Abstract B13: Human pancreatic cancer organoids for functional dependency profiling

Pancreatic ductal adenocarcinoma is a deadly disease with few effective targeted therapies. As such, there is great interest in the development of in vitro and in vivo models from patient-derived samples to better understand disease drivers and to identify potential therapeutic targets. In collaboration with the Division of Gastrointestinal Oncology at the Dana-Farber Cancer Institute and the Cancer Cell Line Factory at the Broad Institute we have developed a pipeline to culture primary pancreatic tumor specimens as patient-derived xenografts (PDXs), organoids, and cell lines. We have established a cohort of 18 PDXs from primary pancreatic tumors and 3 from metastatic specimens. In addition, we have initiated a panel of 10 3D organoid cultures, including from core biopsies and fine needle aspirates, and have also attempted 2D culture of 17 tumor specimens using the conditionally reprogrammed cell (CRC) culture protocol, with successful generation of 5 tumor cell lines. In cases where a 2D cell line could not be established from the primary specimen, outgrowth of fibroblasts associated with the tumor was a common mode of failure. Consequently, we now enrich for the epithelial tumor population through several passages in 3D organoid culture before adapting to 2D surfaces to enable more efficient cell line generation. We are characterizing organoids and cell lines by targeted amplicon and/or whole exome sequencing for comparison to the primary specimen. Pancreatic tumors are notable for having a pronounced stromal response, but the impact of extracellular matrix (ECM)-mediated signaling on tumor cell behavior remains unclear. As such, one goal of our efforts is to characterize and understand how the ECM environment influences tumor cell signaling and drug responses. To this end, we have performed compound screening of a 3D organoid line in parallel with a matched 2D cell line to identify novel therapeutic targets and to begin to dissect therapeutic sensitivities that may be specific to the culture environment. Our preliminary results suggest that while there is significant concordance in drug sensitivity of cells cultured in 2D and 3D contexts, there are also several dependencies that are unique to the specific environmental context. We are performing RNA sequencing and additional molecular analyses of cells in these various adhesive conditions to identify key molecules or pathways that mediate these differential responses. The combination of compound and genetic screening in a variety of environmental contexts using these novel patient-derived culture models will improve our understanding of pancreatic cancer biology and facilitate more comprehensive pancreatic cancer dependency profiling. Citation Format: Srivatsan Raghavan, Shubhroz Gill, Andrew J. Aguirre, Yuen-Yi M. Tseng, Anson Peng, Paula Keskula, Xiaoyun Wu, Coyin Oh, Jamie Cheah, Gregory Kryukov, Ewa Sicinska, Brian M. Wolpin, Matthew H. Kulke, Charles S. Fuchs, Paul Clemons, Todd R. Golub, Stuart Schreiber, Jesse S. Boehm, William C. Hahn. Human pancreatic cancer organoids for functional dependency profiling. [abstract]. In: Proceedings of the AACR Special Conference: Patient-Derived Cancer Models: Present and Future Applications from Basic Science to the Clinic; Feb 11-14, 2016; New Orleans, LA. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(16_Suppl):Abstract nr B13.