Gene-Based Therapeutics for Inherited Retinal Diseases

Inherited retinal degeneration in Malay and Indian populations of Singapore and Malaysia: a prospective multicentre study

PURPOSE

To analyze the phenotypic and genotypic characteristics of inherited retinal degeneration (IRD) patients of Malay and Indian ethnicity from Singapore and Malaysia.

METHODS

Ethnic Malay and Indian IRD patients were consecutively enrolled from retina clinics in Singapore and Malaysia. Phenotypic and genetic data were reviewed.

RESULTS

A total of 100 unrelated individuals (Malay: n = 46, Indian: n = 54) were enrolled. Sixteen distinct IRD phenotypes were identified, with nonsyndromic retinitis pigmentosa (RP) comprising 46% of all cases. Stargardt disease and cone-rod dystrophy accounted for 20% and 11% of cases, respectively. Exome sequencing yielded genotypes in 64.3% of Malay and 68.9% of Indian cases. Variants in ABCA4 were the most common cause of IRD overall. Recurrent variants were identified in ABCA4, GUCY2D, PRPH2, and TULP1 for Malays, and in ABCA4 and MFSD8 (CLN7) for Indians. Homozygosity was more frequent among Indians than Malays (58.1% vs. 19.2%; p = 0.003).

CONCLUSIONS

This study demonstrated diverse phenotypic and genotypic outcomes in Malay and Indian populations of Singapore and Malaysia, with distinct differences between them. Homozygosity was common among ethnic Indian IRD cases, explaining phenotypic diversity. These findings inform the identification of regionally relevant IRDs for developing targeted therapies in Malay and Indian patients from Southeast Asia.

Rescue of the disease-associated phenotype in CRISPR-corrected hiPSCs as a therapeutic approach for inherited retinal dystrophies

Inherited retinal dystrophies (IRDs), such as retinitis pigmentosa and Stargardt disease, are a group of rare diseases caused by mutations in more than 300 genes that currently have no treatment in most cases. They commonly trigger blindness and other ocular affectations due to retinal cell degeneration. Gene editing has emerged as a promising and powerful strategy for the development of IRD therapies, allowing the permanent correction of pathogenic variants. Using clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 and transcription activator-like effector nucleases (TALEN) gene-editing tools, we precisely corrected seven hiPS cell lines derived from IRD patients carrying mutations in ABCA4, BEST1, PDE6A, PDE6C, RHO, or USH2A. Homozygous mutations and point insertions/deletions resulted in the highest homology-directed repair efficiencies, with at least half of the clones repaired properly without off-target effects. Strikingly, correction of a heterozygous pathogenic variant was achieved using the wild-type allele of the patient as the template for DNA repair. These results suggest the unexpected potential application of CRISPR as a donor template-free strategy for single-nucleotide modifications. Additionally, the corrected clones exhibited a reversion of the disease-associated phenotype in retinal cellular models. These data strengthen the study and application of gene editing-based approaches for IRD treatment.

Clinical Exome Sequencing in Pediatric Patients

INTRODUCTION

The development of genomic sequencing techniques has led to the effective diagnosis of genetic diseases. In this study, clinical exome sequencing (CES) results applied to genetic disorders are reported.

METHODS

The CES results of pediatric patients with different system involvements and whose complaints were thought to be of genetic origin were evaluated retrospectively.

RESULTS

Significant variants associated with complaints were detected in 41 (60%) of 68 patients. Copy number variations were detected in two patients, and single nucleotide variants (SNVs) were detected in the other 39 patients. A total of 46 SNVs were detected in these 39 patients. Sixteen of the detected SNVs were previously reported in the literature, but 30 were novel.

CONCLUSIONS

This study shows that CES can provide a high diagnosis rate (60%) in childhood genetic diseases. Novel mutations (30) have contributed to the mutation profiles of genetic disorders.

Characterisation of SLC38A8 and Its Role in Retinal Pathways and Disease

BACKGROUND

This study investigates the role of the SLC38A8 gene. SLC38A8 facilitates glutamine influx, which converts to glutamate in the visual pathway. Mutations in SLC38A8 are associated with FHONDA syndrome, a subtype of foveal hypoplasia with congenital nystagmus and optic-nerve-decussation defects without pigmentation leading to severe vision loss.

METHODS

In vivo and in vitro methods were conducted using retinal cell lines overexpressing SLC38A8, and Slc38a8/Slc38a7 gene-edited mice to evaluate visual function and physiological changes. Statistical analyses included two-way ANOVA, multiple regression, and ANCOVA.

RESULTS

In vitro, SLC38A8 overexpression influenced retinal gene expression, light detection, and visual perception, as well as glutamine and glutamate dynamics. In Y79SNAT8-OE cells, glutamate levels were significantly higher under light conditions compared to dark conditions at 12 h (3.4 ± 0.16 nmol/μl vs. 3.9 ± 0.17 nmol/μl, p = 0.0011) and 17 h (3.6 ± 0.22 nmol/μl vs. 4.5 ± 0.24 nmol/μl, p = 0.0001), a pattern not observed in control cells. SLC38A8 expression also increased significantly (RQ = 2.1 ± 0.11, p < 0.05) in Y79 cells under glutamine deprivation. In vivo, Slc38a8-truncated gene mice exhibited altered testicular morphology, with significantly reduced volume (70.9 ± 5.1 mm3 vs. 85.5 ± 6.7 mm3, p = 0.023), and reduced length (4.8 ± 0.2 mm vs. 5.4 ± 0.4 mm, p = 0.0169), alongside degenerative changes in germinal epithelium, and elevated liver enzyme. Despite normal eye morphology, retinal thickness, and visual evoked potentials, electroretinogram and behavioural tests indicated enhanced scotopic responsiveness with significant increases in a-wave (162.98 ± 14.1 μv vs. 133.9 ± 36.9 μv, p = 1.5e-07) and b-wave amplitudes (274.82 ± 25.2 μv vs. 199.9 ± 56.1 μv, p = 3.02e-09).

