Research into reprogrammed stem cells: an interactive timeline

By Ed Yong | February 2, 2011 1:01 pm

Our bodies are made up of hundreds of different types of cells, but stem cells can become all of them. Over the last five years, scientists have made great advances in reprogramming specialised adult cells back into a stem-like state, turning back the clock and restoring their lost potential. These “induced pluripotent stem cells” or iPSCs could be used to create personalised treatments for diseases, or even new body parts, which are tailored to an individual’s genome.

The journal Science named iPSCs as its Breakthrough of the Year in 2008. Since their discovery in 2006, research on these cells has rocketed ahead and this timeline charts the progress of this exciting field, right up to today’s latest discovery. For readers who are using Readers or phones and cannot see the timeline, all of its content is available as text below.

This timeline was inspired by John Rennie’s manifesto on how to improve science journalism, by looking at the stories that lead up to new discoveries, rather than focusing on every new paper in isolation.

Aug 26, 2005 – The seeds are planted

Kevin Eggan at Harvard University found that he could reprogram adult skin cells into an embryonic state by fusing them with actual embryonic stem cells. The term iPSC hadn’t even been coined yet, but this was an important step. It showed that adult cells can regain some of their lost potential and become more ‘stem-like’. It also showed that embryonic stem cells have something inside them that can help adult cells on their way. The challenge was to find these elusive chemicals…

Aug 10, 2006 – The first iPSCs

Shinya Yamanaka from Kyoto University fired the starting pistol. His team was the first to successfully turn back the clock on adult cells. They transformed skin cells from the tails of adult mice into those that looked a lot like embryonic stem cells. Like true embryonic stem cells, these “induced pluripotent stem cells” (iPSCs) could divide into a wide variety of cells and tissues. The technique depended on just four genes – Oct4, Sox2, c-Myc and Klf4 – a quartet that would come to be known as Yamanaka factors.

Jun 6, 2007 – iPSCs work in mouse embryos

Yamanaka expanded on his earlier work, along with two other teams led by Rudolf Jaenisch at MIT and Konrad Hochedinger of the Harvard Stem Cell Institute. For the first time, the three teams showed that the iPSCs could help to produce adult cells if they were injected into mouse embryos. They were even more like embryonic stem cells than Yamanaka’s earlier paper had suggested.

Unfortunately, and this is a problem that will continue to rear its head for years, some of the animals went on to develop cancers. The team used viruses to insert the Yamanaka factors into the mouse genomes. If these end up in the wrong place, they could cause genetic chaos and ultimately cancer. It doesn’t help that one of the four genes – c-Myc – is involved in cancer.

And so far, no one had been able to create human iPSCs. Yet…

Nov 20, 2007 – Human iPSCs arrive

A major milestone: two independent groups managed to create iPSCs from human cells in a photo-finish tie. Yamanaka, naturally, was one of them. He used the same four genes from his mouse experiments to transform skin cells taken from the face of a 36-year-old woman and connective tissue from a 69-year-old man. He even managed to coax the resulting iPSCs into neurons and heart muscle cells. Meanwhile, James Thomson from the University of Wisconsin managed to reprogram skin cells from a foetus and from the foreskin of a baby boy. And a month later, George Daley’s group from Harvard Medical School became the third to produce human iPSCs. In the next two years, scientists would go on to create iPSCs from a variety of human tissues, including stomach, pancreatic, liver and immune cells, as well as neurons.

These studies raised some important issues. Yamanaka used the same quartet of genes in his mouse experiments, but Thomson swapped out c-Myc and Klf4 for Nanog and Lin28. That was important, for c-Myc is linked to several cancers. Just ten days later, Yamanaka showed that he could produce iPSCs without Myc, using only the three other genes.

Meanwhile, Yamanaka found big differences in the activity of 4% of the iPSC genes, compared to those of true embryonic stem cells. Are these cells really the same?

Dec 6, 2007 – iPSCs cure sickle cell anaemia in mice

From hype to reality. Rudolf Jaenisch cured mice of a genetic disorder called sickle cell anaemia using personalised stem cells. His team took cells from the skin of the rodents’ tails, reprogrammed them, corrected their genetic defect, and injected them back into the mice. Just four weeks later, the iPSCs had begun producing normal blood cells and the mice were no longer anaemic. It was a powerful ‘proof-of-principle’ that iPSCs could one day fulfil their potential in fighting human disease.

