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Garanto A, Collin RWJ. Design and In Vitro Use of Antisense Oligonucleotides to Correct Pre-mRNA Splicing Defects in Inherited Retinal Dystrophies. Methods Mol Biol 2018; 1715:61-78. [PMID: 29188506 DOI: 10.1007/978-1-4939-7522-8_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Antisense oligonucleotides (AONs) are small molecules able to bind to the pre-mRNA and modulate splicing. The increasing amount of intronic mutations leading to pseudoexon insertion in genes underlying inherited retinal dystrophies (IRDs) has highlighted the potential of AONs as a therapeutic tool for these disorders. Here we describe how to design and test AON molecules in vitro in order to correct pre-mRNA splicing defects involved in IRDs.
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Affiliation(s)
- Alejandro Garanto
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Rob W J Collin
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
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52
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Albert S, Garanto A, Sangermano R, Khan M, Bax NM, Hoyng CB, Zernant J, Lee W, Allikmets R, Collin RW, Cremers FP. Identification and Rescue of Splice Defects Caused by Two Neighboring Deep-Intronic ABCA4 Mutations Underlying Stargardt Disease. Am J Hum Genet 2018. [PMID: 29526278 DOI: 10.1016/j.ajhg.2018.02.008] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Sequence analysis of the coding regions and splice site sequences in inherited retinal diseases is not able to uncover ∼40% of the causal variants. Whole-genome sequencing can identify most of the non-coding variants, but their interpretation is still very challenging, in particular when the relevant gene is expressed in a tissue-specific manner. Deep-intronic variants in ABCA4 have been associated with autosomal-recessive Stargardt disease (STGD1), but the exact pathogenic mechanism is unknown. By generating photoreceptor precursor cells (PPCs) from fibroblasts obtained from individuals with STGD1, we demonstrated that two neighboring deep-intronic ABCA4 variants (c.4539+2001G>A and c.4539+2028C>T) result in a retina-specific 345-nt pseudoexon insertion (predicted protein change: p.Arg1514Leufs∗36), likely due to the creation of exonic enhancers. Administration of antisense oligonucleotides (AONs) targeting the 345-nt pseudoexon can significantly rescue the splicing defect observed in PPCs of two individuals with these mutations. Intriguingly, an AON that is complementary to c.4539+2001G>A rescued the splicing defect only in PPCs derived from an individual with STGD1 with this but not the other mutation, demonstrating the high specificity of AONs. In addition, a single AON molecule rescued splicing defects associated with different neighboring mutations, thereby providing new strategies for the treatment of persons with STGD1. As many genes associated with human genetic conditions are expressed in specific tissues and pre-mRNA splicing may also rely on organ-specific factors, our approach to investigate and treat splicing variants using differentiated cells derived from individuals with STGD1 can be applied to any tissue of interest.
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53
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Shimada H, Lu Q, Insinna-Kettenhofen C, Nagashima K, English MA, Semler EM, Mahgerefteh J, Cideciyan AV, Li T, Brooks BP, Gunay-Aygun M, Jacobson SG, Cogliati T, Westlake CJ, Swaroop A. In Vitro Modeling Using Ciliopathy-Patient-Derived Cells Reveals Distinct Cilia Dysfunctions Caused by CEP290 Mutations. Cell Rep 2018; 20:384-396. [PMID: 28700940 DOI: 10.1016/j.celrep.2017.06.045] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 05/03/2017] [Accepted: 06/19/2017] [Indexed: 02/06/2023] Open
Abstract
Mutations in CEP290, a transition zone protein in primary cilia, cause diverse ciliopathies, including Leber congenital amaurosis (LCA) and Joubert-syndrome and related disorders (JSRD). We examined cilia biogenesis and function in cells derived from CEP290-LCA and CEP290-JSRD patients. CEP290 protein was reduced in LCA fibroblasts with no detectable impact on cilia; however, optic cups derived from induced pluripotent stem cells (iPSCs) of CEP290-LCA patients displayed less developed photoreceptor cilia. Lack of CEP290 in JSRD fibroblasts resulted in abnormal cilia and decreased ciliogenesis. We observed selectively reduced localization of ADCY3 and ARL13B. Notably, Hedgehog signaling was augmented in CEP290-JSRD because of enhanced ciliary transport of Smoothened and GPR161. These results demonstrate a direct correlation between the extent of ciliogenesis defects in fibroblasts and photoreceptors with phenotypic severity in JSRD and LCA, respectively, and strengthen the role of CEP290 as a selective ciliary gatekeeper for transport of signaling molecules in and out of the cilium.
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Affiliation(s)
- Hiroko Shimada
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Quanlong Lu
- Laboratory of Cell and Developmental Signaling, National Cancer Institute - Frederick, Frederick, MD 21702, USA
| | | | - Kunio Nagashima
- Electron Microscope Laboratory, Leidos Biomedical Research, Inc., National Cancer Institute - Frederick, Frederick, MD 21702, USA
| | - Milton A English
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elizabeth M Semler
- Laboratory of Cell and Developmental Signaling, National Cancer Institute - Frederick, Frederick, MD 21702, USA
| | - Jacklyn Mahgerefteh
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Artur V Cideciyan
- Department of Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tiansen Li
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brian P Brooks
- Pediatric, Developmental, and Genetic Eye Disease Branch, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Meral Gunay-Aygun
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; Department of Pediatrics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Samuel G Jacobson
- Department of Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tiziana Cogliati
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christopher J Westlake
- Laboratory of Cell and Developmental Signaling, National Cancer Institute - Frederick, Frederick, MD 21702, USA.
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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54
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Antisense Oligonucleotide-Based Splicing Correction in Individuals with Leber Congenital Amaurosis due to Compound Heterozygosity for the c.2991+1655A>G Mutation in CEP290. Int J Mol Sci 2018. [PMID: 29518907 PMCID: PMC5877614 DOI: 10.3390/ijms19030753] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Leber congenital amaurosis (LCA) is a rare inherited retinal disorder affecting approximately 1:50,000 people worldwide. So far, mutations in 25 genes have been associated with LCA, with CEP290 (encoding the Centrosomal protein of 290 kDa) being the most frequently mutated gene. The most recurrent LCA-causing CEP290 mutation, c.2991+1655A>G, causes the insertion of a pseudoexon into a variable proportion of CEP290 transcripts. We previously demonstrated that antisense oligonucleotides (AONs) have a high therapeutic potential for patients homozygously harbouring this mutation, although to date, it is unclear whether rescuing one single allele is enough to restore CEP290 function. Here, we assessed the AON efficacy at RNA, protein and cellular levels in samples that are compound heterozygous for this mutation, together with a protein-truncating mutation in CEP290. We demonstrate that AONs can efficiently restore splicing and increase protein levels. However, due to a high variability in ciliation among the patient-derived cell lines, the efficacy of the AONs was more difficult to assess at the cellular level. This observation points towards the importance of the severity of the second allele and possibly other genetic variants present in each individual. Overall, AONs seem to be a promising tool to treat CEP290-associated LCA, not only in homozygous but also in compound heterozygous carriers of the c.2991+1655A>G variant.