CONCLUSIONS

Our findings underscore SLC38A8 role in retinal function and glutamine-glutamate metabolism, with clinical implications for FHONDA and potential future dietary intervention targeting glutamine or glutamate.

Phenotypic Distinctions Between EYS- and USH2A-Associated Retinitis Pigmentosa in an Asian Population

Purpose

This study compares clinical characteristics of retinitis pigmentosa (RP) associated with mutations in the EYS and USH2A genes in a Southeast Asian cohort.

Methods

Prospective single-center study of families with EYS- or USH2A-associated RP seen at the Singapore National Eye Centre. Comprehensive ophthalmic evaluations, multimodal imaging, genetic testing, and longitudinal follow-up identified clinically useful differentiating features between the two genotypes.

Results

A total of 300 families with RP were enrolled, with EYS- and USH2A-associated RP, accounting for 24.7% of all probands and 50.7% of solved or likely solved cases. USH2A cases were predominantly nonsyndromic RP (75%). EYS-associated RP was more severe in functional and structural outcomes, and patients were more myopic than USH2A (SE -3.31 vs. -0.69; P < 0.0001). EYS RP displayed peripapillary nasal sparing on autofluorescence imaging more frequently than USH2A (57.6% vs. 26.7%; P = 0.006), whereas USH2A cases more often had a parafoveal ring (73.3% vs. 30.3%; P = 0.0002). Multiple logistic regression identified diagnostic features with 83.2% accuracy in distinguishing between EYS and USH2A, validated in a second unrelated clinical cohort.

Conclusions

EYS- and USH2A-associated RP have overlapping clinical presentations but can often be distinguished based on a constellation of phenotypic features including disease onset and severity, refractive error, and fundus autofluorescence. These diagnostic features may support a more effective diagnostic strategy for these common forms of RP.

Translational Relevance

Distinct clinical features differentiating EYS- and USH2A-associated RP provide valuable diagnostic tools that may inform personalized management and facilitate targeted interventions in clinical practice.

From Cellular to Metabolic: Advances in Imaging of Inherited Retinal Diseases

Background: Inherited retinal diseases (IRDs) are a genetically complex group of disorders, usually resulting in progressive vision loss due to retinal degeneration. Traditional imaging methods help in structural assessments, but limitations exist in early functional cellular-level detection that are crucial for guiding new therapies. Methods: This review includes a systematic search of PubMed and Google Scholar for studies on advanced imaging techniques for IRDs. Results: Key modalities covered are adaptive optics, fluorescence lifetime imaging ophthalmoscopy, polarization-sensitive optical coherence tomography, optoretinography, mitochondrial imaging, flavoprotein fluorescence imaging, and retinal oximetry. Each imaging method covers its principles, acquisition techniques, data from healthy eyes, applications in IRDs with specific examples, and current challenges and future directions. Conclusions: Emerging technologies, including adaptive optics and metabolic imaging, offer promising potential for cellular-level imaging and functional correlation in IRDs, allowing for earlier intervention and improved therapeutic targeting. Their integration into clinical practice may significantly improve IRD management and patient outcomes.

When do patients with retinitis pigmentosa present to ophthalmologists? A multi-centre retrospective study

BACKGROUND

Planned gene therapies for retinitis pigmentosa (RP) depend on viable photoreceptors for efficacy. Understanding disease severity at presentation, and drivers that influence time to presentation is important when planning interventions. We examined features that influence RP severity at initial presentation.

METHODS

Multi-centre retrospective cohort study of RP patients at initial presentation. Disease severity was scored using ellipsoid zone (EZ) width on SD-OCT and logistic regression used to determine risk factors for advanced disease at presentation.

RESULTS

A total of 146 unrelated RP patients were included. Median age at onset and presentation was 40.5 (range 1-74) and 50.1 (range 3.9-81.8), respectively. Severe disease (<5° of remaining EZ width) was present in 28.1% of cases at presentation. Patients with family history of RP had greater odds of severe disease (OR 3.29, 95% CI 1.56, 6.95; p = 0.002), while male gender, race, age, syndromic features, and socioeconomic status did not. Patients with affected siblings (median EZ width 6.2°; p = 0.01), but not affected parents (median EZ width 9.4°; p = 0.99), presented with severe EZ loss compared to patients without family history (median EZ width 13.1°). Patients with affected siblings had delayed presentation (≥5 years; OR 5.76, 95% CI 1.817, 18.262; p = 0.003) compared to patients without family history.

CONCLUSIONS

Family history influences the stage of disease at which RP patients initially seek ophthalmology review. This has implications for patient counselling and the number of patients who may benefit from future therapies.

Inherited retinal dystrophies and orphan designations in the European Union

Inherited Retinal Dystrophies (IRD) are diverse rare diseases that affect the retina and lead to visual impairment or blindness. Research in this field is ongoing, with over 60 EU orphan medicinal products designated in this therapeutic area by the Committee for Orphan Medicinal Products (COMP) at the European Medicines Agency (EMA). Up to now, COMP has used traditional disease terms, like retinitis pigmentosa, for orphan designation regardless of the product's mechanism of action. The COMP reviewed the designation approach for IRDs taking into account all previous Orphan Designations (OD) experience in IRDs, the most relevant up to date scientific literature and input from patients and clinical experts. Following the review, the COMP decided that there should be three options available for orphan designation concerning the condition: i) an amended set of OD groups for therapies that might be used in a broad spectrum of conditions, ii) a gene-specific designation for targeted therapies, and iii) an occasional term for products that do not fit in the above two categories. The change in the approach to orphan designation in IRDs caters for different scenarios to allow an optimum approach for future OD applications including the option of a gene-specific designation. By applying this new approach, the COMP increases the regulatory clarity, efficiency, and predictability for sponsors, aligns EU regulatory tools with the latest scientific and medical developments in the field of IRDs, and ensures that all potentially treatable patients will be included in the scope of an OD.

