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Origins and implications of pluripotent stem cell variability and heterogeneity

Nature Reviews Molecular Cell Biology volume 14, pages 357–368 (2013)Cite this article

Subjects

Key Points

  • There are marked differences in the in vitro differentiation capacity of pluripotent stem cell lines, including embryonic stem (ES) cells and induced pluripotent stem (iPS) cells. These differences currently limit their possible application in the clinic and as a research tool.

  • The molecular underpinnings of these functional differences are unclear. In some cases, the differences can be ameliorated by altering culture conditions by adding or removing specific growth factors and/or signalling molecules.

  • Pluripotent stem cells derived using the same method have highly similar gene expression profiles, yet can exhibit functional differences. This suggests that genetic or epigenetic changes are silent in the pluripotent state.

  • Most genetic differences between founder and reprogrammed cells seem to pre-exist in a minor population of the founder cells.

  • Epigenetic differences between ES cells and iPS cells are both residual (that is, they maintain the same epigenetic state as their respective founder cell type) and aberrant (that is, resembling neither ES cells nor founder cells), and both types of differences may have an impact on the in vitro differentiation process.

  • It remains unclear whether gene expression heterogeneity within a clonal pluripotent stem cell line is a crucial feature of pluripotency, and whether this gene expression heterogeneity is associated with functional differences between different pluripotent cell lines.

Abstract

Pluripotent stem cells constitute a platform to model disease and developmental processes and can potentially be used in regenerative medicine. However, not all pluripotent cell lines are equal in their capacity to differentiate into desired cell types in vitro. Genetic and epigenetic variations contribute to functional variability between cell lines and heterogeneity within clones. These genetic and epigenetic variations could 'lock' the pluripotency network resulting in residual pluripotent cells or alter the signalling response of developmental pathways leading to lineage bias. The molecular contributors to functional variability and heterogeneity in both embryonic stem (ES) cells and induced pluripotent stem (iPS) cells are only beginning to emerge, yet they are crucial to the future of the stem cell field.

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Figure 1: Model of the mouse pluripotency network.

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Acknowledgements

G.Q.D. is supported by grants from the US National Institutes of Health (NIH) (UO1-HL100001 Progenitor cell biology consortium, R24-DK092760, P50HG005550 and special funds from the ARRA stimulus package- RC2-HL102815, RC4DK 090913), the Roche Foundation for Anemia Research, Alex's Lemonade Stand Foundation, Doris Duke Charitable Foundation and the Ellison Medical Foundation. G.Q.D. is an affiliate member of the Broad Institute and an investigator of the Manton Center for Orphan Disease Research and the Howard Hughes Medical Institute. P.C. is supported by grants T32HL007623 and 2T32HL66987-11 from the National Heart, Lung, and Blood Institute (NHLBI). The authors would like to thank R. Zhao and A. De Los Angeles for helpful discussions.

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  1. Division of Pediatric Hematology and Oncology, Department of Biological Chemistry and Molecular Pharmacology, Stem Cell Transplantation Program, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Harvard Stem Cell Institute, Boston, 02115, Massachusetts, USA

    Patrick Cahan & George Q. Daley

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Correspondence to George Q. Daley.

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G.Q.D. is a member of the scientific advisory boards of the following companies: Johnson & Johnson, Verastem, Epizyme, Inc., iPierian, Inc., Solasia K.K. and MPM Capital, LLP. P.C. declares no competing financial interests.

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FURTHER INFORMATION

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Glossary

Teratomas

Localized tumours in which germ layer derivatives are apparent, often in highly organized patterns resembling normal tissues.

Trophectoderm

The first cells to differentiate from the fertilized egg and that form the outer layer of the blastocyst. They give rise to extra-embryonic tissues, including the placenta.

Unsupervised analysis

Unsupervised analysis methods, such as clustering, discover groups in data without being informed of group labels.This is in contrast to supervised analysis methods, such as the analysis of variance (ANOVA), which find features that distinguish groups.

Seminomas

Malignant but highly treatable germ cell tumours of the testis.

Episome method

A method to force the ectopic expression of reprogramming factors. This method relies on transient transfection of plasmids that encode reprogramming factors.

Embryoid bodies

Three-dimensional, semi-organized aggregates of differentiating pluripotent stem cells.

CpG bisulphite sequencing

Identification of CpG methylation by targeted sequencing of bisulphite-treated genomic DNA. Bisulphite treatment causes the conversion of cytosine to uracil. Because uracil is not a genomic residue, it can be used to infer cytosine methylation.

Dlk1–Dio3 locus

An imprinted region of mouse chromosome 12qF1 containing multiple dosage-sensitive, protein-coding and non-coding genes.

Genetic mosaicism

Genetic heterogeneity of a cellular population that has arisen due to the presence of distinct founder clones. Can occur at the tissue, organ or organism level, or in the dish.

Exome

The nucleotide sequence of the protein-coding portion of a genome as determined by targeted next-generation sequencing.

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Cahan, P., Daley, G. Origins and implications of pluripotent stem cell variability and heterogeneity. Nat Rev Mol Cell Biol 14, 357–368 (2013). https://doi.org/10.1038/nrm3584

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