Oncogenic and tumor-suppressive forces converge on a progenitor-orchestrated niche to shape early tumorigenesis

SUMMARY The benign-to-malignant transition is a defining step in cancer progression. To investigate when and how malignancy initiation occurs and tissue reorganization proceeds, we combine single-cell and spatial transcriptomic profiling in mouse models of pancreatic ductal adenocarcinoma (PDAC) that capture spontaneous p53 loss. Among Kras-mutant cells, we find that oncogenic and tumor-suppressive programs, including those controlled by p53, CDKN2A, and SMAD4, are co-activated in a discrete progenitor-like population, engaging senescence-like responses. Using a framework we develop for spatial analysis, we show that a niche centered on these cells undergoes stepwise remodeling during tumor progression, mirroring invasive PDAC. Transient KRAS inhibition depletes progenitor-like cells and dismantles their niche, delaying malignancy initiation. Conversely, p53 suppression enables progenitor cell expansion, epithelial–mesenchymal reprogramming, and immune-privileged niche formation. These findings position the progenitor-like state at the convergence of cancer-driving mutations, plasticity and tissue remodeling, revealing a critical window for intercepting malignancy. Competing Interest Statement S.W.L. has equity in and provides external consultancy for Oric Pharmaceuticals, Blueprint Medicines, Faeth Therapeutics and PMV Pharmaceuticals. D.P. reports equity interests and provision of services for Insitro, Inc., and is an editorial board member for Cell. P.B.R provides compensated professional services and activities for EMD Serono, Faeth Therapeutics, Urogen Pharma, Incyte, and Natera Inc, as well as uncompensated professional services and activities for 10x Genomics, XRad Therapeutics, and the HPV Alliance and Anal Cancer Foundation. C.B. reports stock ownership in Roche. R.C. is on the Scientific Advisory Board of Sanavia Oncology and LevitasBio, and is a compensated consultant for the Gerson Lehrman Group. The other authors declare no competing interests. Footnotes ↵16 Senior author ↵17 Lead Contact The revised manuscript incorporates: 1. Additional evidence for the existence of a progenitor-like niche in human disease with a quantitative analysis of new multiplexed IF data. 2. Analysis of long-term consequences of acute oncogenic KRAS inhibition in the premalignant stage of pancreatic cancer development. 3. Perturbation experiments to evaluate the functional role of microenvironmental cells and signals in sustaining progenitor-like states and niches. 4. Multiome analysis of premalignant cells. 5. Quantification of all immunofluorescence data. Our revised manuscript now fully addresses their comments. We have clarified the novel aspects of our work (Reviewer 1), and provided strong additional evidence for the existence of a progenitor-like niche in human disease with a quantitative analysis of new multiplexed IF data from 67 samples of patients with pancreatitis (Reviewers 1 and 3). As we discussed, it would take over a year to generate and test mouse models for manipulating specific epithelial or stromal cell populations. Instead, we confirm that niche progression is functionally relevant to malignant outcomes (Reviewer 2) with exciting new long-term data showing that mice treated briefly with oncogenic Kras inhibitor during premalignancy exhibit significantly delayed PDAC onset. To define reciprocal interactions between the progenitor state and TME (Reviewers 2 and 3), we have depleted macrophages in mice using anti-CSF1R and show that this immune population is involved in maintaining progenitor-like populations. Finally, we add new single-cell multiome data and analysis that provides tantalizing insights into the p53 targets linked to sporadic tumor suppression.