A Comparative Analysis of Models for AAV-Mediated Gene Therapy for Inherited Retinal Diseases

Inherited retinal diseases (IRDs) represent a diverse group of genetic disorders leading to progressive degeneration of the retina due to mutations in over 280 genes. This review focuses on the various methodologies for the preclinical characterization and evaluation of adeno-associated virus (AAV)-mediated gene therapy as a potential treatment option for IRDs, particularly focusing on gene therapies targeting mutations, such as those in the RPE65 and FAM161A genes. AAV vectors, such as AAV2 and AAV5, have been utilized to deliver therapeutic genes, showing promise in preserving vision and enhancing photoreceptor function in animal models. Despite their advantages-including high production efficiency, low pathogenicity, and minimal immunogenicity-AAV-mediated therapies face limitations such as immune responses beyond the retina, vector size constraints, and challenges in large-scale manufacturing. This review systematically compares different experimental models used to investigate AAV-mediated therapies, such as mouse models, human retinal explants (HREs), and induced pluripotent stem cell (iPSC)-derived retinal organoids. Mouse models are advantageous for genetic manipulation and detailed investigations of disease mechanisms; however, anatomical differences between mice and humans may limit the translational applicability of results. HREs offer valuable insights into human retinal pathophysiology but face challenges such as tissue degradation and lack of systemic physiological effects. Retinal organoids, on the other hand, provide a robust platform that closely mimics human retinal development, thereby enabling more comprehensive studies on disease mechanisms and therapeutic strategies, including AAV-based interventions. Specific outcomes targeted in these studies include vision preservation and functional improvements of retinas damaged by genetic mutations. This review highlights the strengths and weaknesses of each experimental model and advocates for their combined use in developing targeted gene therapies for IRDs. As research advances, optimizing AAV vector design and delivery methods will be critical for enhancing therapeutic efficacy and improving clinical outcomes for patients with IRDs.

Utility of multimodal imaging in the clinical diagnosis of inherited retinal degenerations

Inherited retinal degeneration (IRD) is a heterogeneous group of genetic disorders of variable onset and severity, with vision loss being a common endpoint in most cases. More than 50 distinct IRD phenotypes and over 280 causative genes have been described. Establishing a clinical phenotype for patients with IRD is particularly challenging due to clinical variability even among patients with similar genotypes. Clinical phenotyping provides a foundation for understanding disease progression and informing subsequent genetic investigations. Establishing a clear clinical phenotype for IRD cases is required to corroborate the data obtained from exome and genome sequencing, which often yields numerous variants in genes associated with IRD. In the current work, we review the use of contemporary retinal imaging modalities, including ultra-widefield and autofluorescence imaging, optical coherence tomography, and multispectral imaging, in the diagnosis of IRD.

Update on Clinical Trial Endpoints in Gene Therapy Trials for Inherited Retinal Diseases

Inherited retinal diseases (IRDs) encompass a wide spectrum of rare conditions characterized by diverse phenotypes associated with hundreds of genetic variations, often leading to progressive visual impairment and profound vision loss. Multiple natural history studies and clinical trials exploring gene therapy for various IRDs are ongoing. Outcomes for ophthalmic trials measure visual changes in three main categories-structural, functional, and patient-focused outcomes. Since IRDs may range from congenital with poor central vision from birth to affecting the peripheral retina initially and progressing insidiously with visual acuity affected late in the disease course, typical outcome measures such as central visual acuity and ocular coherence tomography (OCT) imaging of the macula may not provide adequate representation of therapeutic outcomes including alterations in disease course. Thus, alternative unique outcome measures are necessary to assess loss of peripheral vision, color vision, night vision, and contrast sensitivity in IRDs. These differences have complicated the assessment of clinical outcomes for IRD therapies, and the clinical trials for IRDs have had to design novel specialized endpoints to demonstrate treatment efficacy. As genetic engineering and gene therapy techniques continue to advance with growing investment from industry and accelerated approval tracks for orphan conditions, the clinical trials must continue to improve their assessments to demonstrate safety and efficacy of new gene therapies that aim to come to market. Here, we will provide an overview of the current gene therapy approaches, review various endpoints for measuring visual function, highlight those that are utilized in recent gene therapy trials, and provide an overview of stage 2 and 3 IRD trials through the second quarter of 2024.

Optogenetics and Targeted Gene Therapy for Retinal Diseases: Unravelling the Fundamentals, Applications, and Future Perspectives

With a common aim of restoring physiological function of defective cells, optogenetics and targeted gene therapies have shown great clinical potential and novelty in the branch of personalized medicine and inherited retinal diseases (IRDs). The basis of optogenetics aims to bypass defective photoreceptors by introducing opsins with light-sensing capabilities. In contrast, targeted gene therapies, such as methods based on CRISPR-Cas9 and RNA interference with noncoding RNAs (i.e., microRNA, small interfering RNA, short hairpin RNA), consists of inducing normal gene or protein expression into affected cells. Having partially leveraged the challenges limiting their prompt introduction into the clinical practice (i.e., engineering, cell or tissue delivery capabilities), it is crucial to deepen the fields of knowledge applied to optogenetics and targeted gene therapy. The aim of this in-depth and novel literature review is to explain the fundamentals and applications of optogenetics and targeted gene therapies, while providing decision-making arguments for ophthalmologists. First, we review the biomolecular principles and engineering steps involved in optogenetics and the targeted gene therapies mentioned above by bringing a focus on the specific vectors and molecules for cell signalization. The importance of vector choice and engineering methods are discussed. Second, we summarize the ongoing clinical trials and most recent discoveries for optogenetics and targeted gene therapies for IRDs. Finally, we then discuss the limits and current challenges of each novel therapy. We aim to provide for the first time scientific-based explanations for clinicians to justify the specificity of each therapy for one disease, which can help improve clinical decision-making tasks.

