Exocrine Pancreas Cell Plasticity in Injury, Regeneration, and Precancerous Initiation

Abstract

The pancreas poses challenges for single-cell transcriptomic profiling due to acinar cell production of digestive enzymes, resulting in underrepresentation of critical cell types. To overcome this, we developed FixNCut, a reversible fixation method that uses dithiobis(succinimidyl propionate) (DSP) to preserve transcriptomes, enabling high quality single-cell profiling of the pancreas. We applied FixNCut to understand pancreatic cancer initiation and exocrine pancreas diseases known to increase risk of pancreatic cancer, including acute, recurrent, and chronic pancreatitis. We identified a conserved transcriptional program of acinar plasticity, termed acinar-to-ductal metaplasia (ADM), across these diverse pancreatic stressors. We characterized ADM states, including a transitional gateway state (gADM), and uncovered PanIN heterogeneity including populations with classical- and basal-like gene expression profiles emerging prior to tumor formation. Immune profiling revealed an initial inflammatory response to acute pancreatitis in the wildtype and oncogenic Kras context. However, oncogenic Kras uniquely triggered a second wave of inflammation, marked by proinflammatory neutrophils, activated macrophages, fibroblast reprogramming, and regulatory T cell emergence, fostering a precancerous niche. Together, we provide a comprehensive atlas of pancreatic cellular plasticity, identifying conserved pathways and novel cell states linked in injury, regeneration, and cancer initiation.