Turning back the clock
First systematic look at protein changes during cellular reprogramming to induced pluripotency
Scientists have known for about half a century that it’s possible to effectively put cells in a time machine, ‘winding back’ their development to the point when they were stem cells. Those stem cells can then be coaxed into becoming a different type of cell altogether, so the process – called reprogramming to induced pluripotency – holds such promise that its pioneers were awarded the 2012 Nobel Prize in Physiology or Medicine. But in spite of tremendous advances, researchers still don’t have a full answer to a seemingly crucial question: What exactly happens inside a cell as it changes from a specific type to one that can turn into virtually anything?
“People have been looking at this a lot, primarily at the level of how genes are expressed and controlled. No-one’s really looked at what happens to proteins,” says Jeroen Krijgsveld from EMBL Heidelberg. As Team Leader in the Genome Biology Unit and head of the Proteomics Core Facility at EMBL Heidelberg, Jeroen was ideally poised to launch an investigation into the matter, published in Cell Reports in December.
Jenny Hansson, a post-doctoral scientist in Jeroen’s group, used mass spectrometry to monitor how the production of 8000 different proteins changed over the two weeks it took to reprogram skin cells back into stem cells. But first, the EMBL scientists had to contend with a shortcoming of reprogramming. Even the best-honed methods for turning cells back into stem cells are very inefficient: only about 1% of cells in each experiment go through the transformation. Under such conditions, attempting to follow protein changes in all the cells in a pluripotency experiment would be wasteful. Working with Konrad Hochedlinger from Massachussets General Hospital in the USA, who had previously developed a sorting method for the purpose, the scientists were able to fish out the cells that were likely to become stem cells, and thus study only what they were truly interested in.
In general, they found that the amount of most proteins the cells produce varies tremendously between the start and end of the reprogramming process: either going from being produced in high numbers at the beginning to hardly being produced at all, or the other way around. Thus, scientists now have more precise information about the molecular processes that take place at different stages of reprogramming.
The study also turned up some surprises. “We saw some changes that there was no hint of when people looked at gene expression,” says Jenny, “the genes for these proteins are not getting turned up or down, but the amounts of proteins are changing in unexpected ways.”
Jenny and Jeroen are keen to point out that this is just a starting-point. They and others can now mine this data for patterns of protein change, and for proteins that inexplicably deviate from those patterns. For instance, Jeroen and Jenny, together with Sina Rafiee in Jeroen’s group, have already discovered that a protein called Nup210, a nuclear pore protein that was recently shown to be essential for stem cells to differentiate into neurons, is also crucial for the transition back to stem cells.
Of the multitude of questions to explore, Jeroen would love for someone to answer: why does reprogramming take 15 days? What happens in those middle days when nothing much seems to be going on? “And ultimately, can we speed up the process? When you’re talking about taking cells from patients, having to wait two to three weeks is wasted time,” he muses.
"Highly coordinated proteome dynamics during reprogramming of somatic cells to pluripotency" - Hansson, J., Reiland, S., Rafiee, M.R., Polo, J., Gehring, J., Okawa, S., Huber, W., Hochedlinger, K., Krijgsveld, J. Cell Reports, 20 December 2012
- 2012 Nobel Prize in Physiology or Medicine
- More information on the work of the Krijgsveld team
- More information on the EMBL Proteomics Core Facility