCA4 variants alters the pre-mRNA splicing process. Antisense oligonucleotides (AONs) are an attractive yet mutation-specific therapeutic strategy to restore these splicing defects. In this study, we experimentally assessed the potential of a splicing modulation therapy to target multiple intronic ABCA4 variants. AONs were inserted into U7snRNA gene cassettes and tested in midigene-based splice assays. Five potent antisense sequences were selected to generate a multiple U7snRNA cassette construct, and this combination vector showed substantial rescue of all of the splicing defects. Therefore, the combination cassette was used for viral synthesis and assessment in patient-derived photoreceptor precursor cells (PPCs). Simultaneous delivery of several modified U7snRNAs through a single AAV, however, did not show substantial splicing correction, probably due to suboptimal transduction efficiency in PPCs and/or a heterogeneous viral population containing incomplete AAV genomes. Overall, these data demonstrate the potential of the U7snRNA system to rescue multiple splicing defects, but also suggest that AAV-associated challenges are still a limiting step, underscoring the need for further optimization before implementing this strategy as a potential treatment for STGD1.
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Affiliation(s)
- Nuria Suárez-Herrera
- Radboud University Medical Center, Department of Human Genetics, 6525GA Nijmegen, the Netherlands
| | - Iris B Riswick
- Radboud University Medical Center, Department of Human Genetics, 6525GA Nijmegen, the Netherlands
| | - Irene Vázquez-Domínguez
- Radboud University Medical Center, Department of Human Genetics, 6525GA Nijmegen, the Netherlands
| | - Lonneke Duijkers
- Radboud University Medical Center, Department of Human Genetics, 6525GA Nijmegen, the Netherlands
| | - Dyah W Karjosukarso
- Radboud University Medical Center, Department of Human Genetics, 6525GA Nijmegen, the Netherlands
| | | | - 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
| | | | - Alejandro Garanto
- Radboud University Medical Center, Department of Human Genetics, 6525GA Nijmegen, the Netherlands; Radboud University Medical Center, Amalia Children's Hospital, Department of Pediatrics, Nijmegen 6252GA, the Netherlands
| | - Rob W J Collin
- Radboud University Medical Center, Department of Human Genetics, 6525GA Nijmegen, the Netherlands.
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17
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Hanany M, Shalom S, Ben-Yosef T, Sharon D. Comparison of Worldwide Disease Prevalence and Genetic Prevalence of Inherited Retinal Diseases and Variant Interpretation Considerations. Cold Spring Harb Perspect Med 2024; 14:a041277. [PMID: 37460155 PMCID: PMC10835612 DOI: 10.1101/cshperspect.a041277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
One of the considerations in planning the development of novel therapeutic modalities is disease prevalence that is usually defined by studying large national/regional populations. Such studies are rare and might suffer from inaccuracies and challenging clinical characterization in heterogeneous diseases, such as inherited retinal diseases (IRDs). Here we collected reported disease prevalence information on various IRDs in different populations. The most common IRD, retinitis pigmentosa, has an average disease prevalence of ∼1:4500 individuals, Stargardt disease ∼1:17,000, Usher syndrome ∼1:25,000, Leber congenital amaurosis ∼1:42,000, and all IRDs ∼1:3450. We compared these values to genetic prevalence (GP) calculated based on allele frequency of autosomal-recessive IRD mutations. Although most values did correlate, some differences were observed that can be explained by discordant, presumably null mutations that are likely to be either nonpathogenic or hypomorphic. Our analysis highlights the importance of performing additional disease prevalence studies and to couple them with population-dependent allele frequency data.
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Affiliation(s)
- Mor Hanany
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120001, Israel
| | - Sapir Shalom
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120001, Israel
- Department of Military Medicine and "Tzameret," Faculty of Medicine, Hebrew University of Jerusalem and Medical Corps, Israel Defense Forces, Jerusalem 9112102, Israel
| | - Tamar Ben-Yosef
- Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120001, Israel
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18
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Dueñas Rey A, Del Pozo Valero M, Bouckaert M, Wood KA, Van den Broeck F, Daich Varela M, Thomas HB, Van Heetvelde M, De Bruyne M, Van de Sompele S, Bauwens M, Lenaerts H, Mahieu Q, Josifova D, Rivolta C, O'Keefe RT, Ellingford J, Webster AR, Arno G, Ayuso C, De Zaeytijd J, Leroy BP, De Baere E, Coppieters F. Combining a prioritization strategy and functional studies nominates 5'UTR variants underlying inherited retinal disease. Genome Med 2024; 16:7. [PMID: 38184646 PMCID: PMC10771650 DOI: 10.1186/s13073-023-01277-1] [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: 06/16/2023] [Accepted: 12/15/2023] [Indexed: 01/08/2024] Open
Abstract
BACKGROUND 5' untranslated regions (5'UTRs) are essential modulators of protein translation. Predicting the impact of 5'UTR variants is challenging and rarely performed in routine diagnostics. Here, we present a combined approach of a comprehensive prioritization strategy and functional assays to evaluate 5'UTR variation in two large cohorts of patients with inherited retinal diseases (IRDs). METHODS We performed an isoform-level re-analysis of retinal RNA-seq data to identify the protein-coding transcripts of 378 IRD genes with highest expression in retina. We evaluated the coverage of their 5'UTRs by different whole exome sequencing (WES) kits. The selected 5'UTRs were analyzed in whole genome sequencing (WGS) and WES data from IRD sub-cohorts from the 100,000 Genomes Project (n = 2397 WGS) and an in-house database (n = 1682 WES), respectively. Identified variants were annotated for 5'UTR-relevant features and classified into seven categories based on their predicted functional consequence. We developed a variant prioritization strategy by integrating population frequency, specific criteria for each category, and family and phenotypic data. A selection of candidate variants underwent functional validation using diverse approaches. RESULTS Isoform-level re-quantification of retinal gene expression revealed 76 IRD genes with a non-canonical retina-enriched isoform, of which 20 display a fully distinct 5'UTR compared to that of their canonical isoform. Depending on the probe design, 3-20% of IRD genes have 5'UTRs fully captured by WES. After analyzing these regions in both cohorts, we prioritized 11 (likely) pathogenic variants in 10 genes (ARL3, MERTK, NDP, NMNAT1, NPHP4, PAX6, PRPF31, PRPF4, RDH12, RD3), of which 7 were novel. Functional analyses further supported the pathogenicity of three variants. Mis-splicing was demonstrated for the PRPF31:c.-9+1G>T variant. The MERTK:c.-125G>A variant, overlapping a transcriptional start site, was shown to significantly reduce both luciferase mRNA levels and activity. The RDH12:c.-123C>T variant was found in cis with the hypomorphic RDH12:c.701G>A (p.Arg234His) variant in 11 patients. This 5'UTR variant, predicted to introduce an upstream open reading frame, was shown to result in reduced RDH12 protein but unaltered mRNA levels. CONCLUSIONS This study demonstrates the importance of 5'UTR variants implicated in IRDs and provides a systematic approach for 5'UTR annotation and validation that is applicable to other inherited diseases.
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Affiliation(s)
- Alfredo Dueñas Rey
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Marta Del Pozo Valero
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Manon Bouckaert
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Katherine A Wood
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Filip Van den Broeck
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
| | - Malena Daich Varela
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Huw B Thomas
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Mattias Van Heetvelde
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Marieke De Bruyne
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Stijn Van de Sompele
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Miriam Bauwens
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Hanne Lenaerts
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Quinten Mahieu
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | | | - Carlo Rivolta
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Raymond T O'Keefe
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Jamie Ellingford
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
- Genomics England, London, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Andrew R Webster
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - Gavin Arno
- UCL Institute of Ophthalmology, University College London, London, UK
- Moorfields Eye Hospital, London, UK
| | - 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), Instituto de Salud Carlos III, Madrid, Spain
| | - Julie De Zaeytijd
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
| | - Bart P Leroy
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
- Department of Head & Skin, Ghent University, Ghent, Belgium
- Division of Ophthalmology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elfride De Baere
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium
| | - Frauke Coppieters
- Center for Medical Genetics Ghent (CMGG), Ghent University Hospital, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent, 9000, Belgium.
- Department of Pharmaceutics, Ghent University, Ghent, Belgium.
