Genomics and Functional Characterization of NF1-mutated Lung Cancer

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Project Summary/Abstract Summary: Lung cancer is the biggest cancer killer and we do not yet have targeted therapeutic strategies for most patients. We do, however, understand the genomic changes that lead to lung cancer in unprecedented and ever-improving detail. The NF1 gene encodes a negative regulator of RAS proteins, and is frequently mutated in lung cancer. This important, large (>10%) patient subset is currently not “actionable” with targeted therapy. This will identify and characterize genes and combinations of genes that drive the formation of lung cancers with NF1 mutations, enabling us to prioritize these co-drivers for therapeutic targeting. We will use clinical sequencing and functional screens in relevant models to identify genes that cooperate with NF1 to cause lung cancer, and use novel in vivo systems to validate and clinically prioritize these targets. Background: Approximately 15 percent of patients have targeted treatment options, but most do not, despite the fact that we know targeted options are often more effective and less toxic than the alternatives. We have shown that many lung cancers harbor mutations in the NF1 gene, but that these mutations are insufficient to cause cancer by themselves in the mouse. Our goal is to understand how NF1 mutations contribute, likely with other, actionable genomic or epigenomic events, to lung adenocarcinoma formation and maintenance, in order to devise new, targeted options for the disease. Methods: First we will dive deeply into human samples to understand the clonality of NF1 mutation at the levels of tumor genomic DNA, and RNA as well as cell free DNA from patients we have selected for targeted therapy based on their tumor's NF1 mutation. We will then use cutting edge functional screening to activate transcription of endogenous genes in both the NF1-deleted and NF1-intact contexts. Finally, we will validate genes that we suspect work with NF1 loss to drive lung adenocarcinoma in immunocompetent mice. Impact: This project focuses on a common and poorly-studied mutation in lung cancer, the biggest cancer killer worldwide, by far. More than 15,000 Americans die each year with NF1-mutated lung cancer, and do so without being offered targeted therapy against their tumor's genotype. We will clarify the role NF1 mutation plays in lung cancer and will identify genes that cooperate with NF1 loss in oncogenic dyads. As such, this project will foster development of therapies targeting newly identified cancer driver genes that cooperate with NF1 mutations, one of the most common, but currently not actionable, lung cancer mutations we know of.