American Association for Cancer Research
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Figure S1 from Single-Cell Transcriptomics of Pancreatic Cancer Precursors Demonstrates Epithelial and Microenvironmental Heterogeneity as an Early Event in Neoplastic Progression

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journal contribution
posted on 2023-03-31, 21:26 authored by Vincent Bernard, Alexander Semaan, Jonathan Huang, F. Anthony San Lucas, Feven C. Mulu, Bret M. Stephens, Paola A. Guerrero, Yanqing Huang, Jun Zhao, Nabiollah Kamyabi, Subrata Sen, Paul A. Scheet, Cullen M. Taniguchi, Michael P. Kim, Ching-Wei Tzeng, Matthew H. Katz, Aatur D. Singhi, Anirban Maitra, Hector A. Alvarez

(A) Correlation of gene expression levels in a pancreatic cancer cell line between single cells, bulk cells, and across independent replicates. (Single cell vs Bulk, R2: 0.915 and R2:0.9 for genesBoth {greater than or equal to}1 (N=14,922) and {greater than or equal to}10 (N=11,574) respectively. Independent Cell Replicates, R2: 0.937 and R2: 0.955 for genesBoth {greater than or equal to}1 (N=13,791) and {greater than or equal to}10 (N=10,609) respectively). (B) Scatter plots of number of UMIs against number of genes expressed and percentage of mitochondrial genes expressed per single cell across independent tissue samples from pancreatic lesions (different colors). (C) Violin plots of number of genes, UMIs, and percentage of mitochondrial genes expressed per single cell from tissue samples profiled in this study. (D) Principal components (PC) elbow plot to determine the elbow between the standard deviation of the PC and the number of PCs (11).



Cancer Prevention and Research Institute of Texas

German Research Foundation



Early detection of pancreatic ductal adenocarcinoma (PDAC) remains elusive. Precursor lesions of PDAC, specifically intraductal papillary mucinous neoplasms (IPMNs), represent a bona fide pathway to invasive neoplasia, although the molecular correlates of progression remain to be fully elucidated. Single-cell transcriptomics provides a unique avenue for dissecting both the epithelial and microenvironmental heterogeneities that accompany multistep progression from noninvasive IPMNs to PDAC. Single-cell RNA sequencing was performed through droplet-based sequencing on 5,403 cells from 2 low-grade IPMNs (LGD-IPMNs), 2 high-grade IPMNs (HGD-IPMN), and 2 PDACs (all surgically resected). Analysis of single-cell transcriptomes revealed heterogeneous alterations within the epithelium and the tumor microenvironment during the progression of noninvasive dysplasia to invasive cancer. Although HGD-IPMNs expressed many core signaling pathways described in PDAC, LGD-IPMNs harbored subsets of single cells with a transcriptomic profile that overlapped with invasive cancer. Notably, a proinflammatory immune component was readily seen in low-grade IPMNs, composed of cytotoxic T cells, activated T-helper cells, and dendritic cells, which was progressively depleted during neoplastic progression, accompanied by infiltration of myeloid-derived suppressor cells. Finally, stromal myofibroblast populations were heterogeneous and acquired a previously described tumor-promoting and immune-evading phenotype during invasive carcinogenesis. This study demonstrates the ability to perform high-resolution profiling of the transcriptomic changes that occur during multistep progression of cystic PDAC precursors to cancer. Notably, single-cell analysis provides an unparalleled insight into both the epithelial and microenvironmental heterogeneities that accompany early cancer pathogenesis and might be a useful substrate to identify targets for cancer interception.See related commentary by Hernandez-Barco et al., p. 2027