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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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2
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Cideciyan AV, Jacobson SG, Ho AC, Swider M, Sumaroka A, Roman AJ, Wu V, Russell RC, Viarbitskaya I, Garafalo AV, Schwartz MR, Girach A. Durable vision improvement after a single intravitreal treatment with antisense oligonucleotide in CEP290-LCA: Replication in two eyes. Am J Ophthalmol Case Rep 2023; 32:101873. [PMID: 37388818 PMCID: PMC10302566 DOI: 10.1016/j.ajoc.2023.101873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/15/2023] [Accepted: 06/11/2023] [Indexed: 07/01/2023] Open
Abstract
Purpose An intravitreally injected antisense oligonucleotide, sepofarsen, was designed to modulate splicing within retinas of patients with severe vision loss due to deep intronic c.2991 + 1655A > G variant in the CEP290 gene. A previous report showed vision improvements following a single injection in one eye with unexpected durability lasting at least 15 months. The current study evaluated durability of efficacy beyond 15 months in the previously treated left eye. In addition, peak efficacy and durability were evaluated in the treatment-naive right eye, and re-injection of the left eye 4 years after the first injection. Observations Visual function was evaluated with best corrected standard and low-luminance visual acuities, microperimetry, dark-adapted chromatic perimetry, and full-field sensitivity testing. Retinal structure was evaluated with OCT imaging. At the fovea, all visual function measures and IS/OS intensity of the OCT showed transient improvements peaking at 3-6 months, remaining better than baseline at ∼2 years, and returning to baseline by 3-4 years after each single injection. Conclusions and Importance These results suggest that sepofarsen reinjection intervals may need to be longer than 2 years.
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Affiliation(s)
- Artur V. Cideciyan
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Samuel G. Jacobson
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Allen C. Ho
- Wills Eye Hospital, Thomas Jefferson University, Philadelphia, USA
| | - Malgorzata Swider
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexander Sumaroka
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alejandro J. Roman
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vivian Wu
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert C. Russell
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Iryna Viarbitskaya
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexandra V. Garafalo
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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3
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Kruczek K, Swaroop A. Patient stem cell-derived in vitro disease models for developing novel therapies of retinal ciliopathies. Curr Top Dev Biol 2023; 155:127-163. [PMID: 38043950 DOI: 10.1016/bs.ctdb.2023.09.003] [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] [Indexed: 12/05/2023]
Abstract
Primary cilia are specialized organelles on the surface of almost all cells in vertebrate tissues and are primarily involved in the detection of extracellular stimuli. In retinal photoreceptors, cilia are uniquely modified to form outer segments containing components required for the detection of light in stacks of membrane discs. Not surprisingly, vision impairment is a frequent phenotype associated with ciliopathies, a heterogeneous class of conditions caused by mutations in proteins required for formation, maintenance and/or function of primary cilia. Traditionally, immortalized cell lines and model organisms have been used to provide insights into the biology of ciliopathies. The advent of methods for reprogramming human somatic cells into pluripotent stem cells has enabled the generation of in vitro disease models directly from patients suffering from ciliopathies. Such models help us in investigating pathological mechanisms specific to human physiology and in developing novel therapeutic approaches. In this article, we review current protocols to differentiate human pluripotent stem cells into retinal cell types, and discuss how these cellular and/or organoid models can be utilized to interrogate pathobiology of ciliopathies affecting the retina and for testing prospective treatments.
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Affiliation(s)
- Kamil Kruczek
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, United States.
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, United States.
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4
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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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5
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Whelan L, Dockery A, Stephenson KAJ, Zhu J, Kopčić E, Post IJM, Khan M, Corradi Z, Wynne N, O' Byrne JJ, Duignan E, Silvestri G, Roosing S, Cremers FPM, Keegan DJ, Kenna PF, Farrar GJ. Detailed analysis of an enriched deep intronic ABCA4 variant in Irish Stargardt disease patients. Sci Rep 2023; 13:9380. [PMID: 37296172 PMCID: PMC10256698 DOI: 10.1038/s41598-023-35889-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Over 15% of probands in a large cohort of more than 1500 inherited retinal degeneration patients present with a clinical diagnosis of Stargardt disease (STGD1), a recessive form of macular dystrophy caused by biallelic variants in the ABCA4 gene. Participants were clinically examined and underwent either target capture sequencing of the exons and some pathogenic intronic regions of ABCA4, sequencing of the entire ABCA4 gene or whole genome sequencing. ABCA4 c.4539 + 2028C > T, p.[= ,Arg1514Leufs*36] is a pathogenic deep intronic variant that results in a retina-specific 345-nucleotide pseudoexon inclusion. Through analysis of the Irish STGD1 cohort, 25 individuals across 18 pedigrees harbour ABCA4 c.4539 + 2028C > T and another pathogenic variant. This includes, to the best of our knowledge, the only two homozygous patients identified to date. This provides important evidence of variant pathogenicity for this deep intronic variant, highlighting the value of homozygotes for variant interpretation. 15 other heterozygous incidents of this variant in patients have been reported globally, indicating significant enrichment in the Irish population. We provide detailed genetic and clinical characterization of these patients, illustrating that ABCA4 c.4539 + 2028C > T is a variant of mild to intermediate severity. These results have important implications for unresolved STGD1 patients globally with approximately 10% of the population in some western countries claiming Irish heritage. This study exemplifies that detection and characterization of founder variants is a diagnostic imperative.
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Affiliation(s)
- Laura Whelan
- The School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland.
| | - Adrian Dockery
- The School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
- Next Generation Sequencing Laboratory, Pathology Department, The Mater Misericordiae University Hospital, Dublin 7, Ireland
| | - Kirk A J Stephenson
- Department of Ophthalmology, Royal Victoria Eye and Ear Hospital, Dublin 2, Ireland
- Mater Clinical Ophthalmic Genetics Unit, The Mater Misericordiae University Hospital, Dublin 7, Ireland
| | - Julia Zhu
- Mater Clinical Ophthalmic Genetics Unit, The Mater Misericordiae University Hospital, Dublin 7, Ireland
| | - Ella Kopčić
- The School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
| | - Iris J M Post
- The School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
| | - Mubeen Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- International Max Planck Research School for Language Sciences, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Zelia Corradi
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Academic Alliance Genetics, Radboud University Medical Center, Nijmegen, and Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Niamh Wynne
- Department of Ophthalmology, Royal Victoria Eye and Ear Hospital, Dublin 2, Ireland
| | - James J O' Byrne
- Mater Clinical Ophthalmic Genetics Unit, The Mater Misericordiae University Hospital, Dublin 7, Ireland
- International Max Planck Research School for Language Sciences, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- National Centre for Inherited Metabolic Disorders, The Mater Misericordiae University Hospital, Dublin 7, Ireland
- School of Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Emma Duignan
- Department of Ophthalmology, Royal Victoria Eye and Ear Hospital, Dublin 2, Ireland
| | - Giuliana Silvestri
- Centre for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK
- School of Medicine, University College Dublin, Dublin 4, Ireland
- Department of Ophthalmology, The Royal Victoria Hospital, Belfast, Northern Ireland, UK
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Academic Alliance Genetics, Radboud University Medical Center, Nijmegen, and Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Academic Alliance Genetics, Radboud University Medical Center, Nijmegen, and Maastricht University Medical Center+, Maastricht, The Netherlands
| | - David J Keegan
- Mater Clinical Ophthalmic Genetics Unit, The Mater Misericordiae University Hospital, Dublin 7, Ireland
| | - Paul F Kenna
- The School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
- Department of Ophthalmology, Royal Victoria Eye and Ear Hospital, Dublin 2, Ireland
| | - G Jane Farrar
- The School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
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6
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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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7
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RNA-targeting strategies as a platform for ocular gene therapy. Prog Retin Eye Res 2023; 92:101110. [PMID: 35840489 DOI: 10.1016/j.preteyeres.2022.101110] [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: 04/25/2022] [Revised: 06/28/2022] [Accepted: 07/06/2022] [Indexed: 02/01/2023]
Abstract
Genetic medicine is offering hope as new therapies are emerging for many previously untreatable diseases. The eye is at the forefront of these advances, as exemplified by the approval of Luxturna® by the United States Food and Drug Administration (US FDA) in 2017 for the treatment of one form of Leber Congenital Amaurosis (LCA), an inherited blindness. Luxturna® was also the first in vivo human gene therapy to gain US FDA approval. Numerous gene therapy clinical trials are ongoing for other eye diseases, and novel delivery systems, discovery of new drug targets and emerging technologies are currently driving the field forward. Targeting RNA, in particular, is an attractive therapeutic strategy for genetic disease that may have safety advantages over alternative approaches by avoiding permanent changes in the genome. In this regard, antisense oligonucleotides (ASO) and RNA interference (RNAi) are the currently popular strategies for developing RNA-targeted therapeutics. Enthusiasm has been further fuelled by the emergence of clustered regularly interspersed short palindromic repeats (CRISPR)-CRISPR associated (Cas) systems that allow targeted manipulation of nucleic acids. RNA-targeting CRISPR-Cas systems now provide a novel way to develop RNA-targeted therapeutics and may provide superior efficiency and specificity to existing technologies. In addition, RNA base editing technologies using CRISPR-Cas and other modalities also enable precise alteration of single nucleotides. In this review, we showcase advances made by RNA-targeting systems for ocular disease, discuss applications of ASO and RNAi technologies, highlight emerging CRISPR-Cas systems and consider the implications of RNA-targeting therapeutics in the development of future drugs to treat eye disease.
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8
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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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9
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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:cells11223640. [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] [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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10
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Kamenarova K, Mihova K, Veleva N, Mermeklieva E, Mihaylova B, Dimitrova G, Oscar A, Shandurkov I, Cherninkova S, Kaneva R. Panel-based next-generation sequencing identifies novel mutations in Bulgarian patients with inherited retinal dystrophies. Mol Genet Genomic Med 2022; 10:e1997. [PMID: 35656873 PMCID: PMC9356554 DOI: 10.1002/mgg3.1997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 04/07/2022] [Accepted: 05/13/2022] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Next-generation sequencing (NGS)-based method is being used broadly for genetic testing especially for clinically and genetically heterogeneous disorders, such as inherited retinal degenerations (IRDs) but still not routinely used for molecular diagnostics in Bulgaria. Consequently, the purpose of this study was to evaluate the effectiveness of a molecular diagnostic approach, based on targeted NGS for the identification of the disease-causing mutations in 16 Bulgarian patients with different IRDs. METHODS We applied a customized NGS panel, including 125 genes associated with retinal and other eye diseases to the patients with hereditary retinopathies. RESULTS Systematic filtering approach coupled with copy number variation analysis and segregation study lead to the identification of 16 pathogenic and likely pathogenic variants in 12/16 (75%) of IRD patients, 2 of which novel (12.5%): ABCA4-c.668delA (p.K223Rfs18) and RР1-c.2015dupA (p.K673Efs*25). Mutations in the ABCA4, PRPH2, USH2A, BEST1, RР1, CDHR1, and RHO genes were detected reaching a diagnostic yield between 42.9% for Retinitis pigmentosa cases and 100% for macular degeneration, Usher syndrome, and cone-rod dystrophy patients. CONCLUSION Our results confirm the usefulness of targeted NGS approach based on frequently mutated genes as a comprehensive and successful genetic diagnostic tool for IRDs with significant impact on patients counseling.
