The overarching goal of this project is to test the hypothesis that modulation of phosphorylation-mediated signaling events in response to perturbations can establish new cellular states by altering their epigenetic landscapes. To achieve this goal, we propose performing mass spectrometry (MS)-based proteomic assays that specifically target quantitative readouts of phosphosignaling and chromatin modifications in cells on > 15,000 perturbational conditions. These perturbations will focus on modulation of signaling cascades and epigenetic marks by small molecules and gene inactivations. We will study several different cellular model systems, including comprehensive studies neuronal lineage differentiation starting from human embryonic stem cells. We propose to establish a center in order to develop the necessary infrastructure, pipelines, data management, and analytics required to perform what would be the largest set of related experiments with MS proteomic read outs to date. We will also explore next-generation MS acquisition technologies to establish a permanently minable MS data resource that will be accessible to the public. We will contribute the resulting data and tools to the Library of Integrated Network-based Cellular Signatures (LINCS) program for the purpose of making connections among disparate perturbations through phosphoproteomic and chromatin modification signatures in concert with other data types to be contributed to LINCS by other centers. The resulting analyses will help identify novel therapeutic opportunities and synergies, as dysregulation of phosphosignaling and epigenetic systems are two of the most common molecular etiologies identified in a growing number of genetic, developmental, and environmental diseases. In this component of the project we describe how we will solicit interactions with the community to allow for input in our scientific direction, allow new directions to be discovered, enhance public data generation capabilities, and allow for laboratories external to our center to contribute their own data to the LINCS program. We discuss methods that will allow users to understand our data and tools, and to replicate the assays we perform.
This project is relevant because we will learn how to develop new drugs that target the common ways that diseases like cancer are caused in the cells of our bodies. We will use cutting edge scientific techniques to understand how these diseases cause normally healthy cells to become sick, and identify possible ways to block or reverse these effects.
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|Egertson, Jarrett D; MacLean, Brendan; Johnson, Richard et al. (2015) Multiplexed peptide analysis using data-independent acquisition and Skyline. Nat Protoc 10:887-903|