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Winner of Crowd-Sourced Breast Cancer Prognosis Challenge Offers Hope for Improved Diagnosis and Prognosis in All Cancers

News — New York, NY鈥擜pril 17, 2013鈥擟olumbia Engineering researchers, led by Dimitris Anastassiou, Charles Batchelor Professor in Electrical Engineering and member of the Columbia Initiative in Systems Biology, have developed a new computational model that is highly predictive of breast cancer survival. The team, who won the Sage Bionetworks/DREAM Breast Cancer Prognosis Challenge for this work, published their results鈥�"Development of a Prognostic Model for Breast Cancer Survival in an Open Challenge Environment")鈥攊n the April 17 issue of Science Translational Medicine.

In earlier work, Anastassiou and his team had identified what he calls 鈥渁ttractor metagenes,鈥� gene signatures that are present in nearly identical form in many cancer types. Working with his PhD students Wei-Yi Cheng and Tai-Hsien Ou Yang, he took these signatures and tested them in the Sage Bionetworks/DREAM Breast Cancer Prognosis Challenge, a crowd-sourced effort for accurate breast cancer prognosis using molecular and clinical data. The team developed a prognostic model that showed that these signatures of cancer, when properly combined, were strong predictors for breast cancer survival.

鈥淭hese signatures manifest themselves in specific genes that are turned on together in the tissues of some patients in many different cancer types,鈥� explains Anastassiou. 鈥淎nd if these general cancer signatures are useful in breast cancer, as we proved in this Challenge, then why not in other types of cancer as well? I think that the most significant鈥攁nd exciting鈥攊mplication of our work is the hope that these signatures can be used for improved diagnostic, prognostic, and eventually, therapeutic products, applicable to multiple cancers.鈥�

Currently there are already widely used biomarker products that look at specific genes in biopsies of cancer patients, so that doctors can decide if particular treatments are appropriate. 鈥淪ome of these genes are related to those in our signatures,鈥� he says, 鈥渟o it鈥檚 worth finding out if replacing such genes with our precise 鈥榩an-cancer鈥� signatures will improve the accuracy of these products.鈥�

Anastassiou, who works in systems biology, an emergent interdisciplinary field that focuses on interactions within biological systems, hopes to collaborate with medical researchers studying the biological mechanisms behind these cancer signatures. He thinks of these signatures as 鈥渂ioinformatic hallmarks of cancer,鈥� a term first coined by Jessica Kandel, R. Peter Altman Professor of Surgery and Pediatrics in Columbia鈥檚 Institute for Cancer Genetics, with whom he collaborates.

鈥淭he hallmarks of cancer,鈥� he explains, 鈥渁re unifying biological capabilities present in all cancers, as described in some seminal papers. We think that we have now reached the point where systems biology can also identify such hallmarks.鈥�

"We are thrilled that Anastassiou's innovative metagenes approach won the Challenge and is getting the visibility it rightly deserves,鈥� says Stephen H. Friend, president and co-founder, Sage Bionetworks. 鈥淎nastassiou's team demonstrated gumption and a thoughtful understanding of what was needed to develop a 鈥榞eneralizable鈥� model that achieved the top CCI score against the newly generated Challenge validation data set."

Anastassiou and his team found the Sage Bionetworks/DREAM Challenge a very productive way to focus on a specific research task. He said that the Challenge provided a vibrant research environment where numerous participants were openly submitting their models and had access to others鈥� models as they were developed. The teams were also encouraged to incorporate the other models into their own. Three- hundred-fifty four participants from more than 35 countries registered for the Challenge and submitted more than 1700 models.

The study was funded by the University鈥檚 allocation for inventor鈥檚 research 鈥攑atents from what Anastassiou calls his 鈥減revious lifetime,鈥� when he was doing research on a totally different topic: digital television. His patents are now used in the international standards for all forms of DVDs including Blu-ray HDTV discs and digital television broadcasting.

Columbia EngineeringColumbia University's Fu Foundation School of Engineering and Applied Science, founded in 1864, offers programs in nine departments to both undergraduate and graduate students. With facilities specifically designed and equipped to meet the laboratory and research needs of faculty and students, Columbia Engineering is home to NSF-NIH funded centers in genomic science, molecular nanostructures, materials science, and energy, as well as one of the world鈥檚 leading programs in financial engineering. These interdisciplinary centers are leading the way in their respective fields while individual groups of engineers and scientists collaborate to solve some of modern society鈥檚 more difficult challenges.

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