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McClements ME, Elsayed MEAA, Major L, de la Camara CMF, MacLaren RE. Gene Therapies in Clinical Development to Treat Retinal Disorders. Mol Diagn Ther 2024:10.1007/s40291-024-00722-0. [PMID: 38955952 DOI: 10.1007/s40291-024-00722-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2024] [Indexed: 07/04/2024]
Abstract
Gene therapies have emerged as promising treatments in clinical development for various retinal disorders, offering hope to patients with inherited degenerative eye conditions. Several gene therapies have already shown remarkable success in clinical trials, with significant improvements observed in visual acuity and the preservation of retinal function. A multitude of gene therapies have now been delivered safely in human clinical trials for a wide range of inherited retinal disorders but there are some gaps in the reported trial data. Some of the most exciting treatment options are not under peer review and information is only available in press release form. Whilst many trials appear to have delivered good outcomes of safety, others have failed to meet primary endpoints and therefore not proceeded to phase III. Despite this, such trials have enabled researchers to learn how best to assess and monitor patient outcomes, which will guide future trials to greater success. In this review, we consider recent and ongoing clinical trials for a variety of potential retinal gene therapy treatments and discuss the positive and negative issues related to these trials. We discuss the treatment potential following clinical trials as well as the potential risks of some treatments under investigation. As these therapies continue to advance through rigorous testing and regulatory approval processes, they hold the potential to revolutionise the landscape of retinal disorder treatments, providing renewed vision and enhancing the quality of life for countless individuals worldwide.
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Affiliation(s)
- Michelle E McClements
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Wellington Square, Oxford, OX1 2JD, UK.
- Oxford University Hospital NIHR Biomedical Research Centre, Oxford, UK.
| | - Maram E A Abdalla Elsayed
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Wellington Square, Oxford, OX1 2JD, UK
- Oxford University Hospital NIHR Biomedical Research Centre, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Lauren Major
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Wellington Square, Oxford, OX1 2JD, UK
- Oxford University Hospital NIHR Biomedical Research Centre, Oxford, UK
| | - Cristina Martinez-Fernandez de la Camara
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Wellington Square, Oxford, OX1 2JD, UK
- Oxford University Hospital NIHR Biomedical Research Centre, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Robert E MacLaren
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Wellington Square, Oxford, OX1 2JD, UK
- Oxford University Hospital NIHR Biomedical Research Centre, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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Lin S, Vermeirsch S, Pontikos N, Martin-Gutierrez MP, Daich Varela M, Malka S, Schiff E, Knight H, Wright G, Jurkute N, Simcoe MJ, Yu-Wai-Man P, Moosajee M, Michaelides M, Mahroo OA, Webster AR, Arno G. Spectrum of Genetic Variants in the Most Common Genes Causing Inherited Retinal Disease in a Large Molecularly Characterized United Kingdom Cohort. Ophthalmol Retina 2024; 8:699-709. [PMID: 38219857 DOI: 10.1016/j.oret.2024.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/12/2023] [Accepted: 01/08/2024] [Indexed: 01/16/2024]
Abstract
PURPOSE Inherited retinal disease (IRD) is a leading cause of blindness. Recent advances in gene-directed therapies highlight the importance of understanding the genetic basis of these disorders. This study details the molecular spectrum in a large United Kingdom (UK) IRD patient cohort. DESIGN Retrospective study of electronic patient records. PARTICIPANTS Patients with IRD who attended the Genetics Service at Moorfields Eye Hospital between 2003 and July 2020, in whom a molecular diagnosis was identified. METHODS Genetic testing was undertaken via a combination of single-gene testing, gene panel testing, whole exome sequencing, and more recently, whole genome sequencing. Likely disease-causing variants were identified from entries within the genetics module of the hospital electronic patient record (OpenEyes Electronic Medical Record). Analysis was restricted to only genes listed in the Genomics England PanelApp R32 Retinal Disorders panel (version 3.24), which includes 412 genes associated with IRD. Manual curation ensured consistent variant annotation and included only plausible disease-associated variants. MAIN OUTCOME MEASURES Detailed analysis was performed for variants in the 5 most frequent genes (ABCA4, USH2A, RPGR, PRPH2, and BEST1), as well as for the most common variants encountered in the IRD study cohort. RESULTS We identified 4415 individuals from 3953 families with molecularly diagnosed IRD (variants in 166 genes). Of the families, 42.7% had variants in 1 of the 5 most common IRD genes. Complex disease alleles contributed to disease in 16.9% of affected families with ABCA4-associated retinopathy. USH2A exon 13 variants were identified in 43% of affected individuals with USH2A-associated IRD. Of the RPGR variants, 71% were clustered in the ORF15 region. PRPH2 and BEST1 variants were associated with a range of dominant and recessive IRD phenotypes. Of the 20 most prevalent variants identified, 5 were not in the most common genes; these included founder variants in CNGB3, BBS1, TIMP3, EFEMP1, and RP1. CONCLUSIONS We describe the most common pathogenic IRD alleles in a large single-center multiethnic UK cohort and the burden of disease, in terms of families affected, attributable to these variants. Our findings will inform IRD diagnoses in future patients and help delineate the cohort of patients eligible for gene-directed therapies under development. FINANCIAL DISCLOSURE(S) Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
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Affiliation(s)
- Siying Lin
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Sandra Vermeirsch
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom
| | - Nikolas Pontikos
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Maria Pilar Martin-Gutierrez
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom
| | - Malena Daich Varela
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Samantha Malka
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Elena Schiff
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Hannah Knight
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Genevieve Wright
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Neringa Jurkute
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom; Department of Neuro-Ophhalmology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Mark J Simcoe
- UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Patrick Yu-Wai-Man
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Mariya Moosajee
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Michel Michaelides
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Omar A Mahroo
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom; Department of Ophthalmology, St Thomas' Hospital, London, United Kingdom
| | - Andrew R Webster
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Gavin Arno
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom.
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Lin YW, Huang YS, Lin CY, Lin CW, Wu CC, Yang CH, Yang CM, Chen PL, Chen TC. High prevalence of exon-13 variants in USH2A-related retinal dystrophies in Taiwanese population. Orphanet J Rare Dis 2024; 19:238. [PMID: 38879497 PMCID: PMC11179209 DOI: 10.1186/s13023-024-03238-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 06/04/2024] [Indexed: 06/19/2024] Open
Abstract
BACKGROUND Biallelic pathogenic variants in USH2A lead to Usher syndrome or non-syndromic retinitis pigmentosa, and shown to have geographical and ethnical distribution in previous studies. This study provided a deeper understanding of the detailed clinical features using multimodal imaging, genetic spectrum, and genotype-phenotype correlations of USH2A-related retinal dystrophies in Taiwan. RESULTS In our cohort, the mean age at first visit was 47.66 ± 13.54 years, and the mean age at symptom onset, which was referred to the onset of nyctalopia and/or visual field constriction, was 31.21 ± 15.24 years. Among the variants identified, 23 (50%) were missense, 10 (22%) were splicing variants, 8 (17%) were nonsense, and 5 (11%) were frameshift mutations. The most predominant variant was c.2802T>G, which accounted for 21% of patients, and was located in exon 13. Patients with truncated alleles had significantly earlier symptom onset and seemly poorer disease progression regarding visual acuity, ellipsoid zone line length, and hypofluorescent lesions in the macula than those who had the complete gene. However, the clinical presentation revealed similar progression between patients with and without the c.2802T>G variant. During long-term follow-up, the patients had different ellipsoid zone line progression rates and were almost evenly distributed in the fast, moderate, and slow progression subgroups. Although a younger onset age and a smaller baseline intact macular area was observed in the fast progression subgroup, the results showed no significant difference. CONCLUSIONS This is the first cohort study to provide detailed genetic and longitudinal clinical analyses of patients with USH2A-related retinal dystrophies in Taiwan. The mutated allele frequency in exon 13 was high in Taiwan due to the predominant c.2802T>G variant. Moreover, truncated variants greatly impacted disease progression and determined the length of therapeutic windows. These findings provide insight into the characteristics of candidates for future gene therapies.
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Affiliation(s)
- Yu-Wei Lin
- Department of Medical Education, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Shu Huang
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Ophthalmology, National Taiwan University Hospital, No 7, Chung-Shan S. Rd, Taipei, Taiwan
| | - Chien-Yu Lin
- Department of Ophthalmology, National Taiwan University Hospital, No 7, Chung-Shan S. Rd, Taipei, Taiwan
| | - Chao-Wen Lin
- Department of Ophthalmology, National Taiwan University Hospital, No 7, Chung-Shan S. Rd, Taipei, Taiwan
| | - Chen-Chi Wu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chang-Hao Yang
- Department of Ophthalmology, National Taiwan University Hospital, No 7, Chung-Shan S. Rd, Taipei, Taiwan
| | - Chung-May Yang
- Department of Ophthalmology, National Taiwan University Hospital, No 7, Chung-Shan S. Rd, Taipei, Taiwan
| | - Pei-Lung Chen
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.
- Graduate Institute of Medical Genomics and Proteomics, Medical College, National Taiwan University, No. 2, Xuzhou Road, 5F., Taipei, Taiwan.
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.
| | - Ta-Ching Chen
- Department of Ophthalmology, National Taiwan University Hospital, No 7, Chung-Shan S. Rd, Taipei, Taiwan.
- Center of Frontier Medicine, National Taiwan University Hospital, Taipei, Taiwan.
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Zhang Y, Gao Z, Yang X, Xu Q, Lu Y. Leveraging high-throughput screening technologies in targeted mRNA delivery. Mater Today Bio 2024; 26:101101. [PMID: 38883419 PMCID: PMC11176929 DOI: 10.1016/j.mtbio.2024.101101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/06/2024] [Accepted: 05/25/2024] [Indexed: 06/18/2024] Open
Abstract
Messenger ribonucleic acid (mRNA) has emerged as a promising molecular preventive and therapeutic approach that opens new avenues for healthcare. Although the use of delivery systems, especially lipid nanoparticles (LNPs), greatly improves the efficiency and stability of mRNA, mRNA tends to accumulate in the liver and hardly penetrates physiological barriers to reach the target site after intravenous injection. Hence, the rational design of targeting strategies aimed at directing mRNA to specific tissues and cells remains an enormous challenge in mRNA therapy. High-throughput screening (HTS) is a cutting-edge targeted technique capable of synthesizing chemical compound libraries for the large-scale experiments to validate the efficiency of mRNA delivery system. In this review, we firstly provide an overview of conventional low-throughput targeting strategies. Then the latest advancements in HTS techniques for mRNA targeted delivery, encompassing optimizing structures of large-scale delivery vehicles and developing large-scale surface ligands, as well as the applications of HTS techniques in extrahepatic systemic diseases are comprehensively summarized. Moreover, we illustrate the selection of administration routes for targeted mRNA delivery. Finally, challenges in the field and potential solutions to tackle them are proposed, offering insights for future development toward mRNA targeted therapy.
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Affiliation(s)
- Yuchen Zhang
- The Second School of Clinical Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China
| | - Zhifei Gao
- The Second School of Clinical Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China
| | - Xiao Yang
- The Second School of Clinical Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China
| | - Qinglong Xu
- The Second School of Clinical Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China
| | - Yao Lu
- Department of Joint and Orthopedics, Orthopedic Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China
- Clinical Research Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China
- The Second School of Clinical Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, 510282, China
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Ashworth KE, Weisbrod J, Ballios BG. Inherited Retinal Diseases and Retinal Organoids as Preclinical Cell Models for Inherited Retinal Disease Research. Genes (Basel) 2024; 15:705. [PMID: 38927641 PMCID: PMC11203130 DOI: 10.3390/genes15060705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/15/2024] [Accepted: 05/17/2024] [Indexed: 06/28/2024] Open
Abstract
Inherited retinal diseases (IRDs) are a large group of genetically and clinically diverse blinding eye conditions that result in progressive and irreversible photoreceptor degeneration and vision loss. To date, no cures have been found, although strides toward treatments for specific IRDs have been made in recent years. To accelerate treatment discovery, retinal organoids provide an ideal human IRD model. This review aims to give background on the development and importance of retinal organoids for the human-based in vitro study of the retina and human retinogenesis and retinal pathologies. From there, we explore retinal pathologies in the context of IRDs and the current landscape of IRD treatment discovery. We discuss the usefulness of retinal organoids in this context (as a patient-derived cell model for IRDs) to precisely understand the pathogenesis and potential mechanisms behind a specific IRD-causing variant of interest. Finally, we discuss the importance and promise of retinal organoids in treatment discovery for IRDs, now and in the future.
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Affiliation(s)
- Kristen E. Ashworth
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 3H2, Canada;
- Donald K. Johnson Eye Institute, Toronto Western Hospital, Toronto, ON M5T 2S8, Canada;
| | - Jessica Weisbrod
- Donald K. Johnson Eye Institute, Toronto Western Hospital, Toronto, ON M5T 2S8, Canada;
| | - Brian G. Ballios
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 3H2, Canada;
- Donald K. Johnson Eye Institute, Toronto Western Hospital, Toronto, ON M5T 2S8, Canada;
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON M5T 3A9, Canada
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6
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Kurzawa-Akanbi M, Tzoumas N, Corral-Serrano JC, Guarascio R, Steel DH, Cheetham ME, Armstrong L, Lako M. Pluripotent stem cell-derived models of retinal disease: Elucidating pathogenesis, evaluating novel treatments, and estimating toxicity. Prog Retin Eye Res 2024; 100:101248. [PMID: 38369182 DOI: 10.1016/j.preteyeres.2024.101248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 02/20/2024]
Abstract
Blindness poses a growing global challenge, with approximately 26% of cases attributed to degenerative retinal diseases. While gene therapy, optogenetic tools, photosensitive switches, and retinal prostheses offer hope for vision restoration, these high-cost therapies will benefit few patients. Understanding retinal diseases is therefore key to advance effective treatments, requiring in vitro models replicating pathology and allowing quantitative assessments for drug discovery. Pluripotent stem cells (PSCs) provide a unique solution given their limitless supply and ability to differentiate into light-responsive retinal tissues encompassing all cell types. This review focuses on the history and current state of photoreceptor and retinal pigment epithelium (RPE) cell generation from PSCs. We explore the applications of this technology in disease modelling, experimental therapy testing, biomarker identification, and toxicity studies. We consider challenges in scalability, standardisation, and reproducibility, and stress the importance of incorporating vasculature and immune cells into retinal organoids. We advocate for high-throughput automation in data acquisition and analyses and underscore the value of advanced micro-physiological systems that fully capture the interactions between the neural retina, RPE, and choriocapillaris.
