Role of nonsense mediated RNA decay in pancreatic cancer

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Nonsense mediated RNA decay (NMD) is a mechanism to rapidly degrade select mRNAs. Recent studies have found that the UPF1 gene, required for NMD, is strikingly mutated and inactivated in >80% of adenosquamous pancreatic cancer (ASPC), a particularly aggressive form of pancreatic cancer. We have determined that UPF1 mutations in pancreatic cancer result in decreased UPF1 expression. Other mutations recently reported to inactivate NMD are found in pancreatic ductal adenocarcinoma, and we have reported that many of the stresses commonly found in pancreatic cancer repress NMD activity. NMD inhibition promotes the growth of transformed cells in soft agar, subcutaneous explants, and in an orthotopic pancreatic transplant model. Our overall goal is to better understand how NMD inhibition augments tumor growth and explore how we can exploit NMD inhibition for therapeutic gain in pancreatic cancer. RNA stability screens, RNAseq, and metabolomics screens have identified Notch signaling and Glycolysis as NMD regulated pathways. Both Notch signaling and Glycolysis play an important role in pancreatic cancer in general, and recent pancreatic cancer molecular classification studies indicate that these two pathways are particularly active in ASPC, where NMD is typically genetically inactivated. Importantly these pathways can also be targeted. In Aim 1 we will identify the mechanism and significance of NMD inhibition on Notch activation in pancreatic cancer. Based on our preliminary data we hypothesize that reduced NMD inhibition expression stabilizes Notch ligands and receptors, and the activation of Notch signaling represses e-cadherin expression to play a key role in metastases and chemo-resistance. However we also hypothesize that NMD inhibited pancreatic cancers will be particularly susceptible to Notch inhibitors. In Aim 2 we will determine how reduced NMD inhibition regulates metabolic pathways and exploit this for therapeutic gain. Based on our preliminary data, we hypothesize that NMD inhibition stabilizes alternatively spliced transcripts encoding members of the mitochondrial respiration system, and this activates glycolysis and the pentose phosphate shunt. The activation of these pathways should render tumors with UPF1 mutations more sensitive to clinically available mitochondrial inhibitors and other metabolic inhibitors, as indicated by preliminary focused shRNA synthetic lethality screens. For both Aims we will use a variety of in vitro cell biology, biochemical, and molecular techniques. We will validate our in vitro findings with unique ASPC tissue arrays, as well as a novel genetically engineered mouse in which we can temporally down-regulate UPF1 expression in pancreas, and can thus faithfully model the consequences of UPF1 mutations found in ASPC.