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Ng BW, Kaukonen MK, McClements ME, Shamsnajafabadi H, MacLaren RE, Cehajic-Kapetanovic J. Genetic therapies and potential therapeutic applications of CRISPR activators in the eye. Prog Retin Eye Res 2024:101289. [PMID: 39127142 DOI: 10.1016/j.preteyeres.2024.101289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 08/05/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
Conventional gene therapy involving supplementation only treats loss-of-function diseases and is limited by viral packaging sizes, precluding therapy of large genes. The discovery of CRISPR/Cas has led to a paradigm shift in the field of genetic therapy, with the promise of precise gene editing, thus broadening the range of diseases that can be treated. The initial uses of CRISPR/Cas have focused mainly on gene editing or silencing of abnormal variants via utilising Cas endonuclease to trigger the target cell endogenous non-homologous end joining. Subsequently, the technology has evolved to modify the Cas enzyme and even its guide RNA, leading to more efficient editing tools in the form of base and prime editing. Further advancements of this CRISPR/Cas technology itself have expanded its functional repertoire from targeted editing to programmable transactivation, shifting the therapeutic focus to precise endogenous gene activation or upregulation with the potential for epigenetic modifications. In vivo experiments using this platform have demonstrated the potential of CRISPR-activators (CRISPRa) to treat various loss-of-function diseases, as well as in regenerative medicine, highlighting their versatility to overcome limitations associated with conventional strategies. This review summarises the molecular mechanisms of CRISPRa platforms, the current applications of this technology in vivo, and discusses potential solutions to translational hurdles for this therapy, with a focus on ophthalmic diseases.
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Affiliation(s)
- Benjamin Wj Ng
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Maria K Kaukonen
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; Department of Medical and Clinical Genetics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Michelle E McClements
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Hoda Shamsnajafabadi
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Robert E MacLaren
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford UK; NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Jasmina Cehajic-Kapetanovic
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford UK; NIHR Oxford Biomedical Research Centre, Oxford, UK.
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Varner LR, Chaya T, Maeda Y, Tsutsumi R, Zhou S, Tsujii T, Okuzaki D, Furukawa T. The deubiquitinase Otud7b suppresses cone photoreceptor degeneration in mouse models of retinal degenerative diseases. iScience 2024; 27:109380. [PMID: 38510130 PMCID: PMC10951987 DOI: 10.1016/j.isci.2024.109380] [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: 09/05/2023] [Revised: 01/15/2024] [Accepted: 02/27/2024] [Indexed: 03/22/2024] Open
Abstract
Primary and secondary cone photoreceptor death in retinal degenerative diseases, including age-related macular degeneration (AMD) and retinitis pigmentosa (RP), leads to severe visual impairment and blindness. Although the cone photoreceptor protection in retinal degenerative diseases is crucial for maintaining vision, the underlying molecular mechanisms are unclear. Here, we found that the deubiquitinase Otud7b/Cezanne is predominantly expressed in photoreceptor cells in the retina. We analyzed Otud7b-/- mice, which were subjected to light-induced damage, a dry AMD model, or were mated with an RP mouse model, and observed increased cone photoreceptor degeneration. Using RNA-sequencing and bioinformatics analysis followed by a luciferase reporter assay, we found that Otud7b downregulates NF-κB activity. Furthermore, inhibition of NF-κB attenuated cone photoreceptor degeneration in the light-exposed Otud7b-/- retina and stress-induced neuronal cell death resulting from Otud7b deficiency. Together, our findings suggest that Otud7b protects cone photoreceptors in retinal degenerative diseases by modulating NF-κB activity.
