Integrated Molecular Characterization of Intraductal Papillary Mucinous Neoplasms: An NCI Cancer Moonshot Precancer Atlas Pilot Project

Abstract

Intraductal papillary mucinous neoplasms (IPMNs) are cystic precursor lesions to pancreatic ductal adenocarcinoma (PDAC). IPMNs undergo multistep progression from low grade (LG) to high grade (HG) dysplasia, culminating in invasive neoplasia. While patterns of IPMN progression have been analyzed using multi-region sequencing for somatic mutations, there is no integrated assessment of molecular events, including copy number alterations (CNAs) and transcriptomics changes, that accompany IPMN progression. We performed laser capture microdissection on surgically resected IPMNs of varying grades of histological dysplasia obtained from 24 patients (total of 74 independent histological lesions), followed by whole exome and whole transcriptome sequencing. Overall, HG IPMNs displayed a significantly greater aneuploidy score than LG lesions, with chromosome 1q amplification, in particular, being associated with HG progression and with cases that harbored co-occurring PDAC. Furthermore, the combined assessment of single nucleotide variants (SNVs) and CNAs identified both linear and branched evolutionary trajectories, underscoring the heterogeneity in the progression of LG lesions to HG and PDAC. At the transcriptome level, upregulation of MYC-regulated targets and downregulation of transcripts associated with the MHC class I antigen presentation machinery was a common feature of progression to HG. Taken together, this work emphasizes the role of 1q copy number amplification as a putative biomarker of high-risk IPMNs, underscores the importance of immune evasion even in non-invasive precursor lesions, and supports a previously underappreciated role of CNA-driven branching evolution as an avenue for IPMN progression. Our study provides important molecular context for risk stratification and cancer interception opportunities in IPMNs.

Spatial Transcriptomics of Intraductal Papillary Mucinous Neoplasms of The Pancreas Identifies NKX6-2 as a Driver of Gastric Differentiation and Indolent Biological Potential

“…LG gastric IPMN and the gastric stomach isthmus-pit cell transcriptome was striking. The NKX6-2 associated GIP signature was also observed in an independent RNA sequencing cohort of archival IPMN samples conducted as part of the NCI Cancer Moonshot Precancer Atlas Pilot project (14).…”

“…Even though gastric IPMN is morphologically similar to gastric epithelium, the remarkable similarity between the NKX6-2 expressing LG gastric IPMN and the gastric stomach isthmus-pit cell transcriptome was striking. The NKX6-2 associated GIP signature was also observed in an independent RNA sequencing cohort of archival IPMN samples conducted as part of the NCI Cancer Moonshot Precancer Atlas Pilot project (14). Moreover, Nkx6-2 expression was also observed in IPMN lesions collected from a genetically engineered IPMN model (13), with enrichment of the GIP signature also detected in spots of high Nkx6-2 expression.…”

“…B) Representative COMET images showing co-staining of NKX6-2, MUC5AC, and TFF1 in three different LG IPMN samples. C) Heatmap showing expression of NKX6-2 and the GIP signature in 23 archival IPMN tissue areas from the NCI Cancer Moonshot PCAPP dataset (14). Samples are ranked by NKX6-2 expression from right to left.…”

“…To validate whether NKX6-2 expression in IPMNs correlates with a gastric transcriptional program, we analyzed an independent dataset of RNA sequencing obtained following laser-capture microdissection (LCM) of 23 archival IPMNs, conducted as part of the NCI Cancer Moonshot PreCancer Atlas Pilot Project (PCAPP) (14). Remarkably, majority of the transcripts that comprise the aforementioned GIP signature (including TFF1, GKN1, GKN2 , and MUC5AC , amongst several others), as well as the prototypal classical-like transcript GATA6 were also positively correlated with NKX6-2 expression in the PCAPP dataset ( Fig.…”

“…Notably, we identified that elevated levels of transcripts encoding the transcription factor NKX6-2 (NK6 homeobox 2) were localized to the epithelium of LG IPMNs and were associated with a gene signature recapitulating the gastric pit and isthmus epithelium, which we have termed gastric isthmus-pit (GIP) signature. We validated the GIP signature associated with elevated NKX6-2 expression using multiple orthogonal approaches, including RNA sequencing performed on archival microdissected IPMN samples and cross-species spatial transcriptomics performed in a genetically engineered model of IPMNs (13,14). Moreover, using a quantitative high-plex platform for protein profiling on archival material (Lunaphore COMET assay), we confirmed that elevated nuclear NKX6-2 was a feature of the gastric subtype of IPMNs, wherein this transcription was co-localized with markers of gastric foveolar mucin (TFF1 and MUC5AC), and with nuclear GATA6, a prototypal marker of so-called “classical” differentiation within pancreatic neoplasms (15).…”