Transcriptional analyses of Barrett's metaplasia and normal upper GI mucosae

Abstract

Over the last two decades, the incidence of esophageal adenocarcinoma (EA) has increased dramatically in the US and Western Europe. It has been shown that EAs evolve from premalignant Barrett's esophagus (BE) tissue by a process of clonal expansion and evolution. However, the molecular phenotype of the premalignant metaplasia, and its relationship to those of the normal upper gastrointestinal (GI) mucosae, including gastric, duodenal, and squamous epithelium of the esophagus, has not been systematically characterized. Therefore, we used oligonucleotide-based microarrays to characterize gene expression profiles in each of these tissues. The similarity of BE to each of the normal tissues was compared using a series of computational approaches. Our analyses included esophageal squamous epithelium, which is present at the same anatomic site and exposed to similar conditions as Barrett's epithelium, duodenum that shares morphologic similarity to Barrett's epithelium, and adjacent gastric epithelium. There was a clear distinction among the expression profiles of gastric, duodenal, and squamous epithelium whereas the BE profiles showed considerable overlap with normal tissues. Furthermore, we identified clusters of genes that are specific to each of the tissues, to the Barrett's metaplastic epithelia, and a cluster of genes that was distinct between squamous and non-squamous epithelia.

Figure 1

Hierarchical clustering of tissues based on point estimates of the Pearson correlation coefficients using all the genes represented by the entire probe set of the Affymetrix (Hu6800 and HuGeneFL) arrays. All samples in italics (Sq1–4, DUO1, GAS1, and BE1–4) were hybridized to Hu6800 arrays, whereas Sq5, DUO2,3, GAS2,3, and BE5 were hybridized to HuGeneFL arrays.

Figure 2

(A) Expression profiles of five tissue-specific clusters (the expression profiles of all eight clusters are available at http://www.fhcrc.org/science/phs/barretts/neoplasia). The horizontal axis represents the pooled samples of the different tissues analyzed, and the vertical axis represents the normalized expression levels (see Materials and Methods). A high normalized expression level indicates relatively high expression levels compared to other experiments for the same gene. Within each of the five clusters (I–V), the average normalized expression levels (solid lines) ± 1 SD (dotted lines) across the 16 experiments are shown. (B) Visualization of the five clusters in a reduced dimensional space. The reduced dimensional space is formed by the first three principal components (PCs), which capture most of the variation in the original data and are therefore typically used in visualization of high dimensional data from multiple experiments. In the present study, 67% of the variation from the 16 separate hybridizations was captured in the first three PCs. BE-specific cluster (orange filled circles); gastric-specific cluster (purple circles); duodenum-specific cluster (filled pink rectangles); squamous-specific cluster (green rectangles); nonsquamous epithelium cluster (green crosses).