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19
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Li CHZ, Pas JAAH, Corradi Z, Hitti-Malin RJ, Hoogstede A, Runhart EH, Dhooge PPA, Collin RWJ, Cremers FPM, Hoyng CB. Study of Late-Onset Stargardt Type 1 Disease: Characteristics, Genetics, and Progression. Ophthalmology 2024; 131:87-97. [PMID: 37598860 DOI: 10.1016/j.ophtha.2023.08.011] [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: 04/12/2023] [Revised: 07/07/2023] [Accepted: 08/09/2023] [Indexed: 08/22/2023] Open
Abstract
PURPOSE Late-onset Stargardt disease is a subtype of Stargardt disease type 1 (STGD1), defined by an age of onset of 45 years or older. We describe the disease characteristics, underlying genetics, and disease progression of late-onset STGD1 and highlight the differences from geographic atrophy. DESIGN Retrospective cohort study. PARTICIPANTS Seventy-one patients with late-onset STGD1. METHODS Medical files were reviewed for clinical data including age at onset, initial symptoms, and best-corrected visual acuity. A quantitative and qualitative assessment of retinal pigment epithelium (RPE) atrophy was performed on fundus autofluorescence images and OCT scans. MAIN OUTCOME MEASURES Age at onset, genotype, visual acuity, atrophy growth rates, and loss of external limiting membrane, ellipsoid zone, and RPE. RESULTS Median age at onset was 55.0 years (range, 45-82 years). A combination of a mild and severe variant in ATP-binding cassette subfamily A member 4 (ABCA4) was the most common genotype (n = 49 [69.0%]). The most frequent allele, c.5603A→T (p.Asn1868Ile), was present in 43 of 71 patients (60.6%). No combination of 2 severe variants was found. At first presentation, all patients have flecks. Foveal-sparing atrophy was present in 33.3% of eyes, whereas 21.1% had atrophy with foveal involvement. Extrafoveal atrophy was present in 38.9% of eyes, and no atrophy was evident in 6.7% of eyes. Time-to-event curves showed a median duration of 15.4 years (95% confidence interval, 11.1-19.6 years) from onset to foveal involvement. The median visual acuity decline was -0.03 Snellen decimal per year (interquartile range [IQR], -0.07 to 0.00 Snellen decimal; 0.03 logarithm of the minimum angle of resolution). Median atrophy growth was 0.590 mm2/year (IQR, 0.046-1.641 mm2/year) for definitely decreased autofluorescence and 0.650 mm2/year (IQR, 0.299-1.729 mm2/year) for total decreased autofluorescence. CONCLUSIONS Late-onset STGD1 is a subtype of STGD1 with most commonly 1 severe and 1 mild ABCA4 variant. The general patient presents with typical fundus flecks and retinal atrophy in a foveal-sparing pattern with preserved central vision. Misdiagnosis as age-related macular degeneration should be avoided to prevent futile invasive treatments with potential complications. In addition, correct diagnosis lends patients with late-onset STGD1 the opportunity to participate in potentially beneficial therapeutic trials for STGD1. FINANCIAL DISCLOSURE(S) The author(s) have no proprietary or commercial interest in any materials discussed in this article.
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Affiliation(s)
- Catherina H Z Li
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jeroen A A H Pas
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Zelia Corradi
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands; Academic Alliance Genetics, Radboud University Medical Center, Nijmegen, and Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Rebekkah J Hitti-Malin
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands; Academic Alliance Genetics, Radboud University Medical Center, Nijmegen, and Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Anne Hoogstede
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - 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
| | - Patty P A Dhooge
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rob W J Collin
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Human Genetics, Radboud University Nijmegen 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
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands; Academic Alliance Genetics, Radboud University Medical Center, Nijmegen, and Maastricht University Medical Center+, Maastricht, 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.
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20
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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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21
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Keuthan CJ, Karma S, Zack DJ. Alternative RNA Splicing in the Retina: Insights and Perspectives. Cold Spring Harb Perspect Med 2023; 13:a041313. [PMID: 36690463 PMCID: PMC10547393 DOI: 10.1101/cshperspect.a041313] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Alternative splicing is a fundamental and highly regulated post-transcriptional process that enhances transcriptome and proteome diversity. This process is particularly important in neuronal tissues, such as the retina, which exhibit some of the highest levels of differentially spliced genes in the body. Alternative splicing is regulated both temporally and spatially during neuronal development, can be cell-type-specific, and when altered can cause a number of pathologies, including retinal degeneration. Advancements in high-throughput sequencing technologies have facilitated investigations of the alternative splicing landscape of the retina in both healthy and disease states. Additionally, innovations in human stem cell engineering, specifically in the generation of 3D retinal organoids, which recapitulate many aspects of the in vivo retinal microenvironment, have aided studies of the role of alternative splicing in human retinal development and degeneration. Here we review these advances and discuss the ongoing development of strategies for the treatment of alternative splicing-related retinal disease.
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Affiliation(s)
- Casey J Keuthan
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Sadik Karma
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Donald J Zack
- Departments of Ophthalmology, Wilmer Eye Institute, Neuroscience, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
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22
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Rodríguez-Hidalgo M, de Bruijn SE, Corradi Z, Rodenburg K, Lara-López A, Valverde-Megías A, Ávila-Fernández A, Fernandez-Caballero L, Del Pozo-Valero M, Corominas J, Gilissen C, Irigoyen C, Cremers FPM, Ayuso C, Ruiz-Ederra J, Roosing S. ABCA4 c.6480-35A>G, a novel branchpoint variant associated with Stargardt disease. Front Genet 2023; 14:1234032. [PMID: 37779911 PMCID: PMC10539688 DOI: 10.3389/fgene.2023.1234032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 08/15/2023] [Indexed: 10/03/2023] Open
Abstract
Introduction: Inherited retinal dystrophies (IRDs) can be caused by variants in more than 280 genes. The ATP-binding cassette transporter type A4 (ABCA4) gene is one of these genes and has been linked to Stargardt disease type 1 (STGD1), fundus flavimaculatus, cone-rod dystrophy (CRD), and pan-retinal CRD. Approximately 25% of the reported ABCA4 variants affect RNA splicing. In most cases, it is necessary to perform a functional assay to determine the effect of these variants. Methods: Whole genome sequencing (WGS) was performed in one Spanish proband with Stargardt disease. The putative pathogenicity of c.6480-35A>G on splicing was investigated both in silico and in vitro. The in silico approach was based on the deep-learning tool SpliceAI. For the in vitro approach we used a midigene splice assay in HEK293T cells, based on a previously established wild-type midigene (BA29) containing ABCA4 exons 46 to 48. Results: Through the analysis of WGS data, we identified two candidate variants in ABCA4 in one proband: a previously described deletion, c.699_768+342del (p.(Gln234Phefs*5)), and a novel branchpoint variant, c.6480-35A>G. Segregation analysis confirmed that the variants were in trans. For the branchpoint variant, SpliceAI predicted an acceptor gain with a high score (0.47) at position c.6480-47. A midigene splice assay in HEK293T cells revealed the inclusion of the last 47 nucleotides of intron 47 creating a premature stop codon and allowed to categorize the variant as moderately severe. Subsequent analysis revealed the presence of this variant as a second allele besides c.1958G>A p.(Arg653His) in an additional Spanish proband in a large cohort of IRD cases. Conclusion: A splice-altering effect of the branchpoint variant, confirmed by the midigene splice assay, along with the identification of this variant in a second unrelated individual affected with STGD, provides sufficient evidence to classify the variant as likely pathogenic. In addition, this research highlights the importance of studying non-coding regions and performing functional assays to provide a conclusive molecular diagnosis.
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Affiliation(s)
- María Rodríguez-Hidalgo
- Department of Neuroscience, Biodonostia Health Research Institute, Donostia-San Sebastián, Spain
- Department of Genetic, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Leioa, Spain
| | - Suzanne E. de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Zelia Corradi
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Kim Rodenburg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | | | | | - Almudena Ávila-Fernández
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Lidia Fernandez-Caballero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Del Pozo-Valero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Jordi Corominas
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Cristina Irigoyen
- Department of Neuroscience, Biodonostia Health Research Institute, Donostia-San Sebastián, Spain
- Ophthalmology Service, Donostia Universy Hospital, Donostia-San Sebastián, Spain
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Carmen Ayuso
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Javier Ruiz-Ederra
- Department of Neuroscience, Biodonostia Health Research Institute, Donostia-San Sebastián, Spain
- Department of Ophthalmology, University of the Basque Country (UPV/EHU), San Sebastián, Spain
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
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Shi J, Tian L, Sun T, Zhang X, Xu K, Xie Y, Peng X, Tang X, Jin ZB, Li Y. Comprehensive Genetic Analysis Unraveled the Missing Heritability and a Founder Variant of BEST1 in a Chinese Cohort With Autosomal Recessive Bestrophinopathy. Invest Ophthalmol Vis Sci 2023; 64:37. [PMID: 37747403 PMCID: PMC10528473 DOI: 10.1167/iovs.64.12.37] [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: 04/18/2023] [Accepted: 09/02/2023] [Indexed: 09/26/2023] Open
Abstract
Purpose To describe the genetic landscape of BEST1 for a large Chinese cohort with autosomal recessive bestrophinopathy (ARB), identify the missing heritability, and report a common Chinese founder variant. Methods We recruited 65 patients from 63 families with a clinical diagnosis of ARB. All patients underwent ophthalmic examinations and comprehensive genetic analyses, including Sanger DNA sequencing of BEST1 and whole genome sequencing (WGS). The effects of deep intronic variants (DIVs) on splicing were assessed using in vitro splicing assays in HEK293T cells and patient-derived peripheral blood mononuclear cells. Haplotype mapping was performed for 17 unrelated patients harboring variant c.867+97G>A. Results We identified 54 distinct disease-causing variants of BEST1 in 63 pedigrees, 62 probands with biallelic variants, and one family with monoallelic variants. Sanger DNA sequencing of BEST1 initially detected 51 variants in 61 pedigrees, including 19 probands with one heterozygous variant. Subsequent WGS, combined with supplementary Sanger sequencing, revealed three missing DIVs (c.1101-491A>G, c.867+97G>A, and c.867+97G>T) in 20 families. The novel DIV c.1101-491A>G caused an abnormal splicing resulting in a 204-nt pseudoexon (PE) insertion, whereas c.867+97G>A/T relatively strengthened an alternative donor site, resulting in a 203-nt intron retention (IR). The PE and IR generated a premature termination codon downstream. Haplotype analysis identified c.867+97G>A as a common founder variant with an allele frequency of 16%. Conclusions Our results expand the pathogenic variant spectrum of BEST1, and DIVs can explain almost all of the missing heritability. The c.867+97G>A DIV is a common founder variant for Chinese patients with ARB.