Mar 7, 2008 – One that failed

Nature reported that a Californian biotech company called PrimeGen claimed to be able to create iPSCs using carbon nanotubes. The tubes would act as a vehicle for shuttling the reprogramming genes into the cells. The claims were made at a conference of investors, many scientists were skeptical, and no published peer-reviewed paper has come of it

Apr 15, 2008 – Rat model of Pakinson’s

Jaenisch tried to repeat his sickle cell success with Parkinson’s disease. He coaxed iPSCs into becoming neurons and transplanted them into the brain of a rat, displaying signs of Parkinson’s disease. The new neurons integrated into the brains of their hosts and the rats’ symptoms improved. However, some of them developed tumours, highlighting again the potential risks of this technique.

Jun 22, 2008 – Small molecules boost efficiency

When Yamanaka tried to create iPSCs without the potential cancer-causing Myc gene, he found that the process worked but slowly and inefficiently. Douglas Melton from Harvard University found a solution. With a suite of small molecules, such as valproic acid, he managed to boost the efficiency of the Myc-less technique by more than 100 times.

Jul 15, 2008 – ALS cells reprogrammed

Building on successes in mice, Kevin Eggan from Harvard University created iPSCs from skin cells taken from an 82-year old woman with amyotrophic lateral sclerosis (ALS). This is the same condition that has paralysed Stephen Hawking. Even after a lifetime of chronic disease, the adult cells could still be reverted to a stem-like state. Eggan then converted the iPSCs into motor neurons, the same cells affected by the donor’s disease.

The results were a boon for ALS researchers, and an example of one of the big benefits of iPSCs. Research into ALS is slow because it’s nigh impossible to obtain a decent supply of living neurons affected by the condition. This study changed all of that, and it was just the beginning…

Aug 7, 2008 – Diseases ahoy

Two months after Eggan’s group produced iPSCs from a patient with ALS, George Daley announced the creation of iPSCs from ten genetic disorders. The list includes a who’s who of important inherited diseases including Huntington Diseases, Down syndrome, Duchenne muscular dystrophy, and others with a strong genetic component, such as juvenile-onset type 1 diabetes and Parkinson disease. As with the ALS iPSCs, these aren’t breakthrough in themselves. Instead, they open doors for future discoveries.

Sep 25, 2008 – A safer method?

Previously, scientists had created iPSCs using viruses that shove their DNA cargo into a cell’s own genome. This approach is risky. If the DNA ends up in the wrong place and disrupts the wrong gene, the result could be cancer. But this isn’t necessary. Konrad Hochedlinger from Harvard University managed to do the same thing with adenoviruses, a group of viruses that stay out of their hosts’ DNA. There was a catch – the process was slower and less efficient.

Dec 22, 2008 – SMA cells reprogrammed

Clive Svendsen from the University of Wisconsin took skin cells taken from a patient with spinal muscular atrophy (SMA) and reprogrammed them into iPSCs. Others had created many such lines from people with other diseases, but Svendsen went one step further. He showed that the reprogrammed cells kept their genetic defects and produced neurons with the same problems. And that makes them a valuable resource for studying the disease in the lab. For example, scientists can expose these cells to experimental drugs to see how they respond.

Jan 12, 2009 – iPSCs treat haemophilia in mice

Yupo Ma from the Nevada Cancer Institute used iPSCs to treat a genetic disease called haemophilia A in mice. The disease is caused by a single faulty gene that stops blood from clotting properly. Ma created iPSCs using three of the Yamanaka factors (without Myc) and transplanted them into the haemophiliac mice. Normally, these animals would bleed to death within a few hours if they get a small cut in their tails. After the iPSC treatment, they could survive a cut for several months.

This was the second genetic disorder to be treated with iPSCs, but it’s still only a triumph in mice. Before human trials can start, there are still many big safety issues to address.

Feb 12, 2009 – iPSCs into beating heart cells

Transforming cells into iPSCs is one thing; turning them back into other types of cells is quite another. Tim Kamp from the University of Wisconsin managed to turn iPSCs into various types of heart cells, which could even be seen beating in a dish.

Mar 1, 2009 – No viruses needed

Scientists have reprogrammed cells with two different types of viruses. But two groups led by Andras Nagy from Mount Sinai Hospital and Keisuke Kaji from the University of Edinburgh managed to produce iPSCs without any viruses at all. They loaded Yamanaka factors into a DNA “cassette” that could jump into the genome of a host cell. Once the cells had been transformed, the cassette could be cut back out.

Apr 23, 2009 – No genes needed

iPSCs can be made without using genes at all. Sheng Ding from the Scripps Research Institute took the proteins encoded by the four Yamanaka factors and tagged them with a backstage-pass – a molecule that gave them entry into mouse cells. A month later, Kwang-Soo Kim from Harvard Medical School managed to do the same thing using human cells.

