The Niche

“Now we have the technology that can make a cloned child” reads the headline of the most-read article in the Independent right now. But the article does not actually break any news, nor does it use the common method of cloning; rather it discusses a well-understood implication of that recent reprogramming breakthroughs might yield yet another weird way of making a baby.

If a technician wanted to do this, here’s how it would work: First, cells would be gathered from an existing human, probably through a skin biopsy. Second, these cells would be reprogrammed to an embryonic like state. (Current techniques to do this require engineered viruses to insert copies of genes into the reprogrammed cells. This makes the cells’ behavior less predictable and more prone to form tumours, but many scientists believe that new reprogramming techniques will soon be available that don’t require genetic modification.) Next, the reprogrammed cells would be merged with an early stage embryo, created by sperm fusing with egg in a laboratory dish. The “chimeric” embryo would be cultured for a few days and then implanted into a woman. If a baby was born, he or she would contain cells from two genetic individuals: the embryo and the human who supplied the cells. The baby would have three parents: two who gave the gametes for the embryo, one who gave the cells from a biopsy. (Such an individual would not be a clone. However, it is feasible that the chimeric embryo could be manipulated such that the original embryo only forms placenta and the reprogrammed cells form the body. This has been accomplished with mixtures mouse embryonic stem cells and mouse embryos, but not with mixtures of reprogrammed mouse cells and mouse embryos. )

The results of some quick internet research suggests that using human iPS cells this way would not be allowed: In the UK, creating or using embryos outside the body requires a special license from the government, so I’d guess that permission would need to happen proactively. The US lacks legislation on reproductive cloning, though some individual states ban it. Australia distinguishes between research embryos (created through technical manipulation or by mixing genes from three or more people) and reproductive embryos (created through fusion of sperm and egg) and allows only reproductive embryos to used to create an embryo. A document dated to 2004 from Japan banned, among other things, the creation of chimeric human-human embryos for research.

Continue reading "Cloning by reprogramming?" »

Posted by Monya Baker on April 15, 2008
Categories: Cloning, Ethics, Reprogramming/Pluripotency | Permalink | Comments (2) | TrackBacks (0)

Skin cells taken from patients with some eight different diseases have been reprogrammed to an embryonic-like state. These could be invaluable for studying disease and testing drugs.

Here’s the statement from the UK’s Science Media Centre, which announced the result:
‘Dr Willy Lensch from the Children's Hospital in Boston and colleagues in his laboratory have generated stem cell lines from iPS cells with the genetic characteristics of more than six different diseases, including Huntingdon’s disease, Down’s syndrome and a type of muscular dystrophy. These can be used to study how these diseases affect fundamental development. They also can be used for surrogate testing for drug development, accelerating the development of therapies for devastating diseases.’ The announcement has been reported by the BBC. UPDATE: When I asked folks at Children's Hospital about this, I was told that the work wasn't ready for coverage; it had simply been mentioned at a seminar, and the fact that the UK press picked it up was surprising.

Reprogramming human cells was first reported in November, using cell cultures that could be bought commercially. Converting cells from a fresh patient biopsy was reported the following month by the lab led by George Daley and where Willy Lensch works as a senior scientist. By now, multiple labs have independently reported reprogramming cells, demonstrating that the technique is reliable and reproducible.

There are a variety of steps that will need to happen before the cells will start yielding information that will be useful for clinical applications. These are discussed in a commentary by the California Institute of Regenerative Medicine and a feature article written after mouse cells were fully reprogrammed.

The cells will need to be differentiated into the cell types that are affected in the various diseases. According to the BBC, a team at Nottingham University is already using reprogrammed cells to study heart conditions. Human cells differentiate very slowly compared to mouse cells. Turning embryonic stem cells into apparent photoreceptors, for example, took close to a year.

The first step in telling if cells are differentiating is checking out the molecules they display on their surfaces. Then comes the much more arduous task of looking at cells’ shape and function. (If it’s a nerve cell, does it release neurotransmitters? If it’s a heart cell, does it beat?) Even then scientists worry whether the cells in a dish behave like the ones in the body.

Other obstacles are getting enough of the cells and purifying the differentiated cells away from other cells growing in the dish that have not transformed fully.

Finally, drugs that are known to treat particular diseases will be tested on the differentiated cells. Results from these cell-based tests will be compared to established tests, most likely tests carried out on mice and rats.

Developing cells to become therapies (transplanting them to perk up or replace diseased hearts, brains, or other organs) will require considerably more work than developing cells to test therapies. One worry is that techniques to reprogram cells change them genetically, and clinical work in gene therapy resulted in patients’ deaths, making researchers leery of trying again.

Posted by Monya Baker on April 07, 2008
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I’ve gotten a couple of emails about an editorial Nature recently ran urging scientists in the iPS field not to rush. It starts by relating an anonymous attack against Shinya Yamanaka for a minor problem. That’s supposed to get folks’ attention, but it is absolutely not the point of the article, which is to urge caution to everyone who is in and rushing into a very hot, very young field that is also politically charged.

The article is not questioning Shinya Yamanaka as a scientist. (It’s common for mistakes to slip through, and there are mechanisms to correct that.) The editorial is about what happens (confusion) and can sometimes happen (fraud) in hot, new fields, and this is going to be even worse for stem cell scientists because the field is politically charged as well. Shinya Yamanaka has already dealt with the accusations in a way that seems to have satisfied Science, and so delving any more into them would actually elevate the accusations of an anonymous emailer, giving the accusations more attention than they deserve.