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Affiliation(s)
- Jie Shi
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Lu Tian
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Tengyang Sun
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Xiao Zhang
- 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
| | - Yue Xie
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Xiaoyan Peng
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Xin Tang
- 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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24
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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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25
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Gupta P, Nakamichi K, Bonnell AC, Yanagihara R, Radulovich N, Hisama FM, Chao JR, Mustafi D. Familial co-segregation and the emerging role of long-read sequencing to re-classify variants of uncertain significance in inherited retinal diseases. NPJ Genom Med 2023; 8:20. [PMID: 37558662 PMCID: PMC10412581 DOI: 10.1038/s41525-023-00366-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 08/02/2023] [Indexed: 08/11/2023] Open
Abstract
Phasing genetic variants is essential in determining those that are potentially disease-causing. In autosomal recessive inherited retinal diseases (IRDs), reclassification of variants of uncertain significance (VUS) can provide a genetic diagnosis in indeterminate compound heterozygote cases. We report four cases in which familial co-segregation demonstrated a VUS resided in trans to a known pathogenic variant, which in concert with other supporting criteria, led to the reclassification of the VUS to likely pathogenic, thereby providing a genetic diagnosis in each case. We also demonstrate in a simplex patient without access to family members for co-segregation analysis that targeted long-read sequencing can provide haplotagged variant calling. This can elucidate if variants reside in trans and provide phase of genetic variants from the proband alone without parental testing. This emerging method can alleviate the bottleneck of haplotype analysis in cases where genetic testing of family members is unfeasible to provide a complete genetic diagnosis.
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Affiliation(s)
- Pankhuri Gupta
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Kenji Nakamichi
- Department of Ophthalmology and Roger and Karalis Johnson Retina Center, University of Washington, Seattle, WA, 98109, USA
| | - Alyssa C Bonnell
- Department of Ophthalmology and Roger and Karalis Johnson Retina Center, University of Washington, Seattle, WA, 98109, USA
| | - Ryan Yanagihara
- Department of Ophthalmology and Roger and Karalis Johnson Retina Center, University of Washington, Seattle, WA, 98109, USA
| | - Nick Radulovich
- Department of Ophthalmology and Roger and Karalis Johnson Retina Center, University of Washington, Seattle, WA, 98109, USA
| | - Fuki M Hisama
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Jennifer R Chao
- Department of Ophthalmology and Roger and Karalis Johnson Retina Center, University of Washington, Seattle, WA, 98109, USA
| | - Debarshi Mustafi
- Department of Ophthalmology and Roger and Karalis Johnson Retina Center, University of Washington, Seattle, WA, 98109, USA.
- Division of Ophthalmology, Seattle Children's Hospital, Seattle, WA, 98105, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, 98195, USA.
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26
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McClinton B, Watson CM, Crinnion LA, McKibbin M, Ali M, Inglehearn CF, Toomes C. Haplotyping Using Long-Range PCR and Nanopore Sequencing to Phase Variants: Lessons Learned From the ABCA4 Locus. J Transl Med 2023; 103:100160. [PMID: 37088464 DOI: 10.1016/j.labinv.2023.100160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/11/2023] [Accepted: 04/17/2023] [Indexed: 04/25/2023] Open
Abstract
Short-read next-generation sequencing has revolutionized our ability to identify variants underlying inherited diseases; however, it does not allow the phasing of variants to clarify their diagnostic interpretation. The advent of widespread, increasingly accurate long-read sequencing has opened up new applications not currently available through short-read next-generation sequencing. One such use is the ability to phase variants to clarify their diagnostic interpretation and to investigate the increasingly prevalent role of cis-acting variants in the pathogenesis of the inherited disease, so-called complex alleles. Complex alleles are becoming an increasingly prevalent part of the study of genes associated with inherited diseases, for example, in ABCA4-related diseases. We sought to establish a cost-effective method to phase contiguous segments of the 130-kb ABCA4 locus by long-read sequencing of overlapping amplification products. Using the comprehensively characterized CEPH sample, NA12878, we verified the accuracy and robustness of our assay. However, in-field assessment of its utility using clinical test cases was hampered by the paucity and distribution of identified variants and by PCR chimerism, particularly where the number of PCR cycles was high. Despite this, we were able to construct robust phase blocks of up to 94.9 kb, representing 73% of the ABCA4 locus. We conclude that, although haplotype analysis of variants located within discrete amplification products was robust and informative, the stitching together of larger phase blocks using overlapping single-molecule reads remained practically challenging.
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Affiliation(s)
- Benjamin McClinton
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK
| | - Christopher M Watson
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK; North East and Yorkshire Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, UK
| | - Laura A Crinnion
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK; North East and Yorkshire Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, UK
| | - Martin McKibbin
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK; Department of Ophthalmology, St. James's University Hospital, Leeds, UK
| | - Manir Ali
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK
| | - Chris F Inglehearn
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK
| | - Carmel Toomes
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK.
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27
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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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28
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Lenassi E, Carvalho A, Thormann A, Abrahams L, Arno G, Fletcher T, Hardcastle C, Lopez J, Hunt SE, Short P, Sergouniotis PI, Michaelides M, Webster A, Cunningham F, Ramsden SC, Kasperaviciute D, Fitzpatrick DR, Black GC, Ellingford JM. EyeG2P: an automated variant filtering approach improves efficiency of diagnostic genomic testing for inherited ophthalmic disorders. J Med Genet 2023; 60:810-818. [PMID: 36669873 PMCID: PMC10423522 DOI: 10.1136/jmg-2022-108618] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 12/16/2022] [Indexed: 01/21/2023]
Abstract
BACKGROUND Genomic variant prioritisation is one of the most significant bottlenecks to mainstream genomic testing in healthcare. Tools to improve precision while ensuring high recall are critical to successful mainstream clinical genomic testing, in particular for whole genome sequencing where millions of variants must be considered for each patient. METHODS We developed EyeG2P, a publicly available database and web application using the Ensembl Variant Effect Predictor. EyeG2P is tailored for efficient variant prioritisation for individuals with inherited ophthalmic conditions. We assessed the sensitivity of EyeG2P in 1234 individuals with a broad range of eye conditions who had previously received a confirmed molecular diagnosis through routine genomic diagnostic approaches. For a prospective cohort of 83 individuals, we assessed the precision of EyeG2P in comparison with routine diagnostic approaches. For 10 additional individuals, we assessed the utility of EyeG2P for whole genome analysis. RESULTS EyeG2P had 99.5% sensitivity for genomic variants previously identified as clinically relevant through routine diagnostic analysis (n=1234 individuals). Prospectively, EyeG2P enabled a significant increase in precision (35% on average) in comparison with routine testing strategies (p<0.001). We demonstrate that incorporation of EyeG2P into whole genome sequencing analysis strategies can reduce the number of variants for analysis to six variants, on average, while maintaining high diagnostic yield. CONCLUSION Automated filtering of genomic variants through EyeG2P can increase the efficiency of diagnostic testing for individuals with a broad range of inherited ophthalmic disorders.
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Affiliation(s)
- Eva Lenassi
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Ana Carvalho
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Medical Genetic Unit, Pediatric Hospital, Coimbra Hospital and Universitary Centre (CHUC), Coimbra, Portugal
| | - Anja Thormann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | | | - Gavin Arno
- UCL Institute of Ophthalmology, University College London, London, UK
- Department of Ophthalmology, Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Tracy Fletcher
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Claire Hardcastle
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | | | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | | | - Panagiotis I Sergouniotis
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Michel Michaelides
- UCL Institute of Ophthalmology, University College London, London, UK
- Department of Ophthalmology, Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Andrew Webster
- UCL Institute of Ophthalmology, University College London, London, UK
- Department of Ophthalmology, Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Simon C Ramsden
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | | | - David R Fitzpatrick
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Graeme C Black
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Jamie M Ellingford
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Genomics England Ltd, London, UK
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29
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Nakamichi K, Van Gelder RN, Chao JR, Mustafi D. Targeted adaptive long-read sequencing for discovery of complex phased variants in inherited retinal disease patients. Sci Rep 2023; 13:8535. [PMID: 37237007 PMCID: PMC10219926 DOI: 10.1038/s41598-023-35791-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/24/2023] [Indexed: 05/28/2023] Open
Abstract
Inherited retinal degenerations (IRDs) are a heterogeneous group of predominantly monogenic disorders with over 300 causative genes identified. Short-read exome sequencing is commonly used to genotypically diagnose patients with clinical features of IRDs, however, in up to 30% of patients with autosomal recessive IRDs, one or no disease-causing variants are identified. Furthermore, chromosomal maps cannot be reconstructed for allelic variant discovery with short-reads. Long-read genome sequencing can provide complete coverage of disease loci and a targeted approach can focus sequencing bandwidth to a genomic region of interest to provide increased depth and haplotype reconstruction to uncover cases of missing heritability. We demonstrate that targeted adaptive long-read sequencing on the Oxford Nanopore Technologies (ONT) platform of the USH2A gene from three probands in a family with the most common cause of the syndromic IRD, Usher Syndrome, resulted in greater than 12-fold target gene sequencing enrichment on average. This focused depth of sequencing allowed for haplotype reconstruction and phased variant identification. We further show that variants obtained from the haplotype-aware genotyping pipeline can be heuristically ranked to focus on potential pathogenic candidates without a priori knowledge of the disease-causing variants. Moreover, consideration of the variants unique to targeted long-read sequencing that are not covered by short-read technology demonstrated higher precision and F1 scores for variant discovery by long-read sequencing. This work establishes that targeted adaptive long-read sequencing can generate targeted, chromosome-phased data sets for identification of coding and non-coding disease-causing alleles in IRDs and can be applicable to other Mendelian diseases.