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Affiliation(s)
- Kunka Kamenarova
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria.,Laboratory of Genomic Diagnostics, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
| | - Kalina Mihova
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria.,Laboratory of Genomic Diagnostics, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
| | - Nevyana Veleva
- Department of Ophthalmology, University Hospital "Alexandrovska", Medical University of Sofia, Sofia, Bulgaria
| | - Elena Mermeklieva
- Clinic of Ophthalmology, University Hospital "Lozenetz", Medical Faculty, Sofia University "St. Kliment Ohridski", Sofia, Bulgaria
| | | | - Galina Dimitrova
- Department of Ophthalmology, University Hospital "Alexandrovska", Medical University of Sofia, Sofia, Bulgaria
| | - Alexander Oscar
- Department of Ophthalmology, University Hospital "Alexandrovska", Medical University of Sofia, Sofia, Bulgaria
| | | | - Sylvia Cherninkova
- Department of Neurology, University hospital "Alexandrovska", Medical University of Sofia, Sofia, Bulgaria
| | - Radka Kaneva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria.,Laboratory of Genomic Diagnostics, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
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11
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Russell SR, Drack AV, Cideciyan AV, Jacobson SG, Leroy BP, Van Cauwenbergh C, Ho AC, Dumitrescu AV, Han IC, Martin M, Pfeifer WL, Sohn EH, Walshire J, Garafalo AV, Krishnan AK, Powers CA, Sumaroka A, Roman AJ, Vanhonsebrouck E, Jones E, Nerinckx F, De Zaeytijd J, Collin RWJ, Hoyng C, Adamson P, Cheetham ME, Schwartz MR, den Hollander W, Asmus F, Platenburg G, Rodman D, Girach A. Intravitreal antisense oligonucleotide sepofarsen in Leber congenital amaurosis type 10: a phase 1b/2 trial. Nat Med 2022; 28:1014-1021. [PMID: 35379979 PMCID: PMC9117145 DOI: 10.1038/s41591-022-01755-w] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 02/18/2022] [Indexed: 02/05/2023]
Abstract
CEP290-associated Leber congenital amaurosis type 10 (LCA10) is a retinal disease resulting in childhood blindness. Sepofarsen is an RNA antisense oligonucleotide targeting the c.2991+1655A>G variant in the CEP290 gene to treat LCA10. In this open-label, phase 1b/2 ( NCT03140969 ), 12-month, multicenter, multiple-dose, dose-escalation trial, six adult patients and five pediatric patients received ≤4 doses of intravitreal sepofarsen into the worse-seeing eye. The primary objective was to evaluate sepofarsen safety and tolerability via the frequency and severity of ocular adverse events (AEs); secondary objectives were to evaluate pharmacokinetics and efficacy via changes in functional outcomes. Six patients received sepofarsen 160 µg/80 µg, and five patients received sepofarsen 320 µg/160 µg. Ten of 11 (90.9%) patients developed ocular AEs in the treated eye (5/6 with 160 µg/80 µg; 5/5 with 320 µg/160 µg) versus one of 11 (9.1%) in the untreated eye; most were mild in severity and dose dependent. Eight patients developed cataracts, of which six (75.0%) were categorized as serious (2/3 with 160 µg/80 µg; 4/5 with 320 µg/160 µg), as lens replacement was required. As the 160-µg/80-µg group showed a better benefit-risk profile, higher doses were discontinued or not initiated. Statistically significant improvements in visual acuity and retinal sensitivity were reported (post hoc analysis). The manageable safety profile and improvements reported in this trial support the continuation of sepofarsen development.
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Affiliation(s)
- Stephen R Russell
- University of Iowa Institute for Vision Research, University of Iowa, Iowa City, IA, USA.
| | - Arlene V Drack
- University of Iowa Institute for Vision Research, University of Iowa, Iowa City, IA, USA
| | - Artur V Cideciyan
- Department of Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Samuel G Jacobson
- Department of Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Bart P Leroy
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
- Division of Ophthalmology and Center for Cellular & Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Allen C Ho
- Wills Eye Hospital/Mid Atlantic Retina, Philadelphia, PA, USA
| | - Alina V Dumitrescu
- University of Iowa Institute for Vision Research, University of Iowa, Iowa City, IA, USA
| | - Ian C Han
- University of Iowa Institute for Vision Research, University of Iowa, Iowa City, IA, USA
| | - Mitchell Martin
- University of Iowa Institute for Vision Research, University of Iowa, Iowa City, IA, USA
| | - Wanda L Pfeifer
- University of Iowa Institute for Vision Research, University of Iowa, Iowa City, IA, USA
| | - Elliott H Sohn
- University of Iowa Institute for Vision Research, University of Iowa, Iowa City, IA, USA
| | - Jean Walshire
- University of Iowa Institute for Vision Research, University of Iowa, Iowa City, IA, USA
| | - Alexandra V Garafalo
- Department of Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Arun K Krishnan
- Department of Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christian A Powers
- Department of Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexander Sumaroka
- Department of Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alejandro J Roman
- Department of Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Eva Vanhonsebrouck
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Eltanara Jones
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Fanny Nerinckx
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Julie De Zaeytijd
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Rob W J Collin
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Carel Hoyng
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
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12
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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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13
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Pollara L, Sottile V, Valente EM. Patient-derived cellular models of primary ciliopathies. J Med Genet 2022; 59:517-527. [DOI: 10.1136/jmedgenet-2021-108315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/21/2022] [Indexed: 11/09/2022]
Abstract
Primary ciliopathies are rare inherited disorders caused by structural or functional defects in the primary cilium, a subcellular organelle present on the surface of most cells. Primary ciliopathies show considerable clinical and genetic heterogeneity, with disruption of over 100 genes causing the variable involvement of several organs, including the central nervous system, kidneys, retina, skeleton and liver. Pathogenic variants in one and the same gene may associate with a wide range of ciliopathy phenotypes, supporting the hypothesis that the individual genetic background, with potential additional variants in other ciliary genes, may contribute to a mutational load eventually determining the phenotypic manifestations of each patient. Functional studies in animal models have uncovered some of the pathophysiological mechanisms linking ciliary gene mutations to the observed phenotypes; yet, the lack of reliable human cell models has previously limited preclinical research and the development of new therapeutic strategies for primary ciliopathies. Recent technical advances in the generation of patient-derived two-dimensional (2D) and three-dimensional (3D) cellular models give a new spur to this research, allowing the study of pathomechanisms while maintaining the complexity of the genetic background of each patient, and enabling the development of innovative treatments to target specific pathways. This review provides an overview of available models for primary ciliopathies, from existing in vivo models to more recent patient-derived 2D and 3D in vitro models. We highlight the advantages of each model in understanding the functional basis of primary ciliopathies and facilitating novel regenerative medicine, gene therapy and drug testing strategies for these disorders.
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14
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Schneider N, Sundaresan Y, Gopalakrishnan P, Beryozkin A, Hanany M, Levanon EY, Banin E, Ben-Aroya S, Sharon D. Inherited retinal diseases: Linking genes, disease-causing variants, and relevant therapeutic modalities. Prog Retin Eye Res 2021; 89:101029. [PMID: 34839010 DOI: 10.1016/j.preteyeres.2021.101029] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/11/2022]
Abstract
Inherited retinal diseases (IRDs) are a clinically complex and heterogenous group of visual impairment phenotypes caused by pathogenic variants in at least 277 nuclear and mitochondrial genes, affecting different retinal regions, and depleting the vision of affected individuals. Genes that cause IRDs when mutated are unique by possessing differing genotype-phenotype correlations, varying inheritance patterns, hypomorphic alleles, and modifier genes thus complicating genetic interpretation. Next-generation sequencing has greatly advanced the identification of novel IRD-related genes and pathogenic variants in the last decade. For this review, we performed an in-depth literature search which allowed for compilation of the Global Retinal Inherited Disease (GRID) dataset containing 4,798 discrete variants and 17,299 alleles published in 31 papers, showing a wide range of frequencies and complexities among the 194 genes reported in GRID, with 65% of pathogenic variants being unique to a single individual. A better understanding of IRD-related gene distribution, gene complexity, and variant types allow for improved genetic testing and therapies. Current genetic therapeutic methods are also quite diverse and rely on variant identification, and range from whole gene replacement to single nucleotide editing at the DNA or RNA levels. IRDs and their suitable therapies thus require a range of effective disease modelling in human cells, granting insight into disease mechanisms and testing of possible treatments. This review summarizes genetic and therapeutic modalities of IRDs, provides new analyses of IRD-related genes (GRID and complexity scores), and provides information to match genetic-based therapies such as gene-specific and variant-specific therapies to the appropriate individuals.
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Affiliation(s)
- Nina Schneider
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Yogapriya Sundaresan
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Prakadeeswari Gopalakrishnan
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Avigail Beryozkin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Mor Hanany
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Shay Ben-Aroya
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel.
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15
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Hernández-Juárez J, Rodríguez-Uribe G, Borooah S. Toward the Treatment of Inherited Diseases of the Retina Using CRISPR-Based Gene Editing. Front Med (Lausanne) 2021; 8:698521. [PMID: 34660621 PMCID: PMC8517184 DOI: 10.3389/fmed.2021.698521] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/19/2021] [Indexed: 12/26/2022] Open
Abstract
Inherited retinal dystrophies [IRDs] are a common cause of severe vision loss resulting from pathogenic genetic variants. The eye is an attractive target organ for testing clinical translational approaches in inherited diseases. This has been demonstrated by the approval of the first gene supplementation therapy to treat an autosomal recessive IRD, RPE65-linked Leber congenital amaurosis (type 2), 4 years ago. However, not all diseases are amenable for treatment using gene supplementation therapy, highlighting the need for alternative strategies to overcome the limitations of this supplementation therapeutic modality. Gene editing has become of increasing interest with the discovery of the CRISPR-Cas9 platform. CRISPR-Cas9 offers several advantages over previous gene editing technologies as it facilitates targeted gene editing in an efficient, specific, and modifiable manner. Progress with CRISPR-Cas9 research now means that gene editing is a feasible strategy for the treatment of IRDs. This review will focus on the background of CRISPR-Cas9 and will stress the differences between gene editing using CRISPR-Cas9 and traditional gene supplementation therapy. Additionally, we will review research that has led to the first CRISPR-Cas9 trial for the treatment of CEP290-linked Leber congenital amaurosis (type 10), as well as outline future directions for CRISPR-Cas9 technology in the treatment of IRDs.
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Affiliation(s)
- Jennifer Hernández-Juárez
- Jacobs Retina Center, Shiley Eye Institute, University of California San Diego, San Diego, CA, United States
| | - Genaro Rodríguez-Uribe
- Medicine and Psychology School, Autonomous University of Baja California, Tijuana, Mexico.,Department of Ocular Genetics and Research, CODET Vision Institute, Tijuana, Mexico
| | - Shyamanga Borooah
- Jacobs Retina Center, Shiley Eye Institute, University of California San Diego, San Diego, CA, United States
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16
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Kalatzis V, Roux AF, Meunier I. Molecular Therapy for Choroideremia: Pre-clinical and Clinical Progress to Date. Mol Diagn Ther 2021; 25:661-675. [PMID: 34661884 DOI: 10.1007/s40291-021-00558-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2021] [Indexed: 12/01/2022]
Abstract
Choroideremia is an inherited retinal disease characterised by a degeneration of the light-sensing photoreceptors, supporting retinal pigment epithelium and underlying choroid. Patients present with the same symptoms as those with classic rod-cone dystrophy: (1) night blindness early in life; (2) progressive peripheral visual field loss, and (3) central vision decline with a slow progression to legal blindness. Choroideremia is monogenic and caused by mutations in CHM. Eight clinical trials (three phase 1/2, four phase 2, and one phase 3) have started (four of which are already finished) to evaluate the therapeutic efficacy of gene supplementation mediated by subretinal delivery of an adeno-associated virus serotype 2 (AAV2/2) vector expressing CHM. Furthermore, one phase 1 clinical trial has been initiated to evaluate the efficiency of a novel AAV variant to deliver CHM to the outer retina following intravitreal delivery. Lastly, a non-viral-mediated CHM replacement strategy is currently under development, which could lead to a future clinical trial. Here, we summarise the rationale behind these various studies, as well as any results published to date. The diversity of these trials currently places choroideremia at the forefront of the retinal gene therapy field. As a consequence, the trial outcomes, regardless of the results, have the potential to change the landscape of gene supplementation for inherited retinal diseases.
