Abstract 1402: Single cell transcriptomic profiling of ex vivo tumoroid models reveal therapeutic vulnerabilities of pancreatic ductal adenocarcinoma
Authors: Bernard Vincent , Lucas F. Anthony San , Huang Jonathan , Powell Reid T. , Guerrero Paola A. , Semaan Alexander , Stephan Clifford C. , Davies Peter , Varadhachary Gauri R. , Katz Matthew H. , Taniguchi Cullen M. , Alvarez Hector A. , Muthuswamy Senthil , Maitra Anirban 
Published: August 2019

Abstract
By 2030, pancreatic ductal adenocarcinoma (PDAC) will likely become the second leading cause of cancer-related death. A lack of actionable mutations continues to be a significant challenge in addressing the disease in a precision medicine setting. As a result, current treatment options are often limited to genotype-independent cytotoxic agents. Patient derived tumor organoid (PDOs) models have gained traction as potential tools for therapeutic stratification. We characterized single cell gene expression profiles of PDOs and applied an in silico therapeutic drug prediction model to identify and validate combinatorial strategies targeting heterogeneous subpopulations. Four established PDOs from PDAC were profiled through single cell RNA-Seq analysis in order to identify subpopulations of cancer cells with differing therapeutic response. The PDOs were then subjected to a high-throughput drug screen of 764 agency approved candidates. Top candidates, including combinatorial drug selections, were orthogonally validated through single cell gene expression analysis and evaluated for efficacy and synergistic interactions. Single-cell transcriptomic profiling of PDOs revealed unique subpopulations of cancer cells with differential expression of DNA Damage response, protein and fatty acid metabolism, and inflammatory related pathways. Effective combinatorial therapies were projected based on pharmacogenomic predictions targeting opposite gene expression patterns of each subpopulation and validated through drug library screens. In a PDO, common sensitivity nodes utilizing epigenetic modifiers were detected among all tumor derived subpopulations. A synergy matrix seeded with PDOs and evaluated using Bliss independence revealed that combinatorial treatment with HDAC-inhibitors and PARP1-inhibitors produced the most profound synergistic result. Mechanistically, HDAC inhibitors limit the activity of DNA repair proteins which in conjunction with PARP-inhibition leads to synergistic outcomes. We have demonstrated the utility of single cell transcriptomic profiling from PDOs in identifying viable treatment options using a pharmacogenomic strategy. The sophisticated heterogeneity of PDOs, revealed the necessity of using combinatorial strategies to target all relevant subpopulations. Furthermore, this strategy revealed an exciting synergistic interplay between HDAC and PARP1 inhibitors, an interaction that has never before been shown in a PDAC case. Looking forward, our model not only may be a vehicle used to discover new drug candidates and elucidate novel mechanisms, but may also be the first step towards the establishment of a true precision medicine paradigm for PDAC.
Citation Format: Vincent Bernard, F. Anthony San Lucas, Jonathan Huang, Reid T. Powell, Paola A. Guerrero, Alexander Semaan, Clifford C. Stephan, Peter Davies, Gauri R. Varadhachary, Matthew H. Katz, Cullen M. Taniguchi, Hector A. Alvarez, Senthil Muthuswamy, Anirban Maitra. Single cell transcriptomic profiling of ex vivo tumoroid models reveal therapeutic vulnerabilities of pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1402.