Identification of synthetic lethal interactors in pancreatic cancer

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 DESCRIPTION (provided by applicant): The goal of research supported by this FOA is "to identify targets whose inhibition would induce synthetic lethality in cancers dependent on the expression of mutant KRas alleles", with a "focus on one or more of the four most frequently observed alleles...in one or more of the predominant mutant KRas-dependent cancers e.g., pancreas...", and utilizing advanced screens "that go beyond the current screens in 2D tissue culture". To accomplish this goal, we have assembled a well-integrated team of five investigators at three institutions. Our team will apply three complementary and highly innovative advanced screens to identify and validate targets whose inhibition would induce synthetic lethality in KRAS-mutant pancreatic ductal adenocarcinoma (PDAC). Each of our screens differs substantially from those in previously published RNAi-based synthetic lethal screens. We will focus not only on K-Ras G12D and G12V but also on G12R, the third most frequent KRAS mutation in PDAC and one whose properties we believe differ from those of other G12 mutants. We propose three specific aims: (1) a robust chemical library screen to convert pharmacologic inhibitors of K-Ras effector signaling from cytostatic to cytotoxic activities; (2) a focused genetic screen to identify cancer signaling pathway components whose activation overcomes addiction to mutant K-Ras; and (3) an unbiased, genome-wide gain-of-function insertional mutagenesis screen to identify genes whose overexpression overcomes addiction to mutant KRAS. Aim 1 will use a powerful chemical library screen (Drug Sensitivity and Resistance Testing, DSRT) of compounds selected specifically to allow rapid clinical transition of positive results. Aims 2 and 3 will employ complementary innovative gain-of-function genetic screens. Aim 2 will take a signaling-centric approach (Cancer Toolkit) shown in preliminary data to be able to identify both known and unknown mechanisms of inhibitor resistance, whereas Aim 3 will apply a genome-wide unbiased approach (CDt/MS) that is mass spectrometry-based and uniquely reads out at the protein level, thereby enabling a cheaper, faster and more informative process than conventional functional genomic screens. Aims 1 and 2 share a signaling focus, whereas Aims 2 and 3 share a conceptual theme. We will utilize low passage KRAS-mutant pancreatic cancer patient-derived xenograft (PDX)-derived cell lines throughout our studies. While the initial Aim 1 screens will be done in conventional high throughput 2D assays, validation of the hits will be done in 3D culture models including pancreatic organoids. Aim 2 and 3 screens will be done in both 2D and 3D culture as well as in vivo in tumor-bearing mice, and hits will be validated in 2D and 3D culture. The top hits from Aims 1-3 will then be further validated in PDX orthotopic pancreatic cancer models. We will apply pathway and network analysis, and expect to find significant overlap of important hits among the three screening approaches. Information from each of these strategies will be integrated across all platforms to identify the best synthetic lethal targets for pharmacologic inhibition and induction of cytotoxicity in KRAS-mutant pancreatic cancer cells.