Lipid Nanoparticle-Mediated Delivery of mRNA Into the Mouse and Human Retina and Other Ocular Tissues

Purpose

Lipid nanoparticles (LNPs) show promise in their ability to introduce mRNA to drive protein expression in specific cell types of the mammalian eye. Here, we examined the ability of mRNA encapsulated in LNPs with two distinct formulations to drive gene expression in mouse and human retina and other ocular tissues.

Methods

We introduced mRNA-carrying LNPs into two biological systems. Intravitreal injections were tested to deliver LNPs into the mouse eye. Human retinal pigment epithelium (RPE) and retinal explants were used to assess mRNA expression in human tissue. We analyzed specificity of expression using histology, immunofluorescence, and imaging.

Results

In mice, mRNAs encoding GFP and ciliary neurotrophic factor (CNTF) were specifically expressed by Müller glia and RPE. Acute inflammatory changes measured by microglia distribution (Iba-1) or interleukin-6 (IL-6) expression were not observed 6 hours post-injection. Human RPE also expressed high levels of GFP. Human retinal explants expressed GFP in cells with apical and basal processes consistent with Müller glia and in perivascular cells consistent with macrophages.

Conclusions

We demonstrated the ability to reliably transfect subpopulations of retinal cells in mouse eye tissues in vivo and in human ocular tissues. Of significance, intravitreal injections were sufficient to transfect the RPE in mice. To our knowledge, we demonstrate delivery of mRNA using LNPs in human ocular tissues for the first time.

Translational Relevance

Ocular gene-replacement therapies using non-viral vector methods are a promising alternative to adeno-associated virus (AAV) vectors. Our studies show that mRNA LNP delivery can be used to transfect retinal cells in both mouse and human tissues without inducing significant inflammation. This methodology could be used to transfect retinal cell lines, tissue explants, mice, or potentially as gene-replacement therapy in a clinical setting in the future.

Self-Reported Functional Vision in USH2A-Associated Retinal Degeneration as Measured by the Michigan Retinal Degeneration Questionnaire

Purpose

The purpose of this study was to evaluate self-reported functional vision (FV) and the impact of vision loss in patients with USH2A-associated retinal degeneration using a patient-reported outcome (PRO) measure, the Michigan Retinal Degeneration Questionnaire (MRDQ), to correlate MRDQ scores with well-established visual function measurements.

Design

An observational cross-sectional study (n = 93) of participants who had Usher Syndrome Type 2 (USH2, n = 55) or autosomal recessive non-syndromic retinitis pigmentosa (ARRP; n = 38) associated with biallelic variants in the USH2A gene.

Methods

The study protocol was approved by all ethics boards and informed consent was obtained from each participant. Participants completed the MRDQ at the 48-month study follow-up visit. Disease duration was self-reported by participants. One-way ANOVA was used to compare subgroups (clinical diagnosis, age, disease duration, and full-field stimulus threshold [FST] Blue-Red mediation) on mean scores per domain. Spearman correlation coefficients were used to assess associations between MRDQ domains and visual/retinal function assessments.

Results

Of the study sample, 58% were female participants and the median disease duration was 13 years. MRDQ domains were sensitive to differences between subgroups of clinical diagnosis, age, disease duration, and FST Blue-Red mediation. MRDQ domains correlated with static perimetry, microperimetry, full-field stimulus testing, and best-corrected visual acuity (BCVA).

Conclusions

Self-reported FV measured by the MRDQ, when applied to USH2 and ARRP participants, had good distributional characteristics and correlated well with visual function tests. MRDQ adds a new dimension of understanding on vision-related functioning and establishes this PRO tool as an informative measure in evaluating USH2A outcomes.

Structure-based network analysis predicts pathogenic variants in human proteins associated with inherited retinal disease

Advances in gene sequencing technologies have accelerated the identification of genetic variants, but better tools are needed to understand which are causal of disease. This would be particularly useful in fields where gene therapy is a potential therapeutic modality for a disease-causing variant such as inherited retinal disease (IRD). Here, we apply structure-based network analysis (SBNA), which has been successfully utilized to identify variant-constrained amino acid residues in viral proteins, to identify residues that may cause IRD if subject to missense mutation. SBNA is based entirely on structural first principles and is not fit to specific outcome data, which makes it distinct from other contemporary missense prediction tools. In 4 well-studied human disease-associated proteins (BRCA1, HRAS, PTEN, and ERK2) with high-quality structural data, we find that SBNA scores correlate strongly with deep mutagenesis data. When applied to 47 IRD genes with available high-quality crystal structure data, SBNA scores reliably identified disease-causing variants according to phenotype definitions from the ClinVar database. Finally, we applied this approach to 63 patients at Massachusetts Eye and Ear (MEE) with IRD but for whom no genetic cause had been identified. Untrained models built using SBNA scores and BLOSUM62 scores for IRD-associated genes successfully predicted the pathogenicity of novel variants (AUC = 0.851), allowing us to identify likely causative disease variants in 40 IRD patients. Model performance was further augmented by incorporating orthogonal data from EVE scores (AUC = 0.927), which are based on evolutionary multiple sequence alignments. In conclusion, SBNA can used to successfully identify variants as causal of disease in human proteins and may help predict variants causative of IRD in an unbiased fashion.

Retinal Imaging Findings in Inherited Retinal Diseases

Inherited retinal diseases (IRDs) represent one of the major causes of progressive and irreversible vision loss in the working-age population. Over the last few decades, advances in retinal imaging have allowed for an improvement in the phenotypic characterization of this group of diseases and have facilitated phenotype-to-genotype correlation studies. As a result, the number of clinical trials targeting IRDs has steadily increased, and commensurate to this, the need for novel reproducible outcome measures and endpoints has grown. This review aims to summarize and describe the clinical presentation, characteristic imaging findings, and imaging endpoint measures that are being used in clinical research on IRDs. For the purpose of this review, IRDs have been divided into four categories: (1) panretinal pigmentary retinopathies affecting rods or cones; (2) macular dystrophies; (3) stationary conditions; (4) hereditary vitreoretinopathies.

