Weglarz-Tomczak E(1), Rijlaarsdam DJ(1), Tomczak JM(2), Brul S(1). Author information:
(1)Swammerdam Institute for Life Sciences, Faculty of Science, University of
Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands.
(2)Department of Computer Science, Vrije Universiteit Amsterdam, De Boelelaan
1111, 1081 HV Amsterdam, The Netherlands.
Cancer cell metabolism is dependent on cell-intrinsic factors, such as genetics, and cell-extrinsic factors, such nutrient availability. In this context, understanding how these two aspects interact and how diet influences cellular metabolism is important for developing personalized treatment. In order to achieve this goal, genome-scale metabolic models (GEMs) are used; however, genetics and nutrient availability are rarely considered together. Here, we propose integrated metabolic profiling, a framework that allows enriching GEMs with metabolic gene expression data and information about nutrients. First, the RNA-seq is converted into Reaction Activity Score (RAS) to further scale reaction bounds. Second, nutrient availability is converted to Maximal Uptake Rate (MUR) to modify exchange reactions in a GEM. We applied our framework to the human osteosarcoma cell line (U2OS). Osteosarcoma is a common and primary malignant form of bone cancer with poor prognosis, and, as indicated in our study, a glutamine-dependent type of cancer.
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