Aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) is a photoreceptor-specific chaperone that stabilizes the effector enzyme of phototransduction, cGMP phosphodiesterase 6 (PDE6). Mutations in the AIPL1 gene cause a severe inherited retinal dystrophy, Leber congenital amaurosis type 4 (LCA4), that manifests as the loss of vision during the first year of life. In this study, we generated three-dimensional (3D) retinal organoids (ROs) from human induced pluripotent stem cells (hiPSCs) derived from an LCA4 patient carrying a Cys89Arg mutation in AIPL1. This study aimed to (i) explore whether the patient hiPSC-derived ROs recapitulate LCA4 disease phenotype, and (ii) generate a clinically relevant resource to investigate the molecular mechanism of disease and safely test novel therapies for LCA4 in vitro. We demonstrate reduced levels of the mutant AIPL1 and PDE6 proteins in patient organoids, corroborating the findings in animal models; however, patient-derived organoids maintained retinal cell cytoarchitecture despite significantly reduced levels of AIPL1. Hereditary retinal degenerations are clinically and genetically heterogeneous and constitute a major cause of incurable visual impairment in working age adults. Unfortunately, this group of diseases currently lacks effective treatment options. Among the divergent clinical phenotypes, Leber congenital amaurosis (LCA) accounts for ∼5% of all inherited retinopathies and is among the most severe, with patients exhibiting visual dysfunction and losing electroretinogram signals during the early years of age 1. Patients typically present nystagmus (repetitive, uncontrolled movements of the eyes), poor pupillary light response, and fundus abnormalities 2. Currently, as many as 25 genes have been identified as causing LCA (https://sph.uth.edu/retnet/) primarily in an autosomal recessive manner; however, genetic defects have not been identified in almost 30% of LCA patients 2. All known causative genes are expressed in photoreceptors and/or the retinal pigment epithelium (RPE) and associated with a wide range of functions, including phototransduction, retinoid cycling, protein trafficking, and ciliary transport. Mutations in the aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) gene lead to early onset retinal disease and account for up to 5-10% of all mutations causing LCA 3 resulting in a clinically severe form, LCA type 4 (LCA4, OMIM #604393) 4. The AIPL1 gene locates to chromosome 17, with 79 mutations identified to date as causing LCA (Human Genome Mutation Database). AIPL1 encodes a 384 amino acid protein expressed only in photoreceptors and the pineal gland 5. The protein has an FK506-binding protein (FKBP)-like domain within the N terminus, a tetratricopeptide (TPR) domain with three TPR repeats, and a primate unique proline-rich domain

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The SWI/SNF family of ATP-dependent chromatin remodeling complexes is implicated in multiple DNA damage response mechanisms and frequently mutated in cancer. The BAF, PBAF and ncBAF complexes are three major types of SWI/SNF complexes that are functionally distinguished by their exclusive subunits. Accumulating evidence suggests that double-strand breaks (DSBs) in transcriptionally active DNA are preferentially repaired by a dedicated homologous recombination pathway. We show that different BAF, PBAF and ncBAF subunits promote homologous recombination and are rapidly recruited to DSBs in a transcription-dependent manner. The PBAF and ncBAF complexes promote RNA polymerase II eviction near DNA damage to rapidly initiate transcriptional silencing, while the BAF complex helps to maintain this transcriptional silencing. Furthermore, ARID1A-containing BAF complexes promote RNaseH1 and RAD52 recruitment to facilitate R-loop resolution and DNA repair. Our results highlight how multiple SWI/SNF complexes perform different functions to enable DNA repair in the context of actively transcribed genes.