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Affiliation(s)
- Leah Rie Varner
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Taro Chaya
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Yamato Maeda
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Ryotaro Tsutsumi
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Shanshan Zhou
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Toshinori Tsujii
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Takahisa Furukawa
- Laboratory for Molecular and Developmental Biology, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
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Jolly JK, Rodda BM, Edwards TL, Ayton LN, Ruddle JB. Optical coherence tomography in children with inherited retinal disease. Clin Exp Optom 2024; 107:255-266. [PMID: 38252959 DOI: 10.1080/08164622.2023.2294807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 12/06/2023] [Indexed: 01/24/2024] Open
Abstract
Recent advances have led to therapeutic options becoming available for people with inherited retinal disease. In particular, gene therapy has been shown to hold great promise for slowing vision loss from inherited retinal disease. Recent studies suggest that gene therapy is likely to be most effective when implemented early in the disease process, making consideration of paediatric populations important. It is therefore necessary to have a comprehensive understanding of retinal imaging in children with inherited retinal diseases, in order to monitor disease progression and to determine which early retinal biomarkers may be used as outcome measures in future clinical trials. In addition, as many optometrists will review children with an inherited retinal disease, an understanding of the expected imaging outcomes can improve clinical care. This review focuses on the most common imaging modality used in research assessment of paediatric inherited retinal diseases: optical coherence tomography. Optical coherence tomography findings can be used in both the clinical and research setting. In particular, the review discusses current knowledge of optical coherence tomography findings in eight paediatric inherited retinal diseases - Stargardt disease, Bests disease, Leber's congenital amaurosis, choroideremia, RPGR related retinitis pigmentosa, Usher syndrome, X-linked retinoschisis and, Batten disease.
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Affiliation(s)
- Jasleen K Jolly
- Vision and Eye Research Institute, Anglia Ruskin University, Cambridge, UK
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Brent M Rodda
- Department of Optometry and Vision Sciences, The University of Melbourne, Carlton, Victoria, Australia
| | - Thomas L Edwards
- Ophthalmology, Department of Surgery, The University of Melbourne, East Melbourne, Victoria, Australia
- Centre for Eye Research Australia, The Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Lauren N Ayton
- Department of Optometry and Vision Sciences, The University of Melbourne, Carlton, Victoria, Australia
- Ophthalmology, Department of Surgery, The University of Melbourne, East Melbourne, Victoria, Australia
- Centre for Eye Research Australia, The Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Jonathan B Ruddle
- Centre for Eye Research Australia, The Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
- Department of Ophthalmology, Royal Children's Hospital, Parkville, Victoria, Australia
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Lam BL, Pennesi ME, Kay CN, Panda S, Gow JA, Zhao G, MacLaren RE. Assessment of Visual Function with Cotoretigene Toliparvovec in X-Linked Retinitis Pigmentosa in the Randomized XIRIUS Phase 2/3 Study. Ophthalmology 2024:S0161-6420(24)00162-3. [PMID: 38423215 DOI: 10.1016/j.ophtha.2024.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 03/02/2024] Open
Abstract
PURPOSE Cotoretigene toliparvovec (BIIB112/AAV8-RPGR) is an investigational vector-based gene therapy designed to provide a full-length, codon-optimized retinitis pigmentosa GTPase regulator (RPGR) protein to individuals with RPGR-associated X-linked retinitis pigmentosa (XLRP). We assessed efficacy and tolerability of cotoretigene toliparvovec subretinal gene therapy. DESIGN Part 2 of the XIRIUS trial (ClinicalTrials.gov identifier, NCT03116113) was a phase 2/3, 12-month, randomized (1:1:1) dose-expansion study. PARTICIPANTS Male patients ≥10 years of age with RPGR-associated XLRP were included. METHODS Participants were randomized 1:1:1 to receive low-dose subretinal cotoretigene toliparvovec (5 × 1010 vector genomes/eye), high-dose cotoretigene toliparvovec (2.5 × 1011 vector genomes/eye) or to be an untreated control participant. MAIN OUTCOME MEASURES The primary end point was the percentage of participants meeting microperimetry responder criteria (≥ 7-dB improvement at ≥ 5 of 16 central loci). Secondary end points included change from baseline in retinal sensitivity at the central 16 loci and the entire 68 loci at 12 months and change from baseline in low-luminance visual acuity (LLVA) at 12 months, as well as the proportion of eyes with a ≥ 15-Early Treatment Diabetic Retinopathy Study ETDRS letter LLVA and ≥ 10-ETDRS letter LLVA change from baseline at month 12. RESULTS Because of the impact of the COVID-19 pandemic, enrollment ended before reaching the initial target, leaving the trial underpowered. Twenty-nine participants were included (low-dose group, n = 10; high-dose group, n = 10; control group, n = 9). At month 12, the percentage of participants meeting microperimetry responder criteria was not significantly different between either cotoretigene toliparvovec group (low dose, 37.5% [P = 0.3181]; high dose, 25.0% [P = 0.5177]) and the control group (22.2%). However, the mean change from baseline in microperimetry sensitivity improved significantly with the low-dose group versus the control group at month 12 (P = 0.0350). Significant improvement in LLVA occurred in the low-dose group versus the control group at month 12 (33.3% difference [80% confidence interval, 14.7%-55.2%]; P = 0.0498). Three ocular-related serious adverse events (SAEs) occurred in the low-dose group versus 7 SAEs in the high-dose group. CONCLUSIONS The primary microperimetry end point was not met. Significant improvements in LLVA and mean microperimetry were observed compared with controls and fewer SAEs occured with low-dose compared with high dose cotoretigene toliparvovec. 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)
- Byron L Lam
- Bascom Palmer Eye Institute, University of Miami, Miami, Florida
| | - Mark E Pennesi
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon
| | | | | | | | | | - Robert E MacLaren
- University of Oxford and NIHR Oxford Biomedical Research Center, Oxford, United Kingdom.
