Gene subnetworks predict cancer spread

December 15, 2008

The metastasis or spread of breast cancer to other tissues in the body can be predicted more accurately by examining subnetworks of gene expression patterns in a patient's tumor, than by conventional gene expression microarrays, according to a presentation at the American Society for Cell Biology (ASCB) 48th Annual Meeting, Dec. 13-17, 2008 in San Francisco.

The subnetworks provide new prognostic markers representing sets of co-functional genes, say scientists at the University of California at San Diego (UCSD), Trey Ideker and Han-Yu Chuang, who worked with Eunjung Lee and Doehaon Lee of the Korean Advanced Institute of Science and Technology in Daejeon, South Korea.

The U.S.-Korea researchers identified the subnetworks by using bioinformatic algorithms to crunch through mountains of gene expression profiles from large cohorts of women with breast cancer.

The data represented women with breast cancer metastasis as well as patients whose tumors had not spread.

The gene expression profiles were then mapped to the extensive networks of signaling pathways and protein complexes in human cells that had been revealed in previous studies.

Searching the data, the researchers identified subnetworks in which aggregate gene expression patterns distinguished one patient group from another.

They also uncovered many genes associated with breast cancer that had not been identified by previous gene microarray profiles.

Thanks to rapid microarray technology, cancers can now be classified according to their gene expression, or activity patterns.

However, disease classification by gene expression is imprecise because cells taken from a single tumor sample often are heterogeneous; genes switched on in cells from one part of the tumor may not be active elsewhere in the tumor.

In addition, the expression profiles from a range of patients with the "same" type and grade of tumor can differ significantly.

Ideker and Chuang's approach may change diagnostics so that a patient's diagnosis could go beyond, for example, estrogen responsive breast cancer to a particular subtype of estrogen responsive breast cancer with poor or good prognosis.

The U.S.-Korean researchers are now extending their new integrated analysis to other cancers including leukemia, prostate cancer and lung cancer.

They are identifying "condition-responsive" genes within signaling and transcriptional pathways that could be used as a measure of activation levels and could provide another useful tool for diagnosis and prognosis, they say.

Source: American Society for Cell Biology

Explore further: Keeping cells in good shape

Related Stories

Keeping cells in good shape

September 28, 2015

People often talk about how important it is to stay in shape, something humans usually can accomplish with exercise and a healthy diet, and other habits. But chances are, few of us ever think about the shape of our individual ...

Scientists create rice variety with high folate stability

September 22, 2015

Researchers from Ghent University succeeded in stabilizing folates in biofortified rice in order to prevent their degradation upon long term storage. They used two strategies: by linking folates with folate binding proteins ...

Student tackles labeling RNA without genetic modification

September 21, 2015

Overcoming limitations of super-resolution microscopy to optimize imaging of RNA in living cells is a key motivation for physics graduate student Takuma Inoue, who works in the lab of MIT assistant professor of physics Ibrahim ...

MicroRNAs are digested, not absorbed

September 8, 2015

There has been a lot of controversy in recent years over the issue of whether exogenous microRNA molecules can be absorbed from food and even have a physiological effect. A new study by ETH professor Markus Stoffel using ...

Recommended for you

How the finch changes its tune

August 3, 2015

Like top musicians, songbirds train from a young age to weed out errors and trim variability from their songs, ultimately becoming consistent and reliable performers. But as with human musicians, even the best are not machines. ...

Machine Translates Thoughts into Speech in Real Time

December 21, 2009

( -- By implanting an electrode into the brain of a person with locked-in syndrome, scientists have demonstrated how to wirelessly transmit neural signals to a speech synthesizer. The "thought-to-speech" process ...


Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.