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Affiliation(s)
- Kenji Nakamichi
- Department of Ophthalmology, Roger and Karalis Johnson Retina Center, University of Washington, Seattle, WA, 98109, USA
| | - Russell N Van Gelder
- Department of Ophthalmology, Roger and Karalis Johnson Retina Center, University of Washington, Seattle, WA, 98109, USA
| | - Jennifer R Chao
- Department of Ophthalmology, Roger and Karalis Johnson Retina Center, University of Washington, Seattle, WA, 98109, USA
| | - Debarshi Mustafi
- Department of Ophthalmology, Roger and Karalis Johnson Retina Center, University of Washington, Seattle, WA, 98109, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, 98195, USA.
- Division of Ophthalmology, Seattle Children's Hospital, Seattle, WA, 98105, USA.
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30
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Sullivan PJ, Gayevskiy V, Davis RL, Wong M, Mayoh C, Mallawaarachchi A, Hort Y, McCabe MJ, Beecroft S, Jackson MR, Arts P, Dubowsky A, Laing N, Dinger ME, Scott HS, Oates E, Pinese M, Cowley MJ. Introme accurately predicts the impact of coding and noncoding variants on gene splicing, with clinical applications. Genome Biol 2023; 24:118. [PMID: 37198692 PMCID: PMC10190034 DOI: 10.1186/s13059-023-02936-7] [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: 03/30/2022] [Accepted: 04/10/2023] [Indexed: 05/19/2023] Open
Abstract
Predicting the impact of coding and noncoding variants on splicing is challenging, particularly in non-canonical splice sites, leading to missed diagnoses in patients. Existing splice prediction tools are complementary but knowing which to use for each splicing context remains difficult. Here, we describe Introme, which uses machine learning to integrate predictions from several splice detection tools, additional splicing rules, and gene architecture features to comprehensively evaluate the likelihood of a variant impacting splicing. Through extensive benchmarking across 21,000 splice-altering variants, Introme outperformed all tools (auPRC: 0.98) for the detection of clinically significant splice variants. Introme is available at https://github.com/CCICB/introme .
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Affiliation(s)
- Patricia J Sullivan
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Velimir Gayevskiy
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia
| | - Ryan L Davis
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia
- Department of Neurogenetics, Kolling Institute, St. Leonards, NSW, Australia
- Sydney Medical School-Northern, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Marie Wong
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
| | - Chelsea Mayoh
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
| | - Amali Mallawaarachchi
- Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, Australia
- Clinical Genetics Unit, Institute of Precision Medicine and Bioinformatics, Sydney Local Health District, Sydney, Australia
| | - Yvonne Hort
- Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, Australia
| | - Mark J McCabe
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia
| | - Sarah Beecroft
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
| | - Matilda R Jackson
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia
- Australian Genomics, Parkville, VIC, Australia
| | - Peer Arts
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia
| | - Andrew Dubowsky
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia
| | - Nigel Laing
- Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia
| | - Marcel E Dinger
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Hamish S Scott
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, Australia
- Australian Genomics, Parkville, VIC, Australia
- School of Medicine, University of Adelaide, Adelaide, SA, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, An Alliance Between SA Pathology and the University of South Australia, Adelaide, SA, Australia
| | - Emily Oates
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Mark Pinese
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
| | - Mark J Cowley
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia.
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia.
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31
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Ullah M, Rehman AU, Folcher M, Ullah A, Usman F, Rashid A, Khan B, Quinodoz M, Ansar M, Rivolta C. A Novel Intronic Deletion in PDE6B Causes Autosomal Recessive Retinitis Pigmentosa by Interfering with RNA Splicing. Ophthalmic Res 2023; 66:878-884. [PMID: 37094557 DOI: 10.1159/000530800] [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: 02/16/2023] [Accepted: 04/17/2023] [Indexed: 04/26/2023]
Abstract
INTRODUCTION Retinitis pigmentosa (RP) is a rare degenerative retinal disease caused by mutations in approximately seventy genes. Currently, despite the availability of large-scale DNA sequencing technologies, ∼30-40% of patients still cannot be diagnosed at the molecular level. In this study, we investigated a novel intronic deletion of PDE6B, encoding the beta subunit of phosphodiesterase 6 in association with recessive RP. METHODS Three unrelated consanguineous families were recruited from the northwestern part of Pakistan. Whole exome sequencing was performed for the proband of each family, and the data were analyzed according to an in-house computer pipeline. Relevant DNA variants in all available members of these families were assessed through Sanger sequencing. A minigene-based splicing assay was also performed. RESULTS The clinical phenotype for all patients was compatible with rod cone degeneration, with the onset during childhood. Whole exome sequencing revealed a homozygous 18 bp intronic deletion (NM_000283.3:c.1921-20_1921-3del) in PDE6B, which co-segregated with disease in 10 affected individuals. In vitro splicing tests showed that this deletion causes aberrant RNA splicing of the gene, leading to the in-frame deletion of 6 codons and, likely, to disease. CONCLUSION Our findings further expand the mutational spectrum of the PDE6B gene.
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Affiliation(s)
- Mukhtar Ullah
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Atta Ur Rehman
- Department of Zoology, Faculty of Biological and Health Sciences, Hazara University Mansehra, Mansehra, Pakistan
| | - Marc Folcher
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Adnan Ullah
- Department of Zoology, Islamia College Peshawar, Peshawar, Pakistan
| | - Faisal Usman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological and Health Sciences, Hazara University Mansehra, Mansehra, Pakistan
| | - Abdur Rashid
- Department of Higher Education, Archives and Libraries Peshawar, Peshawar, Pakistan
| | - Bilal Khan
- Medical Teaching Institution Khyber Teaching Hospital Peshawar, Peshawar, Pakistan
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Muhammad Ansar
- Department of Ophthalmology, Jules Gonin Eye Hospital, Fondation Asile Des Aveugles, University of Lausanne, Lausanne, Switzerland
- Advanced Molecular Genetics and Genomics Disease Research and Treatment Centre, Dow University of Health Sciences, Karachi, Pakistan
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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Kaltak M, de Bruijn P, Piccolo D, Lee SE, Dulla K, Hoogenboezem T, Beumer W, Webster AR, Collin RW, Cheetham ME, Platenburg G, Swildens J. Antisense oligonucleotide therapy corrects splicing in the common Stargardt disease type 1-causing variant ABCA4 c.5461-10T>C. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:674-688. [PMID: 36910710 PMCID: PMC9999166 DOI: 10.1016/j.omtn.2023.02.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 02/15/2023] [Indexed: 02/20/2023]
Abstract
Stargardt disease type 1 (STGD1) is the most common hereditary form of maculopathy and remains untreatable. STGD1 is caused by biallelic variants in the ABCA4 gene, which encodes the ATP-binding cassette (type 4) protein (ABCA4) that clears toxic byproducts of the visual cycle. The c.5461-10T>C p.[Thr1821Aspfs∗6,Thr1821Valfs∗13] variant is the most common severe disease-associated variant, and leads to exon skipping and out-of-frame ABCA4 transcripts that prevent translation of functional ABCA4 protein. Homozygous individuals typically display early onset STGD1 and are legally blind by early adulthood. Here, we applied antisense oligonucleotides (AONs) to promote exon inclusion and restore wild-type RNA splicing of ABCA4 c.5461-10T>C. The effect of AONs was first investigated in vitro using an ABCA4 midigene model. Subsequently, the best performing AONs were administered to homozygous c.5461-10T>C 3D human retinal organoids. Isoform-specific digital polymerase chain reaction revealed a significant increase in correctly spliced transcripts after treatment with the lead AON, QR-1011, up to 53% correct transcripts at a 3 μM dose. Furthermore, western blot and immunohistochemistry analyses identified restoration of ABCA4 protein after treatment. Collectively, we identified QR-1011 as a potent splice-correcting AON and a possible therapeutic intervention for patients harboring the severe ABCA4 c.5461-10T>C variant.