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Leber Congenital Amaurosis Associated with Mutations in CEP290, Clinical Phenotype, and Natural History in Preparation for Trials of Novel Therapies. Ophthalmology 2018; 125:894-903. [PMID: 29398085 PMCID: PMC5974693 DOI: 10.1016/j.ophtha.2017.12.013] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 12/01/2017] [Accepted: 12/07/2017] [Indexed: 11/21/2022] Open
Abstract
PURPOSE To investigate and describe in detail the demographics, functional and anatomic characteristics, and clinical course of Leber congenital amaurosis (LCA) associated with mutations in the CEP290 gene (LCA-CEP290) in a large cohort of adults and children. DESIGN Retrospective case series. PARTICIPANTS Patients with mutations in CEP290 identified at a single UK referral center. METHODS Review of case notes and results of retinal imaging (color fundus photography, fundus autofluorescence [FAF] imaging, OCT), electrophysiologic assessment, and molecular genetic testing. MAIN OUTCOME MEASURES Molecular genetic testing, clinical findings including visual acuity and retinal imaging, and electrophysiologic assessment. RESULTS Forty patients with LCA-CEP290 were identified. The deep intronic mutation c.2991+1655 A>G was the most common disease-causing variant (23/40 patients) identified in the compound heterozygous state in 20 patients (50%) and homozygous in 2 patients (5%). Visual acuity (VA) varied from 6/9 to no perception of light, and only 2 of 12 patients with longitudinal VA data showed deterioration in VA in their better-seeing eye over time. A normal fundus was found at diagnosis in younger patients (mean age, 1.9 years), with older patients showing white flecks (mean age, 5.9 years) or pigmentary retinopathy (mean age, 21.7 years). Eleven of 12 patients (92%) with OCT imaging had preservation of foveal architecture. Ten of 12 patients (83%) with FAF imaging had a perifoveal hyperautofluorescent ring. Having 2 nonsense CEP290 mutations was associated with worse final VA and the presence of nonocular features. CONCLUSIONS Detailed analysis of the clinical phenotype of LCA-CEP290 in a large cohort confirms that there is a window of opportunity in childhood for therapeutic intervention based on relative structural preservation in the central cone-rich retina in a significant proportion of patients, with the majority harboring the deep intronic variant potentially tractable to several planned gene editing approaches.
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56
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Sangermano R, Khan M, Cornelis SS, Richelle V, Albert S, Garanto A, Elmelik D, Qamar R, Lugtenberg D, van den Born LI, Collin RWJ, Cremers FPM. ABCA4 midigenes reveal the full splice spectrum of all reported noncanonical splice site variants in Stargardt disease. Genome Res 2018. [PMID: 29162642 DOI: 10.1101/gr.226621.117/-/dc1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Stargardt disease is caused by variants in the ABCA4 gene, a significant part of which are noncanonical splice site (NCSS) variants. In case a gene of interest is not expressed in available somatic cells, small genomic fragments carrying potential disease-associated variants are tested for splice abnormalities using in vitro splice assays. We recently discovered that when using small minigenes lacking the proper genomic context, in vitro results do not correlate with splice defects observed in patient cells. We therefore devised a novel strategy in which a bacterial artificial chromosome was employed to generate midigenes, splice vectors of varying lengths (up to 11.7 kb) covering almost the entire ABCA4 gene. These midigenes were used to analyze the effect of all 44 reported and three novel NCSS variants on ABCA4 pre-mRNA splicing. Intriguingly, multi-exon skipping events were observed, as well as exon elongation and intron retention. The analysis of all reported NCSS variants in ABCA4 allowed us to reveal the nature of aberrant splicing events and to classify the severity of these mutations based on the residual fraction of wild-type mRNA. Our strategy to generate large overlapping splice vectors carrying multiple exons, creating a toolbox for robust and high-throughput analysis of splice variants, can be applied to all human genes.
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Affiliation(s)
- Riccardo Sangermano
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Mubeen Khan
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands.,Department of Biosciences, COMSATS Institute of Information Technology, Islamabad 45550, Pakistan
| | - Stéphanie S Cornelis
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Valerie Richelle
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Silvia Albert
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Alejandro Garanto
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Duaa Elmelik
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Raheel Qamar
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad 45550, Pakistan
| | - Dorien Lugtenberg
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - L Ingeborgh van den Born
- The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands.,The Rotterdam Ophthalmic Institute, 3011 BH Rotterdam, 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
| | - 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
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57
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Thompson JA, De Roach JN, McLaren TL, Lamey TM. A Mini-Review: Leber Congenital Amaurosis: Identification of Disease-Causing Variants and Personalised Therapies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1074:265-271. [DOI: 10.1007/978-3-319-75402-4_32] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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58
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ABCA4 midigenes reveal the full splice spectrum of all reported noncanonical splice site variants in Stargardt disease. Genome Res 2017; 28:100-110. [PMID: 29162642 PMCID: PMC5749174 DOI: 10.1101/gr.226621.117] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 11/17/2017] [Indexed: 12/13/2022]
Abstract
Stargardt disease is caused by variants in the ABCA4 gene, a significant part of which are noncanonical splice site (NCSS) variants. In case a gene of interest is not expressed in available somatic cells, small genomic fragments carrying potential disease-associated variants are tested for splice abnormalities using in vitro splice assays. We recently discovered that when using small minigenes lacking the proper genomic context, in vitro results do not correlate with splice defects observed in patient cells. We therefore devised a novel strategy in which a bacterial artificial chromosome was employed to generate midigenes, splice vectors of varying lengths (up to 11.7 kb) covering almost the entire ABCA4 gene. These midigenes were used to analyze the effect of all 44 reported and three novel NCSS variants on ABCA4 pre-mRNA splicing. Intriguingly, multi-exon skipping events were observed, as well as exon elongation and intron retention. The analysis of all reported NCSS variants in ABCA4 allowed us to reveal the nature of aberrant splicing events and to classify the severity of these mutations based on the residual fraction of wild-type mRNA. Our strategy to generate large overlapping splice vectors carrying multiple exons, creating a toolbox for robust and high-throughput analysis of splice variants, can be applied to all human genes.
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59
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Huang D, Fletcher S, Wilton SD, Palmer N, McLenachan S, Mackey DA, Chen FK. Inherited Retinal Disease Therapies Targeting Precursor Messenger Ribonucleic Acid. Vision (Basel) 2017; 1:vision1030022. [PMID: 31740647 PMCID: PMC6836112 DOI: 10.3390/vision1030022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 07/24/2017] [Accepted: 08/24/2017] [Indexed: 02/07/2023] Open
Abstract
Inherited retinal diseases are an extremely diverse group of genetically and phenotypically heterogeneous conditions characterized by variable maturation of retinal development, impairment of photoreceptor cell function and gradual loss of photoreceptor cells and vision. Significant progress has been made over the last two decades in identifying the many genes implicated in inherited retinal diseases and developing novel therapies to address the underlying genetic defects. Approximately one-quarter of exonic mutations related to human inherited diseases are likely to induce aberrant splicing products, providing opportunities for the development of novel therapeutics that target splicing processes. The feasibility of antisense oligomer mediated splice intervention to treat inherited diseases has been demonstrated in vitro, in vivo and in clinical trials. In this review, we will discuss therapeutic approaches to treat inherited retinal disease, including strategies to correct splicing and modify exon selection at the level of pre-mRNA. The challenges of clinical translation of this class of emerging therapeutics will also be discussed.