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Wang YZ, Juroch K, Chen Y, Ying GS, Birch DG. Deep Learning-Facilitated Study of the Rate of Change in Photoreceptor Outer Segment Metrics in RPGR-Related X-Linked Retinitis Pigmentosa. Invest Ophthalmol Vis Sci 2023; 64:31. [PMID: 37988107 PMCID: PMC10668621 DOI: 10.1167/iovs.64.14.31] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/02/2023] [Indexed: 11/22/2023] Open
Abstract
Purpose The aim of this retrospective cohort study was to obtain three-dimensional (3D) photoreceptor outer segment (OS) metrics measurements with the assistance of a deep learning model (DLM) and to evaluate the longitudinal change in OS metrics and associated factors in retinitis pigmentosa GTPase regulator (RPGR) X-linked retinitis pigmentosa (XLRP). Methods The study included 34 male patients with RPGR-associated XLRP who had preserved ellipsoid zone (EZ) within their spectral-domain optical coherence tomography volume scans and an approximate 2-year or longer follow-up. Volume scans were segmented using a DLM with manual correction for EZ and apical retinal pigment epithelium (RPE). OS metrics were measured from 3D EZ-RPE layers of volume scans. Linear mixed-effects models were used to calculate the rate of change in OS metrics and the associated factors, including baseline age, baseline OS metrics, and follow-up duration. Results The mean (standard deviation) of progression rates were -0.28 (0.43) µm/y, -0.73 (0.61) mm2/y, and -0.014 (0.012) mm3/y for OS thickness, EZ area, and OS volume, respectively. In multivariable analysis, the progression rates of EZ area and OS volume were strongly associated with their baseline values, with faster decline in eyes with larger baseline values (P ≤ 0.003), and nonlinearly associated with the baseline age (P ≤ 0.003). OS thickness decline was not associated with its baseline value (P = 0.32). Conclusions These results provide evidence to support using OS metrics as biomarkers to assess the progression of XLRP and as the outcome measures of clinical trials. Given that their progression rates are dependent on their baseline values, the baseline EZ area and OS volume should be considered in the design and statistical analysis of future clinical trials. Deep learning may provide a useful tool to reduce the burden of human graders to analyze OCT scan images and to facilitate the assessment of disease progression and treatment trials for retinitis pigmentosa.
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Affiliation(s)
- Yi-Zhong Wang
- Retina Foundation of the Southwest, Dallas, Texas, United States
- Department of Ophthalmology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States
| | - Katherine Juroch
- Retina Foundation of the Southwest, Dallas, Texas, United States
| | - Yineng Chen
- Center for Preventive Ophthalmology and Biostatistics, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Gui-Shuang Ying
- Center for Preventive Ophthalmology and Biostatistics, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - David G. Birch
- Retina Foundation of the Southwest, Dallas, Texas, United States
- Department of Ophthalmology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States
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Buckley TM, Jolly JK, Josan AS, Wood LJ, Cehajic‐Kapetanovic J, MacLaren RE. Clinical applications of microperimetry in RPGR-related retinitis pigmentosa: a review. Acta Ophthalmol 2021; 99:819-825. [PMID: 33783139 DOI: 10.1111/aos.14816] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 12/16/2020] [Accepted: 02/02/2021] [Indexed: 01/05/2023]
Abstract
Microperimetry, or fundus-tracked perimetry, is a precise static-automated perimetric technique to assess central retinal function. As visual acuity only deteriorates at a late disease stage in RPGR-related retinitis pigmentosa (RP), alternative markers for disease progression are of great utility. Microperimetry assessment has been of critical value as an outcome measure in a recently reported phase I/II gene therapy trial for RPGR-related RP, both in terms of detecting safety and efficacy signals. Here, we performed a review of the literature. We describe the principles of microperimetry before outlining specific parameters that may be useful as outcome measures in clinical trial settings. The current state of structure-function correlations between short-wavelength autofluorescence, optical coherence tomography and adaptive optics in RPGR-related retinitis pigmentosa are also summarized.
