Abstract 1701: Identification of epigenetic modifiers able to suppress growth of pancreatic ductal adenocarcinoma: A patient-oriented <i>in vivo</i> functional platform
Authors: Alessandro Carugo, Giannicola Genovese, Sahil Seth, Luigi Nezi, Johnathon L. Rose, Andrea Viale, Piergiorgio F. Pettazzoni, Angelo Cicalese, Daniela Bossi, Wantong Yao, Jason B. Fleming, Luisa Lanfrancone, Timothy P. Heffernan, Giulio F. Draetta
Journal: Cancer Research (2015)

Abstract We have seen great advances in our knowledge of the genetic regulation of various cancers in recent years, thanks in large part to large-scale genome sequencing efforts. As we catalogue and characterize the genomic aberrations associated with cancers with increasing detail and accuracy, we are faced with the challenge of having to cull bystanders from biologically active drivers and establish relevant disease context in which these drivers are rate-limiting. To address this challenge, we have adapted a loss-of-function screening approach to function in the context of an intact tumor microenvironment using patient-derived tumors that more faithfully recapitulate the human disease compared to established cell lines. Due to the genetic heterogeneity between human tumors, we have integrated independent screening approaches in a flexible platform for the interrogation of patient-derived samples as well as GEM models in exactly the same experimental conditions. The goal of this platform is to identify context-specific genetic vulnerabilities and translate these findings into drug discovery opportunities. As proof of concept, we developed an in vivo loss-of-function screen to systematically interrogate epigenetic dependencies in pancreatic ductal adenocarcinoma (PDAC). The screening system utilizes tumor cells isolated from low-passage xenograft tissue and a lentiviral library of pooled shRNAs targeting 230 “druggable” epigenetic regulators. The custom-designed shRNA library (10 shRNAs per gene) was engineered with unique molecular barcodes that allow quantitation of each clone by deep sequencing. To date, we have completed a total of 5 in vivo screens using diverse PDAC models that have informed on novel epigenetic dependencies. So far, the main limitation for the systematic exploitation of in vivo loss-of-function screens come from the limited number of human cells contributing to tumor establishment in a transplantation setting. The frequency of these tumor initiating cells (TICs) is commonly estimated by limiting dilution assays and may consistently vary between tumor origins. With this in mind, we have integrated in our platform a system based on scrambled barcoded libraries that allow to directly assess the required coverage of screening libraries in each model. Our coverage study demonstrated to be a powerful tool to identify the minimal number of cells/barcode required to sustain a complex library and at the same time a step forward to personalize the in vivo screening patient by patient. We optimized a comprehensive data analytics pipeline and developed a high-throughput validation scheme to triage “hits” that emerge from each screen. The most potent “hits” have been enrolled in both functional and clinico-pathological validation studies to determine the highest priority targets for this devastating disease. Results from these studies will be presented. Note: This abstract was not presented at the meeting. Citation Format: Alessandro Carugo, Giannicola Genovese, Sahil Seth, Luigi Nezi, Johnathon L. Rose, Andrea Viale, Piergiorgio F. Pettazzoni, Angelo Cicalese, Daniela Bossi, Wantong Yao, Jason B. Fleming, Luisa Lanfrancone, Timothy P. Heffernan, Giulio F. Draetta. Identification of epigenetic modifiers able to suppress growth of pancreatic ductal adenocarcinoma: A patient-oriented in vivo functional platform. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1701. doi:10.1158/1538-7445.AM2015-1701