Precise Correction of the Dystrophin Gene in Duchenne Muscular Dystrophy Patient Induced Pluripotent Stem Cells by TALEN and CRISPR-Cas9

TLDR

The study aims to evaluate the safety of correcting DMD patient‑derived iPSCs using TALENs or CRISPR‑Cas9. Using a unique k‑mer database, the authors identified a low‑off‑target target region, applied exon skipping, frameshifting, and exon knock‑in to DMD‑derived iPSCs—finding exon knock‑in most effective—and then assessed genomic integrity via karyotyping, CNV array, and exome sequencing to select clones with minimal mutations. The authors successfully corrected the dystrophin frameshift in patient‑derived iPSCs with TALENs or CRISPR‑sgRNAs, achieved minimal off‑target mutations, and demonstrated full‑length dystrophin expression after myogenic differentiation, establishing a framework for iPSC‑based DMD gene therapy.

Abstract

Highlights•A unique k-mer database was used to identify unique targetable regions in human genome•A dystrophin frameshift was corrected using TALENs or CRISPR-sgRNAs in iPSCs•Genomic integrity tests identified minimum off-target mutagenesis by the nucleases•Dystrophin protein was detected by myogenic differentiation in the corrected iPSCsSummaryDuchenne muscular dystrophy (DMD) is a severe muscle-degenerative disease caused by a mutation in the dystrophin gene. Genetic correction of patient-derived induced pluripotent stem cells (iPSCs) by TALENs or CRISPR-Cas9 holds promise for DMD gene therapy; however, the safety of such nuclease treatment must be determined. Using a unique k-mer database, we systematically identified a unique target region that reduces off-target sites. To restore the dystrophin protein, we performed three correction methods (exon skipping, frameshifting, and exon knockin) in DMD-patient-derived iPSCs, and found that exon knockin was the most effective approach. We further investigated the genomic integrity by karyotyping, copy number variation array, and exome sequencing to identify clones with a minimal mutation load. Finally, we differentiated the corrected iPSCs toward skeletal muscle cells and successfully detected the expression of full-length dystrophin protein. These results provide an important framework for developing iPSC-based gene therapy for genetic disorders using programmable nucleases.Graphical abstract