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Affiliation(s)
| | - Jasleen K. Jolly
- Oxford Eye Hospital Oxford University Hospitals NHS Trust Oxford UK
- Nuffield Laboratory of Ophthalmology Nuffield Department of Clinical Neurosciences Oxford Biomedical Research Centre University of Oxford Oxford UK
| | - Amandeep Singh Josan
- Oxford Eye Hospital Oxford University Hospitals NHS Trust Oxford UK
- Nuffield Laboratory of Ophthalmology Nuffield Department of Clinical Neurosciences Oxford Biomedical Research Centre University of Oxford Oxford UK
| | - Laura J. Wood
- Oxford Eye Hospital Oxford University Hospitals NHS Trust Oxford UK
- Nuffield Laboratory of Ophthalmology Nuffield Department of Clinical Neurosciences Oxford Biomedical Research Centre University of Oxford Oxford UK
| | - Jasmina Cehajic‐Kapetanovic
- Oxford Eye Hospital Oxford University Hospitals NHS Trust Oxford UK
- Nuffield Laboratory of Ophthalmology Nuffield Department of Clinical Neurosciences Oxford Biomedical Research Centre University of Oxford Oxford UK
| | - Robert E. MacLaren
- Oxford Eye Hospital Oxford University Hospitals NHS Trust Oxford UK
- Nuffield Laboratory of Ophthalmology Nuffield Department of Clinical Neurosciences Oxford Biomedical Research Centre University of Oxford Oxford UK
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Yang J, Zhou L, Ouyang J, Xiao X, Sun W, Li S, Zhang Q. Genotype-Phenotype Analysis of RPGR Variations: Reporting of 62 Chinese Families and a Literature Review. Front Genet 2021; 12:600210. [PMID: 34745198 PMCID: PMC8565807 DOI: 10.3389/fgene.2021.600210] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 04/27/2021] [Indexed: 02/05/2023] Open
Abstract
Purpose RPGR is the most common cause of X-linked retinitis pigmentosa (RP), of which female carriers are also frequently affected. The aim of the current study was to explore the RPGR variation spectrum and associated phenotype based on the data from our lab and previous studies. Methods Variants in RPGR were selected from exome sequencing data of 7,092 probands with different eye conditions. The probands and their available family members underwent comprehensive ocular examinations. Similar data were collected from previous reports through searches in PubMed, Web of Science, and Google Scholar. Systematic analyses of genotypes, phenotypes and their correlations were performed. Results A total of 46 likely pathogenic variants, including nine missense and one in-frame variants in RCC1-like domain and 36 truncation variants, in RPGR were detected in 62 unrelated families in our in-house cohort. In addition, a total of 585 variants, including 491 (83.9%) truncation variants, were identified from the literature. Systematic analysis of variants from our in-house dataset, literature, and gnomAD suggested that most of the pathogenic variants of RPGR were truncation variants while pathogenic missense and in-frame variants were enriched in the RCC1-like domain. Phenotypic variations were present between males and female carriers, including more severe refractive error but better best corrected visual acuity (BCVA) in female carriers than those in males. The male patients showed a significant reduction of BCVA with increase of age and males with exon1-14 variants presented a better BCVA than those with ORF15 variants. For female carriers, the BCVA also showed significant reduction with increase of age, but BCVA in females with exon1-14 variants was not significant difference compared with those with ORF15 variants. Conclusion Most pathogenic variants of RPGR are truncations. Missense and in-frame variants located outside of the RCC1-like domain might be benign and the pathogenicity criteria for these variants should be considered with greater caution. The BCVA and refractive error are different between males and female carriers. Increase of age and location of variants in ORF15 contribute to the reduction of BCVA in males. These results are valuable for understanding genotypes and phenotypes of RPGR.
