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Cancers are caricatures of normal development. Yet, for most organs we are only beginning to learn about the molecular events underlying the embryonic antecedents of organogenesis and when differentiation into the cell types found in the adult actually begins. Here, we will focus on the powerful single-cell RNA sequencing and Assay for Transposase Accessible DNA by DNA sequencing (ATAC-seq) that we and others have been using to decipher the key regulators and signal transduction pathways involved in normal mammary development. We will first describe the techniques we use to identify, dissect, and isolate embryonic mammary rudiments and their constituent cells. We then describe the methods we have employed to perform single-cell RNA-seq and single-nucleus ATAC-seq using the small number of cells obtainable from mouse embryos. Finally, we will discuss the bioinformatic techniques we have used to interpret the vast amount of data obtained with these methods., (© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Background and Aims: Eicosanoids, oxidized fatty acids that serve as cell-signaling molecules, have been broadly implicated in tumorigenesis. Here, we aimed to identify eicosanoids associated with pancreatic tumorigenesis and the cell types responsible for their synthesis., Methods: We profiled normal pancreas and pancreatic ductal adenocarcinoma (PDAC) in mouse models and patient samples using mass spectrometry. We interrogated RNA sequencing datasets for eicosanoid synthase or receptor expression. Findings were confirmed by immunostaining., Results: In murine models, we identified elevated levels of PGD 2 , prostacyclin, and thromboxanes in neoplasia while PGE 2 , 12-HHTre, HETEs, and HDoHEs are elevated specifically in tumors. Analysis of scRNA-seq datasets suggests that PGE 2 and prostacyclins are derived from fibroblasts, PGD 2 and thromboxanes from myeloid cells, and PGD 2 and 5-HETE from tuft cells. In patient samples, we identified a transition from PGD 2 to PGE 2 -producing enzymes in the epithelium during the transition to PDAC, fibroblast/tumor expression of PTGIS, and myeloid/tumor cell expression of TBXAS1., Conclusions: Our analyses identify key changes in eicosanoid species during pancreatic tumorigenesis and the cell types that contribute to their synthesis. Thromboxane and prostacyclin expression is conserved between animal models and human disease and may represent new druggable targets., Competing Interests: Conflicts of interest: The authors disclose no conflicts.

Background & Aims: Development of pancreatic ductal adenocarcinoma (PDA) involves acinar to ductal metaplasia and genesis of tuft cells. It has been a challenge to study these rare cells because of the lack of animal models. We investigated the role of tuft cells in pancreatic tumorigenesis., Methods: We performed studies with LSL-Kras G12D/+ ;Ptf1a Cre/+ mice (KC; develop pancreatic tumors), KC mice crossed with mice with pancreatic disruption of Pou2f3 (KPouC mice; do not develop tuft cells), or mice with pancreatic disruption of the hematopoietic prostaglandin D synthase gene (Hpgds, KHC mice) and wild-type mice. Mice were allowed to age or were given caerulein to induce pancreatitis; pancreata were collected and analyzed by histology, immunohistochemistry, RNA sequencing, ultrastructural microscopy, and metabolic profiling. We performed laser-capture dissection and RNA-sequencing analysis of pancreatic tissues from 26 patients with pancreatic intraepithelial neoplasia (PanIN), 19 patients with intraductal papillary mucinous neoplasms (IPMNs), and 197 patients with PDA., Results: Pancreata from KC mice had increased formation of tuft cells and higher levels of prostaglandin D 2 than wild-type mice. Pancreas-specific deletion of POU2F3 in KC mice (KPouC mice) resulted in a loss of tuft cells and accelerated tumorigenesis. KPouC mice had increased fibrosis and activation of immune cells after administration of caerulein. Pancreata from KPouC and KHC mice had significantly lower levels of prostaglandin D 2 , compared with KC mice, and significantly increased numbers of PanINs and PDAs. KPouC and KHC mice had increased pancreatic injury after administration of caerulein, significantly less normal tissue, more extracellular matrix deposition, and higher PanIN grade than KC mice. Human PanIN and intraductal papillary mucinous neoplasm had gene expression signatures associated with tuft cells and increased expression of Hpgds messenger RNA compared with PDA., Conclusions: In mice with KRAS-induced pancreatic tumorigenesis, loss of tuft cells accelerates tumorigenesis and increases the severity of caerulein-induced pancreatic injury, via decreased production of prostaglandin D 2 . These data are consistent with the hypothesis that tuft cells are a metaplasia-induced tumor attenuating cell type., (Copyright © 2020 AGA Institute. Published by Elsevier Inc. All rights reserved.)

Chronic pancreatitis, a known risk factor for the development of pancreatic ductal adenocarcinoma (PDA), is a serious, widespread medical condition characterized by inflammation, fibrosis, and acinar to ductal metaplasia (ADM). ADM is a cell type transdifferentiation event where pancreatic acinar cells become ductal-like under conditions of injury or oncogenic mutation. Here, we show that chronic pancreatitis and ADM in genetically wild type mice results in the formation of a significant population of chemosensory tuft cells. Transcriptomic analyses of pancreatitis tuft cells identify expression of inflammatory mediators, consistent with a role for tuft cells in injury progression and/or resolution. Though similar to tuft cell populations in other organs and disease systems, we identified a number of key differences that suggest context-specific tuft cell functions. We evaluated seven different mouse strains for tuft cell formation in response to chronic injury and identified significant heterogeneity reflecting varying proclivity for epithelial plasticity between strains. These results have interesting implications in the role of epithelial plasticity and heterogeneity in pancreatitis and highlight the importance of mouse strain selection when modeling human disease., (Copyright © 2020 DelGiorno, Naeem, Fang, Chung, Ramos, Luhtala, O’Connor, Hunter, Manor and Wahl.)