Jun 23, 2009 – iPSCs make mice

In perhaps the ultimate test of the potential of iPSCs, two teams used these reprogrammed cells to produce living mice. Qi Zhou from the Chinese Academy of Sciences created a mouse called Xiao Xiao by implanting iPSCs into a developing embryo when it was still a ball of cells. He transplanted the embryo into a surrogate mother, which gave birth to a healthy pup 20 days later. All in all, Zhou reared 27 pups from iPSCs transplants and 12 of these survived to adulthood and have produced young of their own. A second group led Shaorong Gao of the Chinese Academy of Medical Sciences achieved the same feat.

Aug 9, 2009 – Immortality helps

No fewer than five separate groups (including Yamanaka’s and Hochedlinger’s) hit on the same way of producing iPSCs more efficiently – making them immortal. All of them focused on p53, the so-called “guardian of the genome”, which prevents cells from becoming cancerous. By knocking out this guardian, or other genes that work together with it, the teams managed to turn a far greater proportion of adult cells into iPSCs. The approach has clear risks and it will never be used to create stem cells for treating patients. But it could help scientists to create more iPSCs for use in their research.

Oct 11, 2009 -  Separating wheat from chaff

When adult cells are reprogrammed into iPSCs, not all of them make the full transition. George Daley and Thorsten Schlaeger found a set of molecules that can tell the fully-reprogrammed cells from their incomplete cousins. They even managed to see these molecules under the microscopy by using glowing antibodies designed to find and stick to them. With these glowing signposts, they could watch the fate of their iPSCs on a live broadcast.

Nov 10, 2009 – Speeding it up

Right from Yamanaka’s first experiments, only a small proportion of adult cells could ever be transformed into iPSCs. Some wondered if only a small proportion of cells had the potential to regain their potential. But Rudolf Janiesch showed that it was just a matter of time. It’s a constant and random process. Give it long enough – say 18 weeks – and almost all cells can be reprogrammed. Janiesch also found ways of speeding up the transformations, either by making the cells divide faster, or by cutting down the number of divisions it takes before they transform.

Feb 11, 2010 – Stem cells not as we know them

As research with iPSCs blazes ahead, some scientists start to report important problems. Sun-Chun Zhang from the University of Wisconsin found that iPSCs produce neurons at a slower pace than true embryonic stem cells. In the same week, Robert Lanza from Stem Cell and Regenerative Medicine International found the same thing for blood cells. Not only that, but the cells they did produce were more likely to grow slowly, age prematurely and die spontaneously. One month later, another group found one of the reasons behind these problems…

Mar 31, 2010 – A genetic flaw

Konrad Hochedlinger found a set of important genetic differences that separate mouse iPSCs from genuine embryonic stem cells. On their 12th chromosome, they have a cluster of genes that is much less active. If human iPSCs have similar silenced genes, this could explain why they aren’t as good as embryonic stem cells at producing other types of cells. The true scale of these differences would become clear in a few months…

Jun 21, 2010 – Forget genes, just use viruses

Some scientists have found ways of producing iPSCs without any viruses, using either the Yamanaka factors or the proteins that they encode. But Andrew Baker at the University of Glasgow went the other way. At the annual meeting of the International Society for Stem Cell Research, he announced that he could create iPSCs form human skin cells using only viruses, without any of Yamanaka factors or any other reprogramming genes. It was like saying you could use a car without a driver. Not everyone was convinced, but Baker’s results were published four months later.

Jul 19, 2010 – Memories of past lives

It’s not so easy to turn back the clock. Even after they’ve been reprogrammed, iPSCs carry a memory of their past identities that constrains their future. George Daley’s group found that iPSCs still carry molecular marks that annotate their DNA. These “epigenetic” changes mean that it is easier, for example, to produce blood cells from iPSCs that themselves came from blood cells, rather than those derived from connective tissue or brain cells.

This explains a lot of earlier results, including the differences in gene activity between iPSCs and true embryonic stem cells. There are a few possible ways around these problems. You could use chemicals to try and strip away the epigenetic marks. Or, as Hochedlinger’s group found, you could simply grow the cells for a long time.

Nov 17, 2010 – iPSCs tag jumping genes

By creating iPSCs from cells with genetic disorders, scientists were supposedly creating important tools for studying these diseases. Alysson Muotri and Maria Marchetto from The Salk Institute proved that point by studying a genetic disorder called Rett syndrome. The disease stops neurons from developing properly, and the duo suspected the involvement of DNA sequences called L1s, which can jump around the genome. To test that, they took cells from girls with or without Rett syndrome and transformed them all into iPSCs. They tagged the L1 gene so that it gave off a green glow and watched it hopped around the genome. The telltale fireflies revealed that Rett syndrome neurons have twice as much active L1 as those from the other children.

