Stem-cell reprogramming method not to blame for mutations: Scripps scientists

October 7, 2011

Scientists at the Scripps Research Institute have discovered that a reprogramming method is not to blame for dangerous mutations found within Induced Pluripotent Stem Cells (iPSC) — adult stem cells that have been genetically coaxed into behaving like embryonic stem cells. The discovery may help narrow down the exact cause of the mutations, long a roadblock to iPSC’s widespread use.

There have been a number of puzzling genetic mutations in iPSCs that some scientists say call into question just how reliable non-embryonic stem cells are. Some believe that the mutations  might be caused by current reprogramming techniques. While little is known about how these mutations would effect how the cells could be used in medicine, it has made researchers cautious as they develop reprogrammed adult cells into treatments. Many, in fact, use embryonic stem cells in tandem to check their work.

Eliminating DNA mutations

Now, Kristin Baldwin, associate professor at The Scripps Research Institute’s Dorris Neuroscience Center, said their research shows that fears over the reprogramming method may be unwarranted.

“We’ve shown that the standard reprogramming method can generate induced pluripotent stem cells that have very few DNA structural mutations, which are often linked to dangerous cell changes such as tumorigenesis,” said Baldwin, whose lab collaborated with Ira M. Hall, an assistant professor of biochemistry and molecular genetics at the University of Virginia.

To push adult stem cells taken from the patient into behaving like embryonic ones, scientists insert four special genes. The Scripps Research team followed this process, but sought to minimize other potential sources of DNA mutations that might have influenced some previously reported results. The donor cells they selected were not decades-old human skin cells, but relatively error-free fibroblast cells from fetal mice. The researchers also kept these fibroblast cells only briefly in lab dishes before reprogramming them.

New chromosomal error-mapping methods

They used sensitive new chromosomal error-mapping methods to distinguish which mutations were present in rare donor fibroblast cells vs. which ones were newly acquired during reprogramming. Instead of finding more mutations, they found almost none. “We sequenced three iPSC lines at very high resolution, and were surprised to find that very few changes to the chromosomal sequence had appeared during reprogramming,” said Michael J. Boland, a research associate in the Scripps Research Baldwin lab

Some of the mutations seen in human iPSCs in previous studies might have been due to incomplete reprogramming that impaired the cells’ DNA-maintenance mechanisms. In this study using mouse iPSCs, however, there was no doubt that a complete reprogramming to an embryonic state had occurred.

Baldwin’s lab now is trying to determine whether a reprogramming method similar to the one used with mouse iPSCs in this study could also yield relatively error-free human iPSCs. “If our results with these mouse cells are applicable to human cells, then selecting better donor cells and using more sensitive genome-survey techniques should allow us to identify reprogramming methods that can produce human iPSCs that will be safer or more useful for therapies than current lines,” she said.

Ref.: Aaron R. Quinlan et al., Genome Sequencing of Mouse Induced Pluripotent Stem Cells Reveals Retroelement Stability and Infrequent DNA Rearrangement during Reprogramming, Cell Stem Cell, Volume 9, Issue 4, 366-373, 4 October 2011