Abstract B074: scRNA-seq from FFPE tissue resolves the tumor microenvironment of intraductal papillary mucinous neoplasms

Abstract Intraductal papillary mucinous neoplasms (IPMN) are precancerous cysts representing the only radiographically identifiable precursor to pancreatic ductal adenocarcinoma (PDAC). Successful interception of PDAC requires identifying high-risk disease, which accounts for approximately 15-20% of IPMN. Currently, this is only achieved by detecting high-grade dysplasia (HGD) in the epithelial lining of the cyst, which is challenging due to the heterogeneity of the disease. Minute foci of HGD can reside adjacent to abundant low-grade dysplasia (LGD), making it nearly impossible to detect HGD without histopathological review of a surgically resected lesion. Additionally, IPMN-associated PDAC is often detected only after surgical removal. The heterogeneity of these lesions has hindered efforts to accurately profile pure HGD or invasive regions, leading to unsuccessful attempts to identify diagnostic biomarkers. The predominant pathology in many IPMN lesions is LGD. Therefore, we hypothesized that if there are differences between the low-grade regions of low-risk, high-risk, and invasive IPMN, we could identify a diagnostic biomarker without the need to detect HGD or PDAC specifically. While single-cell RNA-sequencing (scRNA-seq) presents an attractive approach for characterizing IPMNs, it has been limited by the inability to sequence IPMN samples with confirmed pathology. Recently, 10X Genomics introduced a scRNA-seq method for formalin-fixed, paraffin-embedded (FFPE) tissues, mitigating the challenge of sequencing these highly heterogeneous samples prior to histological annotation. We employed this scRNA-seq assay on 13 FFPE tissue blocks confirmed to harbor LGD epithelium only. These blocks were derived from five patients with only LGD within the entire specimen (low-risk), five patients who had focal HGD detected in other blocks from the same specimen (high-risk), and four patients who had invasive cancer detected in other blocks. We also included two samples containing LGD, HGD, and PDAC within the same specimen for comparative analysis. Overall, we profiled 90,950 cells, the largest known IPMN single-cell sequencing effort to date. We identified a cell population indicative of acinar-to-ductal metaplasia (ADM) in low-risk samples that disappeared through disease progression. Moreover, we discovered that populations of immune cells differed between the low-grade lesions of low-risk, high-risk, and invasive IPMN. For instance, low-risk samples had the highest proportion of effector memory CD8+ T cells, high-risk samples had the highest proportion of pro-inflammatory macrophages, and invasive samples had the highest proportion of B cells. Furthermore, we analyzed inferred cell–cell interactions and identified differences in signaling strength between distinct ductal, stromal, and immune cell populations across these sample groups. These results demonstrate the first instance of resolving and comparing the microenvironment surrounding LGD lesions in low-risk, high-risk, and invasive IPMN. Citation Format: Ashley A. Fletcher, Erika J. Crosby, Daniel P. Nussbaum, Margaret O'Connor, Elishama N. Kanu, Peter J. Allen. scRNA-seq from FFPE tissue resolves the tumor microenvironment of intraductal papillary mucinous neoplasms [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research—Emerging Science Driving Transformative Solutions; Boston, MA; 2025 Sep 28-Oct 1; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85(18_Suppl_3):Abstract nr B074.