Allele-specific antisense oligonucleotides for the treatment of BEST1-related dominantly inherited retinal diseases: An in vitro model

Retinal dystrophies are a common health problem worldwide that are currently incurable due to the inability of retinal cells to regenerate. Inherited retinal diseases (IRDs) are a diverse group of disorders characterized by progressive vision loss caused by photoreceptor cell dysfunction. The eye has always been an attractive organ for the development of novel therapies due to its independent access to the systemic pathway. Moreover, anti-sense oligonucleotides (ASOs), which facilitate manipulation of unwanted mRNAs via degradation or splicing, are undergoing rapid development and have been clinically deployed for the treatment of several diseases. The primary aim of this study was to establish a reliable in vitro model utilizing induced photoreceptor-like cells (PRCs) for assessing the efficacy and safety of ASOs targeting the BEST1 gene. Despite advances in gene therapy, effective treatments for a broad range of IRDs remain limited. An additional aim was to develop an in vitro model for evaluating RNA-based therapeutics, specifically ASOs, for the treatment in IRDs. Firstly, a cell culture model was established by induction of PRCs from dermal fibroblasts via direct programming. The induced PRCs were characterized at both the transcriptomic and protein level. Then, a common single nucleotide polymorphism (SNP) was identified in the BEST1 gene (rs1800007) for targeting with ASOs. ASOs were designed using the GapmeR strategy to target multiple alleles of this SNP, which is potentially suitable for a large proportion of the population. The efficacy and possible off-target effects of these ASOs were also analyzed in the induced PRC model. The findings show that the selected ASOs achieved allele-specific mRNA degradation with virtually no off-target effects on the global transcriptome profile, indicating their potential as safe and effective therapeutic agents. The presented in vitro model is a valuable platform for testing personalized IRD treatments and should inspire further research on RNA-based therapeutics. To the best of our knowledge this study is the first to test RNA-based therapeutics involving the use of ASOs in an induced PRC model. Based on the present findings, it will be possible to establish an ex vivo disease model using dermal fibroblast samples from affected individuals. In other words, the disease model and the ASOs that were successfully designed in this study can serve as a useful platform for the testing of personalized treatments for IRDs.

Predicted deleterious variants in the human genome relevant to gene therapy with adeno-associated virus vectors

Based on the observation that humans have variable responses of gene expression with the same dose of an adeno-associated vector, we hypothesized that there are deleterious variants in genes coding for processes required for adeno-associated virus (AAV)-mediated gene transfer/expression that may hamper or enhance the effectiveness of AAV-mediated gene therapy. To assess this hypothesis, we evaluated 69,442 whole genome sequences from three populations (European, African/African American, and Qatari) for predicted deleterious variants in 62 genes known to play a role in AAV-mediated gene transfer/expression. The analysis identified 5,564 potentially deleterious mutations of which 27 were classified as common based on an allele frequency ≥1% in at least one population studied. Many of these deleterious variants are predicated to prevent while others enhance effective AAV gene transfer/expression, and several are linked to known hereditary disorders. The data support the hypothesis that, like other drugs, human genetic variability contributes to the person-to-person effectiveness of AAV gene therapy and the screening for genetic variability should be considered as part of future clinical trials.

The economic burden of inherited retinal disease in Singapore: a prevalence-based cost-of-illness study

OBJECTIVE

To assess the economic impact of inherited retinal disease (IRD) among Singaporeans.

METHODS

IRD prevalence was calculated using population-based data. Focused surveys were conducted for sequentially enrolled IRD patients from a tertiary hospital. The IRD cohort was compared to the age- and gender-matched general population. Economic costs were expanded to the national IRD population to estimate productivity and healthcare costs.

RESULTS

National IRD caseload was 5202 cases (95% CI, 1734-11273). IRD patients (n = 95) had similar employment rates to the general population (67.4% vs. 70.7%; p = 0.479). Annual income was lower among IRD patients than the general population (SGD 19,500 vs. 27,161; p < 0.0001). Employed IRD patients had lower median income than the general population (SGD 39,000 vs. 52,650; p < 0.0001). Per capita cost of IRD was SGD 9382, with a national burden of SGD 48.8 million per year. Male gender (beta of SGD 6543, p = 0.003) and earlier onset (beta of SGD 150/year, p = 0.009) predicted productivity loss. Treatment of the most economically impacted 10% of IRD patients with an effective IRD therapy required initial treatment cost of less than SGD 250,000 (USD 188,000) for cost savings to be achieved within 20 years.

CONCLUSIONS

Employment rates among Singaporean IRD patients were the same as the general population, but patient income was significantly lower. Economic losses were driven in part by male patients with early age of onset. Direct healthcare costs contributed relatively little to the financial burden.

[Diagnostics and management of patients with inherited retinal diseases in Germany : Results of a nationwide survey of university and non-university eye departments and specialized practices]

BACKGROUND

Inherited retinal diseases (IRDs) refer to a heterogeneous group of rare disorders that potentially lead to blindness. Emerging therapeutic options have led to a growing interest in IRDs; however, there are insufficient systematic studies on IRDs in Germany characterizing the demographics and management in clinical practice.

OBJECTIVE

To characterize the care for IRD patients in Germany, to assess the applied diagnostics, the use of databases and the implementation of education in ophthalmic genetics.

METHODS

The anonymous online survey (SoSci Survey GmbH) was sent to all German ophthalmology departments listed on the website of the German Ophthalmological Society and to three practices focusing on IRDs.