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Affiliation(s)
- Vasiliki Kalatzis
- Institute for Neurosciences of Montpellier, Univ Montpellier, Inserm U1298, Hôpital St Eloi, 80 Avenue Augustin Fliche, 34091, Montpellier, France.
| | - Anne-Françoise Roux
- Institute for Neurosciences of Montpellier, Univ Montpellier, Inserm U1298, Hôpital St Eloi, 80 Avenue Augustin Fliche, 34091, Montpellier, France.,Molecular Genetics Laboratory, Univ Montpellier, CHU Montpellier, Montpellier, France
| | - Isabelle Meunier
- Institute for Neurosciences of Montpellier, Univ Montpellier, Inserm U1298, Hôpital St Eloi, 80 Avenue Augustin Fliche, 34091, Montpellier, France.,National Reference Centre for Inherited Sensory Diseases, University of Montpellier, CHU Montpellier, Montpellier, France
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17
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Shughoury A, Ciulla TA, Bakall B, Pennesi ME, Kiss S, Cunningham ET. Genes and Gene Therapy in Inherited Retinal Disease. Int Ophthalmol Clin 2021; 61:3-45. [PMID: 34584043 DOI: 10.1097/iio.0000000000000377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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18
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Abstract
Antisense oligonucleotides (AON) are synthetic single-stranded fragments of nucleic acids that bind to a specific complementary messenger RNA (mRNA) sequence and change the final gene product. AON were initially approved for treating cytomegalovirus retinitis and have shown promise in treating Mendelian systemic disease. AON are currently being investigated as a treatment modality for many ophthalmic diseases, including inherited retinal disorders (IRD), inflammatory response and wound healing after glaucoma surgery, and macular degeneration. They provide a possible solution to gene therapy for IRD that are not candidates for adeno-associated virus (AAV) delivery. This chapter outlines the historical background of AON and reviews clinical applications and ongoing clinical trials.
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Affiliation(s)
- Kevin Ferenchak
- Inherited Retinal Disorders Service, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, United States
| | - Iris Deitch
- Inherited Retinal Disorders Service, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, United States
| | - Rachel Huckfeldt
- Inherited Retinal Disorders Service, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, United States
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19
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Stokman MF, Saunier S, Benmerah A. Renal Ciliopathies: Sorting Out Therapeutic Approaches for Nephronophthisis. Front Cell Dev Biol 2021; 9:653138. [PMID: 34055783 PMCID: PMC8155538 DOI: 10.3389/fcell.2021.653138] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/19/2021] [Indexed: 12/13/2022] Open
Abstract
Nephronophthisis (NPH) is an autosomal recessive ciliopathy and a major cause of end-stage renal disease in children. The main forms, juvenile and adult NPH, are characterized by tubulointerstitial fibrosis whereas the infantile form is more severe and characterized by cysts. NPH is caused by mutations in over 20 different genes, most of which encode components of the primary cilium, an organelle in which important cellular signaling pathways converge. Ciliary signal transduction plays a critical role in kidney development and tissue homeostasis, and disruption of ciliary signaling has been associated with cyst formation, epithelial cell dedifferentiation and kidney function decline. Drugs have been identified that target specific signaling pathways (for example cAMP/PKA, Hedgehog, and mTOR pathways) and rescue NPH phenotypes in in vitro and/or in vivo models. Despite identification of numerous candidate drugs in rodent models, there has been a lack of clinical trials and there is currently no therapy that halts disease progression in NPH patients. This review covers the most important findings of therapeutic approaches in NPH model systems to date, including hypothesis-driven therapies and untargeted drug screens, approached from the pathophysiology of NPH. Importantly, most animal models used in these studies represent the cystic infantile form of NPH, which is less prevalent than the juvenile form. It appears therefore important to develop new models relevant for juvenile/adult NPH. Alternative non-orthologous animal models and developments in patient-based in vitro model systems are discussed, as well as future directions in personalized therapy for NPH.
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Affiliation(s)
- Marijn F Stokman
- Department of Genetics, University Medical Center Utrecht, Utrecht, Netherlands
- Université de Paris, Imagine Institute, Laboratory of Inherited Kidney Diseases, INSERM UMR 1163, Paris, France
| | - Sophie Saunier
- Université de Paris, Imagine Institute, Laboratory of Inherited Kidney Diseases, INSERM UMR 1163, Paris, France
| | - Alexandre Benmerah
- Université de Paris, Imagine Institute, Laboratory of Inherited Kidney Diseases, INSERM UMR 1163, Paris, France
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20
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Tomkiewicz TZ, Suárez-Herrera N, Cremers FPM, Collin RWJ, Garanto A. Antisense Oligonucleotide-Based Rescue of Aberrant Splicing Defects Caused by 15 Pathogenic Variants in ABCA4. Int J Mol Sci 2021; 22:ijms22094621. [PMID: 33924840 PMCID: PMC8124656 DOI: 10.3390/ijms22094621] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/16/2022] Open
Abstract
The discovery of novel intronic variants in the ABCA4 locus has contributed significantly to solving the missing heritability in Stargardt disease (STGD1). The increasing number of variants affecting pre-mRNA splicing makes ABCA4 a suitable candidate for antisense oligonucleotide (AON)-based splicing modulation therapies. In this study, AON-based splicing modulation was assessed for 15 recently described intronic variants (three near-exon and 12 deep-intronic variants). In total, 26 AONs were designed and tested in vitro using a midigene-based splice system. Overall, partial or complete splicing correction was observed for two variants causing exon elongation and all variants causing pseudoexon inclusion. Together, our results confirm the high potential of AONs for the development of future RNA therapies to correct splicing defects causing STGD1.
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Affiliation(s)
- Tomasz Z. Tomkiewicz
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands; (T.Z.T.); (N.S.-H.); (F.P.M.C.); (R.W.J.C.)
| | - Nuria Suárez-Herrera
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands; (T.Z.T.); (N.S.-H.); (F.P.M.C.); (R.W.J.C.)
| | - Frans P. M. Cremers
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands; (T.Z.T.); (N.S.-H.); (F.P.M.C.); (R.W.J.C.)
| | - Rob W. J. Collin
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands; (T.Z.T.); (N.S.-H.); (F.P.M.C.); (R.W.J.C.)
| | - Alejandro Garanto
- Departments of Pediatrics and Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands
- Correspondence:
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21
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Chiu W, Lin TY, Chang YC, Isahwan-Ahmad Mulyadi Lai H, Lin SC, Ma C, Yarmishyn AA, Lin SC, Chang KJ, Chou YB, Hsu CC, Lin TC, Chen SJ, Chien Y, Yang YP, Hwang DK. An Update on Gene Therapy for Inherited Retinal Dystrophy: Experience in Leber Congenital Amaurosis Clinical Trials. Int J Mol Sci 2021; 22:ijms22094534. [PMID: 33926102 PMCID: PMC8123696 DOI: 10.3390/ijms22094534] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/22/2021] [Accepted: 04/22/2021] [Indexed: 12/20/2022] Open
Abstract
Inherited retinal dystrophies (IRDs) are a group of rare eye diseases caused by gene mutations that result in the degradation of cone and rod photoreceptors or the retinal pigment epithelium. Retinal degradation progress is often irreversible, with clinical manifestations including color or night blindness, peripheral visual defects and subsequent vision loss. Thus, gene therapies that restore functional retinal proteins by either replenishing unmutated genes or truncating mutated genes are needed. Coincidentally, the eye’s accessibility and immune-privileged status along with major advances in gene identification and gene delivery systems heralded gene therapies for IRDs. Among these clinical trials, voretigene neparvovec-rzyl (Luxturna), an adeno-associated virus vector-based gene therapy drug, was approved by the FDA for treating patients with confirmed biallelic RPE65 mutation-associated Leber Congenital Amaurosis (LCA) in 2017. This review includes current IRD gene therapy clinical trials and further summarizes preclinical studies and therapeutic strategies for LCA, including adeno-associated virus-based gene augmentation therapy, 11-cis-retinal replacement, RNA-based antisense oligonucleotide therapy and CRISPR-Cas9 gene-editing therapy. Understanding the gene therapy development for LCA may accelerate and predict the potential hurdles of future therapeutics translation. It may also serve as the template for the research and development of treatment for other IRDs.
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Affiliation(s)
- Wei Chiu
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan; (W.C.); (S.-C.L.); (S.-C.L.); (K.-J.C.); (Y.-B.C.); (C.-C.H.)
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (T.-Y.L.); (H.I.-A.M.L.); (C.M.); (A.A.Y.); (T.-C.L.); (S.-J.C.)
| | - Ting-Yi Lin
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (T.-Y.L.); (H.I.-A.M.L.); (C.M.); (A.A.Y.); (T.-C.L.); (S.-J.C.)
- School of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Yun-Chia Chang
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 11217, Taiwan;
| | - Henkie Isahwan-Ahmad Mulyadi Lai
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (T.-Y.L.); (H.I.-A.M.L.); (C.M.); (A.A.Y.); (T.-C.L.); (S.-J.C.)
- Institute of Pharmacology, College of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Shen-Che Lin
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan; (W.C.); (S.-C.L.); (S.-C.L.); (K.-J.C.); (Y.-B.C.); (C.-C.H.)
| | - Chun Ma
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (T.-Y.L.); (H.I.-A.M.L.); (C.M.); (A.A.Y.); (T.-C.L.); (S.-J.C.)
- Department of Medicine, National Taiwan University, Taipei 10617, Taiwan
| | - Aliaksandr A. Yarmishyn
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (T.-Y.L.); (H.I.-A.M.L.); (C.M.); (A.A.Y.); (T.-C.L.); (S.-J.C.)
| | - Shiuan-Chen Lin
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan; (W.C.); (S.-C.L.); (S.-C.L.); (K.-J.C.); (Y.-B.C.); (C.-C.H.)
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (T.-Y.L.); (H.I.-A.M.L.); (C.M.); (A.A.Y.); (T.-C.L.); (S.-J.C.)
| | - Kao-Jung Chang
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan; (W.C.); (S.-C.L.); (S.-C.L.); (K.-J.C.); (Y.-B.C.); (C.-C.H.)
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (T.-Y.L.); (H.I.-A.M.L.); (C.M.); (A.A.Y.); (T.-C.L.); (S.-J.C.)
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Yu-Bai Chou
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan; (W.C.); (S.-C.L.); (S.-C.L.); (K.-J.C.); (Y.-B.C.); (C.-C.H.)
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 11217, Taiwan;
| | - Chih-Chien Hsu
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan; (W.C.); (S.-C.L.); (S.-C.L.); (K.-J.C.); (Y.-B.C.); (C.-C.H.)