The idea for the editorial started after PrimeGen decided to publish its findings on viral-free reprogramming by press release. Here was an accomplishment that the whole community was waiting for, but no one could assess it, and so Nature felt that we needed to say something about how people need to be more patient in a hot field. And then a few days later, the anonymous email got sent to many journalists and journal editors, and it seemed a call for caution was even more necessary.

So again, the editorial is urging caution in a hot, politically charged field. It is not about one of the field’s best-loved and most-respected scientists.

I’ll blog again as I get more feedback and hear more thoughts, but I wanted to get this up quickly. In the meantime, I want to say that much thought went into this editorial. You might be interested in how I think some decisions are made. (I don’t have first-hand knowledge of much of this, but I think I can guess.) Also, I should emphasize that stuff I've written above is just me; I haven't yet weighed in on the collective wisdom of NPG.

Continue reading "Recent editorial is meant to urge caution, not attack a scientist" »

Posted by Monya Baker on March 27, 2008
Categories: Community, Reprogramming/Pluripotency | Permalink | Comments (1) | TrackBacks (0)

Here's an accounting of how an interesting Nature paper, published online this Sunday, came to be.

Sadhan Majumder (pictured right) sought a better understanding of childhood brain cancer. He ended up finding a new regulator of self-renewal in embryonic stem cells along with a previously unknown mechanism of how this state is maintained.

While working on one of the most malignant childhood brain tumours, medulloblastoma, Majumder and his group thought much of the blame for the cancer might lie on a protein called REST (which has the burdensome full name of repressor element-1 silencing transcription factor/neuron-restrictive silencing factor). REST was originally believed to repress the final stages of neuronal differentiation. “We were working on REST in neurogenesis like everyone else,” Majumder recalls, “and we found that in medulloblastoma, abnormal expression of REST maintains the proliferative state of neural stem or progenitor cells and blocks their differentiation. Basically, it maintains the ‘stemness’ of these cells.” In fact, if REST is introduced artificially into neural stem cells, he says, they will not differentiate. “That told us that it may have a role in self-renewal,” says Majumder. “Then this paper from Gail Mandel came out that showed REST was expressed in embryonic stem cells.” He laughs as he described how he decided on his next experiments. “I have a tremendous grasp of the obvious.”

Continue reading "A new protein in the pluripotency circuit represses microRNA" »

Posted by Monya Baker on March 23, 2008
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Forbes has just reported a company’s announcement that it can reprogram adult human cells to an embryonic-stem-cell-like state without using viruses. All reported successes so far use viruses to introduce new genes into the cells, a technique that most believe make them unsuitable for clinical use. At a stem-cell conference in New York, PrimeGen, based in Irvine-Calif, said that it got the technique to work by attaching “carbon-based delivery vehicles” to the proteins that the genes encode and putting the proteins inside the cells. Unusually, it announced its results outside a peeri-reviewed journal without disclosing many of the details leading to its conclusions. That means that the results are likely to be met with high skepticism from the scientific community.

There are a lot of researchers trying to reprogram cells by introducing the proteins directly. Problems that they have encountered include the fact that some proteins enter and persist in cells better than others, and it’s hard to get enough proteins in for a long enough time and in the proper ratios, which are still not understood. Research in mouse cells indicate that the proteins from the viruses need to persist for a week or more in order for reprogramming to occur.

I haven’t read anything on this specifically but the Forbes article, but here are my thoughts based on my understanding of the researchers who have successfully reprogrammed human skin cells (Kyoto University’s Shinya Yamanaka, the University of Wisconsin’s James Thomson, Harvard’s George Daley, and the University of California, Los Angeles's Kathin Plath) and mouse skin cells (Yamanaka, Plath, Harvard’s Konrad Hochedlinger, MIT’s Rudy Jaenisch).

One problem is that it’s a lot easier to get the cells to just divide really fast than to reprogram, and these can initially resemble reprogrammed cells. The PrimeGen researchers don’t describe the techniques used to conclude that the cells as reaching the embryonic-like state. It implies that the cells have not been tested to see if they can make teratomas, weird tumors that make cells characteristic of the three main types of tissue and the most rigorous test available for human cells. PrimeGen does say that perhaps cells don’t need to be fully reprogrammed to be clinically useful.

According to the Forbes article, PrimeGen says it is collaborating with James Thomson, the scientists who first created human embryonic stem cells and leader of one of the teams that first reprogrammed differentiated cells. Thomson told Forbes he knows little about the company and denies he’s a collaborator.

The researchers say that they have reprogrammed testicular, skin, and retinal cells. There’s some evidence that testicular cells (depending on the actual type) are amenable over time in culture to becoming highly flexible cells, though less flexible than embryonic stem cells. There are several kinds of skin cells. Shinya Yamanaka recently showed that epithelial cells (cells that cover or line organs, and include some skin cells) can be reprogrammed using fewer copies of the viral genes than cultured skin cells (fibroblasts) need, which would make some cell types more amenable to being reprogrammed with proteins than others. Also, Daley found that one problem in reprogramming is that viral genes are silenced too quickly, thus inserting proteins directly might pose some advantages.

PrimeGen said that it made its announcement in order to attract investors. If a company has technology this hot, one would expect a company to approach investors with non-disclosure contracts in hand, not announce it so openly. Also, they say they need partners to expand the cells, but embryonic stem cells should be able to expand indefinitely. Also, the partners aren’t going to want to expand the cells until they know what they are. Embryonic stem cells are hard to grow, so possibly, researchers who could create the cells would have trouble growing them.

