S0002 Developing a Multimodal Platform for Precision Medicine Using Endoscopic Fine Needle Biopsies in Pancreatic Cancer

Abstract

INTRODUCTION: Pancreatic ductal adenocarcinoma (PDAC) is the 4th leading cause of cancer-related death in the US. Unfortunately, prognosis remains dismal with an average survival of only 6–9 months after diagnosis. Historically studies investigating the biology of PDAC have been limited to surgically resected tumors, which only captures a minority of patients with resectable disease. Recently, the development of single cell technologies and 3-dimensional in vitro organoid culture allows for in-depth profiling using small amounts of tissue, raising the potential to develop precision medicine tools at time of endoscopic fine needle biopsy. We have employed single-cell RNA sequencing, mass cytometry, and organoid culture to developed a rich pre-clinical precision platform using specimens from endoscopic fine needle biopsies of PDAC tumors. METHODS: Patients were consented according to IRB HUM00041280 or HUM00025339. Up to three additional fine needle biopsies were obtained for research use after sufficient biopsies obtained for clinical purposes. Tissue was digested into clusters of cells for organoid culture or single cell-suspension for mass cytometry and single cell RNA sequencing. For mass cytometry, cells were stained with a basic immune panel to map the immune landscape of tumor tissue. For single-cell RNA sequencing, cells were sorted through a Live-Dead Macs column, then processed through a 10X Genomics Chromium platform, a droplet-based single cell sequencing technique utilizing barcoding. For organoid culture, cells were plated in 100% growth factor reduced matrigel covered with Human Complete Feeding Medium. RESULTS: We have successfully performed single-cell RNA sequencing (scRNAseq) on 11 PDAC patients and mass cytometry on 22 PDAC patients. Additionally, we have 5 robust PDAC organoid lines growing which have been passaged at least 20 times in culture. Preliminary analysis of our data show patient-specific heterogeneity of immune checkpoints in T cells, thus implicating the possibility of individualized immunotherapeutic targets. CONCLUSION: There is an urgent need for better tailored therapies for pancreatic cancer patients. We have developed a platform using endoscopic fine needle biopsies to map the landscape of PDAC which has potential to be used as a precision medicine tool. The use of endoscopic biopsies broadens the applicability of our platform to all PDAC patients, regardless of how far their disease has progressed.