Genomic Signal Processing May Provide Insights into Cancer Treatment

Dan Schonfeld, professor of electrical and computer engineering at the University of Illinois at Chicago (IL, USA), and a leading expert in image and video analysis, is studying gene expression and interactions in ways that are analogous to the workings of electrical or computer networks. He is project director and lead investigator of a four-year, US$1.2 million National Institutes of Health (Bethesda, MD, USA) grant.

"The idea is that DNA gives expression to proteins, and the amount and level of proteins dictates the state of the organism,” Dr. Schonfeld said.”If the expression level of one DNA goes up, it might reduce the expression level of another. There is this symbiotic relation between the genes in a network and the expression level of each of the proteins depends on one another.”

Dr. Schonfeld envisions this dynamic behavior leading to production of either good or bad proteins. He envisions that using the tools of mathematics and engineering will lead to a way to control this protein production. To achieve this, he and his colleagues model gene regulatory networks as a Markov chain--a statistical modeling tool frequently used in software development. They monitor the network over time and make slight changes or perturbations that may provide a level of control. "We've actually formed a new subarea of inverse perturbation theory where we say we know where we want to go, what is the smallest change in the network that we need to impose in order to guarantee that wherever we are, we're going to end up where we'd like to be,” he said.

Dr. Schonfeld reported that his objective is to take the results of mathematic analysis, convert them into a protocol for making small changes by putting specific chemicals into the cell resulting in a small change in the network, and then monitor its behavior over time to see whether it generates results predicted from the mathematic analysis.

Their hypothetic model will be tested on melanoma cells using RNA interference and plasmid molecules designed to regulate the expression levels of specific genes in a melanoma network. "We need to perturb and affect the influence of one gene on the other in order to move it in a better direction,” he said. "The successful outcome of the proposed approach to the treatment of malignant melanoma cells could serve as a foundation for development of intervention strategies in other cancer networks.”

Dr. Schonfeld noted that an interdisciplinary approach is "essential to an effective plan for developing novel treatment and clinical decision making in cancer research.”

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