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Acquired genetic changes in human pluripotent stem cells: origins and consequences

Abstract

In the 20 years since human embryonic stem cells, and subsequently induced pluripotent stem cells, were first described, it has become apparent that during long-term culture these cells (collectively referred to as ‘pluripotent stem cells’ (PSCs)) can acquire genetic changes, which commonly include gains or losses of particular chromosomal regions, or mutations in certain cancer-associated genes, especially TP53. Such changes raise concerns for the safety of PSC-derived cellular therapies for regenerative medicine. Although acquired genetic changes may not be present in a cell line at the start of a research programme, the low sensitivity of current detection methods means that mutations may be difficult to detect if they arise but are present in only a small proportion of the cells. In this Review, we discuss the types of mutations acquired by human PSCs and the mechanisms that lead to their accumulation. Recent work suggests that the underlying mutation rate in PSCs is low, although they also seem to be particularly susceptible to genomic damage. This apparent contradiction can be reconciled by the observations that, in contrast to somatic cells, PSCs are programmed to die in response to genomic damage, which may reflect the requirements of early embryogenesis. Thus, the common genetic variants that are observed are probably rare events that give the cells with a selective growth advantage.

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Fig. 1: Cultured human pluripotent stem cells can acquire a variety of mutations.
Fig. 2: Nature of tumours derived from pluripotent stem cells.
Fig. 3: Mechanisms of variant growth advantage.
Fig. 4: Overview of the origins of mutation in human pluripotent stem cells.

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Acknowledgements

This work was funded in part by grants from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 668724 and from the UK Regenerative Medicine Platform, MRC reference MR/R015724/1.

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Correspondence to Ivana Barbaric or Peter W. Andrews.

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Glossary

Age-related macular degeneration

A common cause of blindness in elderly people due to degeneration of the retinal pigment epithelium underlying the retina.

Mosaic culture

A culture containing two or more genetically distinct cell types; for example, an original cell type and a genetic variant derived from it.

Population bottleneck

A situation occurring during successive passaging of cell cultures in which a culture is derived from a very small number of cells from the preceding culture.

Driver genes

Genes whose altered expression provides the main selective growth advantage associated with a particular genomic variant.

Clonogenic assays

Assays in which clones of cells are grown out from isolated single cells to assess the properties of the different cells composing a mosaic culture.

Aneuploidy

An unbalanced genome caused by the presence of an abnormal number of chromosomes or fragments of chromosomes in a cell; it does not include abnormal numbers of chromosomes that are exact multiples of the haploid set of chromosomes (that is, 23 in human cells).

Interstitial duplications

A type of chromosomal aberration in which a duplicated DNA segment is inserted in the same chromosome.

Whole-exome sequencing

A method of sequencing all of the protein-coding regions (exome) in the genome.

Epiblast

Embryonic tissue that gives rise to all of the fetal tissues, including the germ line.

Xenograft tumours

Tumours developing from cells transplanted to a host of a different species; in this Review, typically tumours produced by human cells in an immunodeficient mouse host.

Primitive endoderm

Cells found in teratomas and closely resembling cells of the extraembryonic endoderm found in the pre-implantation embryo.

Amplicon

A discrete region of the genome that has been duplicated one or more times.

Hitchhiker genes

Genes present on amplified or deleted chromosome segments with no effect on the growth advantage of the variant cell.

Cell competition

Cell–cell interaction mechanism leading to elimination of cells that are viable in their homotypic environment in the presence of comparatively fitter cells.

Isochromosome

A chromosomal rearrangement in which one whole arm of a chromosome is replaced by a complete copy of the other arm, resulting in a loss of the genes located on the first arm and duplication of the genes located on the other arm.

Clinical grade

A loose and ill-defined term that identifies cell lines that have been developed and maintained in ways that will satisfy regulatory authorities for clinical application; it is commonly applied to pluripotent stem cell lines that have been derived according to good manufacturing practice.

Indels

Genomic changes involving the insertion or deletion of a sequence of one or more nucleotides.

RB1–E2F checkpoint

Controls the entry into S phase and the initiation of DNA replication during the cell cycle; dependent on the retinoblastoma tumour suppressor protein, RB1, regulating expression of the transcription factor E2F.

G1/S checkpoint

Also known as the restriction point, safeguards entry into S phase during the cell cycle, where DNA synthesis occurs.

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Halliwell, J., Barbaric, I. & Andrews, P.W. Acquired genetic changes in human pluripotent stem cells: origins and consequences. Nat Rev Mol Cell Biol 21, 715–728 (2020). https://doi.org/10.1038/s41580-020-00292-z

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