February 01, 1996
So Many Genes, So Little Time
In order to determine which genes a yeast spore inherits from its two parents, Patrick Brown's research team created a "microarray" of yeast DNA. Each of the 240 spots in this array contains DNA from a different gene from Chromosome V of baker's yeast.
Researchers with the Human Genome Project and various commercial
ventures are racing to sequence the genomes of organisms in an effort
to catalog all their genes. But genes and partial gene sequences are
being found at a rate far faster than anyone can decipher their
function.
Two groups of Hughes researchers have been attacking that bottleneck
with automated programs designed to shed light on the function of newly
found genes and the expression patterns of known genes.
Patrick O. Brown, a
Hughes investigator at Stanford University School of Medicine, has
developed a technique that can tell him instantaneously which of the
many thousands of genes present in a cell are switched on at a given
moment in time.
Bert
Vogelstein, a Hughes investigator at the Johns Hopkins Oncology
Center, in collaboration with Kenneth W. Kinzler, also of the Johns
Hopkins Oncology Center, has devised a "genetic bar code" to identify
unknown genes and measure gene expression.
Brown's technique, which was published in the October 20, 1995 issue
of Science, will allow researchers to gather important data
about a gene's biology much more rapidly than was previously possible.
"Researchers have done a great job of determining the sequences of a
huge number of our genes," Brown said. "The problem is, we have the
sequences of so many genes socked away in our data bases, but we don't
know what they're there for or what the body wants to use them
for."
Using the plant Arabidopsis thaliana (mouse-ear cress) that
has become the model plant for genetic studies, Brown's group has
applied the new technique to compare the levels of expression of
certain genes in root tissues with those in leaf tissues. Their results
have been found to match those obtained using the traditional northern
blot method for measuring gene expression. Northern blots of a single
gene may take hours or days. Using Brown's new method, a single
scientist could gather expression data on more than 1,000 genes in the
same time.
The new method hinges upon the use of a speedy robot designed to
imprint small glass slides with arrays of up to 20,000 precisely placed
microscopic DNA samples. Each sample in the array carries a known DNA
sequence corresponding to a particular gene.
After washing the array with a fluorescently labeled mixture
prepared from the messenger RNA (mRNA) of the cells under study, the
scientists can tell which genes are being expressed in the cells and at
what level. "The brighter a dot glows, the higher that gene's level of
expression," Brown said.
Brown's team is now collaborating with scientists from the NIH to
use the technique to study nearly 1,000 genes whose expression patterns
are thought to influence tumor development.
Brown is optimistic that his microarray technique will prove
beneficial to clinicians. Detecting gene expression changes in white
blood cells, for example, might provide an important new window on the
disease defenses of the immune system. "White blood cells circulate
through our bodies with little 'antennas' out, asking, 'How's
everything going out there? Should we be kicking into gear to deal with
a potentially threatening situation?' They have a sensing system that
allows them to react to pathological conditions — and what they sense
is reflected in gene expression," Brown said.
"If we can figure out how these changes in gene expression reflect
the body's condition, we could use white blood cells as little spies
wandering through the body and reporting back to us," he said.
A different variation of "genes as reporters" was detailed in the
same issue of Science by Bert Vogelstein and his colleagues at
the Johns Hopkins Oncology Center. Their approach, analogous to a
genetic bar code, is called SAGE (serial analysis of gene expression).
Vogelstein and Kinzler have assigned a simple nine base pair sequence
to each gene, which can be thought of as being that gene's "bar code."
Powerful computers and gene sequencers are employed to read the bar
codes in tissue samples.
To demonstrate the technology, the scientists have tested SAGE on
pancreas and liver tissue. Once perfected, it took only a few days to
obtain thousands of bar codes and identifiy genes that were
specifically expressed in each of the two tissues. In addition to
detecting expressed genes of known function, the researchers discovered
several new genes which had not been observed previously.
Vogelstein and Kinzler plan to begin using the new technique to
compare gene expression patterns in colon cancer cells to those of
normal colon cells in an attempt to identify genes that are expressed
only in cancer cells. If successful, this approach may lead to better
forms of cancer therapy and better diagnostic tests for colon
cancer.
Image: Patrick O. Brown
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