A team in Australia thinks it may have found the differences between “cancer systems and normal systems”, to help identify treatment targets that would not have otherwise been considered.
Systems are not usually studied; it’s more a question of genes and how they express themselves. But researchers now think even more could be learned about cancer by studying the ways in which genes act in systems.
By using computational systems biology, the University of Queensland (UK) researchers decided to explore the networks of gene regulation, Jennifer Foreshew writes in The Australian.
Led by Mark Ragan from UQ's Institute for Molecular Bioscience (IMB), the team is using computers to untangle the intricacies of cancer biology to detect new targets for treatment. They studied ovarian cancer data.
Professor Ragan, who leads the genomics and computational biology division, said cancer was known as a "disease of systems".
“We are trying to reconstruct, reverse-engineer these systems based on gene-expression data," he told Foreshew. "Then find how our models indicate that there could be differences between cancer systems and normal systems."
All cancers occur due to abnormalities in DNA sequence, according to the Cancer Genome Project at the Sanger Institute, part of UQ. That’s why all cancer research begins there. And most of us are terrified, as was I, when I heard that dreaded word, “malignant” seven years ago, and then again, five years later.
A total of 1,638,910 new cancer cases and 577,190 deaths from cancer are predicted to occur in the United States in 2012.
The IMB team analyzed nine different computational methods, then applied the method judged most effective to real ovarian cancer data. The most exciting part of the research, Foreshew writes, was the team’s evaluation “demonstrated it was possible in some cases to use computational methods to gain insights into cancer biology.”
"Computational methods let us look very broadly at big new data sets that are coming out from new DNA technologies," Professor Ragan said. "We can look more broadly at all or a very big part of the data that these new technologies make available."
ScienceDaily reports that “the idea of using DNA molecules -- the material genes are made of -- to perform computations is not new; scientists have been working on it for over a decade.” The article notes that DNA is such a powerful element because it has the ability “to store much more data than conventional silicon-based computers, as well as the potential to perform calculations in a biological environment -- inside a live cell, for example.”
There is still much work to be done, however the technology is limited, the team noted. Professor Ragan told Foreshew that the challenge lies in determining the accuracy of such methods. "Although we were quite happy with the results in this case, it remains to be seen how more generally applicable this or similar methods will be in other data sets,” he said in the story. "These approaches are helping us to ask different questions of greater generality about systems or pathways rather than just genes."
Edited by Brooke Neuman