Project description:Using genetically modifed mice to express fluorescent reporter in proglucagon expressing cells (GluVenus) or in all enteroendocrine cells (NeuroD1), we purifed positive and negative cells by FACS from duodenal epithelial cells and identified transcripts enriched in positive populations
Project description:We generated knock-in mice expressing GFP under the control of the endogenous GIP (Glucose-dependent Insulinotropic Polypeptide) promoter that enable the isolation of a purified population of small intestine K cells. Using RNA-Seq, we comprehensively characterized the transcriptomes of GIP-GFP cells as well as the entire enteroendocrine lineage derived from Neurogenin3 (Ngn3)-expressing progenitors. We interrogated the whole transcriptome of FACS-isolated small intestine GIPGFP cells using high-throughput mRNA sequencing. We also obtained the global gene expression patterns of the entire enteroendocrine cell lineage as well as the non-enteroendocrine cell population, comprising enterocytes, goblet cells and Paneth cells. To achieve this, small intestine epithelial cells from male mice resulting from the breeding of Neurogenin3 (Ngn3)-Cre mice with ROSA26-LoxP-STOP-LoxP-tomato indicator mice were isolated based on Tomato fluorescence and negative staining for CD45. Due to the small cell numbers, we constructed each of the three RNA-Seq libraries (GIPGFP, Ngn3TOMATO, and Ngn3-) using a pool of equal amounts of individual RNA samples without RNA amplification.
Project description:An indepth analysis of Paneth cell transcriptome at single cell level has not been available. Existing intestinal epithelial cell scRNA dataset contain many cell types, where Paneth cells represent a small portion. We used a flow cytometry based approach to enrich and isolate relatively pure Panethc cells from a newly developed Paneth cell reporter mouse line (Lyz1-3'UTR-IRES-CreER; Rosa26R-tdTomato). Single cell RNA sequencing was performed on purified duodenal and ileal Paneth cells of mice housed under specific pathogen free condition.
Project description:To elucidate the role of duodenal microenvironment in Common variable immunodeficiency pathogenesis (CVID), we sought to explore the transcriptome regulation in duodenal biopsies.
Project description:Background: Duodenal adenoma/adenocarcinomas are rare, and the global gene expression changes associated with the initial stages of carcinogenesis of these neoplasms have not been elucidated. Results: To comprehensively analyze genetic markers and pathways specific to early-stage duodenal adenoma/adenocarcinomas, transcriptional profiles of 4 fresh-frozen non-ampullary duodenal adenoma/adenocarcinomas and surrounding duodenal normal mucosa were compared. Key features of gene expression analysis demonstrated a strong correlation between these tumors and colorectal adenomas, as well as the Wnt/β-catenin pathway. These results shed new light on the transcriptional changes that occur during the early stages of duodenal tumorigenesis. All samples were obtained prior to treatment in order to minimize effects of cauterization, and immediately fresh-frozen.
Project description:To examine the role of Rb1 in gastrointestinal (GI) tumors we generated mice with an Apc1638N allele, Rbtm2brn floxed alleles, and a villlin-cre transgene (RBVCA). These mice had reduced median survival due to an increase in tumor incidence and multiplicity in the cecum and the proximal colon; they differed from murine intestinal tumors of the Apc1638N type which normally arise solely in the small intestine. We have examined by micro-array analysis three cecal tumors from these mice (probable adenomas), and compared them to three duodenal tumors (probable adenocarcinomas). Expression profiles of duodenal and cecal tumors relative to each other show unique gene subsets up and down regulated. The two tumor types were subsequently shown to differentially regulate distinct sets of genes over expressed in a majority of human colorectal carcinomas. Experiment Overall Design: We have compared 3 cecal tumors with 3 duodenal tumors from Rb1 deficient Apc1638N mice.
Project description:We report here the transcriptome of a population enriched in enteroendocrine cells from human jejunum from patients before or after gastrectomy. We analyze the effect of surgery on gene expression and found very little effect on EEC transcriptome
Project description:We report here the transcriptome of sorted enteroendocrine cells from duodenum, ileum and colon from mice after vertical sleeve gastrectomy or sham operation, weight matched or not. We analyze the effect of region of origin and surgery and gene expression and found that only region of origin had an impact on EEC transcriptome
Project description:Progression of duodenal polyposis into cancer is an important cause of morbidity and mortality in the inherited tumour syndromes Familial Adenomatous Polyposis (FAP) and MUTYH-associated Polyposis (MAP), yet this process remains poorly understood. This study aimed to identify genes that are mutated in FAP and MAP duodenal adenomas and to characterise the cellular consequences for duodenal tumorigenesis.