Ethical "Embryonic" Stem Cells from Your Skin

First it was mouse fibroblasts, and now human dermal fibroblasts have been reprogrammed to have pluripotent ES-like potential. Again, as in murine cells, ectopic expression of the fantastic transcription factor foursome of c-myc, Sox4, Klf4, and Oct3/4 will do the trick. Alternatively, Klf4 and c-myc can be substituted with Nanog and Lin28. Either way it's personalized stem cells from your skin. I'm going to get to work on mine right now...

Fresh Science at Nature Precedings

A pre-print manuscript that caught my eye at Nature Precedings; Derivation of Multi-Potent Stem Cells from Fibroblasts Following Treatment with an ES Cell Extract - A lot of buzz was recently generated when it was shown that forced expression of 4 transcription factors could transform fibroblasts into ES-like cells. Now, a group publishing their pre-print manuscript on Nature Precedings claims to have achieved a similar result by transiently permeabilizing fibroblasts in the presence of a cell-free extract from ES cells. Potentially a very simple way to make multi-potent cells for basic research and regenerative therapy. Also could be a great model to find reprogramming factors in the ES cell extracts. This is not really my field so I don't have much criticism to offer, but if you work in this field, take the chance to review their findings and contribute to the discussion by following the link to the paper above.

Another blow to the stem cell hypothesis

You know the immortal strand hypothesis, which says that stem cells keep the "template" DNA when they replicate asymmetrically and send off the new and therefore mutation ridden strand to the daughter cell. Well it turns out to be wrong, thus undermining the use of BrdU as a way to isolate stem cells. These findings were published in the latest Nature: "Sequential administration of 5-chloro-2-deoxyuridine and 5-iodo-2-deoxyuridine indicated that all HSCs segregate their chromosomes randomly. Division of individual HSCs in culture revealed no asymmetric segregation of the label. Thus, HSCs cannot be identified on the basis of BrdU-label retention and do not retain older DNA strands during division, indicating that these are not general properties of stem cells."

In fact this article quotes the researchers as saying:

[BrdU is] ... "a very insensitive and nonspecific marker."

and

"This study suggests that researchers should test BrdU label retention as a marker before assuming it can be used to identify stem cells in other tissues"

Histone Code Cracked?

This report in Nature presents genome-wide CHIP maps of a variety of histone modifications in a few types of embryonic and stem cell lineages. Seems like they found some very interesting signatures that correlated well with gene expression status. For example, trimethylation at lysines 4 and 27 could discriminate expressed versus inducible versus repressed genes, whereas the same modification at lysines 4 and 9 marks imprinted regions. Very cool. Of course we'll have to see what the AC has to say for the expert opinion.

I once proposed a similar project in a mock post-doc grant proposal for a systems biology grad class I took (except with the added minor step of cloning mice by somatic cell nuclear transfer). It got pretty bad reviews. Apparently some people thought it was too ambitious. Go figure. This one only took 15 authors...

Introducing: bayblab definitions

schmer·oid (smîr'oid', směr'-) n. : Aggregate of cells, that vaguely ressembles a sphere, resulting from mistreating your tissue culture. They are thought to have mystical powers to differentiate into anything, including brain, kidney, ipod or a rock, provided you pray to the right gods. But mostly, they are just balls of cells. If you count them, sometimes you can be rewarded with a cell paper or a microscope-induced headache.

functional definition:
-ability for self-denial
-ability to solve differential equations

see also: transit-pimping cells, commited prudo-genitals and terminally disoriented cells.

New stem cell journal from "Cell"

It was bound to happen, cell, the top tier journal when it comes to cell biology spun off a new journal dedicated to stem cells last week. It took a few days for the university to get access, but I was finally able to peruse it today. I had a little bit of a double take actually regarding the landmark paper published in this first edition. You may have heard that Myc, sox2, oct4 and klf4 are sufficient to reprogram fibroblasts into stem cells. In fact you may have heard of it a full year ago, as this experiment was done by a Japanese group (Takahashi K, Yamanaka S.) and published in Cell. This new paper seems to be almost the same experiments except it takes 12 American scientists to do the work of 2 Japanese :). And if that wasn't confusing enough, another team from the Whitehead Institute also published similar findings last week in nature. This latter group is a proponent of the bivalent histone code regulation of key stem-cell factor. The idea is that both repressive and active histone modifications mark the promoters of these factors making them easily inducible but also primed for repression may the cell wish to differentiate. As talked about previously on the bayblab, these bivalent promoters may be suceptible to dysregulation by epigenetic factors (trithorax/polycomb) over time and may be one of the mechanisms to transformation...
While we have talked about sox2, klf4, c-myc and oct4 when the first paper came around there are a few things worth highlighting this time around... While the ectopic expression of these transcription factors is required for the reprogramming it is not really sufficient. There was a large lag period between the expression and the reprogramming, suggesting there is an additional stochastic event that needs to occur. Also, c-myc is the odd one of these transcription factor as it tends to regulate very large areas of chromatin rather than just specific genes. Perhaps the lag is due to chance remodelling event over large areas. For example the authors show that the inactive X chromosome is re-activated by these factors. So this begs the question: what happens to the chromatin, how is the histone code changed, what is the lag for, would expression of members of the trithorax/polycomb make the process more efficient?

More on that later....

Embryonic Stem Cells (tm) by Invitrogen

Caught a great talk today at the OHRI by visiting speaker Mahendra S. Rao, who is probably the world's leading scientist in embryonic/neural stem cell therapies. The talk featured an overwhelmingly impressive wealth of data on neural stem cell biology, particularly pertaining to transplant studies. Most of this work was done in his former capacity as head of the NIH's stem cell program.

What was most interesting about the talk was the work Rao is now leading as VP Stem Cell research at Invitrogen Corp (in the more ES-cell research friendly state of California). He recently took up this post after leaving the NIH as a result of their decision to abandon ES cell research in light of the Bush administration's strong anti ES cell research policies. From what he presented of his new project at Invitrogen, it's obvious they are now about to kick some serious ass in the arena of clinical therapeutic development. They've got GMP-friendly, FDA-approved and production-scalable technologies and ES cell lines ready to go. Couple with that Invitrogen's recent moves that has established the company as the leader in gene expression and cell culture technologies, and what you have is imminent domination of the biological therapies scene. Looks like one of the first applications they will go after is Parkinson's disease, using ES-derived neurons to replenish dopamine producers in the substantia nigra.

Interestingly, while transplanted ES-derived neurons are suitable for applications such as Parkinson's as they can survive long-term in recipient's brain, Rao mentioned that their potential in other regenerative therapies is limited by the fact that we do not yet know how to make the transplanted cells properly integrate into existing neuronal circuitry. Strong impetus for a lot of interesting research in probing neural connectivity...