Turning blood cells into brain stem cells wound back their epigenetic age, but slowly

Every cell in your body carries the same DNA, but it is decorated with small chemical tags, methyl groups, that help decide which genes are used. The pattern of these tags shifts with age in such a regular way that researchers can read it like a clock. An epigenetic clock takes a sample of DNA and estimates how old the cells are; in blood from healthy people, the estimate usually lands close to the person’s real age.

For about two decades it has been possible to turn adult cells back into induced pluripotent stem cells (iPS cells), cells that behave like those of an early embryo and can become any tissue. This trick, called reprogramming, also wipes the epigenetic clock back to an embryo-like age. A second route, direct conversion, skips the embryo-like stage and turns one cell type straight into another. Some directly converted cells keep the age of the cells they came from, which is useful for studying diseases of old age. A team at the University of Bonn had earlier found that one kind of direct conversion, from blood cells into neural stem cells (immature cells that can become nerve cells and their support cells), seemed to make the cells younger. In this study they asked how, and how fast.

What they did

The team took blood from 15 donors, from newborns to a 101-year-old. From each blood sample they grew erythroid progenitors, young cells on their way to becoming red blood cells. Then they switched on two genes, SOX2 and cMYC, carried in by a virus that the cells were later cleared of. Within about two weeks the cells looked and behaved like neural stem cells. For comparison, they also made neural stem cells from the same blood through the classic iPS route.

They then measured the cells’ epigenetic age at several points during the conversion, read out which genes were active, and checked for common signs of aged cells: changes in the scaffolding around the nucleus, DNA damage, faulty recycling of cell parts (autophagy) and genes linked to cells that have permanently stopped dividing.

What they found

• A large drop in epigenetic age. Soon after conversion, the new neural stem cells had an epigenetic age of on average about 13% of the donor’s real age. After much longer growth in the dish, it was about 5%. The cells made via the iPS route were reset to an embryo-like age, as expected.
• It was slow. In cells from three donors aged 50 to 101, the clock kept falling for weeks. It took about 50 days of conversion until most of the age-related tags were reset, more than twice as long as the roughly 20-day reset during iPS reprogramming.
• It didn’t depend on cell division. One idea was that the cells simply “diluted out” their old tags by dividing many times. To test this, the team slowed division with two chemicals (glycerol and thymidine) in cells from three donors aged 81 to 86, or pushed the cells to become non-dividing nerve cells. In both experiments the epigenetic age fell about as much as in normally dividing cells.
• The new identity also took weeks to settle. The cells looked like neural stem cells within about two weeks, but their gene activity and methylation kept shifting toward a mature neural stem cell pattern long after that.
• No obvious signs of old age. In cell lines from donors aged 0, 87 and 101, the team found no clear differences in these markers of aged cells between the converted cells and the iPS-made ones. Differences in gene activity between young and old donors, large in the original blood cells, almost disappeared after conversion.

What to keep in mind

• A clock is not the whole story. The authors stress that epigenetic age is only a stand-in for biological age and “does certainly not capture the full picture”, especially how well cells work.
• Changing cell type may fool the clock. The researchers say they cannot rule out that switching from blood to neural cells itself shifts the tags the clock reads. There are no truly aged neural stem cells to compare with, and the clock is known to read lower in brain tissue than in blood, which could make the drop look bigger than it is.
• Oxygen changed during the experiment. Cells grew at low oxygen for the first five weeks and at normal air oxygen later; the authors note this could also have contributed.
• Small groups. The time-course and division experiments used cells from three donors each, and the youngest gene-activity group had only three newborns.
• Cells in a dish. Nothing here was done in people or animals, and it is not a way to make a body younger.

Why it matters

Scientists would like to know what actually resets the aging marks on DNA, because that might one day point to ways of slowing or reversing aging in tissues. With iPS reprogramming the reset is fast and tied up with the cell becoming embryo-like, which makes the two hard to tell apart. Here the reset was spread over weeks and continued even when cells stopped dividing. The authors suggest this slow process could serve as a model for studying how cells lose their age marks, and as an alternative to “partial reprogramming”, where the iPS process is stopped early.