Spatial Biology and Organoid Technologies Reveal a Potential Therapy-Resistant Cancer Stem Cell Population in Pancreatic Ductal Adenocarcinoma
bioRxiv. 2025. DOI 10.1101/2025.05.22.655586. PMID 40661496. PMCID PMC12258720.
How to cite
AMA
Adhikary P, Chakrabarti J, Wang J, Ezuma-Igwe U, Sun X, Bastian WC, et al. Spatial Biology and Organoid Technologies Reveal a Potential Therapy-Resistant Cancer Stem Cell Population in Pancreatic Ductal Adenocarcinoma. bioRxiv. 2025. doi:10.1101/2025.05.22.655586APA
Adhikary, P., Chakrabarti, J., Wang, J., Ezuma-Igwe, U., Sun, X., Bastian, W. C., et al. (2025). Spatial Biology and Organoid Technologies Reveal a Potential Therapy-Resistant Cancer Stem Cell Population in Pancreatic Ductal Adenocarcinoma. bioRxiv. https://doi.org/10.1101/2025.05.22.655586BibTeX
@article{adhikary2025spatial,
title = {Spatial Biology and Organoid Technologies Reveal a Potential Therapy-Resistant Cancer Stem Cell Population in Pancreatic Ductal Adenocarcinoma},
author = {Adhikary, Pritha and Chakrabarti, Jayati and Wang, Jiang and Ezuma-Igwe, Ugonna and Sun, Xi and Bastian, Willian C. and others},
journal = {bioRxiv},
year = {2025},
doi = {10.1101/2025.05.22.655586},
pmid = {40661496}
}Pancreatic ductal adenocarcinoma is among the deadliest cancers, with a 5-year survival rate below 10%, and chemotherapy often fails because the tumor's dense, immunosuppressive microenvironment shields resistant cells. Understanding that resistance means seeing which cells sit where inside the tumor, not just measuring the tumor as a whole.
The team paired spatial imaging of treated and metastatic patient tissue with patient-derived organoid co-cultures that rebuild the microenvironment in a dish. Testing the drug cabozantinib alongside the immunotherapy pembrolizumab, they saw cancer cells die as immune-suppressing cells were depleted, yet a stubborn cancer stem cell population marked by CD44 variant 9 survived in both patient tissue and the lab models, pointing to a new therapeutic target.
Key findings
- Spatial profiling exposed distinct cellular niches in metastatic PDAC. In metastatic liver tissue, the authors resolved niches of mesenchymal stem cells and fibroblasts (including myCAFs and iCAFs) alongside cancer stem cells expressing CD44 and TROP2.
- Cabozantinib plus anti-PD-1 killed cancer cells and relieved immune suppression in organoid co-cultures. In patient-derived organoid co-cultures (PDO/CAF/IMM), cabozantinib combined with the anti-PD-1 antibody pembrolizumab enhanced cancer cell death by depleting myeloid-derived suppressor cells and promoted cytotoxic T lymphocyte proliferation.
- A therapy-resistant CD44v9+ cancer stem cell population persisted across tissues and models. Across both patient tissues and treated co-cultures, a standard-of-care-resistant cancer stem cell population emerged that expressed CD44 variant 9 (CD44v9), nominating it as a candidate therapeutic target.
Orion in the methods
“The Rarecyte Orion™ multiplex immunofluorescence (MxIF) platform, capable of high-plex, high-throughput spatial profiling, was used to analyze human and mouse paraffin embedded (FFPE) tumor tissues and produce a comprehensive visualization of biomarker expression within the tumor microenvironment. Human tumor tissues were formalin fixed (3.7%), paraffin embedded (FFPE) and serially sectioned at a 5 micron thickness. Orion multiplex immunofluorescence was first performed using an 18-marker antibody panel in addition to Hoechst 33342.”
— Adhikary et al., bioRxiv (2025), Methods, “Rarecyte Orion™ Multiplex Immunofluorescence”
Why it matters for Orion users
If you are weighing Orion for a tumor study, look at the job its multiplex immunofluorescence arm was given here. The question was not how much of a marker a tumor carries, but where specific cells sit inside an intact, treatment-scarred pancreatic tumor and its metastases. Orion carried the in-situ protein layer: an 18-marker antibody panel, plus a 14-marker panel, imaged on whole formalin-fixed sections at 20X, spanning tumor, immune, stromal and proliferation markers, so every cell keeps its position and its neighborhood. In those whole-slide images the authors localized CD44v9 marking the therapy-resistant cancer stem cells, SMA and vimentin marking fibroblasts and mesenchymal stem cells, and GFAP marking glial cells beside the tumor, read in place rather than dissociated. A paired spatial-transcriptomic readout and patient-derived organoid co-cultures did the wider cell-type census and the drug testing; Orion supplied the protein map, not the transcript layer. For your own work the takeaway is concrete: when a question turns on cellular neighborhoods in FFPE tissue you cannot dissociate, whole-slide multiplex immunofluorescence is the measurement that answers it.