RESULTS

The overall response rate was 44.8%. Almost all institutions (93.6%) reported seeing IRD patients, but university and non-university hospitals differed in the number of patients. Databases are used in 60% of universities but only in 5.9% of non-university hospitals. Regarding the number of patients with genetic diagnostics, 53% of the non-university and 12% of the university sites reported that 20% at most of their patients had received a molecular genetic diagnosis. The results of the IRD practices are comparable with the university hospitals. Patients with biallelic RPE65 mutations-associated IRD, potential candidates for treatment with voretigene neparvovec (Luxturna®), were followed in 9/25 participating university departments.

CONCLUSION

This survey highlights the deficits in the management of IRD patients. In particular, we found a clear difference between university and non-university hospitals in the rate of patients with known molecular genetic results. Improvements should be initiated in the latter, especially because of existing and emerging therapeutic options.

Lipid nanoparticles with PEG-variant surface modifications mediate genome editing in the mouse retina

Ocular delivery of lipid nanoparticle (LNPs) packaged mRNA can enable efficient gene delivery and editing. We generated LNP variants through the inclusion of positively charged-amine-modified polyethylene glycol (PEG)-lipids (LNPa), negatively charged-carboxyl-(LNPz) and carboxy-ester (LNPx) modified PEG-lipids, and neutral unmodified PEG-lipids (LNP). Subretinal injections of LNPa containing Cre mRNA in the mouse show tdTomato signal in the retinal pigmented epithelium (RPE) like conventional LNPs. Unexpectedly, LNPx and LNPz show 27% and 16% photoreceptor transfection, respectively, with striking localization extending from the photoreceptor synaptic pedicle to the outer segments, displaying pan-retinal distribution in the photoreceptors and RPE. LNPx containing Cas9 mRNA and sgAi9 leads to the formation of an oval elongated structure with a neutral charge resulting in 16.4% editing restricted to RPE. Surface modifications of LNPs with PEG variants can alter cellular tropism of mRNA. LNPs enable genome editing in the retina and in the future can be used to correct genetic mutations that lead to blindness.

Electrical, Electromagnetic, Ultrasound Wave Therapies, and Electronic Implants for Neuronal Rejuvenation, Neuroprotection, Axonal Regeneration, and IOP Reduction

The peripheral nervous system (PNS) of mammals and nervous systems of lower organisms possess significant regenerative potential. In contrast, although neural plasticity can provide some compensation, the central nervous system (CNS) neurons and nerves of adult mammals generally fail to regenerate after an injury or damage. However, use of diverse electrical, electromagnetic and sonographic energy waves are illuminating novel ways to stimulate neuronal differentiation, proliferation, neurite growth, and axonal elongation/regeneration leading to various levels of functional recovery in animals and humans afflicted with disorders of the CNS, PNS, retina, and optic nerve. Tools such as acupuncture, electroacupuncture, electroshock therapy, electrical stimulation, transcranial magnetic stimulation, red light therapy, and low-intensity pulsed ultrasound therapy are demonstrating efficacy in treating many different maladies. These include wound healing, partial recovery from motor dysfunctions, recovery from ischemic/reperfusion insults and CNS and ocular remyelination, retinal ganglion cell (RGC) rejuvenation, and RGC axonal regeneration. Neural rejuvenation and axonal growth/regeneration processes involve activation or intensifying of the intrinsic bioelectric waves (action potentials) that exist in every neuronal circuit of the body. In addition, reparative factors released at the nerve terminals and via neuronal dendrites (transmitter substances), extracellular vesicles containing microRNAs and neurotrophins, and intercellular communication occurring via nanotubes aid in reestablishing lost or damaged connections between the traumatized tissues and the PNS and CNS. Many other beneficial effects of the aforementioned treatment paradigms are mediated via gene expression alterations such as downregulation of inflammatory and death-signal genes and upregulation of neuroprotective and cytoprotective genes. These varied techniques and technologies will be described and discussed covering cell-based and animal model-based studies. Data from clinical applications and linkage to human ocular diseases will also be discussed where relevant translational research has been reported.

RETINITIS PIGMENTOSA ASSOCIATED WITH THE EYS C2139Y VARIANT : An Important Cause of Blindness in East Asian Populations

PURPOSE

The study aimed to describe the phenotypic features of retinitis pigmentosa (RP) associated with the previously described EYS C2139Y variant in Singaporeans and establish the importance of this variant as a prevalent cause of RP among East Asians.

METHODS

A clinical phenotyping and exome-sequencing study was conducted on consecutive patients with nonsyndromic RP. Epidemiological analysis was performed using Singaporean and global population-based genetic data.

RESULTS

A study of 150 consecutive unrelated individuals with nonsyndromic RP found that 87 (58%) of cases had plausible genotypes. A previously described missense variant in the EYS gene, 6416G>A (C2139Y), occurred heterozygously or homozygously in 17 of 150 families (11.3%), all with autosomal recessive RP. Symptom onset in EYS C2139Y-related RP ranged from 6 to 45 years, with visual acuity ranging from 20/20 at 21 years to no light perception by 48 years. C2139Y-related RP had typical findings, including sectoral RP in cases with EYS E2703X in trans . The median age at presentation was 45 years and visual fields declined to less than 20° (Goldmann V4e isopter) by age 65 years. Intereye correlation for visual acuity, fields, and ellipsoid band width was high (r 2 = 0.77-0.95). Carrier prevalence was 0.66% (allele frequency of 0.33%) in Singaporean Chinese and 0.34% in East Asians, suggesting a global disease burden exceeding 10,000 individuals.

CONCLUSION

The EYS C2139Y variant is common in Singaporean RP patients and other ethnic Chinese populations. Targeted molecular therapy for this single variant could potentially treat a significant proportion of RP cases worldwide.

Lipid nanoparticle-mediated delivery of mRNA into the mouse and human retina and other ocular tissues

Purpose

Lipid nanoparticles (LNPs) show promise in their ability to introduce mRNA to drive protein expression in specific cell types of the mammalian eye. Here, we examined the ability of mRNA encapsulated in lipid nanoparticles (LNPs) with two distinct formulations to drive gene expression in mouse and human retina and other ocular tissues.