The Forbes article quotes several scientists saying they cannot evaluate the work until they see results in more detail. PrimeGen says it will soon be publishing its results in a peer-reviewed journal.

Posted by Monya Baker on February 27, 2008
Categories: Reprogramming/Pluripotency | Permalink | Comments (0) | TrackBacks (0)

The former head of President Bush’s council on bioethics, now says there shouldn’t be a ban against cloning human embryos for research. Instead, there should be a five-year moratorium against the process. Writing in the Weekly Standard, Leon Kass decries the fact that the US Congress did not pass a law blocking all forms of human cloning, and then says that this stricter form of the law is unnecessary now that researchers can turn to alternate ways of reprogramming.

Instead, he argues for a law that would ban “all attempts to conceive a child save by the union of egg and sperm (both taken from adults).” That’s because the new reprogramming techniques mean that a skin cell could generate egg and sperm cells, whether taken from a man or a woman (or a boy or a girl, for that matter).

Embryos created for the purposes of research would not be outlawed, but instead banned for four or five years as researchers are given more funds to perfect the reprogramming techniques. He does not rebut, because he does not raise, the argument that stopping work the creation of embryos for research through somatic cell nuclear transfer will delay efforts to prefect reprogramming techniques.

Kass writes “Cloning for the purpose of biomedical research has lost its chief scientific raison d'être” (i.e. making a pluripotent cell line genetically matched to a patient.) That’s because it will probably be much easier to reprogram whole cells from adult biopsies than it will be to pull out an adult cell’s nucleus, plop it into a donated egg, grow that “reconstituted embryo” to a blastocyst and make embryonic stem cells.

Kass is probably right, but he fails to mention two caveats.

First, while many scientists are hopeful that so-called induced pluripotent stem cells will really behave like embryonic stem cells, they still aren’t sure. Possibly, a reprogrammed skin cell could be coaxed into a pancreas cell or a heart cell, transplanted, and then “remember” that it started out as a skin cell. Also, no one wants to use the current technique (using viruses to insert genes at random places in the cells’ chromosomes) to make cells that would actually get put into people. Those are serious problems, but most scientists think they can be overcome.

Second, and more important, many scientists think that to understand how reprogramming works with viruses, they have to understand how reprogramming works in an egg. Most people think that requires transferring adult nuclei into eggs or early embryos, and trying to figure out what happens.

Just a little quibble: Kass says that recent success by Stemagen in cloning a human blastocyst depended on the technique that Shoukhrat Mitalipov’s team in Oregon used to clone monkey blastocysts to make embryonic stem cells . Actually, Stemagen did not use this technique but credits its success not with a new technique but with a supply of high quality eggs.

Posted by Monya Baker on February 21, 2008
Categories: Cloning, Ethics, Policy, Reprogramming/Pluripotency | Permalink | Comments (0) | TrackBacks (0)

The possibility of reprogramming adult cells to behave like embryonic stem cells without overexpressing cancer genes or relying on hard-to-control viruses has gotten a bit closer. Publishing in Science, Shinya Yamanaka and colleagues from Kyoto University, in Japan (see From skin cells to stem cells), show that the reprogramming techniques he previously demonstrated on cultured mouse skin cells also work on two other mouse cell types: those that line the stomach and those from the liver1.

Because far fewer than 1 in 100 treated cells are successfully reprogrammed, several stem cell scientists had raised concerns that reprogramming does not work on fully differentiated cells but rather on rare stem cells residing undetected within the culture. That would make the reprogrammed cells less interesting scientifically and, potentially, therapeutically. To address this concern, Yamanaka used a genetic marking system that permanently labeled liver cells once they differentiated enough to express albumin, and he found that these cells could be reprogrammed to so-called induced pluripotent stem (iPS) cells that can contribute to all cell types in an adult mouse.

“The old question in cloning was exactly the same: was Dolly derived from a fully differentiated cell?” said Rudolf Jaenisch of the Whitehead Institute, in Cambridge, Massachusetts, who showed that mice can be cloned from terminally differentiated cells such as neurons. Yamanaka provides “good evidence” that reprogramming works in differentiated cells, said Jaenisch, but that conclusion assumes both a reliable labeling system and that only mature cells express the albumin gene. Yamanaka himself stopped short of calling the initial cells fully differentiated: “Our data showed that lineage-committed albumin-producing cells can be reprogrammed.”

Perhaps more interesting, Yamanaka also shows that the epithelial cells lining the stomach can generate iPS cells using a less rigorous screening system than that used with cultured skin cells or fibroblasts. Reprogramming currently uses viruses to insert several copies of three or more pluripotency genes into cells, one of which is particularly implicated in cancer. Tumours develop in about a third of mice created using iPS cells derived from fibroblasts; no tumours were found in mice created from iPS cells derived from stomach and liver cells. Though viruses were less efficient at infecting the stomach-lining cells with the necessary genes, the cells that were transformed contained fewer copies of the transgenes compared with fibroblasts, perhaps because epithelial cells are more similar to embryonic stem cells than fibroblasts are. (These mice were more likely to die in utero, but live-born mice appeared healthy.)

Yamanaka found that the transgenes do not need to be inserted into specific sites within the genome for liver and stomach cells to be reprogrammed. “This is encouraging to those of us who are seeking a nonviral means of generating iPS cells,” said George Daley of Children’s Hospital Boston, who recently compared the efficiencies of reprogramming human fibroblasts from different sources.