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7
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Kandoi S, Martinez C, Chen KX, Mehine M, Reddy LVK, Mansfield BC, Duncan JL, Lamba DA. Disease modeling and pharmacological rescue of autosomal dominant retinitis pigmentosa associated with RHO copy number variation. eLife 2024; 12:RP90575. [PMID: 38661530 PMCID: PMC11045220 DOI: 10.7554/elife.90575] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024] Open
Abstract
Retinitis pigmentosa (RP), a heterogenous group of inherited retinal disorder, causes slow progressive vision loss with no effective treatments available. Mutations in the rhodopsin gene (RHO) account for ~25% cases of autosomal dominant RP (adRP). In this study, we describe the disease characteristics of the first-ever reported mono-allelic copy number variation (CNV) in RHO as a novel cause of adRP. We (a) show advanced retinal degeneration in a male patient (68 years of age) harboring four transcriptionally active intact copies of rhodopsin, (b) recapitulated the clinical phenotypes using retinal organoids, and (c) assessed the utilization of a small molecule, Photoregulin3 (PR3), as a clinically viable strategy to target and modify disease progression in RP patients associated with RHO-CNV. Patient retinal organoids showed photoreceptors dysgenesis, with rod photoreceptors displaying stunted outer segments with occasional elongated cilia-like projections (microscopy); increased RHO mRNA expression (quantitative real-time PCR [qRT-PCR] and bulk RNA sequencing); and elevated levels and mislocalization of rhodopsin protein (RHO) within the cell body of rod photoreceptors (western blotting and immunohistochemistry) over the extended (300 days) culture time period when compared against control organoids. Lastly, we utilized PR3 to target NR2E3, an upstream regulator of RHO, to alter RHO expression and observed a partial rescue of RHO protein localization from the cell body to the inner/outer segments of rod photoreceptors in patient organoids. These results provide a proof-of-principle for personalized medicine and suggest that RHO expression requires precise control. Taken together, this study supports the clinical data indicating that RHO-CNV associated adRPdevelops as a result of protein overexpression, thereby overloading the photoreceptor post-translational modification machinery.
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Affiliation(s)
- Sangeetha Kandoi
- Department of Ophthalmology, University of California, San FranciscoSan FranciscoUnited States
- Eli and Edythe Broad Center of Regeneration Medicine & Stem Cell Research University of California, San FranciscoSan FranciscoUnited States
| | - Cassandra Martinez
- Department of Ophthalmology, University of California, San FranciscoSan FranciscoUnited States
- Eli and Edythe Broad Center of Regeneration Medicine & Stem Cell Research University of California, San FranciscoSan FranciscoUnited States
| | - Kevin Xu Chen
- Eli and Edythe Broad Center of Regeneration Medicine & Stem Cell Research University of California, San FranciscoSan FranciscoUnited States
| | | | - L Vinod K Reddy
- Department of Ophthalmology, University of California, San FranciscoSan FranciscoUnited States
- Eli and Edythe Broad Center of Regeneration Medicine & Stem Cell Research University of California, San FranciscoSan FranciscoUnited States
| | - Brian C Mansfield
- Section on Cellular Differentiation, Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of HealthBethesdaUnited States
| | - Jacque L Duncan
- Department of Ophthalmology, University of California, San FranciscoSan FranciscoUnited States
| | - Deepak A Lamba
- Department of Ophthalmology, University of California, San FranciscoSan FranciscoUnited States
- Eli and Edythe Broad Center of Regeneration Medicine & Stem Cell Research University of California, San FranciscoSan FranciscoUnited States
- Immunology and Regenerative Medicine, GenentechSouth San FranciscoUnited States
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Miskalis A, Shirguppe S, Winter J, Elias G, Swami D, Nambiar A, Stilger M, Woods WS, Gosstola N, Gapinske M, Zeballos A, Moore H, Maslov S, Gaj T, Perez-Pinera P. SPLICER: A Highly Efficient Base Editing Toolbox That Enables In Vivo Therapeutic Exon Skipping. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587650. [PMID: 38883727 PMCID: PMC11178003 DOI: 10.1101/2024.04.01.587650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Exon skipping technologies enable exclusion of targeted exons from mature mRNA transcripts, which has broad applications in molecular biology, medicine, and biotechnology. Existing exon skipping techniques include antisense oligonucleotides, targetable nucleases, and base editors, which, while effective for specific applications at some target exons, remain hindered by shortcomings, including transient effects for oligonucleotides, genotoxicity for nucleases and inconsistent exon skipping for base editors. To overcome these limitations, we created SPLICER, a toolbox of next-generation base editors consisting of near-PAMless Cas9 nickase variants fused to adenosine or cytosine deaminases for the simultaneous editing of splice acceptor (SA) and splice donor (SD) sequences. Synchronized SA and SD editing with SPLICER improves exon skipping, reduces aberrant outcomes, including cryptic splicing and intron retention, and enables skipping of exons refractory to single splice-site editing. To demonstrate the therapeutic potential of SPLICER, we targeted APP exon 17, which encodes the amino acid residues that are cleaved to form the Aβ plaques in Alzheimer's disease. SPLICER reduced the formation of Aβ42 peptides in vitro and enabled efficient exon skipping in a mouse model of Alzheimer's disease. Overall, SPLICER is a widely applicable and efficient toolbox for exon skipping with broad therapeutic applications.
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De Angeli P, Flores-Tufiño A, Stingl K, Kühlewein L, Roschi E, Wissinger B, Kohl S. Splicing defects and CRISPR-Cas9 correction in isogenic homozygous photoreceptor precursors harboring clustered deep-intronic ABCA4 variants. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102113. [PMID: 38274366 PMCID: PMC10809099 DOI: 10.1016/j.omtn.2023.102113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024]
Abstract
Splicing defects from deep-intronic variants significantly contribute to the mutational spectrum in ABCA4-associated inherited retinal diseases, necessitating functional validation for their pathological classification. Typically, minigene assays in HEK293(T) can qualitatively assess splicing defects, yet they often fail to quantitatively reproduce the resulting mis-splicing patterns, leaving uncertainty on severity and pathogenicity. As a potential cellular model derived from patient cells, photoreceptor precursor cells (PPCs) play a pivotal role in assessing the severity of specific splicing mutations. Nevertheless, the accessibility of biosamples is commonly constrained, and their establishment is costly and laborious. In this study, we combined and investigated the use of a minigene assay and isogenic PPCs, as superior qualitative and more accessible cellular models for the assessment of splicing defects. Specifically, we focused on the clustered c.5196+1013A>G, c.5196+1056A>G, and c.5196+1216C>A deep-intronic variants in intron 36 of ABCA4, comparing their resulting (mis)splicing patterns in minigene-transfected cells and isogenic CRISPR-Cas9-knocked-in PPCs harboring these pathogenic variants in homozygous state. Moreover, we demonstrate the successful correction of these three splicing defects in homozygous mutant PPCs using a single pair of guide RNAs to target Cas9 cleavage, thereby identifying an efficient gene editing strategy for therapeutic applications.
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Affiliation(s)
- Pietro De Angeli
- Institute for Ophthalmic Research, Centre for Ophthalmology, University Clinics Tübingen, Elfriede-Aulhorn-Str. 7, 72076 Tübingen, Germany
| | - Arturo Flores-Tufiño
- Institute for Ophthalmic Research, Centre for Ophthalmology, University Clinics Tübingen, Elfriede-Aulhorn-Str. 7, 72076 Tübingen, Germany
| | - Katarina Stingl
- University Eye Hospital, Centre for Ophthalmology, University Clinics Tübingen, Elfriede-Aulhorn-Str. 7, 72076 Tübingen, Germany
| | - Laura Kühlewein
- University Eye Hospital, Centre for Ophthalmology, University Clinics Tübingen, Elfriede-Aulhorn-Str. 7, 72076 Tübingen, Germany
| | - Eleonora Roschi
- Institute for Ophthalmic Research, Centre for Ophthalmology, University Clinics Tübingen, Elfriede-Aulhorn-Str. 7, 72076 Tübingen, Germany
- Wellcome Sanger Institute, Hinxton CB10 1RQ, Saffron Walden, UK
| | - Bernd Wissinger
- Institute for Ophthalmic Research, Centre for Ophthalmology, University Clinics Tübingen, Elfriede-Aulhorn-Str. 7, 72076 Tübingen, Germany
| | - Susanne Kohl
- Institute for Ophthalmic Research, Centre for Ophthalmology, University Clinics Tübingen, Elfriede-Aulhorn-Str. 7, 72076 Tübingen, Germany
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Appell MB, Pejavar J, Pasupathy A, Rompicharla SVK, Abbasi S, Malmberg K, Kolodziejski P, Ensign LM. Next generation therapeutics for retinal neurodegenerative diseases. J Control Release 2024; 367:708-736. [PMID: 38295996 PMCID: PMC10960710 DOI: 10.1016/j.jconrel.2024.01.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 01/05/2024] [Accepted: 01/28/2024] [Indexed: 02/13/2024]
Abstract
Neurodegenerative diseases affecting the visual system encompass glaucoma, macular degeneration, retinopathies, and inherited genetic disorders such as retinitis pigmentosa. These ocular pathologies pose a serious burden of visual impairment and blindness worldwide. Current treatment modalities include small molecule drugs, biologics, or gene therapies, most of which are administered topically as eye drops or as injectables. However, the topical route of administration faces challenges in effectively reaching the posterior segment and achieving desired concentrations at the target site, while injections and implants risk severe complications, such as retinal detachment and endophthalmitis. This necessitates the development of innovative therapeutic strategies that can prolong drug release, deliver effective concentrations to the back of the eye with minimal systemic exposure, and improve patient compliance and safety. In this review, we introduce retinal degenerative diseases, followed by a discussion of the existing clinical standard of care. We then delve into detail about drug and gene delivery systems currently in preclinical and clinical development, including formulation and delivery advantages/drawbacks, with a special emphasis on potential for clinical translation.
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Affiliation(s)
- Matthew B Appell
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Jahnavi Pejavar
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Ashwin Pasupathy
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Sri Vishnu Kiran Rompicharla
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Saed Abbasi
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Kiersten Malmberg
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Patricia Kolodziejski
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Laura M Ensign
- Center for Nanomedicine at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21231, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Departments of Gynecology and Obstetrics, Biomedical Engineering, Oncology, and Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA.
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11
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Ye X, Yang S, Tu J, Xu L, Wang Y, Chen H, Yu R, Huang P. Leveraging baseline transcriptional features and information from single-cell data to power the prediction of influenza vaccine response. Front Cell Infect Microbiol 2024; 14:1243586. [PMID: 38384303 PMCID: PMC10879619 DOI: 10.3389/fcimb.2024.1243586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 01/11/2024] [Indexed: 02/23/2024] Open
Abstract
Introduction Vaccination is still the primary means for preventing influenza virus infection, but the protective effects vary greatly among individuals. Identifying individuals at risk of low response to influenza vaccination is important. This study aimed to explore improved strategies for constructing predictive models of influenza vaccine response using gene expression data. Methods We first used gene expression and immune response data from the Immune Signatures Data Resource (IS2) to define influenza vaccine response-related transcriptional expression and alteration features at different time points across vaccination via differential expression analysis. Then, we mapped these features to single-cell resolution using additional published single-cell data to investigate the possible mechanism. Finally, we explored the potential of these identified transcriptional features in predicting influenza vaccine response. We used several modeling strategies and also attempted to leverage the information from single-cell RNA sequencing (scRNA-seq) data to optimize the predictive models. Results The results showed that models based on genes showing differential expression (DEGs) or fold change (DFGs) at day 7 post-vaccination performed the best in internal validation, while models based on DFGs had a better performance in external validation than those based on DEGs. In addition, incorporating baseline predictors could improve the performance of models based on days 1-3, while the model based on the expression profile of plasma cells deconvoluted from the model that used DEGs at day 7 as predictors showed an improved performance in external validation. Conclusion Our study emphasizes the value of using combination modeling strategy and leveraging information from single-cell levels in constructing influenza vaccine response predictive models.
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Affiliation(s)
- Xiangyu Ye
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Sheng Yang
- Department of Biostatistics, National Vaccine Innovation Platform, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Junlan Tu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Lei Xu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yifan Wang
- Department of Infectious Disease, Jurong Hospital Affiliated to Jiangsu University, Jurong, China
| | - Hongbo Chen
- Department of Infectious Disease, Jurong Hospital Affiliated to Jiangsu University, Jurong, China
| | - Rongbin Yu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Peng Huang
- Department of Epidemiology, National Vaccine Innovation Platform, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
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12
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Verdoodt D, van Wijk E, Broekman S, Venselaar H, Aben F, Sels L, De Backer E, Gommeren H, Szewczyk K, Van Camp G, Ponsaerts P, Van Rompaey V, de Vrieze E. Rational design of a genomically humanized mouse model for dominantly inherited hearing loss, DFNA9. Hear Res 2024; 442:108947. [PMID: 38218018 DOI: 10.1016/j.heares.2023.108947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/04/2023] [Accepted: 12/30/2023] [Indexed: 01/15/2024]
Abstract
DFNA9 is a dominantly inherited form of adult-onset progressive hearing impairment caused by mutations in the COCH gene. COCH encodes cochlin, a crucial extracellular matrix protein. We established a genomically humanized mouse model for the Dutch/Belgian c.151C>T founder mutation in COCH. Considering upcoming sequence-specific genetic therapies, we exchanged the genomic murine Coch exons 3-6 for the corresponding human sequence. Introducing human-specific genetic information into mouse exons can be risky. To mitigate unforeseen consequences on cochlin function resulting from the introduction of the human COCH protein-coding sequence, we converted all human-specific amino acids to mouse equivalents. We furthermore optimized the recognition of the human COCH exons by the murine splicing machinery during pre-mRNA splicing. Subsequent observations in mouse embryonic stem cells revealed correct splicing of the hybrid Coch transcript. The inner ear of the established humanized Coch mice displays correctly-spliced wild-type and mutant humanized Coch alleles. For a comprehensive study of auditory function, mice were crossbred with C57BL/6 Cdh23753A>G mice to remove the Cdh23ahl allele from the genetic background of the mice. At 9 months, all humanized Coch genotypes showed hearing thresholds comparable to wild-type C57BL/6 Cdh23753A>G mice. This indicates that both the introduction of human wildtype COCH, and correction of Cdh23ahl in the humanized Coch lines was successful. Overall, our approach proved beneficial in eliminating potential adverse events of genomic humanization of mouse genes, and provides us with a model in which sequence-specific therapies directed against the human mutant COCH alle can be investigated. With the hearing and balance defects anticipated to occur late in the second year of life, a long-term follow-up study is ongoing to fully characterize the humanized Coch mouse model.
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Affiliation(s)
- Dorien Verdoodt
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium; Laboratory of Experimental Hematology, Vaccine and Infectious Disease Institute (Vaxinfectio), University of Antwerp, Antwerp, Belgium
| | - Erwin van Wijk
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Nijmegen, GA 6525, the Netherlands
| | - Sanne Broekman
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Nijmegen, GA 6525, the Netherlands
| | - Hanka Venselaar
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, GA 6525, the Netherlands
| | - Fien Aben
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium; Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Nijmegen, GA 6525, the Netherlands
| | - Lize Sels
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Evi De Backer
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium; Department of Otorhinolaryngology and Head & Neck Surgery, Antwerp University Hospital, Antwerp, Belgium
| | - Hanne Gommeren
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Krystyna Szewczyk
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Guy Van Camp
- Center for Medical Genetics, University of Antwerp, Antwerp 2000, Belgium
| | - Peter Ponsaerts
- Laboratory of Experimental Hematology, Vaccine and Infectious Disease Institute (Vaxinfectio), University of Antwerp, Antwerp, Belgium
| | - Vincent Van Rompaey
- Department of Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium; Department of Otorhinolaryngology and Head & Neck Surgery, Antwerp University Hospital, Antwerp, Belgium
| | - Erik de Vrieze
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, Nijmegen, GA 6525, the Netherlands.
