Genome-wide expression patterns of invasion front, inner tumor mass and surrounding normal epithelium of colorectal tumors

Abstract

Colorectal tumors have characteristic genome-wide expression patterns that allow their distinction from normal colon epithelia and facilitate clinical prognosis. The expression heterogeneity within a primary colorectal tumor has not been studied on a genome scale yet. Here we investigated three compartments of colorectal tumors, the invasion front, the inner tumor mass, and surrounding normal epithelial tissue by microdissection and microarray-based expression profiling. In both tumor compartments many genes were differentially expressed when compared to normal epithelium. The sets of significantly deregulated genes in both compartments overlapped to a large extent and revealed various interesting known and novel pathways that could have contributed to tumorigenesis. Cells from the invasion front and inner tumor mass, however, did not show significant differences in their expression profile, neither on the single gene level nor on the pathway level. Instead, gene expression differences between individuals are more pronounced as all patient-matched tumor samples clustered in close proximity to each other. With respect to invasion front and inner tumor mass we conclude that the specific tumor cell micro-environment does not have a strong influence on expression patterns: largely similar genome-wide expression programs operate in the invasion front and interior compartment of a colorectal tumor.

Figure 1

Principal component analysis of tumor samples from the invasion front (IT), the inner tumor mass (RT) and from neighbored normal epithelium (N) based on the expression patterns of 7433 genes. Note that normal epithelia cluster closely together to the exclusion of all tumor samples.

Figure 2

Two-way hierarchical clustering of tumor and normal epithelia samples based on expression profiles of 7433 genes. (A) The heat map shows expression changes relative to the average signal in normal tissues. Red means up-regulation, green means down-regulation (see expression ratio color bar at the bottom). (B) The dendrogram shows the hierarchical order of similarities between patient samples. Note that all normal samples are separated from tumors and both samples of a patient that stem from different tumor compartments clustered as neighbors.

Figure 3

Histograms of p-value distributions for pair-wise comparisons between three tissue groups. Note that the p-value distributions for gene-wise comparisons between tumor compartments (RT, IT) and normal epithelia (N) have a peak at p-values approaching 0 that is typical for situations in which multiple genes have highly significant p-values (like tumor-normal comparisons). In contrast, the p-value distribution of the invasion front (IT) vs. inner tumor (RT) comparison lacks this peak and p-values are uniformly distributed, just as if one would have labeled the experiments randomly. This means that there are no gross differences in gene expression between the two tumor compartments.