Reprogrammed stem cells carry a memory of their past identities

By Ed Yong | July 19, 2010 1:00 pm

Embryonic-stem-cells

Imagine trying to rewind the clock and start your life anew, perhaps by moving to a new country or starting a new career. You would still be constrained by your past experiences and your existing biases, skills and knowledge. History is difficult to shake off, and lost potential is not easily regained. This is a lesson that applies not just to our life choices, but to stem cell research too.

Over the last four years, scientists have made great advances in reprogramming specialised adult cells into stem-like ones, giving them the potential to produce any of the various cells in the human body. It’s the equivalent of erasing a person’s past and having them start life again.

But a large group of American scientists led by Kitai Kim have found a big catch. Working in mice, they showed that these reprogrammed cells, formally known as “induced pluripotent stem cells” or iPSCs, still retain a memory of their past specialities. A blood cell, for example, can be reverted back into a stem cell, but it carries a record of its history that constrains its future. It would be easier to turn this converted stem cell back into a blood cell than, say, a brain cell.

The history of iPSCs is written in molecular marks that annotate its DNA. These ‘epigenetic’ changes can alter the way a gene behaves even though its DNA sequence is still the same. It’s the equivalent of sticking Post-It notes in a book to tell a reader which parts to read or ignore, without actually editing the underlying text. Epigenetic marks separate different types of cells from one another, influencing which genes are switched on and which are inactivated. And according to Kim, they’re not easy to remove, even when the cell has apparently been reprogrammed into a stem-like state.

But reprogramming adult cells is just one of two ways of making stem cells tailored to a person’s genetic make-up. The other is known as nuclear transfer. It involves transplanting a nucleus (and the DNA inside it) from one person’s cell into an empty egg. The egg becomes an embryo, which yields stem cells containing the donor’s genome. Kim has found that these cells (known as nuclear transfer embryonic stem cells or ntESCs) are much more like genuine embryonic stem cells than the reprogrammed iPSCs. They’re ‘stemmier’, for lack of a better word.

Kim’s research tells us that creating stem cells through nuclear transfer is not a technique that’s easily disregarded. It certainly steers into trickier ethical territory since harvesting ntESCs destroys the embryo. And it is still trailing behind technically; so far, it has only been successfully done in monkeys and other non-human mammals, and it has been mired in scientific scandal.

Meanwhile, work on iPSCs has raced ahead. The starting pistol was fired in 2006, when a group of Japanese scientists first showed that it was possible to create these cells in mice. The race intensified in 2007, when two research groups independently managed to do the same for human cells. In 2009, mouse iPSCs were used to produce live animals, passing the ultimate test of their stem-like status.  Various groups have made the technique more efficient, sped it up, found ways of sorting out the most promising cells, and changed the details so that it doesn’t use viruses (or uses only viruses).

But all along, scientists have realised that there are subtle differences between iPSCs and genuine embryonic stem cells and, indeed, between iPSCs produced from different tissues. For a start, some types of cell are easier to reprogram than others – skin, stomach or liver cells, for example, are easier to convert than cells from connective tissues. And the older or more specialised the cells are, the harder the task becomes.

Kim’s team found that once the cells are converted, there are further issues. They found it easier to produce blood cells from iPSCs that themselves came from blood cells, rather than those derived from connective tissue or brain cells. By contrast, iPSCs made from connective tissue were the better choice for producing bone cells.

Kim thinks that this is because the widely used reprogramming techniques fail to strip away a cell’s epigenetic markers. He focused on one such marker – the presence of methyl groups on DNA, which typically serve to switch off genes, like Post-it notes that say “Ignore this”. Kim found that the methylation patterns of iPSCs are very different depending on the cells they came from. Those that come from brain or connective cells, for example, have methyl groups at places that are needed to produce blood cells, and vice versa. Even iPSCs that come from slightly different lineages of blood cells carry distinctive patterns of methyl marks.

In all of these tests, ntESCs (those produced by nuclear transfer) were far more similar to genuine embryonic stem cells than any of the iPSCs. Their patterns of methylation were a closer match and they were easier to convert into any type of adult cell. This certainly makes sense – when the nucleus is transferred into an empty shell, it its DNA is rapidly and actively stripped of its methyl groups. Its history is erased with far greater efficiency than the reprogrammed iPSCs.

This seems like a clear win for the nuclear transfer method, but Kim thinks there are ways of improving the reprogramming technique to get around this problem. For a start, you can efficiently convert iPSCs derived from one type of cell into another via another round of programming and reprogramming. For example, you could reprogram a brain cell into an iPSC, convert it into a blood cell, reprogram it back into an iPSC again, and get a stock that’s very good at creating blood cells. This does, however, seem like a very roundabout strategy – why not start with blood cells in the first place?