Dec 12, 2010 – iPSCs into intestinal tissue

iPSCs have been transformed into various types of cells, but typically in a dish. James Wells from the Cincinnati Children’s Hospital Medical Center went one step further by turning iPSCs into three-dimensional pieces of intestinal tissue. He did it using a cocktail of growth factors, delivered at a precise schedule. His “organoids” should help scientists to study human organs in the confines of a lab.

Feb 01, 2011 – Reprogramming errors, lots of them

Like Daley last year, Joseph Ecker’s group from The Salk Institute found epigenetic differences between iPSCs and true embryonic stem cells, but this time in human cells. By comparing methyl marks across the entire genomes of iPSC lines, embryonic stem cells and adult cells, Ecker found reprogramming errors that were more extensive than anyone had suspected. Many of these errors were common to all iPSC lines, and some were unique to individual ones. They could be passed on to daughter cells created form the iPSCs.

The abnormal marks seemed to cluster around structures are the centre and tips of chromosomes –the centromeres and telomeres. Ecker thinks the DNA at these places might be packaged and folded in such a way that makes methyl marks harder to remove. Now, they’re testing chemicals that target or open up these areas, in the hope of producing a ‘stemmier’ breed of iPSCs.

Still to come – ?

Comments (17)

  1. Pablo

    Sincere congratulations about the timeline, and the idea of starting to apply the terms exposed in John Reinne’s manifesto. This way the general context can be easily grabbed, and transmits a sense of coherence can not possibly be achieved by the sporadical publication of “hot” breakthroughs. Thanks for the extra effort.

  2. Thanks! Time will tell if it’s worth it or not. My hope is that people can constantly refer and link back to this post as the story unfolds.

    But the timeline took ages to do, around 4 times as long as a standard post. It’s a significant investment and I’ll be interested to see how it plays out.

  3. I think background stories like this are fascinating from a media studies point of view, but also possibly really important for a load of different types of news storytelling. How many times have you been too busy to ‘follow’ a story on a particular issue, only to then find yourself confused when it develops into something you later want to hear more about?

    The various rhythms of traditional news output don’t always provide a space for catchup, because it’s all about the new. And yes, perhaps this is especially important in science, where people might not have bothered to follow a story when it seems more esoteric but then, when it does seem interesting, they feel alienated by missing the background. Of course, it’s easier to trawl through archives now they are on online, but people won’t always bother – it’s different from having a story told for you.

    (what I’m saying is I can see how this helps in terms of by Rennie’s challenge, but also more).

    Interestingly (though I guess not surprisingly) kids news like Newsround sometimes do this reasonably well, especially for long-running issues like Northern Ireland, when they know their audience weren’t paying attention ten years ago, simply because they weren’t alive! They don’t necessarily tell such stories as a time-line – there are a variety of ways of telling this sort of content, but they do make an effort to pull out more than just the ‘what’s new’ element to the story.

    Things like this also take a load of time to compile, as you said on twitter, but maybe systems like dipity (and low-tech versions like the Guardian’s story tracker) if updated as people go along, will make things easier.

  4. ME

    I notice you didn’t mention the reprogramming using synthetic mRNA! Maybe this wasn’t as big on other people’s radars, but I’ve always had a soft spot for siRNA.

    http://www.ncbi.nlm.nih.gov/pubmed/20888316

  5. @Alice

    …perhaps this is especially important in science, where people might not have bothered to follow a story when it seems more esoteric but then, when it does seem interesting, they feel alienated by missing the background.

    Great comment and I totally agree. The Egypt story currently unfolding is a case in point. I had to go to Wikipedia to get enough background before I could start reading the new stuff.

  6. Aurora

    This is a great approach. I especially like how, as a reader, you can easily choose which bits of the story to look into, depending on your interests and/or prior knowledge – you can catch up on the bits you’ve missed much easier than if you had to look for them in a feature-length text.
    Also, kudos Ed for thinking up so many good headlines!
    (Not sure I want to contemplate how long something like this takes to put together, though…)

  7. It took around 7 hours, including writing all the content (the long bit) and uploading it to Dipity (the short bit). Amusingly, I’ve already been forced to update it thanks to new research :-/

  8. Ken

    The 7 hours were well spent, Ed. Work like yours allows the public to see beyond the headline-of-the-day. Your timeline allows readers to understand the limitations of iPSCs while at the same time demonstrating how scientific research works to both discover those limitations and overcome them. Keep up the good (hard) work.

