1. Predicting ligand-dependent tumors from multi-dimensional signaling features
- Author
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Jens Timmer, Violette Paragas, Mark Sevecka, John E. Allen, Emily Pace, Joerg Stelling, Gavin MacBeath, Helge Hass, Kristina Masson, Birgit Schoeberl, Sibylle Wohlgemuth, and Andreas Raue
- Subjects
0301 basic medicine ,medicine.medical_treatment ,Receptor expression ,Systems biology ,Biology ,Bioinformatics ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,0302 clinical medicine ,In vivo ,Drug Discovery ,medicine ,Receptor ,lcsh:QH301-705.5 ,Tumor microenvironment ,Oncogene ,Applied Mathematics ,Growth factor ,Ligand (biochemistry) ,Computer Science Applications ,030104 developmental biology ,lcsh:Biology (General) ,Cell culture ,030220 oncology & carcinogenesis ,Modeling and Simulation ,Cancer research - Abstract
Targeted therapies have shown significant patient benefit in about 5–10% of solid tumors that are addicted to a single oncogene. Here, we explore the idea of ligand addiction as a driver of tumor growth. High ligand levels in tumors have been shown to be associated with impaired patient survival, but targeted therapies have not yet shown great benefit in unselected patient populations. Using an approach of applying Bagged Decision Trees (BDT) to high-dimensional signaling features derived from a computational model, we can predict ligand dependent proliferation across a set of 58 cell lines. This mechanistic, multi-pathway model that features receptor heterodimerization, was trained on seven cancer cell lines and can predict signaling across two independent cell lines by adjusting only the receptor expression levels for each cell line. Interestingly, for patient samples the predicted tumor growth response correlates with high growth factor expression in the tumor microenvironment, which argues for a co-evolution of both factors in vivo., npj Systems Biology and Applications, 3, ISSN:2056-7189
- Published
- 2017
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