“Not just the FACS, ma’am, not just the FACS.” These words could have come from investigators who have applied a new technique to assess gene expression in stem cells. FACS, or fluorescence-activated cell sorting, is used to remove cells from their native environment and purify them for analysis. Another, newer technique, however, may better reflect stem cells’ in vivo state.
The new technique, which labels newly transcribed RNA in vivo, has been applied by scientists based at Stanford University School of Medicine. According to these scientists, the in vivo approach reveals transcriptional nuances that cannot be captured by FACS, whether this isolation procedure is combined with ordinary culture techniques, or specialized techniques that temporarily arrest transcription.
The Stanford team, led by Thomas Rando, M.D., Ph.D., professor of neurology and neurological sciences, focused on muscle stem cells (MuSCs) in mice. When snug in the body, MuSCs tend to remain quiescent, actively maintaining a state that looks dormant, but isn’t. When extracted from the body, MuSCs tend to become slightly roused, even if they remain quiescent.
“Historically, we’ve thought of quiescence as an ‘everything off,’ or dormant, state,” said Dr. 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.
Stem Cells in Body Transcriptionally Distinct from Those Extracted for Study