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 11217, Taiwan;
| | - Tai-Chi Lin
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (T.-Y.L.); (H.I.-A.M.L.); (C.M.); (A.A.Y.); (T.-C.L.); (S.-J.C.)
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 11217, Taiwan;
| | - Shih-Jen Chen
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (T.-Y.L.); (H.I.-A.M.L.); (C.M.); (A.A.Y.); (T.-C.L.); (S.-J.C.)
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 11217, Taiwan;
| | - Yueh Chien
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (T.-Y.L.); (H.I.-A.M.L.); (C.M.); (A.A.Y.); (T.-C.L.); (S.-J.C.)
- Division of Basic Research, Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- Correspondence: (Y.C.); (Y.-P.Y.); (D.-K.H.)
| | - Yi-Ping Yang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (T.-Y.L.); (H.I.-A.M.L.); (C.M.); (A.A.Y.); (T.-C.L.); (S.-J.C.)
- Division of Basic Research, Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- Institute of Food Safety and Health Risk Assessment, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Correspondence: (Y.C.); (Y.-P.Y.); (D.-K.H.)
| | - De-Kuang Hwang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan; (T.-Y.L.); (H.I.-A.M.L.); (C.M.); (A.A.Y.); (T.-C.L.); (S.-J.C.)
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 11217, Taiwan;
- Correspondence: (Y.C.); (Y.-P.Y.); (D.-K.H.)
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22
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Han RC, Fry LE, Kantor A, McClements ME, Xue K, MacLaren RE. Is subretinal AAV gene replacement still the only viable treatment option for choroideremia? Expert Opin Orphan Drugs 2021; 9:13-24. [PMID: 34040899 PMCID: PMC7610829 DOI: 10.1080/21678707.2021.1882300] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/25/2021] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Choroideremia is an X-linked inherited retinal degeneration resulting from mutations in the CHM gene, encoding Rab escort protein-1 (REP1), a protein regulating intracellular vesicular transport. Loss-of-function mutations in CHM lead to progressive loss of retinal pigment epithelium (RPE) with photoreceptor and choriocapillaris degeneration, leading to progressive visual field constriction and loss of visual acuity. Three hundred and fifty-four unique mutations have been reported in CHM. While gene augmentation remains an ideal therapeutic option for choroideremia, other potential future clinical strategies may exist. AREAS COVERED The authors examine the pathophysiology and genetic basis of choroideremia. They summarize the status of ongoing gene therapy trials and discuss CHM mutations amenable to other therapeutic approaches including CRISPR/Cas-based DNA and RNA editing, nonsense suppression of premature termination codons, and antisense oligonucleotides for splice modification. The authors undertook a literature search in PubMed and NIH Clinical Trials in October 2020. EXPERT OPINION The authors conclude that AAV-mediated gene augmentation remains the most effective approach for choroideremia. Given the heterogeneity of CHM mutations and potential risks and benefits, genome-editing approaches currently do not offer significant advantages. Nonsense suppression strategies and antisense oligonucleotides are exciting novel therapeutic options; however, their clinical viability remains to be determined.
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Affiliation(s)
- Ruofan Connie Han
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Lewis E. Fry
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Ariel Kantor
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | | | - Kanmin Xue
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Robert E. MacLaren
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
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23
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Diakatou M, Dubois G, Erkilic N, Sanjurjo-Soriano C, Meunier I, Kalatzis V. Allele-Specific Knockout by CRISPR/Cas to Treat Autosomal Dominant Retinitis Pigmentosa Caused by the G56R Mutation in NR2E3. Int J Mol Sci 2021; 22:ijms22052607. [PMID: 33807610 PMCID: PMC7961898 DOI: 10.3390/ijms22052607] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 12/18/2022] Open
Abstract
Retinitis pigmentosa (RP) is an inherited retinal dystrophy that causes progressive vision loss. The G56R mutation in NR2E3 is the second most common mutation causing autosomal dominant (ad) RP, a transcription factor that is essential for photoreceptor development and maintenance. The G56R variant is exclusively responsible for all cases of NR2E3-associated adRP. Currently, there is no treatment for NR2E3-related or, other, adRP, but genome editing holds promise. A pertinent approach would be to specifically knockout the dominant mutant allele, so that the wild type allele can perform unhindered. In this study, we developed a CRISPR/Cas strategy to specifically knockout the mutant G56R allele of NR2E3 and performed a proof-of-concept study in induced pluripotent stem cells (iPSCs) of an adRP patient. We demonstrate allele-specific knockout of the mutant G56R allele in the absence of off-target events. Furthermore, we validated this knockout strategy in an exogenous overexpression system. Accordingly, the mutant G56R-CRISPR protein was truncated and mis-localized to the cytosol in contrast to the (peri)nuclear localizations of wild type or G56R NR2E3 proteins. Finally, we show, for the first time, that G56R iPSCs, as well as G56R-CRISPR iPSCs, can differentiate into NR2E3-expressing retinal organoids. Overall, we demonstrate that G56R allele-specific knockout by CRISPR/Cas could be a clinically relevant approach to treat NR2E3-associated adRP.
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Affiliation(s)
- Michalitsa Diakatou
- INM, University of Montpellier, Inserm, 34091 Montpellier, France; (M.D.); (G.D.); (N.E.); (C.S.-S.); (I.M.)
| | - Gregor Dubois
- INM, University of Montpellier, Inserm, 34091 Montpellier, France; (M.D.); (G.D.); (N.E.); (C.S.-S.); (I.M.)
| | - Nejla Erkilic
- INM, University of Montpellier, Inserm, 34091 Montpellier, France; (M.D.); (G.D.); (N.E.); (C.S.-S.); (I.M.)
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, CHU, 34295 Montpellier, France
| | - Carla Sanjurjo-Soriano
- INM, University of Montpellier, Inserm, 34091 Montpellier, France; (M.D.); (G.D.); (N.E.); (C.S.-S.); (I.M.)
| | - Isabelle Meunier
- INM, University of Montpellier, Inserm, 34091 Montpellier, France; (M.D.); (G.D.); (N.E.); (C.S.-S.); (I.M.)
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, CHU, 34295 Montpellier, France
| | - Vasiliki Kalatzis
- INM, University of Montpellier, Inserm, 34091 Montpellier, France; (M.D.); (G.D.); (N.E.); (C.S.-S.); (I.M.)
- Correspondence:
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24
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Perrault I, Hanein S, Gérard X, Mounguengue N, Bouyakoub R, Zarhrate M, Fourrage C, Jabot-Hanin F, Bocquet B, Meunier I, Zanlonghi X, Kaplan J, Rozet JM. Whole Locus Sequencing Identifies a Prevalent Founder Deep Intronic RPGRIP1 Pathologic Variant in the French Leber Congenital Amaurosis Cohort. Genes (Basel) 2021; 12:genes12020287. [PMID: 33670832 PMCID: PMC7922592 DOI: 10.3390/genes12020287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/10/2021] [Accepted: 02/16/2021] [Indexed: 01/04/2023] Open
Abstract
Leber congenital amaurosis (LCA) encompasses the earliest and most severe retinal dystrophies and can occur as a non-syndromic or a syndromic disease. Molecular diagnosis in LCA is of particular importance in clinical decision-making and patient care since it can provide ocular and extraocular prognostics and identify patients eligible to develop gene-specific therapies. Routine high-throughput molecular testing in LCA yields 70%–80% of genetic diagnosis. In this study, we aimed to investigate the non-coding regions of one non-syndromic LCA gene, RPGRIP1, in a series of six families displaying one single disease allele after a gene-panel screening of 722 LCA families which identified 26 biallelic RPGRIP1 families. Using trio-based high-throughput whole locus sequencing (WLS) for second disease alleles, we identified a founder deep intronic mutation (NM_020366.3:c.1468-128T>G) in 3/6 families. We employed Sanger sequencing to search for the pathologic variant in unresolved LCA cases (106/722) and identified three additional families (two homozygous and one compound heterozygous with the NM_020366.3:c.930+77A>G deep intronic change). This makes the c.1468-128T>G the most frequent RPGRIP1 disease allele (8/60, 13%) in our cohort. Studying patient lymphoblasts, we show that the pathologic variant creates a donor splice-site and leads to the insertion of the pseudo-exon in the mRNA, which we were able to hamper using splice-switching antisense oligonucleotides (AONs), paving the way to therapies.
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Affiliation(s)
- Isabelle Perrault
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (X.G.); (N.M.); (R.B.); (J.K.); (J.-M.R.)
- Correspondence:
| | - Sylvain Hanein
- Translational Genetics, Institute of Genetic Diseases, INSERM UMR1163, Imagine and Paris Descartes University, 75015 Paris, France;
| | - Xavier Gérard
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (X.G.); (N.M.); (R.B.); (J.K.); (J.-M.R.)
| | - Nelson Mounguengue
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (X.G.); (N.M.); (R.B.); (J.K.); (J.-M.R.)
| | - Ryme Bouyakoub
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (X.G.); (N.M.); (R.B.); (J.K.); (J.-M.R.)
| | - Mohammed Zarhrate
- Genomics Platform, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France;
| | - Cécile Fourrage
- Bioinformatic Platform, Institute of Genetic Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (C.F.); (F.J.-H.)
| | - Fabienne Jabot-Hanin
- Bioinformatic Platform, Institute of Genetic Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (C.F.); (F.J.-H.)
- Bioinformatics Core Facility, Université Paris Descartes-Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, 75015 Paris, France
| | - Béatrice Bocquet
- Centre de Référence des Affections Sensorielles Génétiques, Institut des Neurosciences de Montpellier, CHU-Saint Eloi Montpellier, 34091 Montpellier, France; (B.B.); (I.M.)
| | - Isabelle Meunier
- Centre de Référence des Affections Sensorielles Génétiques, Institut des Neurosciences de Montpellier, CHU-Saint Eloi Montpellier, 34091 Montpellier, France; (B.B.); (I.M.)
- National Reference Centre for Inherited Sensory Diseases, Univ Montpellier, CHU, 34091 Montpellier, France
| | - Xavier Zanlonghi
- Eye Clinic Jules Verne, 44300 Nantes, France;
- CHU, 35000 Rennes, France
| | - Josseline Kaplan
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (X.G.); (N.M.); (R.B.); (J.K.); (J.-M.R.)
- Ophthalmology Department, University Hospital Henri Mondor, APHP, 94000 Créteil, France
| | - Jean-Michel Rozet
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France; (X.G.); (N.M.); (R.B.); (J.K.); (J.-M.R.)
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25
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The Alter Retina: Alternative Splicing of Retinal Genes in Health and Disease. Int J Mol Sci 2021; 22:ijms22041855. [PMID: 33673358 PMCID: PMC7917623 DOI: 10.3390/ijms22041855] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing of mRNA is an essential mechanism to regulate and increase the diversity of the transcriptome and proteome. Alternative splicing frequently occurs in a tissue- or time-specific manner, contributing to differential gene expression between cell types during development. Neural tissues present extremely complex splicing programs and display the highest number of alternative splicing events. As an extension of the central nervous system, the retina constitutes an excellent system to illustrate the high diversity of neural transcripts. The retina expresses retinal specific splicing factors and produces a large number of alternative transcripts, including exclusive tissue-specific exons, which require an exquisite regulation. In fact, a current challenge in the genetic diagnosis of inherited retinal diseases stems from the lack of information regarding alternative splicing of retinal genes, as a considerable percentage of mutations alter splicing or the relative production of alternative transcripts. Modulation of alternative splicing in the retina is also instrumental in the design of novel therapeutic approaches for retinal dystrophies, since it enables precision medicine for specific mutations.
