Identification of novel spatially resolved markers of malignant transformation in Intraductal Papillary Mucinous Neoplasms

Abstract Objective The current IPMN risk stratification is based on clinical and histological features rather than molecular markers. We aimed to improve the current diagnostic criteria of IPMN performing spatial transcriptomic (ST) on lesions of different grade to identify novel markers that define IPMN degeneration to PDAC. Design We performed ST on two independent cohorts of IPMN samples grouped by morphology and degree of dysplasia using two innovative technologies: Visium ST on a discovery cohort of 18 samples from 14 patients: 4 low-grade IPMN (3 low-grade dysplasia (LGD), 1 intermediate dysplasia/Borderline), 9 high-grade IPMN characterized by a high-grade of dysplasia (HGD), including 4 invasive IPMN with associated PDAC, and 1 PDAC-associated normal duct). GeoMx ST on a validation cohort of 57 IPMN samples: 23 low-grade IPMN (6 low-grade dysplasia (LGD), 17 intermediate dysplasia/Borderline), 34 High-grade IPMN (13 HGD Gastric IPMN and 21 HGD Intestinal IPMN) from 40 patients. Results Novel subtype-specific markers were identified in the discovery cohort: HOXB3 and ZNF117 in LGD ; SPDEF , and gastric neck cell markers in Borderline; NKX6-2 and gastric isthmus cell markers in HGD Gastric IPMN. The spatial trajectory inference implicated NKX6-2 in progression of Gastric IPMN. Transcriptomic dissection highlighted the role of TNFα signalling and Myc activation in IPMN progression. The findings were confirmed in the independent validation cohort by GeoMx analysis. Conclusions Our results identify novel markers associated with IPMN morphology and dysplasia to be explored for clinical utility, to better delineate progression in patients, improve risk stratification and clinical management.