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Affiliation(s)
- Di Huang
- Molecular Therapy Laboratory, Murdoch University, Murdoch 6150, Australia
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Nedlands 6009, Australia
- Perron Institute, 4th Floor A Block, Queen Elizabeth II Medical Centre, Verdun Street, Nedlands 6009, Australia
| | - Sue Fletcher
- Molecular Therapy Laboratory, Murdoch University, Murdoch 6150, Australia
- Perron Institute, 4th Floor A Block, Queen Elizabeth II Medical Centre, Verdun Street, Nedlands 6009, Australia
| | - Steve D. Wilton
- Molecular Therapy Laboratory, Murdoch University, Murdoch 6150, Australia
- Perron Institute, 4th Floor A Block, Queen Elizabeth II Medical Centre, Verdun Street, Nedlands 6009, Australia
| | - Norman Palmer
- Perron Institute, 4th Floor A Block, Queen Elizabeth II Medical Centre, Verdun Street, Nedlands 6009, Australia
| | - Samuel McLenachan
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Nedlands 6009, Australia
| | - David A. Mackey
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Nedlands 6009, Australia
| | - Fred K. Chen
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Nedlands 6009, Australia
- Department of Ophthalmology, Royal Perth Hospital, Perth 6000, Australia
- Correspondence: ; Tel.: +61-8-9381-0817
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60
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Molinari E, Sayer JA. Emerging treatments and personalised medicine for ciliopathies associated with cystic kidney disease. Expert Opin Orphan Drugs 2017. [DOI: 10.1080/21678707.2017.1372282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Elisa Molinari
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - John A. Sayer
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
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61
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Thompson JA, De Roach JN, McLaren TL, Montgomery HE, Hoffmann LH, Campbell IR, Chen FK, Mackey DA, Lamey TM. The genetic profile of Leber congenital amaurosis in an Australian cohort. Mol Genet Genomic Med 2017; 5:652-667. [PMID: 29178642 PMCID: PMC5702575 DOI: 10.1002/mgg3.321] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/27/2017] [Accepted: 06/29/2017] [Indexed: 12/21/2022] Open
Abstract
Background Leber congenital amaurosis (LCA) is a severe visual impairment responsible for infantile blindness, representing ~5% of all inherited retinal dystrophies. LCA encompasses a group of heterogeneous disorders, with 24 genes currently implicated in pathogenesis. Such clinical and genetic heterogeneity poses great challenges for treatment, with personalized therapies anticipated to be the best treatment candidates. Unraveling the individual genetic etiology of disease is a prerequisite for personalized therapies, and could identify potential treatment candidates, inform patient management, and discriminate syndromic forms of disease. Methods We have genetically analyzed 45 affected and 82 unaffected individuals from 34 unrelated LCA pedigrees using predominantly next‐generation sequencing and Array CGH technology. Results We present the molecular findings for an Australian LCA cohort, sourced from the Australian Inherited Retinal Disease Registry & DNA Bank. CEP290 and GUCY2D mutations, each represent 19% of unrelated LCA cases, followed by NMNAT1 (12%). Genetic subtypes were consistent with other reports, and were resolved in 90% of this cohort. Conclusion The high resolution rate achieved, equivalent to recent findings using whole exome/genome sequencing, reflects the progression from hypothesis (LCA Panel) to non‐hypothesis (RD Panel) testing and, coupled with Array CGH analysis, is a highly effective first‐tier test for LCA.
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Affiliation(s)
- Jennifer A Thompson
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - John N De Roach
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia.,Centre for Ophthalmology and Visual Science, The University of Western Australia, Crawley, Western Australia, Australia
| | - Terri L McLaren
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Hannah E Montgomery
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Ling H Hoffmann
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Isabella R Campbell
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Fred K Chen
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia.,Centre for Ophthalmology and Visual Science, The University of Western Australia, Crawley, Western Australia, Australia.,Lions Eye Institute, Nedlands, Western Australia, Australia.,Department of Ophthalmology, Royal Perth Hospital, Perth, Western Australia, Australia
| | - David A Mackey
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia.,Centre for Ophthalmology and Visual Science, The University of Western Australia, Crawley, Western Australia, Australia.,Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Tina M Lamey
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia.,Centre for Ophthalmology and Visual Science, The University of Western Australia, Crawley, Western Australia, Australia
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62
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Molinari E, Srivastava S, Sayer JA, Ramsbottom SA. From disease modelling to personalised therapy in patients with CEP290 mutations. F1000Res 2017; 6:669. [PMID: 28690834 PMCID: PMC5482330 DOI: 10.12688/f1000research.11553.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/10/2017] [Indexed: 01/20/2023] Open
Abstract
Mutations that give rise to premature termination codons are a common cause of inherited genetic diseases. When transcripts containing these changes are generated, they are usually rapidly removed by the cell through the process of nonsense-mediated decay. Here we discuss observed changes in transcripts of the centrosomal protein CEP290 resulting not from degradation, but from changes in exon usage. We also comment on a landmark paper (Drivas et al. Sci Transl Med. 2015) where modelling this process of exon usage may be used to predict disease severity in CEP290 ciliopathies, and how understanding this process may potentially be used for therapeutic benefit in the future.
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Affiliation(s)
- Elisa Molinari
- Institute of Genetic Medicine, Newcastle University, Newcastle, NE1 3BZ, UK
| | - Shalabh Srivastava
- Institute of Genetic Medicine, Newcastle University, Newcastle, NE1 3BZ, UK
| | - John A Sayer
- Institute of Genetic Medicine, Newcastle University, Newcastle, NE1 3BZ, UK.,Renal Services, Newcastle upon Tyne NHS Foundation Trust, Newcastle, NE7 7DN, UK
| | - Simon A Ramsbottom
- Institute of Genetic Medicine, Newcastle University, Newcastle, NE1 3BZ, UK
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63
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Applications of antisense oligonucleotides for the treatment of inherited retinal diseases. Curr Opin Ophthalmol 2017; 28:260-266. [PMID: 28151748 DOI: 10.1097/icu.0000000000000363] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
PURPOSE OF REVIEW Over the last years, antisense oligonucleotides (AONs) have gained attention as a therapeutic tool for the treatment of ocular diseases such as cytomegalovirus retinitis, keratitis-induced corneal neovascularization, and inherited retinal diseases (IRDs). In this review, we summarize the recent key findings, and describe the challenges and opportunities that lie ahead to translate AON-based therapies to the clinic, in particular for IRDs. RECENT FINDINGS The efficacy of AONs to restore splice defects and cellular phenotypes associated with a common mutation in CEP290 was demonstrated in patient-derived optic cups and in a transgenic mouse model, respectively. In addition, allele-specific knockdown of a mutant RHO allele resulted in a delay of photoreceptor cell death and functional preservation of these cells in a transgenic rat model. SUMMARY As demonstrated by several preclinical efficacy studies, AON-based therapy is moving to the clinic for the treatment of some genetic subtypes of IRD. More insights into the delivery of these molecules, the duration of the therapeutic effect, and potential off-target effects will be essential to further shape the transition to the clinic and reveal the true potential of AON-based therapy for retinal diseases.
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64
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Ruan GX, Barry E, Yu D, Lukason M, Cheng SH, Scaria A. CRISPR/Cas9-Mediated Genome Editing as a Therapeutic Approach for Leber Congenital Amaurosis 10. Mol Ther 2017; 25:331-341. [PMID: 28109959 PMCID: PMC5368591 DOI: 10.1016/j.ymthe.2016.12.006] [Citation(s) in RCA: 186] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 12/06/2016] [Accepted: 12/06/2016] [Indexed: 12/18/2022] Open
Abstract
As the most common subtype of Leber congenital amaurosis (LCA), LCA10 is a severe retinal dystrophy caused by mutations in the CEP290 gene. The most frequent mutation found in patients with LCA10 is a deep intronic mutation in CEP290 that generates a cryptic splice donor site. The large size of the CEP290 gene prevents its use in adeno-associated virus (AAV)-mediated gene augmentation therapy. Here, we show that targeted genomic deletion using the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system represents a promising therapeutic approach for the treatment of patients with LCA10 bearing the CEP290 splice mutation. We generated a cellular model of LCA10 by introducing the CEP290 splice mutation into 293FT cells and we showed that guide RNA pairs coupled with SpCas9 were highly efficient at removing the intronic splice mutation and restoring the expression of wild-type CEP290. In addition, we demonstrated that a dual AAV system could effectively delete an intronic fragment of the Cep290 gene in the mouse retina. To minimize the immune response to prolonged expression of SpCas9, we developed a self-limiting CRISPR/Cas9 system that minimizes the duration of SpCas9 expression. These results support further studies to determine the therapeutic potential of CRISPR/Cas9-based strategies for the treatment of patients with LCA10.
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Affiliation(s)
- Guo-Xiang Ruan
- Rare Diseases, Sanofi Genzyme, Framingham, MA 01701, USA.
| | | | - Dan Yu
- Rare Diseases, Sanofi Genzyme, Framingham, MA 01701, USA
| | | | - Seng H Cheng
- Rare Diseases, Sanofi Genzyme, Framingham, MA 01701, USA
| | - Abraham Scaria
- Rare Diseases, Sanofi Genzyme, Framingham, MA 01701, USA
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65
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Simple and complex retinal dystrophies are associated with profoundly different disease networks. Sci Rep 2017; 7:41835. [PMID: 28139756 PMCID: PMC5282568 DOI: 10.1038/srep41835] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 12/28/2016] [Indexed: 12/20/2022] Open
Abstract
Retinopathies are a group of monogenetic or complex retinal diseases associated with high unmet medical need. Monogenic disorders are caused by rare genetic variation and usually arise early in life. Other diseases, such as age-related macular degeneration (AMD), develop late in life and are considered to be of complex origin as they develop from a combination of genetic, ageing, environmental and lifestyle risk factors. Here, we contrast the underlying disease networks and pathological mechanisms of monogenic as opposed to complex retinopathies, using AMD as an example of the latter. We show that, surprisingly, genes associated with the different forms of retinopathies in general do not overlap despite their overlapping retinal phenotypes. Further, AMD risk genes participate in multiple networks with interaction partners that link to different ubiquitous pathways affecting general tissue integrity and homeostasis. Thus AMD most likely represents an endophenotype with differing underlying pathogenesis in different subjects. Localising these pathomechanisms and processes within and across different retinal anatomical compartments provides a novel representation of AMD that may be extended to complex disease in general. This approach may generate improved treatment options that target multiple processes with the aim of restoring tissue homeostasis and maintaining vision.
