Precision Medicine in Pancreatic Cancer: Patient-Derived Organoid Pharmacotyping Is a Predictive Biomarker of Clinical Treatment Response

Abstract

Rationale: Patient-derived organoids (PDOs) are a promising technology to support precision medicine initiatives for patients with pancreatic ductal adenocarcinoma (PDAC). PDOs may improve clinical next-generation sequencing (NGS) and enable rapid ex vivo chemotherapeutic screening (pharmacotyping). Methods: PDOs were derived from tissues obtained during surgical resection and endoscopic biopsies and studied with NGS and pharmacotyping. PDO-specific pharmacotype is assessed prospectively as a predictive biomarker of clinical therapeutic response by leveraging data from a randomized-controlled clinical trial. Results: Clinical sequencing pipelines often fail to detect PDAC-associated somatic mutations in surgical specimens that demonstrate a good pathological response to previously administered chemotherapy. Sequencing the PDOs derived from these surgical specimens, after biomass expansion, improves the detection of somatic mutations and enables quantification of copy number variants. The detection of clinically relevant mutations and structural variants is improved following PDO biomass expansion. On clinical trial, PDOs were derived from biopsies of treatment naïve patients prior to treatment with FOLFIRINOX (FFX). Ex vivo PDO pharmacotyping with FFX components predicted clinical therapeutic response in these patients with borderline resectable or locally advanced PDAC treated in a neoadjuvant or induction paradigm. PDO pharmacotypes suggesting sensitivity to FFX components were associated with longitudinal declines of tumor marker, CA-19-9 and favorable RECIST imaging response. Conclusion: PDOs establishment from tissues obtained from patients previously receiving cytotoxic chemotherapies can be accomplished in a clinically-certified laboratory. Sequencing PDOs following biomass expansion improves clinical sequencing quality. High in-vitro sensitivity to standard-of-care chemotherapeutics predicts good clinical response to systemic chemotherapy in PDAC.

Inflammatory Signaling in Pancreatic Cancer Transfers Between a Single-cell RNA Sequencing Atlas and Co-Culture

“…We previously demonstrated that PDO models of PDAC malignant epithelial cells have the capacity to recapitulate intratumoral heterogeneity and accurately provide clinically-actionable data for chemotherapeutic selection 21,22 . We now aim to use PDOs to further our understanding of tumor biology and mechanisms of inflammation in PDAC.…”

“…To mechanistically test whether fibroblasts induce the inflammatory pattern in malignant epithelial cells that was identified in the atlas, we established a model system of PDAC PDOs co-cultured with patient-derived CAFs. Each matched model leverages our previously published methods for generating PDOs 21,22 while concurrently extracting CAFs from surgical resection specimens (Fig. S10) for co-culture that maintains viability of both cell-types (Fig.…”

“…We further utilized our PDO cultures to validate the inflammatory phenotype identified in the atlas and to interrogate the mechanisms of inflammatory gene expression in the setting of multi-compartmental three-dimensional co-cultures. We previously demonstrated that PDAC PDOs, comprised exclusively of malignant epithelial cells, have the capacity to recapitulate intratumoral heterogeneity and accurately provide clinically-actionable data for chemotherapeutic selection 27,28 . Previous work has also shown that 24 hours of 200ng/mL of IFNγ added into cell media induces MHC-I and PD-L1 upregulation in organoids 29 .…”

“…To evaluate the mechanisms responsible for fibroblast-induced inflammatory signaling towards the malignant epithelial compartment that was identified in the atlas, we established a system of PDAC PDOs co-cultured with patient-derived CAFs. Each patient-matched PDO-CAF co-culture leverages our previously published methods for generating PDOs 27,28 while concurrently extracting CAFs from surgical resection specimens (Supplemental Figure 10) . The three-dimensional cultures were established in Matrigel as the surrogate basement membrane for suspending culture components.…”

Challenges in genomic analysis of model systems and primary tumors of pancreatic ductal adenocarcinoma

“… In the organoid, CNV mean log 2 ratio was remarkably decreased by approximately −6 for CDKN2A and CDKN2B . [56] …”