Need Help?

To determine the mutational impact of the in vitro culture, clonal human adult and pluripotent stem cell lines were subjected to a second clonal step after 3 months of culture. These subclones were whole genome sequenced to identify all the mutations that accumulated during the 3 month culture period.

Genetic changes acquired during culture pose a potential risk for the successful application of stem cells. To assess the risk of in vitro expansion on mutation accumulation we have performed whole genome sequencing of clonally expanded human induced pluripotent stem cells (iPS cells) and adult stem cells (ASCs) to identify all mutations that accumulated over a fixed culture period. We find that ASCs acquire more single nucleotide variants (SNVs) and indels per population doubling than the iPS cells. When compared with ASCs, iPS cells are more vulnerable to mutations in genes and promoters. Mutational analysis revealed a clear in vitro induced mutational signature that is irrespective of stem cell type. This in vitro signature is characterized by C to G transversions that are probably caused by oxidative stress. 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. In conclusion, in vitro culture induces mutation accumulation in iPS cells and ASCs. Culture under low-oxygen tension may help to reduce the number of culture-induced mutations.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
EGAD00001004104 HiSeq X Ten NextSeq 500 11
Publications Citations
5-Fluorouracil treatment induces characteristic T>G mutations in human cancer.
Nat Commun 10: 2019 4571
The mutational impact of culturing human pluripotent and adult stem cells.
Nat Commun 11: 2020 2493
Human induced pluripotent stem cells display a similar mutation burden as embryonic pluripotent cells <i>in vivo</i>.
iScience 25: 2022 103736