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26
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Splicing mutations in inherited retinal diseases. Prog Retin Eye Res 2021. [DOI: 10.1016/j.preteyeres.2020.100874
expr 921883647 + 833887994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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27
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Alvarez MEV, Chivers M, Borovska I, Monger S, Giannoulatou E, Kralovicova J, Vorechovsky I. Transposon clusters as substrates for aberrant splice-site activation. RNA Biol 2020; 18:354-367. [PMID: 32965162 PMCID: PMC7951965 DOI: 10.1080/15476286.2020.1805909] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Transposed elements (TEs) have dramatically shaped evolution of the exon-intron structure and significantly contributed to morbidity, but how recent TE invasions into older TEs cooperate in generating new coding sequences is poorly understood. Employing an updated repository of new exon-intron boundaries induced by pathogenic mutations, termed DBASS, here we identify novel TE clusters that facilitated exon selection. To explore the extent to which such TE exons maintain RNA secondary structure of their progenitors, we carried out structural studies with a composite exon that was derived from a long terminal repeat (LTR78) and AluJ and was activated by a C > T mutation optimizing the 5ʹ splice site. Using a combination of SHAPE, DMS and enzymatic probing, we show that the disease-causing mutation disrupted a conserved AluJ stem that evolved from helix 3.3 (or 5b) of 7SL RNA, liberating a primordial GC 5ʹ splice site from the paired conformation for interactions with the spliceosome. The mutation also reduced flexibility of conserved residues in adjacent exon-derived loops of the central Alu hairpin, revealing a cross-talk between traditional and auxilliary splicing motifs that evolved from opposite termini of 7SL RNA and were approximated by Watson-Crick base-pairing already in organisms without spliceosomal introns. We also identify existing Alu exons activated by the same RNA rearrangement. Collectively, these results provide valuable TE exon models for studying formation and kinetics of pre-mRNA building blocks required for splice-site selection and will be useful for fine-tuning auxilliary splicing motifs and exon and intron size constraints that govern aberrant splice-site activation.
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Affiliation(s)
| | - Martin Chivers
- School of Medicine, University of Southampton, Southampton, UK
| | - Ivana Borovska
- Slovak Academy of Sciences, Institute of Molecular Physiology and Genetics, Bratislava, Slovak Republic
| | - Steven Monger
- Computational Genomics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Eleni Giannoulatou
- Computational Genomics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, Australia.,St. Vincent's Clinical School, University of New South Wales, Sydney, Australia
| | - Jana Kralovicova
- School of Medicine, University of Southampton, Southampton, UK.,Slovak Academy of Sciences, Institute of Molecular Physiology and Genetics, Bratislava, Slovak Republic
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28
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Xue K, MacLaren RE. Antisense oligonucleotide therapeutics in clinical trials for the treatment of inherited retinal diseases. Expert Opin Investig Drugs 2020; 29:1163-1170. [PMID: 32741234 DOI: 10.1080/13543784.2020.1804853] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Antisense oligonucleotides (ASOs) represent a class of drugs which can be rationally designed to complement the coding or non-coding regions of target RNA transcripts. They could modulate pre-messenger RNA splicing, induce mRNA knockdown, or block translation of disease-causing genes, thereby slowing disease progression. The pharmacokinetics of intravitreal delivery may enable ASOs to be effective in the treatment of inherited retinal diseases. AREAS COVERED We review the current status of clinical trials of ASO therapies for inherited retinal diseases, which have demonstrated safety, viable durability, and early efficacy. Future applications are discussed in the context of alternative genetic approaches, including gene augmentation and gene editing. EXPERT OPINION Early efficacy data suggest that the splicing-modulating ASO, sepofarsen, is a promising treatment for Leber congenital amaurosis associated with the common c.2991+1655A>G mutation in CEP290. However, potential variability in clinical response to ASO-mediated correction of splicing defect on one allele in patients who are compound heterozygotes needs to be assessed. ASOs hold great therapeutic potential for numerous other inherited retinal diseases with common deep-intronic and dominant gain-of-function mutations. These would complement viral vector-mediated gene augmentation which is generally limited by the size of the transgene and to the treatment of recessive diseases.
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Affiliation(s)
- Kanmin Xue
- Wellcome Trust Clinical Research Career Development Fellow, Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford & Honorary Consultant Vitreoretinal Surgeon, Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust , Oxford, UK
| | - Robert E MacLaren
- Professor of Ophthalmology, Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford & Honorary Consultant Vitreoretinal Surgeon, Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust , Oxford, UK
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29
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Zhou LY, Qin Z, Zhu YH, He ZY, Xu T. Current RNA-based Therapeutics in Clinical Trials. Curr Gene Ther 2020; 19:172-196. [PMID: 31566126 DOI: 10.2174/1566523219666190719100526] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/26/2019] [Accepted: 07/09/2019] [Indexed: 02/08/2023]
Abstract
Long-term research on various types of RNAs has led to further understanding of diverse mechanisms, which eventually resulted in the rapid development of RNA-based therapeutics as powerful tools in clinical disease treatment. Some of the developing RNA drugs obey the antisense mechanisms including antisense oligonucleotides, small interfering RNAs, microRNAs, small activating RNAs, and ribozymes. These types of RNAs could be utilized to inhibit/activate gene expression or change splicing to provide functional proteins. In the meantime, some others based on different mechanisms like modified messenger RNAs could replace the dysfunctional endogenous genes to manage some genetic diseases, and aptamers with special three-dimensional structures could bind to specific targets in a high-affinity manner. In addition, the recent most popular CRISPR-Cas technology, consisting of a crucial single guide RNA, could edit DNA directly to generate therapeutic effects. The desired results from recent clinical trials indicated the great potential of RNA-based drugs in the treatment of various diseases, but further studies on improving delivery materials and RNA modifications are required for the novel RNA-based drugs to translate to the clinic. This review focused on the advances and clinical studies of current RNA-based therapeutics, analyzed their challenges and prospects.
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Affiliation(s)
- Ling-Yan Zhou
- Department of Pharmacy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, China
| | - Zhou Qin
- Department of Pharmacy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, China
| | - Yang-Hui Zhu
- Department of Pharmacy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, China.,State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Zhi-Yao He
- Department of Pharmacy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, China.,State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Ting Xu
- Department of Pharmacy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, China
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30
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Splicing mutations in inherited retinal diseases. Prog Retin Eye Res 2020; 80:100874. [PMID: 32553897 DOI: 10.1016/j.preteyeres.2020.100874] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 05/30/2020] [Accepted: 05/31/2020] [Indexed: 12/15/2022]
Abstract
Mutations which induce aberrant transcript splicing represent a distinct class of disease-causing genetic variants in retinal disease genes. Such mutations may either weaken or erase regular splice sites or create novel splice sites which alter exon recognition. While mutations affecting the canonical GU-AG dinucleotides at the splice donor and splice acceptor site are highly predictive to cause a splicing defect, other variants in the vicinity of the canonical splice sites or those affecting additional cis-acting regulatory sequences within exons or introns are much more difficult to assess or even to recognize and require additional experimental validation. Splicing mutations are unique in that the actual outcome for the transcript (e.g. exon skipping, pseudoexon inclusion, intron retention) and the encoded protein can be quite different depending on the individual mutation. In this article, we present an overview on the current knowledge about and impact of splicing mutations in inherited retinal diseases. We introduce the most common sub-classes of splicing mutations including examples from our own work and others and discuss current strategies for the identification and validation of splicing mutations, as well as therapeutic approaches, open questions, and future perspectives in this field of research.
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31
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Mechaussier S, Almoallem B, Zeitz C, Van Schil K, Jeddawi L, Van Dorpe J, Dueñas Rey A, Condroyer C, Pelle O, Polak M, Boddaert N, Bahi-Buisson N, Cavallin M, Bacquet JL, Mouallem-Bézière A, Zambrowski O, Sahel JA, Audo I, Kaplan J, Rozet JM, De Baere E, Perrault I. Loss of Function of RIMS2 Causes a Syndromic Congenital Cone-Rod Synaptic Disease with Neurodevelopmental and Pancreatic Involvement. Am J Hum Genet 2020; 106:859-871. [PMID: 32470375 PMCID: PMC7273530 DOI: 10.1016/j.ajhg.2020.04.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/29/2020] [Indexed: 12/13/2022] Open
Abstract
Congenital cone-rod synaptic disorder (CRSD), also known as incomplete congenital stationary night blindness (iCSNB), is a non-progressive inherited retinal disease (IRD) characterized by night blindness, photophobia, and nystagmus, and distinctive electroretinographic features. Here, we report bi-allelic RIMS2 variants in seven CRSD-affected individuals from four unrelated families. Apart from CRSD, neurodevelopmental disease was observed in all affected individuals, and abnormal glucose homeostasis was observed in the eldest affected individual. RIMS2 regulates synaptic membrane exocytosis. Data mining of human adult bulk and single-cell retinal transcriptional datasets revealed predominant expression in rod photoreceptors, and immunostaining demonstrated RIMS2 localization in the human retinal outer plexiform layer, Purkinje cells, and pancreatic islets. Additionally, nonsense variants were shown to result in truncated RIMS2 and decreased insulin secretion in mammalian cells. The identification of a syndromic stationary congenital IRD has a major impact on the differential diagnosis of syndromic congenital IRD, which has previously been exclusively linked with degenerative IRD.