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66
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Moulay G, Leborgne C, Mason AJ, Aisenbrey C, Kichler A, Bechinger B. Histidine-rich designer peptides of the LAH4 family promote cell delivery of a multitude of cargo. J Pept Sci 2017; 23:320-328. [PMID: 28067008 DOI: 10.1002/psc.2955] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 11/23/2016] [Accepted: 11/25/2016] [Indexed: 11/09/2022]
Abstract
The histidine-rich designer peptides of the LAH4 family exhibit potent antimicrobial, transfection, transduction and cell-penetrating properties. They form non-covalent complexes with their cargo, which often carry a negative overall charge at pH 7.4 and include a large range of molecules and structures such as oligonucleotides, including siRNA and DNA, peptides, proteins, nanodots and adeno-associated viruses. These complexes are thought to enter the cells through an endosomal pathway where the acidification of the organelle is essential for efficient endosomal escape. Biophysical measurements indicate that, upon acidification, almost half the peptides are released from DNA cargo, leading to the suggestion of a self-promoted uptake mechanism where the liberated peptides lyse the endosomal membranes. LAH4 derivatives also help in cellular transduction using lentiviruses. Here, we compare the DNA transfection activities of LAH4 derivatives, which vary in overall charge and/or the composition in the hydrophobic core region. In addition, LAH4 is shown to mediate the transport of functional β-galactosidase, a large tetrameric protein of about 0.5 MDa, into the cell interior. Interestingly, the LAH1 peptide efficiently imports this protein, while it is inefficient during DNA transfection assays. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Gilles Moulay
- Genethon, 1bis rue de l'Internationale, 91002, Evry, France
| | | | - A James Mason
- Université de Strasbourg, CNRS, UMR7177, Institut de Chimie, 4, Rue Blaise Pascal, 67070, Strasbourg, France.,Institute of Pharmaceutical Science, King's College London, 150 Stamford Street, London, UK
| | - Christopher Aisenbrey
- Université de Strasbourg, CNRS, UMR7177, Institut de Chimie, 4, Rue Blaise Pascal, 67070, Strasbourg, France
| | - Antoine Kichler
- Genethon, 1bis rue de l'Internationale, 91002, Evry, France.,Faculté de Pharmacie, Laboratoire de Conception et Application de Molécules Bioactives UMR7199 CNRS - Université de Strasbourg, Labex Medalis, 67401, Illkirch, France
| | - Burkhard Bechinger
- Université de Strasbourg, CNRS, UMR7177, Institut de Chimie, 4, Rue Blaise Pascal, 67070, Strasbourg, France
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67
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Gerber S, Ding MG, Gérard X, Zwicker K, Zanlonghi X, Rio M, Serre V, Hanein S, Munnich A, Rotig A, Bianchi L, Amati-Bonneau P, Elpeleg O, Kaplan J, Brandt U, Rozet JM. Compound heterozygosity for severe and hypomorphic NDUFS2 mutations cause non-syndromic LHON-like optic neuropathy. J Med Genet 2016; 54:346-356. [PMID: 28031252 DOI: 10.1136/jmedgenet-2016-104212] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 11/29/2016] [Accepted: 12/01/2016] [Indexed: 11/03/2022]
Abstract
BACKGROUND Non-syndromic hereditary optic neuropathy (HON) has been ascribed to mutations in mitochondrial fusion/fission dynamics genes, nuclear and mitochondrial DNA-encoded respiratory enzyme genes or nuclear genes of poorly known mitochondrial function. However, the disease causing gene remains unknown in many families. The objective of the present study was to identify the molecular cause of non-syndromic LHON-like disease in siblings born to non-consanguineous parents of French origin. METHODS We used a combination of genetic analysis (gene mapping and whole-exome sequencing) in a multiplex family of non-syndromic HON and of functional analyses in patient-derived cultured skin fibroblasts and the yeast Yarrowia lipolytica. RESULTS We identified compound heterozygote NDUFS2 disease-causing mutations (p.Tyr53Cys; p.Tyr308Cys). Studies using patient-derived cultured skin fibroblasts revealed mildly decreased NDUFS2 and complex I abundance but apparently normal respiratory chain activity. In the yeast Y. lipolytica ortholog NUCM, the mutations resulted in absence of complex I and moderate reduction in nicotinamide adenine dinucleotide-ubiquinone oxidoreductase activity, respectively. CONCLUSIONS Biallelism for NDUFS2 mutations causing severe complex I deficiency has been previously reported to cause Leigh syndrome with optic neuropathy. Our results are consistent with the view that compound heterozygosity for severe and hypomorphic NDUFS2 mutations can cause non-syndromic HON. This observation suggests a direct correlation between the severity of NDUFS2 mutations and that of the disease and further support that there exist a genetic overlap between non-syndromic and syndromic HON due to defective mitochondrial function.
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Affiliation(s)
- Sylvie Gerber
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine, Paris Descartes University, Paris, France
| | - Martina G Ding
- Molecular Bioenergetics Group, Goethe-University Medical School, Frankfurt am Main, Germany
| | - Xavier Gérard
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine, Paris Descartes University, Paris, France
| | - Klaus Zwicker
- Institute of Biochemistry I, Goethe-University Medical School, Frankfurt am Main, Germany
| | | | - Marlène Rio
- Department of Genetics, Necker Hospital, Paris, France
| | - Valérie Serre
- UMR7592 CNRS, Jacques Monod Institute, Paris Diderot University, Paris, France.,Laboratory of Genetics in Mitochondrial Diseases, INSERM UMR1163, Institute of Genetic Diseases, Imagine, Paris Descartes University, Paris, France
| | - Sylvain Hanein
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine, Paris Descartes University, Paris, France
| | | | - Agnès Rotig
- Laboratory of Genetics in Mitochondrial Diseases, INSERM UMR1163, Institute of Genetic Diseases, Imagine, Paris Descartes University, Paris, France
| | - Lucas Bianchi
- Laboratory of Genetics in Mitochondrial Diseases, INSERM UMR1163, Institute of Genetic Diseases, Imagine, Paris Descartes University, Paris, France
| | - Patrizia Amati-Bonneau
- Department of Biochemistry and Genetics, UMR CNRS 6214-INSERM U1083, CHU Angers, Angers, France
| | - Orly Elpeleg
- Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Josseline Kaplan
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine, Paris Descartes University, Paris, France
| | - Ulrich Brandt
- Radboud Center for Mitochondrial Medicine (RCMM), Radboud University Medical Center, Nijmegen, The Netherlands.,Cluster of Excellence Frankfurt Macromolecular Complexes, Goethe-University, Frankfurt am Main, Germany
| | - Jean-Michel Rozet
- Laboratory of Genetics in Ophthalmology (LGO), INSERM UMR1163, Institute of Genetic Diseases, Imagine, Paris Descartes University, Paris, France
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68
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Collin RWJ. Unraveling the mysteries of pre-mRNA splicing in the retina via stem cell technology. Stem Cell Investig 2016; 3:72. [PMID: 27868054 DOI: 10.21037/sci.2016.10.05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 10/12/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Rob W J Collin
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
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69
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Bonifert T, Gonzalez Menendez I, Battke F, Theurer Y, Synofzik M, Schöls L, Wissinger B. Antisense Oligonucleotide Mediated Splice Correction of a Deep Intronic Mutation in OPA1. MOLECULAR THERAPY. NUCLEIC ACIDS 2016; 5:e390. [PMID: 27874857 PMCID: PMC5155325 DOI: 10.1038/mtna.2016.93] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/13/2016] [Indexed: 12/13/2022]
Abstract
Inherited optic neuropathies (ION) present an important cause of blindness in the European working-age population. Recently we reported the discovery of four independent families with deep intronic mutations in the main inherited optic neuropathies gene OPA1. These deep intronic mutations cause mis-splicing of the OPA1 pre-messenger-RNA transcripts by creating cryptic acceptor splice sites. As a rescue strategy we sought to prevent mis-splicing of the mutant pre-messenger-RNA by applying 2'O-methyl-antisense oligonucleotides (AONs) with a full-length phosphorothioate backbone that target the cryptic acceptor splice sites and the predicted novel branch point created by the deep intronic mutations, respectively. Transfection of patient-derived primary fibroblasts with these AONs induced correct splicing of the mutant pre-messenger-RNA in a time and concentration dependent mode of action, as detected by pyrosequencing of informative heterozygous variants. The treatment showed strong rescue effects (~55%) using the cryptic acceptor splice sites targeting AON and moderate rescue (~16%) using the branch point targeting AON. The highest efficacy of Splice correction could be observed 4 days after treatment however, significant effects were still seen 14 days post-transfection. Western blot analysis revealed increased amounts of OPA1 protein with maximum amounts at ~3 days post-treatment. In summary, we provide the first mutation-specific in vitro rescue strategy for OPA1 deficiency using synthetic AONs.