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Affiliation(s)
- Melita Kaltak
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, the Netherlands
- Academic Alliance Genetics, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, and Maastricht University Medical Center+, P. Debyelaan 25, 6229 HX Maastricht, the Netherlands
| | - Petra de Bruijn
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | - Davide Piccolo
- UCL, Institute of Ophthalmology, 11-43 Bath Street, EC1V 9EL London, UK
| | - Sang-Eun Lee
- UCL, Institute of Ophthalmology, 11-43 Bath Street, EC1V 9EL London, UK
| | - Kalyan Dulla
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | | | - Wouter Beumer
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | - Andrew R. Webster
- UCL, Institute of Ophthalmology, 11-43 Bath Street, EC1V 9EL London, UK
- Moorfields Eye Hospital, 162 City Road, EC1V 2PD London, UK
| | - Rob W.J. Collin
- Department of Human Genetics, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, the Netherlands
- Academic Alliance Genetics, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, and Maastricht University Medical Center+, P. Debyelaan 25, 6229 HX Maastricht, the Netherlands
| | | | | | - Jim Swildens
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
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Luo X, Wang R, Sun Y, Qiu W, Lu D, Wang Y, Gong Z, Zhang H, Han L, Liang L, Gu X, Yu Y, Xiao B. Deep Intronic PAH Variants Explain Missing Heritability in Hyperphenylalaninemia. J Mol Diagn 2023; 25:284-294. [PMID: 36849017 DOI: 10.1016/j.jmoldx.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/18/2023] [Accepted: 02/02/2023] [Indexed: 02/27/2023] Open
Abstract
Phenylalanine hydroxylase (PAH) deficiency or phenylketonuria (PKU) is the most common cause of hyperphenylalaninemia (HPA), and approximately 5% of patients remain genetically unsolved. Identifying deep intronic PAH variants may help improve their molecular diagnostic rate. Next-generation sequencing was utilized to detect the whole PAH gene in 96 patients with genetically unsolved HPA from 2013 to 2022. The effects of deep intronic variants on pre-mRNA splicing were investigated by minigene-based assay. The allelic phenotype values of recurrent deep intronic variants were calculated. Twelve deep intronic PAH variants, located in intron 5 (c.509+434C>T), intron 6 (c.706+288T>G, c.706+519T>C, c.706+531T>C, c.706+535G>T, c.706+600A>C, c.706+603T>G, and c.706+608A>C), intron 10 (c.1065+241C>A and c.1065+258C>A), and intron 11 (c.1199+502A>T and c.1199+745T>A) were identified in 80.2% (77/96) patients. Ten of the 12 variants were novel, and they all generated pseudoexons in mRNA, leading to frameshift or lengthened proteins. The most prevalent deep intronic variant was c.1199+502A>T, followed by c.1065+241C>A, c.1065+258C>A, and c.706+531T>C. The metabolic phenotypes of the four variants were assigned as classic PKU, mild HPA, mild HPA, and mild PKU, respectively. The results suggest that deep intronic PAH variants improved the diagnostic rate from 95.3% to 99.3% in the overall patients with HPA. Our data demonstrate the importance of assessing noncoding variants in genetic diseases. Pseudoexon inclusion caused by deep intronic variants could represent a recurrent mechanism.
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Affiliation(s)
- Xiaomei Luo
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Institute for Pediatric Research, Shanghai, China
| | - Ruifang Wang
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Institute for Pediatric Research, Shanghai, China
| | - Yu Sun
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Institute for Pediatric Research, Shanghai, China
| | - Wenjuan Qiu
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Institute for Pediatric Research, Shanghai, China
| | - Deyun Lu
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Institute for Pediatric Research, Shanghai, China
| | - Yu Wang
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Institute for Pediatric Research, Shanghai, China
| | - Zhuwen Gong
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Institute for Pediatric Research, Shanghai, China
| | - Huiwen Zhang
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Institute for Pediatric Research, Shanghai, China
| | - Lianshu Han
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Institute for Pediatric Research, Shanghai, China
| | - Lili Liang
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Institute for Pediatric Research, Shanghai, China
| | - Xuefan Gu
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Institute for Pediatric Research, Shanghai, China
| | - Yongguo Yu
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Institute for Pediatric Research, Shanghai, China.
| | - Bing Xiao
- Department of Pediatric Endocrinology and Genetic Metabolism, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Institute for Pediatric Research, Shanghai, China.
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34
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Horton AE, Lunke S, Sadedin S, Fennell AP, Stark Z. Elusive variants in autosomal recessive disease: how can we improve timely diagnosis? Eur J Hum Genet 2023; 31:371-374. [PMID: 36732660 PMCID: PMC10133393 DOI: 10.1038/s41431-023-01293-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Affiliation(s)
- Ari E Horton
- Monash Genetics, Monash Health, Melbourne, VIC, Australia.,Monash Heart and Monash Children's Hospital, Monash Health, Melbourne, VIC, Australia.,Monash Cardiovascular Research Centre, Victorian Heart Institute, Melbourne, VIC, Australia.,Department of Paediatrics, Monash University, Melbourne, VIC, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,University of Melbourne, Melbourne, VIC, Australia.,Australian Genomics, Melbourne, VIC, Australia
| | - Simon Sadedin
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Andrew P Fennell
- Monash Genetics, Monash Health, Melbourne, VIC, Australia.,Department of Paediatrics, Monash University, Melbourne, VIC, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC, Australia. .,University of Melbourne, Melbourne, VIC, Australia. .,Australian Genomics, Melbourne, VIC, Australia.
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Viering DH, Hureaux M, Neveling K, Latta F, Kwint M, Blanchard A, Konrad M, Bindels RJ, Schlingmann KP, Vargas-Poussou R, de Baaij JH. Long-Read Sequencing Identifies Novel Pathogenic Intronic Variants in Gitelman Syndrome. J Am Soc Nephrol 2023; 34:333-345. [PMID: 36302598 PMCID: PMC10103101 DOI: 10.1681/asn.2022050627] [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: 05/30/2022] [Accepted: 10/17/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Gitelman syndrome is a salt-losing tubulopathy characterized by hypokalemic alkalosis and hypomagnesemia. It is caused by homozygous recessive or compound heterozygous pathogenic variants in SLC12A3 , which encodes the Na + -Cl - cotransporter (NCC). In up to 10% of patients with Gitelman syndrome, current genetic techniques detect only one specific pathogenic variant. This study aimed to identify a second pathogenic variant in introns, splice sites, or promoters to increase the diagnostic yield. METHODS Long-read sequencing of SLC12A3 was performed in 67 DNA samples from individuals with suspected Gitelman syndrome in whom a single likely pathogenic or pathogenic variant was previously detected. In addition, we sequenced DNA samples from 28 individuals with one variant of uncertain significance or no candidate variant. Midigene splice assays assessed the pathogenicity of novel intronic variants. RESULTS A second likely pathogenic/pathogenic variant was identified in 45 (67%) patients. Those with two likely pathogenic/pathogenic variants had a more severe electrolyte phenotype than other patients. Of the 45 patients, 16 had intronic variants outside of canonic splice sites (nine variants, mostly deep intronic, six novel), whereas 29 patients had an exonic variant or canonic splice site variant. Midigene splice assays of the previously known c.1670-191C>T variant and intronic candidate variants demonstrated aberrant splicing patterns. CONCLUSION Intronic pathogenic variants explain an important part of the missing heritability in Gitelman syndrome. Long-read sequencing should be considered in diagnostic workflows for Gitelman syndrome.
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Affiliation(s)
- Daan H.H.M. Viering
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marguerite Hureaux
- Reference Center for Hereditary Kidney and Childhood Diseases (Maladies Rénales Héréditaires de l’Enfant et de l’Adulte, MARHEA), Paris, France
- Department of Genetics, Hôpital Européen Georges-Pompidou, Assistance Publique Hôpitaux de Paris, Paris, France
- Paris CardioVascular Research Center, Institut National de la Santé et de Recherche Médicale (INSERM) U970, Paris City University, Paris, France
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Femke Latta
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Michael Kwint
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Anne Blanchard
- Reference Center for Hereditary Kidney and Childhood Diseases (Maladies Rénales Héréditaires de l’Enfant et de l’Adulte, MARHEA), Paris, France
- Clinical Investigations Center, Hôpital Européen Georges-Pompidou, Assistance Publique Hôpitaux de Paris, Paris, France
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, University of Paris, Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Martin Konrad
- Department of General Pediatrics, University Children’s Hospital, Münster, Germany
| | - René J.M. Bindels
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Rosa Vargas-Poussou
- Reference Center for Hereditary Kidney and Childhood Diseases (Maladies Rénales Héréditaires de l’Enfant et de l’Adulte, MARHEA), Paris, France
- Department of Genetics, Hôpital Européen Georges-Pompidou, Assistance Publique Hôpitaux de Paris, Paris, France
- Clinical Investigations Center, Hôpital Européen Georges-Pompidou, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Jeroen H.F. de Baaij
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
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36
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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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Tomkiewicz TZ, Nieuwenhuis SE, Cremers FPM, Garanto A, Collin RWJ. Correction of the Splicing Defect Caused by a Recurrent Variant in ABCA4 (c.769-784C>T) That Underlies Stargardt Disease. Cells 2022; 11:3947. [PMID: 36552712 PMCID: PMC9777113 DOI: 10.3390/cells11243947] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/23/2022] [Accepted: 11/26/2022] [Indexed: 12/13/2022] Open
Abstract
Stargardt disease is an inherited retinal disease caused by biallelic mutations in the ABCA4 gene, many of which affect ABCA4 splicing. In this study, nine antisense oligonucleotides (AONs) were designed to correct pseudoexon (PE) inclusion caused by a recurrent deep-intronic variant in ABCA4 (c.769-784C>T). First, the ability of AONs to skip the PE from the final ABCA4 mRNA transcript was assessed in two cellular models carrying the c.769-784C>T variant: a midigene assay using HEK293T cells and patient-derived fibroblasts. Based on the splicing-correcting ability of each individual AON, the three most efficacious AONs targeting independent regions of the PE were selected for a final assessment in photoreceptor precursor cells (PPCs). The final analysis in the PPC model confirmed high efficacy of AON2, -5, and -7 in promoting PE exclusion. Among the three AONs, AON2 is chosen as the lead candidate for further optimization, hereby showcasing the high potential of AONs to correct aberrant splicing events driven by deep-intronic variants.