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Affiliation(s)
- Sabrina Mechaussier
- Laboratory of Genetics in Ophthalmology, INSERM UMR 1163, Institute of Genetic Diseases, Imagine and Paris University, 75015 Paris, France
| | - Basamat Almoallem
- Center for Medical Genetics and Department of Biomolecular Medicine, Ghent University and Ghent University Hospital, 9000 Ghent, Belgium; Department of Ophthalmology, King Abdul-Aziz University Hospital, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Christina Zeitz
- Sorbonne Université, INSERM, Centre National de la Recherche Scientifique, Institut de la Vision, 75012 Paris, France
| | - Kristof Van Schil
- Center for Medical Genetics and Department of Biomolecular Medicine, Ghent University and Ghent University Hospital, 9000 Ghent, Belgium
| | - Laila Jeddawi
- Pediatric Ophthalmology Division, Dhahran Eye Specialist Hospital, Dhahran 34257, Saudi Arabia
| | - Jo Van Dorpe
- Department of Pathology, Ghent University and Ghent University Hospital, 9000 Ghent, Belgium
| | - Alfredo Dueñas Rey
- Center for Medical Genetics and Department of Biomolecular Medicine, Ghent University and Ghent University Hospital, 9000 Ghent, Belgium
| | - Christel Condroyer
- Sorbonne Université, INSERM, Centre National de la Recherche Scientifique, Institut de la Vision, 75012 Paris, France
| | - Olivier Pelle
- Cell Sorting Facility, INSERM UMR 1163, Institute of Genetic Diseases, Imagine and Paris University, 75015 Paris, France
| | - Michel Polak
- Endocrinology, Gynecology, and Pediatric Diabetology Department, University Hospital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France
| | - Nathalie Boddaert
- Department of Pediatric Radiology, University Hospital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France
| | - Nadia Bahi-Buisson
- Pediatric Neurology Department, University Hospital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France
| | - Mara Cavallin
- Laboratory of Embryology and Genetics of Human Malformation, INSERM UMR 1163, Institute of Genetic Diseases, Imagine and Paris University, 75015 Paris, France
| | - Jean-Louis Bacquet
- Service d'Ophtalmologie, Centre Hospitalier Intercommunal de Créteil, Assistance Publique-Hôpitaux de Paris, 94000 Créteil, France
| | - Alexandra Mouallem-Bézière
- Service d'Ophtalmologie, Centre Hospitalier Intercommunal de Créteil, Assistance Publique-Hôpitaux de Paris, 94000 Créteil, France
| | - Olivia Zambrowski
- Service d'Ophtalmologie, Centre Hospitalier Intercommunal de Créteil, Assistance Publique-Hôpitaux de Paris, 94000 Créteil, France; Ophthalmology Department, University Hospital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France
| | - José Alain Sahel
- Sorbonne Université, INSERM, Centre National de la Recherche Scientifique, Institut de la Vision, 75012 Paris, France; Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, INSERM, Direction de l'Hospitalisation et de l'Organisation des Soins (DHOS), Centres d'Investigations Cliniques (CIC) 1423, 75012 Paris, France; Fondation Ophtalmologique Adolphe de Rothschild, 75019 Paris, France; Académie des Sciences, Institut de France, 75006 Paris, France; Department of Ophthalmology, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, PA 15213, USA
| | - Isabelle Audo
- Sorbonne Université, INSERM, Centre National de la Recherche Scientifique, Institut de la Vision, 75012 Paris, France; Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, INSERM, Direction de l'Hospitalisation et de l'Organisation des Soins (DHOS), Centres d'Investigations Cliniques (CIC) 1423, 75012 Paris, France; Institute of Ophthalmology, University College of London, London EC1V 9EL, UK
| | - Josseline Kaplan
- Laboratory of Genetics in Ophthalmology, INSERM UMR 1163, Institute of Genetic Diseases, Imagine and Paris University, 75015 Paris, France; Service d'Ophtalmologie, Centre Hospitalier Intercommunal de Créteil, Assistance Publique-Hôpitaux de Paris, 94000 Créteil, France
| | - Jean-Michel Rozet
- Laboratory of Genetics in Ophthalmology, INSERM UMR 1163, Institute of Genetic Diseases, Imagine and Paris University, 75015 Paris, France
| | - Elfride De Baere
- Center for Medical Genetics and Department of Biomolecular Medicine, Ghent University and Ghent University Hospital, 9000 Ghent, Belgium.
| | - Isabelle Perrault
- Laboratory of Genetics in Ophthalmology, INSERM UMR 1163, Institute of Genetic Diseases, Imagine and Paris University, 75015 Paris, France.
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Cremers FPM, Lee W, Collin RWJ, Allikmets R. Clinical spectrum, genetic complexity and therapeutic approaches for retinal disease caused by ABCA4 mutations. Prog Retin Eye Res 2020; 79:100861. [PMID: 32278709 PMCID: PMC7544654 DOI: 10.1016/j.preteyeres.2020.100861] [Citation(s) in RCA: 162] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/13/2020] [Accepted: 03/18/2020] [Indexed: 12/18/2022]
Abstract
The ABCA4 protein (then called a “rim protein”) was first
identified in 1978 in the rims and incisures of rod photoreceptors. The
corresponding gene, ABCA4, was cloned in 1997, and variants
were identified as the cause of autosomal recessive Stargardt disease (STGD1).
Over the next two decades, variation in ABCA4 has been
attributed to phenotypes other than the classically defined STGD1 or fundus
flavimaculatus, ranging from early onset and fast progressing cone-rod dystrophy
and retinitis pigmentosa-like phenotypes to very late onset cases of mostly mild
disease sometimes resembling, and confused with, age-related macular
degeneration. Similarly, analysis of the ABCA4 locus uncovered
a trove of genetic information, including >1200 disease-causing mutations
of varying severity, and of all types – missense, nonsense, small
deletions/insertions, and splicing affecting variants, of which many are located
deep-intronic. Altogether, this has greatly expanded our understanding of
complexity not only of the diseases caused by ABCA4 mutations,
but of all Mendelian diseases in general. This review provides an in depth
assessment of the cumulative knowledge of ABCA4-associated retinopathy –
clinical manifestations, genetic complexity, pathophysiology as well as current
and proposed therapeutic approaches.
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Affiliation(s)
- Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, PO Box 9104, 6500 HE, Nijmegen, the Netherlands.
| | - Winston Lee
- Department of Ophthalmology, Columbia University, New York, NY, 10032, USA; Department of Genetics & Development, Columbia University, New York, NY, 10032, USA
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, PO Box 9104, 6500 HE, Nijmegen, the Netherlands
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, NY, 10032, USA; Department of Pathology & Cell Biology, Columbia University, New York, NY, 10032, USA.
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Barny I, Perrault I, Michel C, Soussan M, Goudin N, Rio M, Thomas S, Attié-Bitach T, Hamel C, Dollfus H, Kaplan J, Rozet JM, Gerard X. Basal exon skipping and nonsense-associated altered splicing allows bypassing complete CEP290 loss-of-function in individuals with unusually mild retinal disease. Hum Mol Genet 2019; 27:2689-2702. [PMID: 29771326 DOI: 10.1093/hmg/ddy179] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 05/02/2018] [Accepted: 05/06/2018] [Indexed: 12/18/2022] Open
Abstract
CEP290 mutations cause a spectrum of ciliopathies from Leber congenital amaurosis type 10 (LCA10) to embryo-lethal Meckel syndrome (MKS). Using panel-based molecular diagnosis testing for inherited retinal diseases, we identified two individuals with some preserved vision despite biallelism for presumably truncating CEP290 mutations. The first one carried a homozygous 1 base pair deletion in Exon 17, introducing a premature termination codon (PTC) in Exon 18 (c.1666del; p.Ile556Phefs*17). mRNA analysis revealed a basal exon skipping (BES) of Exon 18, providing mutant cells with the ability to escape protein truncation, while disrupting the reading frame in controls. The second individual harbored compound heterozygous nonsense mutations in Exon 8 (c.508A>T, p.Lys170*) and Exon 32 (c.4090G>T, p.Glu1364*), respectively. Some CEP290 lacking Exon 8 were detected in mutant fibroblasts but not in controls whereas some skipping of Exon 32 occurred in both lines, but with higher amplitude in the mutant. Considering that the deletion of either exon maintains the reading frame in either line, skipping in mutant cells likely involves nonsense-associated altered splicing alone (Exon 8), or with BES (Exon 32). Skipping of PTC-containing exons in mutant cells allowed production of CEP290 isoforms with preserved ability to assemble into a high molecular weight complex and to interact efficiently with proteins important for cilia formation and intraflagellar trafficking. In contrast, studying LCA10 and MKS fibroblasts we show moderate to severe cilia alterations, providing support for a correlation between disease severity and the ability of cells to express shortened, yet functional, CEP290 isoforms.
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Affiliation(s)
- Iris Barny
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases
| | - Isabelle Perrault
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases
| | - Christel Michel
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases
| | - Mickael Soussan
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases
| | - Nicolas Goudin
- Cell Imaging Core Facility of the Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Imagine and Paris Descartes University, Paris, France
| | - Marlène Rio
- Department of Genetics, IHU Necker-Enfants Malades, University Paris Descartes, Paris, France
| | - Sophie Thomas
- Laboratory of Embryology and Genetics of Human Malformation, INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, Paris, France
| | - Tania Attié-Bitach
- Laboratory of Embryology and Genetics of Human Malformation, INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, Paris, France
| | - Christian Hamel
- Centre de Référence des Affections Sensorielles Génétiques, Institut des Neurosciences de Montpellier, CHU-Saint Eloi Montpellier, Montpellier, France
| | - Hélène Dollfus
- Centre de Référence pour les Affections Génétiques Ophtalmologiques CARGO, CHRU Strasbourg, INSERM 1112, Université de Strasbourg, Strasbourg, France
| | - Josseline Kaplan
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases
| | - Jean-Michel Rozet
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases
| | - Xavier Gerard
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases
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Prevalence of ABCA4 Deep-Intronic Variants and Related Phenotype in An Unsolved "One-Hit" Cohort with Stargardt Disease. Int J Mol Sci 2019; 20:ijms20205053. [PMID: 31614660 PMCID: PMC6829239 DOI: 10.3390/ijms20205053] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/24/2019] [Accepted: 10/09/2019] [Indexed: 02/06/2023] Open
Abstract
We investigated the prevalence of reported deep-intronic variants in a French cohort of 70 patients with Stargardt disease harboring a monoallelic pathogenic variant on the exonic regions of ABCA4. Direct Sanger sequencing of selected intronic regions of ABCA4 was conducted. Complete phenotypic analysis and correlation with the genotype was performed in case a known intronic pathogenic variant was identified. All other variants found on the analyzed sequences were queried for minor allele frequency and possible pathogenicity by in silico predictions. The second mutated allele was found in 14 (20%) subjects. The three known deep-intronic variants found were c.5196+1137G>A in intron 36 (6 subjects), c.4539+2064C>T in intron 30 (4 subjects) and c.4253+43G>A in intron 28 (4 subjects). Even though the phenotype depends on the compound effect of the biallelic variants, a genotype-phenotype correlation suggests that the c.5196+1137G>A was mostly associated with a mild phenotype and the c.4539+2064C>T with a more severe one. A variable effect was instead associated with the variant c.4253+43G>A. In addition, two novel variants, c.768+508A>G and c.859-245_859-243delinsTGA never associated with Stargardt disease before, were identified and a possible splice defect was predicted in silico. Our study calls for a larger cohort analysis including targeted locus sequencing and 3D protein modeling to better understand phenotype-genotype correlations associated with deep-intronic changes and patients’ selection for clinical trials.
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Cehajic Kapetanovic J, Barnard AR, MacLaren RE. Molecular Therapies for Choroideremia. Genes (Basel) 2019; 10:genes10100738. [PMID: 31548516 PMCID: PMC6826983 DOI: 10.3390/genes10100738] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/14/2019] [Accepted: 09/20/2019] [Indexed: 01/03/2023] Open
Abstract
Advances in molecular research have culminated in the development of novel gene-based therapies for inherited retinal diseases. We have recently witnessed several groundbreaking clinical studies that ultimately led to approval of Luxturna, the first gene therapy for an inherited retinal disease. In parallel, international research community has been engaged in conducting gene therapy trials for another more common inherited retinal disease known as choroideremia and with phase III clinical trials now underway, approval of this therapy is poised to follow suit. This chapter discusses new insights into clinical phenotyping and molecular genetic testing in choroideremia with review of molecular mechanisms implicated in its pathogenesis. We provide an update on current gene therapy trials and discuss potential inclusion of female carries in future clinical studies. Alternative molecular therapies are discussed including suitability of CRISPR gene editing, small molecule nonsense suppression therapy and vision restoration strategies in late stage choroideremia.
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Affiliation(s)
- Jasmina Cehajic Kapetanovic
- Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford OX3 9DU, UK; (A.R.B.); (R.E.M.)
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
- Correspondence:
| | - Alun R. Barnard
- Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford OX3 9DU, UK; (A.R.B.); (R.E.M.)
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Robert E. MacLaren
- Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford OX3 9DU, UK; (A.R.B.); (R.E.M.)
