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  • Review Article
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Progress in understanding reprogramming to the induced pluripotent state

Nature Reviews Genetics volume 12, pages 253–265 (2011)Cite this article

Subjects

Key Points

  • This Review summarizes the progress to date on efforts to understand the molecular mechanisms underlying transcription factor-induced reprogramming of somatic cells to a pluripotent state (known as the induced pluripotent stem cell (iPSC) state).

  • We discuss potential causes for the inefficiency of the reprogramming process and highlight epigenetic barriers that cannot be easily overcome by the reprogramming factors.

  • New technologies and experiments are helping to determine the chronology of steps leading from loss of the somatic state to gain of pluripotency.

  • We are gaining mechanistic insights into the role of each of the reprogramming factors during the progression to pluripotency.

  • This Review also highlights the role of repressive chromatin as an inhibitor of reprogramming and discusses how chromatin states change at various stages of the process.

  • Studies of X chromosome inactivation and reactivation underscore the degree of chromatin remodelling that occurs during reprogramming. Failure to reactivate the somatically silent X chromosome in female human iPSCs is suggestive of differences in the developmental state between human and mouse embryonic stem cells (ESCs) and iPSCs.

  • Molecular comparisons of ESCs and iPSCs have uncovered various differences between these cell types, and some are informative about the mechanisms underlying the reprogramming process.

  • Finally, we speculate that a combination of novel technologies will accurately define all the molecular events of reprogramming.

Abstract

Induction of pluripotency by transcription factors has become a commonplace method to produce pluripotent stem cells. Great strides have been made in our understanding of the mechanism by which this occurs — particularly in terms of transcriptional and chromatin-based events — yet only a small part of the complete picture has been revealed. Understanding the mechanism of reprogramming to pluripotency will have important implications for improving the efficiency and quality of reprogramming and advancing therapeutic application of induced pluripotent stem cells. It will also help to reveal the machinery that stabilizes cell identity and to instruct the design of directed differentiation or lineage switching strategies. To inform the next phase in understanding reprogramming, we review the latest findings, highlight ongoing debates and outline future challenges.

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Figure 1: The generation of induced pluripotent stem cells is a multistep process.
Figure 2: Roles of the reprogramming factors and their interaction with chromatin during the final step of reprogramming.
Figure 3: X chromosome inactivation and reprogramming.

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Acknowledgements

K.P. is supported by the US National Institutes of Health (NIH) Director's Young Innovator Award (DP2OD001686) and a California Institute for Regenerative Medicine Young Investigator Award (RN1-00564). W.E.L. is the Maria Rowena Ross Professor of Cell Biology and Biochemistry and is supported by the NIH, The March of Dimes, and the Fuller Foundation. K.P. and W.E.L. are supported by the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at the University of California Los Angeles.

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Authors and Affiliations

  1. Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, California, USA

    Kathrin Plath

  2. Jonsson Comprehensive Cancer Center, University of California Los Angeles, California, USA

    Kathrin Plath & William E. Lowry

  3. Molecular Biology Institute, University of California Los Angeles, California, USA

    Kathrin Plath & William E. Lowry

  4. Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, California, USA

    Kathrin Plath & William E. Lowry

  5. Department of Molecular Cell and Developmental Biology, University of California Los Angeles, California, USA

    William E. Lowry

  6. William E. Lowry

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  1. Kathrin Plath
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Nature Reviews Genetics Focus issue on Stem cells

UCLA Broad Stem Cell Research Center

Glossary

Induced pluripotent stem cells

Pluripotent cells that can be generated from many different types of somatic cells by expression of only a few pluripotency-related transcription factors, and that have properties of embryonic stem cells. They serve as an ideal platform to produce patient-specific pluripotent cells.

Pluripotency

The ability of a cell to give rise to all cells of the embryo.

Embryonic stem cells

Pluripotent cells derived from epiblast cells of the blastocyst upon explantation in culture.

Reprogramming factors

Four transcription factors (OCT4, SOX2, KLF4 and MYC), first described by Shinya Yamanaka, that when forcibly expressed in somatic cells are capable of driving these cells into the induced pluripotent stem cell state.

Epigenetic memory

The idea that at least a portion of somatic post-translational modifications on histones and DNA is retained despite reprogramming to a more immature state. This memory is thought to make cells adopt facets of physiology that are representative of a previous cellular state.

Faithful reprogramming

Complete reprogramming to induced pluripotent stem cells, defined by endogenous expression of pluripotency-related genes (such as Nanog and Oct4). Presence of markers such as alkaline phosphatase or the surface antigen stage-specific embryonic antigen 1 (SSEA1), often used to assess reprogramming, mark partially as well as faithfully reprogrammed cells.

Polycistronic cassette

DNA-containing sequence that codes for multiple genes expressed from a single promoter. These coding regions are sometimes separated by sequences that are cleaved during translation to produce individual protein products.

Secondary reprogramming system

A system in which induced pluripotent stem cells are first generated from somatic cells with virally encoded inducible reprogramming factors, then differentiated again to obtain somatic cell populations that can express these factors in all cells and be used for secondary reprogramming experiments upon re-induction of the programming factors.

Pre-iPSCs

Partially reprogrammed cells that arise in reprogramming cultures. They have efficiently silenced somatic genes but have not induced the endogenous pluripotency programme.

NANOG

A transcription factor that is highly expressed in pluripotent cells and is essential for the establishment of embryonic stem cells but not for their maintenance. Although not belonging to the original Yamanaka set of reprogramming factors, NANOG overexpression enhances mouse cell reprogramming at the late step and has been used with OCT4 and SOX2 to reprogramme human cells.

Mesenchymal-to-epithelial transition

Mesenchymal and epithelial cells are distinguished by, among other traits, their gene expression, morphology and cell adhesion properties. Transitions between these two states are thought to have key roles in development, cancer and, more recently, in reprogramming.

Enhancers

DNA regions that positively control gene expression and that can be located upstream, downstream or even within the genes that they regulate. They are often bound by cell-type-specific transcription factors (such as OCT4 and NANOG in embryonic stem cells) and have a specific chromatin signature.

X chromosome inactivation

Transcriptional silencing of one of the two X chromosomes in female mammalian cells, initiated during development when epiblast cells of the blastocyst differentiate.

Naive pluripotent state

This stage of pluripotency is captured in vitro in the form of mouse embryonic stem cells or induced pluripotent stem cells. These cells can differentiate in vitro into many different cell types and, upon injection into blastocysts, can give rise to all tissues of the mouse, including the germ line.

Primed pluripotent state

This stage of pluripotency is captured in vitro in the form of mouse epiblast stem cells and is considered developmentally more advanced than naive pluripotency, with respect to X-inactivation, signalling dependence, gene expression and the inability to contribute to chimeric animals. Human embryonic stem cells are more similar to mouse epiblast stem cells.

Epiblast stem cells

Primed pluripotent cells derived from the post-implantation mouse epiblast of day 5.5–6.5 embryos.

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Plath, K., Lowry, W. Progress in understanding reprogramming to the induced pluripotent state. Nat Rev Genet 12, 253–265 (2011). https://doi.org/10.1038/nrg2955

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