Examining Epigenetics in Induced Stem Cells

Epigenetics is one of the ways in which genes can be turned on or off in different cell types.  And if a cell divides, so it's split into two daughter cells, this also inherits the same epigenetic programme.  So, what happens when we used specialised mature adult cells like a skin cell to make adult stem cells that we can then for instance turn into brain cells or heart cells to treat diseases?  Are the epigenetic markers alreset correctly in the process?  Well, it's looking like the answer could be no.  From the University of Western Australia, Ryan Lister.

Ryan -   When people started making these adult stem cells which are able to turn into many different types of cells, the essential question was, do these adult stem cells look like embryonic stem cells which you can then turn into many different types of cells? 

This is an important question because we want to know when you start with these adult stem cells, do they start from this clean slate where you're then able to then turn them into any differentiated cell type that you wish? Or they start with any residual marks of a hangover of originally being a different cell in the body?

So, what we actually did was to profile the genomes of these induced pluripotent stem cells, they're called adult stem cells and look at exactly where the methylation marks,  it's chemical tags were throughout the 3 billion bases of the human genome and compared this to embryonic stem cells to see if there were any differences between the adult stem cells and the embryonic stem cells.

It turns out that there are hundreds of differences in these chemical tags, its epigenetic tags, between the adult stem cells and the embryonic stem cells.  What happens is that you have some memory of the adult cell type, the adult stem cell that you've derived from say, a skin cell in a couple of hundred places in the genome has these chemical tags which still look like the tags as you would find them in the skin cell, and look different, the pattern of these tags that you would find in these stem cells.

Chris -   What do you think the consequence of that could be?

Ryan -   Well, the potential consequence of that is that, ideally, what we want to do is to take these adult stem cells and turn them into different cell types that we require for therapeutic purposes in our body for repair's sake. You may take a skin cell and turn it into a cell required for repair of your heart.  Now, if the adult stem cells that you derive from the skin cell has these epigenetic tags which prevent certain genes being turned on which may need to be turned on when the cell was turned into a heart cell, then it potentially could cause problems for deriving fully functional heart cells from the adult stem cells.

Chris -   Do we know why they don't set those tags right?  Is it that the reprograming that we're doing is incomplete in some way?

Ryan -   That's right.  So, it appears that there may be certain regions of the genome which may be difficult to reprogram.  So, this reprogramming process where you create an adult stem cell typically involves taking a very small number of genes, for example, four genes and turn them back on in the skin cell, and these genes are able to bind in many places in the genome, and sort of kick start it into a different pattern of activities, so that it becomes like a stem cell. 

Some very recent work showed that certain regions of the genome, when this reprograming process is taking place, are quite resistant to being bound by these reprograming factors.  And interestingly, those regions are where we found many of these differences in these epigenetic tags between the adult stem cells and the embryonic stem cells. 

Chris -   Scientists have got a number of different ways of making these so-called IPS or induced pluripotent stem cells when you take a skin cell and turn it back into this stem cell-like state.  Some involve using viruses to put these four genes in, others involve just putting the four genes in via, what we call transfection - you just put the DNA into the cell.  Does it make a difference, how you make the cells, whether or not you get this washing clean of the genetic slate or not?  Do some methods work better than others?

Ryan -   Well, from what we've seen so far, you find this memory no matter what methodology you use.  That's not to say there aren't approaches that will produce perfectly reprogramed adult stem cells, but so far, from the different methodologies that we've looked at, IPS cells created with these different methodologies, we find these consistent differences between IPS cells and embryonic stem cells in all of them.

Chris -   Is it just that we need to put more of these resetting factors in?  Is it just a shortage of supply or is there something fundamentally missing that we need to get on top of?

Ryan -   I'm not sure that it's a shortage of supply.  It could be that we need to pre-treat the adult cells, the differentiated cells in order to make these certain resistant parts of the genome more amenable to binding these reprogramming factors.  This is something we don't know at this stage, but they're potentially ways that we can poke the cell beforehand to try to put it into a state which is more amenable to reprogramming, but certainly an area which a lot of research is going into at this stage.

Chris -   So, if in the future we wanted to use these cells, would we make a huge batch of them and then go through, using the techniques you use, and find the ones that have got the best epigenetic profile, and say, "those are the pool we'll use and we'll just discard the ones that have got a less attractive profile."?

Ryan -   Yeah, I think potentially - there may be say, three different approaches that we could use in the future, and we may be able to identify reprogramming conditions which create IPS cells which look - to all intents and purposes - just like the embryonic stem cells.  We may alternately be able to create many IPS cells from a skin cell for example and it might be that a small percentage of them look perfectly like an embryonic stem cell, but it's just that we need to check say, a large panel of them to find the one which looks very good.  Or maybe that we are able in the future to develop methods to specifically reprogram or correct epigenetic patterns precisely where we want.  And so, we could take an adult stem cell, an IPS cell, and identify through this epigenome sequencing methodologies where differences exist between the IPS cell and the embryonic stem cell, and then go in and correct them, and subsequently use them.

Chris -   That's Ryan Lister from the University of Western Australia.