The Niche

Two transcription factors and a chromatin remodeller help make mouse cardiomyocytes

{Here's a highlight of work recently published online in Nature}

Ever since researchers turned cultured cells into muscle, scientists have been searching for ways to do something similar to make heart cells.[1] That’s because, at least in the developed world, heart disease kills more people than anything else — in part because adult hearts are not able to replace damaged cells. Now, Jun Takeuchi and Benoit Bruneau at the Gladstone Institute of Cardiovascular Disease in San Francisco have found that adding cardiac-specific genes to developing mouse embryos can make even some extra-embryonic parts become beating cardiomyocytes[2].

Continue reading "A recipe for heart cells from amnion and more" »

Posted by Monya Baker on April 30, 2009
Categories: Regenerative medicine | Permalink | Comments (0) | TrackBacks (0)

Science is going even more global, and that means more face-to-face and online get together. Here’s some help with both.

Travel grants to UK
It seems every American scientist is busy writing a grant right now. U.S. stem cell scientists looking for funds to go to the UK may want to gear up for another, very short grant A small travel grant program allows UK and US researchers to meet face-to-face and discuss potential collaborations. In this latest round, the program is inviting applications from academic researchers who want to visit industry partners.

Applications are due by May 8. Get more information here.

New online cell characterization tool
A new online resource allows the storage and analysis of various kinds of data associated with cell, cell line and tissue characterization across different species The Characterization Tool , housed at the Charité University Medicine Berlin, is now available; it is linked with the European Embryonic Stem Cell Registry but also includes mesenchymal stem cell lines and non-stem cell lines.

A recent feature profiled what it takes to turn data sets into information. Obviously, a big set is having the information.

Here are some other online tools and registries. If I’ve left out some of your favorites, please email me at theniche[at]nature.com

Continue reading "A new stem-cell online resource; upcoming deadline for short travel grant to UK" »

Posted by Monya Baker on April 27, 2009
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In a testament to the pace of the field, on the very day two features on induced pluripotent stem cells publish, so does a new paper showing how to reprogram without DNA, perhaps the most obvious milestone in the reprogramming race.. (See the previous blog post)

Here are related stories on Nature Reports. The links are divided into four sections. The first lists overarching stories, including my two features and lovely Q&As with Tom Graf and James Thomson. The others key off the specific research publications noted. They are grouped according to 1) reprogramming techniques 2) understanding pluripotency 3) embryonic stem cell behavior in culture.

Such lists are always incomplete. Send comments to theniche[at]nature.com

Related Nature Reports features, Q&As and commentaries

What does reprogramming do?
Researchers grapple with the factors that make cells pluripotent

Stem cells: fast and furious (Subscription required)
The field of induced pluripotent stem cells has gone from standing start to headlong rush in less than three years.

Continue reading "Induced pluripotent stem cells, reading list" »

Posted by Monya Baker on April 23, 2009
Categories: Reprogramming/Pluripotency | Permalink | Comments (0) | TrackBacks (0)

Researchers make iPS cells without inserting DNA

For the first time, researchers have reprogrammed cells to pluripotency without using DNA. Ever since Shinya Yamanaka of Kyoto University in Japan showed that cultured skin cells could be made to behave like embryonic stem cells by inserting additional pluripotency genes, researchers have been trying to find ways to avoid genetic engineering as a reprogramming strategy. The additional genes make the cells less predictable, more variable and more prone to undergo unwanted proliferation. Even if DNA is not inserted into the cells, researchers worry that undetected integration could occur and could change the behaviour of those cells, limiting their use in cell therapy, drug screening and disease modelling.

An obvious alternative would be to add the proteins for the gene products instead of the genes themselves, but for that to happen, proteins would have to be made not only to enter cells but also to enter the nucleus, a particularly difficult task. Furthermore, the proteins would have to persist at high enough levels in the nucleus for the duration of the reprogramming process.

Now, researchers led by Sheng Ding of The Scripps Research Institute in La Jolla, California, have found a way to overcome this barrier in mouse fibroblasts. Besides Scripps scientists, the team included Hans Schöler of the Max Planck Institute for Molecular Biomedicine in Münster, Germany, who has published with Ding before, as well as scientists from two California-based companies — Proteomtech, in Costa Mesa, and LD Biopharma, in San Diego1.