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13
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Cideciyan AV, Jacobson SG, Ho AC, Swider M, Sumaroka A, Roman AJ, Wu V, Russell RC, Viarbitskaya I, Garafalo AV, Schwartz MR, Girach A. Durable vision improvement after a single intravitreal treatment with antisense oligonucleotide in CEP290-LCA: Replication in two eyes. Am J Ophthalmol Case Rep 2023; 32:101873. [PMID: 37388818 PMCID: PMC10302566 DOI: 10.1016/j.ajoc.2023.101873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/15/2023] [Accepted: 06/11/2023] [Indexed: 07/01/2023] Open
Abstract
Purpose An intravitreally injected antisense oligonucleotide, sepofarsen, was designed to modulate splicing within retinas of patients with severe vision loss due to deep intronic c.2991 + 1655A > G variant in the CEP290 gene. A previous report showed vision improvements following a single injection in one eye with unexpected durability lasting at least 15 months. The current study evaluated durability of efficacy beyond 15 months in the previously treated left eye. In addition, peak efficacy and durability were evaluated in the treatment-naive right eye, and re-injection of the left eye 4 years after the first injection. Observations Visual function was evaluated with best corrected standard and low-luminance visual acuities, microperimetry, dark-adapted chromatic perimetry, and full-field sensitivity testing. Retinal structure was evaluated with OCT imaging. At the fovea, all visual function measures and IS/OS intensity of the OCT showed transient improvements peaking at 3-6 months, remaining better than baseline at ∼2 years, and returning to baseline by 3-4 years after each single injection. Conclusions and Importance These results suggest that sepofarsen reinjection intervals may need to be longer than 2 years.
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Affiliation(s)
- Artur V. Cideciyan
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Samuel G. Jacobson
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Allen C. Ho
- Wills Eye Hospital, Thomas Jefferson University, Philadelphia, USA
| | - Malgorzata Swider
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexander Sumaroka
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alejandro J. Roman
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vivian Wu
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert C. Russell
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Iryna Viarbitskaya
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexandra V. Garafalo
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Nam DW, Song YK, Kim JH, Lee EK, Park KH, Cha J, Choi BY, Lee JH, Oh SH, Jo DH, Lee SY. Allelic hierarchy for USH2A influences auditory and visual phenotypes in South Korean patients. Sci Rep 2023; 13:20239. [PMID: 37981655 PMCID: PMC10658080 DOI: 10.1038/s41598-023-47166-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 11/09/2023] [Indexed: 11/21/2023] Open
Abstract
When medical genetic syndromes are influenced by allelic hierarchies, mutant alleles have distinct effects on clinical phenotypes. Genotype-phenotype correlations for Usher syndrome type 2 (USH2) suggest that the USH2A gene exhibits an allelic hierarchy. Here, we analyzed the phenotypes and genotypes of 16 South Korean patients with USH2A biallelic variants to investigate an allelic hierarchy from audiological and ophthalmological perspectives. Using whole exome and genome sequencing, 18 mutant alleles, including 4 novel alleles, were identified and implicated in USH2A-related disorders. Truncated alleles were linked to earlier onset of subjective hearing loss and more severe thresholds; biallelic truncated alleles had more severe effects. Truncated alleles were also associated with retinal structure degeneration and severe functional deterioration. However, younger patients (aged < 16 years) did not exhibit overt retinitis pigmentosa even when they had biallelic truncated alleles, suggesting that USH2A-related USH2 can mimic nonsyndromic hearing loss. For truncated alleles, there was a clear correlation between mean hearing threshold and 30-Hz flicker electroretinography implicit time. This study provides the first evidence of an USH2A-related allelic hierarchy among South Korean patients; our data yield valuable insights concerning the natural courses of clinical phenotypes and how genotype-based therapies may be used.
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Affiliation(s)
- Dong Woo Nam
- Department of Otorhinolaryngology, Chungbuk National University Hospital, Cheongju, Republic of Korea
| | - Yong Keun Song
- Department of Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jeong Hun Kim
- Fight Against Angiogenesis-Related Blindness (FARB) Laboratory, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Ophthalmology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Eun Kyoung Lee
- Department of Ophthalmology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyu Hyung Park
- Department of Ophthalmology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - JuHyuen Cha
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, 101, Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Byung Yoon Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Jun Ho Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, 101, Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Seung Ha Oh
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, 101, Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Dong Hyun Jo
- Department of Anatomy and Cell Biology, Seoul National University College of Medicine, 103, Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
| | - Sang-Yeon Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul National University College of Medicine, 101, Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, Republic of Korea.
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15
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Kandoi S, Martinez C, Chen KX, Reddy LVK, Mehine M, Mansfield BC, Duncan JL, Lamba DA. Disease modeling and pharmacological rescue of autosomal dominant Retinitis Pigmentosa associated with RHO copy number variation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.27.23286248. [PMID: 36909455 PMCID: PMC10002783 DOI: 10.1101/2023.02.27.23286248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Retinitis pigmentosa (RP), a heterogenous group of inherited retinal disorder causes slow progressive vision loss with no effective treatments available. Mutations in the rhodopsin gene (RHO), account for ~25% cases of autosomal dominant RP (adRP). In this study, we describe the disease characteristics of the first ever reported mono-allelic copy number variation (CNV) in RHO as a novel cause of adRP. We (1) show advanced retinal degeneration in a male patient (60-70 year old) harboring four transcriptionally active intact copies of rhodopsin, (2) recapitulated the clinical phenotypes using retinal organoids, and (3) assessed the utilization of a small molecule, Photoregulin3 (PR3), as a clinically viable strategy to target and modify disease progression in RP patients associated with RHO-CNV. Patient retinal organoids showed photoreceptors dysgenesis, with rod photoreceptors displaying stunted outer segments with occasional elongated cilia-like projections (microscopy); increased RHO mRNA expression (qRT-PCR and bulk RNA-sequencing); and elevated levels and mislocalization of rhodopsin protein (RHO) within the cell body of rod photoreceptors (western blotting and immunohistochemistry) over the extended (300-days) culture time period when compared against control organoids. Lastly, we utilized PR3 to target NR2E3, an upstream regulator of RHO, to alter RHO expression and observed a partial rescue of RHO protein localization from the cell body to the inner/outer segments of rod photoreceptors in patient organoids. These results provide a proof-of-principle for personalized medicine and suggest that RHO expression requires precise control. Taken together, this study supports the clinical data indicating that adRP due to RHO-CNV develops due protein overexpression overloading the photoreceptor post-translational modification machinery.
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Affiliation(s)
- Sangeetha Kandoi
- Department of Ophthalmology, University of California San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine & Stem Cell Research, University of California San Francisco, CA, USA
| | - Cassandra Martinez
- Department of Ophthalmology, University of California San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine & Stem Cell Research, University of California San Francisco, CA, USA
| | - Kevin Xu Chen
- Eli and Edythe Broad Center of Regeneration Medicine & Stem Cell Research, University of California San Francisco, CA, USA
| | - L Vinod K. Reddy
- Department of Ophthalmology, University of California San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine & Stem Cell Research, University of California San Francisco, CA, USA
| | | | - Brian C. Mansfield
- Section on Cellular Differentiation, Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
| | - Jacque L. Duncan
- Department of Ophthalmology, University of California San Francisco, CA, USA
| | - Deepak A. Lamba
- Department of Ophthalmology, University of California San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine & Stem Cell Research, University of California San Francisco, CA, USA
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16
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Sanjurjo-Soriano C, Jimenez-Medina C, Erkilic N, Cappellino L, Lefevre A, Nagel-Wolfrum K, Wolfrum U, Van Wijk E, Roux AF, Meunier I, Kalatzis V. USH2A variants causing retinitis pigmentosa or Usher syndrome provoke differential retinal phenotypes in disease-specific organoids. HGG ADVANCES 2023; 4:100229. [PMID: 37654703 PMCID: PMC10465966 DOI: 10.1016/j.xhgg.2023.100229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/03/2023] [Indexed: 09/02/2023] Open
Abstract
There is an emblematic clinical and genetic heterogeneity associated with inherited retinal diseases (IRDs). The most common form is retinitis pigmentosa (RP), a rod-cone dystrophy caused by pathogenic variants in over 80 different genes. Further complexifying diagnosis, different variants in individual RP genes can also alter the clinical phenotype. USH2A is the most prevalent gene for autosomal-recessive RP and one of the most challenging because of its large size and, hence, large number of variants. Moreover, USH2A variants give rise to non-syndromic and syndromic RP, known as Usher syndrome (USH) type 2, which is associated with vision and hearing loss. The lack of a clear genotype-phenotype correlation or prognostic models renders diagnosis highly challenging. We report here a long-awaited differential non-syndromic RP and USH phenotype in three human disease-specific models: fibroblasts, induced pluripotent stem cells (iPSCs), and mature iPSC-derived retinal organoids. Moreover, we identified distinct retinal phenotypes in organoids from multiple RP and USH individuals, which were validated by isogenic-corrected controls. Non-syndromic RP organoids showed compromised photoreceptor differentiation, whereas USH organoids showed a striking and unexpected cone phenotype. Furthermore, complementary clinical investigations identified macular atrophy in a high proportion of USH compared with RP individuals, further validating our observations that USH2A variants differentially affect cones. Overall, identification of distinct non-syndromic RP and USH phenotypes in multiple models provides valuable and robust readouts for testing the pathogenicity of USH2A variants as well as the efficacy of therapeutic approaches in complementary cell types.
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Affiliation(s)
- Carla Sanjurjo-Soriano
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, INSERM, Montpellier, France
| | - Carla Jimenez-Medina
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, INSERM, Montpellier, France
| | - Nejla Erkilic
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, INSERM, Montpellier, France
| | - Luisina Cappellino
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, INSERM, Montpellier, France
| | - Arnaud Lefevre
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, CHU, Montpellier, France
| | - Kerstin Nagel-Wolfrum
- Institute of Molecular Physiology, Molecular Cell Biology, and Photoreceptor Cell Biology, Johannes Gutenberg University Mainz, Mainz, Germany
- Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Uwe Wolfrum
- Institute of Molecular Physiology, Molecular Cell Biology, and Photoreceptor Cell Biology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Erwin Van Wijk
- Department of Otorhinolaryngology, Hearing, & Genes, Radboud University Medical Center, Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition, and Behavior, Nijmegen, the Netherlands
| | - Anne-Françoise Roux
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, INSERM, Montpellier, France
- Molecular Genetics Laboratory, University of Montpellier, CHU, Montpellier, France
| | - Isabelle Meunier
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, INSERM, Montpellier, France
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, CHU, Montpellier, France
| | - Vasiliki Kalatzis
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, INSERM, Montpellier, France
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17
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Keuthan CJ, Karma S, Zack DJ. Alternative RNA Splicing in the Retina: Insights and Perspectives. Cold Spring Harb Perspect Med 2023; 13:a041313. [PMID: 36690463 PMCID: PMC10547393 DOI: 10.1101/cshperspect.a041313] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Alternative splicing is a fundamental and highly regulated post-transcriptional process that enhances transcriptome and proteome diversity. This process is particularly important in neuronal tissues, such as the retina, which exhibit some of the highest levels of differentially spliced genes in the body. Alternative splicing is regulated both temporally and spatially during neuronal development, can be cell-type-specific, and when altered can cause a number of pathologies, including retinal degeneration. Advancements in high-throughput sequencing technologies have facilitated investigations of the alternative splicing landscape of the retina in both healthy and disease states. Additionally, innovations in human stem cell engineering, specifically in the generation of 3D retinal organoids, which recapitulate many aspects of the in vivo retinal microenvironment, have aided studies of the role of alternative splicing in human retinal development and degeneration. Here we review these advances and discuss the ongoing development of strategies for the treatment of alternative splicing-related retinal disease.
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Affiliation(s)
- Casey J Keuthan
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Sadik Karma
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Donald J Zack
- Departments of Ophthalmology, Wilmer Eye Institute, Neuroscience, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
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18
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Toms M, Toualbi L, Almeida PV, Harbottle R, Moosajee M. Successful large gene augmentation of USH2A with non-viral episomal vectors. Mol Ther 2023; 31:2755-2766. [PMID: 37337429 PMCID: PMC10491995 DOI: 10.1016/j.ymthe.2023.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 05/09/2023] [Accepted: 06/14/2023] [Indexed: 06/21/2023] Open
Abstract
USH2A mutations are a common cause of autosomal recessive retinitis pigmentosa (RP) and Usher syndrome, for which there are currently no approved treatments. Gene augmentation is a valuable therapeutic strategy for treating many inherited retinal diseases; however, conventional adeno-associated virus (AAV) gene therapy cannot accommodate cDNAs exceeding 4.7 kb, such as the 15.6-kb-long USH2A coding sequence. In the present study, we adopted an alternative strategy to successfully generate scaffold/matrix attachment region (S/MAR) DNA plasmid vectors containing the full-length human USH2A coding sequence, a GFP reporter gene, and a ubiquitous promoter (CMV or CAG), reaching a size of approximately 23 kb. We assessed the vectors in transfected HEK293 cells and USH2A patient-derived dermal fibroblasts in addition to ush2au507 zebrafish microinjected with the vector at the one-cell stage. pS/MAR-USH2A vectors drove persistent transgene expression in patient fibroblasts with restoration of usherin. Twelve months of GFP expression was detected in the photoreceptor cells, with rescue of Usher 2 complex localization in the photoreceptors of ush2au507 zebrafish retinas injected with pS/MAR-USH2A. To our knowledge, this is the first reported vector that can be used to express full-length usherin with functional rescue. S/MAR DNA vectors have shown promise as a novel non-viral retinal gene therapy, warranting further translational development.
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Affiliation(s)
- Maria Toms
- Development, Ageing, and Disease, UCL Institute of Ophthalmology, London EC1V 9EL, UK; Ocular Genomics and Therapeutics, The Francis Crick Institute, London NW1 1AT, UK
| | - Lyes Toualbi
- Development, Ageing, and Disease, UCL Institute of Ophthalmology, London EC1V 9EL, UK; Ocular Genomics and Therapeutics, The Francis Crick Institute, London NW1 1AT, UK
| | - Patrick V Almeida
- DNA Vector Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Richard Harbottle
- DNA Vector Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Mariya Moosajee
- Development, Ageing, and Disease, UCL Institute of Ophthalmology, London EC1V 9EL, UK; Ocular Genomics and Therapeutics, The Francis Crick Institute, London NW1 1AT, UK; Department of Genetics, Moorfields Eye Hospital, NHS Foundation Trust, London EC1V 2PD, UK.
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19
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Kelley RA, Wu Z. Utilization of the retinal organoid model to evaluate the feasibility of genetic strategies to ameliorate retinal disease(s). Vision Res 2023; 210:108269. [PMID: 37295270 DOI: 10.1016/j.visres.2023.108269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/12/2023] [Accepted: 05/12/2023] [Indexed: 06/12/2023]
Abstract
Organoid models have quickly become a popular research tool to evaluate novel therapeutics on 3-D recapitulated tissue. This has enabled researchers to use physiologically relevant human tissue in vitro to augment the standard use of immortalized cells and animal models. Organoids can also provide a model when an engineered animal cannot recreate a specific disease phenotype. In particular, the retinal research field has taken advantage of this burgeoning technology to provide insight into inherited retinal disease(s) mechanisms and therapeutic intervention to ameliorate their effects. In this review we will discuss the use of both wild-type and patient-specific retinal organoids to further gene therapy research that could potentially prevent retinal disease(s) progression. Furthermore, we will discuss the pitfalls of current retinal organoid technology and present potential solutions that could overcome these hurdles in the near future.