  9. I’m awed to think that my remarks did anything to inspire you along these lines, Ed. Thanks for daring to experiment.

    Beyond complimenting you on doing this timeline, though, I think all of us with markers in this game need to mull over what we can learn from your experience with doing it. Yes, it’s a first-rate piece of science journalism and a treat for readers. But as you’ve noted, it took a lot of time to research and produce, and it keeps screaming out to be updated. So maybe—maybe—we should conclude that a timeline like this is not something we should routinely try to emulate, at least for research topics that are “live” enough to demand ongoing, timely attention. Maybe those are better handled by some kind of wiki or, as you’ve suggested elsewhere, I think, by freelancers who aren’t chasing any one particular news peg or deadline.

    Don’t get me wrong: I don’t want to discourage people from doing what Ed has done here, or to imply in any way that Ed’s timeline is a failure. (If it were, I only wish my failures were this brilliant!) Rather, this was an experiment, and we should try to draw real lessons from it.

    Thanks again, Ed.

  10. Aurora

    @John Rennie: I see your point. There wouldn’t be enough hours even in Ed’s day to do this for every topic. But I guess for subjects that are often ‘in the news’ (or that a writer often touches on), it might also be seen as an investment – next time there’s an interesting development in the field of reprogrammed stem cells, Ed can add/link it to this timeline, and readers landing on that piece of news for the first time will have the treat of being able to access all this background information, and seeing things in context – and Ed will ‘only’ have had to write up that latest development.

    Also, Ken’s comment made me realize this sort of approach might also go some way towards showing people ‘science as process’, as we’re always saying we should…

  11. @Aurora: Yes, I think you’re right about all that. For journalists or journalistic publications that can justify doing something like the timeline as reusable resource, it may make very good sense. A writer who handles stem cells steadily as part of her “beat” would probably find this less burdensome than someone like Ed whose interests point everywhere.

    In the future, science journalism probably shouldn’t depend on any one default model so strongly as it has in the past. Think how much more exciting and informative science coverage can be!

    (And the point that Ken and you made about portraying the process of scientific discovery is also very good.)

  12. @Aurora and John – Yes, the hope is that as this topic grows, I will have a resource that I can continually reuse. Context-in-a-can, as it were. A couple of observations about the timeline idea:

    It’s got to serve the story. I left out a lot of potential stuff because the timeline, like any feature, isn’t meant to be a review of the field. It’s meant to tell a story, about science as a process. I think this topic was a good fit because it’s recent, it’s taking off and by looking at the timeline, you can see some emergent themes. The same research groups turn up. People are breaking down barriers while trying to optimise old techniques. There’s intense competition because many of the discoveries involve multiple groups publishing at the same time. These things come out when you look at the flow of the research rather than individual moments.

    When I was looking at old news stories to link to from the timeline, I was struck by how repetitive they are. All of them mention Yamanaka’s initial breakthrough (and yes, I think that word is justified), they talk about the wider policy implications, they have quotes from people saying that this new study is great yadda yadda. That’s all necessary, but I think that there are better ways of providing that context more richly than just hitting the same points in a few paragraphs for each new event.

    Ian Sample pointed out that the timeline only looks at research and not the broader policy events around these cells. I agree – I made that decision due to time constraints and if I had the chance, I’d put in more wider-world stuff to put the context in context. Also, nice little things like Science naming iPSCs as breakthrough of the year in 2008, and Yamanaka scooping prize after prize in recent years.

  13. Eskimo

    This is a valuable resource. Thanks for putting it together.
    I’m a university-based science writer who may have to tackle this area soon.

  14. Well done, Ed. Well done.

  15. Nathan Myers

    Robert Becker’s work in the ’70s, causing newt cells to de-differentiate to pluripotent stem cells, seems relevant, at least as an early missed opportunity. At the time, to mention any hint of biological sensitivity to small electric currents was career death. Maybe it still is.

  16. Ed, I love your site and your work. As a teacher of IB Biology (High School), your writing and articles are a great link to many of the topics we study. I’ve featured and promoted your blog many many times – including this post: http://sciencevideos.wordpress.com/2011/02/13/deeply-dipity-about-interactive-timelines/

    Thanks for your outstanding work. You are an inspiration!

  17. Hi Ed, great work done on stem cells and ipsc. Awesome work and thank for your great contribution and sharing. Will get my kids to use your site for reference.

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