Systems approaches to understanding the relationships between genotype, signaling, and therapeutic efficacy

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Project Summary/Abstract The promise of precision medicine is that a physician can tailor a therapeutic regimen to suit each individual patient. In the case of cancer, this means a personalized therapeutic strategy based on the molecular features of an individual's cancer. But while successes in precision medicine have garnered significant attention in recent years, precision medicine has not made an impact for the vast majority of cancer patients. Our overarching goal is to use proteomics and systems biology to understand the relationships between cancer genotype and therapeutic response, with the long-term goal of expanding the prospects of precision medicine. Our study focuses primary on cancers expressing mutant forms of K-Ras, the most commonly mutated oncoprotein in cancer and one of the best biomarkers for the failure of a cancer to respond to therapy. Using a variety of experimental and computational approaches, this project will address three key questions related to K-Ras and the promise of precision medicine. First, we will exploit a relatively rare circumstance in which colorectal cancers expressing a specific mutant form of K-Ras are uniquely sensitive to inhibition of the MEK kinase. We will use mass spectrometry and computational modeling to determine why cancers expressing K-RasG12D and K-RasA146T are differentially sensitive to inhibition of MEK. Next, we will address the limitation of univariate genetic prediction of therapeutic efficacy by determining how genetic and epigenetic factors interact to establish network signaling state. We will use mass cytometry and computational modeling to explore how signaling downstream of mutant K-Ras is affected by cellular lineage and by secondary mutations in oncogenes and tumor suppressor genes. Finally, we will move beyond genotype as a predictor of therapeutic efficacy by developing an algorithm to predict sensitivity to kinase inhibition based on phospho-proteomic measurements. We will validate the computational approach via preclinical therapeutics studies in patient-derived xenografts. Altogether these studies will utilize state-of-the-art experimental and computational approaches to make personalized medicine a realistic goal for patients suffering from K-Ras mutant cancer.