References
1. Aoi, T. et al. Generation of pluripotent stem cells from adult mouse liver and stomach cell. Science published online 14 February 2008; doi:10.1126/science.1154884

Posted by Monya Baker on February 14, 2008
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An independent laboratory has been able to reprogram differentiated human skin cells to an embryonic-like state using the method originally reported by Shinya Yamanaka of Kyoto University.1,2 Also late last year, two other laboratories announced reprogramming differentiated human cells via slightly different methods.3,4 The latest work, by Kathrin Plath of the University of California, Los Angeles, indicates that the technique is broadly feasible and introduces a potentially easier method to pluck reprogrammed cells from culture.5

Notably, all the groups that have reported success with this method have experience working with embryonic stem cells. At least two have derived human embryonic stem cells, and the genes that must be introduced to reprogram cells were identified through embryonic stem cells.

Meanwhile, the California Institute of Regenerative Medicine announced that it has received 50 applications for up to 16 grants totaling $25 million for creating new human pluripotent cell lines either from embryos from fertility clinics or from other sources of cells. In an executive order and his state of the union address, President Bush has directed the NIH to direct more funds to methods to create pluripotent stem cell lines without destroying embryos, but no dedicated funding programs have yet been announced.

The scientist leading the work just published in the Proceedings of the National Academy of Sciences has received a $1.5 million NIH grant set aside for “exceptionally innovative investigators.” Only 41 such grants were awarded, less than one of 50 applicants including biomedical researchers across the nation. She also received a $2.2 million grant from CIRM to study how reprogramming works in mice. Two other scientists who have successfully reprogrammed human cells (Yamanaka and James Thomson) have part-time appointments in California that will allow them to access some funds from the CIRM Medicine, but Plath is the first full-time faculty California to lead such an effort.

Plath’s team infected cultured skin cells originally collected from circumcisions and infected them with retroviruses carrying the four genes originally identified in reprogramming work. After about two weeks they began to see colonies proliferating. They looked clearly different from the cultured skin cells, but they did not go on to become induced pluripotent cells, and analysis showed that they had not taken in copies of all four genes. Colonies of cells destined to become reprogrammed lines showed up about 21 days after infection; they clustered together as human embryonic stem cells do, and they also displayed a variety of cell-surface markers characteristic of ES cells. A week later, Plath and researchers hand-selected colonies staining positive for one particular cell-surface marker. All cells analyzed from these colonies contained copies of all four genes.

Of the 30 colonies isolated, cells from seven were closely analyzed. As expected, all of these cells were expressing endogenous genes associated with pluripotency, and the viral genes were silenced. Though the cells express markers of the three main types of tissues forming the body, the team has not yet tested the functionality of the cells by differentiating them into teratomas or other cell types.

1. Takahashi K. et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell advance online publication 20 November 2007. doi: 10.1016/j.cell.2007.11.019 | Article |
2. Takahashi K. & Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–76 (2006) | Article | PubMed | ISI | ChemPort |
3. Yu, J. et al. Induced pluripotent stem cell lines derived from human somatic cells. Science advance online publication 20 November 2007. doi: 10.1126/science.1151526 | Article |
4. Park, I. H. et al. Reprogramming of human somatic cells to pluripotency with defined factors. Nature advance online publication, doi:doi: 10.1038/nature06534 (23 December 2007).
5. Lowry, W.E. et al. Generation of human-induced pluripotent cells from dermal fibroblasts. Advance online publication www.pnas.org_cgi_doi_10.1073_pnas.0711983105 11 February 2008

Posted by Monya Baker on February 10, 2008
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I’ve been reading the coverage on making embryonic-like stem cells without embryos in the religious press, and two quotes going through my mind, both sarcastic. One is “Shocked! Shocked!” (from Casablanca) and the other is “Oh, Lord! Make me pure, but not just yet.” (from St. Augustine).

Continue reading "Inconsistent Christian views on reprogramming" »

Posted by Monya Baker on January 22, 2008
Categories: Ethics, Reprogramming/Pluripotency | Permalink | Comments (0) | TrackBacks (0)

George Daley, author of a paper published online today in Nature says that a simple skin biopsy can yield stem cells specific to an individual patient, and may mean that a bank of genetically matched stem cell lines is possible. Further, any group that knows how to keep human or mouse embryonic stem cells alive will probably be able to make and maintain induced pluripotent stem (iPS) cells.

Here's an advance peak of an article that will appear on our site in January 2008.

In January 2007, George Daley of Harvard University published proof of principle that pluripotent stem cells could be created so that they would not cause an immune response when differentiated for cell transplantation1. His forthcoming publication in January 2008 shows much the same thing, but through an entirely different technique. The first paper used unfertilized mouse eggs; the more recent one uses a skin biopsy from a human volunteer2. It is the first to demonstrate such complete reprogramming without starting from embryos or cell cultures available from commercial vendors.

These bookends highlight the major stem cell advance of this year: multiple laboratories have now shown that adult human skin cells can be reprogrammed to an embryonic stem-cell-like state.

Daley’s lab began work shortly after Kyoto University’s Shinya Yamanaka announced the four genes that could transform cultured mouse skins cells, or fibroblasts, into an embryonic-like state3. This summer, Yamanaka and two other groups proved that the mouse fibroblasts could be made truly pluripotent by showing that the cells could become sperm and eggs4-6. (See Skin cell to stem cell)

Meanwhile, labs across the world were racing to reprogram human cells. This November, Yamanaka and James Thomson of the University of Wisconsin-Madison became the first labs to announce that they had done so7,8. “Our paper was already submitted when the others were published,” Daley says. “It was frustrating, but the point is that this is a robust technology that lots of people can reduce to practice.” Indeed, he says, any group that knows how to keep human or mouse embryonic stem cells alive will probably be able to make and maintain induced pluripotent stem (iPS) cells.

