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.
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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

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Figure 2

Comparison of transcriptomes of invasive and noninvasive organoids reveals differentially expressed genes that are enhanced in invasive protrusions.

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Comparison of transcriptomes of invasive and noninvasive organoids revea...
(A) A sample-to-sample distance plot (Spearman’s correlation) of the variance-stabilizing transform (VST) gene expression for each sample (n = 23). (B) Differentially expressed (DE) genes between all invasive organoids (n = 12) and noninvasive organoids (n = 11) (adjusted-P threshold of 0.05). OLR1, SPOCK1, MMP8, and COL7A1 were all upregulated in invasive organoids compared with the noninvasive organoids. (C) SPOCK1 mRNA expression in indicated organoid groups. Each dot represents an organoid culture. In the box-and-whisker plot, the box boundaries represent the 25th to 75th percentiles, horizontal lines represent medians, and whiskers extend to 1.5 × IQR. (D) Phase and immunofluorescence images of pan-CK, SPOCK1, and DAPI staining in invasive and noninvasive organoids. Scale bars: 50 μm. (E) Immunofluorescence images of pan-CK, SPOCK1, and DAPI staining in primary PDAC tissue sections. Scale bar: 50 μm.