The secret to getting the proteins across the cell and nuclear membrane turns out to be adding a sort of transportation tag to each of the four proteins (c-Myc, Klf4, Oct4 and Sox2) that is typically used to reprogram cells. The tag consisted of 11 linked copies of the amino acid arginine, a highly polar species that helped the proteins pass through membranes. In addition, the researchers added valproic acid, which has been shown to boost reprogramming rates both for induced pluripotent stem cells and in somatic cell nuclear transfer. The proteins were added 4 times over 6 days at 36-hour intervals. Researchers observed the cells over 30 passages and found that they were “morphologically indistinguishable” from embryonic stem cells and expressed similar markers. Though the researchers have not yet completed the step showing that the cells can form viable sperm and eggs, the cells did pass a related test. When the cells were mixed in with normal mouse embryos and allowed to develop in a surrogate mother, the reprogrammed cells contributed to the germ layers in 13.5-day-old embryos.

Though the work has not yet been reported in human cells, and other groups will need to replicate the results, Ding predicts that his and similar techniques will replace those requiring DNA, partially because it does not require the preparation of viruses and plasmids. “Whenever you use a genetic method, even if you claim there's nothing left [of the added DNA], it's still not as convenient as using chemically defined methods.”

Nonetheless, Ding and other researchers agree that further studies are essential to assessing induced pluripotent stem cells made by various methods. “At the end of the day, what you want to do is just make normal cells and reduce the risk of things like mutation,” says James Thomson of the University of Wisconsin–Madison, who recently published a technique to reprogram cells without requiring any genetic integration.2 There will eventually be many ways of making the cells, he says. “Evaluating the cells — that’s going to be the hard part.”

Nonetheless, techniques like this are essential to such evaluation. “Once the cells are vector free,” says Thomson, “they can be characterized by a lot of labs.”

Related articles
What does reprogramming do?

Small molecules boost reprogramming rates

References
1. Zhou, H. et al. Generation of induced pluripotent stem cells using recombinant proteins. Cell Stem Cell doi:10.1016/j.stem.2009.04.005 (published online 23 April 2009).
2. Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science doi:10.1126/science.1172482 (published online 26 March 2009).

Further reading
iPS reading list

Author affiliation
Monya Baker is editor of Nature Reports Stem Cells.

Posted by Monya Baker on April 23, 2009
Categories: Reprogramming/Pluripotency | Permalink | Comments (1) | TrackBacks (0)

I just got off a teleconference discussing draft guidelines about what kinds of human embryonic stem cell lines the NIH will fund. Research advocates still have some work to do for final guidelines due out just after the 4th of July. Here's a link to the NIH draft guidelines.

Right now, here's what's not fundable: lines created from parthenotes (made by stimulating an unfertilized egg to divide; these have been created), lines created from cloned human embryo (made by taking an unfertilized egg and replacing its nucleus with that of another person, then using that to make a genetically matched line of embryo; these have not been created), also any embryos made for the purposes of research (i.e. fertilizing eggs with sperm with the intention of using the resultant embryo for deriving stem cell lines; these have not been created as far as I know, and doing so is prohibited in widely accepted scientific guidelines). The embryos used for deriving lines are typically blastocysts (hollow balls of cells, about 5 days old). Much more rarely, younger embryos (solid balls of cells) are used.

Here is what's fundable : all of those lines that have been made from embryos that would otherwise have been discarded by fertility clinic including those diagnosed with certain genetic diseases, provided researchers can document certain conditions: That the embryo donors knew what would happen to the embryos when the lines are made (the balls of cells are typically destroyed), that donors knew the lines would be maintained for years and that if any commercial benefits developed from the lines, the donors would not get them. Interestingly, the NIH did not talk about grandfathering in any of the hES cell lines that were fundable under the Bush administration, and consent issues have been raised surrounding some of those lines. (See When the past catches up with the present)

This is a big expansion of the lines available, though researchers very much want to compare lines between embryos produced from cloning and left-over embryos to try to figure out what controls the machinery that maintains cells in an embryonic state. Interestingly, when Bill Clinton had the NIH issue guidelines during his presidency, the draft forms did allow funding of embryonic stem cell lines created for research purposes, but, after public comment, the final guidelines restricted funding to left-over embryos from IVF. The Bush Administration withdrew these guidelines when it issued its more-restrictive policy. These guidelines wre based on the kinds of research that enjoyed broad public support.