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Affiliation(s)
- Ryan A Kelley
- PTC Therapeutics, 100 Corporate Ct #2400, South Plainfield, NJ 07080, USA.
| | - Zhijian Wu
- PTC Therapeutics, 100 Corporate Ct #2400, South Plainfield, NJ 07080, USA
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20
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Kaltak M, Blanco-Garavito R, Molday LL, Dhaenens CM, Souied EE, Platenburg G, Swildens J, Molday RS, Cremers FPM. Stargardt disease-associated in-frame ABCA4 exon 17 skipping results in significant ABCA4 function. J Transl Med 2023; 21:546. [PMID: 37587475 PMCID: PMC10428568 DOI: 10.1186/s12967-023-04406-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 08/01/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND ABCA4, the gene implicated in Stargardt disease (STGD1), contains 50 exons, of which 17 contain multiples of three nucleotides. The impact of in-frame exon skipping is yet to be determined. Antisense oligonucleotides (AONs) have been investigated in Usher syndrome-associated genes to induce skipping of in-frame exons carrying severe variants and mitigate their disease-linked effect. Upon the identification of a STGD1 proband carrying a novel exon 17 canonical splice site variant, the activity of ABCA4 lacking 22 amino acids encoded by exon 17 was examined, followed by design of AONs able to induce exon 17 skipping. METHODS A STGD1 proband was compound heterozygous for the splice variant c.2653+1G>A, that was predicted to result in in-frame skipping of exon 17, and a null variant [c.735T>G, p.(Tyr245*)]. Clinical characteristics of this proband were studied using multi-modal imaging and complete ophthalmological examination. The aberrant splicing of c.2653+1G>A was investigated in vitro in HEK293T cells with wild-type and mutant midigenes. The residual activity of the mutant ABCA4 protein lacking Asp864-Gly885 encoded by exon 17 was analyzed with all-trans-retinal-activated ATPase activity assay, along with its subcellular localization. To induce exon 17 skipping, the effect of 40 AONs was examined in vitro in WT WERI-Rb-1 cells and 3D human retinal organoids. RESULTS Late onset STGD1 in the proband suggests that c.2653+1G>A does not have a fully deleterious effect. The in vitro splice assay confirmed that this variant leads to ABCA4 transcripts without exon 17. ABCA4 Asp864_Gly863del was stable and retained 58% all-trans-retinal-activated ATPase activity compared to WT ABCA4. This sequence is located in an unstructured linker region between transmembrane domain 6 and nucleotide-binding domain-1 of ABCA4. AONs were designed to possibly reduce pathogenicity of severe variants harbored in exon 17. The best AON achieved 59% of exon 17 skipping in retinal organoids. CONCLUSIONS Exon 17 deletion in ABCA4 does not result in the absence of protein activity and does not cause a severe STGD1 phenotype when in trans with a null allele. By applying AONs, the effect of severe variants in exon 17 can potentially be ameliorated by exon skipping, thus generating partial ABCA4 activity in STGD1 patients.
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Affiliation(s)
- Melita Kaltak
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- ProQR Therapeutics, Leiden, The Netherlands
| | - Rocio Blanco-Garavito
- Department of Ophthalmology, Intercommunal Hospital Center and Henri Mondor Hospital, Paris-Est Créteil University, Creteil, France
| | - Laurie L Molday
- Department of Biochemistry and Molecular Biology, Department of Ophthalmology and Visual Sciences, Centre for Macular Research, University of British Columbia, Vancouver, BC, Canada
| | - Claire-Marie Dhaenens
- University of Lille, Inserm, CHU Lille, U1172-LilNCog-Lille Neuroscience & Cognition, Lille, France
| | - Eric E Souied
- Department of Ophthalmology, Intercommunal Hospital Center and Henri Mondor Hospital, Paris-Est Créteil University, Creteil, France
| | | | | | - Robert S Molday
- Department of Biochemistry and Molecular Biology, Department of Ophthalmology and Visual Sciences, Centre for Macular Research, University of British Columbia, Vancouver, BC, Canada
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
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21
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Stephenson KAJ, Whelan L, Zhu J, Dockery A, Wynne NC, Cairns RM, Kirk C, Turner J, Duignan ES, O'Byrne JJ, Silvestri G, Kenna PF, Farrar GJ, Keegan DJ. Usher Syndrome on the Island of Ireland: A Genotype-Phenotype Review. Invest Ophthalmol Vis Sci 2023; 64:23. [PMID: 37466950 PMCID: PMC10362925 DOI: 10.1167/iovs.64.10.23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023] Open
Abstract
Purpose Usher syndrome (USH) is a genetically heterogeneous group of autosomal recessive (AR) syndromic inherited retinal degenerations (IRDs) representing 50% of deaf-blindness. All subtypes include retinitis pigmentosa, sensorineural hearing loss, and vestibular abnormalities. Thorough phenotyping may facilitate genetic diagnosis and intervention. Here we report the clinical/genetic features of an Irish USH cohort. Methods USH patients were selected from the Irish IRD registry (Target 5000). Patients were examined clinically (deep-phenotyping) and genetically using a 254 IRD-associated gene target capture sequencing panel, USH2A exon, and whole genome sequencing. Results The study identified 145 patients (24.1% USH1 [n = 35], 73.8% USH2 [n = 107], 1.4% USH3 [n = 2], and 0.7% USH4 [n = 1]). A genetic diagnosis was reached in 82.1%, the majority (80.7%) being MYO7A or USH2A genotypes. Mean visual acuity and visual field (VF) were 0.47 ± 0.58 LogMAR and 31.3° ± 32.8°, respectively, at a mean age of 43 years. Legal blindness criteria were met in 40.7%. Cataract was present in 77.4%. ADGRV1 genotypes had the most VF loss, whereas USH2A patients had greater myopia and CDH23 had the most astigmatism. Variants absent from gnomAD non-Finnish Europeans and ClinVar represented more than 20% of the variants identified and were detected in ADGRV1, ARSG, CDH23, MYO7A, and USH2A. Conclusions USH is a genetically diverse group of AR IRDs that have a profound impact on affected individuals and their families. The prevalence and phenotype/genotype characteristics of USH in Ireland have, as yet, gone unreported. Understanding the genotype of Irish USH patients may guide clinical and genetic characterization facilitating access to existing/novel therapeutics.
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Affiliation(s)
- Kirk A J Stephenson
- Clinical Ophthalmic Genetics Unit, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Laura Whelan
- The School of Genetics & Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Julia Zhu
- Clinical Ophthalmic Genetics Unit, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Adrian Dockery
- Next Generation Sequencing Laboratory, Pathology Department, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Niamh C Wynne
- The Research Foundation, Royal Victoria Eye & Ear Hospital, Dublin, Ireland
| | - Rebecca M Cairns
- Ophthalmology Department, Belfast Health and Social Care Trust Hospitals, Belfast, Northern Ireland
| | - Claire Kirk
- Ophthalmology Department, Belfast Health and Social Care Trust Hospitals, Belfast, Northern Ireland
| | - Jacqueline Turner
- Clinical Ophthalmic Genetics Unit, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Emma S Duignan
- The Research Foundation, Royal Victoria Eye & Ear Hospital, Dublin, Ireland
| | - James J O'Byrne
- Clinical Ophthalmic Genetics Unit, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Giuliana Silvestri
- Ophthalmology Department, Belfast Health and Social Care Trust Hospitals, Belfast, Northern Ireland
| | - Paul F Kenna
- The School of Genetics & Microbiology, Trinity College Dublin, Dublin, Ireland
- The Research Foundation, Royal Victoria Eye & Ear Hospital, Dublin, Ireland
| | - G Jane Farrar
- The School of Genetics & Microbiology, Trinity College Dublin, Dublin, Ireland
| | - David J Keegan
- Clinical Ophthalmic Genetics Unit, Mater Misericordiae University Hospital, Dublin, Ireland
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22
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Khorkova O, Stahl J, Joji A, Volmar CH, Wahlestedt C. Amplifying gene expression with RNA-targeted therapeutics. Nat Rev Drug Discov 2023; 22:539-561. [PMID: 37253858 PMCID: PMC10227815 DOI: 10.1038/s41573-023-00704-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2023] [Indexed: 06/01/2023]
Abstract
Many diseases are caused by insufficient expression of mutated genes and would benefit from increased expression of the corresponding protein. However, in drug development, it has been historically easier to develop drugs with inhibitory or antagonistic effects. Protein replacement and gene therapy can achieve the goal of increased protein expression but have limitations. Recent discoveries of the extensive regulatory networks formed by non-coding RNAs offer alternative targets and strategies to amplify the production of a specific protein. In addition to RNA-targeting small molecules, new nucleic acid-based therapeutic modalities that allow highly specific modulation of RNA-based regulatory networks are being developed. Such approaches can directly target the stability of mRNAs or modulate non-coding RNA-mediated regulation of transcription and translation. This Review highlights emerging RNA-targeted therapeutics for gene activation, focusing on opportunities and challenges for translation to the clinic.
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Affiliation(s)
- Olga Khorkova
- OPKO Health, Miami, FL, USA
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
| | - Jack Stahl
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Aswathy Joji
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
- Department of Chemistry, University of Miami, Miami, FL, USA
| | - Claude-Henry Volmar
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA
| | - Claes Wahlestedt
- Center for Therapeutic Innovation, University of Miami, Miami, FL, USA.
- Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, USA.
- Department of Chemistry, University of Miami, Miami, FL, USA.
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23
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Zhu A, Chiba S, Shimizu Y, Kunitake K, Okuno Y, Aoki Y, Yokota T. Ensemble-Learning and Feature Selection Techniques for Enhanced Antisense Oligonucleotide Efficacy Prediction in Exon Skipping. Pharmaceutics 2023; 15:1808. [PMID: 37513994 PMCID: PMC10384346 DOI: 10.3390/pharmaceutics15071808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 07/30/2023] Open
Abstract
Antisense oligonucleotide (ASO)-mediated exon skipping has become a valuable tool for investigating gene function and developing gene therapy. Machine-learning-based computational methods, such as eSkip-Finder, have been developed to predict the efficacy of ASOs via exon skipping. However, these methods are computationally demanding, and the accuracy of predictions remains suboptimal. In this study, we propose a new approach to reduce the computational burden and improve the prediction performance by using feature selection within machine-learning algorithms and ensemble-learning techniques. We evaluated our approach using a dataset of experimentally validated exon-skipping events, dividing it into training and testing sets. Our results demonstrate that using a three-way-voting approach with random forest, gradient boosting, and XGBoost can significantly reduce the computation time to under ten seconds while improving prediction performance, as measured by R2 for both 2'-O-methyl nucleotides (2OMe) and phosphorodiamidate morpholino oligomers (PMOs). Additionally, the feature importance ranking derived from our approach is in good agreement with previously published results. Our findings suggest that our approach has the potential to enhance the accuracy and efficiency of predicting ASO efficacy via exon skipping. It could also facilitate the development of novel therapeutic strategies. This study could contribute to the ongoing efforts to improve ASO design and optimize gene therapy approaches.
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Affiliation(s)
- Alex Zhu
- Phillips Academy, Andover, MA 01810, USA
- Department of Medical Generics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Shuntaro Chiba
- HPC- and AI-Driven Drug Development Platform Division, RIKEN Center for Computational Science, Yokohama 230-0045, Japan
| | - Yuki Shimizu
- Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Katsuhiko Kunitake
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo 187-8551, Japan
| | - Yasushi Okuno
- HPC- and AI-Driven Drug Development Platform Division, RIKEN Center for Computational Science, Yokohama 230-0045, Japan
- Department of Biomedical Data Intelligence, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Yoshitsugu Aoki
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo 187-8551, Japan
| | - Toshifumi Yokota
- Department of Medical Generics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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24
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Schellens RT, Broekman S, Peters T, Graave P, Malinar L, Venselaar H, Kremer H, De Vrieze E, Van Wijk E. A protein domain-oriented approach to expand the opportunities of therapeutic exon skipping for USH2A-associated retinitis pigmentosa. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:980-994. [PMID: 37313440 PMCID: PMC10258241 DOI: 10.1016/j.omtn.2023.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 05/17/2023] [Indexed: 06/15/2023]
Abstract
Loss-of-function mutations in USH2A are among the most common causes of syndromic and non-syndromic retinitis pigmentosa (RP). We previously presented skipping of USH2A exon 13 as a promising treatment paradigm for USH2A-associated RP. However, RP-associated mutations are often private, and evenly distributed along the USH2A gene. In order to broaden the group of patients that could benefit from therapeutic exon skipping strategies, we expanded our approach to other USH2A exons in which unique loss-of-function mutations have been reported by implementing a protein domain-oriented dual exon skipping strategy. We first generated zebrafish mutants carrying a genomic deletion of the orthologous exons of the frequently mutated human USH2A exons 30-31 or 39-40 using CRISPR-Cas9. Excision of these in-frame combinations of exons restored usherin expression in the zebrafish retina and rescued the photopigment mislocalization typically observed in ush2a mutants. To translate these findings into a future treatment in humans, we employed in vitro assays to identify and validate antisense oligonucleotides (ASOs) with a high potency for sequence-specific dual exon skipping. Together, the in vitro and in vivo data demonstrate protein domain-oriented ASO-induced dual exon skipping to be a highly promising treatment option for RP caused by mutations in USH2A.
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Affiliation(s)
- Renske T.W. Schellens
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, 6500 GL Nijmegen, the Netherlands
| | - Sanne Broekman
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Theo Peters
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Pam Graave
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Lucija Malinar
- Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Hanka Venselaar
- Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Hannie Kremer
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, 6500 GL Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Erik De Vrieze
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, 6500 GL Nijmegen, the Netherlands
| | - Erwin Van Wijk
- Department of Otorhinolaryngology, Hearing and Genes, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
- Donders Institute for Brain, Cognition and Behaviour, 6500 GL Nijmegen, the Netherlands
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25
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Stemerdink M, Broekman S, Peters T, Kremer H, de Vrieze E, van Wijk E. Generation and Characterization of a Zebrafish Model for ADGRV1-Associated Retinal Dysfunction Using CRISPR/Cas9 Genome Editing Technology. Cells 2023; 12:1598. [PMID: 37371069 DOI: 10.3390/cells12121598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/26/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Worldwide, around 40,000 people progressively lose their eyesight as a consequence of retinitis pigmentosa (RP) caused by pathogenic variants in the ADGRV1 gene, for which currently no treatment options exist. A model organism that mimics the human phenotype is essential to unravel the exact pathophysiological mechanism underlying ADGRV1-associated RP, and to evaluate future therapeutic strategies. The introduction of CRISPR/Cas-based genome editing technologies significantly improved the possibilities of generating mutant models in a time- and cost-effective manner. Zebrafish have been recognized as a suitable model to study Usher syndrome-associated retinal dysfunction. Using CRISPR/Cas9 technology we introduced a 4bp deletion in adgrv1 exon 9 (adgrv1rmc22). Immunohistochemical analysis showed that Adgrv1 was absent from the region of the photoreceptor connecting cilium in the adgrv1rmc22 zebrafish retina. Here, the absence of Adgrv1 also resulted in reduced levels of the USH2 complex members usherin and Whrnb, suggesting that Adgrv1 interacts with usherin and Whrnb in zebrafish photoreceptors. When comparing adgrv1rmc22 zebrafish with wild-type controls, we furthermore observed increased levels of aberrantly localized rhodopsin in the photoreceptor cell body, and decreased electroretinogram (ERG) B-wave amplitudes which indicate that the absence of Adgrv1 results in impaired retinal function. Based on these findings we present the adgrv1rmc22 zebrafish as the first ADGRV1 mutant model that displays an early retinal dysfunction. Moreover, the observed phenotypic changes can be used as quantifiable outcome measures when evaluating the efficacy of future novel therapeutic strategies for ADGRV1-associated RP.
