We identified and validated ligands with significant phenotypic effects on PDAC tumor cell state via a compressed ligand perturbation screen on patient-derived PDAC organoids followed by single ligand follow-ups. Our findings include a gene expression program (GEP) robustly induced by IL-4 and IL-13 in malignant PDAC cells that displays little similarity to existing gene signatures of type 2 cytokines.

CS: We conducted two PDAC organoid CSs with the same model, ligand library, and compression scheme (replicates = 5, mean pool size = 4.75), but distinct ligand poolings. 

Validation screen: To validate our CS results, we individually tested the 11 top-scoring ligands (IL-1A, IL-1B, TNF-α, IL-4, IL-13, ADIPOQ, TGF-β1, INHBB, IFN-γ, WNT7A, and RSPO3) significantly associated with 5 of the GEPs (NF-κβ response, PDAC IL-4/IL-13 response, TGF-β response, IFN- γ response, and ribosomal module). We conducted two validation experiments on separate days (biological replicates) by screening six replicates of all ligands, including a set of negative control organoids in each run.