A Genetically Engineered Human Organoid Model Reveals Distinct Genetic and Epigenetic Barriers of Lineage Plasticity in Early PDAC Transformation

Zhang, X.; Wong, W.; Cho, H. S.; Yang, D.; Dixon, G.; Luo, R.; Liu, D.; Torre, D.; Umeda, S.; Gonzalez, F.; Askan, G.; Yavas, A.; Damodaran, J. R.; Rickert, R. W.; Kappagantula, R.; Pan, F. C.; Aveson, V. G.; Grimont, A.; Pulecio Rojas, J. A.; Kaplan, S. J.; Pan, H.; Leach, S. D.; Iacobuzio-Donahue, C. A.; Chandwani, R.; Leslie, C. S.; Huangfu, D.

doi:10.64898/2026.03.09.710586

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bioRxiv · 10.64898/2026.03.09.710586

A Genetically Engineered Human Organoid Model Reveals Distinct Genetic and Epigenetic Barriers of Lineage Plasticity in Early PDAC Transformation

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Abstract

The lack of accurate, human-based models recapitulating early-stage pancreatic ductal adenocarcinoma (PDAC) has hindered therapeutic development. Using pluripotent stem cell-derived pancreatic progenitor organoids, we established a human PDAC model that faithfully reproduces the genetic, epigenetic, and transcriptomic trajectory of tumor initiation and progression in vitro, validated against clinical datasets and histopathology. We demonstrate that CDKN2A loss, nearly universal in patients but dispensable in mouse models, is essential for neoplastic transformation when combined with KRAS and TP53 mutations, while SMAD4 loss promotes tumor progression. Multi-omics profiling reveals epigenetic repression of pancreatic lineage program during PDAC initiation, alongside oncogenic AP-1-driven chromatin remodeling. Notably, we identify TET1 suppression as a mechanistic link between oncogenic ERK signaling and the hypermethylation and silencing of essential pancreatic transcription factors. This model captures the genetic and epigenetic determinants of human PDAC, reveals antagonism between oncogenic and lineage restriction programs, and supports TET-based lineage restoration as a promising early intervention strategy for high-risk individuals.

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Zhang, X., Wong, W., Cho, H. S., Yang, D., Dixon, G., Luo, R., Liu, D., Torre, D., Umeda, S., Gonzalez, F., Askan, G., Yavas, A., Damodaran, J. R., Rickert, R. W., Kappagantula, R., Pan, F. C., Aveson, V. G., Grimont, A., Pulecio Rojas, J. A., Kaplan, S. J., Pan, H., Leach, S. D., Iacobuzio-Donahue, C. A., Chandwani, R., Leslie, C. S., Huangfu, D.. 2026-03-11. A Genetically Engineered Human Organoid Model Reveals Distinct Genetic and Epigenetic Barriers of Lineage Plasticity in Early PDAC Transformation. https://doi.org/10.64898/2026.03.09.710586

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