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Affiliation(s)
- Merel Stemerdink
- Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Sanne Broekman
- Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Theo Peters
- Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Hannie Kremer
- Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Erik de Vrieze
- Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Erwin van Wijk
- Department of Otorhinolaryngology, Hearing & Genes, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
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26
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Duncan JL, Cheng P, Maguire MG, Ayala AA, Birch DG, Cheetham JK, Durham TA, Fahim AT, Hoyng CB, Ishikawa H, Michaelides M, Pennesi ME, Sahel JA, Stingl K, Weng CY. Static Perimetry in the Rate of Progression in USH2A-related Retinal Degeneration (RUSH2A) Study: Assessment Through 2 Years. Am J Ophthalmol 2023; 250:103-110. [PMID: 36764426 PMCID: PMC10705000 DOI: 10.1016/j.ajo.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/01/2022] [Accepted: 02/02/2023] [Indexed: 02/12/2023]
Abstract
PURPOSE To evaluate disease progression using static perimetry (SP) in patients with USH2A-related retinal degeneration, including Usher syndrome type 2 (USH2) and nonsyndromic autosomal recessive retinitis pigmentosa. DESIGN Prospective, observational cohort study. METHODS A total of 102 patients with biallelic disease-causing sequence variants in USH2A with baseline best-corrected visual acuity (BCVA) letter score ≥54 were recruited from 16 clinical sites in Europe and North America. SP, BCVA, full-field stimulus thresholds, spectral domain optical coherence tomography macular scans, and fundus-guided mesopic microperimetry were performed at baseline and annually. The main outcome measures were total hill of vision (VTOT), hill of vision in the central 30° (V30), VTOT minus V30 (VPERIPH), and mean sensitivity. RESULTS The average decline (95% CI) was 2.05 (1.40, 2.70) decibel-steradian (dB-sr)/y for VTOT, 0.48 (0.32, 0.65) dB-sr/y for V30, 1.53 (0.97, 2.08) dB-sr/y for VPERIPH, and 0.55 (0.40, 0.71) dB/y for mean sensitivity. Average percentage decline per year was 8.3 (5.5, 11.1) for VTOT, 5.2 (3.0, 7.4) for V30, 16.0 (9.5, 22.0) for VPERIPH, and 5.1 (3.5, 6.7) for mean sensitivity. Changes from baseline to year 2 in all SP measures were highly correlated (r's ranging from 0.52 [V30 vs VPERIPH] to 0.98 [VTOT vs VPERIPH]). CONCLUSIONS Quantitative measures of SP declined significantly over 2 years in USH2A-related retinal degeneration. The annual percentage rate of change was greatest for VTOT and VPERIPH, whereas V30 and mean sensitivity changed least, reflecting earlier and more severe peripheral degeneration compared with central loss.
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Affiliation(s)
- Jacque L Duncan
- From the University of California, San Francisco (J.L.D.), San Francisco, California, USA
| | - Peiyao Cheng
- Jaeb Center for Health Research (P.C., M.G.M., A.A.A.), Tampa, Florida, USA
| | - Maureen G Maguire
- Jaeb Center for Health Research (P.C., M.G.M., A.A.A.), Tampa, Florida, USA
| | - Allison A Ayala
- Jaeb Center for Health Research (P.C., M.G.M., A.A.A.), Tampa, Florida, USA.
| | - David G Birch
- Retina Foundation of the Southwest (D.G.B.), Dallas, Texas, USA
| | - Janet K Cheetham
- Foundation Fighting Blindness (J.K.C., T.A.D.), Columbia, Maryland, USA
| | - Todd A Durham
- Foundation Fighting Blindness (J.K.C., T.A.D.), Columbia, Maryland, USA
| | - Abigail T Fahim
- Kellogg Eye Center, University of Michigan (A.T.F.), Ann Arbor, Michigan, USA
| | - Carel B Hoyng
- Radboud University Medical Center (C.B.H.), Nijmegen, the Netherlands
| | - Hiroshi Ishikawa
- Casey Eye Institute, Oregon Health & Science University (H.I., M.E.P.), Portland, Oregon, USA
| | - Michel Michaelides
- Moorfields Eye Hospital and UCL Institute of Ophthalmology (M.M.), London, United Kingdom
| | - Mark E Pennesi
- Casey Eye Institute, Oregon Health & Science University (H.I., M.E.P.), Portland, Oregon, USA
| | - José-Alain Sahel
- Institut de la Vision, Sorbonne Université, INSERM, CNRS (J.A.-S.), Paris, France; Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, INSERM-DGOS CIC1423 (J.A.-S.), Paris, France; Department of Ophthalmology, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Katarina Stingl
- University Eye Hospital, Center for Ophthalmology, University of Tübingen (K.S.), Tübingen, Germany; Center for Rare Eye Diseases, University of Tübingen, Tübingen (K.S.), Germany
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Micevych PS, Wong J, Zhou H, Wang RK, Porco TC, Carroll J, Roorda A, Duncan JL. Cone Structure and Function in RPGR- and USH2A-Associated Retinal Degeneration. Am J Ophthalmol 2023; 250:1-11. [PMID: 36646238 PMCID: PMC10308738 DOI: 10.1016/j.ajo.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023]
Abstract
PURPOSE To compare cone structure and function between RPGR- and USH2A-associated retinal degeneration. DESIGN Retrospective, observational, cross-sectional study. METHODS This multicenter study included 13 eyes (9 participants) with RPGR-related X-linked retinitis pigmentosa (RPGR), 15 eyes (10 participants) with USH2A-related Usher syndrome type 2 (USH2), 16 eyes (9 participants) with USH2A-related autosomal recessive retinitis pigmentosa (ARRP), and 7 normal eyes (6 participants). Structural measures included cone spacing and density from adaptive optics scanning laser ophthalmoscopy and photoreceptor inner segment (IS), outer segment (OS), and outer nuclear layer (ONL) thickness from optical coherence tomography (OCT) images. OCT angiography images were used to study choriocapillaris flow deficit percent (CCFD). Cone function was assessed by fundus-guided microperimetry. Measures were compared at designated regions using analysis of variance with pairwise comparisons among disease groups, adjusted for disease duration and eccentricity. RESULTS OCT segmentation revealed shorter OS and IS, with reduced ONL thickness in RPGR compared to normal (OS: P < .001, IS: P = .001, ONL: P = .005), USH2 (OS: P = .01, IS: P = .03, ONL: P = .03), or ARRP (OS: P = .001, ONL: P = .03). Increased cone spacing was observed in both RPGR (P = .03) and USH2 compared with normal (P = .048). The mean CCFD in RPGR was greater than in USH2 (P = .02). Microperimetry demonstrated below-normal regional sensitivity in RPGR (P = .004), USH2 (P = .02), and ARRP (P = .009), without significant intergroup differences. CONCLUSIONS Outer retinal structure and choriocapillaris perfusion were more abnormal in RPGR- than USH2A-related retinal degenerations, whereas there were no significant differences in below-normal regional sensitivity between each rod-cone degeneration associated with variants in these 2 genes expressed at the photoreceptor-connecting cilium.
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Affiliation(s)
- Paul S Micevych
- From the Department of Ophthalmology, University of California (P.S.M., J.W., T.C.P., J.L.D.), San Francisco, California
| | - Jessica Wong
- From the Department of Ophthalmology, University of California (P.S.M., J.W., T.C.P., J.L.D.), San Francisco, California
| | - Hao Zhou
- Department of Bioengineering, University of Washington (H.Z., R.K.W.), Seattle, Washington
| | - Ruikang K Wang
- Department of Bioengineering, University of Washington (H.Z., R.K.W.), Seattle, Washington
| | - Travis C Porco
- From the Department of Ophthalmology, University of California (P.S.M., J.W., T.C.P., J.L.D.), San Francisco, California; Francis I. Proctor Foundation, Department of Ophthalmology, University of California (T.C.P.), San Francisco, California
| | - Joseph Carroll
- Department of Ophthalmology & Visual Sciences, Medical College of Wisconsin Eye Institute (J.C.), Milwaukee, Wisconsin
| | - Austin Roorda
- Herbert Wertheim School of Optometry & Vision Science, University of California Berkeley (A.R.), Berkeley, California, USA
| | - Jacque L Duncan
- From the Department of Ophthalmology, University of California (P.S.M., J.W., T.C.P., J.L.D.), San Francisco, California.
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Bellingrath JS, McClements ME, Fischer MD, MacLaren RE. Programmable RNA editing with endogenous ADAR enzymes - a feasible option for the treatment of inherited retinal disease? Front Mol Neurosci 2023; 16:1092913. [PMID: 37293541 PMCID: PMC10244592 DOI: 10.3389/fnmol.2023.1092913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 04/27/2023] [Indexed: 06/10/2023] Open
Abstract
RNA editing holds great promise for the therapeutic correction of pathogenic, single nucleotide variants (SNV) in the human transcriptome since it does not risk creating permanent off-targets edits in the genome and has the potential for innovative delivery options. Adenine deaminases acting on RNA (ADAR) enzymes catalyse the most widespread form of posttranscriptional RNA editing in humans and their ability to hydrolytically deaminate adenosine to inosine in double stranded RNA (dsRNA) has been harnessed to change pathogenic single nucleotide variants (SNVs) in the human genome on a transcriptional level. Until now, the most promising target editing rates have been achieved by exogenous delivery of the catalytically active ADAR deaminase domain (ADARDD) fused to an RNA binding protein. While it has been shown that endogenous ADARs can be recruited to a defined target site with the sole help of an ADAR-recruiting guide RNA, thus freeing up packaging space, decreasing the chance of an immune response against a foreign protein, and decreasing transcriptome-wide off-target effects, this approach has been limited by a low editing efficiency. Through the recent development of novel circular ADAR-recruiting guide RNAs as well as the optimisation of ADAR-recruiting antisense oligonucleotides, RNA editing with endogenous ADAR is now showing promising target editing efficiency in vitro and in vivo. A target editing efficiency comparable to RNA editing with exogenous ADAR was shown both in wild-type and disease mouse models as well as in wild-type non-human primates (NHP) immediately following and up to 6 weeks after application. With these encouraging results, RNA editing with endogenous ADAR has the potential to present an attractive option for the treatment of inherited retinal diseases (IRDs), a field where gene replacement therapy has been established as safe and efficacious, but where an unmet need still exists for genes that exceed the packaging capacity of an adeno associated virus (AAV) or are expressed in more than one retinal isoform. This review aims to give an overview of the recent developments in the field of RNA editing with endogenous ADAR and assess its applicability for the field of treatment of IRD.
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Affiliation(s)
- Julia-Sophia Bellingrath
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Michelle E. McClements
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - M. Dominik Fischer
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, Oxford, United Kingdom
| | - Robert E. MacLaren
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- Oxford Eye Hospital, Oxford University Hospitals NHS Trust, Oxford, United Kingdom
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29
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Zhai Y, Xu M, Radziwon A, Dimopoulos IS, Crichton P, Mah R, MacLaren RE, Somani R, Tennant MT, MacDonald IM. AAV2-Mediated Gene Therapy for Choroideremia: 5-Year Results and Alternate Anti-sense Oligonucleotide Therapy. Am J Ophthalmol 2023; 248:145-156. [PMID: 36581191 DOI: 10.1016/j.ajo.2022.12.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 11/03/2022] [Accepted: 12/14/2022] [Indexed: 12/27/2022]
Abstract
PURPOSE To assess the long-term safety and efficacy of AAV2-REP1 in choroideremia (CHM) patients, and to test a potential antisense oligonucleotide therapy for CHM. DESIGN Extended, prospective phase 1/2 clinical trial and laboratory investigation. METHODS Five patients who received a single subfoveal injection of AAV2-REP1 were studied. The long-term safety was evaluated by ophthalmic examination, spectral domain optical coherence tomography, and fundus autofluorescence (FAF) for up to 5 years. Functional and structural changes were determined by different test modalities. Four antisense oligonucleotides (ASOs) were designed to treat the CHM c.1245-521A>G mutation, which was present in 2 patients within this trial. RESULTS Subject P3 experienced a localized intraretinal immune response that resulted in a significant loss of preserved retinal pigment epithelium (RPE). P4 experienced an exacerbation of peripheral retinoschisis. P2 had a constant ≥15-letter best-corrected visual acuity (BCVA) gain in the treated eye, whereas P5 had ≥15-letter BCVA improvement once in the untreated eye. The preserved FAF areas declined more rapidly in the treated eyes compared to the untreated eyes (P = .043). A customized 25-mer ASO recovered 83.2% to 95.0% of the normal RNA and 57.5% of the normal protein in fibroblasts from 2 trial patients. CONCLUSIONS Intraretinal inflammation triggered by AAV2-REP1 subretinal injection stabilized after 2 years but resulted in permanent damage to the retinal structure. Long-term progression of the disease was seen in both treated and untreated eyes, casting doubt as to the effectiveness of this approach in late-stage CHM. Alternative approaches such as ASO may have a therapeutic effect in a subgroup of CHM patients.
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Affiliation(s)
- Yi Zhai
- From the Department of Ophthalmology and Visual Sciences (Y.Z., M.X., A.R., R.S., M.T.T., I.M.M.), University of Alberta, Edmonton, Alberta, Canada
| | - Manlong Xu
- From the Department of Ophthalmology and Visual Sciences (Y.Z., M.X., A.R., R.S., M.T.T., I.M.M.), University of Alberta, Edmonton, Alberta, Canada
| | - Alina Radziwon
- From the Department of Ophthalmology and Visual Sciences (Y.Z., M.X., A.R., R.S., M.T.T., I.M.M.), University of Alberta, Edmonton, Alberta, Canada; Department of Medical Genetics (A.R., I.M.M.), University of Alberta, Edmonton, Alberta, Canada
| | - Ioannis S Dimopoulos
- Department of Ophthalmology (I.S.D., P.C., R.M.), University of Ottawa, Ottawa, Ontario, Canada
| | - Paul Crichton
- Department of Ophthalmology (I.S.D., P.C., R.M.), University of Ottawa, Ottawa, Ontario, Canada
| | - Rachel Mah
- Department of Ophthalmology (I.S.D., P.C., R.M.), University of Ottawa, Ottawa, Ontario, Canada
| | - Robert E MacLaren
- Nuffield Laboratory of Ophthalmology (R.E.M.), Department of Clinical Neurosciences, University of Oxford and NIHR Oxford Biomedical Research Centre, Oxfordshire, UK
| | - Rizwan Somani
- From the Department of Ophthalmology and Visual Sciences (Y.Z., M.X., A.R., R.S., M.T.T., I.M.M.), University of Alberta, Edmonton, Alberta, Canada
| | - Matthew T Tennant
- From the Department of Ophthalmology and Visual Sciences (Y.Z., M.X., A.R., R.S., M.T.T., I.M.M.), University of Alberta, Edmonton, Alberta, Canada
| | - Ian M MacDonald
- From the Department of Ophthalmology and Visual Sciences (Y.Z., M.X., A.R., R.S., M.T.T., I.M.M.), University of Alberta, Edmonton, Alberta, Canada; Department of Medical Genetics (A.R., I.M.M.), University of Alberta, Edmonton, Alberta, Canada.
