Spatial transcriptomics defines the molecular progression, invasion and immune landscape of IPMN and IPMN-derived pancreatic cancer

Background Intraductal papillary mucinous neoplasms (IPMNs) are precursor lesions of pancreatic cancer with highly variable malignant potential. Current understanding of their biology remains incomplete, limiting accurate risk stratification and targeted interventions. Objective This study aimed to characterise the molecular and immune features of IPMN across different dysplasia grades and histological subtypes, with a focus on IPMN-associated invasive carcinoma (IPMN-IC). Design Spatial whole-transcriptome profiling using Digital Spatial Profiling was conducted on 12 patients, capturing the full histological and dysplastic spectrum of IPMN and conventional pancreatic ductal adenocarcinoma. A total of 117 epithelial, immune and stromal areas of interest were analysed. An expanded cohort of 43 patients with IPMN was used to validate selected key markers. Results Transcriptomic analysis unveiled stage-specific molecular alterations and identified two distinct subsets of high-grade (HG) IPMN lesions: one resembling indolent lesions (HG) and the other IC (HG+). Key markers associated with divergent biological behaviours were identified, including MUC5AC and TFF1 in indolent lesions, and Claudin-1 in lesions with invasive potential. Immune profiling revealed a trajectory from activation to suppression during IPMN progression. Several characteristic immune checkpoint molecules, including CEACAM1 and CD44, were identified in IPMN-IC. Conclusion This study provides a spatially resolved molecular map of IPMN progression, delineating key transcriptomic and immune signatures. These findings advance the understanding of IPMN biology and highlight potential biomarkers for risk stratification and therapeutic strategies.