Tuesday, November 20, 2007

We Can Reprogram Skin Cells Into Stem Cells - So Do We Still Need Embryos?

This month we've witnessed the first-time success of two important stem cell research techniques in primate cells. Both techniques were previously developed in mice, but their success in humans and monkeys is important. Stem cells from cloned embryos have been generated from macaque cells. And now this week, two papers (here and here - this last one is a PDF file) have been published that are reporting that adult human skin cells can be reprogrammed to become stem cells. However, do the results of this week's papers mean that we no longer need to get stem cells from embryos? The answer, for now, is a resounding no - reprogrammed skin cells currently have some serious drawbacks that need to be overcome before they can become worth trying in disease treatments.

How do you reprogram a skin cell (in this case, fibroblasts - a very generic, easily handled cell commonly used in labs) to become a stem cell? The key step is to induce 4 genes that produce important master regulators, the transcription factors named Oct3/4, Sox2, Klf4, and c-Myc. These transcription factors are proteins which switch large sets of genes on or off, thus initiating a cascade of genetic signals that enable the fibroblast to transform itself into a stem cell. It's amazing that just these 4 genes can initiate so many substantial changes, but this is a common phenomenon in biology, found even in yeast.

But does this technique now eliminate the need to take stem cells from embryos? Not yet. Contrary to statements by the White house, this research was not a result "the president’s drawing of lines on cloning and embryo use." Without research on embryonic stem cells, we would have had a hard time identifying the role of the 4 transcription factors in the first place. And even with no restrictions on embryo use, researchers would have still tried these important experiments. Science at its best attacks problems using a variety of strategies.

And it's not clear that this technique is going to produce better results in the near future. The process of transferring the 4 regulator genes into fibroblasts involves a type of virus (not a health-threatening virus - it's basically a handy lab tool), which deposits multiple copies of these genes almost at random around the genome. These four genes can end up in good places or bad places in the genome. In bad places, stem cell transplants can develop into cancers, with the c-Myc gene being an especially frequent culprit (it's a gene known to be involved in a variety of cancers). In mice, up to 20% of stem cell recipients develop cancer.

So our ability to manipulate these cells for a useful purpose still lags. We can do a somewhat better job manipulating embryonic stem cells, but in general we have a hard time getting any plutipotent stem cells to produce the exact kind of desired differentiated tissue, such as nerve or heart cells. To improve the process we need to keep working on reprogramming, but we also need to study how stem cells actually work in nature - that is, in embryos.

Monday, November 19, 2007

Monkey Stem Cells From Cloned Embryos - Humans Are Next...

Headlines last week reported that researchers successfully produced stem cells from cloned monkey embryos. Using a process that has become almost routine with mice, scientists can now make make primate embryonic stem cells that are genetically identical to a given DNA donor. Once we learn to do this in humans, the possibility of stem cell based treatments for heart disease, neurodegeneration, and more will be closer to reality. But in the US and elsewhere, can we develop the political will to let this research move forward?

In case you missed the headlines, the story is this: a group of researchers at the Oregon Health and Science University led by Dr. Shoukhrat Mitalipov used the process of somatic cell nuclear transfer (SCNT) to create cloned Rhesus macaque embryonic stem cells. SCNT involves taking the DNA from an adult skin cell and implanting this DNA into an egg cell from which the DNA has been removed. This DNA transplant procedure can produce an embryo without the need for a fertilized egg - and most importantly, it produces an embryo genetically identical the DNA donor, which means that potential therapies using SCNT-derived stem cells wouldn't be rejected by a patient's immune system.

SCNT itself is old news; what is impressive in this research is the new ability to do SCNT with primate cells. This breakthrough was enabled by better imaging technology. SCNT is like a heart transplant where you just rip out the old heart with a giant tug, leaving a lot of damage behind. With the new technology, Dr. Mitalipov's team was able to better see what they were doing as they carried out the procedure.

If it can be done in monkeys, it's just a matter of time before it can be done in humans. Back in 2004 the world thought that human stem cells had been created from such cloned embryos, but that research turned out to be faked. The researcher behind those studies, Woo Suk Hwang from Seoul National University, was exposed as a crook and the already controversial image of human stem cell research was tarnished. Because of this history, Nature and Dr. Mitalipov went to great lengths to prove that the macaque embryonic stem cells reported in this paper are real, including requesting genetic confirmation from an independent group.

Where does this research go from here? Scientifically, we're still some way off from using these cells to replace ailing nerve or heart tissue in patients with terminal diseases. The many political and legal hurdles are even more formidable in the immediate future. To take just one example, at SCNT's current success rates you need hundreds of eggs from donors before you get just one successful embryo. Egg donation is not a pleasant process, and laws in some states prevent researchers from financially compensating donors, unlike other types of research volunteers who are paid for their time and trouble. Success rates will no doubt improve as researchers learn important tweaks in the procedure, but that can't be done without lots of trying. If the US doesn't develop the political will to make it possible for stem cell researchers to do their work, future treatments will be developed elsewhere and the US will lack the expertise in both research and patient treatment. The macaque stem cell paper indicates that the day when we will know how to use embryonic stem cells for medical treatments looms ahead, and unless we make changes in this country, we won't benefit from them.

