Stem cells in the body have a significantly different gene-expression profile than do the same cells when they're isolated in a lab dish, according to Stanford University researchers.
Research published yesterday in Cell Reports suggests that any conclusions about stem cell function based on studies of isolated stem cells may now need to be reconsidered in light of the fact that the cells' biology changes during isolation. In particular, the researchers found that levels of certain RNA molecules increased when stem cells were isolated, whereas the levels of many other RNA molecules decreased.
"The cells in the animal clearly differ from those that are removed for study," said senior author Thomas Rando, M.D., Ph.D., professor of neurology and neurological sciences at Stanford University School of Medicine. "It's likely that some of these notable differences will skew our view of what the quiescent state entails for many types of adult stem cells. We and other researchers will need to rethink about how to profile stem cells in a way that accurately reflects their in vivo state."
Previous studies of stem cell gene expression have been largely based on cells that had been removed from their native environment within an animal and purified through fluorescence-activated cell sorting, or FACS. Researchers then studied the function, biology and RNA content of the isolated cells.
In contrast, Rando and his colleagues used a new technology that allowed them to specifically label RNA molecules at the moment of their birth in muscle stem cells in mice. These molecules could then be rapidly extracted for study, in contrast to the several hours it can take to isolate whole stem cells from an animal. This approach allowed them to distinguish the patterns of gene expression in vivo from those observed in stem cells that have been isolated before analysis of their RNA.
The results confirmed what previous research in Rando's laboratory has shown: Despite their seemingly sleepy lifestyle, muscle stem cells are actually hotbeds of activity concealed by a tranquil outer membrane. The researchers were particularly surprised to learn that many of the RNAs made by the muscle stem cells in vivo are either degraded before they are made into proteins, or they are made into proteins that are then rapidly.
"Historically, we've thought of quiescence as an 'everything off,' or dormant, state," said Rando. "But our work has shown that the reality is quite different. Not only have we been missing transcripts that are present in vivo, but we are also puzzled as to why so many transcripts that are made in vivo are not made into proteins. It's possible that this is one way the cells stay ready to undergo a rapid transformation, either by blocking degradation of RNA or proteins or by swiftly initiating translation of already existing RNA transcripts."