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30
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Lee BJH, Tham YC, Tan TE, Bylstra Y, Lim WK, Jain K, Chan CM, Mathur R, Cheung CMG, Fenner BJ. Characterizing the genotypic spectrum of retinitis pigmentosa in East Asian populations: a systematic review. Ophthalmic Genet 2023; 44:109-118. [PMID: 36856324 DOI: 10.1080/13816810.2023.2182329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
BACKGROUND Ongoing trials for retinitis pigmentosa (RP) are genotype-specific, with most trials conducted on European cohorts. Due to genetic differences across diverse ancestries and populations, these therapies may not be efficacious in East Asians. MATERIALS AND METHODS A literature search was conducted from 1966 to September 2022 for cohort studies on East Asian populations reporting on non-syndromic RP genotypes and variants. Population-weighted prevalence was used to determine the genotypes and individual variants across the entire cohort. The carrier prevalence of common variants was compared against those in Europe. RESULTS A total of 12 articles describing 2,932 clinically diagnosed East Asian RP probands were included. We identified 876 variants across 54 genes. The most common genotypes included USH2A, EYS, RPGR, ABCA4, PRPF31, RHO, RP1, RP2, PDE6B and SNRNP200, with USH2A as the most common (17.1%). Overall, 60.5% of probands with clinically relevant variants were found to have one of the genotypes above, with 543/876 (62.0%) of the variants occurring in these genes. The most frequently reported variant was USH2A missense variant c.2802T>G/p.C934W (4.9%). Carrier prevalence of these variants was significantly different (p < 0.0001) than in Europe. CONCLUSIONS USH2A was the most commonly affected RP gene in this East Asian cohort, although sub-population analysis revealed distinct genotype prevalence patterns. While the genotypes are similar between East Asia and European cohorts, variants are specific to East Asia. The identification of several prevalent variants in USH2A and EYS provides an opportunity for the development of therapeutics that are relevant for East Asia patients.
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Affiliation(s)
- Brian Juin Hsien Lee
- Department of Medical Retina, Singapore National Eye Centre, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Yih-Chung Tham
- Retina Research Group Singapore Eye Research Institute, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Medical School, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Centre for Innovation & Precision Eye Health, Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore
| | - Tien-En Tan
- Department of Medical Retina, Singapore National Eye Centre, Singapore
- Retina Research Group Singapore Eye Research Institute, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Medical School, Singapore
| | - Yasmin Bylstra
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore
| | - Kanika Jain
- POLARIS, Genome Institute of Singapore, Singapore
| | - Choi Mun Chan
- Department of Medical Retina, Singapore National Eye Centre, Singapore
- Retina Research Group Singapore Eye Research Institute, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Medical School, Singapore
| | - Ranjana Mathur
- Department of Medical Retina, Singapore National Eye Centre, Singapore
- Retina Research Group Singapore Eye Research Institute, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Medical School, Singapore
| | - Chui Ming Gemmy Cheung
- Department of Medical Retina, Singapore National Eye Centre, Singapore
- Retina Research Group Singapore Eye Research Institute, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Medical School, Singapore
| | - Beau J Fenner
- Department of Medical Retina, Singapore National Eye Centre, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Retina Research Group Singapore Eye Research Institute, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (EYE ACP), Duke-NUS Medical School, Singapore
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31
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Riley KC, Koleilat A, Dugdale JA, Cooper SA, Christensen TA, Schimmenti LA. Three-Dimensional Structure of Inner Ear Hair Cell Ribbon Synapses in a Zebrafish Model of Usher Syndrome Type 1B. Zebrafish 2023; 20:47-54. [PMID: 37071854 DOI: 10.1089/zeb.2022.0049] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
Our understanding of inner ear hair cell ultrastructure has heretofore relied upon two-dimensional imaging; however, serial block-face scanning electron microscopy (SBFSEM) changes this paradigm allowing for three-dimensional evaluation. We compared inner ear hair cells of the apical cristae in myo7aa-/- null zebrafish, a model of human Usher Syndrome type 1B, to hair cells in wild-type zebrafish by SBFSEM to investigate possible ribbon synapse ultrastructural differences. Previously, it has been shown that compared to wild type, myo7aa-/- zebrafish neuromast hair cells have fewer ribbon synapses yet similar ribbon areas. We expect the recapitulation of these results within the inner ear apical crista hair cells furthering the knowledge of three-dimensional ribbon synapse structure while resolving the feasibility of therapeutically targeting myo7aa-/- mutant ribbons. In this report, we evaluated ribbon synapse number, volume, surface area, and sphericity. Localization of ribbons and their distance from the nearest innervation were also evaluated. We determined that myo7aa-/- mutant ribbon synapses are smaller in volume and surface area; however, all other measurements were not significantly different from wild-type zebrafish. Because the ribbon synapses are nearly indistinguishable between the myo7aa-/- mutant and wild type, it suggests that the ribbons are structurally receptive, supporting that therapeutic intervention may be feasible.
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Affiliation(s)
- Kenneth C Riley
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Alaa Koleilat
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Joseph A Dugdale
- Department of Otorhinolaryngology, Head and Neck Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Shawna A Cooper
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, Minnesota, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Trace A Christensen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
- Microscopy and Cell Analysis Core, and Mayo Clinic, Rochester, Minnesota, USA
| | - Lisa A Schimmenti
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
- Department of Otorhinolaryngology, Head and Neck Surgery, Mayo Clinic, Rochester, Minnesota, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, USA
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Kaltak M, de Bruijn P, Piccolo D, Lee SE, Dulla K, Hoogenboezem T, Beumer W, Webster AR, Collin RW, Cheetham ME, Platenburg G, Swildens J. Antisense oligonucleotide therapy corrects splicing in the common Stargardt disease type 1-causing variant ABCA4 c.5461-10T>C. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:674-688. [PMID: 36910710 PMCID: PMC9999166 DOI: 10.1016/j.omtn.2023.02.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 02/15/2023] [Indexed: 02/20/2023]
Abstract
Stargardt disease type 1 (STGD1) is the most common hereditary form of maculopathy and remains untreatable. STGD1 is caused by biallelic variants in the ABCA4 gene, which encodes the ATP-binding cassette (type 4) protein (ABCA4) that clears toxic byproducts of the visual cycle. The c.5461-10T>C p.[Thr1821Aspfs∗6,Thr1821Valfs∗13] variant is the most common severe disease-associated variant, and leads to exon skipping and out-of-frame ABCA4 transcripts that prevent translation of functional ABCA4 protein. Homozygous individuals typically display early onset STGD1 and are legally blind by early adulthood. Here, we applied antisense oligonucleotides (AONs) to promote exon inclusion and restore wild-type RNA splicing of ABCA4 c.5461-10T>C. The effect of AONs was first investigated in vitro using an ABCA4 midigene model. Subsequently, the best performing AONs were administered to homozygous c.5461-10T>C 3D human retinal organoids. Isoform-specific digital polymerase chain reaction revealed a significant increase in correctly spliced transcripts after treatment with the lead AON, QR-1011, up to 53% correct transcripts at a 3 μM dose. Furthermore, western blot and immunohistochemistry analyses identified restoration of ABCA4 protein after treatment. Collectively, we identified QR-1011 as a potent splice-correcting AON and a possible therapeutic intervention for patients harboring the severe ABCA4 c.5461-10T>C variant.
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Affiliation(s)
- Melita Kaltak
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, the Netherlands
- Academic Alliance Genetics, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, and Maastricht University Medical Center+, P. Debyelaan 25, 6229 HX Maastricht, the Netherlands
| | - Petra de Bruijn
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | - Davide Piccolo
- UCL, Institute of Ophthalmology, 11-43 Bath Street, EC1V 9EL London, UK
| | - Sang-Eun Lee
- UCL, Institute of Ophthalmology, 11-43 Bath Street, EC1V 9EL London, UK
| | - Kalyan Dulla
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | | | - Wouter Beumer
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
| | - Andrew R. Webster
- UCL, Institute of Ophthalmology, 11-43 Bath Street, EC1V 9EL London, UK
- Moorfields Eye Hospital, 162 City Road, EC1V 2PD London, UK
| | - Rob W.J. Collin
- Department of Human Genetics, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, the Netherlands
- Academic Alliance Genetics, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, and Maastricht University Medical Center+, P. Debyelaan 25, 6229 HX Maastricht, the Netherlands
| | | | | | - Jim Swildens
- ProQR Therapeutics, Zernikedreef 9, 2333 CK Leiden, the Netherlands
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Natural Disease Course in Usher Syndrome Patients Harboring USH2A Variant p.Cys870* in Exon 13, Amenable to Exon Skipping Therapy. Genes (Basel) 2023; 14:genes14030652. [PMID: 36980924 PMCID: PMC10048357 DOI: 10.3390/genes14030652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/08/2023] [Accepted: 02/13/2023] [Indexed: 03/08/2023] Open
Abstract
The aim of the study was to determine the rate of retinal degeneration in patients with c.2610C>A (p.Cys870*) in USH2A exon 13, amenable to exon skipping therapy. There were nine patients from seven families, three of whom were male (two were homozygous). Seven patients had follow-up data (median of 11 years). Analysis included best corrected visual acuity (BCVA, decimal Snellen), visual field (Goldmann perimetry target II/4), fundus autofluorescence (FAF), optical coherence tomography (OCT), and microperimetry (MP). The median age at the onset of nyctalopia was 20 years (range, 8–35 years of age). At the first exam, at a median age of 42 years, the median BCVA was 0.5 (0.2–1.0), and the median visual field diameter was 23° (5°–114°). Imaging showed a hyperautofluorescent ring delineating preserved foveal photoreceptors in 78% (7/9) of patients, while 22% (2/9) had a hyperautofluorescent patch or atrophy, reflecting advanced disease. Survival analysis predicted that 50% of patients reach legal blindness based on a visual field diameter < 20° at the age of 52 (95% CI, 45–59) and legal blindness based on a BCVA ≤ 0. 1 (20/200) at the age of 55 (95% CI, 46–66). Visual field constriction occurred at the median rate of radial 1.5 deg/year, and hyperautofluorescent ring constriction occurred at the median rate of 34 μm/year. A non-null second allele was found in two patients: p.Thr4315Pro and p.Arg303His; the patient with p.Arg303His had a milder disease. The rates of progression will be useful in the design and execution of clinical trials.
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Iwasa Y, Klimara MJ, Yoshimura H, Walls WD, Omichi R, West CA, Shibata SB, Ranum PT, Smith RJ. Mutation-agnostic RNA interference with engineered replacement rescues Tmc1-related hearing loss. Life Sci Alliance 2023; 6:6/3/e202201592. [PMID: 36574989 PMCID: PMC9795038 DOI: 10.26508/lsa.202201592] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 12/28/2022] Open
Abstract
Hearing loss is the most common sensory deficit, of which genetic etiologies are a frequent cause. Dominant and recessive mutations in TMC1, a gene encoding the pore-forming subunit of the hair cell mechanotransduction channel, cause DFNA36 and DFNB7/11, respectively, accounting for ∼2% of genetic hearing loss. Previous work has established the efficacy of mutation-targeted RNAi in treatment of murine models of autosomal dominant non-syndromic deafness. However, application of such approaches is limited by the infeasibility of development and validation of novel constructs for each variant. We developed an allele-non-specific approach consisting of mutation-agnostic RNAi suppression of both mutant and WT alleles, co-delivered with a knockdown-resistant engineered WT allele with or without the use of woodchuck hepatitis virus post-transcriptional regulatory element (WPRE) to augment transgene expression. This therapeutic construct was delivered into the mature murine model of DFNA36 with an AAV vector and achieved robust hair cell and auditory brainstem response preservation. However, WPRE-enhanced Tmc1 expression resulted in inferior outcomes, suggesting a role for gene dosage optimization in future TMC1 gene therapy development.
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Affiliation(s)
- Yoichiro Iwasa
- Department of Otorhinolaryngology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Miles J Klimara
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology - Head and Neck Surgery, University of Iowa, Iowa City, IA, USA
| | - Hidekane Yoshimura
- Department of Otolaryngology - Head and Neck Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - William D Walls
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology - Head and Neck Surgery, University of Iowa, Iowa City, IA, USA
| | - Ryotaro Omichi
- Department of Otolaryngology - Head and Neck Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Cody A West
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology - Head and Neck Surgery, University of Iowa, Iowa City, IA, USA
| | - Seiji B Shibata
- Department of Otolaryngology Head and Neck Surgery, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Paul T Ranum
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - Richard Jh Smith
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology - Head and Neck Surgery, University of Iowa, Iowa City, IA, USA
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Tebbe L, Mwoyosvi ML, Crane R, Makia MS, Kakakhel M, Cosgrove D, Al-Ubaidi MR, Naash MI. The usherin mutation c.2299delG leads to its mislocalization and disrupts interactions with whirlin and VLGR1. Nat Commun 2023; 14:972. [PMID: 36810733 PMCID: PMC9944904 DOI: 10.1038/s41467-023-36431-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 02/01/2023] [Indexed: 02/24/2023] Open
Abstract
Usher syndrome (USH) is the leading cause of combined deafness-blindness with type 2 A (USH2A) being the most common form. Knockout models of USH proteins, like the Ush2a-/- model that develops a late-onset retinal phenotype, failed to mimic the retinal phenotype observed in patients. Since patient's mutations result in the expression of a mutant protein and to determine the mechanism of USH2A, we generated and evaluated an usherin (USH2A) knock-in mouse expressing the common human disease-mutation, c.2299delG. This mouse exhibits retinal degeneration and expresses a truncated, glycosylated protein which is mislocalized to the photoreceptor inner segment. The degeneration is associated with a decline in retinal function, structural abnormalities in connecting cilium and outer segment and mislocaliztion of the usherin interactors very long G-protein receptor 1 and whirlin. The onset of symptoms is significantly earlier compared to Ush2a-/-, proving expression of mutated protein is required to recapitulate the patients' retinal phenotype.
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Affiliation(s)
- Lars Tebbe
- Department of Biomedical Engineering, University of Houston, Houston, TX, 77204, USA
| | - Maggie L Mwoyosvi
- Department of Biomedical Engineering, University of Houston, Houston, TX, 77204, USA
- Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Ryan Crane
- Department of Biomedical Engineering, University of Houston, Houston, TX, 77204, USA
| | - Mustafa S Makia
- Department of Biomedical Engineering, University of Houston, Houston, TX, 77204, USA
| | - Mashal Kakakhel
- Department of Biomedical Engineering, University of Houston, Houston, TX, 77204, USA
| | | | - Muayyad R Al-Ubaidi
- Department of Biomedical Engineering, University of Houston, Houston, TX, 77204, USA.
| | - Muna I Naash
- Department of Biomedical Engineering, University of Houston, Houston, TX, 77204, USA.
