Jaenisch’s new, complicated iPS paper in Cell: what the heck does it all mean?

The iPS cell field has had a relatively quiet 2012 so far, but one recent paper has drawn particular attention in the last 10 days. I’m talking about the paper from Jaenisch’s lab on iPS cells in Cell.

Quite a few people are excited, but also scratching their heads a bit as to what this paper means in the big picture.

This study represents a massive amount of work for, at least relatively speaking, “only” 9 authors including Jaenisch.

The paper uses single-cell analysis, a relatively underutilized approach for iPS cell studies, to examine the chain of events that occur leading a fibroblast to be reprogrammed into an iPS cell.

In my mind the biggest take home message from this paper is that there seem to be two phases to cellular reprogramming with the first being largely random (i.e. stochastic) and the second being orderly.

The notion that there is a chaotic element to reprogramming is not new and this theory has been used to explain why only certain rare cells become iPS cells, while others end up partially reprogrammed or have other fates such as being like cancer cells. So in my opinion it’s not a major advance that Jaenisch’s paper identifies a stochastic phase. Still it is interesting albeit logical that this chaos, if you will, occurs early and then things become more orderly later.

It is particularly notable which stem cell player, to anthropomorphize the process somewhat, comes out as the kingpin directing the second more orderly phase. Not Oct4. Not Nanog. Not a host of other likely suspects.


Yes, Sox2 is important and we knew that already in the field. Jaenisch’s study places much more weight on Sox2 over other factors, though, than might have been anticipated. To me this is somewhat surprising, but the data at least in this context seem to back it up and the Bayesian Network analysis is convincing (see their model below).


Some important questions come to mind.

  • I wonder if different labs doing similar studies but using different starting cells or different approaches might find different “kingpins” of iPS cells? 
  • I also wonder: could some of the chaotic nature of the early phase of reprogramming be due to different protein levels of reprogramming factors in every cell? Or is it always going to messy at first and then orderly later?
  • Why would DPPA2-Nanog evolve as a somewhat separable functional unit? 
  • Why such a relatively “minor” role for Oct4, when it seems that most data to date point toward it being the most important factor? Why is it not even part of the model’s network?

I also found it interesting that Jaenisch several times mentions of cells becoming “transformed” as though it is not a big deal to mention this.

I assume that their using this terminology means they are stating as basically accepted fact that the iPS cell process frequently generates oncogenically transformed cells? If so, this is really a big deal and at least so far in the published literature has not been the subject of careful study. In this regard, on page 1211 right column they write (emphasis mine):

Because most cells senesced, became contact inhibited, or transformed after exposure to dox for 6 days, which interfered with single-cell sorting to identify those rare cells that were destined to become iPSCs, we generated secondary cells that, in addition to the Nanog-GFP gene, carried a tdTomato reporter.

And on page 1219:

After 25 days on dox, abundant amounts of transformed cells were found on the plate,

This is also stated elsewhere.

I’m thus surprised they do not talk about this further in the discussion. Why does the iPS cell production process create oncogenically transformed cells and what does this mean for the field?

More on that soon from my lab, but you can take a gander at our new paper here on this topic.

I’d value other people’s thoughts on this interesting Jaenisch paper.