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Affiliation(s)
- Tobias Bonifert
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany.,Graduate School of Cellular and Molecular Neuroscience, University of Tübingen, Tübingen, Germany
| | - Irene Gonzalez Menendez
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany
| | | | - Yvonne Theurer
- Department of Neurodegenerative Diseases and Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Matthis Synofzik
- Department of Neurodegenerative Diseases and Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Ludger Schöls
- Department of Neurodegenerative Diseases and Hertie-Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Bernd Wissinger
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany
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70
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Antisense Oligonucleotide-based Splice Correction for USH2A-associated Retinal Degeneration Caused by a Frequent Deep-intronic Mutation. MOLECULAR THERAPY. NUCLEIC ACIDS 2016; 5:e381. [PMID: 27802265 DOI: 10.1038/mtna.2016.89] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 09/07/2016] [Indexed: 12/21/2022]
Abstract
Usher syndrome (USH) is the most common cause of combined deaf-blindness in man. The hearing loss can be partly compensated by providing patients with hearing aids or cochlear implants, but the loss of vision is currently untreatable. In general, mutations in the USH2A gene are the most frequent cause of USH explaining up to 50% of all patients worldwide. The first deep-intronic mutation in the USH2A gene (c.7595-2144A>G) was reported in 2012, leading to the insertion of a pseudoexon (PE40) into the mature USH2A transcript. When translated, this PE40-containing transcript is predicted to result in a truncated non-functional USH2A protein. In this study, we explored the potential of antisense oligonucleotides (AONs) to prevent aberrant splicing of USH2A pre-mRNA as a consequence of the c.7595-2144A>G mutation. Engineered 2'-O-methylphosphorothioate AONs targeting the PE40 splice acceptor site and/or exonic splice enhancer regions displayed significant splice correction potential in both patient derived fibroblasts and a minigene splice assay for USH2A c.7595-2144A>G, whereas a non-binding sense oligonucleotide had no effect on splicing. Altogether, AON-based splice correction could be a promising approach for the development of a future treatment for USH2A-associated retinitis pigmentosa caused by the deep-intronic c.7595-2144A>G mutation.
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71
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Li L, Khanna H. Stem cells with a view: a look inside a retinal ciliopathy. Stem Cell Investig 2016; 3:62. [PMID: 27868044 DOI: 10.21037/sci.2016.09.19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 09/23/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Linjing Li
- Department of Ophthalmology, UMASS Medical School, Worcester, MA 01605, USA
| | - Hemant Khanna
- Department of Ophthalmology, UMASS Medical School, Worcester, MA 01605, USA
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72
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Parfitt DA, Lane A, Ramsden C, Jovanovic K, Coffey PJ, Hardcastle AJ, Cheetham ME. Using induced pluripotent stem cells to understand retinal ciliopathy disease mechanisms and develop therapies. Biochem Soc Trans 2016; 44:1245-1251. [PMID: 27911706 PMCID: PMC5238943 DOI: 10.1042/bst20160156] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 07/15/2016] [Accepted: 07/19/2016] [Indexed: 12/23/2022]
Abstract
The photoreceptor cells in the retina have a highly specialised sensory cilium, the outer segment (OS), which is important for detecting light. Mutations in cilia-related genes often result in retinal degeneration. The ability to reprogramme human cells into induced pluripotent stem cells and then differentiate them into a wide range of different cell types has revolutionised our ability to study human disease. To date, however, the challenge of producing fully differentiated photoreceptors in vitro has limited the application of this technology in studying retinal degeneration. In this review, we will discuss recent advances in stem cell technology and photoreceptor differentiation. In particular, the development of photoreceptors with rudimentary OS that can be used to understand disease mechanisms and as an important model to test potential new therapies for inherited retinal ciliopathies.
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Affiliation(s)
- David A. Parfitt
- UCL Institute of Ophthalmology, 11-43 Bath Street, London, EC1V 9EL UK
| | - Amelia Lane
- UCL Institute of Ophthalmology, 11-43 Bath Street, London, EC1V 9EL UK
| | - Conor Ramsden
- UCL Institute of Ophthalmology, 11-43 Bath Street, London, EC1V 9EL UK
| | | | - Peter J. Coffey
- UCL Institute of Ophthalmology, 11-43 Bath Street, London, EC1V 9EL UK
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73
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Garanto A, Chung DC, Duijkers L, Corral-Serrano JC, Messchaert M, Xiao R, Bennett J, Vandenberghe LH, Collin RWJ. In vitro and in vivo rescue of aberrant splicing in CEP290-associated LCA by antisense oligonucleotide delivery. Hum Mol Genet 2016; 25:2552-2563. [PMID: 27106101 DOI: 10.1093/hmg/ddw118] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/08/2016] [Accepted: 04/12/2016] [Indexed: 12/29/2022] Open
Abstract
Leber congenital amaurosis (LCA) is a severe disorder resulting in visual impairment usually starting in the first year of life. The most frequent genetic cause of LCA is an intronic mutation in CEP290 (c.2991 + 1655A > G) that creates a cryptic splice donor site resulting in the insertion of a pseudoexon (exon X) into CEP290 mRNA. Previously, we showed that naked antisense oligonucleotides (AONs) effectively restored normal CEP290 splicing in patient-derived lymphoblastoid cells. We here explore the therapeutic potential of naked and adeno-associated virus (AAV)-packaged AONs in vitro and in vivo In both cases, AON delivery fully restored CEP290 pre-mRNA splicing, significantly increased CEP290 protein levels and rescued a ciliary phenotype present in patient-derived fibroblast cells. Moreover, administration of naked and AAV-packaged AONs to the retina of a humanized mutant Cep290 mouse model, carrying the intronic mutation, showed a statistically significant reduction of exon X-containing Cep290 transcripts, without compromising the retinal structure. Together, our data highlight the tremendous therapeutic prospective of AONs for the treatment of not only CEP290-associated LCA but potentially many other subtypes of retinal dystrophy caused by splicing mutations.
