Fig. 1.
PDAC exists on a continuum of epithelial to quasi-mesenchymal gene expression, and cytotoxic chemotherapy shifts toward a mesenchymal phenotype. (A) Expression heatmap to determine an E to QM metascore for each PDAC cell line using a validated gene signature (2). (B) Unsupervised clustering of RNA-seq data from 6 patient-derived PDAC cell lines. [Scale bar, log10(RPM+1).] (C and D) Correlation heatmap of ATAC-seq samples using chromatin accessibility peaks across the genome (C) and at promoter regions (D). (E) Representative images of PDAC cell lines stained with hematoxylin and by RNA-ISH for epithelial (brown) and mesenchymal (red) markers. Quantification of relative E vs. QM expression using the Halo image analysis platform shown below. (F) Schematic of experimental system in which tumor spheroids are grown in 3D culture conditions and treated with a single dose of FOLFIRINOX (FFX). RNA is extracted on day 14 for RNA-seq. (G) Top 5 enriched gene sets procured by computing overlaps between genes induced by FFX treatment across all 6 PDAC cell lines and Hallmark gene sets. (H) Heatmap depicting the relative change in E/QM metascore over time following FFX exposure in each PDAC cell line. Expressed as metascore fold change over untreated. (I) Representative images of PDAC tumors resected following neoadjuvant FFX chemotherapy and stained by RNA-ISH for E (brown) and QM (red) markers. (Scale bars, 100 μm.) Table depicts quantification of E and QM cases in the untreated cohort and the neoadjuvant FFX-treated cohort. P value calculated using Fisher’s exact 2-tailed test.