Citation: Sahoo, D.K.; Borcherding, D.C.; Chandra, L.; Jergens, A.E.; Atherly, T.; Bourgois-Mochel, A.; Ellinwood, N.M.; Snella, E.; Severin, A.J.; Martin, M.; et al. Differential Transcriptomic Profiles Following Stimulation with Lipopolysaccharide in Intestinal Organoids from Dogs with Inflammatory Bowel Disease and Intestinal Mast Cell Tumor. Cancers 2022, 14, 3525. https:// doi.org/10.3390/cancers14143525 Received: 13 June 2022 Accepted: 16 July 2022 Published: 20 July 2022 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). cancers Article Differential Transcriptomic Profiles Following Stimulation with Lipopolysaccharide in Intestinal Organoids from Dogs with Inflammatory Bowel Disease and Intestinal Mast Cell Tumor Dipak Kumar Sahoo 1,2, * , Dana C. Borcherding 1 , Lawrance Chandra 1 , Albert E. Jergens 1 , Todd Atherly 1 , Agnes Bourgois-Mochel 1 , N. Matthew Ellinwood 3 , Elizabeth Snella 3 , Andrew J. Severin 4 , Martin Martin 5 , Karin Allenspach 1 and Jonathan P. Mochel 2, * 1 Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; bdana@wustl.edu (D.C.B.); lawrancecc@gmail.com (L.C.); ajergens@iastate.edu (A.E.J.); atherlyt@gmail.com (T.A.); abmochel@iastate.edu (A.B.-M.); allek@iastate.edu (K.A.) 2 SMART Pharmacology, Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA 3 Department of Animal Science, Iowa State University, Ames, IA 50011, USA; matthew@mpssociety.org (N.M.E.); esnella@iastate.edu (E.S.) 4 Office of Biotechnology’s Genome Informatics Facility, Iowa State University, Ames, IA 50011, USA; severin@iastate.edu 5 Mayo Clinic, Rochester, MN 55905, USA; mmartin@mednet.ucla.edu * Correspondence: dsahoo@iastate.edu or dipaksahoo11@gmail.com (D.K.S.); jmochel@iastate.edu (J.P.M.) Simple Summary: Lipopolysaccharide (LPS) derived from intestinal bacteria is linked to long-lasting inflammation that contributes to the development of intestinal cancer. While much research has been performed on the interplay between LPS and intestinal immune cells, little is known about how LPS influences intestinal epithelial cell structure and function. In this study, we investigated the effects of LPS on the proliferation and function of genes in intestinal organoids derived from dogs with gastrointestinal diseases, including inflammatory bowel disease (IBD) and intestinal mast cell tumor. The goal of this study was to evaluate how LPS affects signaling pathways in intestinal epithelial cells to influence development of a pro-tumor-like environment. Using an ex vivo model system, LPS incubation of organoids activated cancer-causing genes and accelerated the formation of IBD organoids derived from the small and large intestines. In brief, the crosstalk that occurs between the LPS/TLR4 signal transduction pathway and several different metabolic pathways, including primary bile acid biosynthesis and secretion, peroxisome, renin-angiotensin system, glutathione metabolism, and arachidonic acid pathways, may play a prominent role in the development of chronic intestinal inflammation and intestinal cancer. Abstract: Lipopolysaccharide (LPS) is associated with chronic intestinal inflammation and promotes intestinal cancer progression in the gut. While the interplay between LPS and intestinal immune cells has been well-characterized, little is known about LPS and the intestinal epithelium interactions. In this study, we explored the differential effects of LPS on proliferation and the transcriptome in 3D enteroids/colonoids obtained from dogs with naturally occurring gastrointestinal (GI) diseases including inflammatory bowel disease (IBD) and intestinal mast cell tumor. The study objective was to analyze the LPS-induced modulation of signaling pathways involving the intestinal epithelia and contributing to colorectal cancer development in the context of an inflammatory (IBD) or a tumor microenvironment. While LPS incubation resulted in a pro-cancer gene expression pattern and stimulated proliferation of IBD enteroids and colonoids, downregulation of several cancer-associated genes such as Gpatch4, SLC7A1, ATP13A2, and TEX45 was also observed in tumor enteroids. Genes participating in porphyrin metabolism (CP), nucleocytoplasmic transport (EEF1A1), arachidonic acid, and glutathione metabolism (GPX1) exhibited a similar pattern of altered expression between IBD enteroids and IBD colonoids following LPS stimulation. In contrast, genes involved in anion transport, transcription and translation, apoptotic processes, and regulation of adaptive immune Cancers 2022, 14, 3525. https://doi.org/10.3390/cancers14143525 https://www.mdpi.com/journal/cancers