A better solution is to try and strip away the epigenetic marks more directly. Some chemicals can do that, and after treating the iPSCs with such substances for a few days, Kim improved their ability to produce tissues regardless of their origins.

Another group led by Jose Polo found the same epigenetic problem, but they discovered a simpler solution – grow the cells for a long time. When cells are grown in culture, they need to be frequently ‘passaged’. That is, they need to be split among fresh containers so that they don’t run out of room and nutrients. Polo found that continuous passaging solves the epigenetic problem, reprogramming the iPSCs into a far more stem-like state, free from the constraints of their origins. It seems that when iPSCs are created, their epigenetic marks are eventually removed even though the process is gradual and slow.

And after all, the epigenetic memory of reprogrammed cells isn’t necessarily a bad thing. If you want to produce blood in bulk, why not start with iPSCs that are very good at making blood cells but not other types? Indeed, it’s still very difficult to nudge stem cells into becoming specific tissues, and starting off with cells that naturally gravitate towards certain fates could well be a blessing in disguise.

Reference: Nature http://dx.doi.org/10.1038/nature09342 and Nature Biotechnology http://dx.doi.org/10.1038/nbt1667

More on epigenetics:

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Comments (13)

  1. NewEnglandBob

    Life gets “curiouser and curiouser” as we look through the looking glass.

  2. It does get curiouser. One wonders what the implications are for all other “transplants:” blood transfusions, organ donations, bone donations… Clearly we are still in our infancy in understanding how it all works.

  3. Nathan Myers

    I remember how astounded I was in 2002 to learn (1) about DNA methylation and (2) that biologists had known of it for decades and ignored it. It’s still hard to decide which is the more astounding.

  4. “It’s the equivalent of sticking Post-It notes in a book to tell a reader which parts to read or ignore, without actually editing the underlying text”
    I have to say you have a gift for clear metaphors. Or were the authors of the paper to think of that? In any case, clearness 5/5

  5. Heh. Thanks. Post-its are mine – I use it in virtually everything I write on epigenetics. Can’t claim original credit for it though. I expect that lots of writers have used the same analogy and I can’t remember if I heard it from somewhere else first.

  6. Nathan Myers

    I just found out that Richard Dawkins thinks epigenetics is a fad, “a modish buzz-word now enjoying its fifteen minutes of fame” (“The Greatest Show on Earth”, 2009, p. 216). This serves mainly to confirm my prior opinion about him, which had begun to thaw.

  7. @ Nathan Myers:
    “Everyone makes mistakes. That’s why they put erasers on pencils” (Lenny Leonard, The Simpsons)
    Remember, Darwin himself thought that Lamarckian inheritance played a role in evolution (and I am referring to strict, “giraffe stretching necks” Lamarckism, not “neo-Lamarckism” based on epigenetics)

  8. Jeremy

    Just another reason you never invest all authority in one person. No one person is ever always right.

    Am I the only one who first heard ‘Epigenetics’ and thought someone was referring to the DNA of a bee?

  9. amphiox

    And I think Dawkins was referring to what he felt was the excessive and inaccurate use of the word “epigenetics” as opposed to the specific science of the subject itself.

  10. Aurora

    Like Walter S. Andriuzzi above, I too was immediately struck by the post-it metaphor – hope you don’t mind if I ‘steal’ it for future use… (I hadn’t heard/seen it from anyone else, but this could be because I’ve only recently had to start writing about genetics, and so have only recently started noticing such things…)

  11. rick

    There’s also a third way beyond transcription-factor transduction (making iPSC’s) and nuclear transfer called cell fusion.

    Anyone interested at all in this kind of thing, I urge to read

    http://www.nature.com/nature/journal/v465/n7299/abs/nature09229.html

    It’s imminently readable to nonexperts (I’m in cs and enjoyed it) and is a nice review of current ways of getting to pluripotency from differentiated cells.

  12. Kostas Bachas

    What I find astonishing is the way that human imagination and intuition use “trial and error” concepts to come up with solutions that -especially in the case of “roundabout” methods- have no initial logic. Ask an IT technician and they will describe similar thinking patterns when trying to clear a file from bugs or unwanted stored info. Is this a hint that programming seems to have very similar concepts whether in DNA or man-made computer memories?

  13. Your article reminded me of the article “Epigenetic stability” by Erwin Schrodinger et a. In fact, acetylation and methylation status count as to what an extent a DNA will be read (or written). Anyhow, I hope that scientists will surely circumvent this soon.

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