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Mutational impact of culturing human pluripotent and adult stem cells

Kuijk, Ewart and Jager, Myrthe and Roest, Bastiaan van der and Locati, Mauro and Hoeck, Arne Van and Korzelius, Jerome and Janssen, Roel and Besselink, Nicolle and Boymans, Sander and Boxtel, Ruben van and Cuppen, Edwin (2018) Mutational impact of culturing human pluripotent and adult stem cells. [Preprint] (Unpublished) (doi:10.1101/430165) (KAR id:81302)

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Official URL:
https://doi.org/10.1101/430165

Abstract

Genetic changes acquired during in vitro culture 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 vitro mutation accumulation rate of ASCs adds up to ∼1600 base pair substitutions, which is ∼40-fold higher than the in vivo rate of ∼40 base pair substitutions per year. Mutational analysis revealed a distinct in vitro induced mutational signature that is irrespective of stem cell type and distinct from the in vivo mutational signature. This in vitro signature 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 vitro expansion, 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.

Item Type: Preprint
DOI/Identification number: 10.1101/430165
Refereed: No
Other identifier: https://www.biorxiv.org/content/10.1101/430165v1
Name of pre-print platform: bioRxiv
Divisions: Divisions > Division of Natural Sciences > Biosciences
Depositing User: Susan Davies
Date Deposited: 18 May 2020 13:39 UTC
Last Modified: 26 Sep 2023 14:45 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/81302 (The current URI for this page, for reference purposes)

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