Project 3

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PROJECT 3 SUMMARY ROLES AND MECHANISMS OF ACTION OF METABOLIC VULNERABILITIES OF SCLC Small cell lung cancer (SCLC) lacks targeted therapies, and with only 7% overall survival on standard-of-care cisplatin/etoposide chemotherapy, and only 10% survival on immune checkpoint therapy, NCI has classified SCLC as a recalcitrant malignancy. Thus, there is an urgent need to identify new and effective targeted therapies for SCLC. In non-small cell lung cancer (NSCLC) genomic studies led to effective targeted therapies directed at drivers such as mutant EGFR. Unfortunately, drivers of SCLC are undruggable, where there are loss-of-function mutations in the tumor suppressors retinoblastoma protein (RB1), p53 (TP53) and p73, as well as amplification and/or overexpression of MYC oncogenic transcription factors. To identify vulnerabilities for SCLC, we performed unbiased mass spectrometry-based screens for SCLC-specific changes in the ATP-binding proteome via activity-based proteome profiling (ABPP), and in the metabolome (metabolomics and lipidomics) using a large bank of SCLC and NSCLC cell lines, patient-derived xenografts (PDX) and primary tumor tissue. Further, we performed screens with compounds that inhibit different aspects of metabolism. Integrating these data revealed SCLC has highly elevated levels of glycolysis, 1-carbon and purine and lipid metabolism, and that combined treatment with inhibitors of two metabolic regulators – MCT lactate transporters (MCTi) and the glycolytic enzyme PFKFB3 (PFKFB3i) – triggers SCLC cell line metabolic collapse, growth arrest and cell death. Genetic studies validated these findings, and confirmed the paradoxical observation that PFKFB3 inhibition provokes a collapse in oxidative phosphorylation (OxPhos). Given these findings, we will assess the roles of MCTs and PFKFB3 in the metabolism, development and maintenance of SCLC using established (from Project 1) and new (from Core 2) genetically engineered SCLC mouse models (GEMM), SCLC PDX, and circulating SCLC xenografts (CDX) (Aim 1). These SCLC models will also be used to test the safety and efficacy of the MCTi/PFKB3i combination as a therapeutic strategy for SCLC, and we will also assess effects of targeting MCTs and/or PFKB3 on the repertoire and activity of intratumoral immune cells using SCLC GEMM (with Project 4). Further, we will use ABPP, in vivo tracing (with Project 2), metabolic flux, and metabolomics studies (with Core 3) to identify and then target adaptive metabolic changes provoked by the loss or inhibition of MCTs and/or PFKFB3. These studies will define the mechanism by which PFKFB3 inhibition impairs OxPhos, and how combined MCTi/PFKFB3i treatment provokes SCLC metabolic collapse (Aim 2). Importantly, our metabolomic studies of paired sensitive and cisplatin/etoposide-resistant SCLC PDX supports the hypothesis that MCTi/PFKB3i therapy represents an opportunity to treat and prevent emergence of chemoresistant disease, which we will test using these SCLC PDX models and SCLC GEMM (Aim 3). Finally, guided by our ABPP, metabolomic and lipidomic analyses, we will use targeted CRISPR screens to identify new metabolic vulnerabilities in SCLC, which we will validate and characterize using our SCLC models and ABPP, metabolic flux and metabolomics experiments (Aim 4).