Thank you for your interest in our research! This repository accompanies the study "Oncogenic and tumor suppressive forces converge on a progenitor niche at the benign-to-malignant transition", to be published in Cell. We hope that our data and computation will help advance your work.
Please don't hesitate to contact José Reyes (jreyes.lab at gmail.com) if you have any questions.
We found that tumor suppressors preferentially target a rare subpopulation of premalignant epithelial cells that orchestrates the assembly of cancer-like niches during pancreatic tumor initiation. Physiological or pharmacological depletion of this epithelial state collapses their associated niches, blunting malignant transformation.
In this repository, you can find the code that we used to produce key figures and analyses from our manuscript. You can also download tarballs that containing preprocessed single and supporting data to run our code:
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/p53-niche-dynamics/Reyes2026_transcriptomics.tar.gz
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/p53-niche-dynamics/Reyes2026_imaging_kras_inhibition_4h_FigS5.tar.gz
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/p53-niche-dynamics/Reyes2026_imaging_progenitor_niche_Fig3_FigS2.tar.gz
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/p53-niche-dynamics/Reyes2026_multiome_Fig7_FigS6.tar.gz
To quickly download our processed single cell objects in .h5ad, you can use the following links:
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/p53-niche-dynamics/Reyes_KPLOH_SUBSET_pretumor_PDAC__annotated.h5ad
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/p53-niche-dynamics/Reyes_injury_SUBSET_all__annotated.h5ad
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/p53-niche-dynamics/Reyes_Krasi_SUBSET_all__annotated.h5ad
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/p53-niche-dynamics/Reyes_FLEX_SUBSET_all__integrated.h5ad
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/p53-niche-dynamics/Reyes_FLEX_SUBSET_TAM_all__integrated.h5ad
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/p53-niche-dynamics/Reyes_Xenium_TIER_all_SUBSET_all__annotated.h5ad
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/p53-niche-dynamics/Reyes_Xenium_TIER_all_SUBSET_all__spatial_neighborhood.h5ad
https://dp-lab-data-public.s3.us-east-1.amazonaws.com/p53-niche-dynamics/Reyes_Xenium_TIER_tier3_SUBSET_Premalignant0.h5ad