The proposed new NIH policy is both more and less restrictive than policies in the UK and Australia. The UK does not allow research on embryos unless researchers obtain a license from the government, of which very few have been granted. However, these licenses do allow researchers to transfer nuclei into eggs for the purposes of creating embryonic stem cells. In the US, anyone can try such procedures, but they can't get federal money to do so.

I'll post more in a few days as there is more information. A few months ago, Bryn Nelson compared how policy on hES research evolved in the UK, US, and Germany. That seems particularly relevant now. (Persistence pays off)
Also, here's reporting from Reuters.

PS: This came through from the Harvard Stem Cell Institute as I was typing this up.
"The draft guidelines released today clearly reflect a great deal of careful consideration of the scientific and ethical issues involved. We strongly support the development of unambiguous, ethically sound regulation of the field of embryonic stem cell research, and will carefully consider these proposed guidelines and offer detailed response during the public comment period."

Posted by Monya Baker on April 17, 2009
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A commentary from a global group of scholars
International stem cell environments: a world of difference
Stem-cell research represents a patchwork of patchworks. Understanding this can help the research community to manage it effectively

Getting blood stem cells to the heart
Improving engraftment increases survival in a mouse model

What makes a cancer stem cell?
What can cultured balls of cells say about the origin of cancer stem cells?

(Also, last week I ran a series called Stem cells and neurodegenerative disease: cool science and scepticism) Here are some follow-ups.

Continue reading "This week on Nature Reports Stem Cells" »

Posted by Monya Baker on April 17, 2009
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iZumi Biotech has just announced a dream team, but they aren’t saying much about what exact game they’ll be playing with induced pluripotent stem cells. Here is the article in USA Today , announcing a deal with Kyoto University’s Shinya Yamanaka, who figured out how to transform specialized cells to an embryonic-like state. iZumi already has an agreement with the Gladstone Institute in San Francisco, where Yamanaka has a joint appointment.

iZumi will be pursuing iPS cells not for cell therapy but for drug screening. For this application, iPS cells promise all the benefits of ES cells, plus more, because such cells can be readily generated from the cells of patients with a known medical history, and a trackable medical future. The idea is that researchers can take skin cells from people with, say, heart disease, convert them into iPS cells, convert the iPS cells into cardiomyocytes, and then test drugs on cardiomyocytes. This should, in principle, work for just about any disease. iZumi is certainly not the only company in this space.

Related articles
iPS cell technology gains momentum in drug discovery (requires access to Nature Reviews Drug Discovery)
Reprogrammed skin cells provide testing ground for new drugs (requires access to Nature News)
New tools for drug discovery (Though this discusses human embryonic stem cells, most of the players and the problems are the same.)

Posted by Monya Baker on April 14, 2009
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A transplant of blood stem cells in early onset diabetes seems to stop the immune system’s errant attacks on patients’ insulin-producing cells and so allow 20 of 23 patients to forego daily injections.
Read about the new JAMA study in Bloomberg. The work moves forward previous research on diabetic children carried out in Brazil.
The authors have previously reported using this system to stop errant immune attacks in an early study for multiple sclerosis. The strategy of the treatment is not to replace the tissue lost to the disease, but to stop the body from destroying itself.

Posted by Monya Baker on April 14, 2009
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Several sources of new bond funds might be coming into the California Institute for Regenerative Medicine (CIRM), but CIRM’s Don Gibbons emphasizes that none of them are yet “done deals.”

The first funds are expected to be allocated from $6.5 billion in tax-exempt bond sales that occurred through the state two weeks ago, as reported by the San Francisco Chronicle.
The state’s investment board is meeting on April 15th to decide how those funds will be distributed, and CIRM hopes some of those funds will be used to pay off some prior debt and to award $43 million pending for one of CIRM’s facilities grants, says Gibbons.

The state is scheduled to begin selling more bonds, this time taxable bonds, on April 20th, and CIRM hopes to use funds from those sales to cover new research and educational grants. But neither the amount to be sold nor its allocation has been determined yet, says Gibbons. “We’re not going to presuppose how much we’ll get.”

