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bioRxiv · 10.1101/222943

Characterizing Cancer Drug Response andBiological Correlates: A Geometric NetworkApproach

Tannenbaum, A.·Pouryahya, M.·Oh, J. H.·Mathews, J.·Deasy, J.
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Abstract

In the present work, we consider a geometric network approach to study common biological features of anticancer drug response. We use for this purpose the panel of 60 human cell lines (NCI-60) provided by the National Cancer Institute. Our study suggests that utilization of mathematical tools for network-based analysis can provide novel insights into drug response and cancer biology. We adopted a discrete notion of Ricci curvature to measure the robustness of biological networks constructed with a pre-treatment gene expression dataset and coupled the results with the GI50 response of the cell lines to the drugs. The link between network robustness and Ricci curvature was implemented using the theory of optimal mass transport. Our hypothesis behind this idea is that robustness in the biological network contributes to tumor drug resistance, thereby enabling us to predict the effectiveness and sensitivity of drugs in the cell lines. Based on the resulting drug response ranking, we assessed the impact of genes that are likely associated with individual drug response. For important genes identified, we performed a gene ontology enrichment analysis using a curated bioinformatics database which resulted in very plausible biological processes associated with drug response across cell lines and cell types from the biological and literature viewpoint. These results demonstrate the potential of using the mathematical network analysis in assessing drug response and in identifying relevant genomic biomarkers and biological processes for precision medicine.

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Tannenbaum, A., Pouryahya, M., Oh, J. H., Mathews, J., Deasy, J.. 2017-11-21. Characterizing Cancer Drug Response andBiological Correlates: A Geometric NetworkApproach. https://doi.org/10.1101/222943

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