Continue reading "Personalizing pluripotency" »

Posted by Monya Baker on December 23, 2007
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Since the recent announcement of successful reprogramming, editorials carrying statements such as “[r]arely has a president - so vilified for a moral stance - been so thoroughly vindicated” have been springing up across the United States. Now the fightback seems to be gearing up.

Key to their argument is the fact that ‘reprogrammed’ cells – where instead of obtaining stem cells from an embryo ‘induced pluripotent stem cells’ are created from adult human skin – are not yet safe for clinical use.

“For doing basic research on human cells, IPS as a method has won - it's huge. But for the ultimate goal of getting cells into a patient, it's a lot less clear. These cells may never be useful for direct therapy,” says George Q. Daley, a stem cell researcher at Children’s Hospital Boston, in the Boston Globe.

Douglas A. Melton, codirector of the Harvard Stem Cell Institute, is even firmer, saying: “It will never be approved [by the FDA] to put these cells in a patient.”

See also our Q&A on the topic with the head of the NIH Stem Cell Task Force and what scientists had to say

Posted by Monya Baker on December 21, 2007
Categories: Policy, Reprogramming/Pluripotency | Permalink | Comments (0) | TrackBacks (0)

This will appear as a regular, archived article on Nature Reports Stem Cells eventually. However, our production cycle will be even slower over the holidays, and I wanted to put this up as soon as possible. --Monya

Nature Reports: Did the induced pluripotent stem (iPS) cell breakthrough happen faster than you thought?

Landis: Yes.

Nature Reports: What do you think of the public response to this breakthrough?

Landis: It’s kind of very sad. Instead of focusing on the scientific potential—what you can learn in terms of reprogramming and the epigenetics of the cells—people seem to have focused on “We don’t need embryonic stem cells” or “Oh yes we do need embryonic stem cells”. It’s as if the science has been consumed by the political argument.

Nature Reports: What still needs to be assessed with induced pluripotent stem cells?

Landis: There are a zillion questions. The assumption on the part of a large part of the public that this does away with the need for embryonic stem cells is premature.

I find it hard to believe that you’d get back to the same starting point that a pristine embryonic stem cell would represent. You don’t know what the undifferentiated state actually is and you don’t know how they [the cells] are going to respond to differentiation.

If you’re taking a fibroblast that’s obviously gone through several developmental stages to get to its differentiated state and then you’re getting it to go back to its undifferentiated state, I would be surprised if it took the same pathway backwards.

[Regarding pluripotent stem cells as disease models] An interesting catch could be that the mutations that give rise to the disease could interfere with the ability to reprogram. Everyone has just assumed that they won’t, but I don’t think we have any data on that.

Nature Reports: How can researchers compare human iPS cells to embryonic stem cells?

Landis: Given that they’ve had the mouse embryonic stem cells and mouse iPS cells for some time and have not yet completed the epigenetic comparison, I think it will take a lot to do the human.

Nature Reports: But comparisons can’t be funded for the newer human embryonic stem cell lines.

Landis: You would be constrained to the identified lines that are available for funding. Obviously it would be better to have more lines. Jamie Thomson[who led one of the groups making the reprogramming breakthrough and was the first to generate human embryonic stem cells] has pointed out that one of the major disadvantages of the limited number of lines is that they come from a pretty narrow genetic repertoire.

Nature Reports: Scientists have called for comparisons between iPS and hES cells, but there is some ambiguity about what kinds of these studies the NIH could fund. For example, can people use data or RNA or techniques from newer embryonic stem cell lines that aren’t eligible for NIH funding?

Landis: That’s kind of outside my paygrade, that kind of regulation. Apparently Harvard has a very good policy that’s written up that outlines what Harvard feels are the appropriate safeguards to make sure that you don’t violate the NIH policy.

Nature Reports: What’s going to happen now in terms of what science is being done and who’s doing it?

Landis: [The buzz makes it sound] like it’s really easy and that anyone who’s cultured cells should be able to make their own pluripotent stem cells. In talking to people on the phone, it sounds like it’s much more complicated than that. Jamie Thompson said that it took him four years.

There will be new grant applications to take advantage of this scientific advance, whether or not they will be outstanding grant applications is unclear. Also, with the advance of SCNT [somatic cell nuclear transfer] in primates, I expect we’ll get more grant applications based on that.

Since this is a new area, and not many investigators have the expertise to make pluripotent stem cell lines, the issue won’t be that there are too many [grant applications] that are outstanding but that there won’t be enough that are outstanding.

Nature Reports: How will grants be chosen?

Landis: One of the most contentious issues at NIH is how much money is assigned by what the review says is the scientific merit of the grant versus how much money is assigned based on programmatic considerations.

If 50 grants come in and none of them are deemed outstanding, the institutes can then say ‘none of them make the payline, but this [research] is absolutely critical.’

Nature Reports: How do you feel about NIH’s leadership role in global science?

Landis: Do we want therapeutic advances using human embryonic research to come out of Singapore, China, Britain? That’s a piece of the tension that exists.

I don’t think that the NIH can do anything except talk about the fact that the science does not support the President’s policy and at the same time to implement the President’s policy.

