Comparative gene expression analysis of the rat gastrointestinal tract epithelia

Background: The molecular basis of segment specific epithelial functions of the stomach and bowel has not been established. Regionally unique molecular properties of epithelial cells can be identified using cell-specific gene expression in each epithelial region by comparative mRNA analysis. Aim: To describe segment-specific epithelial mRNA content by comparative mRNA analysis of purified epithelial cell suspensions of stomach, small and large bowel. Results: 12% of all annotated genes show segment specific enrichment. The gastric (>3000 genes) and ileal (519 genes) mucosa show the most diverse expression profile. (a) Stomach: The gastric mucosa expresses the machinery for acid secretion, digestive enzyme release, and hormone release by gastric enteroendocrine cells. Associated with acid secretion is a specific set of K+, Cl-, and bicarbonate channels. Novel is a pathway for glucose and fatty acid sensing, iodine and glutamate uptake, and taurine synthesis. Specific sets of transcription factors control epithelial (Barx1, Runx) and enteroendocrine (FoxA2/N4) cell differentiation. (b) Small Bowel: This epithelium expresses genes coding for a unique fructose/glucose uptake and utilization mechanism. Enteroendocrine signalling to the gastric function is present. The upper portion expresses genes for iron uptake, bicarbonate secretion, and detoxification of food contents. Epithelial differentiation is transcriptionally controlled by Meis2/Pdx1 and Onecut 2. Expression of digestive enzymes, lipid/bile acid uptake and utilization increases distally. The ileal epithelium is also involved in innate and acquired immune defence, regulation of motility, and electrolyte and water re-absorption. Transcriptional regulation of enterocyte and goblet cell differentiation is mainly controlled by increasing expression of Cdx1 and 2. (c) Colon: This epithelium is mainly involved in Ca++-, K+, and water re-absorption, fatty acid uptake and sensing, and innate and acquired immune defence. Epithelial differentiation is controlled by Hox transcription factors in addition to Cdx1/2. Conclusion: This regional survey of gene expression by the GI tract epithelium reveals unique epithelial properties, raising several important questions as to the role of the proteins encoded in gut physiology. Rat stomach, small, and large bowel segments were inverted and subjected to a short pronase digestion and elutriation to obtain purified mucosal cells. RNA was isolated, labelled for microarray hybridization, and comparative whole rat genome expression analysis (Agilent) performed. 3 independent isolations of mucosal cell total RNA, labeled with either cy3 or cy5 were performed. All microarrays are scanned and the intensities normalized over background using a microarray scanner from Agilent Technologies including proprietary software. All microarray data sets (single channel) are imported into the microarray data analysis software Genespring 7.3 (Agilent, USA) and normalized intensities compared. Each individual normalized intensity was divided by the median of intensity of all 15 data points and the statistical significance of difference of the mean calculated using Genespring 7.3 microarray analysis software (Agilent). A p-value of less than < 0.05 was considered as a significant difference.