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
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Cideciyan AV, Jacobson SG. Leber Congenital Amaurosis (LCA): Potential for Improvement of Vision. Invest Ophthalmol Vis Sci 2019; 60:1680-1695. [PMID: 31009524 PMCID: PMC6892385 DOI: 10.1167/iovs.19-26672] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Artur V Cideciyan
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Samuel G Jacobson
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
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37
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Vázquez-Domínguez I, Garanto A, Collin RWJ. Molecular Therapies for Inherited Retinal Diseases-Current Standing, Opportunities and Challenges. Genes (Basel) 2019; 10:genes10090654. [PMID: 31466352 PMCID: PMC6770110 DOI: 10.3390/genes10090654] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/23/2019] [Accepted: 08/26/2019] [Indexed: 12/15/2022] Open
Abstract
Inherited retinal diseases (IRDs) are both genetically and clinically highly heterogeneous and have long been considered incurable. Following the successful development of a gene augmentation therapy for biallelic RPE65-associated IRD, this view has changed. As a result, many different therapeutic approaches are currently being developed, in particular a large variety of molecular therapies. These are depending on the severity of the retinal degeneration, knowledge of the pathophysiological mechanism underlying each subtype of IRD, and the therapeutic target molecule. DNA therapies include approaches such as gene augmentation therapy, genome editing and optogenetics. For some genetic subtypes of IRD, RNA therapies and compound therapies have also shown considerable therapeutic potential. In this review, we summarize the current state-of-the-art of various therapeutic approaches, including the pros and cons of each strategy, and outline the future challenges that lie ahead in the combat against IRDs.
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Affiliation(s)
- Irene Vázquez-Domínguez
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands
| | - Alejandro Garanto
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands.
| | - Rob W J Collin
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands.
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Winter J, Luu A, Gapinske M, Manandhar S, Shirguppe S, Woods WS, Song JS, Perez-Pinera P. Targeted exon skipping with AAV-mediated split adenine base editors. Cell Discov 2019; 5:41. [PMID: 31636954 PMCID: PMC6796986 DOI: 10.1038/s41421-019-0109-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 06/28/2019] [Accepted: 07/02/2019] [Indexed: 01/26/2023] Open
Abstract
Techniques for exclusion of exons from mature transcripts have been applied as gene therapies for treating many different diseases. Since exon skipping has been traditionally accomplished using technologies that have a transient effect, it is particularly important to develop new techniques that enable permanent exon skipping. We have recently shown that this can be accomplished using cytidine base editors for permanently disabling the splice acceptor of target exons. We now demonstrate the application of CRISPR-Cas9 adenine deaminase base editors to disrupt the conserved adenine within splice acceptor sites for programmable exon skipping. We also demonstrate that by altering the amino acid sequence of the linker between the adenosine deaminase domain and the Cas9-nickase or by coupling the adenine base editor with a uracil glycosylase inhibitor, the DNA editing efficiency and exon-skipping rates improve significantly. Finally, we developed a split base editor architecture compatible with adeno-associated viral packaging. Collectively, these results represent significant progress toward permanent in vivo exon skipping through base editing and, ultimately, a new modality of gene therapy for the treatment of genetic diseases.
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Affiliation(s)
- Jackson Winter
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Alan Luu
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Michael Gapinske
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Sony Manandhar
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Shraddha Shirguppe
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Wendy S. Woods
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Jun S. Song
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Pablo Perez-Pinera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Carle Illinois College of Medicine, Champaign, IL 61820 USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
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Targeted exon skipping rescues ciliary protein composition defects in Joubert syndrome patient fibroblasts. Sci Rep 2019; 9:10828. [PMID: 31346239 PMCID: PMC6658666 DOI: 10.1038/s41598-019-47243-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 07/12/2019] [Indexed: 12/19/2022] Open
Abstract
Joubert syndrome (JBTS) is an incurable multisystem ciliopathy syndrome. The most commonly mutated gene in JBTS patients with a cerebello-retinal-renal phenotype is CEP290 (alias JBTS5). The encoded CEP290 protein localises to the proximal end of the primary cilium, in the transition zone, where it controls ciliary protein composition and signalling. We examined primary cilium structure and composition in fibroblast cells derived from homozygous and compound heterozygous JBTS5 patients with nonsense mutations in CEP290 and show that elongation of cilia, impaired ciliogenesis and ciliary composition defects are typical features in JBTS5 cells. Targeted skipping of the mutated exon c.5668 G > T using antisense oligonucleotide (ASO) therapy leads to restoration of CEP290 protein expression and functions at the transition zone in homozygous and compound heterozygous JBTS5 cells, allowing a rescue of both cilia morphology and ciliary composition. This study, by demonstrating that targeted exon skipping is able to rescue ciliary protein composition defects, provides functional evidence for the efficacy of this approach in the treatment of JBTS.
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40
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Chen HY, Welby E, Li T, Swaroop A. Retinal disease in ciliopathies: Recent advances with a focus on stem cell-based therapies. ACTA ACUST UNITED AC 2019; 4:97-115. [PMID: 31763178 PMCID: PMC6839492 DOI: 10.3233/trd-190038] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ciliopathies display extensive genetic and clinical heterogeneity, varying in severity, age of onset, disease progression and organ systems affected. Retinal involvement, as demonstrated by photoreceptor dysfunction or death, is a highly penetrant phenotype among a vast majority of ciliopathies. Photoreceptor cells possess a specialized and modified sensory cilium with membrane discs where efficient photon capture and ensuing signaling cascade initiate the visual process. Disruptions of cilia biogenesis and protein transport lead to impairment of photoreceptor function and eventually degeneration. Despite advances in elucidation of ciliogenesis and photoreceptor cilia defects, we have limited understanding of pathogenic mechanisms underlying retinal phenotype(s) observed in human ciliopathies. Patient-derived induced pluripotent stem cell (iPSC)-based approaches offer a unique opportunity to complement studies with model organisms and examine cilia disease relevant to humans. Three-dimensional retinal organoids from iPSC lines feature laminated cytoarchitecture, apical-basal polarity and emergence of a ciliary structure, thereby permitting pathogenic modeling of human photoreceptors in vitro. Here, we review the biology of photoreceptor cilia and associated defects and discuss recent progress in evolving treatment modalities, especially using patient-derived iPSCs, for retinal ciliopathies.
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Affiliation(s)
- Holly Yu Chen
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Emily Welby
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tiansen Li
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, USA
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41
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Garanto A, Duijkers L, Tomkiewicz TZ, Collin RWJ. Antisense Oligonucleotide Screening to Optimize the Rescue of the Splicing Defect Caused by the Recurrent Deep-Intronic ABCA4 Variant c.4539+2001G>A in Stargardt Disease. Genes (Basel) 2019; 10:genes10060452. [PMID: 31197102 PMCID: PMC6628380 DOI: 10.3390/genes10060452] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/04/2019] [Accepted: 06/11/2019] [Indexed: 12/17/2022] Open
Abstract
Deep-sequencing of the ABCA4 locus has revealed that ~10% of autosomal recessive Stargardt disease (STGD1) cases are caused by deep-intronic mutations. One of the most recurrent deep-intronic variants in the Belgian and Dutch STGD1 population is the c.4539+2001G>A mutation. This variant introduces a 345-nt pseudoexon to the ABCA4 mRNA transcript in a retina-specific manner. Antisense oligonucleotides (AONs) are short sequences of RNA that can modulate splicing. In this work, we designed 26 different AONs to perform a thorough screening to identify the most effective AONs to correct splicing defects associated with c.4539+2001G>A. All AONs were tested in patient-derived induced pluripotent stem cells (iPSCs) that were differentiated to photoreceptor precursor cells (PPCs). AON efficacy was assessed through RNA analysis and was based on correction efficacy, and AONs were grouped and their properties assessed. We (a) identified nine AONs with significant correction efficacies (>50%), (b) confirmed that a single nucleotide mismatch was sufficient to significantly decrease AON efficacy, and (c) found potential correlations between efficacy and some of the parameters analyzed. Overall, our results show that AON-based splicing modulation holds great potential for treating Stargardt disease caused by splicing defects in ABCA4.
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Affiliation(s)
- Alejandro Garanto
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands.
| | - Lonneke Duijkers
- Department of Human Genetics, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands.
| | - Tomasz Z Tomkiewicz
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands.
| | - Rob W J Collin
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525GA Nijmegen, The Netherlands.
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42
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Barny I, Perrault I, Michel C, Goudin N, Defoort-Dhellemmes S, Ghazi I, Kaplan J, Rozet JM, Gerard X. AON-Mediated Exon Skipping to Bypass Protein Truncation in Retinal Dystrophies Due to the Recurrent CEP290 c.4723A > T Mutation. Fact or Fiction? Genes (Basel) 2019; 10:E368. [PMID: 31091803 PMCID: PMC6562928 DOI: 10.3390/genes10050368] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/09/2019] [Accepted: 05/09/2019] [Indexed: 01/09/2023] Open
Abstract
Mutations in CEP290 encoding a centrosomal protein important to cilia formation cause a spectrum of diseases, from isolated retinal dystrophies to multivisceral and sometimes embryo-lethal ciliopathies. In recent years, endogenous and/or selective non-canonical exon skipping of mutant exons have been documented in attenuated retinal disease cases. This observation led us to consider targeted exon skipping to bypass protein truncation resulting from a recurrent mutation in exon 36 (c.4723A > T, p.Lys1575*) causing isolated retinal ciliopathy. Here, we report two unrelated individuals (P1 and P2), carrying the mutation in homozygosity but affected with early-onset severe retinal dystrophy and congenital blindness, respectively. Studying skin-derived fibroblasts, we observed basal skipping and nonsense associated-altered splicing of exon 36, producing low (P1) and very low (P2) levels of CEP290 products. Consistent with a more severe disease, fibroblasts from P2 exhibited reduced ciliation compared to P1 cells displaying normally abundant cilia; both lines presented however significantly elongated cilia, suggesting altered axonemal trafficking. Antisense oligonucleotides (AONs)-mediated skipping of exon 36 increased the abundance of the premature termination codon (PTC)-free mRNA and protein, reduced axonemal length and improved cilia formation in P2 but not in P1 expressing higher levels of skipped mRNA, questioning AON-mediated exon skipping to treat patients carrying the recurrent c.4723A > T mutation.
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Affiliation(s)
- Iris Barny
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France.
| | - Isabelle Perrault
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France.
| | - Christel Michel
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France.
| | - Nicolas Goudin
- Cell Imaging Core Facility of the Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Imagine and Paris Descartes University, 75015 Paris, France.
| | - Sabine Defoort-Dhellemmes
- Service D'exploration de la Vision et Neuro-Ophtalmologie, Pôle D'imagerie et Explorations Fonctionnelles, CHRU de Lille, 59037 Lille, France.
| | - Imad Ghazi
- Department of Ophthalmology, IHU Necker-Enfants Malades, 75015 Paris, France.
| | - Josseline Kaplan
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France.
| | - Jean-Michel Rozet
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France.
| | - Xavier Gerard
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, 75015 Paris, France.
- Unit of Retinal Degeneration and Regeneration, Department of Ophthalmology, University of Lausanne, Hôpital Ophtalmique Jules Gonin, Fondation Asile des Aveugles, 1004 Lausanne, Switzerland.