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Affiliation(s)
- Junxing Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Lin Zhou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.,Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
| | - Jiamin Ouyang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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Wang YZ, Wu W, Birch DG. A Hybrid Model Composed of Two Convolutional Neural Networks (CNNs) for Automatic Retinal Layer Segmentation of OCT Images in Retinitis Pigmentosa (RP). Transl Vis Sci Technol 2021; 10:9. [PMID: 34751740 PMCID: PMC8590180 DOI: 10.1167/tvst.10.13.9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Purpose We propose and evaluate a hybrid model composed of two convolutional neural networks (CNNs) with different architectures for automatic segmentation of retina layers in spectral domain optical coherence tomography (SD-OCT) B-scans of retinitis pigmentosa (RP). Methods The hybrid model consisted of a U-Net for initial semantic segmentation and a sliding-window (SW) CNN for refinement by correcting the segmentation errors of U-Net. The U-Net construction followed Ronneberger et al. (2015) with an input image size of 256 × 32. The SW model was similar to our previously reported approach. Training image patches were generated from 480 horizontal midline B-scans obtained from 220 patients with RP and 20 normal participants. Testing images were 160 midline B-scans from a separate group of 80 patients with RP. The Spectralis segmentation of B-scans was manually corrected for the boundaries of the inner limiting membrane, inner nuclear layer, ellipsoid zone (EZ), retinal pigment epithelium, and Bruch's membrane by one grader for the training set and two for the testing set. The trained U-Net and SW, as well as the hybrid model, were used to classify all pixels in the testing B-scans. Bland–Altman and correlation analyses were conducted to compare layer boundary lines, EZ width, and photoreceptor outer segment (OS) length and area determined by the models to those by human graders. Results The mean times to classify a B-scan image were 0.3, 65.7, and 2.4 seconds for U-Net, SW, and the hybrid model, respectively. The mean ± SD accuracies to segment retinal layers were 90.8% ± 4.8% and 90.7% ± 4.0% for U-Net and SW, respectively. The hybrid model improved mean ± SD accuracy to 91.5% ± 4.8% (P < 0.039 vs. U-Net), resulting in an improvement in layer boundary segmentation as revealed by Bland–Altman analyses. EZ width, OS length, and OS area measured by the models were highly correlated with those measured by the human graders (r > 0.95 for EZ width; r > 0.83 for OS length; r > 0.97 for OS area; P < 0.05). The hybrid model further improved the performance of measuring retinal layer thickness by correcting misclassification of retinal layers from U-Net. Conclusions While the performances of U-Net and the SW model were comparable in delineating various retinal layers, U-Net was much faster than the SW model to segment B-scan images. The hybrid model that combines the two improves automatic retinal layer segmentation from OCT images in RP. Translational Relevance A hybrid deep machine learning model composed of CNNs with different architectures can be more effective than either model separately for automatic analysis of SD-OCT scan images, which is becoming increasingly necessary with current high-resolution, high-density volume scans.
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Affiliation(s)
- Yi-Zhong Wang
- Retina Foundation of the Southwest, Dallas, TX, USA.,Department of Ophthalmology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Wenxuan Wu
- Retina Foundation of the Southwest, Dallas, TX, USA
| | - David G Birch
- Retina Foundation of the Southwest, Dallas, TX, USA.,Department of Ophthalmology, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
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Shurygina MF, Khoteeva AM. [Diagnostics of inherited retinal degenerations by gene therapy]. Vestn Oftalmol 2021; 137:145-151. [PMID: 34410070 DOI: 10.17116/oftalma2021137041145] [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: 11/18/2022]
Abstract
The article presents recent worldwide achievements in the area of diagnosis and treatment of inherited retinal degenerations (IRDs) from the standpoint of ophthalmic genetics. Clinical studies conducted in patients with Leber congenital amaurosis and retinitis pigmentosa caused by biallelic mutations in the RPE65 gene have provided the basis for future genes studies associated with IRDs. The conducted studies highlight the importance of fundamental understanding of function of the gene, timely diagnosis and study of natural history of the disease. Currently, surgical techniques are being improved for the efficient delivery of gene preparations to target cells, as well as the criteria for evaluating treatment outcomes.
