Core O: HIGH THROUGHPUT SEQUENCING

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A central theme in this proposal is a generic experimental design that investigates NSAID responses in five model systems, yeast, human cells, fish, mice, and man (see experimental design in the Systems Pharmacology Core). Each of these model systems offers advantages to inform NSAID responses. Because yeast don't have cyclooxygenases (COXs), but do have powerful genetics, we are using them to identify the genes and networks that regulate off target effects. We propose using human cells to understand how NSAIDs regulate cell autonomous network function in multiple cell types. Zebrafish and mice are ideal model systems for studying physiology relevant to NSAID response, e.g. how NSAIDs modify pain and blood pressure. Furthermore, they are excellent systems to find modifier genes that impact NSAID action. While zebrafish have elegant forward genetic screens, the mouse is the dominant organism for reverse genetics, and we have an array of conditional knockout mice available in this grant. Our final model system, human subjects, is the bedrock on which these studies lay. We will study NSAID response in human subjects focusing on physiological parameters such as response to pain and blood pressure. Furthermore, we will investigate individual differences in these human subjects. In all systems, we will integrate genomic information with drug levels and prostanoids and unbiased (e.g. metabolomic and lipidomic) quantitative outputs reflecting drug exposure and response. Most investigation of the physiological effects of NSAIDs has focused on the role of one or a few genes in a single model system. Here we develop a 21st-century approach that studies drug response at the network level across model systems. To do this, we need common technologies. In the Molecular Profiling Core, we propose using lipidomics, metabolomics, and proteomics to study how these small molecules are metabolized, influence prostaglandin signaling, and change the expression of proteins in a variety of experimental designs. In this core, we leverage recent advances in high throughput sequencing that now enable whole genome analysis of RNA expression dynamics, chromatin modifications, microbiome regulation, and genome sequence. This is a rapidly moving area. To ensure we stay relevant, we've enlisted Eric Schadt, Chief Scientific Officer of PacBio and Professor at UCSF, who is developing third-generation technologies to address these issues.