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Affiliation(s)
- Alejandro Garanto
- Department of Human Genetics.,Donders Center for NeurosciencesRadboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Daniel C Chung
- F.M. Kirby Center for Molecular Ophthalmology and Center for Advanced Retinal and Ophthalmic Therapeutics, Scheie Eye Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | | | - Julio C Corral-Serrano
- Department of Human Genetics.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Muriël Messchaert
- Department of Human Genetics.,Donders Center for NeurosciencesRadboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Ru Xiao
- Grousbeck Gene Therapy Center, Department of Ophthalmology, Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA
| | - Jean Bennett
- F.M. Kirby Center for Molecular Ophthalmology and Center for Advanced Retinal and Ophthalmic Therapeutics, Scheie Eye Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Luk H Vandenberghe
- Grousbeck Gene Therapy Center, Department of Ophthalmology, Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA
| | - Rob W J Collin
- Department of Human Genetics .,Donders Center for NeurosciencesRadboud University Medical Center, 6525 GA Nijmegen, The Netherlands
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74
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Antisense Oligonucleotide Therapy for Inherited Retinal Dystrophies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 854:517-24. [PMID: 26427454 DOI: 10.1007/978-3-319-17121-0_69] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Inherited retinal dystrophies (IRDs) are an extremely heterogeneous group of genetic diseases for which currently no effective treatment strategies exist. Over the last decade, significant progress has been made utilizing gene augmentation therapy for a few genetic subtypes of IRD, although several technical challenges so far prevent a broad clinical application of this approach for other forms of IRD. Many of the mutations leading to these retinal diseases affect pre-mRNA splicing of the mutated genes . Antisense oligonucleotide (AON)-mediated splice modulation appears to be a powerful approach to correct the consequences of such mutations at the pre-mRNA level , as demonstrated by promising results in clinical trials for several inherited disorders like Duchenne muscular dystrophy, hypercholesterolemia and various types of cancer. In this mini-review, we summarize ongoing pre-clinical research on AON-based therapy for a few genetic subtypes of IRD , speculate on other potential therapeutic targets, and discuss the opportunities and challenges that lie ahead to translate splice modulation therapy for retinal disorders to the clinic.
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75
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Parfitt DA, Lane A, Ramsden CM, Carr AJF, Munro PM, Jovanovic K, Schwarz N, Kanuga N, Muthiah MN, Hull S, Gallo JM, da Cruz L, Moore AT, Hardcastle AJ, Coffey PJ, Cheetham ME. Identification and Correction of Mechanisms Underlying Inherited Blindness in Human iPSC-Derived Optic Cups. Cell Stem Cell 2016; 18:769-781. [PMID: 27151457 PMCID: PMC4899423 DOI: 10.1016/j.stem.2016.03.021] [Citation(s) in RCA: 235] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 02/08/2016] [Accepted: 03/29/2016] [Indexed: 12/14/2022]
Abstract
Leber congenital amaurosis (LCA) is an inherited retinal dystrophy that causes childhood blindness. Photoreceptors are especially sensitive to an intronic mutation in the cilia-related gene CEP290, which causes missplicing and premature termination, but the basis of this sensitivity is unclear. Here, we generated differentiated photoreceptors in three-dimensional optic cups and retinal pigment epithelium (RPE) from iPSCs with this common CEP290 mutation to investigate disease mechanisms and evaluate candidate therapies. iPSCs differentiated normally into RPE and optic cups, despite abnormal CEP290 splicing and cilia defects. The highest levels of aberrant splicing and cilia defects were observed in optic cups, explaining the retinal-specific manifestation of this CEP290 mutation. Treating optic cups with an antisense morpholino effectively blocked aberrant splicing and restored expression of full-length CEP290, restoring normal cilia-based protein trafficking. These results provide a mechanistic understanding of the retina-specific phenotypes in CEP290 LCA patients and potential strategies for therapeutic intervention. Generation of 3D optic cups with opsin-expressing photoreceptors and outer segments A CEP290-LCA intronic mutation creates a cryptic exon that impairs ciliogenesis Aberrant splicing is increased in photoreceptors compared to other cell types Antisense oligonucleotide can block the cryptic exon and restore CEP290 function
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Affiliation(s)
- David A Parfitt
- Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Amelia Lane
- Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Conor M Ramsden
- Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK; Moorfields Eye Hospital, 162 City Road, London EC1V 2PD, UK
| | - Amanda-Jayne F Carr
- Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Peter M Munro
- Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Katarina Jovanovic
- Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Nele Schwarz
- Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Naheed Kanuga
- Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Manickam N Muthiah
- Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK; Moorfields Eye Hospital, 162 City Road, London EC1V 2PD, UK
| | - Sarah Hull
- Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK; Moorfields Eye Hospital, 162 City Road, London EC1V 2PD, UK
| | - Jean-Marc Gallo
- Maurice Wohl Clinical Neurosciences Institute, Institute of Psychiatry, Psychology, and Neuroscience, Kings College London, London SE5 9NU, UK
| | - Lyndon da Cruz
- Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK; Moorfields Eye Hospital, 162 City Road, London EC1V 2PD, UK
| | - Anthony T Moore
- Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK; Moorfields Eye Hospital, 162 City Road, London EC1V 2PD, UK
| | - Alison J Hardcastle
- Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Peter J Coffey
- Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Michael E Cheetham
- Ocular Biology and Therapeutics, UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK.
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76
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Intravitreal Injection of Splice-switching Oligonucleotides to Manipulate Splicing in Retinal Cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2015; 4:e250. [PMID: 26325627 PMCID: PMC4877449 DOI: 10.1038/mtna.2015.24] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 07/22/2015] [Indexed: 12/25/2022]
Abstract
Leber congenital amaurosis is a severe hereditary retinal dystrophy responsible for neonatal blindness. The most common disease-causing mutation (c.2991+1655A>G; 10-15%) creates a strong splice donor site that leads to insertion of a cryptic exon encoding a premature stop codon. Recently, we reported that splice-switching oligonucleotides (SSO) allow skipping of the mutant cryptic exon and the restoration of ciliation in fibroblasts of affected patients, supporting the feasibility of a SSO-mediated exon skipping strategy to correct the aberrant splicing. Here, we present data in the wild-type mouse, which demonstrate that intravitreal administration of 2'-OMePS-SSO allows selective alteration of Cep290 splicing in retinal cells, including photoreceptors as shown by successful alteration of Abca4 splicing using the same approach. We show that both SSOs and Cep290 skipped mRNA were detectable for at least 1 month and that intravitreal administration of oligonucleotides did not provoke any serious adverse event. These data suggest that intravitreal injections of SSO should be considered to bypass protein truncation resulting from the c.2991+1655A>G mutation as well as other truncating mutations in genes which like CEP290 or ABCA4 have a mRNA size that exceed cargo capacities of US Food and Drug Administration (FDA)-approved adeno-associated virus (AAV)-vectors, thus hampering gene augmentation therapy.
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Perrault I, Halbritter J, Porath JD, Gérard X, Braun DA, Gee HY, Fathy HM, Saunier S, Cormier-Daire V, Thomas S, Attié-Bitach T, Boddaert N, Taschner M, Schueler M, Lorentzen E, Lifton RP, Lawson JA, Garfa-Traore M, Otto EA, Bastin P, Caillaud C, Kaplan J, Rozet JM, Hildebrandt F. IFT81, encoding an IFT-B core protein, as a very rare cause of a ciliopathy phenotype. J Med Genet 2015; 52:657-65. [PMID: 26275418 PMCID: PMC4621372 DOI: 10.1136/jmedgenet-2014-102838] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 06/15/2015] [Indexed: 11/06/2022]
Abstract
Background Bidirectional intraflagellar transport (IFT) consists of two major protein complexes, IFT-A and IFT-B. In contrast to the IFT-B complex, all components of IFT-A have recently been linked to human ciliopathies when defective. We therefore hypothesised that mutations in additional IFT-B encoding genes can be found in patients with multisystemic ciliopathies. Methods We screened 1628 individuals with reno-ocular ciliopathies by targeted next-generation sequencing of ciliary candidate genes, including all IFT-B encoding genes. Results Consequently, we identified a homozygous mutation in IFT81 affecting an obligatory donor splice site in an individual with nephronophthisis and polydactyly. Further, we detected a loss-of-stop mutation with extension of the deduced protein by 10 amino acids in an individual with neuronal ceroid lipofuscinosis-1. This proband presented with retinal dystrophy and brain lesions including cerebellar atrophy, a phenotype to which the IFT81 variant might contribute. Cultured fibroblasts of this latter affected individual showed a significant decrease in ciliated cell abundance compared with controls and increased expression of the transcription factor GLI2 suggesting deranged sonic hedgehog signalling. Conclusions This work describes identification of mutations of IFT81 in individuals with symptoms consistent with the clinical spectrum of ciliopathies. It might represent the rare case of a core IFT-B complex protein found associated with human disease. Our data further suggest that defects in the IFT-B core are an exceedingly rare finding, probably due to its indispensable role for ciliary assembly in development.