Thursday, November 15, 2007

Making a Weed that Eats Explosives

RDX is a common military explosive, and it’s dangerous not just because it explodes - it’s also toxic. Places where RDX is used, produced, or stored often present a serious hazardous waste problem, such at the Massachusetts Military Reservation on Cape Cod, where the local aquifer has been contaminated with RDX. A group of researchers from the University of York in the UK and Canada’s Biotechnology Research Institute have shown how it might be possible to clean up RDX with explosives-eating transgenic plants.

Plants that use man-made explosives as a nitrogen source are not so easy to find in nature. In this case, the researchers genetically engineered two key bacterial proteins into the thale cress Arabidopsis thaliana. Plants that produce these proteins are able to take up RDX from soil and metabolize it. But how did these researchers find such useful bacterial proteins?

The answer is that they searched in the obvious place - contaminated soil where bacteria that metabolize explosives are likely to evolve. Bacteria reproduce extremely quickly and live in fairly large populations, thus it is not uncommon for a bacterium with just the right mutation to turn up and outcompete its peers in a new environment. The researchers found a bacterial strain of R. rhodochrous that was able to use RDX as its sole nitrogen source. Explosives are nitrogen-rich compounds, so this bacterial strain has evolved to take advantage of an abundant nutrient in its environment.

And it turns out that not many mutational changes were required to make this strain of R. rhodochrous an explosives-eater. All organisms contain many versions of a versatile class of electron-shuttling proteins called cytochrome P450s. This class of proteins is involved in some of the most sophisticated chemistry in the cell, including the synthesis of steroids and various vitamins. These cytochromes have been tweaked by evolution to perform an astounding range of chemical jobs. The explosives-degrading R. rhodochrous harbors a variant cytochrome P450 that is able to break an N-NO2 bond, something rarely encountered in nature but present in RDX.

Once they had the bacterial gene in hand, the researchers attempted to express it in the Arabidopsis plant. Since the plant itself has plenty of cytochrome P450s, it was easily able to properly synthesize the bacterial version in quantities large enough to start metabolizing RDX from the soil. This was a straightforward use of evolution and biochemistry to create a useful genetically engineered organism. It's possible that this approach could be successful a range of environmental problems. Given the chemical sophistication and diversity of the metabolic pathways found in nature, the chances of finding a solution to other pollution problems like this one are good.

Wednesday, November 14, 2007

Intelligent Design's Day in Court on NOVA

Last night the PBS series NOVA featured a two-hour show on the 2005 Dover, PA Intelligent Design trial. If you missed it, go check out clips and some great evolution resources at the show's website. As a creation/evolution junkie, I had previously read all of the trial transcripts, but reading transcripts was no substitute for seeing and hearing the major participants on camera. And while the big players from the Discovery Institute refused to be interviewed, NOVA managed to get just about everyone else on camera, including one of the defense's expert witnesses and the two ex-school board members who started the whole mess. These guys made it abundantly clear in their own words that intelligent design in Dover was not about improving science education - it was all about pushing creationism among the students.

The show was generally well done, in spite of some badly acted (not to mention tacky) courtroom reenactments. There were excellently illustrated segments discussing science's success in some areas where intelligent design advocates have claimed there are problems, such as transitional fossils and the bacterial flagellum. I was happy to see that the show also spent time discussing how the development of genetics, and much later, genomics, were big tests of evolution. Darwin's ideas enabled scientists to make predictions that were borne out decades later in scientific fields that Darwin knew nothing about.

The most entertaining part of the show were the interviews with the two ex-school board members (who were caught lying during the trial) and a local Dover pastor. The founders of intelligent design have gone to great lengths to paint their ideas as serious science, not creationism. And yet on the show we hear Dover's local intelligent design advocates explain that they pushed intelligent design in school because they were concerned that the malleable students of Dover were having their good Christian faith weakened by evolution - not because the board members cared (or knew anything about) a good science education. Alan Bonsell and Bill Buckingham made it repeatedly clear that their main beef with evolution is that it offends their religious beliefs.

Judge John Jones, who presided over the trial, made a sobering statement towards the end of the show. He said that before this case he would have never have imagined that he would receive threats after an Establishment Clause case. Jones and his family were placed under the protection of the US Marshals for a time after his ruling, due to threats of physical harm Jones received. Of course I'm biased, but I can't imagine that Jones would have received such threats had he ruled the other way. And while I have no doubt that the overwhelming majority of creationists would never, ever make such threats, much less act on them, the incident does expose the hatred that some people feel towards those who work to keep our science curricula untainted by religious dogma. This was a nasty episode in creation/evolution history, but with luck this trial will produce a lull in the battle for a couple of years. Unfortunately, we all know that this controversy is not over.