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Affiliation(s)
- Tomasz Z. Tomkiewicz
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Sara E. Nieuwenhuis
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Frans P. M. Cremers
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Alejandro Garanto
- Departments of Pediatrics, Amalia Children’s Hospital, Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Rob W. J. Collin
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
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Suga A, Yoshitake K, Minematsu N, Tsunoda K, Fujinami K, Miyake Y, Kuniyoshi K, Hayashi T, Mizobuchi K, Ueno S, Terasaki H, Kominami T, Nao-I N, Mawatari G, Mizota A, Shinoda K, Kondo M, Kato K, Sekiryu T, Nakamura M, Kusuhara S, Yamamoto H, Yamamoto S, Mochizuki K, Kondo H, Matsushita I, Kameya S, Fukuchi T, Hatase T, Horiguchi M, Shimada Y, Tanikawa A, Yamamoto S, Miura G, Ito N, Murakami A, Fujimaki T, Hotta Y, Tanaka K, Iwata T. Genetic characterization of 1210 Japanese pedigrees with inherited retinal diseases by whole-exome sequencing. Hum Mutat 2022; 43:2251-2264. [PMID: 36284460 DOI: 10.1002/humu.24492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/18/2022] [Accepted: 10/21/2022] [Indexed: 01/25/2023]
Abstract
Inherited retinal diseases (IRDs) comprise a phenotypically and genetically heterogeneous group of ocular disorders that cause visual loss via progressive retinal degeneration. Here, we report the genetic characterization of 1210 IRD pedigrees enrolled through the Japan Eye Genetic Consortium and analyzed by whole exome sequencing. The most common phenotype was retinitis pigmentosa (RP, 43%), followed by macular dystrophy/cone- or cone-rod dystrophy (MD/CORD, 13%). In total, 67 causal genes were identified in 37% (448/1210) of the pedigrees. The first and second most frequently mutated genes were EYS and RP1, associated primarily with autosomal recessive (ar) RP, and RP and arMD/CORD, respectively. Examinations of variant frequency in total and by phenotype showed high accountability of a frequent EYS missense variant (c.2528G>A). In addition to the two known EYS founder mutations (c.4957dupA and c.8805C>G) of arRP, we observed a frequent RP1 variant (c.5797C>T) in patients with arMD/CORD.
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Affiliation(s)
- Akiko Suga
- Division of Molecular and Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Kazutoshi Yoshitake
- Division of Molecular and Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan.,Laboratory of Aquatic Molecular Biology and Biotechnology, Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Naoko Minematsu
- Division of Molecular and Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Kazushige Tsunoda
- Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Kaoru Fujinami
- Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | | | - Kazuki Kuniyoshi
- Department of Ophthalmology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Takaaki Hayashi
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, Japan
| | - Kei Mizobuchi
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, Japan
| | - Shinji Ueno
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Department of Ophthalmology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Hiroko Terasaki
- Nagoya University, Institutes of Innovation for Future Society, Nagoya, Japan
| | - Taro Kominami
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nobuhisa Nao-I
- Department of Ophthalmology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Go Mawatari
- Department of Ophthalmology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Atsushi Mizota
- Department of Ophthalmology, Teikyo University School of Medicine, Teikyo, Japan
| | - Kei Shinoda
- Department of Ophthalmology, Teikyo University School of Medicine, Teikyo, Japan.,Department of Ophthalmology, Saitama Medical University, Iruma-gun, Japan
| | - Mineo Kondo
- Department of Ophthalmology, Mie University Graduate School of Medicine, Tsu, Japan
| | - Kumiko Kato
- Department of Ophthalmology, Mie University Graduate School of Medicine, Tsu, Japan
| | - Tetsuju Sekiryu
- Department of Ophthalmology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Makoto Nakamura
- Division of Ophthalmology, Department of Surgery, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Sentaro Kusuhara
- Division of Ophthalmology, Department of Surgery, Kobe University Graduate School of Medicine, Kobe, Japan
| | | | | | - Kiyofumi Mochizuki
- Department of Ophthalmology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Hiroyuki Kondo
- Department of Ophthalmology, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Itsuka Matsushita
- Department of Ophthalmology, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Shuhei Kameya
- Nippon Medical School Chiba Hokusoh Hospital, Chiba, Japan
| | - Takeo Fukuchi
- Division of Ophthalmology and Visual Science, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Tetsuhisa Hatase
- Division of Ophthalmology and Visual Science, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | | | - Yoshiaki Shimada
- Department of Ophthalmology, Fujita Health University, Fujita, Japan
| | - Atsuhiro Tanikawa
- Department of Ophthalmology, Fujita Health University, Fujita, Japan
| | - Shuichi Yamamoto
- Department of Ophthalmology and Visual Science, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Gen Miura
- Department of Ophthalmology and Visual Science, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Nana Ito
- Department of Ophthalmology and Visual Science, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Akira Murakami
- Department of Ophthalmology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Japan
| | - Takuro Fujimaki
- Department of Ophthalmology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Japan.,Kohinata Eye Clinic, Tokyo, Japan
| | - Yoshihiro Hotta
- Department of Ophthalmology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Koji Tanaka
- Division of Ophthalmology, Department of Visual Sciences, Nihon University School of Medicine, Chiyoda-ku, Japan
| | - Takeshi Iwata
- Division of Molecular and Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
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Huang D, Thompson JA, Chen SC, Adams A, Pitout I, Lima A, Zhang D, Jeffery RCH, Attia MS, McLaren TL, Lamey TM, De Roach JN, McLenachan S, Aung-Htut MT, Fletcher S, Wilton SD, Chen FK. Characterising splicing defects of ABCA4 variants within exons 13-50 in patient-derived fibroblasts. Exp Eye Res 2022; 225:109276. [PMID: 36209838 DOI: 10.1016/j.exer.2022.109276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/12/2022] [Accepted: 09/28/2022] [Indexed: 12/29/2022]
Abstract
The ATP-binding cassette subfamily A member 4 gene (ABCA4)-associated retinopathy, Stargardt disease, is the most common monogenic inherited retinal disease. Given the pathogenicity of numerous ABCA4 variants is yet to be examined and a significant proportion (more than 15%) of ABCA4 variants are categorized as splice variants in silico, we therefore established a fibroblast-based splice assay to analyze ABCA4 variants in an Australian Stargardt disease cohort and characterize the pathogenic mechanisms of ABCA4 variants. A cohort of 67 patients clinically diagnosed with Stargardt disease was recruited. Genomic DNA was analysed using a commercial panel for ABCA4 variant detection and the consequences of ABCA4 variants were predicted in silico. Dermal fibroblasts were propagated from skin biopsies, total RNA was extracted and the ABCA4 transcript was amplified by RT-PCR. Our analysis identified a total of 67 unique alleles carrying 74 unique variants. The most prevalent splice-affecting complex allele c.[5461-10T>C; 5603A>T] was carried by 10% of patients in a compound heterozygous state. ABCA4 transcripts from exon 13 to exon 50 were readily detected in fibroblasts. In this region, aberrant splicing was evident in 10 out of 57 variant transcripts (18%), carried by 19 patients (28%). Patient-derived fibroblasts provide a feasible platform for identification of ABCA4 splice variants located within exons 13-50. Experimental evidence of aberrant splicing contributes to the pathogenic classification for ABCA4 variants. Moreover, identification of variants that affect splicing processes provides opportunities for intervention, in particular antisense oligonucleotide-mediated splice correction.
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Affiliation(s)
- Di Huang
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Western Australia, Australia; Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Jennifer A Thompson
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Shang-Chih Chen
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Abbie Adams
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Western Australia, Australia
| | - Ianthe Pitout
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Western Australia, Australia
| | - Alanis Lima
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Western Australia, Australia
| | - Dan Zhang
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Rachael C Heath Jeffery
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, Western Australia, Australia; Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Western Australia, Australia; Royal Victorian Eye and Ear Hospital, Centre for Eye Research Australia, East Melbourne, Victoria, Australia
| | - Mary S Attia
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Terri L McLaren
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia; Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Tina M Lamey
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia; Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
| | - John N De Roach
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia; Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Samuel McLenachan
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, Western Australia, Australia; Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
| | - May Thandar Aung-Htut
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Western Australia, Australia; Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Western Australia, Australia; Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Australia; PYC Therapeutics, Harry Perkins Institute of Medical Research, Verdun St, Nedlands, Western Australia, Australia
| | - Steve D Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Western Australia, Australia; Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Australia
| | - Fred K Chen
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, 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; Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Western Australia, Australia; Department of Ophthalmology, Royal Perth Hospital, Perth, Western Australia, Australia; Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, Victoria, Australia; Royal Victorian Eye and Ear Hospital, Centre for Eye Research Australia, East Melbourne, Victoria, Australia.
