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1.  The glucose-deprivation network counteracts lapatinib-induced toxicity in resistant ErbB2-positive breast cancer cells 
This study implicates the glucose deprivation response in breast cancer cell resistance to lapatinib and high relapse rates in Her2-positive patients. Identification of these compensatory networks suggests novel strategies to target cancer signaling and metabolism.
Increased expression of the glucose deprivation response network, including glucagon signaling, glucose uptake, gluconeogenesis and unfolded protein response genes is found in breast cancer cells with acquired resistance to lapatinib.The glucose deprivation response gene network correlated significantly with high clinical relapse rates in ErbB2-positive breast cancer patients.Chemical genomics bioinformatics data mining identified drugs that target the glucose deprivation response networks to reduced survival of resistant cells.
Dynamic interactions between intracellular networks regulate cellular homeostasis and responses to perturbations. Targeted therapy is aimed at perturbing oncogene addiction pathways in cancer, however, development of acquired resistance to these drugs is a significant clinical problem. A network-based computational analysis of global gene expression data from matched sensitive and acquired drug-resistant cells to lapatinib, an EGFR/ErbB2 inhibitor, revealed an increased expression of the glucose deprivation response network, including glucagon signaling, glucose uptake, gluconeogenesis and unfolded protein response in the resistant cells. Importantly, the glucose deprivation response markers correlated significantly with high clinical relapse rates in ErbB2-positive breast cancer patients. Further, forcing drug-sensitive cells into glucose deprivation rendered them more resistant to lapatinib. Using a chemical genomics bioinformatics mining of the CMAP database, we identified drugs that specifically target the glucose deprivation response networks to overcome the resistant phenotype and reduced survival of resistant cells. This study implicates the chronic activation of cellular compensatory networks in response to targeted therapy and suggests novel combinations targeting signaling and metabolic networks in tumors with acquired resistance.
doi:10.1038/msb.2012.25
PMCID: PMC3421441  PMID: 22864381
bioinformatics; computational methods; functional genomics; metabolic and regulatory networks; signal transduction
2.  Kinome siRNA-phosphoproteomic screen identifies networks regulating AKT signaling 
Oncogene  2011;30(45):4567-4577.
To identify regulators of intracellular signaling we targeted 541 kinases and kinase-related molecules with siRNAs and determined their effects on signaling with a functional proteomics reverse phase protein array (RPPA) platform assessing 42 phospho and total proteins. The kinome wide screen demonstrated a strong inverse correlation between phosphorylation of AKT and MAPK with 115 genes that when targeted by siRNAs demonstrated opposite effects on MAPK and AKT phosphorylation. Network based analysis identified the MAPK subnetwork of genes along with p70S6K and FRAP1 as the most prominent targets that increased phosphorylation of AKT, a key regulator of cell survival. The regulatory loops induced by the MAPK pathway are dependent on TSC2 but demonstrate a lesser dependence on p70S6K than the previously identified FRAP1 feedback loop. The siRNA screen also revealed novel bi-directionality in the AKT and GSK3 interaction, whereby genetic ablation of GSK3 significantly blocks AKT phosphorylation, an unexpected observation as GSK3 has only been predicted to be downstream of AKT. This method uncovered novel modulators of AKT phosphorylation and facilitated the mapping of regulatory loops.
doi:10.1038/onc.2011.164
PMCID: PMC3175328  PMID: 21666717
AKT; MAPK; proteomics; signaling networks; siRNA
3.  The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks 
PLoS Computational Biology  2008;4(2):e1000005.
Reconstructing cellular signaling networks and understanding how they work are major endeavors in cell biology. The scale and complexity of these networks, however, render their analysis using experimental biology approaches alone very challenging. As a result, computational methods have been developed and combined with experimental biology approaches, producing powerful tools for the analysis of these networks. These computational methods mostly fall on either end of a spectrum of model parameterization. On one end is a class of structural network analysis methods; these typically use the network connectivity alone to generate hypotheses about global properties. On the other end is a class of dynamic network analysis methods; these use, in addition to the connectivity, kinetic parameters of the biochemical reactions to predict the network's dynamic behavior. These predictions provide detailed insights into the properties that determine aspects of the network's structure and behavior. However, the difficulty of obtaining numerical values of kinetic parameters is widely recognized to limit the applicability of this latter class of methods.
Several researchers have observed that the connectivity of a network alone can provide significant insights into its dynamics. Motivated by this fundamental observation, we present the signaling Petri net, a non-parametric model of cellular signaling networks, and the signaling Petri net-based simulator, a Petri net execution strategy for characterizing the dynamics of signal flow through a signaling network using token distribution and sampling. The result is a very fast method, which can analyze large-scale networks, and provide insights into the trends of molecules' activity-levels in response to an external stimulus, based solely on the network's connectivity.
We have implemented the signaling Petri net-based simulator in the PathwayOracle toolkit, which is publicly available at http://bioinfo.cs.rice.edu/pathwayoracle. Using this method, we studied a MAPK1,2 and AKT signaling network downstream from EGFR in two breast tumor cell lines. We analyzed, both experimentally and computationally, the activity level of several molecules in response to a targeted manipulation of TSC2 and mTOR-Raptor. The results from our method agreed with experimental results in greater than 90% of the cases considered, and in those where they did not agree, our approach provided valuable insights into discrepancies between known network connectivities and experimental observations.
Author Summary
Many cellular behaviors including growth, differentiation, and movement are influenced by external stimuli. Such external stimuli are obtained, processed, and carried to the nucleus by the signaling network—a dense network of cellular biochemical reactions. Beyond being interesting for their role in directing cellular behavior, deleterious changes in a cell's signaling network can alter a cell's responses to external stimuli, giving rise to devastating diseases such as cancer. As a result, building accurate mathematical and computational models of cellular signaling networks is a major endeavor in biology. The scale and complexity of these networks render them difficult to analyze by experimental techniques alone, which has led to the development of computational analysis methods. In this paper, we present a novel computational simulation technique that can provide qualitatively accurate predictions of the behavior of a cellular signaling network without requiring detailed knowledge of the signaling network's parameters. Our approach makes use of recent discoveries that network structure alone can determine many aspects of a network's dynamics. When compared against experimental results, our method correctly predicted 90% of the cases considered. In those where it did not agree, our approach provided valuable insights into discrepancies between known network structure and experimental observations.
doi:10.1371/journal.pcbi.1000005
PMCID: PMC2265486  PMID: 18463702

Results 1-3 (3)