Abstract PO-010: Elucidating intratumoral heterogeneity and predicting effective combination regimens in PDAC PDOs using scRNA-seq and snATAC-seq

Abstract

Abstract Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer-related death in the United States. The overwhelming majority of patients (up to 85%) present with unresectable disease, and the 5-year survival rate stands at a dire 9%. Current chemotherapeutic regimens extend survival by only a few months, and the molecular underpinnings of treatment failure in advanced disease remain largely unknown. Recently, single-cell sequencing techniques have emerged as highly effective methods to uncover intratumoral heterogeneity across many cancer types, including PDAC. These studies, and our own unpublished data, have reiterated profound transcriptomic subclonal diversity in PDAC, which likely underlies the divergent therapeutic responses and eventual treatment failure. Using a patient-derived organoid (PDO) platform, we have characterized, on the single cell level, gene expression and regulation profiles to understand the heterogeneity and clinical utility of this model. We applied predictive RNA-seq-based algorithms (CMap) to our initial PDO profiling data to design “custom” PDO combinatorial regimens as a true precision medicine-based approach. We are in the process of validating these predictions in vitro; however, preliminary single-cell RNA (scRNA-seq) data shows treatment PDOs with CMap-predicted compounds induced dramatic transcriptomic shifts in subclones reflective of an efficacious treatment strategy. Additionally, we conducted single-nuclei ATAC sequencing (snATAC-seq) of PDOs pre- and post-treatment with CMap-predicted compounds. This data, coupled to our scRNA-seq, allowed for construction of chromatin regulatory maps, and determined alterations in chromatin accessibility and gene regulation induced by targeted combinatorial therapeutics. These findings provide meaningful insight to biological processes driven by treatment-induced chromatin accessibility, and its relationship to heterogeneous transcriptional architecture. Our data suggests that differential regulation across PDO subclones may drive responses to therapy and acquired resistance mechanisms observed in the clinic, which could be predicted and therapeutically targeted with scRNA sequencing. Thus, this work represents the importance of leveraging subclonal architecture in the preclinical space to ensure both treatment efficacy and the consideration of novel therapeutic combinations in PDAC patients. Citation Format: Paola A. Guerrero, Anirban Maitra, Maria E. Monberg, Jaewon J Lee, Vincent Bernard-Pagan, Senthil Muthuswamy. Elucidating intratumoral heterogeneity and predicting effective combination regimens in PDAC PDOs using scRNA-seq and snATAC-seq [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2020 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2020;80(22 Suppl):Abstract nr PO-010.