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36
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Cellular and Molecular Mechanisms of Pathogenesis Underlying Inherited Retinal Dystrophies. Biomolecules 2023; 13:biom13020271. [PMID: 36830640 PMCID: PMC9953031 DOI: 10.3390/biom13020271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/23/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
Inherited retinal dystrophies (IRDs) are congenital retinal degenerative diseases that have various inheritance patterns, including dominant, recessive, X-linked, and mitochondrial. These diseases are most often the result of defects in rod and/or cone photoreceptor and retinal pigment epithelium function, development, or both. The genes associated with these diseases, when mutated, produce altered protein products that have downstream effects in pathways critical to vision, including phototransduction, the visual cycle, photoreceptor development, cellular respiration, and retinal homeostasis. The aim of this manuscript is to provide a comprehensive review of the underlying molecular mechanisms of pathogenesis of IRDs by delving into many of the genes associated with IRD development, their protein products, and the pathways interrupted by genetic mutation.
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Whole genome sequencing for USH2A-associated disease reveals several pathogenic deep-intronic variants that are amenable to splice correction. HGG ADVANCES 2023; 4:100181. [PMID: 36785559 PMCID: PMC9918427 DOI: 10.1016/j.xhgg.2023.100181] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
A significant number of individuals with a rare disorder such as Usher syndrome (USH) and (non-)syndromic autosomal recessive retinitis pigmentosa (arRP) remain genetically unexplained. Therefore, we assessed subjects suspected of USH2A-associated disease and no or mono-allelic USH2A variants using whole genome sequencing (WGS) followed by an improved pipeline for variant interpretation to provide a conclusive diagnosis. One hundred subjects were screened using WGS to identify causative variants in USH2A or other USH/arRP-associated genes. In addition to the existing variant interpretation pipeline, a particular focus was put on assessing splice-affecting properties of variants, both in silico and in vitro. Also structural variants were extensively addressed. For variants resulting in pseudoexon inclusion, we designed and evaluated antisense oligonucleotides (AONs) using minigene splice assays and patient-derived photoreceptor precursor cells. Biallelic variants were identified in 49 of 100 subjects, including novel splice-affecting variants and structural variants, in USH2A or arRP/USH-associated genes. Thirteen variants were shown to affect USH2A pre-mRNA splicing, including four deep-intronic USH2A variants resulting in pseudoexon inclusion, which could be corrected upon AON treatment. We have shown that WGS, combined with a thorough variant interpretation pipeline focused on assessing pre-mRNA splicing defects and structural variants, is a powerful method to provide subjects with a rare genetic condition, a (likely) conclusive genetic diagnosis. This is essential for the development of future personalized treatments and for patients to be eligible for such treatments.
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RNA-targeting strategies as a platform for ocular gene therapy. Prog Retin Eye Res 2023; 92:101110. [PMID: 35840489 DOI: 10.1016/j.preteyeres.2022.101110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/28/2022] [Accepted: 07/06/2022] [Indexed: 02/01/2023]
Abstract
Genetic medicine is offering hope as new therapies are emerging for many previously untreatable diseases. The eye is at the forefront of these advances, as exemplified by the approval of Luxturna® by the United States Food and Drug Administration (US FDA) in 2017 for the treatment of one form of Leber Congenital Amaurosis (LCA), an inherited blindness. Luxturna® was also the first in vivo human gene therapy to gain US FDA approval. Numerous gene therapy clinical trials are ongoing for other eye diseases, and novel delivery systems, discovery of new drug targets and emerging technologies are currently driving the field forward. Targeting RNA, in particular, is an attractive therapeutic strategy for genetic disease that may have safety advantages over alternative approaches by avoiding permanent changes in the genome. In this regard, antisense oligonucleotides (ASO) and RNA interference (RNAi) are the currently popular strategies for developing RNA-targeted therapeutics. Enthusiasm has been further fuelled by the emergence of clustered regularly interspersed short palindromic repeats (CRISPR)-CRISPR associated (Cas) systems that allow targeted manipulation of nucleic acids. RNA-targeting CRISPR-Cas systems now provide a novel way to develop RNA-targeted therapeutics and may provide superior efficiency and specificity to existing technologies. In addition, RNA base editing technologies using CRISPR-Cas and other modalities also enable precise alteration of single nucleotides. In this review, we showcase advances made by RNA-targeting systems for ocular disease, discuss applications of ASO and RNAi technologies, highlight emerging CRISPR-Cas systems and consider the implications of RNA-targeting therapeutics in the development of future drugs to treat eye disease.
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Kim KS, Koo HY, Bok J. Alternative splicing in shaping the molecular landscape of the cochlea. Front Cell Dev Biol 2023; 11:1143428. [PMID: 36936679 PMCID: PMC10018040 DOI: 10.3389/fcell.2023.1143428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/16/2023] [Indexed: 03/06/2023] Open
Abstract
The cochlea is a complex organ comprising diverse cell types with highly specialized morphology and function. Until now, the molecular underpinnings of its specializations have mostly been studied from a transcriptional perspective, but accumulating evidence points to post-transcriptional regulation as a major source of molecular diversity. Alternative splicing is one of the most prevalent and well-characterized post-transcriptional regulatory mechanisms. Many molecules important for hearing, such as cadherin 23 or harmonin, undergo alternative splicing to produce functionally distinct isoforms. Some isoforms are expressed specifically in the cochlea, while some show differential expression across the various cochlear cell types and anatomical regions. Clinical phenotypes that arise from mutations affecting specific splice variants testify to the functional relevance of these isoforms. All these clues point to an essential role for alternative splicing in shaping the unique molecular landscape of the cochlea. Although the regulatory mechanisms controlling alternative splicing in the cochlea are poorly characterized, there are animal models with defective splicing regulators that demonstrate the importance of RNA-binding proteins in maintaining cochlear function and cell survival. Recent technological breakthroughs offer exciting prospects for overcoming some of the long-standing hurdles that have complicated the analysis of alternative splicing in the cochlea. Efforts toward this end will help clarify how the remarkable diversity of the cochlear transcriptome is both established and maintained.
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Affiliation(s)
- Kwan Soo Kim
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
- Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hei Yeun Koo
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jinwoong Bok
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea
- Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Republic of Korea
- *Correspondence: Jinwoong Bok,
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40
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Tomkiewicz TZ, Nieuwenhuis SE, Cremers FPM, Garanto A, Collin RWJ. Correction of the Splicing Defect Caused by a Recurrent Variant in ABCA4 (c.769-784C>T) That Underlies Stargardt Disease. Cells 2022; 11:3947. [PMID: 36552712 PMCID: PMC9777113 DOI: 10.3390/cells11243947] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/23/2022] [Accepted: 11/26/2022] [Indexed: 12/13/2022] Open
Abstract
Stargardt disease is an inherited retinal disease caused by biallelic mutations in the ABCA4 gene, many of which affect ABCA4 splicing. In this study, nine antisense oligonucleotides (AONs) were designed to correct pseudoexon (PE) inclusion caused by a recurrent deep-intronic variant in ABCA4 (c.769-784C>T). First, the ability of AONs to skip the PE from the final ABCA4 mRNA transcript was assessed in two cellular models carrying the c.769-784C>T variant: a midigene assay using HEK293T cells and patient-derived fibroblasts. Based on the splicing-correcting ability of each individual AON, the three most efficacious AONs targeting independent regions of the PE were selected for a final assessment in photoreceptor precursor cells (PPCs). The final analysis in the PPC model confirmed high efficacy of AON2, -5, and -7 in promoting PE exclusion. Among the three AONs, AON2 is chosen as the lead candidate for further optimization, hereby showcasing the high potential of AONs to correct aberrant splicing events driven by deep-intronic variants.
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Affiliation(s)
- Tomasz Z. Tomkiewicz
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Sara E. Nieuwenhuis
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Frans P. M. Cremers
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Alejandro Garanto
- Departments of Pediatrics, Amalia Children’s Hospital, Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Rob W. J. Collin
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
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41
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Karali M, Testa F, Di Iorio V, Torella A, Zeuli R, Scarpato M, Romano F, Onore ME, Pizzo M, Melillo P, Brunetti-Pierri R, Passerini I, Pelo E, Cremers FPM, Esposito G, Nigro V, Simonelli F, Banfi S. Genetic epidemiology of inherited retinal diseases in a large patient cohort followed at a single center in Italy. Sci Rep 2022; 12:20815. [PMID: 36460718 PMCID: PMC9718770 DOI: 10.1038/s41598-022-24636-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 11/17/2022] [Indexed: 12/04/2022] Open
Abstract
Inherited retinal diseases (IRDs) are the leading cause of vision loss in the working-age population. We performed a retrospective epidemiological study to determine the genetic basis of IRDs in a large Italian cohort (n = 2790) followed at a single referral center. We provided, mainly by next generation sequencing, potentially conclusive molecular diagnosis for 2036 patients (from 1683 unrelated families). We identified a total of 1319 causative sequence variations in 132 genes, including 353 novel variants, and 866 possibly actionable genotypes for therapeutic approaches. ABCA4 was the most frequently mutated gene (n = 535; 26.3% of solved cases), followed by USH2A (n = 228; 11.2%) and RPGR (n = 102; 5.01%). The other 129 genes had a lower contribution to IRD pathogenesis (e.g. CHM 3.5%, RHO 3.5%; MYO7A 3.4%; CRB1 2.7%; RPE65 2%, RP1 1.8%; GUCY2D 1.7%). Seventy-eight genes were mutated in five patients or less. Mitochondrial DNA variants were responsible for 2.1% of cases. Our analysis confirms the complex genetic etiology of IRDs and reveals the high prevalence of ABCA4 and USH2A mutations. This study also uncovers genetic associations with a spectrum of clinical subgroups and highlights a valuable number of cases potentially eligible for clinical trials and, ultimately, for molecular therapies.
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Affiliation(s)
- Marianthi Karali
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy ,grid.9841.40000 0001 2200 8888Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Pansini 5, 80131 Naples, Italy
| | - Francesco Testa
- grid.9841.40000 0001 2200 8888Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Pansini 5, 80131 Naples, Italy
| | - Valentina Di Iorio
- grid.9841.40000 0001 2200 8888Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Pansini 5, 80131 Naples, Italy
| | - Annalaura Torella
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy ,grid.410439.b0000 0004 1758 1171Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Roberta Zeuli
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy
| | - Margherita Scarpato
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy
| | - Francesca Romano
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy
| | - Maria Elena Onore
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy
| | - Mariateresa Pizzo
- grid.410439.b0000 0004 1758 1171Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Paolo Melillo
- grid.9841.40000 0001 2200 8888Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Pansini 5, 80131 Naples, Italy
| | - Raffaella Brunetti-Pierri
- grid.9841.40000 0001 2200 8888Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Pansini 5, 80131 Naples, Italy
| | - Ilaria Passerini
- grid.24704.350000 0004 1759 9494Department of Genetic Diagnosis, Careggi Teaching Hospital, Florence, Italy
| | - Elisabetta Pelo
- grid.24704.350000 0004 1759 9494Department of Genetic Diagnosis, Careggi Teaching Hospital, Florence, Italy
| | - Frans P. M. Cremers
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Gabriella Esposito
- grid.4691.a0000 0001 0790 385XDepartment of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy ,CEINGE-Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Vincenzo Nigro
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy ,grid.410439.b0000 0004 1758 1171Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Francesca Simonelli
- grid.9841.40000 0001 2200 8888Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Pansini 5, 80131 Naples, Italy
| | - Sandro Banfi
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy ,grid.410439.b0000 0004 1758 1171Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
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Robillard KN, de Vrieze E, van Wijk E, Lentz JJ. Altering gene expression using antisense oligonucleotide therapy for hearing loss. Hear Res 2022; 426:108523. [PMID: 35649738 DOI: 10.1016/j.heares.2022.108523] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 04/20/2022] [Accepted: 05/14/2022] [Indexed: 12/12/2022]
Abstract
Hearing loss affects more than 430 million people, worldwide, and is the third most common chronic physical condition in the United States and Europe (GBD Hearing Loss Collaborators, 2021; NIOSH, 2021; WHO, 2021). The loss of hearing significantly impacts motor and cognitive development, communication, education, employment, and overall quality of life. The inner ear houses the sensory organs for both hearing and balance and provides an accessible target for therapeutic delivery. Antisense oligonucleotides (ASOs) use various mechanisms to manipulate gene expression and can be tailor-made to treat disorders with defined genetic targets. In this review, we discuss the preclinical advancements within the field of the highly promising ASO-based therapies for hereditary hearing loss disorders. Particular focus is on ASO mechanisms of action, preclinical studies on ASO treatments of hearing loss, timing of therapeutic intervention, and delivery routes to the inner ear.
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Affiliation(s)
| | - Erik de Vrieze
- Department of Otorhinolaryngology, RUMC, Geert Grooteplein 10, Route 855, GA, Nijmegen 6525, the Netherlands; Donders Institute for Brain, Cognition, and Behavior, RUMC, Nijmegen, NL
| | - Erwin van Wijk
- Department of Otorhinolaryngology, RUMC, Geert Grooteplein 10, Route 855, GA, Nijmegen 6525, the Netherlands; Donders Institute for Brain, Cognition, and Behavior, RUMC, Nijmegen, NL.
| | - Jennifer J Lentz
- Neuroscience Center of Excellence, LSUHSC, New Orleans, LA, USA; Department of Otorhinolaryngology, LSUHSC, 2020 Gravier Street, Lions Building, Room 795, New Orleans, LA, USA.
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43
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Altay HY, Ozdemir F, Afghah F, Kilinc Z, Ahmadian M, Tschopp M, Agca C. Gene regulatory and gene editing tools and their applications for retinal diseases and neuroprotection: From proof-of-concept to clinical trial. Front Neurosci 2022; 16:924917. [PMID: 36340792 PMCID: PMC9630553 DOI: 10.3389/fnins.2022.924917] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 09/26/2022] [Indexed: 09/11/2023] Open
Abstract
Gene editing and gene regulatory fields are continuously developing new and safer tools that move beyond the initial CRISPR/Cas9 technology. As more advanced applications are emerging, it becomes crucial to understand and establish more complex gene regulatory and editing tools for efficient gene therapy applications. Ophthalmology is one of the leading fields in gene therapy applications with more than 90 clinical trials and numerous proof-of-concept studies. The majority of clinical trials are gene replacement therapies that are ideal for monogenic diseases. Despite Luxturna's clinical success, there are still several limitations to gene replacement therapies including the size of the target gene, the choice of the promoter as well as the pathogenic alleles. Therefore, further attempts to employ novel gene regulatory and gene editing applications are crucial to targeting retinal diseases that have not been possible with the existing approaches. CRISPR-Cas9 technology opened up the door for corrective gene therapies with its gene editing properties. Advancements in CRISPR-Cas9-associated tools including base modifiers and prime editing already improved the efficiency and safety profile of base editing approaches. While base editing is a highly promising effort, gene regulatory approaches that do not interfere with genomic changes are also becoming available as safer alternatives. Antisense oligonucleotides are one of the most commonly used approaches for correcting splicing defects or eliminating mutant mRNA. More complex gene regulatory methodologies like artificial transcription factors are also another developing field that allows targeting haploinsufficiency conditions, functionally equivalent genes, and multiplex gene regulation. In this review, we summarized the novel gene editing and gene regulatory technologies and highlighted recent translational progress, potential applications, and limitations with a focus on retinal diseases.
