As many of us, you are likely an avid google user, and know your way around the web. Perhaps you are even an expert web crawler, and can find just about anything on the web. But can you find new ways to help cancer patients? Well, a group of German researchers did just that.
Christof Winter, from Dresden University of Technology, led a team of researchers, which included Helmut Friess from Technische Universität München, that modified Google's PageRank algorithm to rank about 20,000 proteins based on their genetic importance in the progression of pancreatic cancer. In their study, published on May 17 in PLoS Computational Biology, they found seven proteins that can be used to determine the aggressiveness of a patient's tumor. This information can then help doctors decide whether to use chemotherapy or not.
The proteins in question are called biomarkers and are produced by cancer cells, so doctors use them to detect early stages of cancer. However, biomarkers are usually hard and time consuming to find. But now, with this novel approach, finding new biomarkers can potentially be as easy as searching your favorite website. OK maybe not that easy, but it certainly speeds things up.
The new strategy relies on Google's search approach that takes into account not only the content of a webpage but also how the webpage is connected to other websites via hyperlinks. Using this as a model, the research team designed a search approach that takes into account not only the composition of a protein but also how they are connected within a cell to other proteins through physical and regulatory interactions.
"Once we added the network information in our analysis, our biomarkers became more reproducible," said Christof Winter.
This new technique promises to speed up the process of finding useful biomarkers for cancer and other diseases. There is, of course, a lot of work left to do, such as validating these biomarkers on clinical trials, but this work represents a positive step forward. Winter's team is now working with the Dresden-based biotech company RESprotect, which performs clinical trials on a pancreas cancer drug, to test their results.
The work was a cooperation between the bioinformatics group of Prof. Dr. Michael Schroeder and the medical groups of Dr. Christian Pilarsky and Prof. Robert Grützmann.