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:

• Shutting off a single gene could improve fertility by activating dormant egg-producing cells
• Crickets forewarn their offspring about predators before they’re born
• Alcohol tastes and smells better to those who get their first sips in the womb
• Child abuse permanently modifies stress genes in brains of suicide victims
• Obesity amplifies across generations; can folate-rich diets stop it?

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