We assessed genotype–phenotype correlations among the visual, auditory, and olfactory phenotypes of 127 participants with Usher syndrome (USH2) (n =80) or nonsyndromic autosomal recessive retinitis pigmentosa (ARRP) (n = 47) due to USH2A variants, using clinical data and molecular diagnostics from the Rate of Progression in USH2A Related Retinal Degeneration (RUSH2A) study. USH2A truncating alleles were associated with USH2 and had a dose‐dependent effect on hearing loss severity with no effect on visual loss severity within the USH2 subgroup. A group of missense alleles in an interfibronectin domain appeared to be hypomorphic in ARRP. These alleles were associated with later age of onset, larger visual field area, better sensitivity thresholds, and better electroretinographic responses. No effect of genotype on the severity of olfactory deficits was observed. This study unveils a unique, tissue‐specific USH2A allelic hierarchy with important prognostic implications for patient counseling and treatment trial endpoints. These findings may inform clinical care or research approaches in others with allelic disorders or pleiotropic phenotypes.

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Tissue‐specific genotype–phenotype correlations among USH2A‐related disorders in the RUSH2A study

The precise processes causing photoreceptor cell death in retinal degeneration (RD) are still largely unknown but are likely to follow a variety of degenerative mechanisms. While different genetic insults can trigger distinct molecular pathways, eventually these may converge into a limited number of common cell death mechanisms. These mechanisms often involve deregulation of cyclic guanosine monophosphate (cGMP)-signaling and proteostasis, which both may increase photoreceptor energy expenditure. Comprehensive information on these mechanisms may allow for targeted interventions to delay or prevent photoreceptor loss. Here, we review the current knowledge on photoreceptor degenerative mechanisms, focusing on processes triggered by aberrant cGMP-signaling, proteostasis, and energy metabolism. Afterward, we discuss how these pathways could potentially be used to treat photoreceptor degeneration, highlighting data from a number of recent studies on inhibitory cGMP analogs, proteostasis blockers, and interventions aimed at fortifying energetic status. Finally, we provide perspectives on how such experimental approaches could be translated into future clinical applications.

Pathomechanisms of Inherited Retinal Degeneration and Perspectives for Neuroprotection.

Abstract The prime editor (PE) can edit genomes with almost any intended changes, including all 12 possible types of base substitutions, small insertions and deletions, and their combinations, without the requirement for double strand breaks or exogenous donor templates. PE demonstrates the possibility of correcting a variety of disease-causing mutations and might expand the therapeutic application of gene editing. In this study, PE was optimized based on a dual-adeno-associated virus (AAV) split-intein system in vitro by screening different split sites and split inteins. We found that splitting PE before amino acid 1105(Ser) of SpCas9 with Rma intein resulted in the highest on-target editing. The orientations of pegRNA and nicking sgRNA in the AAV vector were further optimized. To test the in vivo performance of the optimized dual-AAV split-PE3, it was delivered by subretinal injection in rd12 mice with inherited retinal disease Leber congenital amaurosis. The prime editors corrected the pathogenic mutation with up to 16% efficiency in a precise way, with no detectable off-target edits, restored RPE65 expression, rescued retinal and visual function, and preserved photoceptors. Our findings establish a framework for the preclinical development of PE and motivate further testing of PE for the treatment of inherited retinal diseases caused by various mutations. 

https://www.nature.com/articles/s41392-022-01234-1.pdf

Dual-AAV split prime editor corrects the mutation and phenotype in mice with inherited retinal degeneration

ABSTRACT Background/aims To investigate the natural history of PRPF31-related retinitis pigmentosa (RP11). Materials and methods We identified individuals with RP11 and collected retrospective data from disease onset to present date including genetics, demographic data, Goldmann visual field areas, and visual acuity measurements. Visual fields were evaluated as summed squared degrees and best-corrected visual acuity was converted to logMAR. We performed linear mixed model regression analysis to evaluate annual disease progression, and survival analysis to evaluate the age of legal blindness. Results We included 46 subjects with RP11. Median age of disease onset was 10 years (range 5–65). Follow-up spanned from 0 to 36 years with a median of 8 years. Median Goldmann visual field areas decreased by 10.0% per year (95% CI 7.5%−12.4%) with target IV4e, 7.9% (95% CI 4.5% − 11.2%) with target III4e, and 9.3% (95% CI: 7.0% −11.5%) when combining target sizes. Individuals with RP11 maintained good visual acuity until late stage of disease. Legal blindness was reached at a median age of 57 years (95% CI 50–75 years). Conclusions PRPF31 variants cause autosomal dominant retinitis pigmentosa that most commonly manifests in childhood with a variable disease progression. Visual field area deteriorates faster than visual acuity and was the major cause of legal blindness in our study population. This study characterizes disease progression in retinitis pigmentosa caused by PRPF31-variants and demonstrates the importance of differentiation between specific genotypes when counselling patients and conducting natural history studies of RP.

https://figshare.com/articles/journal_contribution/Disease_progression_of_retinitis_pigmentosa_caused_by_i_PRPF31_i_variants_in_a_Nordic_population_a_retrospective_study_with_up_to_36_years_follow-up/21212561/1/files/37614815.pdf

Disease progression of retinitis pigmentosa caused by PRPF31 variants in a Nordic population: a retrospective study with up to 36 years follow-up

Purpose Bietti crystalline dystrophy (BCD) is a rare monogenic autosomal recessive (AR) chorioretinal degenerative disease caused by biallelic mutations in CYP4V2. The aim of the current study was to perform an in-depth calculation of worldwide carrier frequency and genetic prevalence of BCD using gnomAD data and comprehensive literature CYP4V2 analysis. Methods CYP4V2 gnomAD data and reported mutations were used to calculate carrier frequency of each variant. An evolutionary-based sliding window analysis was used to detect conserved protein regions. Potential exonic splicing enhancers (ESEs) were identified using ESEfinder. Results We identified 1171 CYP4V2 variants, 156 of which were considered pathogenic, including 108 reported in patients with BCD. Carrier frequency and genetic prevalence calculations confirmed that BCD is more common in the East Asian population, with ∼19 million healthy carriers and 52,000 individuals who carry biallelic CYP4V2 mutations and are expected to be affected. Additionally, we generated BCD prevalence estimates of other populations, including African, European, Finnish, Latino, and South Asian. Worldwide, the estimated overall carrier frequency of CYP4V2 mutation is 1:210, and therefore, ∼37 million individuals are expected to be healthy carriers of a CYP4V2 mutation. The estimated genetic prevalence of BCD is about 1:116,000, and we predict that ∼67,000 individuals are affected with BCD worldwide. Conclusions Our analysis estimates BCD prevalence and revealed large differences among various populations. Moreover, it highlights advantages and limitations of the gnomAD database. Translational Relevance This analysis is likely to have important implications for genetic counseling in each studied population and for developing clinical trials for potential BCD treatments.

Prakadeeswari Gopalakrishnan

Papers

Inherited retinal diseases: Linking genes, disease-causing variants, and relevant therapeutic modalities.