And CIRM is also moving ahead with plans to issue its own private bonds, says Gibbons. Under current law, any CIRM-funded projects that yield products will need to pay some portion of revenues back to the state. That requirement means that the bonds issued will have to be taxable. Such bonds, he says, might be easier to place privately than publicly.

As previously described in the Great Beyond, the state has authorized the sale of $400 million in private bonds by CIRM, and CIRM’s Board has met to discuss funding priorities, based on expectations that $100 million bonds would be sold. For example, it decided to delay funding of $40.6 million in grants awarded in January destined for graduate students, postdoctoral and clinical fellows already working in stem cell research labs.

Gibbons acknowledged the possibility that some programs might need to be scaled back, but said that CIRM was not obsessing over the bond sales. “The feeling here is that the money will come through for us when we need it. That someone will find a way.”

California’s plans to sell taxable bonds are described in The Bond Buyer . And the Los Angeles Times. I found both articles through the California Stem Cell Report, which has several posts on April 6 and 7 discussing how these funds might be applied to the California Institute of Regenerative Medicine.

See also a previous post on CIRM finances and private bond sales.

Posted by Monya Baker on April 08, 2009
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In a rebuttal to a statement by members of President Bush’s Council of Bioethics, statementdefended the Bush policy on human embryonic stem cell research, William Hoffman, coauthor of The Stem Cell Dilemma, counters that the U.S. has now rejoined the world’s scientific mainstream.

He writes, “The consensus view of countries that have deliberated and established policy is that research on stem cell lines derived from human embryos donated by fertility clinics with consent of the donors is legal and can be funded with public money.”

For the past seveal years, Hoffman has maintained color-coded maps tracking countries’ stem cell policies. In his commentary, he recounts:

“By 2007 34 countries representing some 3.5 billion people – more than half the earth’s population – had policies that permitted public funds to be spent for stem cell research using embryos donated by fertility clinics with consent of the donors. The United States was not among them. Today it is on its way.”

Hoffman’s commentary is posted on the Bioethics Forum of the Hasting’s Center, which also posted the original statement and another opposing commentary by bioethicist Insoo Hyun.

Even as the amount of research grows, it’s worth noting that a friendlier research environment may not translate into a friendlier business environment. Though the work is tightly regulated and requires researchers to obtain national licenses, the UK is one of the more permissive countries for human embryonic stem cell research. However, researchers at the University of Nottingham have studied the commercialization of stem-cell therapy in the UK and found that the resources to turn research into products are likely insufficient.
As noted in the press release: “the industry is dominated by small, young companies lacking the resources to bring products easily and successfully to market and those that do struggle to make sales.”

Posted by Monya Baker on April 06, 2009
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Hi everyone, We've got this Cell Stem Cell article slated to go up as a story in a couple Thursdays, but the press release is really making the rounds. So here's the reported story by Asher Mullard.

The origins of cancer stem cells have long been elusive and controversial. While some researchers think that they are stem cells gone awry, others suspect that cancer stem cells arise from differentiated cells that have been reprogrammed. In support of the reprogramming theory, a tissue-culture study suggests that mutant mouse embryonic fibroblast (MEF) cells that lack retinoblastoma proteins are reprogrammed when they are cultured in suspension, and come to resemble cancer stem cells.

The retinoblastoma 1 (RB1) pathway is crucial for detecting cell-cell contact and regulating cell cycle arrest. Consequently, whereas cultured MEFs normally grow in a monolayer, MEFs lacking RB1 grow into mounds of cells that eventually detach and form colonies of free-floating ‘spheres’. The RB1 pathway is also frequently lost in cancers. These and other observations set Douglas Dean of Brown Cancer Center in Louisville, USA, and his colleagues wondering whether spheres had a role in reprogramming differentiated cells into cancer stem cells.

Reporting in Cell Stem Cell, Dean and his colleagues show that when RB1–/– cells are forced to grow in spheres for 2 weeks, a new cellular morphology emerges[1]. Moreover, some cells from 2 week old spheres, but not from younger spheres or from the original monolayer, persistently express embryonic stem cell genes, including Oct4 and Nanog as well as cancer stem cell markers. “It’s like a switch has been flipped,” says Dean. Thus, he argues that spheres might enable reprogramming of cancer stem cells. “There may be a technique down the road for producing an inducible pluripotent stem cell from a fibroblast using this technique,” he adds excitedly.

