Bioinformatic Analysis of Epithelial:Mesenchymal Crosstalk during Mouse Gut Development and Patterning

Abstract

ABSTRACT BIOINFORMATIC ANALYSIS OF EPITHELIAL:MESENCHYMAL CROSSTALK DURING MOUSE GUT DEVELOPMENT AND PATTERNING

By

Xing Li

Chair: Deborah L. Gumucio

The small intestine develops from a tube of endoderm wrapped by mesoderm. Crosstalk between the endodermally derived epithelium and the underlying mesenchyme is required for regional patterning and proper differentiation of the developing intestine. In this thesis, microarray technology was combined with bioinformatics techniques to study two aspects of small intestinal organogenesis. First, the transcriptomes of the separate mesenchymal and epithelial compartments of the perinatal mouse intestine were examined. It was found that the vast majority of soluble inhibitors and modulators of signaling pathways such as Hedgehog, BMP, Wnt, Fgf, and Igf are expressed predominantly or exclusively by the mesenchyme, accounting for its known ability to dominate instructional crosstalk. Additionally, while epithelially enriched genes tended to be highly tissue restricted in their expression pattern, mesenchymally enriched genes were broadly expressed in multiple tissues. Thus, the unique tissue-specific signature that characterizes the intestinal epithelium is instructed and supported by a mesenchyme that itself expresses genes that are largely non-tissue specific. In a second study, gene expression profiles were analyzed during the formation of the pyloric border. At E14.5, before this border is established, gene expression patterns in stomach and nearby duodenum were similar. However, at E16.5, border formation was accompanied by the up-regulation of about 2000 genes specifically in the duodenum. Combining the results from these two microarray experiments revealed that >95% of up-regulated genes were epithelial. This work establishes for the first time that epithelial border formation occurs via a massive change in duodenal (not stomach) character. Genes that are specifically expressed at the border (Nkx2.5, Gata3, nephrocan) and might be involved in border specification were identified, as were transcription factors (Hnf4, Hnf4, Tcfec, Creb3l3, etc.) that are likely to be important in establishment of intestinal identity, a process herein called “intestinalization”. Taken together, the results of these studies provide new insights into tissue crosstalk and the specific transcriptional networks that are responsible for intestinal organogenesis.