Methods

We introduced mRNA carrying LNPs into two biological systems. Intravitreal injections were tested to deliver LNPs into the mouse eye. Human retinal pigment epithelium (RPE) and retinal explants were used to assess mRNA expression in human tissue. We analyzed specificity of expression using histology, immunofluorescence, and imaging.

Results

In mice, mRNAs encoding GFP and ciliary neurotrophic factor (CNTF) were specifically expressed by Müller glia and retinal pigment epithelium (RPE). Acute inflammatory changes measured by microglia distribution (Iba-1) or interleukin-6 (IL-6) expression were not observed 6 hours post-injection. Human RPE also expressed high levels of GFP. Human retinal explants expressed GFP in cells with apical and basal processes consistent with Müller glia and in perivascular cells consistent with macrophages.

Conclusions

We demonstrated the ability to reliably transfect subpopulations of retinal cells in mice eye tissues in vivo and in human ocular tissues. Of significance, intravitreal injections were sufficient to transfect the RPE in mice. To our knowledge we demonstrate delivery of mRNA using LNPs in human ocular tissues for the first time.

Structure-based network analysis predicts mutations associated with inherited retinal disease

With continued advances in gene sequencing technologies comes the need to develop better tools to understand which mutations cause disease. Here we validate structure-based network analysis (SBNA)1,2 in well-studied human proteins and report results of using SBNA to identify critical amino acids that may cause retinal disease if subject to missense mutation. We computed SBNA scores for genes with high-quality structural data, starting with validating the method using 4 well-studied human disease-associated proteins. We then analyzed 47 inherited retinal disease (IRD) genes. We compared SBNA scores to phenotype data from the ClinVar database and found a significant difference between benign and pathogenic mutations with respect to network score. Finally, we applied this approach to 65 patients at Massachusetts Eye and Ear (MEE) who were diagnosed with IRD but for whom no genetic cause was found. Multivariable logistic regression models built using SBNA scores for IRD-associated genes successfully predicted pathogenicity of novel mutations, allowing us to identify likely causative disease variants in 37 patients with IRD from our clinic. In conclusion, SBNA can be meaningfully applied to human proteins and may help predict mutations causative of IRD.

Management of keratoconus: an updated review

Keratoconus is the most common corneal ectatic disorder. It is characterized by progressive corneal thinning with resultant irregular astigmatism and myopia. Its prevalence has been estimated at 1:375 to 1:2,000 people globally, with a considerably higher rate in the younger populations. Over the past two decades, there was a paradigm shift in the management of keratoconus. The treatment has expanded significantly from conservative management (e.g., spectacles and contact lenses wear) and penetrating keratoplasty to many other therapeutic and refractive modalities, including corneal cross-linking (with various protocols/techniques), combined CXL-keratorefractive surgeries, intracorneal ring segments, anterior lamellar keratoplasty, and more recently, Bowman's layer transplantation, stromal keratophakia, and stromal regeneration. Several recent large genome-wide association studies (GWAS) have identified important genetic mutations relevant to keratoconus, facilitating the development of potential gene therapy targeting keratoconus and halting the disease progression. In addition, attempts have been made to leverage the power of artificial intelligence-assisted algorithms in enabling earlier detection and progression prediction in keratoconus. In this review, we provide a comprehensive overview of the current and emerging treatment of keratoconus and propose a treatment algorithm for systematically guiding the management of this common clinical entity.

Repurposing small molecules for Nephronophthisis and related renal ciliopathies

Nephronophthisis is an autosomal recessive tubulo-interstitial nephropathy, belonging to the ciliopathy disorders, characterized by fibrosis and/or cysts. It is the most common genetic cause of renal failure in children and young adults. Clinically and genetically heterogeneous, it is caused by variants in ciliary genes resulting in either an isolated kidney disease or syndromic forms in association with other manifestations of ciliopathy disorders. No curative treatment is currently available. Over the past two decades, advances in understanding disease mechanisms have identified several dysregulated signaling pathways, some shared with other cystic kidney diseases. Notably, molecules previously developed to target these pathways have shown promising beneficial effects in orthologous mouse models. In addition to these knowledge-based repurposing approaches, unbiased "in cellulo" phenotypic screens of "repurposing" libraries identified small molecules able to rescue the ciliogenesis defects observed in nephronophthisis conditions. Those compounds appeared to act on relevant pathways and, when tested, showed beneficial nephronophthisis-associated kidney and/or extra-renal defects in mice. In this review, we have summarized those studies which highlight the drug repurposing strategies in the context of a rare disorders such as nephronophthisis-related ciliopathies, with broad genetic heterogeneity and systemic manifestations but with shared disease mechanisms.

Nanotechnology Lighting the Way for Gene Therapy in Ophthalmopathy: From Opportunities toward Applications

Hereditary ophthalmopathy is a well-described threat to human visual health affecting millions of people. Gene therapy for ophthalmopathy has received widespread attention with the increasing understanding of pathogenic genes. Effective and safe delivery of accurate nucleic acid drugs (NADs) is the core of gene therapy. Efficient nanodelivery and nanomodification technologies, appropriate targeted genes, and the choice of drug injection methods are the guiding lights of gene therapy. Compared with traditional drugs, NADs can specifically change the expression of specific genes or restore the normal function of mutant genes. Nanodelivery carriers can improve targeting and nanomodification can improve the stability of NADs. Therefore, NADs, which can fundamentally solve pathogeny, hold great promise in the treatment of ophthalmopathy. This paper reviews the limitations of ocular disease treatment, discusses the classification of NADs in ophthalmology, reveals the delivery strategies of NADs to improve bioavailability, targeting, and stability, and summarizes the mechanisms of NADs in ophthalmopathy.

Characterizing the genotypic spectrum of retinitis pigmentosa in East Asian populations: a systematic review

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.

