In his very cool talk up here at the Till & McCulloch Meeting on Stem Cells yesterday, Andras Nagy characterized the reprogramming process to make iPS cells as “jailbreaking” cell fate. Nagy described some intriguing studies done on reprogramming by his lab together in collaboration with an international consortium.
I especially appreciated the fact that Nagy (see pic at left, credit to Peter Raaymakers) tackled head on an “elephant in the room” issue in the iPS cell field: cellular reprogramming produces a heterogeneous mix of stem cell types. This unfortunate reality has been quietly reported on in papers and discussed at stem cell meetings for years. Many of colonies produced by the most common iPS cell reprogramming methods are not iPS cells and this phenomenon has meaning.
What are these other colonies?
Some are pre-iPS cells, which didn’t quite make it to full pluripotency. Others are likely iPS cells that made it to full pluripotency, but were unstable and differentiated. Still other byproducts of the iPS cell process are colonies of cancer cells. I noted the similarity of iPS cell methodology to “old-fashioned” oncogenic foci assays used to study tumorigenesis in a review 4 years ago and then in a somewhat controversial research paper, Induced Pluripotency and Oncogenic Transformation Are Related Processes, about 10 months ago.
Nagy focused in his talk on two main types of stem cells produced by the reprogramming process: true iPS cells and so-called “F cells”.
The F class stem cells made by reprogramming are in fact nearly pluripotent, Nagy reported. They are able to form “beautiful” teratoma, but they don’t form chimeric mice so in fact they are not quite as fully pluripotent.
When Nagy’s team looked at gene expression changes in the F cells compared to starting fibroblasts, the alterations tended to more extreme in F cells as opposed to iPS cells. It’s almost as if in the F cells the reprogramming factors did their jobs but went too far to yield too much of a good thing leading to a suboptimal result.
They asked if they could find small molecules that would make the F cells behave more like iPS cells and found that histone deacetylase (HDAC) inhibitors did the trick, now making the F cells able to form chimeric embryos. Thus, Nagy asserted that genomic acetylation is an obstacle to reprogramming.
In an effort that he himself has dubbed “Project Grandiose”, Nagy’s team is throwing everything but the kitchen sink in the way of Omics assays at iPS cells and F cells in a dynamic time course of reprogramming.
The results so far are intriguing with one conclusion being that most of the elements of reprogramming happen surprisingly fast, except for DNA methylation changes. This is interesting at least in part because they do see transcription changes happen fast, well before changes in DNA methylation even though DNA methylation is of course thought to change gene expression. So it seems that there is more to DNA methylation’s role in reprogramming than impacting transcription.
I can’t wait to see more on the Nagy teams efforts in this area.