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Affiliation(s)
- Halit Yusuf Altay
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, Istanbul, Turkey
| | - Fatma Ozdemir
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, Istanbul, Turkey
| | - Ferdows Afghah
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, Istanbul, Turkey
| | - Zeynep Kilinc
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, Istanbul, Turkey
| | - Mehri Ahmadian
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, Istanbul, Turkey
| | - Markus Tschopp
- Department of Ophthalmology, Cantonal Hospital Aarau, Aarau, Switzerland
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Cavit Agca
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, Istanbul, Turkey
- Nanotechnology Research and Application Center (SUNUM), Sabanci University, Istanbul, Turkey
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44
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Transcriptomics and RNA-Based Therapeutics as Potential Approaches to Manage SARS-CoV-2 Infection. Int J Mol Sci 2022; 23:ijms231911058. [PMID: 36232363 PMCID: PMC9570475 DOI: 10.3390/ijms231911058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/24/2022] Open
Abstract
SARS-CoV-2 is a coronavirus family member that appeared in China in December 2019 and caused the disease called COVID-19, which was declared a pandemic in 2020 by the World Health Organization. In recent months, great efforts have been made in the field of basic and clinical research to understand the biology and infection processes of SARS-CoV-2. In particular, transcriptome analysis has contributed to generating new knowledge of the viral sequences and intracellular signaling pathways that regulate the infection and pathogenesis of SARS-CoV-2, generating new information about its biology. Furthermore, transcriptomics approaches including spatial transcriptomics, single-cell transcriptomics and direct RNA sequencing have been used for clinical applications in monitoring, detection, diagnosis, and treatment to generate new clinical predictive models for SARS-CoV-2. Consequently, RNA-based therapeutics and their relationship with SARS-CoV-2 have emerged as promising strategies to battle the SARS-CoV-2 pandemic with the assistance of novel approaches such as CRISPR-CAS, ASOs, and siRNA systems. Lastly, we discuss the importance of precision public health in the management of patients infected with SARS-CoV-2 and establish that the fusion of transcriptomics, RNA-based therapeutics, and precision public health will allow a linkage for developing health systems that facilitate the acquisition of relevant clinical strategies for rapid decision making to assist in the management and treatment of the SARS-CoV-2-infected population to combat this global public health problem.
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De Angeli P, Reuter P, Hauser S, Schöls L, Stingl K, Wissinger B, Kohl S. Effective splicing restoration of a deep-intronic ABCA4 variant in cone photoreceptor precursor cells by CRISPR/SpCas9 approaches. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:511-524. [PMID: 35991315 PMCID: PMC9375153 DOI: 10.1016/j.omtn.2022.07.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/20/2022] [Indexed: 12/26/2022]
Affiliation(s)
- Pietro De Angeli
- Institute for Ophthalmic Research, Centre for Ophthalmology, University Hospital Tübingen, 72076 Tübingen, Germany
- Corresponding author Pietro De Angeli, Institute for Ophthalmic Research, Centre for Ophthalmology, Elfriede-Aulhorn-Strasse 5–7, 72076 Tübingen, Germany.
| | - Peggy Reuter
- Institute for Ophthalmic Research, Centre for Ophthalmology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Stefan Hauser
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, 72076 Tübingen, Germany
| | - Ludger Schöls
- German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
- Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, 72076 Tübingen, Germany
| | - Katarina Stingl
- Centre for Ophthalmology, University Hospital Tübingen, 72076 Tübingen, Germany
- Center for Rare Eye Diseases, University of Tübingen, 72076 Tübingen, Germany
| | - Bernd Wissinger
- Institute for Ophthalmic Research, Centre for Ophthalmology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Susanne Kohl
- Institute for Ophthalmic Research, Centre for Ophthalmology, University Hospital Tübingen, 72076 Tübingen, Germany
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46
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Li W, Jiang XS, Han DM, Gao JY, Yang ZT, Jiang L, Zhang Q, Zhang SH, Gao Y, Wu JH, Li JK. Genetic Characteristics and Variation Spectrum of USH2A-Related Retinitis Pigmentosa and Usher Syndrome. Front Genet 2022; 13:900548. [PMID: 36110214 PMCID: PMC9468824 DOI: 10.3389/fgene.2022.900548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
Purposes: We aimed to characterize the USH2A genotypic spectrum in a Chinese cohort and provide a detailed genetic profile for Chinese patients with USH2A-IRD.Methods: We designed a retrospective study wherein a total of 1,334 patients diagnosed with IRD were included as a study cohort, namely 1,278 RP and 56 USH patients, as well as other types of IEDs patients and healthy family members as a control cohort. The genotype-phenotype correlation of all participants with USH2A variant was evaluated.Results: Etiological mutations in USH2A, the most common cause of RP and USH, were found in 16.34% (n = 218) genetically solved IRD patients, with prevalences of 14.87% (190/1,278) and 50% (28/56). After bioinformatics and QC processing, 768 distinct USH2A variants were detected in all participants, including 136 disease-causing mutations present in 665 alleles, distributed in 5.81% of all participants. Of these 136 mutations, 43 were novel, nine were founder mutations, and two hot spot mutations with allele count ≥10. Furthermore, 38.5% (84/218) of genetically solved USH2A-IRD patients were caused by at least one of both c.2802T>G and c.8559–2 A>G mutations, and 36.9% and 69.6% of the alleles in the RP and USH groups were truncating, respectively.Conclusion: USH2A-related East Asian-specific founder and hot spot mutations were the major causes for Chinese RP and USH patients. Our study systematically delineated the genotype spectrum of USH2A-IRD, enabled accurate genetic diagnosis, and provided East Asian and other ethnicities with baseline data of a Chinese origin, which would better serve genetic counseling and therapeutic targets selection.
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Affiliation(s)
- Wei Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
- *Correspondence: Wei Li, ; Ya Gao, ; Ji-Hong Wu, ; Jian-Kang Li,
| | - Xiao-Sen Jiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Dong-Ming Han
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Jia-Yu Gao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Zheng-Tao Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Li Jiang
- Department of Ophthalmology, Laizhou City People’s Hospital, Yantai, China
| | - Qian Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Sheng-Hai Zhang
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China
| | - Ya Gao
- BGI-Shenzhen, Shenzhen, China
- *Correspondence: Wei Li, ; Ya Gao, ; Ji-Hong Wu, ; Jian-Kang Li,
| | - Ji-Hong Wu
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China
- *Correspondence: Wei Li, ; Ya Gao, ; Ji-Hong Wu, ; Jian-Kang Li,
| | - Jian-Kang Li
- BGI-Shenzhen, Shenzhen, China
- *Correspondence: Wei Li, ; Ya Gao, ; Ji-Hong Wu, ; Jian-Kang Li,
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Chien JY, Huang SP. Gene therapy in hereditary retinal dystrophy. Tzu Chi Med J 2022; 34:367-372. [PMID: 36578644 PMCID: PMC9791861 DOI: 10.4103/tcmj.tcmj_78_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/25/2022] [Accepted: 06/07/2022] [Indexed: 11/07/2022] Open
Abstract
Hereditary retinal dystrophies (HRDs), such as retinitis pigmentosa, Leber's congenital amaurosis (LCA), Usher syndrome, and retinoschisis, are a group of genetic retinal disorders exhibiting both genetic and phenotypic heterogeneity. Symptoms include progressive retinal degeneration and constricted visual field. Some patients will be legal or completely blind. Advanced sequencing technologies improve the genetic diagnosis of HRD and lead to a new era of research into gene-targeted therapies. Following the first Food and Drug Administration approval of gene augmentation therapy for LCA caused by RPE65 mutations, multiple clinical trials are currently underway applying different techniques. In this review, we provide an overview of gene therapy for HRD and emphasize four distinct approaches to gene-targeted therapy that have the potential to slow or even reverse retinal degeneration: (1) viral vector-based and nonviral gene delivery, (2) RNA-based antisense oligonucleotide, (3) genome editing by the Clustered Regularly Interspaced Short Palindromic Repeat/cas9 system, and (4) optogenetics gene therapy.
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Affiliation(s)
- Jia-Ying Chien
- Institute of Medical Science, Tzu Chi University, Hualien, Taiwan
| | - Shun-Ping Huang
- Institute of Medical Science, Tzu Chi University, Hualien, Taiwan,Department of Molecular Biology and Human Genetics, Tzu Chi University, Hualien, Taiwan,Department of Ophthalmology, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung, Taiwan,Address for correspondence: Dr. Shun-Ping Huang, Department of Molecular Biology and Human Genetics, Tzu Chi University, 701, Zhongyang Road, Section 3, Hualien, Taiwan. E-mail:
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Su BN, Shen RJ, Liu ZL, Li Y, Jin ZB. Global spectrum of USH2A mutation in inherited retinal dystrophies: Prompt message for development of base editing therapy. Front Aging Neurosci 2022; 14:948279. [PMID: 36034145 PMCID: PMC9399374 DOI: 10.3389/fnagi.2022.948279] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/07/2022] [Indexed: 01/10/2023] Open
Abstract
Purpose Mutation in the USH2A gene is the most common cause of inherited retinal dystrophy (IRD), including non-syndromic retinitis pigmentosa (RP) and Usher syndrome II (USH2). Gene editing and therapy targeting USH2A, especially the hotspot region, would benefit a large proportion of IRD patients. In this study, we comprehensively analyzed the genetic spectrum of the USH2A gene, aiming to identify global hot spot mutations in USH2A-related IRDs and differences in hot spot regions across continents. Materials and methods A retrospective USH2A-related IRD study was conducted, including our IRD cohort, and reported USH2A studies worldwide. Results A total of 3,972 mutated USH2A alleles of approximately 1,935 patients were collected from 33 cohort studies worldwide, containing 102 alleles of 51 patients in our IRD cohort. Mutations in exon 13 were the most common, reaching 18.4% globally and a higher frequency of 22% in America, 19.2% in Europe, and a lower 12% in East Asia. Pathogenic mutations that affected 10 of the 72 exons of USH2A, exon 2, exon 13, exon 41–43, exon 50, exon 54, exon 57, exon 61, and exon 63 in total were responsible for half of global USH2A mutant alleles. With base editors including adenine base editor (ABE), cytidine base editor (CBE), and glycosylase base editor (GBE), 76.3% of single nucleotide variations (SNVs) and 58% of all mutations in USH2A are correctable. Meantime, four novel pathogenic mutations were revealed in our IRD cohort, p. (Val1130Cysfs*72), p. (Ala2139fs*14), p. (Gly4139Arg), and p. (Val4166Cysfs*7). Conclusion In this study, we revealed four novel mutations, expanding the spectrum of USH2A mutations, and importantly presented global hotspot exons and mutations of USH2A as well as the proportion of SNVs that can be restored by different base editors, providing a perspective for exploring high-efficiency and broader-reaching gene editing and gene therapies.
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Affiliation(s)
- Bing-Nan Su
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Beijing Institute of Ophthalmology, Capital Medical University, Beijing, China
- Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing, China
| | - Ren-Juan Shen
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Beijing Institute of Ophthalmology, Capital Medical University, Beijing, China
- Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing, China
| | - Zhuo-Lin Liu
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Beijing Institute of Ophthalmology, Capital Medical University, Beijing, China
- Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing, China
| | - Yang Li
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Beijing Institute of Ophthalmology, Capital Medical University, Beijing, China
- Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing, China
| | - Zi-Bing Jin
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Beijing Institute of Ophthalmology, Capital Medical University, Beijing, China
- Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing, China
- *Correspondence: Zi-Bing Jin,
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Cross N, van Steen C, Zegaoui Y, Satherley A, Angelillo L. Current and Future Treatment of Retinitis Pigmentosa. Clin Ophthalmol 2022; 16:2909-2921. [PMID: 36071725 PMCID: PMC9441588 DOI: 10.2147/opth.s370032] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 07/14/2022] [Indexed: 12/16/2022] Open
Abstract
Retinitis Pigmentosa (RP) is a group of inherited retinal dystrophies (IRDs) characterised by progressive vision loss. Patients with RP experience a significant impact on daily activities, social interactions, and employment, reducing their quality of life. Frequent delays in referrals and no standard treatment for most patients also contribute to the high unmet need for RP. This paper aims to describe the evolving therapeutic landscape for RP including the rationale for advanced therapy medicinal products (ATMPs). A review of available data was conducted in three stages: (1) a search of publicly available literature; (2) qualitative research with physicians treating RP patients in France, Germany, Italy, Spain, and the UK; and (3) a review of leading candidates in the RP pipeline. Globally, there are currently over 100 drugs in development for RP; 50% of which are ATMPs. Amongst the 15 cell and gene therapies in late-stage development, 5 leading candidates have been selected to profile based on the development stage, drug target and geography: gene therapies AGN-151597, GS-030 and VMCO-1 and human stem cell therapies jCell and ReN-003. Hereditary retinal diseases are suitable for treatment with cell and gene therapies due to the accessibility of the retina and its immune privilege and compartmentalisation. Therapeutic approaches that aim to rescue photoreceptors (eg gene therapies) require that non-functional target cells are still present, whereas other therapies (eg cell therapies) are not reliant on the presence of viable photoreceptors. Gene therapies may be attractive as their fundamental goal is to restore vision; however, cell therapies will likely have a broader application and do not rely on genetic testing, which can delay treatment. Ensuring effective therapeutic options for RP patients across disease stages requires the continued diversification and advancement of the development pipeline, and sustained efforts to promote early patient identification and timely diagnosis.
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Affiliation(s)
| | - Cécile van Steen
- Market Access, Health Technology Assessment & Health Economics and Outcome Research, Europe, the Middle East and Africa, Santen GmbH, Munich, Bavaria, Germany
| | - Yasmina Zegaoui
- Market Access, Lightning Health, London, UK
- Correspondence: Yasmina Zegaoui, Market Access, Lightning Health, 8 Devonshire Square, London, EC2M 4PL, UK, Tel +44 7770918748, Email
| | | | - Luigi Angelillo
- Market Access, Health Technology Assessment & Health Economics and Outcome Research, Europe, the Middle East and Africa, Santen GmbH, Munich, Bavaria, Germany
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Zebrafish and inherited photoreceptor disease: Models and insights. Prog Retin Eye Res 2022; 91:101096. [PMID: 35811244 DOI: 10.1016/j.preteyeres.2022.101096] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/20/2022] [Accepted: 06/23/2022] [Indexed: 11/21/2022]
Abstract
Photoreceptor dysfunctions and degenerative diseases are significant causes of vision loss in patients, with few effective treatments available. Targeted interventions to prevent or reverse photoreceptor-related vision loss are not possible without a thorough understanding of the underlying mechanism leading to disease, which is exceedingly difficult to accomplish in the human system. Cone diseases are particularly challenging to model, as some popular genetically modifiable model animals are nocturnal with a rod-dominant visual system and cones that have dissimilarities to human cones. As a result, cone diseases, which affect visual acuity, colour perception, and central vision in patients, are generally poorly understood in terms of pathology and mechanism. Zebrafish (Danio rerio) provide the opportunity to model photoreceptor diseases in a diurnal vertebrate with a cone-rich retina which develops many macular degeneration-like pathologies. Zebrafish undergo external development, allowing early-onset retinal diseases to be detected and studied, and many ophthalmic tools are available for zebrafish visual assessment during development and adulthood. There are numerous zebrafish models of photoreceptor disease, spanning the various types of photoreceptor disease (developmental, rod, cone, and mixed photoreceptor diseases) and genetic/molecular cause. In this review, we explore the features of zebrafish that make them uniquely poised to model cone diseases, summarize the established zebrafish models of inherited photoreceptor disease, and discuss how disease in these models compares to the human presentation, where applicable. Further, we highlight the contributions of these zebrafish models to our understanding of photoreceptor biology and disease, and discuss future directions for utilising and investigating these diverse models.
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