Rates of acquisition of de novo mutations in human pluripotent stem cells under different culture conditions
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA494559 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7961090_1.fastq.gz | Fastqsanger.gz | |||
| SRR7961090_2.fastq.gz | Fastqsanger.gz | |||
| SRR7961100_1.fastq.gz | Fastqsanger.gz | |||
| SRR7961100_2.fastq.gz | Fastqsanger.gz | |||
| SRR7961110_1.fastq.gz | Fastqsanger.gz |
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Project description:The presence of mutations in human pluripotent stem cells (PSC), whether embryonic stem (ESC) cells, or induced pluripotent stem (iPSC) cells, is a concern for their safe use in therapeutic applications. Indeed, in one case, a potential trial of retinal pigment cells from an autologous iPS cell line was abandoned because the cells carried a mutation of unknown significance (Mandai et al. 2017). Certainly some such variants are likely to have been present in the embryos or somatic cells from which particular PSC were derived and can be classed as ‘variants of origin’ (Amps et al. 2011). However, the propensity of PSC to acquire genetic variants on prolonged passage poses additional concerns, not only because of the difficulty for their early detection (Baker et al. 2016), but also their selective growth advantages might presage malignant potential (Andrews et al. 2017). In this study, to determine the rate and types of mutation that occur during culture of human PSC, we have used a cloning strategy coupled with whole genome- and RNA-sequencing to compare two well characterized, clinical grade human ES cell lines, as well as the effects of culture in the presence of a Rho kinase inhibitor, now commonly used in routine culture of human PSC, and of culture under low oxygen (5% O2) conditions. We have tested whether the mutations are randomly distributed throughout the genome or clustered in regions related to chromatin structure and gene expression. Our results indicate that the mutation rate is low compared to estimates in somatic or cancer cells, and can be further reduced by culture under low oxygen conditions. Furthermore, the mutational signature of human PSC is similar to that of other cultured human cells, but low oxygen culture does alter the frequency of some types of base pair change associated with oxidative damage.
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