Tumor-barcoding coupled with high-throughput sequencing of a novel chemoradiation resistant SCLC mouse model

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PROJECT ABSTRACT Limited stage small cell lung cancer (LS SCLC), which is the only curable form of SCLC, is remarkably sensitive to etoposide plus cisplatin combined with radiation (XRT) with response rates of 90%, but recurrence is nearly universal. LS SCLC has only a 20-25% 5-year overall survival and ultimately a strategy for improving long-term outcome in SCLC needs to successfully target the population of cells within tumors destined to survive through standard therapy to inevitably give rise to recurrent disease. However, there is a considerable gap in understanding the specific mechanisms responsible for chemoradiation (chemoXRT) resistance in SCLC. Our project is unique among the current portfolio of SCLC funded programs in that we have focused on chemoXRT resistance to increase cure rates in LS SCLC. Recently, our work has suggested using patient- derived xenograft (PDX) models of SCLC may be an important tool to elucidate these mechanisms of chemoresistance. This approach identified a strongly synergistic anti-SCLC interaction that led to an approved CTEP trial based on our preclinical data - (NCI #10070: PI Hann). Our parent U01 had three Specific Aims: (1) Characterize natural history of response of experimental models of SCLC to chemoXRT in vivo. – where we proposed to determine response rates and recurrence natural histories from a panel of PDXs and available SCLC genetically engineered mouse models (GEMMs); (2) Characterization of molecular underpinnings of SCLC chemoXRT resistance – where we proposed constructing gene regulatory networks and gene expression profiles associated with chemoXRT resistance; and , (3) Pharmacologic and genetic validation of candidate genes for SCLC chemoXRT resistance in vitro and in vivo – where we proposed to validate novel gene candidates for conferring chemoXRT resistance using pharmacologic and genetic approach with SCLC PDX-derived organoids and available SCLC GEMMs. In this revision proposal, we propose additional Specific Aims that are highly complementary to the parent U01 objectives but are completely novel. SCLC has recently been stratified into four molecular subgroups. Currently, there are no GEMMs that reliably represent the SCLC-Y (or -YAP1) subtype and using our novel epithelial-mesenchymal transition (EMT) GEMMs we propose to create a novel SCLC GEMM for the community. Using novel inducible Twist1 and SNAI1 mouse models we will examine whether Twist1 (or SNAI1) can accelerate autochthonous SCLC tumor development and are casual for chemoXRT resistance. Lastly, our revision proposal leverages a new technique, tumor barcoding with barcode deep-sequencing (Tuba-seq), to overcome all of the barriers that limited the feasibility of using SCLC GEMMs for quantitative pharmacogenomic analysis. We will use Tuba-seq, an innovative technique enabling lineage tracing and direct quantification of chemoXRT treatment effects on different genetic backgrounds in vivo to profile the pharmcogenetic landscape of SCLC.