Posted by Monya Baker on December 17, 2007
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Last month, we posted an article that asked how one could declare human cells pluripotent, when the most robust tests are neither ethical nor feasible. Here are some of our favorite responses. If you've got more to say, please add your own comments.

Peter Andrews, Sheffield University

I rather think the discussion is becoming like the Middle Ages' discussions about how many angels can stand on the head of a pin. Does it matter? Sometimes in science it helps to have terms that are not so precisely defined - indeed the term 'gene' is an example. In fact it can mean a variety of subtly different things - which in fact makes it generally useful. When people wanted more precise terms, new ones were invented, like the 'cistron' based upon a very specific assay.

The same may be true of pluripotency. To me it means what it says - the ability of a cell to be capable of generating many cell types by differentiation. When we come to ES (and related EC) cells, we can actually find a very broad range of capacities - ranging from cells that have completely lost their ability to differentiatiate (nullipotent) to those with a very broad range – ultimately all somatic cell types. But we know very little about the molecular basis of pluripotency and what controls the range of cells into which a stem cell can differentiate. On the face of it at the moment I think we have little or no way of identifying which ES cells can generate a whole mouse in the tetraploid assay and which cannot even form the germ line in chimeras. In the face of this type of uncertainty, I would advocate retaining 'pluripotency' as a somewhat vague, term meaning ability to differentiate into a lot of cell types, and then as the need arises invent new terms with precise definitions based on specific assays - very much as the concept of the gene and its associated terminologies evolved.

Shinya Yamanaka, Kyoto University

This is an important, but difficult question. First of all, we don't know whether human ES cells are really ES cells or not. Because the lack of chimera experiments, we will not be able to answer this question. This means we lack a positive control. I have been telling my students that one of the worst experiments you can do is one without positive and negative controls.

In human ES cell field, all the scientists are forced to perform bad experiments without positive control. The best we can do is to describe how the cells are similar to human ES cells. This includes not only teratoma formation, but also surface marker, gene expression, DNA methylation, telomerase activity. You are right that some iPS cells can make teratomas, but do not give rise to germline transmission. However, these cells have different gene expression and DNA methylation.

I don't think it is governments to make definition of pluripotency. It should be scientific community.

Paul Tesar, Laboratory of Molecular Biology, National Institutes of Health, NINDS

Since I’m associated with NIH, I won’t comment on the recent nomenclature alteration.

I do, however, think that the definition of pluripotency sits at the heart of modern biology. Currently it is more of a semantic argument but I think further study will clarify the issue. Existing methodologies such as blastocyst injection and teratoma formation are inclusive but not exclusive when defining pluripotency. Additionally, they require secondary characteristics that are not necessarily involved in pluripotency. For example, cells that do not incorporate into the ICM, maybe because of cell adhesion or cell cycle differences, can not be examined by blastocyst injection. This does not mean that they are not pluripotent. Likewise, cells that do not rapidly proliferate when transplanted to an ectopic site will not form a teratoma. Can quiescent cells be pluripotent? Does growth or cell adhesion have to be linked to pluripotency? I think, thus far, pluripotent cells have satisfied one or the other of these basic assays but it is becoming harder to pinpoint the defining characteristic of pluripotency.
It sounds a bit outlandish but one could imagine something like a ‘pluripotency score’ which could be computed from a variety of cellular characteristics. It is difficult to define what exactly would need to be input, but in a current sense one could imagine looking across the genome at a large number of histone and DNA modifications. The ‘pluripotency score’ would basically be the probability that the chromatin is immediately capable of changing to form a panoply of differentiated tissues. SCNT and iPS cells have shown us that most, if not all, cells are capable of being pluripotent, but only after reprogramming. A much deeper understanding of multiple aspects of cell biology are necessary for something like a ‘pluripotency score’ to be a reliable and predictive measure, but at least it provides a framework to move forward instead of walking away or simply arguing semantics.

William Gunn, Tulane University
I would like to share what the consensus view is trending towards in my field, multipotent stromal cells(aka mesenchymal stem cells, MSCs).

I think the subtlety that is most often missed when talking about differentiation capacity is that differentiation is a cell-intrinsic process, but it's only assayed at the level of a whole culture. In other words, you're assaying a heterogeneous population of cells for phenotypes that different subpopulations possess to various degrees.

Further, these populations interact through cell-cell contacts and paracrine signaling, forming microenvironments which change constituency over time. Outside of ESCs and HSCs, it's an open question whether there's really one cell in a stem cell culture that could make all the various tissues, or if the pluripotency we see is a result of a mixture of progenitors of the various types that we just haven't learned how to distinguish yet. When exactly these progenitors may have become committed to a lineage isn't known.

The heterogeneity and dynamic nature of pluripotent cells is what has been confounding the studies which try to pin down markers of pluripotency or "stemness", and I'm not sure we'll get a satisfying answer until we develop the tools to study these cells on the single-cell level.

Evidence supporting this can be found in the work of Kuznetsov et al,
back in 1997: http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=9286749&ordinalpos=41&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum

Posted by Monya Baker on December 13, 2007
Categories: Reprogramming/Pluripotency | Permalink | Comments (0) | TrackBacks (1)

Over the past few days, I’ve seen a series of press releases from stem cell companies. They’ve taken the excitement generated by recent breakthroughs to draw people’s attention to their existence. And why not latch on to the general sense of euphoria? Two big advances happened within a week of each other, and both were ones that the stem-cell community had been waiting for.