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Vázquez-Domínguez I, Duijkers L, Fadaie Z, Alaerds ECW, Post MA, van Oosten EM, O’Gorman L, Kwint M, Koolen L, Hoogendoorn ADM, Kroes HY, Gilissen C, Cremers FPM, Collin RWJ, Roosing S, Garanto A. The Predicted Splicing Variant c.11+5G>A in RPE65 Leads to a Reduction in mRNA Expression in a Cell-Specific Manner. Cells 2022; 11:3640. [PMID: 36429068 PMCID: PMC9688607 DOI: 10.3390/cells11223640] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/01/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022] Open
Abstract
Pathogenic variants in RPE65 lead to retinal diseases, causing a vision impairment. In this work, we investigated the pathomechanism behind the frequent RPE65 variant, c.11+5G>A. Previous in silico predictions classified this change as a splice variant. Our prediction using novel software's suggested a 124-nt exon elongation containing a premature stop codon. This elongation was validated using midigenes-based approaches. Similar results were observed in patient-derived induced pluripotent stem cells (iPSC) and photoreceptor precursor cells. However, the splicing defect in all cases was detected at low levels and thereby does not fully explain the recessive condition of the resulting disease. Long-read sequencing discarded other rearrangements or variants that could explain the diseases. Subsequently, a more relevant model was employed: iPSC-derived retinal pigment epithelium (RPE) cells. In patient-derived iPSC-RPE cells, the expression of RPE65 was strongly reduced even after inhibiting a nonsense-mediated decay, contradicting the predicted splicing defect. Additional experiments demonstrated a cell-specific gene expression reduction due to the presence of the c.11+5G>A variant. This decrease also leads to the lack of the RPE65 protein, and differences in size and pigmentation between the patient and control iPSC-RPE. Altogether, our data suggest that the c.11+5G>A variant causes a cell-specific defect in the expression of RPE65 rather than the anticipated splicing defect which was predicted in silico.
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Affiliation(s)
- Irene Vázquez-Domínguez
- 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 GD Nijmegen, The Netherlands
| | - Lonneke Duijkers
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Zeinab Fadaie
- 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 GD Nijmegen, The Netherlands
| | - Eef C. W. Alaerds
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Merel A. Post
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GD Nijmegen, The Netherlands
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Edwin M. van Oosten
- Department of Pediatrics, Amalia Children’s Hospital, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Luke O’Gorman
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Michael Kwint
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Louet Koolen
- Department of Ophthalmology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Anita D. M. Hoogendoorn
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Hester Y. Kroes
- Division Laboratories, Pharmacy and Biomedical Genetics, Clinical Genetics, University Medical Center of Utrecht, 3584 CX Utrecht, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - 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 GD Nijmegen, The Netherlands
| | - Rob W. J. Collin
- 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 GD 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 GD Nijmegen, The Netherlands
| | - Alejandro Garanto
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Pediatrics, Amalia Children’s Hospital, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
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Putscher E, Hecker M, Fitzner B, Boxberger N, Schwartz M, Koczan D, Lorenz P, Zettl UK. Genetic risk variants for multiple sclerosis are linked to differences in alternative pre-mRNA splicing. Front Immunol 2022; 13:931831. [PMID: 36405756 PMCID: PMC9670805 DOI: 10.3389/fimmu.2022.931831] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 10/12/2022] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND Multiple sclerosis (MS) is a chronic immune-mediated disease of the central nervous system to which a genetic predisposition contributes. Over 200 genetic regions have been associated with increased disease risk, but the disease-causing variants and their functional impact at the molecular level are mostly poorly defined. We hypothesized that single-nucleotide polymorphisms (SNPs) have an impact on pre-mRNA splicing in MS. METHODS Our study focused on 10 bioinformatically prioritized SNP-gene pairs, in which the SNP has a high potential to alter alternative splicing events (ASEs). We tested for differential gene expression and differential alternative splicing in B cells from MS patients and healthy controls. We further examined the impact of the SNP genotypes on ASEs and on splice isoform expression levels. Novel genotype-dependent effects on splicing were verified with splicing reporter minigene assays. RESULTS We were able to confirm previously described findings regarding the relation of MS-associated SNPs with the ASEs of the pre-mRNAs from GSDMB and SP140. We also observed an increased IL7R exon 6 skipping when comparing relapsing and progressive MS patients to healthy subjects. Moreover, we found evidence that the MS risk alleles of the SNPs rs3851808 (EFCAB13), rs1131123 (HLA-C), rs10783847 (TSFM), and rs2014886 (TSFM) may contribute to a differential splicing pattern. Of particular interest is the genotype-dependent exon skipping of TSFM due to the SNP rs2014886. The minor allele T creates a donor splice site, resulting in the expression of the exon 3 and 4 of a short TSFM transcript isoform, whereas in the presence of the MS risk allele C, this donor site is absent, and thus the short transcript isoform is not expressed. CONCLUSION In summary, we found that genetic variants from MS risk loci affect pre-mRNA splicing. Our findings substantiate the role of ASEs with respect to the genetics of MS. Further studies on how disease-causing genetic variants may modify the interactions between splicing regulatory sequence elements and RNA-binding proteins can help to deepen our understanding of the genetic susceptibility to MS.
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Affiliation(s)
- Elena Putscher
- Rostock University Medical Center, Department of Neurology, Division of Neuroimmunology, Rostock, Germany
| | - Michael Hecker
- Rostock University Medical Center, Department of Neurology, Division of Neuroimmunology, Rostock, Germany
| | - Brit Fitzner
- Rostock University Medical Center, Department of Neurology, Division of Neuroimmunology, Rostock, Germany
| | - Nina Boxberger
- Rostock University Medical Center, Department of Neurology, Division of Neuroimmunology, Rostock, Germany
| | - Margit Schwartz
- Rostock University Medical Center, Department of Neurology, Division of Neuroimmunology, Rostock, Germany
| | - Dirk Koczan
- Rostock University Medical Center, Institute of Immunology, Rostock, Germany
| | - Peter Lorenz
- Rostock University Medical Center, Institute of Immunology, Rostock, Germany
| | - Uwe Klaus Zettl
- Rostock University Medical Center, Department of Neurology, Division of Neuroimmunology, Rostock, Germany
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42
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Daich Varela M, Bellingham J, Motta F, Jurkute N, Ellingford JM, Quinodoz M, Oprych K, Niblock M, Janeschitz-Kriegl L, Kaminska K, Cancellieri F, Scholl HPN, Lenassi E, Schiff E, Knight H, Black G, Rivolta C, Cheetham ME, Michaelides M, Mahroo OA, Moore AT, Webster AR, Arno G. Multidisciplinary team directed analysis of whole genome sequencing reveals pathogenic non-coding variants in molecularly undiagnosed inherited retinal dystrophies. Hum Mol Genet 2022; 32:595-607. [PMID: 36084042 PMCID: PMC9896476 DOI: 10.1093/hmg/ddac227] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/23/2022] [Accepted: 09/04/2022] [Indexed: 02/07/2023] Open
Abstract
The purpose of this paper is to identify likely pathogenic non-coding variants in inherited retinal dystrophy (IRD) genes, using genome sequencing (GS). Patients with IRD were recruited to the study and underwent comprehensive ophthalmological evaluation and GS. The results of GS were investigated through virtual gene panel analysis, and plausible pathogenic variants and clinical phenotype evaluated by the multidisciplinary team (MDT) discussion. For unsolved patients in whom a specific gene was suspected to harbor a missed pathogenic variant, targeted re-analysis of non-coding regions was performed on GS data. Candidate variants were functionally tested by messenger RNA analysis, minigene or luciferase reporter assays. Previously unreported, likely pathogenic, non-coding variants in 7 genes (PRPF31, NDP, IFT140, CRB1, USH2A, BBS10 and GUCY2D), were identified in 11 patients. These were shown to lead to mis-splicing (PRPF31, IFT140, CRB1 and USH2A) or altered transcription levels (BBS10 and GUCY2D). MDT-led, phenotype-driven, non-coding variant re-analysis of GS is effective in identifying the missing causative alleles.
