Quantitative Analysis of Epidermal Growth Factor Receptor Signaling Networks

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Overexpression and mutation of epidermal growth factor receptor (EGFR) and EGFR family members leads to dysregulated signal transduction and has been correlated with increased risk for cancer and poor prognosis for cancer patients due to development of more aggressive cancers (i.e. higher proliferation and metastasis rates). Here we propose to develop an improved mechanistic model of the EGFR signaling network, from which we will be able to identify key nodes in the signaling network which regulate downstream biological response to activated ErbB receptor tyrosine kinases. In this five-year project we will investigate, model, and manipulate the EGFR signaling network to develop an improved mechanistic understanding of cellular signal transduction. In the first phase, we will apply mass spectrometry to quantify temporal phosphorylation profiles for hundreds of phosphorylation sites downstream of EGFR, under a variety of stimulation conditions. In order to link this signaling data to biological outcome, we will acquire phenotypic (migration, proliferation, apoptosis) data for each condition. In the second phase of the project, we will implement a variety of bioinformatic algorithms (hierarchical clustering, SOMs, PLSR) to characterize the data gathered in the first phase of the project. For instance, hierarchical clustering and self-organizing maps will be used to identify co-regulated phosphorylation sites which may function as dynamic modules within the EGFR signaling network. Identification of module components will facilitate assignment of potential biological function to poorly characterized proteins. PLSR will be used to correlate quantitative phosphorylation profiles with downstream biological response data. The result of this method is a functional relationship between the signaling metrics (phosphorylation sites) and biological outcomes (proliferation, migration, and apoptosis); predictions which will be tested experimentally. In this second phase of the project we will construct a mechanistic model of the EGFR signaling network which may then be used to predict behavior of the system. In the third phase of the project, we will attempt to validate model predictions by measuring the response to biological manipulation of the EGFR signaling network. Perturbations may include disrupting the function of various components in the network with RNA interference (RNAi) or small molecule kinase inhibitors (where available), or overexpressing proteins of interest through stable transfection. The final product of this research project will be a more comprehensive and well calibrated mechanistic model of the ErbB signaling network which will have a profound impact on our understanding of oncogenic signaling networks. Overexpression and mutation of epidermal growth factor receptor (EGFR) and EGFR family members have been implicated in many different tumor types, yet our understanding of these signaling networks is still very incomplete. Here we propose to use cutting-edge analysis and modeling tools to develop a more comprehensive mechanistic understanding of these signaling networks and their linkage to biological response. We will use these improved models to predict biological outcome to novel therapeutic interventions, with the goal of establishing new paradigms for cancer treatment.