Do stem cells have memory?

14 August 2014
By Daniel Gaffney and Foad Rouhani

iPS colonies. Credit: Foad Rouhani

iPS colonies. Credit: Foad Rouhani

Human induced pluripotent stem cells (hIPSCs) can be created from skin, blood or other tissues, and can be differentiated into any cell in the human body. Because they can be easily derived from pretty much anyone, hIPSCs have enormous potential for personalised medicine and the study of disease.

However, for reasons we don’t really understand, hIPSCs are highly variable in the lab: some cell lines are almost impossible to work with, but others are relatively trouble-free. One potential problem might be that hIPSCs remember their origins, the skin or blood cells they were originally derived from, long after they’ve been reprogrammed, a phenomenon some people have called “epigenetic memory”.

On the other hand, genetic differences between people also influence the behaviour and character of cells. Although it’s often overlooked, different cell lines probably vary simply because they’re derived from different people.

We wanted to understand whether hIPSC “memory” could really explain some of the variability we see between cell lines and how important this effect was relative to the effects of genetic differences between people. We made hIPSCs in controlled experimental conditions from two different types of skin cells, and blood derived from healthy donors. A key feature of our experiment was that we were able to get multiple tissue types from the same people, allowing us to disentangle the effects of genetics from other experimental factors.

The major result of our paper is that, although epigenetic memory may exist, its effects on hIPSCs look less influential than the effects of normal genetic differences between healthy people. In other words, on average, hIPSCs derived from two different tissues in the same person are more similar than hIPSCs derived from the same tissue in two unrelated people. We did find a handful of genes that showed some evidence of epigenetic memory, but none of these appeared to be the “master regulators”, that can drastically alter every aspect of a cell’s behaviour and morphology.

The results of our study have a few consequences we think are important. The first is that the impact of an entire genome’s worth of genetic differences can’t be ignored when studying, for example, the consequences of an individual mutation. In the future, hIPSCs are likely to be a vital research tool in understanding the functions of disease causing mutations. When faced with the choice of making lots of hIPSC lines from a single individual, or one hIPSC line from lots of individuals, we think that in most experimental scenarios the latter option is the right one. At the Sanger Institute, we’re currently involved in a large project, the Human Induced Pluripotent Stem Cells Initiative, to generate hIPSCs from a large number of healthy people, to provide exactly this type of resource for the research community.

A second point is that the effects of epigenetic memory seem to be pretty modest. This is important because it’s sometimes not possible to ensure that all cell types in a study have all been derived in exactly the same way. Our study suggests that hIPSCs derived from different tissues are comparable although, as always, this should be done cautiously. It also important to point out that our study can’t say really whether epigenetic memory exists or not.

Finally, an intriguing possibility is that some important differences in hIPSC behavior, such as better differentiation into certain cell types, might be driven by genetic differences. Although for the moment this is speculation, analysis of the data generated by the HIPSCI project will give us much better insights into this question. By identifying what causes variation in iPS cells we can design more efficient differentiation protocols and be better able to generate clinically useful cells for treating patients.

Daniel Gaffney is a junior group leader in Computational Genomics at the Wellcome Trust Sanger Institute. His group works on understanding how mutations affect the regulation of gene expression.

Foad Rouhani is a former clinical PhD student under the supervision of Allan Bradley. His research focussed on genetic and transcriptional variations following reprogramming of cells into induced pluripotent stem cells.


  • Rouhani,F et al (2014). Genetic Background Drives Transcriptional Variation in Human Induced Pluripotent Stem Cells. PLOS Genetics. DOI: 10.1371/journal.pgen.1004432

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