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Leber Congenital Amaurosis (LCA16) is a progressive vision loss disorder caused by point mutations in the KCNJ13 gene, which encodes an inward-rectifying potassium channel, Kir7.1. A nonsense mutation, W53X (c.158G>A), leads to premature truncation of the protein, which disrupts K+ conductance and makes retinal pigmented epithelium (RPE) non-functional. While there are no current treatments for LCA16, here we explore CRISPR base editing as a strategy to correct the single base pair pathogenic variant. We show that silica nanoparticle (SNC)-mediated delivery of an adenine base editor (ABE8e) mRNA and single-guide RNA can precisely and efficiently correct the KCNJ13W53X mutation to restore Kir7.1 channel function in an induced pluripotent stem cell-derived RPE (iPSC-RPE) model of LCA16, as well as in patient-derived fibroblasts and in a new LCA16 mouse model. We observed a higher editing efficiency in LCA16 patient-derived fibroblasts (47.38% ± 1.02) than in iPSC-RPE (16.90% ± 1.58) with no detectable off-target editing. The restored channel function in the edited cells resulted in a phenotype comparable to wild-type cells, suggesting the possibility that this treatment could restore vision in LCA16 patients. Injection of ABE8e-carrying SNCs decorated with all-trans retinoic acid (ATRA) ligand into the subretinal space in LCA16 mice showed specific delivery only to RPE and resulted in gene correction in approximately 10% of RPE cells that received the editing machinery. We observed marginal recovery of electroretinogram (ERG) following correction of the W53X allele at the injection site with no further degeneration of RPE. These findings provide a foundation and a proof-of-concept to transition from bench to bedside and support its further development for treating pediatric blindness using a safer mode of SNC-mediated delivery of base editors.

Dominantly inherited disorders are not typically considered therapeutic candidates for gene augmentation. Here, we utilized patient-specific induced pluripotent stem cell-derived retinal pigment epithelium (iPSC-RPE) to test the potential of gene augmentation to treat Best disease, a dominant macular dystrophy caused by over 200 missense mutations in BEST1. Gene augmentation in iPSC-RPE fully restored BEST1 calcium-activated chloride channel activity and improved rhodopsin degradation in iPSC-RPE models of recessive bestrophinopathy and dominant Best disease caused by two different ion binding domain mutations. A dominant Best disease iPSC-RPE model that did not respond to gene augmentation showed normalization of BEST1 channel activity following CRISPR-Cas9 editing of the mutant allele. We then tested gene editing in all three dominant Best disease iPSC-RPE models, which produced premature stop codons exclusively within the mutant BEST1 alleles. Single-cell profiling demonstrated no adverse perturbation of RPE transcriptional programs in any model, although off-target analysis detected a silent genomic alteration in one model. These results suggest that gene augmentation is a viable first-line approach for some dominant Best disease patients and that non-responders are candidates for alternate approaches such as genome editing. However, testing genome editing strategies for on-target efficiency and off-target events using patient-matched iPSC-RPE model systems is warranted. In summary, personalized iPSC-RPE models can be used to select among a growing list of gene therapy options to maximize safety and efficacy while minimizing time and cost. Similar scenarios likely exist for other genotypically diverse channelopathies, expanding the therapeutic landscape for affected patients.SignificanceDominantly inherited disorders pose distinct challenges for gene therapies, particularly in the face of extreme mutational diversity. We tested whether a broad gene replacement strategy could reverse the cellular phenotype of Best disease, a dominant blinding condition that targets retinal pigment epithelium (RPE). Using RPE generated from patient-specific induced pluripotent stem cells (iPSCs), we show that gene replacement functionally overcomes some, but not all, of the tested mutations. In comparison, all dominant Best disease models tested were phenotypically corrected after mutation-specific genome editing, although one off-target genomic alteration was discovered. Our results support a two-tiered approach to gene therapy for Best disease, guided by safety and efficacy testing in iPSC-RPE models to maximize personal and public health value.

PurposeMutations in the KCNJ13 gene are known to cause Leber’s Congenital Amaurosis (LCA16), an inherited pediatric blindness. KCNJ13 gene encodes the Kir7.1 subunit protein which acts as a tetrameric inwardly rectifying potassium ion channel in the retinal pigment epithelium to maintain ionic homeostasis thereby allowing photoreceptors to encode visual information. We sought to determine if genetic approaches might be effective in treating blindness due to mutations in KCNJ13.MethodsWe developed patient-derived hiPSC-RPE carrying an autosomal recessive nonsense mutation in the KCNJ13 gene (c.158G>A, p.Trp53*). We performed biochemical and electrophysiology assays of Kir7.1 function. Both small molecule read-through drug and gene-therapy approaches were tested using this disease-in-a-dish approach.ResultsWe found that the LCA16 hiPSC-RPE had normal morphology but did not express a functional Kir7.1 channel and was unable to demonstrate normal physiology. Following read-through drug treatment, the LCA16 hiPSC cells were hyperpolarized by 30 mV and Kir7.1 current was restored. Similarly, loss-of-function of Kir7.1 channel was circumvented by lentiviral gene delivery to the hiPSC-RPE cells. In either approach, Kir7.1 protein was expressing normally with restoration of membrane potential and Kir7.1 current.ConclusionLoss-of-function mutation in Kir7.1 is a cause of LCA. Using either read-through therapy or gene augmentation, we rescued Kir7.1 channel function in patient-derived iPSC-RPE cells via a precision medicine approach.