Mutational impact of culturing human pluripotent and adult stem cells

Ewart Kuijk, Myrthe Jager, Bastiaan van der Roest, Mauro D. Locati, Arne Van Hoeck, Jerome Korzelius, Roel Janssen, Nicolle Besselink, Sander Boymans, Ruben van Boxtel, Edwin Cuppen

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Oct 25, 2018
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Received Date: 15th October 18

Genetic changes acquired during in vitroculture pose a potential risk for the successful application of stem cells in regenerative medicine. To assess mutation accumulation risks induced by culturing, we determined genetic aberrations in individual human induced pluripotent stem cells (iPS cells) and adult stem cells (ASCs) by whole genome sequencing analyses. Individual iPS cells, intestinal ASCs and liver ASCs accumulated 3.5±0.5, 7.2±1.0 and 8.4±3.6 base substitutions per population doubling, respectively. The annual in vitromutation accumulation rate of ASCs adds up to ~1600 base pair substitutions, which is ~40-fold higher than the in vivorate of ~40 base pair substitutions per year. Mutational analysis revealed a distinct in vitroinduced mutational signature that is irrespective of stem cell type and distinct from the in vivo mutational signature. This in vitrosignature is characterized by C to A changes that have previously been linked to oxidative stress conditions. Additionally, we observed stem cell-specific mutational signatures and differences in transcriptional strand bias, indicating differential activity of DNA repair mechanisms between stem cell types in culture. We demonstrate that the empirically defined mutation rates, spectra, and genomic distribution enable risk assessment by modelling the accumulation of specific oncogenic mutations during typical in vitroexpansion, manipulation or screening experiments using human stem cells. Taken together, we have here for the first time accurately quantified and characterized in vitro mutation accumulation in human iPS cells and ASCs in a direct comparison. These results provide insights for further optimization of culture conditions for safe in vivo utilization of these cell types for regenerative purposes.

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This is an abstract of a preprint hosted on an independent third party site. It has not been peer reviewed but is currently under consideration at Nature Communications.

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