Morphology-guided transcriptomic analysis of human pancreatic cancer organoids reveals microenvironmental signals that enhance invasion
Yea Ji Jeong, … , Joel S. Bader, Laura D. Wood
Yea Ji Jeong, … , Joel S. Bader, Laura D. Wood
Published March 7, 2023
Citation Information: J Clin Invest. 2023;133(8):e162054. https://doi.org/10.1172/JCI162054.
View: Text | PDF
Research Article Gastroenterology Oncology

Morphology-guided transcriptomic analysis of human pancreatic cancer organoids reveals microenvironmental signals that enhance invasion

Abstract

Pancreatic ductal adenocarcinoma (PDAC) frequently presents with metastasis, but the molecular programs in human PDAC cells that drive invasion are not well understood. Using an experimental pipeline enabling PDAC organoid isolation and collection based on invasive phenotype, we assessed the transcriptomic programs associated with invasion in our organoid model. We identified differentially expressed genes in invasive organoids compared with matched noninvasive organoids from the same patients, and we confirmed that the encoded proteins were enhanced in organoid invasive protrusions. We identified 3 distinct transcriptomic groups in invasive organoids, 2 of which correlated directly with the morphological invasion patterns and were characterized by distinct upregulated pathways. Leveraging publicly available single-cell RNA-sequencing data, we mapped our transcriptomic groups onto human PDAC tissue samples, highlighting differences in the tumor microenvironment between transcriptomic groups and suggesting that non-neoplastic cells in the tumor microenvironment can modulate tumor cell invasion. To further address this possibility, we performed computational ligand-receptor analysis and validated the impact of multiple ligands (TGF-β1, IL-6, CXCL12, MMP9) on invasion and gene expression in an independent cohort of fresh human PDAC organoids. Our results identify molecular programs driving morphologically defined invasion patterns and highlight the tumor microenvironment as a potential modulator of these programs.

Authors

Yea Ji Jeong, Hildur Knutsdottir, Fatemeh Shojaeian, Michael G. Lerner, Maria F. Wissler, Elodie Henriet, Tammy Ng, Shalini Datta, Bernat Navarro-Serer, Peter Chianchiano, Benedict Kinny-Köster, Jacquelyn W. Zimmerman, Genevieve Stein-O’Brien, Matthias M. Gaida, James R. Eshleman, Ming-Tseh Lin, Elana J. Fertig, Andrew J. Ewald, Joel S. Bader, Laura D. Wood

×

Figure 5

Application of organoid invasion signatures to primary PDAC scRNA-seq data reveals different cellular compositions in the tumor microenvironment.

Options: View larger image (or click on image) Download as PowerPoint
Application of organoid invasion signatures to primary PDAC scRNA-seq da...
(A) Pancreatic cancer samples from The Cancer Genome Atlas (PAAD from TCGA) ordered by their expression score of tG1 and tG2 genes (the score was calculated using Ucell R package of positive expression of tG2 genes and negative expression of tG1 genes). This gene expression score is annotated in green at the top of the figure. The second annotation bar shows the Moffitt et al. (8) basal and classical subtypes for these samples. (B) A Kaplan-Meier curve of high and low tG1 signature–expressing tumors in TCGA cohort (n = 185). (C) Average fractions and error bars showing SD of neoplastic cells, T and B cells, fibroblasts, macrophages, and other cell types within tG1 (n = 8), tG2 (n = 9), and neither (n = 7) tumors in the Peng et al. (42) scRNA-seq data set. (D) Average fractions and error bars showing SD of fibroblast subpopulations in tG1 (n = 8), tG2 (n = 9), and neither (n = 7) tumors from Peng et al. scRNA-seq data set. (E) Fraction of tumor cells that express tG1 genes (x axis) and tG2 genes(y axis) within each PDAC in the Peng et al. scRNA-seq data set. Each patient’s Moffitt et al. subtype is shown in the color legend. (F) Representative images of immunohistochemical staining showing the density of CD3+ T cells in primary tumors that produce mesenchymal and collective organoids. Scale bars: 200 μm. (G) Quantification of the density of B cells, T cells, myofibroblasts, and macrophages/tumor area (100 μm2) on tissue sections of primary PDACs (6 tumors that generated mesenchymal organoids and 3 that generated the collective organoids), which shows statistically significant differences in fractions of myofibroblasts (P = 0.037, t test) and T cells (P = 0.0042, t test). Each dot represents 1 tumor. In the box-and-whisker plots, the box outlines represent the 25th to 75th percentiles, horizontal lines represent medians, and whiskers extend to 1.5 × IQR.