Phenotype rescue through the restoration of full-length dystrophin using CRISPR/Cas9 genome editing in Duchenne muscular dystrophy patient-derived iPSCs carrying the deletion of two exons

Duchenne muscular dystrophy (DMD) is a X-linked disease affecting skeletal and cardiac muscle and is caused by mutations in the dystrophin gene ( DMD ). Patient-derived induced pluripotent stem cells (iPSCs) serve as reliable in vitro disease models. Their genetic correction by CRISPR/Cas9 allows the generation of isogenic controls and holds promises for gene therapy. However, restoring full-length dystrophin, especially when deletions involve multiple exons, constitutes a technological challenge. This study aimed to fully repair the dystrophin gene from a DMD iPSC line carrying the deletion of exons 49–50 and to characterize the rescue of the cardiac phenotype. We developed an innovative CRISPR/Cas9-based approach involving the insertion of coding sequences of the deleted region, at the 3’ of exon 48, thereby generating a single continuous coding sequence encompassing exons 48-49-50. Subsequently, iPSCs were differentiated into cardiomyocytes and cardiac fibroblasts. Cardiac phenotypes were analysed by western blot, immunofluorescence, ELISA, FACS, Ionoptix, 3D engineered heart tissue (EHT) and single-nuclei RNA-seq. The correction of a two-exons DMD gene deletion in Duchenne iPSCs, using CRISPR/Cas9, enabled the re-expression of a stable and functional full-length dystrophin in cardiomyocytes resulting in the rescue of cardiac pathological phenotypes. Edited cardiomyocytes showed improved morphology, reduced release of the cardiomyocytes damage marker troponin I, and decreased ROS production. Moreover, dystrophin restoration enhanced contractility and ameliorated the Ca 2+ kinetics. Notably, edited iPSC derived fibroblasts showed reduced pro-fibrotic stimuli response. In parallel, we also observed enhanced functioning of a 3D engineered heart tissue and profound change in the transcriptomic profile in both cardiomyocytes and fibroblasts after the re-expression of full-length dystrophin. We developed an innovative approach that enabled the re-expression of full-length dystrophin in a DMD iPSC line with consequent complete rescue of in vitro DMD cardiac phenotypes. On the long term, these results could lay a foundation for future applications of cell therapy or in vivo CRISPR/Cas9-based intervention to treat DMD.