Genomic instability in iPS cells

Author: Chris Kamel, 03/02/11

They’re promising, but not perfect. Induced pluripotent stem cells are perhaps one of the most studied areas of stem cell research today, as researchers work to improve their method of production, but new findings out of Canada and Finland suggests that the process of reprogramming may cause unwanted and irreversible DNA damage. As such, the rush to improve iPS cell generation may, in itself, be partially responsible for decreased integrity of the cells.

To date, several methods of reprogramming have been developed with the partial aim of improving the efficiency of iPS cell generation. The reprogramming process involves the introduction of a key set of genes which, along with turning terminally differentiated cells into stem cells, can alter other aspects of cell biology. For example, one of the genes involved in reprogramming, the oncogene c-Myc, can interact with p53 and p21 activities. This has a positive effect on reprogramming efficiency but can also lead to genomic instability.

One mark of genomic instability is copy number variation (CNV), an abnormal number of copies of DNA caused by the deletion or duplication of regions of the genome. The Canadian-Finnish paper, to be published tomorrow in Nature, demonstrated that human iPS cells have more CNVs than human ES cell lines, and that the number of CNVs decreased as the induced pluripotent cells were passaged in culture. These observations were independent of gene delivery method, original cell source, and the presence or absence of c-Myc, and suggest that generation of CNVs occurs with the reprogramming process. Focussing on copy number variation caused by genomic deletions, the authors found that in “young” iPS cell populations, many deletions were found in regions responsible for mainenance of an undifferentiated state in ES cells. As cells were passaged in culture, these deletions were not found indicating these cells were being selected against and overgrown.

The study demonstrates that the reprogramming process to generate iPS cells is associated with a high mutation rate. While selection deleterious mutations in culture brings the number of CNVs in line with those in human ES cells, it does not exclude the fact that some mutations may, in fact, offer selective advantage and lead to propagation of unwanted traits. The paper offers some new insights into the reprogramming mechanisms and potential downsides of the iPS approach. Better understanding of the reprogramming process and of the genomic integrity of iPS cell lines could lead to more efficient techniques and higher quality iPS cells for use in future research and therapeutic applications.

 

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