Stuck in the past

Molecular remnants may limit potential of reprogrammed stem cells

Barbra Streisand probably wasn’t thinking about reprogrammed stem cells when she crooned “The Way We Were,” but it turns out that the cells also retain misty watercolor memories of their former selves.

By most standards, a cocktail of four proteins can reprogram skin or blood into stem cells nearly indistinguishable from those isolated from embryos (SN: 11/24/07, p. 323; SN Online, 8/24/08). But two new studies show that reprogrammed cells, known as induced pluripotent stem cells or iPS cells, hold on to molecular memories of their former identities.

The findings, published online July 19 in Nature and Nature Biotechnology, could be a blessing and a curse for researchers who hope to transform the reprogrammed cells into adult cell types for transplant into patients or for studying how certain genetic diseases influence cell development.   

All stem cells aren’t equally flexible, scientists have found. Stem cells made from skin cells called fibroblasts taken from the tip of a mouse’s tail aren’t very good at becoming blood cells, for instance, says George Daley, a stem cell biologist at Children’s Hospital Boston and Harvard University who coauthored the Nature paper. His group reprogrammed fibroblasts and bone marrow cells into stem cells that were pluripotent — able to make any type of cell in the body. But when the researchers tried to coax the reprogrammed cells to make blood cells, those that had originally come from bone marrow (where blood is made) had an easier time making blood cells. Reprogrammed fibroblasts were better at making bone cells.

Reprogramming is supposed to wipe a cell’s molecular slate clean, but clearly something was preventing the cells from being as flexible as the embryonic cells they are supposed to resemble. Looking closer, Daley’s group discovered that DNA in the reprogrammed cells still retained some of the molecular tags that block access to some genes in adult cells.

These chemical tags essentially cover DNA just as stickers on a textbook page cover some of the writing. The chemical stickers don’t change the genes themselves, but prevent proteins called transcription factors from reading the genes and turning them on.

In embryonic stem cells the DNA is as tag-free as a new textbook fresh from the printer, giving the cell nearly unlimited potential to become any other type of cell. As more stickers are added, more genes are turned off, and the stem cell becomes more and more limited in its options.

Reprogrammed cells, like used textbooks, still have traces of molecular stickers that the reprogramming process didn’t quite strip away, the researchers found.

“Even though we can get back to a pluripotent state, we haven’t erased all of the history of that cell,” Daley says.

Another team of researchers led by Konrad Hochedlinger of Massachusetts General Hospital in Boston and the Harvard Stem Cell Institute also found that gene activity and DNA tags in reprogrammed cells echoed those of the original cell type. But like memories of lost love, the molecular memories faded over time. Reprogrammed mouse cells held on to molecular memories when grown in a lab dish for two to three weeks, but after a month or two the tags had nearly been erased, the researchers report in Nature Biotechnology.

Daley’s group found that, unlike embryo-derived stem cells, reprogrammed fibroblasts contained 5,304 spots where at least some sticker residue still clung. Stem cells created by cloning, or nuclear transfer, had far fewer residual tags — only 229. Cloned stem cells also were more flexible than induced pluripotent stem cells in the type of cells they could become. Those results indicate that the cloning process — transferring the DNA-containing nucleus from a skin cell to an empty egg — more completely reprograms cells than adding a protein cocktail to adult cells does.

Cloning has not been successful with human cells, but the finding could indicate that eggs have some special way to strip molecular memories bare. Studying the way eggs reprogram cells could lead to better cocktails for making iPS cells, Daley suggests.

Molecular memories might also be useful, says David Scadden, a stem cell biologist at Massachusetts General Hospital and the Harvard Stem Cell Institute who was not involved in either study. Reprogrammed blood cells that still remember being blood could be easier to transform into different types of blood cells. But the old memories could also get in the way of making a former blood cell into a brain cell. Hochedlinger’s work suggests an easy way to get rid of the baggage, he says.

“These distinctions are real and important biologically, but practically, it remains to be seen,” Scadden says. “If just growing an iPS cell a little longer will get you there, that could be OK.”

Because the new studies were done in mice, their full implications for human stem cell research are unclear. Previous research has suggested that human embryonic stem cells are slightly less pluripotent than those from mice, says Louise Laurent, a genomics researcher at the University of California, San Diego. “One could imagine then that reprogramming human cells to full pluripotency could be a little more challenging,” she says.

Tina Hesman Saey is the senior staff writer and reports on molecular biology. She has a Ph.D. in molecular genetics from Washington University in St. Louis and a master’s degree in science journalism from Boston University.

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