First, came the announcement that embryonic stem cells could be made from cloned monkey embryos, a feat that many had deemed impossible. Nature Reports Stem Cells had a feature describing what made the advance possible as well as exclusive information on what the anonymous peer reviewers had to say about the advance. Well before the accomplishment was printed, the Niche had posted expert opinion on whether cloning papers needed additional layers of scrutiny, and Nature had decided on independent verification for cloning papers.

Next, came the announcement that human skin cells could be reprogrammed to pluripotency. Back when the breakthrough was published for mice this summer, Nature Reports Stem Cells covered what would need to happen to generate useful cells through direct reprogramming. A month earlier, we’d explored how pluripotency could be defined for human cells since the most rigorous tests are neither feasible nor ethical for humans. We also ran a profile of Shinya Yamanaka, who found the suite of genes and slogged through the screens showing that differentiated cells could be reset to a state similar to that found in the embryo. A highlight of the papers showing how human cells can be reprogrammed with only three genes.

More Nature articles are listed here.

Posted by Monya Baker on December 04, 2007
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The excitement from the reprogramming and cloning breakthroughs from earlier this month is fading, and people are looking to future paths and profits. Monkey cloner Shoukhrat Mitalipov has teamed up with a start-up company in San Diego, though it’s not exactly clear what it will be doing. Reprogramming cells without eggs or embryos will require less money, skill, and hard-to-procure material, so expect both academics and entrepreneurs to jump into the space. I’ve already seen one stem cell company touting the advance in a press release.
The intellectual property field may be more open as well. One of the teams that reprogrammed human skin cells was led by James Thomson of the University of Wisconsin, who also led the first team to generate human embryonic stem cells from leftover embryos provided by an IVF clinic. His patents covering human embryonic stem cells are controlled by WARF (Wisconsin Alumni Research Foundation) and have raised howls of protest from the community. Thomson says the intellectual property surrounding reprogramming techniques will "be complicated." When I asked WARF what that meant, I was told that the patent situation is complex because two groups made the discovery at the same time and the science is moving very rapidly. Another complicating factor is that the two groups used different techniques to reprogram cells, and whispers of forthcoming techniques are growing into shouts.
That doesn't yet mean patient advocates should be dancing in the streets. To keep us levelheaded, Newsweek’s Sharon Begley has an article that’s informative and easy to read. Also, while several prolife blogs are hoping the end is nigh for embryonic stem cells, the scientists leading the egg-free reprogramming breakthrough are making a strong case that studies of embryonic stem cells hold the keys for using these so-called induced pluripotent cells. See an editorial in Nature and this article from AFP.
For what it’s worth: Of the articles that appeared at the time of announcement, I particularly enjoyed the articles from Bloomberg , Nature, and Science.

Posted by Monya Baker on November 29, 2007
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That’s a paraphrase of what James Thomson at the University of Wisconsin-Madison told reporters at a press conference this morning when he announced that he’d induced human skin cells to take on the trappings of embryonic stem cells. His work is published online today in Science. Tying (or narrowly beating) Thomson is Kyoto University’s Shinya Yamanaka who reports his accomplishment in Cell. A news article from Nature is available here.
Thomson said that other researchers would be hard-pressed to distinguish his cells from human embryonic stem cells (ESCs) but repeated several times that whether these cells differ from ESCs in important ways remains to be seen. It does seem, however, that highly flexible cells could be made without collecting eggs from women and without destroying an early stage embryo.

Moreover, these pluripotent cells could be made from patients with known diseases. If the root causes of disease were genetic that could be a better way to study disease. It could also mean that replacement tissues for, say, diabetes patients using genetically identical cells. Thomson predicted that this research could lead to researchers testing drugs in ‘panels” of cell lines to figure out if toxicity and efficacy varied across genotypes.

Both Yamanaka and Thomson used a suite of four genes to transform cultures of skin cells. Both quartets included OCT3 and SOX2, well known markers of pluripotency. For the other two, Yamanaka used the KLF4 and c-Myc, which he’d shown earlier in mice. Thomson used NANOG (identified a few years ago as a master switch of pluripotency) and LIN28, implicated in processing mRNA. (According to a news article by Science.)

Besides these groups, there are many, many whispers of others about to publish similar accomplishments. Some report overcoming a remaining drawback: the transformed cells contain multiple copies of genes inserted into the genome by engineered viruses. “Nobody thinks we’re going to have those vectors even a year from now,” Thomson told reporters who had called in.

But he said, the major barriers still exist. The manipulations move cells back to what he called “a ground state” but for therapies and drug screening, researchers need a differentiated state. That was something he said was coming.

Synergies with other research

Thomson said that the time, cost, and expertise needed to make embryonic stem cells would likely push researchers to prefer genetically reprogrammed cells. Induced pluirpotent cells made by Yamanaka and Thomson come directly from cultured skin cells. Embryonic stem cells are made by scooping out cells from within an embryo and culturing them. Both types of cells can form teratomas and be differentiated into other cell types. Embryonic stem cells can also be made from cloned embryos, in which the nucleus of a differentiated cell is placed in an oocyte that is then activated to divide to form an embryo.

That feat was never been accomplished in humans (earlier reports were fraudlent). Nature did report it this week.

Thomson said that it would be useful to reprogram cells from the same monkey whose nucleus was used to make the embryonic stem cell lines. Then, cells generated from oocyte-assisted reprogramming and genetically engineered reprogramming could be compared directly.