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Affiliation(s)
- Isabelle Perrault
- Laboratory of Genetics in Ophthalmology, INSERM UMR 1163, Paris, France Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Jan Halbritter
- Division of Endocrinology and Nephrology, Department of Internal Medicine, University Clinic Leipzig, Leipzig, Germany Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan D Porath
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Xavier Gérard
- Laboratory of Genetics in Ophthalmology, INSERM UMR 1163, Paris, France Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Daniela A Braun
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Heon Yung Gee
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Hanan M Fathy
- Pediatric Nephrology Unit, University of Alexandria, Alexandria, Egypt
| | - Sophie Saunier
- Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France INSERM UMR 1163, Molecular bases of hereditary kidney diseases, Nephronophthisis and Hypodysplasia, Paris, France
| | - Valérie Cormier-Daire
- Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France INSERM UMR 1163, Molecular and Physiopathological bases of osteochondrodysplasia, Paris, France
| | - Sophie Thomas
- Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France INSERM UMR 1163, Embryology and genetics of human malformation, Paris, France
| | - Tania Attié-Bitach
- Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France INSERM UMR 1163, Embryology and genetics of human malformation, Paris, France
| | - Nathalie Boddaert
- Department of Pediatric Radiology, Hôpital Necker-Enfants Malades, APHP, Descartes University, Paris, France
| | - Michael Taschner
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Markus Schueler
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Esben Lorentzen
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Richard P Lifton
- Department of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, USA
| | - Jennifer A Lawson
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Meriem Garfa-Traore
- Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France INSERM UMR 1163, Cell imaging platform, Paris, France
| | - Edgar A Otto
- Departments of Pediatrics, University of Michigan, Ann Arbor, USA
| | - Philippe Bastin
- Trypanosome Cell Biology Unit, Institut Pasteur and CNRS, URA 2581, Paris, France
| | | | - Josseline Kaplan
- Laboratory of Genetics in Ophthalmology, INSERM UMR 1163, Paris, France Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Jean-Michel Rozet
- Laboratory of Genetics in Ophthalmology, INSERM UMR 1163, Paris, France Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Friedhelm Hildebrandt
- Division of Nephrology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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Maria M, Ajmal M, Azam M, Waheed NK, Siddiqui SN, Mustafa B, Ayub H, Ali L, Ahmad S, Micheal S, Hussain A, Shah STA, Ali SHB, Ahmed W, Khan YM, den Hollander AI, Haer-Wigman L, Collin RWJ, Khan MI, Qamar R, Cremers FPM. Homozygosity mapping and targeted sanger sequencing reveal genetic defects underlying inherited retinal disease in families from pakistan. PLoS One 2015; 10:e0119806. [PMID: 25775262 PMCID: PMC4361598 DOI: 10.1371/journal.pone.0119806] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 01/13/2015] [Indexed: 11/18/2022] Open
Abstract
Background Homozygosity mapping has facilitated the identification of the genetic causes underlying inherited diseases, particularly in consanguineous families with multiple affected individuals. This knowledge has also resulted in a mutation dataset that can be used in a cost and time effective manner to screen frequent population-specific genetic variations associated with diseases such as inherited retinal disease (IRD). Methods We genetically screened 13 families from a cohort of 81 Pakistani IRD families diagnosed with Leber congenital amaurosis (LCA), retinitis pigmentosa (RP), congenital stationary night blindness (CSNB), or cone dystrophy (CD). We employed genome-wide single nucleotide polymorphism (SNP) array analysis to identify homozygous regions shared by affected individuals and performed Sanger sequencing of IRD-associated genes located in the sizeable homozygous regions. In addition, based on population specific mutation data we performed targeted Sanger sequencing (TSS) of frequent variants in AIPL1, CEP290, CRB1, GUCY2D, LCA5, RPGRIP1 and TULP1, in probands from 28 LCA families. Results Homozygosity mapping and Sanger sequencing of IRD-associated genes revealed the underlying mutations in 10 families. TSS revealed causative variants in three families. In these 13 families four novel mutations were identified in CNGA1, CNGB1, GUCY2D, and RPGRIP1. Conclusions Homozygosity mapping and TSS revealed the underlying genetic cause in 13 IRD families, which is useful for genetic counseling as well as therapeutic interventions that are likely to become available in the near future.
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Affiliation(s)
- Maleeha Maria
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Muhammad Ajmal
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Maleeha Azam
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nadia Khalida Waheed
- Tufts University Medical School, Boston, Massachusetts, United States of America
| | | | - Bilal Mustafa
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
| | - Humaira Ayub
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
| | - Liaqat Ali
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
| | - Shakeel Ahmad
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
| | - Shazia Micheal
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Alamdar Hussain
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
| | - Syed Tahir Abbas Shah
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
| | - Syeda Hafiza Benish Ali
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
- Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan, Pakistan
| | - Waqas Ahmed
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
- University of Haripur, Haripur, Pakistan
| | - Yar Muhammad Khan
- Department of Chemistry, University of Science and Technology, Bannu, Pakistan
| | - Anneke I. den Hollander
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Rob W. J. Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Muhammad Imran Khan
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Raheel Qamar
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
- Al-Nafees Medical College & Hospital, Isra University, Islamabad, Pakistan
| | - Frans P. M. Cremers
- Department of Biosciences, Commission on Science and Technology for Sustainable Development in the South Institute of Information Technology, Islamabad, Pakistan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
- * E-mail:
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Species-dependent splice recognition of a cryptic exon resulting from a recurrent intronic CEP290 mutation that causes congenital blindness. Int J Mol Sci 2015; 16:5285-98. [PMID: 25761237 PMCID: PMC4394476 DOI: 10.3390/ijms16035285] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 02/03/2015] [Accepted: 02/15/2015] [Indexed: 11/17/2022] Open
Abstract
A mutation in intron 26 of CEP290 (c.2991+1655A>G) is the most common genetic cause of Leber congenital amaurosis (LCA), a severe type of inherited retinal degeneration. This mutation creates a cryptic splice donor site, resulting in the insertion of an aberrant exon (exon X) into ~50% of all CEP290 transcripts. A humanized mouse model with this mutation did not recapitulate the aberrant CEP290 splicing observed in LCA patients, suggesting differential recognition of cryptic splice sites between species. To further assess this phenomenon, we generated two CEP290 minigene constructs, with and without the intronic mutation, and transfected these in cell lines of various species. RT-PCR analysis revealed that exon X is well recognized by the splicing machinery in human and non-human primate cell lines. Intriguingly, this recognition decreases in cell lines derived from species such as dog and rodents, and it is completely absent in Drosophila. In addition, other cryptic splicing events corresponding to sequences in intron 26 of CEP290 were observed to varying degrees in the different cell lines. Together, these results highlight the complexity of splice site recognition among different species, and show that care is warranted when generating animal models to mimic splice site mutations in vivo.
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Localizing the RPGR protein along the cilium: a new method to determine efficacies to treat RPGR mutations. Gene Ther 2015; 22:413-20. [PMID: 25630948 DOI: 10.1038/gt.2014.128] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Revised: 12/16/2014] [Accepted: 12/19/2014] [Indexed: 01/18/2023]
Abstract
Retinal dystrophies constitute a group of clinically and genetically heterogeneous diseases that cause visual impairment. As treatments are not readily available, readout assays performed in patient-derived cells can aid in the development and comparative analysis of therapeutic approaches. We describe a new method with which the localization of the retinitis pigmentosa GTPase regulator (RPGR) protein along the cilium can be used as a measure for treatment efficacy. In a patient-derived fibroblast cell line, we found that the RPGR protein is mislocalized along the ciliary axoneme. The patient carried a point mutation that leads to skipping of RPGR exon 10. We confirmed that this skipping is causative for the impaired localization of RPGR using a U7 small nuclear RNA (U7snRNA)-based antisense approach in control cells. Treatment of the patient-derived fibroblasts with therapeutic U1snRNA significantly corrected the proteins' mislocalization. In this proof of principle study, we show that detecting the RPGR protein along the cilium provides a reliable and quantifiable readout assay to evaluate the efficacy of therapies intended to correct or silence RPGR gene mutations. This method opens the possibility to compare different therapeutic agents, and thus facilitate the identification of treatment options for the clinically and molecularly complex RPGR-associated diseases.