But Thea Tlsty, a pathologist at University of California San Francisco, is not convinced for two reasons. In the 2 weeks it took for the new morphology and characteristics to arise, the culture setup might have selected stem-cell-like cells that were already present in the population, rather than enabled de novo reprogramming. And although Dean took precautions to minimize this possibility, he acknowledges it has not yet been definitively ruled out.

And Tlsty is also uncertain about the claim that cells from aged spheres even have the characteristics of cancer stem cells. When Dean transplanted sphere-reared cells into mice, he observed tumour formation, supporting the notion that these cells have cancer stem cell capabilities. Yet this evidence isn’t conclusive, explains Tlsty. “A cancer stem cell phenotype is usually accompanied by an invasive phenotype, and while I saw a growth in vivo, I did not see an examination of invasive phenotypes.”

“To clear up my confusion, I would want them to start with single differentiated somatic cell,” says Tlsty. “And I would want to see some evidence of invasion potential.”

Dean readily notes another limitation of his study. “This is a cell culture based set of studies,” he says. “What we’re doing is trying to put forward a hypothesis that we and others can test in real tumours.”

Related articles
John Dick: Careful assays for cancer stem cells
http://www.nature.com/stemcells//2009/0903/090326/full/stemcells.2009.47.html

Cancer stem cells, becoming common
http://www.nature.com/stemcells/2008/0812/081203/full/stemcells.2008.153.html

Cancer stem cell sightings and slightings
http://www.nature.com/stemcells/2007/0709/070927/full/stemcells.2007.93.html

References
Liu, Y. et al. Mouse fibroblasts lacking RB1 function form spheres and undergo reprogramming to a cancer stem cell phenotype. Cell Stem Cell 4, 336–347 (2009).

Posted by Monya Baker on April 03, 2009
Categories: Cancer | Permalink | Comments (0) | TrackBacks (0)

Here are the stories that just went live

Look now! Human iPS cells with no genetic integration
Six reprogramming factors in a plasmid reach a holy grail

Carbon dating shows humans make new heart cells
The cold war helps settle a hot debate about how hearts grow.

How tissue-specific stem cells keep their fate
Epidermal stem cells stay skin even if alternative programs shed chromatin marks of repression

G-protein signalling is needed for stem cell homing
Protein is vital for engrafting of haematopoietic stem cells
Published online: 02 April 2009; doi:10.1038/stemcells.2009.53

Many intestinal villi from a single stem cell, in culture
Even without a supporting niche, intestinal stem cells can self-organize into a mini-organ in a dish

iPS cell technology gains momentum in drug discovery
Reprogramming of adult cells without viral vectors adds to the excitement about their application of iPS cells in drug development

Posted by Monya Baker on April 03, 2009
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Induced pluripotent stem cells may be capable of forming any imaginable creature, at least in miniature form. Short of funds and unable to buy fibroblast growth factor (FGF) to study her induced pluripotent stem cells, Sheila Nagin of Yount University decided to try something desperate. A herpetologist colleague had been studying the development of scales, and she added some of his reagents to the mix. To her surprise, the cells grew into what appeared, morphologically, to be embryonic stem cells. When she tried to assessing the cells by injecting them into an immunecompromised mouse, the cells grew, not into the expected teratomas, but into small furry lizards. Intrigued, Nagin began new combinations: the shafts of feathers, the eyes of newts, pulverized rhinocerous horn. By testing out various combinations, she was able to create miniature versions of unicorns and griffins. Placing the cells in an immunocompromised cat produced a creature very much like a sphinx.

Further work needs to be done to understand how well the miniature creatures actually mimic their full-size counterparts, says Allen Funt, of Candida College. “The problem is that since these are fictional creatures, we have no ‘gold-standard’ to compare them to.”

Meanwhile, Nagin thinks she may have found a way to satisfy the critics. A combination of match-heads and butterfly wings, she believes, could the factors necessary to produce dragons. “I figure if they breathe fire, everyone will believe they’re the real thing.”

Meanwhile, scores of other researchers are throwing aside FGF in favor of fairy tales. “It just goes to show that we really have no idea how we can make reprogramming work,” says New Carolina University’s Joe King.

For more information, try here.

Posted by Monya Baker on April 01, 2009
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