Systems Pharmacology Dissection of Cholesterol Regulation Reveals Determinants of Large Pharmacodynamic Variability between Cell Lines

23 pages, 7 figures.-- This is an open access article under the CC BY licenseIn individuals, heterogeneous drug-response phenotypes result from a complex interplay of dose, drug specificity, genetic background, and environmental factors, thus challenging our understanding of the underlying processes and optimal use of drugs in the clinical setting. Here, we use mass-spectrometry-based quantification of molecular response phenotypes and logic modeling to explain drug-response differences in a panel of cell lines. We apply this approach to cellular cholesterol regulation, a biological process with high clinical relevance. From the quantified molecular phenotypes elicited by various targeted pharmacologic or genetic treatments, we generated cell-line-specific models that quantified the processes beneath the idiotypic intracellular drug responses. The models revealed that, in addition to drug uptake and metabolism, further cellular processes displayed significant pharmacodynamic response variability between the cell lines, resulting in cell-line-specific drug-response phenotypes. This study demonstrates the importance of integrating different types of quantitative systems-level molecular measurements with modeling to understand the effect of pharmacological perturbations on complex biological processesThis work was supported by the Swiss SystemsX.ch initiative and evaluated by the Swiss National Science Foundation (TPdF 2013/134 to P.B.). The R.A. group is supported by the Swiss National Science Foundation (grant no. 3100A0-688 107679 ), the European Research Council (grants no. ERC-2008-AdG 233226 , and ERC-2014-AdG 670821 ), ETH Zurich, and SystemsX.ch. M.Z. and U.S. were supported by the SystemsX.ch grant TbXPeer reviewe