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Metodiev MD, Gerber S, Hubert L, Delahodde A, Chretien D, Gérard X, Amati-Bonneau P, Giacomotto MC, Boddaert N, Kaminska A, Desguerre I, Amiel J, Rio M, Kaplan J, Munnich A, Rötig A, Rozet JM, Besmond C. Mutations in the tricarboxylic acid cycle enzyme, aconitase 2, cause either isolated or syndromic optic neuropathy with encephalopathy and cerebellar atrophy. J Med Genet 2014; 51:834-8. [DOI: 10.1136/jmedgenet-2014-102532] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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The ciliopathies and their relationship with ophthalmology. ACTA ACUST UNITED AC 2014; 88:165-7. [PMID: 23623015 DOI: 10.1016/j.oftal.2013.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 04/09/2013] [Indexed: 11/24/2022]
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Veltrop M, Aartsma-Rus A. Antisense-mediated exon skipping: taking advantage of a trick from Mother Nature to treat rare genetic diseases. Exp Cell Res 2014; 325:50-5. [PMID: 24486759 DOI: 10.1016/j.yexcr.2014.01.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 01/20/2014] [Accepted: 01/22/2014] [Indexed: 01/16/2023]
Abstract
Rare diseases can be caused by genetic mutations that disrupt normal pre-mRNA splicing. Antisense oligonucleotide treatment to the splicing thus has therapeutic potential for many rare diseases. In this review we will focus on the state of the art on exon skipping using antisense oligonucleotides as a potential therapy for rare genetic diseases, outlining how this versatile approach can be exploited to correct for different mutations.
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Affiliation(s)
- Marcel Veltrop
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands.
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Garanto A, van Beersum SEC, Peters TA, Roepman R, Cremers FPM, Collin RWJ. Unexpected CEP290 mRNA splicing in a humanized knock-in mouse model for Leber congenital amaurosis. PLoS One 2013; 8:e79369. [PMID: 24223178 PMCID: PMC3819269 DOI: 10.1371/journal.pone.0079369] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 09/27/2013] [Indexed: 01/29/2023] Open
Abstract
Leber congenital amaurosis (LCA) is the most severe form of retinal dystrophy with an onset in the first year of life. The most frequent genetic cause of LCA, accounting for up to 15% of all LCA cases in Europe and North-America, is a mutation (c.2991+1655AG) in intron 26 of CEP290. This mutation generates a cryptic splice donor site resulting in the insertion of an aberrant exon (exon X) containing a premature stop codon to CEP290 mRNA. In order to study the pathophysiology of the intronic CEP290 mutation, we generated two humanized knock-in mouse models each carrying ~6.3 kb of the human CEP290 gene, either with or without the intronic mutation. Transcriptional characterization of these mouse models revealed an unexpected splice pattern of CEP290 mRNA, especially in the retina. In both models, a new cryptic exon (coined exon Y) was identified in ~5 to 12% of all Cep290 transcripts. This exon Y was expressed in all murine tissues analyzed but not detected in human retina or fibroblasts of LCA patients. In addition, exon x that is characteristic of LCA in humans, was expressed at only very low levels in the retina of the LCA mouse model. Western blot and immunohistochemical analyses did not reveal any differences between the two transgenic models and wild-type mice. Together, our results show clear differences in the recognition of splice sites between mice and humans, and emphasize that care is warranted when generating animal models for human genetic diseases caused by splice mutations.
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Affiliation(s)
- Alejandro Garanto
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
- Institute for Genetic and Metabolic Disease, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Sylvia E. C. van Beersum
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
- Institute for Genetic and Metabolic Disease, Radboud University Medical Centre, Nijmegen, The Netherlands
- Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Theo A. Peters
- Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
- Department of Otorhinolaryngology, Head and Neck Surgery, Radboud University Medical Centre, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Ronald Roepman
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
- Institute for Genetic and Metabolic Disease, Radboud University Medical Centre, Nijmegen, The Netherlands
- Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
- Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Rob W. J. Collin
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
- Institute for Genetic and Metabolic Disease, Radboud University Medical Centre, Nijmegen, The Netherlands
- Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
- * E-mail:
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Manipulating the pH response of 2,3-diaminopropionic acid rich peptides to mediate highly effective gene silencing with low-toxicity. J Control Release 2013; 172:929-38. [PMID: 24144917 PMCID: PMC3858832 DOI: 10.1016/j.jconrel.2013.09.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 09/06/2013] [Accepted: 09/16/2013] [Indexed: 12/27/2022]
Abstract
Cationic amphipathic pH responsive peptides possess high in vitro and in vivo nucleic acid delivery capabilities and function by forming a non-covalent complex with cargo, protecting it from nucleases, facilitating uptake via endocytosis and responding to endosomal acidification by being released from the complex and inserting into and disordering endosomal membranes. We have designed and synthesised peptides to show how Coulombic interactions between ionizable 2,3-diaminopropionic acid (Dap) side chains can be manipulated to tune the functional pH response of the peptides to afford optimal nucleic acid transfer and have modified the hydrogen bonding capabilities of the Dap side chains in order to reduce cytotoxicity. When compared with benchmark delivery compounds, the peptides are shown to have low toxicity and are highly effective at mediating gene silencing in adherent MCF-7 and A549 cell lines, primary human umbilical vein endothelial cells and both differentiated macrophage-like and suspension monocyte-like THP-1 cells.
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87
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Liang W, Kwok PCL, Chow MYT, Tang P, Mason AJ, Chan HK, Lam JKW. Formulation of pH responsive peptides as inhalable dry powders for pulmonary delivery of nucleic acids. Eur J Pharm Biopharm 2013; 86:64-73. [PMID: 23702276 DOI: 10.1016/j.ejpb.2013.05.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Revised: 05/04/2013] [Accepted: 05/06/2013] [Indexed: 12/22/2022]
Abstract
Nucleic acids have the potential to be used as therapies or vaccines for many different types of disease, but delivery remains the most significant challenge to their clinical adoption. pH responsive peptides containing either histidine or derivatives of 2,3-diaminopropionic acid (Dap) can mediate effective DNA transfection in lung epithelial cells with the latter remaining effective even in the presence of lung surfactant containing bronchoalveolar lavage fluid (BALF), making this class of peptides attractive candidates for delivering nucleic acids to lung tissues. To further assess the suitability of pH responsive peptides for pulmonary delivery by inhalation, dry powder formulations of pH responsive peptides and plasmid DNA, with mannitol as carrier, were produced by either spray drying (SD) or spray freeze drying (SFD). The properties of the two types of powders were characterised and compared using scanning electron microscopy (SEM), next generation impactor (NGI), gel retardation and in vitro transfection via a twin stage impinger (TSI) following aerosolisation by a dry powder inhaler (Osmohaler™). Although the aerodynamic performance and transfection efficacy of both powders were good, the overall performance revealed SD powders to have a number of advantages over SFD powders and are the more effective formulation with potential for efficient nucleic acid delivery through inhalation.
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Affiliation(s)
- Wanling Liang
- Department of Pharmacology & Pharmacy, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Philip C L Kwok
- Department of Pharmacology & Pharmacy, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region; Faculty of Pharmacy, The University of Sydney, Australia
| | - Michael Y T Chow
- Department of Pharmacology & Pharmacy, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Patricia Tang
- Faculty of Pharmacy, The University of Sydney, Australia
| | - A James Mason
- Institute of Pharmaceutical Science, King's College London, United Kingdom
| | - Hak-Kim Chan
- Faculty of Pharmacy, The University of Sydney, Australia
| | - Jenny K W Lam
- Department of Pharmacology & Pharmacy, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region.
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