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Affiliation(s)
- M F Shurygina
- S.N. Fedorov National Medical Research Center «MNTK «Eye Microsurgery», Moscow, Russia.,Center of Genetics and Reproductive Medicine «Genetico», Moscow, Russia
| | - A M Khoteeva
- S.N. Fedorov National Medical Research Center «MNTK «Eye Microsurgery», Moscow, Russia
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10
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Wood LJ, Jolly JK, Josan AS, Buckley TMW, MacLaren RE. Low Luminance Visual Acuity and Low Luminance Deficit in Choroideremia and RPGR-Associated Retinitis Pigmentosa. Transl Vis Sci Technol 2021; 10:28. [PMID: 34003913 PMCID: PMC7900861 DOI: 10.1167/tvst.10.2.28] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 01/07/2021] [Indexed: 11/24/2022] Open
Abstract
Introduction Choroideremia and RPGR-associated retinitis pigmentosa (RP) are two distinct inherited rod-cone degenerations, where good visual acuity (VA) is maintained until late disease stages, limiting its usefulness as a disease marker. Low luminance VA and low luminance deficit (standard VA minus low luminance VA) may be more sensitive visual function measures. Methods Standard VA was obtained using Early Treatment Diabetic Retinopathy Study letter charts (Precision Vision, Bloomington, IL, USA). Low luminance VA was assessed using a 2.0-log unit neutral density filter, with the same chart setup, without formal dark adaptation. Mean central retinal sensitivity was assessed using MAIA microperimetry (Centervue SpA, Padova, Italy). Optical coherence tomography imaging was attained with Heidelberg Eye Explorer software (Heidelberg Engineering, Heidelberg, Germany). Results Twenty-four male participants with confirmed pathogenic RPGR mutations, 44 male participants with confirmed pathogenic CHM mutations, and 62 age-matched controls underwent clinical assessment prior to clinical trial recruitment. Low luminance VA was significantly reduced in both disease groups compared to controls. The low luminance deficit correlated with microperimetry retinal sensitivity and ellipsoid zone width. Eleven participants with moderate VA had poor low luminance VA (subsequently a large low luminance deficit), no detectable microperimetry sensitivity, and severely constricted ellipsoid zone widths. Conclusions Low luminance VA and subsequently low luminance deficit are useful markers of central macular visual function in both choroideremia and RPGR-associated RP, when standard VA is preserved. Translational Relevance Low luminance visual acuity and low luminance deficit are useful vision measures in two distinct rod-cone degenerations and may be useful in other retinal degenerations.
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Affiliation(s)
- Laura J. Wood
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jasleen K. Jolly
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Amandeep S. Josan
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Thomas M. W. Buckley
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Robert E. MacLaren
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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Cehajic-Kapetanovic J, McClements ME, Whitfield J, Shanks M, Clouston P, MacLaren RE. Association of a Novel Intronic Variant in RPGR With Hypomorphic Phenotype of X-Linked Retinitis Pigmentosa. JAMA Ophthalmol 2020; 138:1151-1158. [PMID: 32970112 PMCID: PMC7516822 DOI: 10.1001/jamaophthalmol.2020.3634] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Importance Pathogenic variants in retinitis pigmentosa GTPase regulator (RPGR) gene typically lead to a severe form of X-linked retinitis pigmentosa, which is associated with early severe vision loss. Objective To investigate an X-linked retinal degeneration family with atypical preservation of visual acuity in the presence of a novel deep intronic splice site RPGR c.779-5T>G variant. Design, Setting, and Participants In this case series, 3 members of an X-linked retinal degeneration family were studied by in-depth phenotyping and genetic screening at a single center. Data were collected and analyzed from November 2018 to March 2020. Main Outcomes and Measures Data were collected on full ophthalmic history, examination, and retinal imaging. A full retinitis pigmentosa gene panel was analyzed by next-generation sequencing. The pathogenicity of the RPGR c.779-5T>G variant was assessed by in silico splice prediction tools and by purpose-designed in vitro splicing assay. Results An 84-year-old man was referred with clinical diagnosis of choroideremia and possible inclusion into a gene therapy trial. He presented with late-stage retinal degeneration and unusually preserved visual acuity (78 and 68 ETRDS letters) that clinically resembled choroideremia. His 23-year-old grandson was still in early stages of degeneration but showed a very different clinical picture, typical of retinitis pigmentosa. Next-generation sequencing identified a sole RPGR c.779-5T>G variant of undetermined pathogenicity in both cases. The daughter of the proband showed an RPGR carrier phenotype and was confirmed to carry the same variant. The molecular analysis confirmed that the RPGR c.779-5T>G variation reduced the efficiency of intron splicing compared with wild type, leading to a population of mutant and normal transcripts. The predicted consequences of the pathogenic variant are potential use of an alternative splice acceptor site or complete skipping of exon 8, resulting in truncated forms of the RPGR protein with different levels of glutamylation. Conclusions and Relevance These results support the importance of careful interpretation of inconsistent clinical phenotypes between family members. Using a molecular splicing assay, a new pathogenic variant in a noncoding region of RPGR was associated with a proportion of normal and hypomorphic RPGR, where cones are likely to survive longer than expected, potentially accounting for the preserved visual acuity observed in this family.
