September 12, 2002
Gene Profiling Reveals the Essence of 'Stemness'
An extensive genetic comparison of different types of stem cells and
terminally differentiated cells has revealed that hundreds of genes are
likely to be involved in shaping the characteristic properties of stem
cells. The studies show that embryonic, neural and hematopoietic
(blood-cell-forming) stem cells seem to share a common genetic program
that may be important for “stemness.”
These initial gene-profiling studies provide basic information about
the nature of stem cells that should aid long-term efforts to induce
stem cells to differentiate into cells that can be used to replace
tissue damaged by disease or trauma.
Howard Hughes Medical Institute investigator Douglas
A. Melton and Miguel Ramalho-Santos, Soonsang Yoon, Yumi Matsuzaki,
and Richard C. Mulligan at Harvard University described their findings
in an article in the September 12, 2002, issue of Science
Express, which provides rapid electronic publication of select
articles that will appear in the journal Science.
"There has been a great deal of excitement about the possibility
that adult stem cells are entirely plastic, that is, they are able to
become any tissue in the body," said Melton. "However, there have been
questions about whether such conclusions were correct. This led us to
wonder if we could figure out whether stem cells were, in fact, all
similar. And a related and critical scientific question is what genes
or genetic programs are important for stem cells to have their special
properties, or 'stemness.'"
To get at the answers to those questions, Melton and his colleagues
developed experiments to survey thousands of genes in different kinds
of stem cells and mature cells to determine if there are patterns of
gene activity that are distinct to stem cells.
"We were quite stringent in our criteria for which stem cells to
look at, choosing only those that everyone agreed were, indeed, stem
cells," said Melton. The scientists compared embryonic stem cells,
neural stem cells and hematopoietic stem cells — all from the mouse.
The researchers compared the patterns of gene activity in stem cells to
the gene activity exhibited in differentiated forms of these cells,
including adult brain cells and bone marrow cells. Their studies
identified stem-cell-specific genes that were distinct from those
involved in the normal growth of mature cells.
The researchers performed their surveys by first isolating the
messenger RNA (mRNA) from the cells. The presence of mRNA indicates
that genes are expressed. They then used commercial DNA arrays
containing some 12,000 genes to determine which genes were active in
the cells. Statistical analysis of the results offered insights into
the genetic programs used by stem cells, said Melton.
"First, we showed that there is a common genetic program among bona
fide stem cells," said Melton. "But we also found that these three
types of stem cells were not identical."
The researchers identified 216 "stemness" genes that are active in
each of the three types of stem cells that were studied. An important
sign that the analysis was valid, said Melton, was that the genes that
were enriched in the stem cells included those that are commonly used
as distinguishing markers for the cells.
Melton said the "stemness" genes they found fit into categories that
reflect the activities that stem cells must perform to self-renew and
differentiate. "For example, these stem cells seem to be highly
enriched in gene products involved in dealing with environmental
toxins, which enables them to cope with stress," said Melton. "Beyond
that, they seem to have upregulated genes for receptors that enable
them to receive signals from extracellular proteins. These might be
important for signaling the cells to start differentiating.”
While the scientists did find that the stem cells were genetically
distinct from one another, there were interesting differences between
stem cells and their differentiated counterparts. "One very nice
happenstance was the finding that embryonic stem cells and neural stem
cells are much more similar to each other than they are to their
differentiated counterparts," said Melton. "This fits with a 'default
model' we proposed, which is that the default fate of embryonic stem
cells is to become neurons."
Comparing stem cells with their differentiated counterparts revealed
genetic differences that will offer clues to developing techniques to
induce stem cells to differentiate into adult cells, said Melton.
"These findings provide a starting point to help people think how to
cause stem cells to differentiate down specific pathways, such as
becoming neurons that could rejuvenate brain tissue lost to
neurodegenerative diseases," he said.
According to Melton, the findings are likely to aid the search for
new types of stem cells. "For example, nobody has yet been able to
identify adult pancreatic stem cells — a central effort in our
laboratory," he said. "But now we know that if we're going to isolate
such cells, we should look for those that express many of these
'stemness' genes."
Another significant development, said Melton, was that the studies
revealed that the stem cells expressed large numbers of "expressed
sequence tags," which mark genes of unknown function. "For young
scientists, this finding is especially exciting because it shows that
these stem cells express a large number of genes that no one has a clue
what the gene products do," he said. What's more, said Melton, "it's
easily a decade's worth of work just to define the functions of the
genes that we have defined as characteristically active in these stem
cells."
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