Precise editing of pathogenic nucleotide repeat expansion in iPSCs without inducing DNA double-strand breaks using a prime editor [RNA-Seq]

Nucleotide repeat expansion disorders, a group of genetic diseases characterized by the expansion of specific DNA sequences, pose significant challenges to treatment and therapy development. Here, we present a precise and programmable method called prime editor–mediated correction of nucleotide repeat expansion (PE-CORE) for correcting pathogenic nucleotide repeat expansion. PE-CORE leverages a prime editor and paired pegRNAs to achieve targeted correction of repeat sequences. We demonstrate the effectiveness of PE-CORE in HEK293T cells and patient-derived induced pluripotent stem cells (iPSCs). Specifically, we focus on spinal and bulbar muscular atrophy and spinocerebellar ataxia type, two diseases associated with nucleotide repeat expansion. Our results demonstrate the successful correction of pathogenic expansions in iPSCs and subsequent differentiation into motor neurons. Specifically, we detect distinct downshifts in the size of both the mRNA and protein, confirming the functional correction of the iPSC-derived motor neurons. These findings highlight PE-CORE as a precision tool for addressing the intricate challenges of nucleotide repeat expansion disorders, paving the way for targeted therapies and potential clinical applications. Using PE-CORE, we transfected the iPSC-derived from patient, Spinal and Bulbar Muscular Atrophy (SBMA) and Spinocerebellar Ataxia Type 1 (SCA1), and generated gene-corrected disease iPSCs. We differentiate the Motor Neurons (MNs) from the iPSCs and treat 30 nM dihydrotestosterone (DHT) for 1 week to induce androgen activation. Next, we performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells with biological duplication. Comparative gene expression profiling analysis of RNA-seq data for disease iPSCs and gene-corrected disease iPSCs.