Abstract PR15: Assessment of tumor heterogeneity, clonal evolution, and the stromal microenvironment in metastatic pancreatic ductal adenocarcinoma and matched patient-derived organoids
Authors: Raghavan Srivatsan , Winter Peter S. , Navia Andrew , Kalekar Radha , Galvez-Reyes Jennyfer , Prakadan Sanjay , Wang Junning , Reilly Emma , Brais Lauren , Cleary James M. , Nowak Jonathan , Wolpin Brian M. , Shalek Alex K. , Aguirre Andrew J. , Hahn William C. 
Published: March 2020

Patients with metastatic pancreatic ductal adenocarcinoma (PDAC) have few treatment options and continue to have dismal prognoses due to the rapid development of resistance to both standard-of-care and experimental therapies. Several recent studies have demonstrated that patients with distinct PDAC transcriptional subtypes have differing clinical courses, and that the tumor microenvironment can also contribute to patient outcome. However, deep cellular characterization of metastatic PDAC tumors and their stromal microenvironments has been challenging due to limited tissue availability from metastatic liver biopsies. Here, we present a focused assessment of the PDAC liver metastatic niche—encompassing tumor, immune, and stromal cells—via low-input single-cell transcriptional profiling of patient specimens with the goal of developing a deeper understanding of tumor heterogeneity and the tumor microenvironment. Our pipeline accesses core needle biopsies from liver metastases, splitting each core for 1) single-cell RNA sequencing using Seq-Well and 2) organoid generation. Using this pipeline, we have successfully profiled liver metastases from 15 patients along with matched early-passage organoid models. Assessment of clinically relevant transcriptional signatures reveals extensive heterogeneity at the single-cell level and identifies new, hybrid transcriptional states occupied by these metastases. In addition, we observe evidence of significant crosstalk between stromal and immune populations and tumor cells. Serial samples at different stages of therapy show transcriptional shifts in tumor cells suggestive of significant plasticity that likely contributes to therapeutic resistance. Initial analysis of matched organoids at successive passages demonstrates a skew in their clonal composition, as well as evolution of their transcriptional state as compared to their in vivo phenotypes. Overall, our work provides an important window into the biology of metastatic PDAC, as well as some of the first direct comparisons of clonality and transcriptional phenotypes across in vivo specimens and their in vitro organoid counterparts.

This abstract is also being presented as Poster C43.

Citation Format: Srivatsan Raghavan, Peter S. Winter, Andrew Navia, Radha Kalekar, Jennyfer Galvez-Reyes, Sanjay Prakadan, Junning Wang, Emma Reilly, Lauren Brais, James M. Cleary, Jonathan Nowak, Brian M. Wolpin, Alex K. Shalek, Andrew J. Aguirre, William C. Hahn. Assessment of tumor heterogeneity, clonal evolution, and the stromal microenvironment in metastatic pancreatic ductal adenocarcinoma and matched patient-derived organoids [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2019 Sept 6-9; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2019;79(24 Suppl):Abstract nr PR15.