SummaryHuntington disease (HD) is a dominant neurodegenerative disorder caused by a CAG repeat expansion in HTT. Here we report correction of HD human induced pluripotent stem cells (hiPSCs) using a CRISPR-Cas9 and piggyBac transposon-based approach. We show that both HD and corrected isogenic hiPSCs can be differentiated into excitable, synaptically active forebrain neurons. We further demonstrate that phenotypic abnormalities in HD hiPSC-derived neural cells, including impaired neural rosette formation, increased susceptibility to growth factor withdrawal, and deficits in mitochondrial respiration, are rescued in isogenic controls. Importantly, using genome-wide expression analysis, we show that a number of apparent gene expression differences detected between HD and non-related healthy control lines are absent between HD and corrected lines, suggesting that these differences are likely related to genetic background rather than HD-specific effects. Our study demonstrates correction of HD hiPSCs and associated phenotypic abnormalities, and the importance of isogenic controls for disease modeling using hiPSCs.

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Human induced pluripotent stem cells (hiPSCs) derived from Huntington’s disease (HD) patients provide a physiologically relevant cellular platform for disease modelling and drug screening studies. However, hiPSCs reprogramed from different individuals may exhibit variability in differentiation potential and cellular phenotypes that are independent of the HTT mutation due to variations in genetic background. Thus, in order to accurately detect authentic disease phenotypes and subtle alterations in cell function in hiPSC-based models, the establishment of isogenic controls is necessary. Here we report the scarless correction of an HD iPSC line carrying an expansion of 180 CAG repeats using a CRISPR-Cas9 and piggyBac transposon-based homologous recombination approach. Our results suggest that some molecular changes and phenotypes observed in HD hiPSC models compared with non-related healthy controls in fact reflect differences in the genetic background of the respective lines rather than disease-specific mutant HTT effects. Therefore, our study provides an example of scarless correction of hiPSCs from HD patients and also demonstrates the importance of isogenic controls for disease modelling using hiPSCs.