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Affiliation(s)
- Jasmina Cehajic-Kapetanovic
- Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford, England
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, England
| | - Michelle E. McClements
- Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford, England
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, England
| | - Jennifer Whitfield
- Genetics Laboratories, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, England
| | - Morag Shanks
- Genetics Laboratories, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, England
| | - Penny Clouston
- Genetics Laboratories, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, England
| | - Robert E. MacLaren
- Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford, England
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, England
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Jolly JK, Menghini M, Johal PA, Buckley TMW, Bridge H, Maclaren RE. Inner retinal thickening affects microperimetry thresholds in the presence of photoreceptor thinning in patients with RPGR retinitis pigmentosa. Br J Ophthalmol 2020; 106:256-261. [PMID: 33127827 DOI: 10.1136/bjophthalmol-2020-317692] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Loss of photoreceptors cause degeneration in areas of the retina beyond the photoreceptors. The pattern of changes has implications for disease monitoring and measurement of functional changes. The aim of the study was to study the changes in inner retinal structure associated with photoreceptor disease, and the impact of these on microperimetry threshold. METHODS This retrospective cohort study was conducted on optical coherence tomography (OCT) images and microperimetry tests collected between 2013 and 2019. 22 eyes with RPGR retinitis pigmentosa completed both OCT imaging and microperimetry assessment. 18 control eyes underwent OCT imaging. Photoreceptor layer and inner retinal thickness calculated for different eccentric areas were obtained. The relationship between the photoreceptor layer and inner retinal thickness, and microperimetry threshold was explored. RESULTS Central 1° photoreceptor layer and inner retinal thickness were 96±34 and 139±75 μm in RPGR patients, and 139±15 and 62±14 μm in controls. Photoreceptor layer thickness differed between patient and control groups across increasing visual field areas (p<0.01, Kruskal-Wallis 1-way ANOVA), whereas the inner retinal thickness significantly differed between groups for the central 1° and 3° only. Microperimetry thresholds were explained by a combination of photoreceptor thickness (coefficient 0.15, 95% CI 0.13 to 0.18) and inner retinal thickness (coefficient 0.05, 95% CI 0.03 to 0.06). CONCLUSION OCT shows evidence of remodelling in the inner retinal layers secondary to photoreceptor disease. This appears to have an impact on microperimetry threshold measurements.
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Affiliation(s)
- Jasleen Kaur Jolly
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK .,Oxford Centre for Functional MRI of the Brain (FMRIB), Wellcome Centre for Integrative Neuroimaging, University of Oxford, Oxford OX3 9DU, UK.,Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Moreno Menghini
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK.,Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Piers A Johal
- Oxford Centre for Functional MRI of the Brain (FMRIB), Wellcome Centre for Integrative Neuroimaging, University of Oxford, Oxford OX3 9DU, UK
| | - Thomas M W Buckley
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK.,Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Holly Bridge
- Oxford Centre for Functional MRI of the Brain (FMRIB), Wellcome Centre for Integrative Neuroimaging, University of Oxford, Oxford OX3 9DU, UK
| | - Robert E Maclaren
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK.,Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
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