Much of the speculation about what would need to happen to make the technique useful was reported when Yamanaka and other groups reported the accomplishment in mice. Here is a link to that article .

Posted by Monya Baker on November 20, 2007
Categories: Cloning, Reprogramming/Pluripotency | Permalink | Comments (2) | TrackBacks (0)

The Nobel prize has been awarded to three scientists who created the techniques for “knockout mice”. Here’s one article.

The award announcement acknowledged the powerful cells that made the technique possible. The prize went to Sir Martin Evans at Cardiff University, Oliver Smithies, from the University of North Carolina, and Mario Capecchi, from the University of Utah for "principles for introducing specific gene modifications in mice by the use of embryonic stem cells".

Knockout (and knock-in) mice are one of genetics’ power apps. Scientists create mice with nonfunctioning (or, in some cases, differently functioning) versions of specific genes. In one recent example, scientists knocked out one of many mouse genes that allow neurons to communicate and ended up, surprisingly, with a potential animal model for obsessive compulsive disorder. That’s just one of thousands of experiments using these engineered mice. The technique and its iterations are so routine that it’s hard to imagine biology without it.

Knockout mice are, both directly and indirectly, responsible for the breakthroughs showing that mouse skin cells can be reprogrammed to a state almost exactly like embryonic stem cells. Also, Shinya Yamanaka, the scientist who discovered which genes to insert to cause reprogramming, read about knockout mice well over a decade ago. He was doing classic pharmacology on dogs, but decided to strike out on a completely different path because the ability to pick any gene and delete its function was so intriguing.

When Yamanka attempted to reprogram differentiated cells, he started by genetically modifying mice so that their cells could signal (by growing green) when they had been reprogrammed.

This year’s Nobel Prize in Medicine lauds a tool and technique used by scientists in many disciplines across the world. It also illustrates a powerful platform that already owes its existence to embryonic stem cells. Cell therapies aside, many scientists who hope to study a disease in a dish believe there are more to come.

Posted by Monya Baker on October 08, 2007
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Today, the Human Fertilisation and Embryology Authority (HFEA) in the UK said that scientists could combine human chromosomes with animal eggs and try to make embryonic stem cells. It’s easier to collect unfertilized eggs from, say, cows than it is to collect them from women.

Interested scientists will learn in November if they’ll be licensed to make the attempts, which must be carried out under certain guidelines, but an article this month in Nature Cell Biology reminds us that even if the government says `yes’, some laws of science might say ‘no’.

In chimera-embryos (properly called `cybrid-embryos’ in this context), the chromosomes will be human, but at least some of the mitochondria will not.

Continue reading "Britain gives go-ahead on chimeras. Will science now block the way?" »

Posted by Monya Baker on September 06, 2007
Categories: Cloning, Policy, Reprogramming/Pluripotency | Permalink | Comments (1) | TrackBacks (0)

Horst-Dietrich Elvers, Burkhard Jandrig, and Christof Tannert write:
The Nature News story “Simple switch turns cells embryonic” (Nature 447, 618-619; 2007) presents the results of three independent research teams showing that normal skin cells can be reprogrammed to an embryonic state in mice. If this can be successfully adapted to human cells, the creation of human germ cells out of these pluripotent cells should be possible (as was indicated already by Huebner et al. Science 300, 1251-1256, 2003). Now, the road seems to be prepared to create human tissues for therapeutic purposes without using or destructing human embryos. This is, doubtless, an important progress for the whole field of regenerative medicine and avoids many morally questionable decisions, which so far have led to an international mix of regulatory frameworks. Therefore it is not surprising that excitement is overall huge at the moment.
The published results seem to indicate that the ethical problems of human embryo research are solved now.

Continue reading "Reprogramming breakthrough does not displace ethical debate" »

Posted by Monya Baker on July 09, 2007
Categories: Correspondence, Reprogramming/Pluripotency | Permalink | Comments (2) | TrackBacks (0)

In June, widely publicized work from three labs showed that specialized cells could be reprogrammed after transfection with four genes. In this correspondence, James Trosko suggests an alternative explanation, that the reprogrammed cells identified by groups led by Shinya Yamanaka, Rudolf Jaenisch, and Konrad Hochedlinger and Kathrin Plath could in fact be skin stem cells reprogrammed to an embryonic state.

Another thread discusses how reprogramming work alters perceptions of whether dedifferentiation is active or passive, and adds insight from in silico modeling. http://blogs.nature.com/reports/theniche/2007/07/reprogramming_insights_in_sili.html

Below is the email correspondence between the scientists:

Continue reading "Do induced pluripotent stem cells arise from skin stem cells?" »

Posted by Monya Baker on July 09, 2007
Categories: Correspondence, Reprogramming/Pluripotency | Permalink | Comments (0) | TrackBacks (0)

Eric Werner writes:
The recent results of dedifferentiating adult mouse fibroblast cells into stem cells brings into focus the fundamental question of how differentiation and development are controlled. (Cyranoski, D., Nature 447, 618-9; 2007). (Okita, K., et al. Nature doi 10.1038/nature05934, 2007). The fact that just four regulatory genes inserted into cells using viral vectors, can transform normal, differentiated cells into pluripotent stem cells indicates that for some cell types, at least, the process of dedifferentiation is more a process of activation rather than deactivation (Reik, W., Nature 447, 425-32; 2007). Indeed, this falls in line with in silico studies where stem cells, and, more generally, multicellular differentiation and development are modeled on computers.

Continue reading "Reprogramming insights: in silico modeling sugges