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Affiliation(s)
- Malena Daich Varela
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | | | - Fabiana Motta
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Department of Ophthalmology, Universidade Federal de Sao Paulo, Sao Paulo 04021001, Brazil
| | - Neringa Jurkute
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Jamie M Ellingford
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WL, UK,Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland,Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | | | | | - Lucas Janeschitz-Kriegl
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Hendrik P N Scholl
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Eva Lenassi
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WL, UK,Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | | | | | - Graeme Black
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WL, UK,Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland,Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | | | - Michel Michaelides
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Omar A Mahroo
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Anthony T Moore
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK,University of California, San Francisco, CA 94607, USA
| | - Andrew R Webster
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Gavin Arno
- To whom correspondence should be addressed at: UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1 9EL, UK. Tel: +44 2076086971;
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43
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De Angeli P, Reuter P, Hauser S, Schöls L, Stingl K, Wissinger B, Kohl S. Effective splicing restoration of a deep-intronic ABCA4 variant in cone photoreceptor precursor cells by CRISPR/SpCas9 approaches. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:511-524. [PMID: 35991315 PMCID: PMC9375153 DOI: 10.1016/j.omtn.2022.07.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/20/2022] [Indexed: 12/26/2022]
Affiliation(s)
- Pietro De Angeli
- Institute for Ophthalmic Research, Centre for Ophthalmology, University Hospital Tübingen, 72076 Tübingen, Germany
- Corresponding author Pietro De Angeli, Institute for Ophthalmic Research, Centre for Ophthalmology, Elfriede-Aulhorn-Strasse 5–7, 72076 Tübingen, Germany.
| | - Peggy Reuter
- Institute for Ophthalmic Research, Centre for Ophthalmology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Stefan Hauser
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, 72076 Tübingen, Germany
| | - Ludger Schöls
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, 72076 Tübingen, Germany
| | - Katarina Stingl
- Centre for Ophthalmology, University Hospital Tübingen, 72076 Tübingen, Germany
- Center for Rare Eye Diseases, University of Tübingen, 72076 Tübingen, Germany
| | - Bernd Wissinger
- Institute for Ophthalmic Research, Centre for Ophthalmology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Susanne Kohl
- Institute for Ophthalmic Research, Centre for Ophthalmology, University Hospital Tübingen, 72076 Tübingen, Germany
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Ellingford JM, Ahn JW, Bagnall RD, Baralle D, Barton S, Campbell C, Downes K, Ellard S, Duff-Farrier C, FitzPatrick DR, Greally JM, Ingles J, Krishnan N, Lord J, Martin HC, Newman WG, O'Donnell-Luria A, Ramsden SC, Rehm HL, Richardson E, Singer-Berk M, Taylor JC, Williams M, Wood JC, Wright CF, Harrison SM, Whiffin N. Recommendations for clinical interpretation of variants found in non-coding regions of the genome. Genome Med 2022; 14:73. [PMID: 35850704 PMCID: PMC9295495 DOI: 10.1186/s13073-022-01073-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/16/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The majority of clinical genetic testing focuses almost exclusively on regions of the genome that directly encode proteins. The important role of variants in non-coding regions in penetrant disease is, however, increasingly being demonstrated, and the use of whole genome sequencing in clinical diagnostic settings is rising across a large range of genetic disorders. Despite this, there is no existing guidance on how current guidelines designed primarily for variants in protein-coding regions should be adapted for variants identified in other genomic contexts. METHODS We convened a panel of nine clinical and research scientists with wide-ranging expertise in clinical variant interpretation, with specific experience in variants within non-coding regions. This panel discussed and refined an initial draft of the guidelines which were then extensively tested and reviewed by external groups. RESULTS We discuss considerations specifically for variants in non-coding regions of the genome. We outline how to define candidate regulatory elements, highlight examples of mechanisms through which non-coding region variants can lead to penetrant monogenic disease, and outline how existing guidelines can be adapted for the interpretation of these variants. CONCLUSIONS These recommendations aim to increase the number and range of non-coding region variants that can be clinically interpreted, which, together with a compatible phenotype, can lead to new diagnoses and catalyse the discovery of novel disease mechanisms.
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Affiliation(s)
- Jamie M Ellingford
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, M13 9PT, UK.
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK.
- Genomics England, London, UK.
| | - Joo Wook Ahn
- Cambridge Genomics Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Richard D Bagnall
- Agnes Ginges Centre for Molecular Cardiology at Centenary Institute, University of Sydney, Sydney, Australia
| | - Diana Baralle
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Stephanie Barton
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Chris Campbell
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Kate Downes
- Cambridge Genomics Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
- South West Genomic Laboratory Hub, Exeter Genomic Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Celia Duff-Farrier
- South West NHS Genomic Laboratory Hub, Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, UK
| | - David R FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - John M Greally
- Department of Pediatrics, Division of Pediatric Genetic, Medicine, Children's Hospital at Montefiore/Montefiore Medical Center/Albert, Einstein College of Medicine, Bronx, NY, USA
| | - Jodie Ingles
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Australia
| | - Neesha Krishnan
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Australia
| | - Jenny Lord
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Hilary C Martin
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - William G Newman
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, M13 9PT, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Simon C Ramsden
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Ebony Richardson
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Australia
| | - Moriel Singer-Berk
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jenny C Taylor
- National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Maggie Williams
- South West NHS Genomic Laboratory Hub, Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, UK
| | - Jordan C Wood
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Steven M Harrison
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ambry Genetics, Aliso Viejo, CA, USA
| | - Nicola Whiffin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
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Tian L, Chen C, Song Y, Zhang X, Xu K, Xie Y, Jin ZB, Li Y. Phenotype-Based Genetic Analysis Reveals Missing Heritability of ABCA4-Related Retinopathy: Deep Intronic Variants and Copy Number Variations. Invest Ophthalmol Vis Sci 2022; 63:5. [PMID: 35657619 PMCID: PMC9185996 DOI: 10.1167/iovs.63.6.5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Purpose To identify the missing heritability of ABCA4-related retinopathy in a Chinese cohort. Methods We recruited 33 unrelated patients with ABCA4-related retinopathy carrying a monoallelic variant in ABCA4. All patients underwent ophthalmic examinations. Next-generation sequencing of the whole ABCA4 sequence, including coding and noncoding regions, was performed to detect deep intronic variants (DIVs) and copy number variations (CNVs). Results We identified eight missing pathogenic ABCA4 variants in 60.6% of the patients (20/33), which comprised five DIVs and three CNVs. The five DIVs, including four novel (c.1555-816T>G, c.2919-169T>G, c.2919-884G>T, and c.5461-1321A>G) and one reported (c.4539+1100A>G), accounted for the missing alleles in 51.5% of the patients. Minigene assays showed that four novel DIVs activated cryptic splice sites leading to the insertions of pseudoexons. The three novel CNVs consisted of one gross deletion of 1273 bp (exon 2) and two gross duplications covering 25.2 kb (exons 28-43) and 9.4 kb (exons 38-44). The microhomology domains were identified at the breakpoints and revealed the potential mechanisms of CNV formation. Conclusions DIVs and CNVs explained approximately two-thirds of the unresolved Chinese cases with ABCA4-related retinopathy. Combining results from phenotypic-directed screening, targeting the whole ABCA4 sequencing and in silico tools can help to identify the missing heritability.
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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
| | - Chunjie Chen
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Yuning Song
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Xiaohui Zhang
- 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
| | - 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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46
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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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Cornelis SS, Runhart EH, Bauwens M, Corradi Z, De Baere E, Roosing S, Haer-Wigman L, Dhaenens CM, Vulto-van Silfhout AT, Cremers FP. Personalized genetic counseling for Stargardt disease: Offspring risk estimates based on variant severity. Am J Hum Genet 2022; 109:498-507. [PMID: 35120629 DOI: 10.1016/j.ajhg.2022.01.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/11/2022] [Indexed: 12/21/2022] Open
Abstract
Recurrence risk calculations in autosomal recessive diseases are complicated when the effect of genetic variants and their population frequencies and penetrances are unknown. An example of this is Stargardt disease (STGD1), a frequent recessive retinal disease caused by bi-allelic pathogenic variants in ABCA4. In this cross-sectional study, 1,619 ABCA4 variants from 5,579 individuals with STGD1 were collected and categorized by (1) severity based on statistical comparisons of their frequencies in STGD1-affected individuals versus the general population, (2) their observed versus expected homozygous occurrence in STGD1-affected individuals, (3) their occurrence in combination with established mild alleles in STGD1-affected individuals, and (4) previous functional and clinical studies. We used the sum allele frequencies of these severity categories to estimate recurrence risks for offspring of STGD1-affected individuals and carriers of pathogenic ABCA4 variants. The risk for offspring of an STGD1-affected individual with the "severe|severe" genotype or a "severe|mild with complete penetrance" genotype to develop STGD1 at some moment in life was estimated at 2.8%-3.1% (1 in 36-32 individuals) and 1.6%-1.8% (1 in 62-57 individuals), respectively. The risk to develop STGD1 in childhood was estimated to be 2- to 4-fold lower: 0.68%-0.79% (1 in 148-126) and 0.34%-0.39% (1 in 296-252), respectively. In conclusion, we established personalized recurrence risk calculations for STGD1-affected individuals with different combinations of variants. We thus propose an expanded genotype-based personalized counseling to appreciate the variable recurrence risks for STGD1-affected individuals. This represents a conceptual breakthrough because risk calculations for STGD1 may be exemplary for many other inherited diseases.
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Antisense RNA Therapeutics: A Brief Overview. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2434:33-49. [PMID: 35213008 DOI: 10.1007/978-1-0716-2010-6_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Nucleic acid therapeutics is a growing field aiming to treat human conditions that has gained special attention due to the successful development of mRNA vaccines against SARS-CoV-2. Another type of nucleic acid therapeutics is antisense oligonucleotides, versatile tools that can be used in multiple ways to target pre-mRNA and mRNA. While some years ago these molecules were just considered a useful research tool and a curiosity in the clinical market, this has rapidly changed. These molecules are promising strategies for personalized treatments for rare genetic diseases and they are in development for very common disorders too. In this chapter, we provide a brief description of the different mechanisms of action of these RNA therapeutic molecules, with clear examples at preclinical and clinical stages.
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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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50
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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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