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Antisense Oligonucleotide-Based Splice Correction of a Deep-Intronic Mutation in CHM Underlying Choroideremia. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1074:83-89. [PMID: 29721931 DOI: 10.1007/978-3-319-75402-4_11] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Choroideremia is a progressive genetic eye disorder caused by mutations in the CHM gene that encodes the Rab escort protein-1 (REP-1). One of the many CHM mutations described so far is a deep-intronic variant, c.315-4587T>A, that creates a novel splice acceptor site resulting in the insertion of a 98-bp pseudoexon in the CHM transcript. Antisense oligonucleotides (AONs) are a potential therapeutic tool for correcting splice defects, as they have the properties to bind to the pre-mRNA and redirect the splicing process. Previously, we used AONs to correct aberrant splicing events caused by a recurrent intronic mutation in CEP290 underlying Leber congenital amaurosis. Here, we expand the use of these therapeutic molecules for the c.315-4587T>A deep-intronic mutation in CHM by demonstrating splice correction in patient-derived lymphoblast cells.
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Antisense Oligonucleotide Design and Evaluation of Splice-Modulating Properties Using Cell-Based Assays. Methods Mol Biol 2019; 1828:519-530. [PMID: 30171565 DOI: 10.1007/978-1-4939-8651-4_34] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Antisense oligonucleotide (AON)-based splice modulation has been proven to hold great promise as a therapeutic strategy for a number of hereditary conditions. AONs are small modified single-stranded RNA or DNA molecules that are complementary to splice enhancer or silencer target sites. Upon pre-mRNA binding, AONs will prevent or stimulate binding of the spliceosome thereby modulating splicing events. AONs can be designed and applied for different genes and genetic disorders as the specificity depends on their nucleotide sequence. Here we provide a guideline for setting up AON-based splice-modulation experiments by describing a detailed protocol to design and evaluate AONs using a combination of in silico and in vitro analyses.
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Maeder ML, Stefanidakis M, Wilson CJ, Baral R, Barrera LA, Bounoutas GS, Bumcrot D, Chao H, Ciulla DM, DaSilva JA, Dass A, Dhanapal V, Fennell TJ, Friedland AE, Giannoukos G, Gloskowski SW, Glucksmann A, Gotta GM, Jayaram H, Haskett SJ, Hopkins B, Horng JE, Joshi S, Marco E, Mepani R, Reyon D, Ta T, Tabbaa DG, Samuelsson SJ, Shen S, Skor MN, Stetkiewicz P, Wang T, Yudkoff C, Myer VE, Albright CF, Jiang H. Development of a gene-editing approach to restore vision loss in Leber congenital amaurosis type 10. Nat Med 2019; 25:229-233. [DOI: 10.1038/s41591-018-0327-9] [Citation(s) in RCA: 338] [Impact Index Per Article: 67.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 12/07/2018] [Indexed: 12/18/2022]
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Garanto A. RNA-Based Therapeutic Strategies for Inherited Retinal Dystrophies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1185:71-77. [PMID: 31884591 DOI: 10.1007/978-3-030-27378-1_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Inherited retinal dystrophies (IRDs) are genetic diseases affecting 1 in every 3000 individuals worldwide. Nowadays, more than 250 genes have been associated with different forms of IRD. In the last decade, it has been shown that gene therapy is a promising approach to correct the genetic defects underlying IRD. In fact, voretigene neparvovec-rzyl (Luxturna™), the first commercialized gene therapy drug to treat RPE65-associated Leber congenital amaurosis, has opened new venues. However, IRDs are highly heterogeneous at genetic level making the design of novel strategies complicated. Unfortunately, the size of several frequently mutated genes is not suitable for the approved conventional therapeutic viral vectors; therefore, there is an urgent need for the development of alternatives, such as those targeting the pre-mRNA. In this mini-review, the potential of RNA-based strategies for IRDs is discussed.
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Affiliation(s)
- Alejandro Garanto
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands.
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Barny I, Perrault I, Rio M, Dollfus H, Defoort-Dhellemmes S, Kaplan J, Rozet JM, Gerard X. Description of Two Siblings with Apparently Severe CEP290 Mutations and Unusually Mild Retinal Disease Unrelated to Basal Exon Skipping or Nonsense-Associated Altered Splicing. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1185:189-195. [PMID: 31884610 DOI: 10.1007/978-3-030-27378-1_31] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
CEP290 mutations cause a spectrum of ciliopathies, including Leber congenital amaurosis. Milder retinal diseases have been ascribed to exclusion of CEP290 mutant exons through basal exon skipping (BES) and/or nonsense-associated altered splicing (NAS). Here, we report two siblings with some preserved vision despite biallelism for presumably severe CEP290 mutations: a maternal splice site change in intron 18 (c.1824 + 3A > G) and a paternal c.6869dup (p.Asn2290Lysfs∗6) in exon 50 that introduces a premature termination codon (PTC) within the same exon. Analyzing mRNAs from fibroblasts of the two siblings, we detected no BES or NAS which could have enabled the production of PTC-free CEP290 isoforms from the paternal allele. In contrast, we reveal partial alteration of exon 18 donor splice site, allowing the transcription of some correctly spliced CEP290 mRNAs from the maternal allele which likely account for the mild retinal disease. This observation adds further variability to the mechanisms underlying CEP290 pleiotropy.
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Affiliation(s)
- Iris Barny
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, Paris, France
| | - Isabelle Perrault
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, Paris, France
| | - Marlène Rio
- Department of Genetics, IHU Necker-Enfants Malades, University Paris Descartes, Paris, France
| | - Hélène Dollfus
- Centre des Affections Rares en Génétique Ophtalmologique CARGO, CHRU Strasbourg, INSERM1112, Université de Strasbourg, Strasbourg, France
| | - Sabine Defoort-Dhellemmes
- Service d'exploration de la Vision et Neuro-ophtalmologie, Pôle d'Imagerie et Explorations Fonctionnelles, CHRU de Lille, Lille, France
| | - Josseline Kaplan
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, Paris, France
| | - Jean-Michel Rozet
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, Paris, France.
| | - Xavier Gerard
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetics Diseases, Imagine and Paris Descartes University, Paris, France. .,Unit of Retinal Degeneration and Regeneration, Department of Ophthalmology, University of Lausanne, Hôpital Ophtalmique Jules Gonin, Lausanne, Switzerland.
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48
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Dulla K, Aguila M, Lane A, Jovanovic K, Parfitt DA, Schulkens I, Chan HL, Schmidt I, Beumer W, Vorthoren L, Collin RWJ, Garanto A, Duijkers L, Brugulat-Panes A, Semo M, Vugler AA, Biasutto P, Adamson P, Cheetham ME. Splice-Modulating Oligonucleotide QR-110 Restores CEP290 mRNA and Function in Human c.2991+1655A>G LCA10 Models. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 12:730-740. [PMID: 30114557 PMCID: PMC6092551 DOI: 10.1016/j.omtn.2018.07.010] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 07/18/2018] [Accepted: 07/18/2018] [Indexed: 12/11/2022]
Abstract
Leber congenital amaurosis type 10 (LCA10) is a severe inherited retinal dystrophy associated with mutations in CEP290. The deep intronic c.2991+1655A>G mutation in CEP290 is the most common mutation in LCA10 individuals and represents an ideal target for oligonucleotide therapeutics. Here, a panel of antisense oligonucleotides was designed to correct the splicing defect associated with the mutation and screened for efficacy and safety. This identified QR-110 as the best-performing molecule. QR-110 restored wild-type CEP290 mRNA and protein expression levels in CEP290 c.2991+1655A>G homozygous and compound heterozygous LCA10 primary fibroblasts. Furthermore, in homozygous three-dimensional iPSC-derived retinal organoids, QR-110 showed a dose-dependent restoration of mRNA and protein function, as measured by percentage and length of photoreceptor cilia, without off-target effects. Localization studies in wild-type mice and rabbits showed that QR-110 readily reached all retinal layers, with an estimated half-life of 58 days. It was well tolerated following intravitreal injection in monkeys. In conclusion, the pharmacodynamic, pharmacokinetic, and safety properties make QR-110 a promising candidate for treating LCA10, and clinical development is currently ongoing.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Rob W J Collin
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Alejandro Garanto
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lonneke Duijkers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | | | | | | | - Peter Adamson
- ProQR Therapeutics, Leiden, the Netherlands; UCL Institute of Ophthalmology, London, UK.
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Valkenburg D, van Cauwenbergh C, Lorenz B, van Genderen MM, Bertelsen M, Pott JWR, Coppieters F, de Zaeytijd J, Thiadens AAHJ, Klaver CCW, Kroes HY, van Schooneveld MJ, Preising M, Hoyng CB, Leroy BP, van den Born LI, Collin RWJ. Clinical Characterization of 66 Patients With Congenital Retinal Disease Due to the Deep-Intronic c.2991+1655A>G Mutation inCEP290. ACTA ACUST UNITED AC 2018; 59:4384-4391. [DOI: 10.1167/iovs.18-24817] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Dyon Valkenburg
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Cognitive Neuroscience Department, Nijmegen, The Netherlands
| | - Caroline van Cauwenbergh
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Birgit Lorenz
- Department of Ophthalmology, Giessen University Medical Center, Giessen, Germany
| | | | - Mette Bertelsen
- Department of Ophthalmology, Righospitalet, Glostrup, Denmark
- Department of Clinical Genetics, Righospitalet, Copenhagen, Denmark
| | - Jan-Willem R. Pott
- Department of Ophthalmology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Frauke Coppieters
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Julie de Zaeytijd
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | | | - Caroline C. W. Klaver
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Hester Y. Kroes
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Markus Preising
- Department of Ophthalmology, Giessen University Medical Center, Giessen, Germany
| | - Carel B. Hoyng
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Cognitive Neuroscience Department, Nijmegen, The Netherlands
| | - Bart P. Leroy
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
- Division of Ophthalmology & Center for Cellular & Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | | | - Rob W. J. Collin
- Radboud University Medical Center, Donders Institute for Brain, Cognition and Behavior, Cognitive Neuroscience Department, Nijmegen, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
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50
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Gapinske M, Luu A, Winter J, Woods WS, Kostan KA, Shiva N, Song JS, Perez-Pinera P. CRISPR-SKIP: programmable gene splicing with single base editors. Genome Biol 2018; 19:107. [PMID: 30107853 PMCID: PMC6092781 DOI: 10.1186/s13059-018-1482-5] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 07/13/2018] [Indexed: 01/09/2023] Open
Abstract
CRISPR gene editing has revolutionized biomedicine and biotechnology by providing a simple means to engineer genes through targeted double-strand breaks in the genomic DNA of living cells. However, given the stochasticity of cellular DNA repair mechanisms and the potential for off-target mutations, technologies capable of introducing targeted changes with increased precision, such as single-base editors, are preferred. We present a versatile method termed CRISPR-SKIP that utilizes cytidine deaminase single-base editors to program exon skipping by mutating target DNA bases within splice acceptor sites. Given its simplicity and precision, CRISPR-SKIP will be broadly applicable in gene therapy and synthetic biology.
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Affiliation(s)
- Michael Gapinske
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1406 West Green Street, Urbana, 61801-2918 IL USA
| | - Alan Luu
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801-3080 USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Jackson Winter
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1406 West Green Street, Urbana, 61801-2918 IL USA
| | - Wendy S. Woods
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1406 West Green Street, Urbana, 61801-2918 IL USA
| | - Kurt A. Kostan
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1406 West Green Street, Urbana, 61801-2918 IL USA
| | - Nikhil Shiva
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1406 West Green Street, Urbana, 61801-2918 IL USA
| | - Jun S. Song
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801-3080 USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Pablo Perez-Pinera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1406 West Green Street, Urbana, 61801-2918 IL USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Carle Illinois College of Medicine, Champaign, IL 61820 USA
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