Epigenetic plasticity cooperates with emergent cell-cell interactions to drive neoplastic tissue remodeling in the pancreas [scRNA-seq]

In pancreatic cancer, select cells within a homogeneous epithelium drive tumorigenesis in response to an environmental trigger, suggesting key uncharacterized roles for epigenetics and cellular context. To investigate epigenetic plasticity in early tumorigenesis, we performed single-cell transcriptional and chromatin accessibility sequencing of Kras-mutant pancreatic cancer models, encompassing initiation to malignant stages and wild-type tissue. Our analysis identifies a few progenitor states that correspond to known cells-of-origin, exhibit the greatest measured epigenetic plasticity, and are primed for diverse neoplastic fates. Plasticity is strongly associated with accessibility near receptor and ligand loci. We delineated robust communication modules and a feedback loop between IL33-expressing epithelial and immune cells with broad tissue impacts, which we confirmed by genetic perturbation in mice. Our results promise to nominate early interception strategies for this lethal cancer. Overall design: Characterization of single-cell transcriptional profiles of lineage-traced pancreatic epithelial cells (mKate2+) isolated directly by FACS-sorting from normal (N1), regenerating (N2), pre-neoplastic (K1, K2), bening neoplastic (PanIN, K3, K4), malignant (PDAC, K5) and metastasis (K6) murine pancreatic tissues: To assess the effects of injury-induced inflammation on mutant Kras-expressing or Kras wild-type pancreatic epithelia, cells were sorted from KC;RIK (p48-Cre;RIK;LSLKrasG12D) or C;RIK (p48-Cre;RIK) male mice treated with caerulein or PBS (vehicle control) at 5 weeks of age, using littermates when possibe, and were analyzed 2 o 21 days thereafter. To characterize invasive disease, pancreatic ductal adenocarcinoma (PDAC) cells were isolated from cancer lesions arising in autochthonous transgenic models (KPC;RIK (p48Cre;RIK;LSL-KrasG12D;p53fl/+ or p48Cre;RIK;LSL-KrasG12D;p53R127H/+). 2-3 biological replicates (independent mice) were used per experimental condition.