Therapeutic landscape for inherited ocular diseases: Current and emerging therapies

Inherited ocular diseases comprise a heterogeneous group of rare and complex diseases, including inherited retinal diseases (IRDs) and inherited optic neuropathies. Recent success in adeno-associated virus-based gene therapy, voretigene neparvovec (Luxturna^®) for RPE65-related IRDs, has heralded rapid evolution in gene therapy platform technologies and strategies, from gene augmentation to RNA editing, as well as gene agnostic approaches such as optogenetics. This review discusses the fundamentals underlying the mode of inheritance, natural history studies and clinical trial outcomes, as well as current and emerging therapies covering gene therapy strategies, cell-based therapies and bionic vision.

Gene-agnostic therapeutic approaches for inherited retinal degenerations

Inherited retinal diseases (IRDs) are associated with mutations in over 250 genes and represent a major cause of irreversible blindness worldwide. While gene augmentation or gene editing therapies could address the underlying genetic mutations in a small subset of patients, their utility remains limited by the great genetic heterogeneity of IRDs and the costs of developing individualised therapies. Gene-agnostic therapeutic approaches target common pathogenic pathways that drive retinal degeneration or provide functional rescue of vision independent of the genetic cause, thus offering potential clinical benefits to all IRD patients. Here, we review the key gene-agnostic approaches, including retinal cell reprogramming and replacement, neurotrophic support, immune modulation and optogenetics. The relative benefits and limitations of these strategies and the timing of clinical interventions are discussed.

RNA-targeting strategies as a platform for ocular gene therapy

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.

Nanoneedles Induce Targeted siRNA Silencing of p16 in the Human Corneal Endothelium

Nanoneedles can target nucleic acid transfection to primary cells at tissue interfaces with high efficiency and minimal perturbation. The corneal endothelium is an ideal target for nanoneedle-mediated RNA interference therapy aimed at enhancing its proliferative capacity, necessary for tissue regeneration. This work develops a strategy for siRNA nanoninjection to the human corneal endothelium. Nanoneedles can deliver p16-targeting siRNA to primary human corneal endothelial cells in vitro without toxicity. The nanoinjection of siRNA induces p16 silencing and increases cell proliferation, as monitored by ki67 expression. Furthermore, siRNA nanoinjection targeting the human corneal endothelium is nontoxic ex vivo, and silences p16 in transfected cells. These data indicate that nanoinjection can support targeted RNA interference therapy for the treatment of endothelial corneal dysfunction.

Advancements in ocular gene therapy delivery: vectors and subretinal, intravitreal, and suprachoroidal techniques

INTRODUCTION

: Ocular gene therapy represents fertile ground for rapid innovation, with ever-expanding therapeutic strategies, molecular targets, and indications.

AREAS COVERED

: Potential indications for ocular gene therapy have classically focused on inherited retinal disease (IRD), but more recently include acquired retinal diseases, such as neovascular age-related macular degeneration, geographic atrophy and diabetic retinopathy. Ocular gene therapy strategies have proliferated recently, and include gene augmentation, gene inactivation, gene editing, RNA modulation, and gene-independent gene augmentation. Viral vector therapeutic constructs include adeno-associated virus and lentivirus and continue to evolve through directed evolution and rationale design. Ocular gene therapy administration techniques have expanded beyond pars plana vitrectomy with subretinal injection to intravitreal injection and suprachoroidal injection.

EXPERT OPINION

: The success of treatment for IRD, paired with the promise of clinical research in acquired retinal diseases and in administration techniques, has raised the possibility of in-office gene therapy for common retinal disorders within the next five to ten years.

Gene Therapy for Rhodopsin Mutations

Mutations in RHO, the gene for rhodopsin, account for a large fraction of autosomal-dominant retinitis pigmentosa (adRP). Patients fall into two clinical classes, those with early onset, pan retinal photoreceptor degeneration, and those who experience slowly progressive disease. The latter class of patients are candidates for photoreceptor-directed gene therapy, while former may be candidates for delivery of light-responsive proteins to interneurons or retinal ganglion cells. Gene therapy for RHO adRP may be targeted to the mutant gene at the DNA or RNA level, while other therapies preserve the viability of photoreceptors without addressing the underlying mutation. Correcting the RHO gene and replacing the mutant RNA show promise in animal models, while sustaining viable photoreceptors has the potential to delay the loss of central vision and may preserve photoreceptors for gene-directed treatments.

Deciphering the Retinal Epigenome during Development, Disease and Reprogramming: Advancements, Challenges and Perspectives

Retinal neurogenesis is driven by concerted actions of transcription factors, some of which are expressed in a continuum and across several cell subtypes throughout development. While seemingly redundant, many factors diversify their regulatory outcome on gene expression, by coordinating variations in chromatin landscapes to drive divergent retinal specification programs. Recent studies have furthered the understanding of the epigenetic contribution to the progression of age-related macular degeneration, a leading cause of blindness in the elderly. The knowledge of the epigenomic mechanisms that control the acquisition and stabilization of retinal cell fates and are evoked upon damage, holds the potential for the treatment of retinal degeneration. Herein, this review presents the state-of-the-art approaches to investigate the retinal epigenome during development, disease, and reprogramming. A pipeline is then reviewed to functionally interrogate the epigenetic and transcriptional networks underlying cell fate specification, relying on a truly unbiased screening of open chromatin states. The related work proposes an inferential model to identify gene regulatory networks, features the first footprinting analysis and the first tentative, systematic query of candidate pioneer factors in the retina ever conducted in any model organism, leading to the identification of previously uncharacterized master regulators of retinal cell identity, such as the nuclear factor I, NFI. This pipeline is virtually applicable to the study of genetic programs and candidate pioneer factors in any developmental context. Finally, challenges and limitations intrinsic to the current next-generation sequencing techniques are discussed, as well as recent advances in super-resolution imaging, enabling spatio-temporal resolution of the genome.