Report on EU–USA Workshop: How Systems Biology Can Advance Cancer Research (27 October 2008)
Authors: Aebersold Ruedi , Auffray Charles , Baney Erin , Barillot Emmanuel , Brazma Alvis , Brett Catherine , Brunak Søren , Butte Atul , Califano Andrea , Celis Julio , Čufer Tanja , Ferrell James , Galas David , Gallahan Daniel , Gatenby Robert , Goldbeter Albert , Hace Nataša , Henney Adriano , Hood Lee , Iyengar Ravi , Jackson Vicky , Kallioniemi Ollie , Klingmüller Ursula , Kolar Patrik , Kolch Walter , Kyriakopoulou Christina , Laplace Frank , Lehrach Hans , Marcus Frederick , Matrisian Lynn , Nolan Garry , Pelkmans Lucas , Potti Anil , Sander Chris , Seljak Marija , Singer Dinah , Sorger Peter , Stunnenberg Hendrik , Superti‐Furga Giulio , Uhlen Mathias , Vidal Marc , Weinstein John , Wigle Dennis , Williams Michael , Wolkenhauer Olaf , Zhivotovsky Boris , Zinovyev Andrei , Zupan Blaž 
Published: December 2008

The main conclusion is that systems biology approaches can indeed advance cancer research, having already proved successful in a very wide variety of cancer‐related areas, and are likely to prove superior to many current research strategies. Major points include:

Systems biology and computational approaches can make important contributions to research and development in key clinical aspects of cancer and of cancer treatment, and should be developed for understanding and application to diagnosis, biomarkers, cancer progression, drug development and treatment strategies.

Development of new measurement technologies is central to successful systems approaches, and should be strongly encouraged. The systems view of disease combined with these new technologies and novel computational tools will over the next 5–20years lead to medicine that is predictive, personalized, preventive and participatory (P4 medicine).

Major initiatives are in progress to gather extremely wide ranges of data for both somatic and germ‐line genetic variations, as well as gene, transcript, protein and metabolite expression profiles that are cancer‐relevant. Electronic databases and repositories play a central role to store and analyze these data. These resources need to be developed and sustained.

Understanding cellular pathways is crucial in cancer research, and these pathways need to be considered in the context of the progression of cancer at various stages. At all stages of cancer progression, major areas require modelling via systems and developmental biology methods including immune system reactions, angiogenesis and tumour progression.

A number of mathematical models of an analytical or computational nature have been developed that can give detailed insights into the dynamics of cancer‐relevant systems. These models should be further integrated across multiple levels of biological organization in conjunction with analysis of laboratory and clinical data.

Biomarkers represent major tools in determining the presence of cancer, its progression and the responses to treatments. There is a need for sets of high‐quality annotated clinical samples, enabling comparisons across different diseases and the quantitative simulation of major pathways leading to biomarker development and analysis of drug effects.

Education is recognized as a key component in the success of any systems biology programme, especially for applications to cancer research. It is recognized that a balance needs to be found between the need to be interdisciplinary and the necessity of having extensive specialist knowledge in particular areas.

A proposal from this workshop is to explore one or more types of cancer over the full scale of their progression, for example glioblastoma or colon cancer. Such an exemplar project would require all the experimental and computational tools available for the generation and analysis of quantitative data over the entire hierarchy of biological information. These tools and approaches could be mobilized to understand, detect and treat cancerous processes and establish methods applicable across a wide range of cancers.